ANNUAL REPORT 2017 ANNUAL REPORT 2017 ANNUAL REPORT 2017 4 ORGANISATION OF RESEARCH 14 CONTENTS BASIC RESEARCH 16 Molecular Oncology Programme 18 Tumour Suppression Group 20 Experimental Oncology Group 24 Telomeres and Telomerase Group 28 Cell Division and Cancer Group 32 Genomic Instability Group 36 Chromosome Dynamics Group 40 DNA Replication Group 44 Melanoma Group 48 Microenvironment & Metastasis Junior Group 52 Brain Metastasis Junior Group 54 Metabolism and Cell Signalling Junior Group 56 Cancer Cell Biology Programme 58 Genes, Development and Disease Group 60 Epithelial Carcinogenesis Group 64 Epithelial Cell Biology Junior Group 68 Growth Factors, Nutrients and Cancer Junior Group 70 Seve Ballesteros Foundation-CNIO Brain Tumour Junior Group 72 Structural Biology Programme 74 Macromolecular Complexes In DNA Damage Response Group 76 Cell Signalling and Adhesion Junior Group 80 Structural Bases of Genome Integrity Junior Group 82 Kinases, Protein Phosphorylation and Cancer Junior Group 84 Genome Integrity and Structural Biology Junior Group 86 Spectroscopy and Nuclear Magnetic Resonance Unit 88 Bioinformatics Unit 90 Electron Microscopy Unit 92 Crystallography and Protein Engineering Unit 94 Biological Text Mining Unit 96 Structural Computational Biology Group 98 National Bioinformatics Institute Unit 99 TRANSLATIONAL RESEARCH 100 Human Cancer Genetics Programme 102 Human Genetics Group 104 Hereditary Endocrine Cancer Group 108 Genetic and Molecular Epidemiology Group 112 Familial Cancer Clinical Unit 116 Molecular Cytogenetics and Genome Editing Unit 118 Human Genotyping-CEGEN Unit 120 Clinical Research Programme 122 Breast Cancer Junior Clinical Research Unit 124 Prostate Cancer Junior Clinical Research Unit 126 Molecular Diagnostics Unit 128 H12O-CNIO Haematological Malignancies Clinical Research Unit 130 H12O-CNIO Lung Cancer Clinical Research Unit 134 Biobank 138 FOREWORD 9 VICE DIRECTOR 12 SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 5 INNOVATION 140 Biotechnology Programme 144 Genomics Core Unit 146 Transgenic Mice Core Unit 148 Monoclonal Antibodies Core Unit 150 Molecular Imaging Core Unit 152 Flow Cytometry Core Unit 154 Confocal Microscopy Core Unit 156 Proteomics Core Unit 158 Histopathology Core Unit 160 Animal Facility 162 Experimental Therapeutics Programme 164 Medicinal Chemistry Section 166 Biology Section 170 CNIO - Lilly Cell Signalling Therapies Section 174 CNIO - Lilly Epigenetics Section 176 Technology Transfer and Valorisation Office 178 COMMUNICATION 180 INTERNATIONAL AFFAIRS 192 CNIO OFFICES 196 Dean’s Office 198 CNIO Women in Science Office 200 FACTS & FIGURES 202 Scientific Management 204 Competitive Funding 206 Education and Training Programmes 218 Scientific Events 224 Administration 238 Board of Trustees 238 Scientific Advisory Board 240 Management 242 CNIO Personnel 2017 244 Private Sponsors 248 CNIO FRIENDS 250 CNIO Friends 253 ‘ CNIO Friends ’ Postdoctoral Contracts 254 ‘ Excelentes ’: a book of portraits 255 CNIO opens its doors to ‘ CNIO Friends ’ 256 Benefactor Friends/Sponsor Friends 258 Donations to the CNIO 259 CREATIVE TEAM 260 Communications 182 Press Clippings 184 2017 Social Network Data 187 Invited Guest Speakers 188 Social Events 189 CNIO & The City 190 ANNUAL REPORT 2017 6 SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 7 “ The year 2017 has been a record year in terms of CNIO publications in top journals.” MARIA A. BLASCO Director SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 9 FOREWORD This year, once again, the data on CNIO’s scientific performance illustrate that we are doing a good job in contributing towards scientific breakthroughs. During 2017, the CNIO authored a total of 217 papers, 26 of which were published in journals with impact factors ( IF ) ranging from 10 to 15, and 44 papers in journals with impact factors greater than 15. Comparison with previous years ( 2006-2017 ) indicates that CNIO has continued to increase the numbers of papers it published in top journals with IF greater than 15 ; in fact, 2017 is the year that counts the most publications in these journals in our Centre’s history. Our excellence in research has been bolstered by an institutional effort to establish new alliances and collaborations with important partners all over the world, both from the public and private sectors. The creation of these ties has enabled us to forge a robust research and innovation network that will help the CNIO to retain its position as a key centre of reference in cancer research within the international community. We continue to focus on the importance of attracting new talent from abroad and to safeguarding our strong, competitive position in Europe, opening up our centre to the realm of excellent science worldwide. In this regard, we are implementing new institutional initiatives that will, on one hand, provide better support to our investigators for achieving their objectives, and on the other hand, help us to coordinate all endeavours with the aim of better aligning our research agenda, efforts and strategy with the work programme and goals of the European Commission for research and innovation. We have not forgotten our duties and responsibilities towards other centres in Spain and our own Spanish society ; in this light, we have welcomed the launch of the Severo Ochoa and Maria de Maetzu Alliance, SOMMa, an important Spanish research network, for which we are actively contributing to its mission. With every step we take, we get a bit closer to achieving great impact through science ; our institutional strategy delineates a clear path to meet this goal. In 2017, Manuel Serrano, from the Molecular Oncology Programme, and Alfonso Valencia, from the Structural Biology and Biocomputing Programme, left the CNIO after many years Maria A. Blasco Director FOREWORD ANNUAL REPORT 2017 10 FOREWORD of excellent work and dedication to the CNIO. We want to wholeheartedly thank them for their contribution in making the CNIO a centre of excellence of international reputation and we wish them all the best in their new ventures. I am also happy to mention that we have attracted new talent to the CNIO. During 2017, we incorporated 3 new Groups within the Structural Biology Programme, with the aim of boosting the structural biology activities at the CNIO. We hired Óscar Llorca as the new Director of CNIO’s Structural Biology Programme. Óscar is an international leader in the cryo-EM field and his joining the CNIO has served to re-design this key programme for the Centre, thereby integrating this exciting technology within our existing portfolio ; the Programme is now equipped with a new electron microscope that allows for atomic resolution. Under the leadership of Óscar Llorca, we have hired 2 new Junior Group Leaders for the Programme : Iván Plaza Menacho, former Senior Research associate at the Structural Biology Laboratory at the Biozentrum, Univesity of Basel, Switzerland ; and Rafael Fernández Leiro, coming from the MRC Laboratory of Molecular Biology, Cambridge, UK. The valorisation of the research results generated by CNIO scientists, with the aim of turning them into high-potential diagnostic or therapeutic products and services, is one of our many ways of creating added value for society and boosting public benefit through improving cancer patient outcomes. At CNIO, our scientists perform research on the key biological processes underlying the disease ; these include structural biology, drug development, molecular and cellular biology, animal models, human genetics, and clinical collaborations with hospitals. Importantly, the number of scientists that have joined forces to develop novel drugs relying on the Experimental Therapeutics Programme capacity has grown most notably in 2017. Each one of these activities can lead to know- how and/or goods that can be beneficial to the patients and to the health sector beyond the boundaries of academic research − It is the role of the Direction of Innovation to gear up this transition. This activity is essential to translate our discoveries and to make an impact on the patient community as well as on the health and economic system. Additionally, it contributes to the generation of income for CNIO in the form of royalties, which help the CNIO, its groups and the inventors themselves to further pursue their goals. In 2017, a remarkable step was taken under the leadership of Manuel Serrano ; the start-up of a new company based on his research in the field of senescence, which has applications in cancer treatment and other diseases such as pulmonary fibrosis, took place. A patent based on discoveries made by Nabil Djouder’s group was licensed to the Spanish company Stemtek Therapeutics for the development of compounds to treat and prevent hepatocellular carcinoma and other tumours. CNIO has applied for 5 novel patents covering a wide range of applications such as novel targets, tissue regeneration, nano-systems to deliver cancer drugs to the tumour site, and methods to treat metastasis in the brain. We continue to strengthen our ties with industry, and to build research collaborations to advance research results towards the generation of novel products useful to patients. In 2017, scientists at the CNIO, in collaboration with local industry leaders, presented 5 innovative projects for competitive funding under private-public partnerships. Commercialisation and return on investment in research remain priorities. Royalty income in 2017 raised more than 550 thousand euros. This includes revenues from patent licences as well as from commercialisation of research tools such as monoclonal antibodies. A total of 52 inventors, nearly 15% of the researches at CNIO, have contributed and benefited from this achievement. The CNIO External Scientific Advisory Board ( SAB ), currently chaired by Mariann Bienz, is of utmost importance for guiding the strategic plans of the CNIO as well as for the review of our research groups. In June 2017, 2 Research Programmes were evaluated by the SAB, namely the Clinical Research Programme ( CRP ) and the Cancer Genetics Programme ( CGP ). As a result of this evaluation, we also conducted a review procedure to promote Nabil Djouder from Junior Group Leader to a full CNIO Group Leader position. Congratulations Nabil ! I would like to take this opportunity to thank all those who have helped the CNIO by sponsoring our students, postdoctoral programmes and the stays of several researchers. I hereby extend my gratitude to the Banco Santander Foundation for funding postdoctoral stays at the CNIO and the IE Business School course ; the ”la Caixa ” Foundation for fostering international PhD fellowships as well as for sponsoring the CNIO Frontiers Meetings ; the Seve Ballesteros Foundation that supports the Seve-Ballesteros Foundation-CNIO Brain Tumour Group ; and the Jesus Serra Foundation for supporting the Visiting Scientists Programme as well as the Dean’s Office. During 2017, we hosted Raul Rabadan, Associate Professor of the Department of Biomedical Informatics at the Columbia University of NewYork, USA ; and Wolfgang Weninger, Head of the Department of Dermatology at the Royal Prince Alfred Hospital of Sydney, Australia. I also wish to thank the Foundation Banc Sabadell for sponsoring the Distinguished Seminars hosted at the CNIO and given by ‘ outside-the-box speakers ’ who provided novel perspectives that contribute to the CNIO’s transdisciplinary environment. During 2017, we had the privilege to listen to : Tom Kirkwood, from the Newcastle University Institute for Ageing, UK ; Vera Gorbunova, from the University of Rochester, New York, USA ; José Luis Sanz from the Autonomous University of Madrid ( UAM ), Spain ; Nuria Oliver from the Data-Pop Alliance, New York, USA ; and Óscar Marin, Director of the MRC Centre for Developmental Neurobiology at King’s College, London, UK. I would also like to thank the British Embassy of Madrid for sponsoring a seminar given by Ricardo Baptista, of the Cell and Gene Therapy Catapult, UK. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 11 FOREWORD Furthermore, I would like to highlight the work that is being carried out by the CNIO Women and Science ( WISE ) Office. During 2017, we had the pleasure of listening to Maria Ángeles Durán, ad honorem Professor of the Center for Human and Social Sciences ( CSIC ); Belén Yuste and Sonnia L. Rivas-Caballero, of Rocaviva Eventos, Madrid ; Teresa Jurado and Mariano Nieto of the Plataforma por Permisos Iguales e Intransferibles de Nacimiento y Adopción, Madrid ; Ana Botella, Politician and ex-Mayor of Madrid ; Natalia Flores Sanz, ex player of the Spanish National indoor Football team and Director of the Woman and Sport programme of the Consejo Superior de Deporte ; Katharina Miller, Founder Partner of the 3CCompliance, Madrid ; Ana Requena, Journalist and Columnist at “ El Diario ”; and Margarita de Cos, Head of the Major Donors Relations WWF Spain and CEO of Riansoft SL, Madrid. Moreover, on the occasion of International Women’s Day, a theatre play was performed at the CNIO, namely “ Una Habitación Propia ”, based on Virginia Woolf’s speech, with Maria Ruiz as stage director and Clara Sanchis as actress. In 2017, advances and discoveries made at the CNIO were very well received and attracted broad media coverage, with over 2,300 appearances in the press ( on line and on paper ), and nearly 200 appearances on radio and TV, representing an increase of 63% compared to the previous year. Throughout the year, the featured stories received nearly 52,222 hits ( EurekAlert ! news service ) from around the world. During this year, the CNIO established an agreement with the TV & Media Group Atresmedia, one of the leading media groups in Spain, and the AXA Foundation to disseminate scientific knowledge and to foster scientific values. Through this agreement, CNIO celebrated World Cancer Research Day with the event ‘ Present and Future of Cancer Research ’, which took place at El Matadero – one of the most vibrant and cultural venues in Madrid − and enjoyed the participation of Nobel Prize- winner Harald zur Hausen as guest of honour, as well as Ángela Nieto, from the Institute of Neurosciences ( CSIC-UMH ), Pilar Garrido, Chief Oncologist at the Hospital Ramón y Cajal and myself. The year 2017 has been the year in which we reaffirmed and renewed our image. We adopted a new logo, which can be found on the CNIO website and our social media accounts. This new image is another way of transmitting the values and mission of the CNIO, the picture on our passport. Therefore, we said goodbye to the logo that has served us well since the Centre’s inception, and we have welcomed a new one that is elegant, clear-cut and faithful to our origins at the Carlos III Health Institute. The renewed CNIO branding matches the leading-edge nature of our research and brings our image into the present. The ‘ CNIO Friends ’ initiative, devoted to raising funds for cancer research at the CNIO, celebrated its first 3 years of existence at the end of 2017. At that time, the initiative had about 900 Friends who showed their unwavering commitment at all times. Thanks to them, we were able to put 2 more cancer research grants in place in 2017. In addition to the first 2 ‘ CNIO Friends ’ grants and the Juegaterapia Foundation grant, 2 more researchers were awarded with these two CNIO Friends Grants : Sebastian Thompson, from the Growth Factors, Nutrients and Cancer Group, and Carolina Maestre, from the Cell Division and Cancer Group. Beyond other activities, the CNIO presented the book Excelentes that features artistic photographs and personal stories by some of the most influential people who have visited the Centre in recent years, such as the Nobel laureates Elizabeth Blackburn and Paul Nurse, the physicist Ignacio Cirac or the palaeontologist Juan Luis Arsuaga. The funds collected through this book, on sale at stores like El Corte Inglés, VIPS and the CNIO store, go directly to the ‘ CNIO Friends ’ initiative, which motivates us even more to keep working on the important cause of cancer research. In December, CNIO launched a campaign with the participation of 2 of Spain’s best humourists, José Mota and Mago More, who offered their image and ingenuity to the service of CNIO Friends. Mota and More made their message clear : “ If many of us provide a bit, we will all do a lot.” The CNIO has a rich history when it comes to science outreach activities. In 2017 we launched a new project that aims to centralise all of CNIO’s efforts in terms of bringing science and research to the general public. CNIO & The City seeks to encourage creativity and scientific vocations by providing secondary school students with direct access to science, as well as providing new tools for teachers to consolidate this goal. During its first edition, more than 150 students and teachers took part in this initiative. Last but not least, I would like to thank all the CNIO volunteers who make it possible for us to move our mission forward, and of course, to the entire CNIO Friends community. Combining society’s efforts with the endeavours of the research community can make a significant difference for the future of cancer treatment. Finally, I would like to thank all of those who have once again collaborated on the elaboration of this Annual Report, with especial thanks to Sonia Cerdá who is responsible for this CNIO publication, as well as to our collaborators : the visual artist Amparo Garrido and the Underbau graphic design team. ANNUAL REPORT 2017 OSCAR FERNÁNDEZ-CAPETILLO Vice-Director SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 13 “ During 2017, CNIO scientists have made important contributions that help us to understand why cancer occurs, how we can prevent it, and ultimately how we can treat it if prevention fails.” The end of the year is a good time to look back and reflect on the overall progress that has been made − with a bit of a panoramic view, I can only say that our scientists have, one more year, made amazing contributions to cancer research. We now have mice that can predict where metastasis will emerge, and a better knowledge of how the protein content in the diet or cholesterol levels influence cancer development. We have discovered new therapeutic approaches for cancers with poor prognosis and found that certain cancer treatments might be bad for our hearts, thereby providing clinicians with an important alert of what to watch for in patients treated with these agents. We have understood the paradox of why certain oncogenes lead to tumour development upon their inactivation, and found new mutations that cause neuroendocrine hereditary cancers. We have made progress in understanding the consequences of abnormal DNA replication for mammalian health, and generated new tools to model cancer mutations in the lab. These are all great indicators of the excellence of our science, and illustrate that CNIO is still a superb place to be a scientist. Last but certainly not least, I want to acknowledge that these and other important works would not have been possible without the continuous support provided by all the CNIO personnel who facilitate our daily activities. We are all CNIO. Thank you for your help. ANNUAL REPORT 2017 ORGANISATION OF RESEARCH MARIA A. BLASCO DIRECTOR ÓSCAR FERNÁNDEZ-CAPETILLO VICE-DIRECTOR BASIC RESEARCH MOLECULAR ONCOLOGY PROGRAMME Manuel Serrano Programme Director (until April) Manuel Serrano (until April) Tumour Suppression Group Mariano Barbacid Experimental Oncology Group Maria A. Blasco Telomeres and Telomerase Group Marcos Malumbres Cell Division and Cancer Group Óscar Fernández-Capetillo Genomic Instability Group Ana Losada Chromosome Dynamics Group Juan Méndez DNA Replication Group María S. Soengas Melanoma Group Héctor Peinado Microenvironment and Metastasis Junior Group Manuel Valiente Brain Metastasis Junior Group Alejo Efeyan Metabolism and Cell Signalling Junior Group CANCER CELL BIOLOGY PROGRAMME Erwin F. Wagner Programme Director Erwin F. Wagner Genes, Development and Disease Group Francisco X. Real Epithelial Carcinogenesis Group Mirna Pérez-Moreno Epithelial Cell Biology Junior Group Nabil Djouder Growth Factors, Nutrients and Cancer Junior Group Massimo Squatrito Seve Ballesteros Foundation-CNIO Brain Tumour Junior Group STRUCTURAL BIOLOGY PROGRAMME Óscal Llorca (since July) / Alfonso Valencia (until February) Programme Director Oscar Llorca (since July) Macromolecular Complexes in DNA Damage Response Group Alfonso Valencia (until February) Structural Computational Biology Group Daniel Lietha Cell Signalling and Adhesion Junior Group Santiago Ramón-Maiques (until February) Structural Bases of Genome Integrity Junior Group Ivan Plaza-Menacho (since May) Kinases, Protein Phosphorylation and Cancer Junior Group Rafael Fernández Leiro (since September) Genome Integrity and Structural Biology Junior Group Ramón Campos-Olivas Spectroscopy and Nuclear Magnetic Resonance Unit Fátima Al-Shahrour Bioinformatics Unit Salvador J. Capella Gutierrez (until June) National Bioinformatics Institute Unit Jasminka Boskovic Electron Microscopy Unit Inés Muñoz Crystallography and Protein Engineering Unit Martin Krallinger Biological Text Mining Unit SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 15 TRANSLATIONAL RESEARCH HUMAN CANCER GENETICS PROGRAMME Javier Benítez Programme Director Javier Benítez Human Genetics Group Mercedes Robledo Hereditary Endocrine Cancer Group Núria Malats Genetic and Molecular Epidemiology Group Miguel Urioste Familial Cancer Clinical Unit Sandra Rodríguez Moleculra Cytogenetics and Genome Editing Unit Anna González-Neira Human Genotyping-CEGEN Unit CLINICAL RESEARCH PROGRAMME Miguel Quintela-Fandino Acting Programme Director Miguel Quintela-Fandino Breast Cancer Junior Clinical Research Unit David Olmos Prostate Cancer Junior Clinical Research Unit Luis J. Lombardía Molecular Diagnostics Unit Joaquín Martínez-López H12O-CNIO Haematological Malignancies Clinical Research Unit Luis Paz-Ares H12O-CNIO Lung Cancer Clinical Research Unit BIOBANK Manuel M. Morente Director INNOVATION ÓSCAR FERNÁNDEZ-CAPETILLO DIRECTOR OF INNOVATION BIOTECHNOLOGY PROGRAMME Fernando Peláez Programme Director Orlando Domínguez Genomics Core Unit Sagrario Ortega Transgenic Mice Core Unit Giovanna Roncador Monoclonal Antibodies Core Unit Francisca Mulero Molecular Imaging Core Unit Lola Martínez Flow Cytometry Core Unit Diego Megías Confocal Microscopy Core Unit Javier Muñoz Proteomics Core Unit Vacant Histopathology Core Unit Isabel Blanco Animal Facility ( Vivotecnia Management & Services ) EXPERIMENTAL THERAPEUTICS PROGRAMME Joaquín Pastor Programme Director Sonia Martínez Medicinal Chemistry Section Carmen Blanco Biology Section Susana Velasco CNIO-Lilly Cell Signalling Therapies Section María José Barrero CNIO-Lilly Epigenetics Section TECHNOLOGY TRANSFER AND VALORISATION OFFICE Anabel Sanz Director ANNUAL REPORT 2016 16 Basic Research SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 17 Molecular Oncology Programme 18 Tumour Suppression Group 20 Experimental Oncology Group 24 Telomeres and Telomerase Group 28 Cell Division and Cancer Group 32 Genomic Instability Group 36 Chromosome Dynamics Group 40 DNA Replication Group 44 Melanoma Group 48 Microenvironment & Metastasis Junior Group 52 Brain Metastasis Junior Group 54 Metabolism and Cell Signalling Junior Group 56 Cancer Cell Biology Programme 58 Genes, Development and Disease Group 60 Epithelial Carcinogenesis Group 64 Epithelial Cell Biology Junior Group 68 Growth Factors, Nutrients and Cancer Junior Group 70 Seve Ballesteros Foundation-CNIO Brain Tumour Junior Group 72 Structural Biology Programme 74 Macromolecular Complexes in DNA Damage Response Group 76 Cell Signalling and Adhesion Junior Group 80 Structural Bases of Genome Integrity Junior Group 82 Kinases, Protein Phosphorylation and Cancer Junior Group 84 Genome Integrity and Structural Biology Junior Group 86 Spectroscopy and Nuclear Magnetic Resonance Unit 88 Bioinformatics Unit 90 Electron Microscopy Unit 92 Crystallography and Protein Engineering Unit 94 Biological Text Mining Unit 96 Structural Computational Biology Group 98 National Bioinformatics Institute Unit 99 ANNUAL REPORT 2017 18 BASIC RESEARCH MOLECULAR ONCOLOGY PROGRAMME MANUEL SERRANO ( until April ) Programme Director The time has come for me to say “ good bye ”. I will not be far away and I will often be around, so rather than saying an actual farewell, what I really want to put into words is a big “ THANK YOU ” to the CNIO in general and, in particular, to my colleagues in the Molecular Oncology Programme. I have been with the CNIO since 2003, and looking back at all my time in the Centre, I am amazed by how much I have managed to accomplish scientifically at the CNIO. The CNIO put to my service the best scientific facilities that I could ever have imagined. I am deeply grateful to the superb scientists of the Biotechnology Programme. The Centre has also given me high-level visibility through the constant organisation of meetings, conferences and seminars. But most importantly, I have been surrounded by the best possible colleagues, creative, ambitious and always helpful. The scientists at the CNIO have been my main source of inspiration for new ideas and bestowed me with the necessary confidence for exploring new fields of research. It has been a great satisfaction for me to have served as the Director of the Molecular Oncology Programme since 2012. Despite the complicated times in terms of funding and hiring, with everyone’s help, we have been able to grow with the addition of three new Junior Groups that have brought new topics, new ideas and enthusiasm. Thank you for having joined us ! I will continue to bother you all to ask for your help, advice or reagents ; thanks in advance ! Needless to say, count on me whenever I can be of help to any of you, I’ll do my best ! Let’s keep in touch ! SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 19 MOLECuLAR ONCOLOGy PROGRAMME The Molecular Oncology Programme is the largest basic research programme at the CNIO, encompassing a total of 8 Research Groups and 3 Junior Research Groups. The Programme focuses on the study of some of the most active areas of research in cellular oncology, including DNA and chromosome stability ( Maria A. Blasco, Óscar Fernández-Capetillo, and Ana Losada ), oncogenes and cell cycle kinases ( Mariano Barbacid ), DNA replication ( Juan Méndez ), mitosis ( Marcos Malumbres ), tumour suppressors ( Manuel Serrano ), molecular mechanisms in melanoma ( María S. Soengas ), metabolism and cell signalling ( Alejo Efeyan ), and metastasis ( Manuel Valiente and Héctor Peinado ). This year, the Molecular Oncology Programme has continued to be on the frontline of oncology research. The top-level quality of the research conducted by each of these Groups is detailed in the following pages. In 2017, the Programme has authored a total of 11 papers in Nature journals ( Nature 5×, Nature Medicine, Nature Reviews Cancer, Nature Cell Biology and Nature Communications 3×) and 7 papers in Cell Journals ( Cancer Cell, Cell, Cell Stem Cell 2x, Cell Metabolism 2x and Trends in Cell Biology ); this trend continues with New England Journal of Medicine, Circulation Research, JACS , The Journal of Clinical Investigation and PNAS. Also, during this year, researchers from the Programme have filed several patents, some of which have been licensed, and a spin-off company has been created. Over the year to come we hope to continue to make many exciting discoveries, further increase the quality of scientific production and strive to impact on cancer research and cancer therapeutics. We would like take this opportunity to thank our former Programme Director, Manuel Serrano, who has served as the Director of the Molecular Oncology Programme since 2012. Manuel Serrano and his group left the CNIO in April 2017 to join the Institute for Research in Biomedicine ( IRB Barcelona ). We are thankful to him for his important contributions as well as for his unconditional support in bringing new ideas and challenges to the Programme. Thank you Manuel for having been a part of our CNIO community and we wish you the best in your new position ! A new Director for the Molecular Oncology Programme will be appointed soon. We are confident that, under a new leadership, the Programme will continue to make significant discoveries and generate knowledge that can be translated into better care for cancer patients. Maria A. Blasco, Director Óscar Fernández-Capetillo, Vice Director ANNUAL REPORT 2017 20 BASIC RESEARCH TUMOUR SUPPRESSION GROUP Manuel Serrano Group Leader Associate Investigator ( since May, from the IRB Barcelona ) Staff Scientists Susana Llanos, Bárbara Martínez ( until April ), Cristina Pantoja ( until April ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 21 MOLECuLAR ONCOLOGy PROGRAMME | TUmOUR SUPPRESSION GROUP OVERVIEW Our Group upholds the unifying concept that tumour suppressor genes protect against many types of damage, no matter what the potential detrimental consequences of the damage might be. Tumour suppressors, therefore, confer protection from damage even if that damage is not going to lead to cancer, but to a degenerative disease instead. Cancer protection would thus be just one of the outcomes of tumour suppressors, with other outcomes being protection from degenerative diseases, from nutritional overload, from tissue injuries, or from ageing. We aim to achieve an integrated understanding of the protection provided by tumour suppressors. Our goals are to : ɗ Understand tumour suppression mechanisms and identify new tumour suppressor regulators. ɗ Study the interplay between tumour suppression and ageing. ɗ Characterise cellular senescence as a tumour suppression mechanism. ɗ Investigate cellular pluripotency and the involvement of tumour suppressors in the regulation of reprogramming to pluripotent stem cells. ɗ Explore the role( s ) of cell plasticity in cancer, tissue regeneration, and ageing. ɗ Search for new frontiers in cell plasticity. “ We have developed a strategy for the targeted delivery of drugs that is therapeutically efficient against tumours treated with senescence- inducing chemotherapies.” Post-Doctoral Fellows Timothy Cash ( until July ), Cian J. Lynch ( until April ), Gianluca Varetti ( until April ), Maté Maus ( until April ) Graduate Students Noelia Alcázar, Raquel Bernad ( until April ), Selim Chaib ( until April ), Dafni Chondronasiou ( until July ), Lluc Mosteiro ( until June ), Miguel Rovira ( until July ) Technicians Maribel Muñoz ( until April ) ( TS )*, Yolanda Durán ( since May ) *Titulado Superior ( Advanced Degree ) ANNUAL REPORT 2017 22 BASIC RESEARCH RESEARCH HIGHLIGHTS A novel RNA Polymerase II regulator critical for cell identity The mechanisms underlying cell plasticity are poorly understood. The activation or silencing of enhancers is thought to be at the core of cell identity and, therefore, changes in enhancers underlie cell plasticity. The Mediator complex is critical for the function of enhancers, serving to communicate the enhancers with the RNA polymerase II at promoters. We have characterised a novel regulator of RNA Polymerase II called RPAP1 ( RNA Polymerase II Associated Protein 1 ), which is critical for the interaction between Pol II and Mediator, as well as for the recruitment of the key factor Gdown1 ( FIGURE 1 ). RPAP1 is essential for the expression of cell identity genes and for viability. Depletion of RPAP1 erases cell identity gene expression and triggers cell de-differentiation, facilitates reprogramming towards pluripotency, and impairs differentiation. We have concluded that Mediator-RPAP1-Pol II is an ancient module, conserved from plants to mammals, which is critical for establishing and maintaining cell identity. A new therapeutic strategy for drug delivery into senescent cells Severe or unrepairable cellular damage often triggers a stereotypical cellular response known as senescence. Senescent cells accumulate in many ageing-associated diseases, contributing actively to their pathological manifestations. Genetic ablation of senescent cells delays and ameliorates some ageing-associated diseases, reverts long-term degenerative processes associated to chemotherapy, and extends longevity. The pharmaceutical targeting of senescent cells is emerging as a promising therapeutic approach. We have exploited the characteristic high levels of lysosomal β-galactosidase activity that exist in senescent cells as a vulnerable trait in order to design a drug delivery system that targets senescent cells. This system is based on the encapsulation of drugs with galacto-oligosaccharides ( FIGURE 2 ). We have shown that gal-encapsulated drugs are preferentially released within senescent cells in mice, and that this targeted delivery strategy is therapeutically efficient in vivo. In a model of cancer chemotherapy, gal-encapsulated cytotoxic drugs target tumour cells undergoing chemotherapy-induced senescence and contribute to tumour xenograft regression. In the context of pulmonary fibrosis in mice, gal-encapsulated cytotoxics target senescent cells, reducing collagen deposition and ameliorating pulmonary function. Importantly, gal-encapsulation reduces the systemic toxicity of the cytotoxic drugs. Drug delivery into senescent cells opens up new diagnostic and therapeutic applications in senescence-associated disorders. p16INK 4a and IL6 play a critical role in the interplay between senescence and reprogramming Cellular senescence is a damage response aimed to orchestrate tissue repair. We have recently reported that cellular senescence, through the production of interleukin-6 and other soluble factors, strongly favours cellular reprogramming by Oct4, Sox2, Klf4 and cMyc ( OSKM ). The expression of an OSKM transgene results in senescence and reprogramming in different cell populations, both processes occurring in close proximity. In this system, upon OSKM activation, Ink4/Arf-null tissues cannot undergo senescence, fail to produce IL6 and cannot reprogram efficiently ; whereas the absence of p53 results in extensive tissue damage, high levels of senescence and IL6, and efficient reprogramming. We have explored some genetic determinants of in vivo reprogramming. We have found that Ink4a, but not Arf, is critical for OSKM- induced senescence and, thereby, for the paracrine stimulation of reprogramming. Interestingly, p53 deficiency renders IL6 production and reprogramming independent of Ink4a, as implied by the high levels of IL6 and reprogramming in triply deficient p53/Ink4a/Arf mice. We have also observed that Il6-deficient mice present profoundly reduced levels of reprogramming, therefore, providing genetic proof for the critical role of IL6 in reprogramming. Finally, young female mice present lower efficiency of in vivo reprogramming compared to male mice, and this gender difference disappears with ageing, which is consistent with the anti-inflammatory effect of oestrogens. These findings regarding the interplay between senescence and reprogramming may conceivably apply to other contexts of tissue damage. s SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 23 MOLECuLAR ONCOLOGy PROGRAMME | TUmOUR SUPPRESSION GROUP ∞ PUBLICATIONS ∞ Serrano M ( 2017 ). Understanding aging. New Eng J Med 376, 1083-1085. ∞ Serrano M ( 2017 ). Ageing : Tools to elimi- nate senescent cells. Nature 545, 294-296. ∞ Fernandez-Marcos PJ, Serrano M ( 2017 ). Young and lean : elimination of senescent cells boost adaptive thermogenesis. Cell Metab 25, 226-228. ∞ Kälin S, Becker M, Ott VB, Serr I, Hosp F, Mollah MMH, Keipert S, Lamp D, Roh- ner-Jeanrenaud F, Flynn VK, Scherm MG, Nascimento LFR, Gerlach K, Popp V, Diet- zen S, Bopp T, Krishnamurthy P, Kaplan MH, Serrano M, Woods SC, Tripal P, Palmisano R, Jastroch M, Blüher M, Wolfrum C, Weig- mann B, Ziegler AG, Mann M, Tschöp MH, Daniel C ( 2017 ). A Stat6/Pten Axis Links Regulatory T Cells with Adipose Tissue Function. Cell Metab 26,475-492. ∞ Lozano-Torres B, Galiana I, Rovira M, Gar- rido E, Chaib S, Bernardos A, Muñoz-Espín D, Serrano M, Martínez-Máñez R, San- cenón F ( 2017 ). An OFF-ON Two-Pho- ton Fluorescent Probe for Tracking Cell Senescence in Vivo. J Am Chem Soc 139, 8808-8811. ∞ Horikawa I, Park KY, Isogaya K, Hiyoshi Y, Li H, Anami K, Robles AI, Mondal AM, Fujita K, Serrano M, Harris CC ( 2017 ). Δ133p53 represses p53-inducible senescence genes and enhances the generation of human induced pluripotent stem cells. Cell Death Differ 24, 1017-1028. ∞ Marion RM, Lopez de Silanes I, Mosteiro L, Gamache B, Abad M, Guerra C, Megias D, Serrano M, Blasco MA ( 2017 ). Common telomere changes during in vivo repro- gramming and early stages of tumorigen- esis. Stem Cell Rep 8, 460-475. ∞ Gómez-Cabello D, Checa-Rodríguez C, Abad M, Serrano M, Huertas P ( 2017 ). CtIP-Specific Roles during Cell Repro- gramming Have Long-Term Consequences in the Survival and Fitness of Induced Pluripotent Stem Cells. Stem Cell Rep 8, 432-445. ∞ Evangelou K, Lougiakis N, Rizou SV, Kot- sinas A, Kletsas D, Muñoz-Espín D., Kastri- nakis NG, Pouli N, Marakos P, Townsend P, Serrano M, Bartek J, Gorgoulis VG ( 2017 ). Robust, universal biomarker assay to de- tect senescent cells in biological speci- mens. Aging Cell 16, 192-197. ∞ Mosteiro L, Pantoja C, de Martino A, Serrano M ( 2017 ). Critical role of p16INK 4a and IL6 in the in vivo interplay between senescence and reprogramming. Aging Cell. PMID : 29280266. ∞ Sánchez-Luengo MA, Rovira M, Serrano M, Fernandez-Marcos PJ, Martínez L ( 2017 ). Analysis of the advantages of cis reporters in optimized FACS-Gal. Cytometry A 91, 721-729. ∞ Kannappan K, Matsuda A, Ferreira-Martins J, Zhang E, Palano G, Czarna A, Castro Cabral-Da-Silva M, Bastos-Carvalho A, Sanada F, Ide N, Rota M, Blasco MA, Serrano M, Anversa P, Leri A ( 2017 ). P53 modulates the fate of cardiac progenitor cells ex vivo and in the diabetic heart in vivo. EBioMedicine 16, 224-237. ∞ PATENTS ∞ Martinez Mañez R, Serrano Marugán M, Murguía Ibáñez JR, Bernardos Bau A, Díaz De Greñu Puertas B, Galiana Guillem I, Lozano Torres B, Rovira Del Olmo M, Sancenón Galarza F ( 2017 ). Therapeutic derivatives. PCT/ES2017/070079. ∞ Serrano Marugán M, Llanos Girón S, Chaib AS ( 2017 ). Identification and elimina- tion of damaged and/or senescent cells. EP17382417. ∞ Serrano Marugán M, Muñoz Espín D, Rovira Del Olmo M, Bernardos Bau A, Galiana Guillem I, Lozano Torres B, Martinez Mañez R, Sancenón Galarza F ( 2017 ). Therapeutic nanoparticles. EP17382901.1. Figure 1 Model for RPAP1 function. RPAP1 exists in complex with RNA Pol II, playing an essential role in the Mediator-Pol II regulatory axis. Loss of RPAP1 impairs the association between Mediator and Pol II affecting the ability of enhancers to activate Mediator target genes, thereby, disrupting cell identity. Figure 2 Senescent cells targeted drug delivery system. GalNP beads consist of a mesoporous silica scaffold loaded with different cargoes encapsulated by a coat of galacto-oligosaccharides. Cellular uptake of the GalNP beads occurs via endocytosis and after fusion with lysosomal vesicles the beads are secreted by exocytosis. The release of the cargo requires β-galactosidase- mediated hydrolysis of the cap and this occurs preferentially in senescent cells due to their high levels of lysosomes and β-galactosidase activity. ANNUAL REPORT 2017 24 BASIC RESEARCH EXPERIMENTAL ONCOLOGY GROUP Mariano Barbacid Group Leader Staff Scientists Matthias Drosten, Raquel García- Medina, Carmen Guerra, Monica A. Musteanu SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 25 MOLECuLAR ONCOLOGy PROGRAMME | ExPERImENTAL ONCOLOGy GROUP OVERVIEW KRAS oncogenes have been implicated in one fifth of all human tumours including lung and pancreatic adenocarcinomas, two tumour types with some of the worse prognosis. Unfortunately, identification of suitable therapies to treat these tumours remains elusive and patients are still treated with cytotoxic compounds approved over 2 decades ago. The recent discovery that tumours display intra-tumour heterogeneity adds another layer of complexity that needs to be addressed. Hence, we have decided to search for novel therapeutic targets that contribute to the early stages of tumour development, arguing that they should be present in all tumour cells and not only in evolving clones. In addition, we have continued our quest to validate known targets among the members of the MAPK and PI3K pathways using genetically engineered mouse tumour models with the ultimate goal of establishing rational combination therapies that may provide significant therapeutic benefits in the clinic. “ We have demonstrated that the Capicua transcription factor is a tumour suppressor capable of inducing thymomas. We have also demonstrated that kinase dead B-Raf mutants are oncogenic. Tumours harbouring these BRAF mutants are sensitive to the inhibitors of receptor tyrosine kinases, hence offering novel treatment options for these cancer patients.” Post-Doctoral Fellows Harrys K.C. Jacob ( until March ), Carolina Navas ( since March ), Guillem Paniagua ( since March ) Graduate Students M. Teresa Blasco, Laura De Esteban, Magdolna Djurec, Fernando Fernández, Jing Li, Laura Martín, Lucía Morales ( since November ), Marina Salmón, Manuel Sanclemente Visiting Graduate Students Lavinia Cabras ( Università di Cagliari, Italy ), Zhu Xiao-Xu ( Sun Yat-sun University, Guangzhou, China ) ( since October ) Technicians M. Carmen González ( TS )*, Silvia Jiménez, Marta San Román, Raquel Villar *Titulado Superior ( Advanced Degree ) External Associates Alfredo Carrato ( Hospital Ramón y Cajal, Madrid ), Bruno Sainz ( Universidad Autónoma de Madrid ), Juan Velasco ( Lilly Spain ) ANNUAL REPORT 2017 26 BASIC RESEARCH RESEARCH HIGHLIGHTS A B-Raf kinase inactive mutant is a driver oncogene in lung adenocarcinoma The initiating oncogenic event in almost half of human lung adenocarcinomas is still unknown ; a fact that complicates the development of selective targeted therapies. We have demonstrated that expression of an endogenous B-RafD 631A kinase inactive isoform, present in a significant percentage of human lung tumours, triggers lung adenocarcinoma in vivo, indicating that BRAF inactivating mutations represent novel oncogenic drivers. Moreover, these BRAF mutations have also been identified in a subset of K-RAS driven human lung tumours. Co-expression of K-RasG 12V and B-RafD 631A mutations dramatically enhances tumour initiation, a phenomenon mediated by c-Raf kinase activity and that effectively accelerates tumour progression in advanced lung adenocarcinomas. Concomitant ablation of the wild type B-Raf allele prevents lung adenocarcinoma by inducing oncogenic toxicity. Loss of B-Raf expression in this scenario also induces trans-differentiation of Clara cells, leading to the development of intrabronchiolar lesions that result in the rapid death of the mice. We have also shown that this class of BRAF mutants are sensitive to ERK-mediated feedback and that their activation of signalling is dependent on RAS activation. The dependence of these mutants on RAS suggests that their activation of ERK signalling requires incomplete feedback inhibition of RAS activation. Indeed, these are sensitive to inhibition of RAS activation, which can be achieved by using available inhibitors of tyrosine protein kinase receptors. Inactivation of Capicua in adult mice causes T cell lymphoblastic lymphoma Capicua ( CIC ) is a transcriptional repressor negatively regulated by RAS/MAPK signalling. CIC is inactivated in a variety of human tumours and has recently been implicated in lung metastasis. Here, we describe a mouse model in which we inactivate Cic by blocking its transcriptional repressor activity. Cic function is essential for embryonic development but not for adult homeostasis. Systemic inactivation of Cic in adult mice results in T-cell acute lymphoblastic lymphoma ( T-ALL ) with high penetrance. Although Cic inactivation induces a large transcriptional program, T-ALL is mediated by the selective expression of the Etv4 transcription factor. We also show that a genetic signature indicative of Cic inactivation is enriched in Ras-induced T-ALL. Indeed, Cic mutations render T-ALL insensitive to MEK inhibitors. More importantly, human T-ALL also displays this signature, indicating that CIC inactivation plays a key role in this human malignancy and may confer resistance to inhibitors of the MAPK pathway. In vivo oncogenic conflict triggered by co-existing KRAS and EGFR activating mutations in lung adenocarcinoma Activating mutations in KRAS and EGFR, the two most frequent oncogenic drivers in human lung adenocarcinoma, occur in a mutually exclusive manner suggesting functional redundancy and implying lack of positive selection. By means of a mouse model engineered to induce expression of mutant EGFRL 858R in advanced tumours driven by a resident KrasG 12V oncogene we show that, instead, their co-expression is detrimental for the progression of lung adenocarcinoma. In vivo, expression of EGFRL 858R in KrasG 12V-driven tumours triggers an immediate response with hallmarks of replicative stress resulting in apoptosis. Yet, a fraction of tumour cells survive but enter a transient cytostatic state incompatible with tumour development that is fully reversible upon discontinuation of EGFRL 858R expression. Ultimately, continuous co-expression of both mutants results in the attenuation of the overall oncogenic signalling to levels ∞ PUBLICATIONS ∞ Nieto P, Ambrogio C, Esteban-Burgos L, Gómez-López G, Blasco MT, Yao Z, Marais R, Rosen N, Chiarle R, Pisano DG, Barbacid M, Santamaría D ( 2017 ). A Braf kinase-inactive mutant induces lung ade- nocarcinoma. Nature 548, 239-243. ∞ Yao Z, Yaeger R, Rodrik-Outmezguine VS, Tao A, Torres NM, Chang MT, Dros- ten M, Zhao H, Cecchi F, Hembrough T, Michels J, Baumert H, Miles L, Campbell NM, de Stanchina E, Solit DB, Barbacid M, Taylor BS, Rosen N ( 2017 ). Tumors with class 3 BRAF mutants are sensitive to the inhibition of activated RAS. Nature 548, 234-238. Commentaries for these articles ap- peared in : Cancer Discovery : Research Watch, Inactivating BRAF Mutations Modulate RAS–MAPK Signaling, doi : 10.1158/2159- 8290.CD-RW2017-153. Nature Reviews Clinical Oncology : Even kinase-inactive BRAF is oncogenic, doi :10.1038/nrclinonc.2017.140. ∞ Simón-Carrasco L, Graña O, Salmón M, Jacob HKC, Gutierrez A, Jiménez G, Dros- ten M, Barbacid M ( 2017 ) Inactivation of Capicua in adult mice causes T cell lympho- blastic lymphoma. Genes Dev 31, 1456-1468. This article was recommended in F1000Prime as being of special signifi- cance in its field. This article was selected ‘ Paper of the Month ’ by the Spanish Society of Biochem- istry and Molecular Biology ( SEBBM ). ∞ Papale A, d’Isa R, Menna E, Cerovic M, Solari N, Hardingham N, Cambiaghi M, Cursi M, Barbacid M, Leocani L, Fasano S, Matteoli M, Brambilla R ( 2017 ). Severe Intellectual Disability and Enhanced Gam- ma-Aminobutyric Acidergic Synaptogen- esis in a novel model of rare RASopathies. Biol Psychiat 81, 179-192. ∞ Drosten M, Simón-Carrasco L, Hernán- dez-Porras I, Lechuga CG, Blasco MT, Ja- cob HK, Fabbiano S, Potenza N, Bustelo XR, Guerra C, Barbacid M ( 2017 ). H-Ras and K-Ras oncoproteins induce differ- ent tumor spectra when driven by the same regulatory sequences. Cancer Res 77, 707-718. ∞ Forés M, Simón-Carrasco L, Ajuria L, Samper N, González-Crespo S, Drosten M, Barbacid M, Jiménez G ( 2017 ). A new mode of DNA binding distinguishes Capi- cua from other HMG-box factors and ex- plains its recurrent mutation patterns in cancer. PLoS Genet 13, e1006622. ∞ Ambrogio C, Barbacid M, Santamaría D ( 2017 ). In vivo oncogenic conflict trig- gered by co-existing KRAS and EGFR activating mutations in lung adenocarci- noma. Oncogene 36, 2309-2318. ∞ Drosten M, Guerra C, Barbacid M ( 2017 ). Genetically engineered mouse models of K-Ras driven lung and pancreatic tumors : SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 27 MOLECuLAR ONCOLOGy PROGRAMME | ExPERImENTAL ONCOLOGy GROUP compatible with cell proliferation and tumour growth. In sum, our results indicate that the mutual exclusivity of KRAS and EGFR activating mutations occurs as a combination of cellular toxicity and signal adjustment that results in the lack of selective advantage for those cells expressing both oncogenes. s Figure B-RafD 631A is a driver oncogene in lung adenocarcinoma. ( A ) Co-occurrence of B-RAF hypoactive mutants with NF1 and RAS mutations in human skin cutaneous melanoma and lung adenocarcinoma patients. Sample ID as well as the precise mutation/s identified are indicated. ( B ) Representative images of H&E and SPC and CC10 immunostaining of paraffin embedded lung sections from Ad-Cre- infected B-Raf+/LSLD 631A mice sacrificed at humane end-point. Scale bar 500 mM and 50 mM ( top right panel ). ( C ) Representative images of pErk1/2 immunostaining of paraffin embedded lung sections from Ad-Cre-infected K-Ras+/ LSLG 12Vgeo, K-Ras+/LSLG 12Vgeo ;Trp53lox/lox, B-Raf+/ LSLV 637E or B-Raf+/LSLD 631A mice. Scale bar 100 mM. ( D ) Mice carrying a K-Ras+/FSFG 12V allele were infected intratracheally with Ad-Flp and tumour formation was monitored by CT. Mice bearing CT+ tumours were fed ad libitum a tamoxifen-containing diet to activate expression of the B-RafD 468A kinase dead isoform. Tumour volume increase ( measured as fold change ) was calculated after 8 weeks in continuous diet in K-Ras+/ FSFG 12V ;B-Raf+/LSLD 631A ;Tg.hUbCre-ERT2+/T ; ( KFB, n=29 ) and control K-Ras+/FSFG 12V ;Tg. hUbCre-ERT2+/T ( KF, n=38 ) cohorts. Validation of therapeutic targets. In Ad- ditional Perspectives on Ras and Cancer in the 21st Century ( eds. L. VanAelst, J. Downward and F. McCormick ). Cold Spring Harbour Perspect Med. PMID : 28778964. ∞ Lawler M et al. ( incl. Barbacid M ) ( 2017 ). The European Cancer Patient’s Bill of Rights, update and implementation 2016. ESMO OPEN 1, e000127. ∞ Chirivella L, Kirstein M, Ferrón SR, Domin- go-Muelas A, Durupt FC, Acosta-Uman- zor C, Cano-Jaimez M, Pérez-Sánchez F, Barbacid M, Ortega S, Burks D, Fariñas I ( 2017 ). Cdk4 regulates adult neural stem cell proliferation and differentiation in response to insulin-IRS2 signals. Stem Cells 35, 2403-2416. ∞ Schuhmacher AJ, Hernández-Porras I, García-Medina R, Guerra C ( 2017 ). Lessons learnt from genetic studies in mice into Noonan syndrome. Expert Review of En- docrinology and Metabolism 12, 367-378. ∞ Hernández-Porras I, Guerra C ( 2017 ). Modeling Rasopathies with genetically modified mouse models. Methods Mol Biol 1487, 379-408. ∞ Schreiber J, Grimbergen LA, Overwater I, Vaart TV, Stedehouder J, Schuhmacher AJ, Guerra C, Kushner SA, Jaarsma D, El- gersma Y ( 2017 ). Mechanisms underlying cognitive deficits in a mouse model for Costello Syndrome are distinct from other RASopathy mouse models. Sci Rep 7, 1256. ∞ Marión RM, López de Silanes I, Mosteiro Ll, Gamache B, Abad M, Guerra C, Megías D, Serrano M, Blasco MA. ( 2017 ). Common telomere changes during in vivo repro- gramming and early stages of tumori- genesis. Stem Cell Reports 8, 460-475. ∞ Lechuga CG, Simón-Carrasco L, Jacob HKC, Drosten M ( 2017 ). Genetic validation of cell proliferation via Ras-independent activation of the Raf/Mek/Erk pathway. Methods Mol Biol 1487, 269-276. ∞ Shahbazi MN, Peña-Jimenez D, Antonucci F, Drosten M, Perez-Moreno M ( 2017 ). Clasp2 ensures mitotic fidelity and pre- vents differentiation of epidermal kerat- inocytes. J Cell Sci 130, 683-688. ∞ AWARDS AND RECOGNITION ∞ Burkitt Medal, Trinity College Dublin, Ireland. ∞ Lección Conmemorativa Teófilo Hernando, Madrid, Spain. ∞ Chair, Gordon Research Conference on “ Cell Growth & Proliferation ”, Mount Snow, VT, USA. ∞ Keynote Speaker, Gulbenkian & Brabaham Institutes Joint Retreat, Vimeiro, Portugal. ANNUAL REPORT 2017 28 BASIC RESEARCH TELOMERES AND TELOMERASE GROUP Maria A. Blasco Group Leader Staff Scientists Isabel López De Silanes, Rosa M. Marión, Paula Martínez, Marinela Méndez, Águeda M. Tejera ( until October ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 29 MOLECuLAR ONCOLOGy PROGRAMME | TELOmERES ANd TELOmERASE GROUP OVERVIEW We study the mechanisms by which tumour cells are immortal and normal cells are mortal. Immortality is one of the most universal characteristics of cancer cells. The enzyme telomerase is present in more than 95% of all types of human cancers and absent in normal cells in the body. Telomeres are nucleoprotein complexes located at the ends of chromosomes, essential for chromosome protection and genomic stability. Progressive shortening of telomeres associated with organism ageing leads to ageing. When telomeres are altered adult stem cells have a maimed regenerative capacity. Our research focuses on : ɗ Generating mouse models to validate telomeres and telomerase as therapeutic targets for cancer and age-related diseases. ɗ The interplay between telomeres and DNA repair pathways. ɗ The role and regulation of non-coding telomeric RNAs or TERRA. ɗ Testing telomerase gene therapy in ‘ telomere syndromes ’ and age-related diseases. ɗ The role of telomerase and telomeres in adult stem cell biology and in nuclear reprogramming of differentiated cells to iPS cells. “ We have designed an effective therapeutic strategy for the treatment of glioblastoma multiforme based on targeting telomeres by small molecule inhibition of telomeric protein TRF1.” Post-Doctoral Fellow Kurt Whittemore Graduate Students Leire Bejarano, Aksinya Derevyanko ( until April ), Iole Ferrara, Juan José Montero, Miguel Ángel Muñoz, Raúl Sánchez ( since October ) Technicians Ana Carolina Moises Da Silva ( until November ), Rosa M. Serrano Visiting Student Lydia T. Poluha ( since September ) ( University of Salford, Manchester, UK ) ANNUAL REPORT 2017 30 BASIC RESEARCH RESEARCH HIGHLIGHTS The PI3K/AKT pathway modulates telomere protection We have described a role for PI3K/AKT in the regulation of TRF1, an essential component of the shelterin complex. Small molecule inhibitors of PI3K and AKT significantly reduce TRF1 telomeric foci and lead to increased telomeric DNA damage and fragility. We identified PI3Kα as the PI3K isoform responsible for this TRF1 inhibition. We found TRF1 is phosphorylated at different residues by AKT and that these modifications regulate TRF1 protein stability and TRF1 in vitro binding to telomeric DNA ( FIGURE 1 ), and that they are important for in vivo TRF1 telomere location and cell viability. Patient-derived xenograft ( PDX ) breast cancer mouse models that responded effectively to a PI3Kα-specific inhibitor showed decreased TRF1 levels and increased telomeric DNA damage. Our discovery that the telomeric protein TRF1 is regulated by the PI3K signalling pathway not only functionally connects two of the hallmarks of cancer and ageing, but also pinpoints PI3K and AKT as novel targets for telomere-based therapies in cancer and age-related diseases. Targeting telomeres as a therapeutic strategy for Glioblastoma Multiforme ( GBM ) Glioblastoma multiforme is a deadly and common brain tumour. Its poor prognosis is linked to high proliferation and cell heterogeneity, including glioma stem cells ( GSCs ). Disruption of telomere maintenance is among the most frequent alterations found in human glioblastoma, but no previous studies had validated telomeres as a good target to arrest GBM growth. TRF1 is a shelterin protein essential for both telomere protection and adult and pluripotent stem cells. We demonstrated that disrupting telomere capping through direct inhibition of TRF1 is a promising strategy for the treatment of GBM. We showed that inhibition of TRF1 blocks GBM in both mouse and human models ( FIGURE 2 ). We also established the striking effectiveness of TRF1 inhibition in impairing the growth of glioma stem cells. Our results have a potential impact in cancer treatment as current GBM therapies are unable to kill these cells and patients die because of the strong recurrence of the tumours. TRF1-based gene therapy rescues reduced TRF1 levels with ageing and prolongs mouse health span TRF1 deficiency in the context of different mouse tissues leads to loss of tissue homeostasis due to impaired stem cell function. We have now shown that TRF1 levels decrease during organismal ageing, both in mice and in humans. We also showed that increasing TRF1 expression in both adult and old mice using gene therapy can delay age-associated pathologies. We used the non-integrative adeno-associated serotype 9 vector ( AAV9 ), which allows for moderate and transient TRF1 overexpression. AAV9-TRF1 gene therapy prevented age-related decline in neuromuscular function, glucose tolerance, cognitive function, maintenance of subcutaneous fat, and chronic anaemia. We also found a lower abundance of short telomeres and of telomere- associated DNA damage in some tissues. Rescuing naturally decreased TRF1 levels during mouse ageing results in an improved mouse health span. Common telomere changes during in vivo reprogramming and early stages of tumourigenesis We studied whether tissue dedifferentiation induced by in vivo reprogramming involves changes at telomeres. In the reprogrammed areas, we found telomerase-dependent telomere elongation and telomere length-independent highly upregulated expression of TRF1. TRF1 inhibition reduced in Figure 1 Phosphorylation of TRF1 by AKT stabilises TRF1 telomeric foci. ( A ) AKT phosphorylates TRF1 at T248, T330 and S344 residues. ( B ) Model : PI3K activation leads to AKT-dependent phosphorylation of TRF1 regulating its turn-over and its binding to telomeres. Inhibition of the PI3K pathway results in TRF1 release from telomeres and degradation. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 31 MOLECuLAR ONCOLOGy PROGRAMME | TELOmERES ANd TELOmERASE GROUP ∞ PUBLICATIONS ∞ Bejarano L, Schuhmacher AJ, Méndez-Per- tuz M, Megías M, Blanco-Aparicio C, Martínez S, Pastor J, Squatrito M, Blasco MA ( 2017 ). Inhibition of Trf1 telomere protein impairs tumor initiation and pro- gression in glioblastoma multiform mouse models and patient-derived xenografts. Cancer Cell 32, 590-607. ∞ Marión RM, Blasco MA ( 2017 ). Long Live Partial Reprogramming. Circ Res 120, 1381-1383. ∞ Méndez-Pertuz M, Martínez P, Blan- co-Aparicio C, Gómez-Casero E, García AB, Martínez -Torrecuadrada J, Palafox M, Cortés J, Serra V, Pastor J, Blasco MA ( 2017 ). Modulation of telomere protec- tion by the PI3K/AKT pathway. Nature Communications 8, 1278. ∞ Martínez P, Blasco MA ( 2017 ). Tel- omere-driven diseases and telomere-tar- geting therapies. J Cell Biol 216, 875-887. ∞ Marión RM, López de Silanes I, Mosteiro L, Gamache B, Abad M, Guerra C, Megías D, Serrano M, Blasco MA ( 2017 ). Com- mon Telomere Changes during In Vivo Reprogramming and Early Stages of Tumorigenesis. Stem Cell Reports 8, 460-475. ∞ Derevyanko A, Whittemore K, Schneider RP, Jiménez V, Bosch F, Blasco MA ( 2017 ). Gene therapy with the TRF1 telomere gene rescues decreased TRF1 levels with aging and prolongs mouse health span. Aging Cell 16, 1353-1368. ∞ Quintela-Fandino M, Soberon N, Lluch A, Manso L, Calvo I, Cortes J, Moreno-Antón F, Gil-Gil M, Martinez-Jánez N, Gonza- lez-Martin A, Adrover E, de Andres R, Viñas G, Llombart-Cussac A, Alba E, Mouron S, Guerra J, Bermejo B, Zamora E, García-Saenz JA, Simon SP, Carrasco E, Escudero MJ, Campo R, Colomer R, Blasco MA ( 2017 ). Critically short telomeres and toxicity of chemotherapy in early breast cancer. Oncotarget 8, 21472-21482. ∞ Kannappan R, Matsuda A, Ferreira-Martins J, Zhang E, Palano G, Czarna A, Cabral- Da-Silva MC, Bastos-Carvalho A, Sanada F, Ide N, Rota M, Blasco MA, Serrano M, Anversa P, Leri A ( 2017 ). p53 Modulates the Fate of Cardiac Progenitor Cells Ex Vivo and in the Diabetic Heart In Vivo. EBioMedicine 16, 224-237. ∞ AWARDS AND RECOGNITION ∞ Scientific Merit Award, Generalitat Va- lenciana, Spain. ∞ XIII Health Science Award, Fundación Caja Rural de Granada, Spain. ∞ XXXVI Lección Memorial Fernández-Cruz Award, Fernández-Cruz Foundation, Spain. ∞ Doctorate Honoris Causa, Universidad de Alicante, Alicante, Spain. vivo reprogramming efficiency. We extended the finding of TRF1 upregulation to pathological tissue dedifferentiation associated with neoplasias, specifically, to pancreatic acinar- to-ductal metaplasia, a K-Ras driven process that involves transdifferentiation of adult acinar cells into ductal-like cells. Our findings place telomeres as important players in cellular plasticity both during in vivo reprogramming and in pathological conditions associated with increased plasticity, such as cancer. s Figure 2 TRF1 chemical inhibitors reduce xenograft tumour growth. ( A ) Longitudinal tumour growth follow-up in treated/untreated xenograft models ( right ), representative tumours ( left ). ( B ) Tumour weight ( right ), representative tumours post- mortem. ANNUAL REPORT 2017 32 BASIC RESEARCH CELL DIVISION AND CANCER GROUP Marcos Malumbres Group Leader Staff Scientists Mónica Álvarez, Guillermo de Cárcer Post-Doctoral Research Associate Dario Hermida ( since July ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 33 MOLECuLAR ONCOLOGy PROGRAMME | CELL dIvISION ANd CANCER GROUP OVERVIEW The Cell Division and Cancer Group is interested in deciphering the mechanisms by which cell division and cell proliferation are regulated in mammalian cells. During the last few years, we have used different mouse models to understand the relevance of cell cycle regulators, including cell cycle kinases and phosphatases, as well as of proteins involved in ubiquitin-dependent degradation, in the control of cell division and tissue physiology. Our interests are : i ) to understand the basic control mechanisms that regulate the cell division cycle ; ii ) to characterise the physiological and therapeutic consequences of cell cycle deregulation ; iii ) understanding the function of microRNAs in stem cell biology and tumour development, and iv ) to understand how progenitor cells and cancer stem cells control their self-renewal and proliferative properties. As a final goal, we aim to generate information that may be useful for improving therapeutic strategies against cancer cell proliferation. “ During 2017, we uncovered a new function for the cell cycle kinase Plk1 in vascular postmitotic cells, suggesting unexpected side effects of Plk1 in the treatment of human tumours.” Post-Doctoral Fellows Begoña Hurtado, Carolina Maestre ( until June ), María Salazar Graduate Students Ana F. Batalha Martins, José González ( since May ), María Maroto, Diego Martínez, Beatriz Salvador ( since June ), Belén Sanz ( until November ), María Sanz Technicians Aicha El Bakkali ( PEJ ) *, María Guirola ( until November ) ( TS ) **, Beatriz Ortigosa ( since February ) ( PEJ ) *, Elisabet Zapatero ( TS ) ** *Plan de Empleo Joven ( Youth Employment Plan ) **Titulado Superior ( Advanced Degree ) Visiting Student Javier Gilabert ( since October ) ( Paris Diderot University, France ) ANNUAL REPORT 2017 34 BASIC RESEARCH RESEARCH HIGHLIGHTS Recent research in our laboratory has focused on several aspects of the control of cancer cell proliferation by the cell cycle machinery. We are currently studying the relevance of critical cell cycle kinases such as cyclin-dependent kinases, Plk1 or the PP2A- inhibitory kinase Mastl in cancer cells from different origins. Although mostly overlooked in the past, we are also studying major phosphatases such as PP2A or Cdc14 using genetic models. In addition, we have generated mouse models with gain-of- or loss-of-mutations in miR-203, a microRNA with relevant properties in the control of self-renewal and differentiation properties of stem cells ( Patent EP 17382304.8 ). The cell cycle kinase Plk1 controls vascular homeostasis Among cell cycle enzymes, Polo-like kinase 1 ( Plk1 ) is an essential kinase with multiple roles in centrosome maturation and separation, DNA replication, chromosome segregation, and cytokinesis. In human cancer, Plk1 is upregulated and its expression frequently correlates with poor prognosis in a variety of tumour types such as breast or lung cancer, among others. Pioneering work in model organisms such as flies or mammalian cells in culture demonstrated that inhibition of this kinase resulted in prometaphase arrest due to monopolar spindles or Figure Schematic representation of the involvement of Plk1 in the response to vasoconstrictors and in the cell division cycle. Plk1 participates in the recruitment of the RacGap1- Ect2 complex, thereby leading to the activation of RhoA. This process is mediated by atypical PKCs. Activation of RhoA leads to changes in the actomyosin cytoskeleton required for contraction. In parallel, Plk1 regulates several processes required for mitosis ( M ) such as centrosome maturation, chromosome segregation and cytokinesis, which also involves RhoA- mediated actomyosin contraction. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 35 MOLECuLAR ONCOLOGy PROGRAMME | CELL dIvISION ANd CANCER GROUP misaligned chromosomes, as well as in specific defects during cytokinesis. Not surprisingly, a number of Plk1 small-molecule inhibitors are currently under scrutiny in clinical trials for cancer therapy. One of these inhibitors, volasertib, recently received the Breakthrough Therapy designation by the FDA owing to its therapeutic effect in acute myeloid leukaemia. We have recently analysed the relevance of this kinase using genetically engineered mouse models. Our results uncovered a new function for this protein in the maintenance of the proper structure of the arteries. Plk1 regulates the contractile response of smooth muscle cells to changes in blood pressure. Mechanistically, this kinase regulates the activation of the RhoA GTPase, a central node in the actomyosin changes required for cell contractility ( FIGURE ). This function is actually related to the known role of Plk1 in controlling actomyosin dynamics during the later steps of mitosis and cytokinesis. In fact, the control of myosin contractility by Polo-like kinases is conserved through evolution from yeast to humans. Similarly to its genetic inactivation, the use of Plk1 inhibitors resulted in defects in vascular structure and function in mice. These data do not preclude the use of Plk1 inhibitors in the clinic but suggest that understanding their toxicity effects will be critical for the proper design of therapeutic strategies against cancer. In addition, as RhoA is a critical mediator of major oncogenic and metastatic pathways, the use of low doses of Plk1 inhibitors could be considered as a potential therapeutic strategy to limit the activation of these pathways in cancer cells. Mastl-PP2A in the cell cycle and cancer During the last few years, the cell cycle kinase Mastl ( also known as Greatwall ) has emerged as a key player in the regulation of the PP2A phosphatase during mitosis. Mastl phosphorylates two small proteins, endosulfine ( ENSA ) and ARPP19, which in their phosphorylated form bind and inhibit PP2A-B55 complexes. In vertebrates, PP2A-B55 complexes counteract the phosphorylation of CDK substrates, and Mastl-dependent inhibition of PP2A-B55 prevents the activity of this phosphatase during mitosis, thus contributing to the phosphorylation of mitotic phospho-proteins. Recent data, including our own, suggest that B55 subunits are inactivated and Mastl is overexpressed in specific tumours such as oral squamous cell carcinoma, colon cancer, neuroblastoma and breast tumours. Our recent work also suggests a new function for B55 subunits in the control of chromosome structure during mitosis. Our current efforts are focused on understanding how B55 participates in chromosome segregation and malignant transformation using cellular and in vivo models. s ∞ PUBLICATIONS ∞ Burgess A, Vuong J, Rogers S, Malum- bres M, O’Donoghue SI ( 2017 ). SnapShot : phosphoregulation of mitosis. Cell 169, 1358-1358e1. ∞ de Cárcer G, Wachowicz P, Martín- ez-Martínez S, Oller J, Méndez-Barbero N, Escobar B, González-Loyola A, Takaki T, El Bakkali A, Cámara JA, Jiménez-Bor- reguero LJ, Bustelo X, Cañamero M, Mulero F, Sevilla MdlA, Montero MJ, Redondo JM, Malumbres M ( 2017 ). Plk1 regulates contraction of postmitotic smooth muscle cells and is required for vascular homeo- stasis. Nat Med 23, 964-974. ∞ Salazar-Roa M, Malumbres M ( 2017 ). Fue- ling the cell division cycle. Trends Cell Biol. 27, 69-81. ∞ Ha K, Ma C, Lin H, Tang L, Lian Z, Zhao F, Li J-M, Zhen B, Pei H, Han S, Malumbres M, Jin J, Chen H, Zhao Y, Zhu Q, Zhang P ( 2017 ). The anaphase promoting com- plex impacts repair choice by protecting ubiquitin signaling at DNA damage sites. Nat Commun 8, 15751. ∞ Esteban-Martínez L, Sierra-Filardi E, McG- real RS, Salazar-Roa M, Mariño G, Seco E, Durand S, Enot D, Graña O, Malumbres M, Cvekl A, Cuervo AM, Kroemer G, Boya P ( 2017 ). Programmed mitophagy is es- sential for the glycolytic switch during cell differentiation. EMBO J 36, 1688-1706. ∞ Rattani A, Ballesteros Mejia R, Roberts K, Roig MB, Godwin J, Hopkins M, Eguren M, Sanchez-Pulido L, Okaz E, Ogushi S, Wolna M, Metson J, Pendás AM, Malum- bres M, Novák B, Herbert M, Nasmyth K ( 2017 ). APC/CCdh1 enables removal of shugoshin-2 from the arms of biva- lent chromosomes by moderating cyc- lin-dependent kinase activity. Curr Biol 27, 1462-1476. ∞ PATENT ∞ Malumbres M, Salazar-Roa M, Trakala M, Álvarez-Fernández M ( 2017 ). Method for expanding stemness and differenti- ation potential of pluripotent cells. EP 17382304.8. ∞ AWARDS AND RECOGNITION ∞ Editorial Board Member, Scientific Reports. ANNUAL REPORT 2017 36 BASIC RESEARCH GENOMIC INSTABILITY GROUP Óscar Fernández-Capetillo Group Leader Staff Scientists Emilio Lecona, Bárbara Martínez ( since May ), Matilde Murga, Sergio Ruíz SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 37 MOLECuLAR ONCOLOGy PROGRAMME | GENOmIC INSTAbILITy GROUP OVERVIEW The Genomic Instability laboratory centres its research on understanding how cells respond to a specific type of DNA damage known as replication stress ( RS ), which is the main source of genomic rearrangements in cancer cells. In mammals, RS is sensed and suppressed by a signalling cascade initiated by ATR and CHK1 kinases. Throughout the years, our laboratory has developed a wide battery of cellular and animal tools for the study of RS. These tools include mice with enhanced or limited function of ATR/CHK1 kinases, cell lines in which the RS-response pathway can be activated at will, and chemical inhibitors of ATR. Our studies have enhanced our understanding of the impact of RS on cancer and ageing, and have led to novel drugs with antitumour potential that can exploit the presence of RS in cancer cells. Altogether, our main aim is to understand how genome maintenance is safeguarded – particularly during replication – and to exploit this knowledge as a way to fight against cancer. “ In 2017, we have invested a significant part of our activities in trying to improve the existing technologies for forward genetic screenings in mammalian cells, and have used them ( among others ) to identify new determinants of the sensitivity to ATR inhibitors.” Post-Doctoral Fellow Vanesa Lafarga Graduate Students Antonio Galarreta, Cristina Mayor ( until November ), Isabel Morgado ( until June ), Teresa Olbrich, Laura Sánchez ( since June ), Federica Schiavoni ( until March ), Oleksandra Sirozh, Pablo Valledor ( since October ) Technicians Marta E. Antón, Patricia Cozar, Alicia González ( TS )*, Sara Rodrigo, María Vega *Titulado Superior ( Advanced Degree ) ANNUAL REPORT 2017 38 BASIC RESEARCH RESEARCH HIGHLIGHTS Forward genetic screening ( FGS ) represents one of the most powerful methods for the discovery of new pathways and/or mechanisms of disease. Haploid organisms, such as yeast, have long been the ideal platform for FGS, since mutations in one allele can suffice to reveal a phenotype. The relevance of this approach is exemplified by the high number of Nobel Prizes that have been awarded in the recent decades to investigations that started with yeast studies. While many biological questions are intrinsic to mammals and cannot be approached through yeast, the presence of a diploid genome ( with two copies per gene ) has significantly limited FGS approaches in mammalian cells. The recent development of CRISPR-Cas9 gene editing technologies, together with the isolation of mammalian haploid cell lines, has recently changed this landscape. During 2017, our laboratory contributed to this field by finding ways to stabilise the haploid state in mammalian cells, as well as by developing a new method for the identification of genetrap insertions by RNA sequencing that can be coupled to FGS approaches. TrapSeq : A new method for genetrap-based genetic screenings in mammals Genetraps are one of the most widely used methods to conduct genetic screenings in mammals. In these studies, identifying the genetrap insertion site was an essential step, which was accomplished via inverse PCR-based methods that ( a ) are prone to biases and artefacts, and ( b ) while they are able to identify the insertion site, they do not provide information as to how the insertion affects the expression of the targeted gene. To overcome these limitations, we have now developed an RNA sequencing-based method ( TrapSeq ) that provides a fast, direct and cost-effective pipeline for the identification of a gene-trap insertion mutation, and which also reveals the impact of the genetrap on the expression of the mutated gene ( FIGURE 1 ). We have now used TrapSeq to conduct several genetic screenings in haploid mammalian cells, including the discovery of mutations that increase the resistance to ATR inhibitors. This screening confirmed the key role of the mitosis-promoting phosphatase CDC25A in the response to ATR inhibition that we had previously identified in CRISPR-based screenings ( Ruiz et al., Mol Cell 2016 ), Figure 1 Pipeline for genetrap- based genetic screenings with TrapSeq. ( A ) Scheme followed for the mutagenesis and genetic screenings on the human haploid cell line HAP1. ( B ) Example of the output of TrapSeq in an individual HAP1 clone that was selected for resistance against 6TG. The first track ( red ) indicates the insertion site, and the other ones the expression of the trapped gene ( HPRT ), which is downregulated in the mutant clone. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 39 MOLECuLAR ONCOLOGy PROGRAMME | GENOmIC INSTAbILITy GROUP ∞ PUBLICATIONS ∞ Olbrich T, Mayor-Ruiz C, Vega-Sendino M, Gomez C, Ortega S, Ruiz S, Fernan- dez-Capetillo O ( 2017 ). A p53-dependent response limits the viability of mammalian haploid cells. Proc Natl Acad Sci USA 114, 9367-9372. ∞ Mayor-Ruiz C, Dominguez O, Fernan- dez-Capetillo O ( 2017 ). Trap( Seq ): An RNA sequencing-based pipeline for the identification of gene-trap insertions in mammalian cells. J Mol Biol 429, 2780- 2789. ∞ AWARDS AND RECOGNITION ∞ Erik K. Fernström Award. as well as identified new determinants of the sensitivity to these chemicals such as the oncogene Epithelial Cell Transforming 2 ( ECT2 ). Studies aiming to understand the mechanisms by which the identified mutations alter the response to ATR inhibition are currently underway. Identification of a ‘ Haploidy Checkpoint ’ One important limitation of mammalian haploid cell lines is the rapid loss of the haploid state, resulting in cultures becoming rapidly enriched in diploid cells. This phenomenon has been previously assumed to be due to the ‘ diploidization ’ of the haploid genomes, although how this occurs has remained poorly understood. We have now revealed that the so-called ‘ diploidization ’ is a consequence of a growing disadvantage of haploid cells, which are outcompeted by the few diploids that are present in these cultures. In support of this, single-cell sorting can significantly stabilise the haploid state. We have also discovered that the reduced fitness of mammalian haploid cells arises as a consequence of problems during chromosome segregation in mitosis, which subsequently lead to the activation of a cytotoxic p53-dependent response. Consequently, p53- deletion can increase the stability of haploid cultures in human HAP1 cells or mouse embryonic stem cells. Due to the similarities between our findings and those previously reported in aneuploid or polyploid cells, we propose the existence of a unified p53-dependent ‘ ploidy ’ checkpoint, which is activated as a consequence of the difficulties in segregating a suboptimal chromosomal content during mitosis. s Figure 2 p53 deficiency increases the percentage of haploidy in mouse embryonic stem cells. ( A ) Mouse haploid embryonic stem cells ( mhaESC ) were derived by inducing parthenogenesis with SrCl2 on oocytes from p53+/- female mice. ( B ) While, as previously reported, mhaESC cultures derived from wild type oocytes presented very small percentages of haploid cells ( red ), this was significantly increased in p53-deficient lines. ANNUAL REPORT 2017 40 BASIC RESEARCH CHROMOSOME DYNAMICS GROUP Ana Losada Group Leader Staff Scientist Ana Cuadrado SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 41 MOLECuLAR ONCOLOGy PROGRAMME | CHROmOSOmE dyNAmICS GROUP OVERVIEW Our research focuses on a protein complex named cohesin that embraces DNA and is essential for chromosome organisation. Cohesin mediates sister chromatid cohesion and, thereby, ensures faithful DNA repair by homologous recombination and proper chromosome segregation during cell division. It also plays a major role in the spatial organisation of the genome by promoting long- range DNA looping, which in turn contributes to transcriptional regulation, organisation of DNA replication factories and locus rearrangement by recombination. Mutations in cohesin have been found in several tumour types, most prominently in bladder cancer and acute myeloid leukaemia. Mutations in cohesin and its regulatory factors are also at the origin of a group of human syndromes collectively known as cohesinopathies. Our goal is to understand how cohesin works, how it is regulated and how its dysfunction contributes to cancer and other human diseases. In particular, we are intrigued by the existence of different versions of the cohesin complex in somatic cells. We use mouse models carrying knock out alleles of genes encoding cohesin subunit to investigate their functional specificity both at the cellular level and in the context of an organism. We also take advantage of the Xenopus egg cell-free system to explore additional aspects of cohesin regulation. “ We have defined the specific contributions of cohesin-SA1 and cohesin-SA2 to genome organisation. Our work may uncover vulnerabilities in cancer cells carrying mutations in the gene encoding SA2, which is one of the twelve genes most mutated in cancer.” Graduate Students Aleksandar Kojic, Magali De Koninck, Carmen M. Morales, Miguel Ruiz Technicians Daniel Giménez ( since September ), Miriam Rodríguez, Marta Vargas ( since June ) ANNUAL REPORT 2017 42 BASIC RESEARCH RESEARCH HIGHLIGHTS Cohesin-SA1 and cohesin-SA2 have distinct roles in 3D genome organisation Cohesin consists of four core subunits, SMC1, SMC3, RAD21 and SA. There are two versions of the SA subunit in vertebrate somatic cells, SA1 and SA2. Loss of function mutations in the STAG2 gene encoding SA2 have been identified in bladder cancer, Ewing sarcoma and other tumour types. Cells lacking cohesin-SA2 can proliferate because cohesin-SA1 performs the essential function of cohesin in cohesion. This explains why STAG2 mutant tumours are not aneuploid. However, it is likely that cohesin-SA1 cannot accomplish the other functions of cohesin-SA2 related with chromatin organisation and gene regulation, thereby providing some advantage to the tumour. Importantly, lack of cohesin-SA2 may also generate vulnerabilities that could be exploited in cancer therapy. To characterise the specific functions of the two variant complexes in chromatin architecture and gene regulation we are pursuing two strategies. The first one is the characterisation of cells derived from mouse embryos deficient for SA1 or SA2. A STAG1 knockout allele was obtained a few years ago ( Remeseiro et al., 2012 ), while a conditional STAG2 knockout allele has been generated more recently in collaboration with Francisco X. Real ( CNIO Epithelial Carcinogenesis Group ). The second strategy makes use of non-transformed human cell lines before and after downregulation of SA1 or SA2. In these cells, we have analysed the genome-wide distribution of the two cohesin complexes as well as their transcriptomes. Moreover, in collaboration with M. A. Martí-Renom ( CRG-CNAG ), we have interrogated the genome architecture by Hi-C. From these studies, and in line with our previous work, we conclude that cohesin-SA1 collaborates with CTCF in the demarcation of domain boundaries ( FIGURE 1 ). In contrast, a more dynamic cohesin-SA2 complex promotes cell type-specific interactions between enhancers and promoters within contact domains ( or TADs, for Topologically Associated Domains ) independently of CTCF. Loss of SA2 rewires local chromatin contacts and alters gene expression. We are currently exploring the molecular mechanisms underlying these functional specificities of cohesin-SA1 and cohesin-SA2. Pds5 proteins regulate cohesin distribution and dynamics Two factors associate with chromatin-bound cohesin, Pds5 and Wapl. Wapl promotes cohesin unloading, and in its absence there is an excess of cohesin on chromatin and chromosome organisation is altered, both in interphase and mitosis. The role of Pds5 is less clear. Moreover, there are two versions of Pds5 present in vertebrate cells, Pds5A and Pds5B. In order to explore their specific functions we previously generated murine knock out ( KO ) alleles for these two genes. We showed that both Pds5A and Pds5B contribute to cohesion establishment during S phase by promoting cohesin acetylation and Sororin binding, with Pds5B being specifically required for cohesion at centromeres ( Carretero et al., 2013 ). Now we have analysed how these proteins regulate cohesin distribution and dynamics. We have found that the presence of Pds5A or Pds5B does not specify cohesin localisation, since either one can be found at most cohesin binding sites. However, genome wide distribution of cohesin clearly becomes restricted in the absence of both ( FIGURE 2 ). Under this condition, the dynamic association of cohesin to chromatin, measured in Fluorescence Recovery After Photobleaching ( FRAP ) experiments, is significantly decreased. Much milder effects are observed in cells lacking only Pds5A or Pds5B. Aberrant accumulation of cohesin in axial structures known as vermicelli, previously described in Wapl depleted cells ( Tedeschi et al., 2013 ), can be observed only in the absence of the two Pds5 proteins, although overall accumulation of the complex on chromatin is not as dramatic. From these studies we conclude that Wapl and Pds5 work together in cohesin unloading, but that Pds5 has additional functions. Our current hypothesis is that cohesin acetylation, which is carried out by Cohesin Acetyl Transferases that are recruited to cohesin through Pds5, is essential not only for cohesion establishment during S phase but also for proper cohesin dynamics throughout the cell cycle as well as in non-dividing cells. s ∞ PUBLICATION ∞ Messina G, Atterrato MT, Prozzillo Y, Pia- centini L, Losada A, Dimitri P ( 2017 ). The human Cranio Facial Development Protein 1 ( Cfdp1 ) gene encodes a protein required for the maintenance of higher-order chro- matin organization. Sci Rep 7, 45022. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 43 MOLECuLAR ONCOLOGy PROGRAMME | CHROmOSOmE dyNAmICS GROUP Figure 1 Matrices showing differential interactions along human chromosome 15 comparing control MCF10A cells (mock transfected) with cells downregulated for SA1 or SA2 by siRNA (siSA1 and siSA2, respectively) by means of Hi-C analyses. The absence of cohesin-SA1 increases long range interactions between TADs (red patches outside the diagonal) whereas the absence of cohesin-SA2 increases interactions between neighbouring TADs (close to the diagonal). Figure 2 Snapshot of the UCSC browser showing the distribution of Pds5A and Pds5B in a 200-kb long region of chromosome 15 in wild type ( WT ) mouse embryo fibroblasts, as well as the distribution of cohesin ( Smc1 ) in the presence and absence of either or both Pds5 proteins ( WT, Pds5A/B double KO or Pds5 DKO, Pds5A KO and Pds5B KO ), as obtained by ChIP-seq analyses. Figure 1 Figure 2 ANNUAL REPORT 2017 44 BASIC RESEARCH DNA REPLICATION GROUP Juan Méndez Group Leader Staff Scientist Sara Rodríguez SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 45 MOLECuLAR ONCOLOGy PROGRAMME | dNA REPLICATION GROUP OVERVIEW Up to two thirds of the total mutations detected in tumours are caused by inaccurate DNA replication. Our laboratory studies the process of DNA replication using a combination of biochemistry, cell biology and mouse genetics. Our current interests include : ( 1 ) the genetic and epigenetic elements that define replication origins ; ( 2 ) the cellular responses to replicative stress ( RS ) caused by endogenous elements ( e.g. natural decay of DNA ; collisions between replication and transcription proteins ) or exogenous factors such as UV radiation or DNA-damaging chemical agents. One of the responses to RS is the activation of ‘ dormant ’ origins, whose regulation remains poorly understood ; ( 3 ) the mechanisms that limit DNA replication to only one round in each cell cycle, and the physiological consequences of their malfunction ; and ( 4 ) the role of PrimPol, a recently characterised enzyme with primase and polymerase activities, in the ‘ tolerance ’ mechanisms that enable replication through damaged DNA. “ We have reported that deregulation of CDC6 and CDT1 proteins – a frequent occurrence in cancer cells – leads to DNA over- replication and causes lethal tissue dysplasias.” Graduate Students Elena Blanco ( since June ), Daniel González, Karolina Jodkowska, Sergio Muñoz ( until June ), Patricia Ubieto ( since October ) ANNUAL REPORT 2017 46 BASIC RESEARCH RESEARCH HIGHLIGHTS Genome-wide analysis of replication origin usage upon replicative stress Mammalian DNA replication starts at tens of thousands of points called ‘ origins ’ whose frequency of activation is flexible. Our laboratory reported, several years ago, that stalled replication forks induce the activation of extra origins as a backup mechanism ( Ibarra et al., Proc Natl Acad Sci USA, 2008 ). In collaboration with the group of Dr María Gómez ( Centro de Biología Molecular “ Severo Ochoa ”, Madrid ), we have used a technique called SNS- Seq ( isolation of short nascent DNA strands followed by DNA sequencing ) to map the genomic positions and global efficiency of origins in mouse embryonic stem cells under experimental conditions that trigger extra origin activation. This approach allows a comparative analysis of ‘ constitutive ’ origins that are active in all the tested conditions, as well as the analysis of ‘ responsive ’ origins that become stimulated under stress. We have found that constitutive origins are more frequently associated with open chromatin marks, CpG islands, bivalent promoters and transcription factors than responsive ones. In addition, many replication origins increase their frequency of activation following stress. In collaboration with computational biologists at CNIO and the Barcelona Supercomputing Center, we are working on integrating the linear origin maps into three- dimensional chromatin networks, in order to shed light on the complex hubs of nuclear DNA replication factories. Lethal tissue dysplasias caused by DNA re-replication Activation of oncogenes such as c-Myc affects replication origins through mechanisms that are not well understood. It has been reported that oncogenic stress may lead to origin hyper- activation, which leads to DNA over-replication and possibly gene amplification. Origin activity is largely controlled by the CDC6 and CDT1 proteins responsible for the loading of the MCM DNA helicase onto DNA. In normal cells, the activity of CDC6 and CDT1 is strictly regulated to prevent origin reactivation, but both factors are overexpressed in multiple types of cancer. To investigate the effects of deregulated expression of CDC6 and CDT1 in vivo, we have designed mouse strains that allow the inducible expression of both proteins, alone or in combination. This year, we have reported that simultaneous, but not individual, deregulation of CDC6 and CDT1 is lethal to adult mice due to a striking dysplasia of the intestinal epithelium. The regeneration of intestinal epithelia is driven by transit-amplifying cells derived from stem cell niches located at the bottom of the intestinal crypts. Upon CDC6 and CDT1 deregulation, transit-amplifying progenitors undergo DNA over-replication and cell death, causing rapid intestinal failure ( FIGURE ). A mechanistic insight derived from this study is that lethal DNA over-replication only occurred when CDC6 and CDT1 were deregulated at the same time. Therefore, unleashing CDT1 activity could kill tumour cells that generally express high levels of CDC6, but have no effect on the surrounding tissue that display normal CDC6 expression. At this time, CDT1 stimulation can be achieved by targeting GMN, a CDT1 inhibitor, or by the use of neddylation inhibitors ( e.g. MLN4924 ) that stabilise CDT1. The mouse strains characterised in our study reveal the marked cytotoxicity of DNA re-replication in vivo and may therefore become useful models in pre-clinical studies. PrimPol : a damage tolerance protein with potential applications in cancer therapy We continue to investigate the functions of PrimPol, an enzyme that facilitates replication through damaged DNA. We have found that genetic ablation of PrimPol by Crispr/Cas9 sensitises cells to UV and chemical agents that induce DNA damage. Because PrimPol facilitates cell survival in the presence of DNA lesions, its inhibition could enhance the efficacy of cytotoxic chemotherapeutic agents that trigger cell death by inducing DNA damage. s ∞ PUBLICATIONS ∞ Muñoz S, Búa S, Rodríguez-Acebes S, Megías D, Ortega S, De Martino A, Mén- dez J ( 2017 ). In vivo DNA re-replication elicits lethal tissue dysplasias. Cell Rep 19, 928-938. ∞ Garzón J, Rodríguez R, Kong Z, Chabes A, Rodríguez-Acebes S, Méndez J, Moreno S, García-Higuera I ( 2017 ). Shortage of dNTPs underlies altered replication dy- namics and DNA breakage in the absence of the APC/C cofactor Cdh1. Oncogene 36, 5808-5818. ∞ Muñoz S, Méndez J ( 2017 ). DNA replica- tion stress : from molecular mechanisms to human disease. Chromosoma 126, 1-15. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 47 MOLECuLAR ONCOLOGy PROGRAMME | dNA REPLICATION GROUP Figure DNA re-replication elicits lethal tissue dysplasia. ( A ) Left, bidirectional DNA replication forks starting from an origin, as observed in control cells or after CDC6 or CDT1 deregulation. Right, aberrant origin reactivation caused by simultaneous CDC6 and CDT1 deregulation. ( B ) Haematoxylin-eosin staining in colon sections of control ( left ) or CDC6 and CDT1-overexpressing mice ( right ). Boxes mark areas of inflammatory infiltration. ( C ) Schematic of normal intestinal crypts ( left ) or dysplastic crypts ( right ). SC, stem cells. TA, transit-amplifying cells. Adapted from Muñoz et al. ( 2017 ). ANNUAL REPORT 2017 48 BASIC RESEARCH MELANOMA GROUP María S. SoengasGroup Leader Staff ScientistDavid Olmeda Post-Doctoral Fellows Paula Penacchi, Susana Frago SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 49 MOLECuLAR ONCOLOGy PROGRAMME | mELANOmA GROUP OVERVIEW Melanomas are inherently aggressive cancers for which basic and translational research have significantly improved patient prognosis. Nevertheless, clinical responses are still incomplete. The long-term goals of our Group are to identify new progression biomarkers and therapeutic agents. Focusing on stress response programmes involving apoptosis, autophagy and endosome mobilisation, we have discovered lineage-specific oncogenes that define the melanoma ‘ fingerprint ’. Transcriptomic and proteomic analyses of the melanoma secretome have allowed us to define how tumour cells remodel the ( lymp )angiogenic vasculature and avoid immune recognition. Moreover, we have generated a unique set of animal models for non-invasive imaging of melanoma progression in vivo. These systems have led to the validation of nanoparticle-based treatments which are being currently being tested in clinical trials. Our ultimate objective is to improve the management of patients with otherwise refractory metastatic melanomas. “ We have developed the first-in- class lymphoreporter mouse models of melanoma for in vivo imaging and pharmacological testing of new metastatic agents.” Graduate Students Xavier Catena, Daniela Cerezo, Metehan Cifdaloz ( until March ), Marta Contreras, Panagiotis Karras ( until May ), Raúl Martínez, Cristina Tejedo Technicians Tonantzin Calvo, Estela Cañón ( TS )* *Titulado Superior ( Advanced Degree ) Clinical Collaborators José L Rodríguez-Peralto ( Pathology, Hospital 12 de Octubre, Madrid ), Pablo Ortiz-Romero ( Dermatology, Hospital 12 de Octubre, Madrid ), Erica Riveiro-Falchenback ( Pathology, Hospital 12 de Octubre, Madrid ) ANNUAL REPORT 2017 50 BASIC RESEARCH RESEARCH HIGHLIGHTS CNIO Melanoma Group : Objectives and model systems Melanomas are aggressive solid tumours and a prime example of how integrated basic and clinical research has significantly improved patient prognosis. Nevertheless, despite great success with targeted and immune-based therapies, sustained clinical responses are still limited. Moreover, the field lacks molecular markers of diagnosis, and the knowledge on how melanomas progress and metastasise is largely incomplete. In addition, one of the main hurdles to advance in this disease is the lack of animal models to monitor melanoma initiation and progression in vivo. To this end, our Group focuses on three main areas of research ( FIGURE 1 ): ɗ Aim 1. Oncogenic pathways selectively deregulated in melanoma that may represent new diagnostic indicators. ɗ Aim 2. Risk factors and prognostic markers. ɗ Aim 3. Animal models that allow for non-invasive monitoring of pre-metastatic niches. Lineage-specific oncogenic dependencies in melanoma One of the long-term objectives of the Melanoma Group is to discover new melanoma drivers. We have previously identified a cluster of endolysosomal-associated genes that distinguish melanoma from over 35 additional malignancies ( Alonso-Curbelo et al., Cancer Cell 2014 ; Alonso-Curbelo et al., Oncotarget 2015a and Oncotarget 2015b ). Further analyses of lysosomal-dependent pathways also revealed unique features of autophagy genes ( ATG5 ) in melanoma ( García-Fernández et al., Autophagy 2016 ). Additional contributions of autophagy to melanoma cell survival and response to targeted therapy were generated in collaboration with the Ashani Weeraratna group at the Wistar Institute ( USA ) ( Ndoye et al., Cancer Res 2017 ). Other melanoma-enriched regulatory mechanisms were identified by focusing on RNA binding proteins ( RBPs ). We selected RBPs ( a family of over 950 members ) because they are largely unexplored in melanoma, although this is a tumour characteristically associated with a plethora of changes in mRNA gene expression profiles. Performing a series of genome wide studies ( i.e. genomic, transcriptomic, proteomic and interactomic analyses ) we uncovered new roles of the RBPs CPEB4 and CUGBP1 in the modulation of mRNA stability, with unexpected targets involving master specifiers of the melanocyte lineage ( Perez-Guijarro et al., Nat Commun 2016 ; Cifdaloz et al., Nat Commun 2017 ). Figure 1 Vegfr3Luc ( MetAlert ) mice to test PDX, melanoma cell lines or genetically engineered mice for the visualisation of pre-metastatic niches and as a platform for gene discovery and drug testing ( here shown to visualise the efficacy of the dsRNA- based nanoparticle BO-110 ). SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 51 MOLECuLAR ONCOLOGy PROGRAMME | mELANOmA GROUP ‘ MetAlert ’ mice for the visualisation of premetastatic niches in melanoma and as a platform for gene discovery and target validation We have also made great progress regarding one of the most pressing needs in the melanoma field, namely, the mechanisms that enable melanoma cells to disseminate already from lesions of barely 1 mm in depth. In collaboration with Sagrario Ortega at the CNIO, we have generated a series of mouse models of melanoma that have the unique feature of revealing how these cells act ‘ a distance ’ from very early stages of tumour development, activating the lymphatic vasculature and preparing metastatic niches before their colonisation ( Olmeda et al., Nature 2017 ; see the versatility of these mice for gene discovery and pharmacological analyses in FIGURE 1 ). Using these ‘ MetAlert ’ animals we found the growth factor MIDKINE as a new driver of lymphangiogenesis and melanoma metastasis ( FIGURE 2, A ). The physiological relevance of these data was validated in human clinical biopsies where MIDKINE expression correlated with poor patient prognosis ( FIRGURE 2, B ). This paper of Olmeda et al. was highlighted in Nature, Cancer Discovery, Developmental Cell and other scientific journals, and was awarded the Premio “ Constantes y Vitales ” by the Fundación AtresMedia for the Best Publication in Biomedical Research in 2017. This article was also considered as being among the Top 10 publications in Spain in 2017 by the news agency EFE. This publication, together with others from the Soengas Group, was recognised by the Estela Medrano Memorial Award by the Society of Melanoma Research, which honours the most influential female leaders in the melanoma field. In addition, clinical trials with the compound BO-112 performed by the biotechnology company Bioncotech Therapeutics were considered as being among the 14 Most Relevant Scientific Hits in 2017 by the SINC agency ( the Spanish Information and Scientific News Service ). BO-112 is a derivative of the polyplex BO-110 generated at the CNIO by the Soengas laboratory. s ∞ PUBLICATIONS ∞ Olmeda D, Cerezo-Wallis D, Riveiro-Falk- enbach E, Pennacchi PC, Contreras-Alcal- de M, Ibarz N, Cifdaloz M, Catena X, Calvo TG, Cañón E, Alonso-Curbelo D, Suarez J, Osterloh L, Graña O, Mulero F, Megías D, Cañamero M, Martínez-Torrecuadrada JL, Mondal C, Di Martino J, Lora D, Mar- tinez-Corral I, Bravo-Cordero JJ, Muñoz J, Puig S, Ortiz-Romero P, Rodriguez-Peralto JL, Ortega S, Soengas MS ( 2017 ). Whole body imaging of lymphovascular niches identifies premetastatic roles of midkine. Nature 546, 676-680. Featured in : Hoshino A, Lyden D ( 2017 ). Metastasis : lymphatic detours for cancer. Nature 546, 609-610. Cancer Discovery Research Watch ( 2017 ). A lymphoreporter mouse model identifies midkine as a metastasis driver. Cancer Discovery, doi : 10.1158/2159-8290. CD-RW2017-126. Karaman S, Alitalo K ( 2017 ). Midkine and melanoma metastasis : a malevolent mix. Dev Cell 42, 205-207. Pérez-Guijarro E, Merlino G ( 2017 ). Lymphangiogenesis : from passive dis- seminator to dynamic metastatic enabler. Pigment Cell Melanoma Res, doi : 10.1111/ pcmr.12621. ∞ Soengas MS, Patton EE ( 2017 ). Location, location, location : spatio-temporal cues that define the cell of origin in melanoma. Cell Stem Cell 21, 559-561. ∞ Soengas MS, Hernando E ( 2017 ). TYRP1 mRNA goes fishing for miRNAs in mela- noma. Nat Cell Biol 19, 1311-1312. ∞ Cifdaloz M, Osterloh L, Graña O, Rivei- ro-Falkenbach E, Ximénez-Embún P, Muñoz J, Tejedo C, Calvo TG, Karras P, Olmeda D, Miñana B, Gómez-López G, Cañon E, Eyras E, Guo H, Kappes F, Or- tiz-Romero PL, Rodríguez-Peralto JL, Megías D, Valcárcel J, Soengas MS. ( 2017 ). Systems analysis identifies melanoma-en- riched pro-oncogenic networks controlled by the RNA binding protein CELF1. Nat Commun 8, 2249. ∞ Ndoye A, Budina-Kolomets A, Kugel CH 3rd, Webster MR, Kaur A, Behera R, Re- becca VW, Li L, Brafford PA, Liu Q, Gopal YNV, Davies MA, Mills GB, Xu X, Wu H, Herlyn M, Nicastri MC, Winkler JD, So- engas MS, Amaravadi RK, Murphy ME, Weeraratna AT ( 2017 ). ATG5 mediates a positive feedback loop between Wnt signaling and autophagy in melanoma. Cancer Res 77, 5873-5885. ∞ Riveiro-Falkenbach E, Ruano Y, García- Martín RM, Lora D, Cifdaloz M, Acquadro F, Ballestín C, Ortiz-Romero PL, Soengas MS, Rodríguez-Peralto JL ( 2017 ). DEK oncogene is overexpressed during mela- noma progression. Pigment Cell Melanoma Res 30, 194-202. ∞ AWARDS AND RECOGNITION ∞ Estela Medrano Memorial Award for the most influential female melanoma researcher, the Society for Melanoma Research, USA. ∞ “ Constantes y Vitales ” Award for the Best Publication in Medicine, Fundación Atresmedia, Spain. ∞ “ Premio Executivas de Galicia 2017 ”, Executivas de Galicia, Spain. ∞ Finalist “ Premios MAS Mujeres a Seguir ”, Spain. ∞ Olmeda et al., Nature 2017 ; considered one of the Top 10 scientific publications in Spain in 2017, Agencia EFE. Figure 2 MIDKINE ( MDK ) as pro- metastatic driver and marker of poor prognosis in melanoma. (  A ) Schematic depicting newly-described roles of tumour-secreted MDK on tumour cells and the lymphatic vasculature. ( B ) Kaplan-Meier survival curves of melanoma patients ( Stage II-IV ) classified on the basis of MDK expression in sentinel lymph nodes. ANNUAL REPORT 2017 52 BASIC RESEARCH MICROENVIRONMENT & METASTASIS JUNIOR GROUP OVERVIEW Our laboratory is interested in analysing the main mechanisms involved in tumour-microenvironment communication during metastasis. Extracellular vesicles ( EVs ) and soluble factors are key players during this process. Tumour cells benefit from the secretion of these factors partly by influencing the behaviour of neighbouring cells in the tumour microenvironment. We are exploring the role of secreted factors and vesicles in metastasis using different approaches : 1 ) decoding the messages packaged in tumour-derived exosomes during melanoma metastasis, 2 ) defining novel factors involved in the crosstalk between adipose tissue and tumour, and 3 ) testing new therapies to prevent metastasis in rare diseases such as neurofibromatosis. “ We aim to block tumour- microenvironment communication as a novel way to control metastatic progression.” Héctor Peinado Junior Group Leader Staff Scientist Susana García Post-Doctoral Fellows Marta Hergueta, Claudia Savini SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 53 MOLECuLAR ONCOLOGy PROGRAMME | mICROENvIRONmENT & mETASTASIS JUNIOR GROUP RESEARCH HIGHLIGHTS Decoding tumour-microenvironment communication in metastasis Tumour-secreted extracellular vesicles constitute a network of communication secreted by primary tumours favouring metastasis. In melanoma, tumour-adjacent lymph nodes ( a.k.a. sentinel lymph nodes ) are normally the first sites of metastasis. In this project, we are focused on unravelling the role of tumour- derived exosomes as entities promoting cellular and molecular alterations in the lymph node microenvironment, facilitating metastasis ( FIGURE ). In particular, we are investigating the effects of tumour exosomes in the lymphatic vasculature. In addition, we are developing nanoparticles ( FIGURE B, left panel ) as sensors of pre-metastatic niches mimicking tumour-derived exosomes ( FIGURE B, right panel ) that will help to identify future areas of metastasis. These studies will lead to the development of novel technologies and therapies to block metastatic disease. Fatal triage : adipose tissue, coagulation and metastasis Over the past few decades, the incidence of overweight and obesity has been increasing very rapidly in both developed and developing countries, making obesity one of the most serious health problems worldwide. Increasing evidences have revealed a link between obesity and the development of certain types of cancer ; still the impact of obesity on metastasis is not well established. Recent data support a role for secreted factors [ e.g. soluble factors and EVs ] in the communication between tumour cells and adipose tissue during tumour metastasis. In this project, we are investigating the local crosstalk between the adipose tissue and tumour cells, analysing secreted factors and EVs as well as the role of platelets as systemic players in the metastatic process. Testing new therapies to prevent metastasis Neurofibromatosis type 1 ( NF1 ) is a genetic disorder which can progress to Malignant Peripheral Nerve Sheath Tumour ( MPNST ), a highly aggressive sarcoma. In this project, we are analysing the main pathways involved in tumour- microenvironment crosstalk during metastatic progression. In order to find potential biomarkers and candidates to target the progression of the disease, we investigated the molecular signature of exosomes secreted by MPNST cell lines. We have identified several candidates and we are currently performing a multidrug screening in combination with these markers in order to find new therapies for the treatment of this disease. s Graduate Students Ana I. Amor, Teresa González, Alberto Hernández ( since September ), Olwen Leaman ( March-October ), Lucía Robado Technicians Marina Mazariegos, Cristina Merino, Sara Sánchez-Redondo Students in Practice Ainhoa Almeida ( February-June ), Alberto Hernández ( January-June ), Alicia Teijeira ( since October ) ∞ PUBLICATIONS ∞ Peinado H et al. ( 2017 ). Pre-metastatic niches : organ-specific homes for metas- tases. Nat Rev Cancer 17, 302-317. ∞ Huang Y et al. ( incl. Peinado H ) ( 2017 ). A proangiogenic signaling axis in myeloid cells promotes malignant progression of glioma. J Clin Invest 127, 1826-1838. ∞ A-Gonzalez N et al. ( incl.García-Silva S, Mazariegos M, Peinado H ) ( 2017 ). Phagocytosis imprints heterogeneity in tissue-resident macrophages. J Exp Med 214, 1281-1296. ∞ Santamaría PG et al. ( incl. Peinado H ). Ly- syl oxidase-like 3 is required for melanoma cell survival by maintaining genomic sta- bility. Cell Death Differ. PMID : 29229995. ∞ Nogués L, Benito-Martin A, Hergueta-Re- dondo M, Peinado H ( 2017 ). The influence of tumour-derived extracellular vesicles on local and distal metastatic dissemination. Mol Aspects Med. PMID : 29196097. ∞ Colletti M et al. ( incl. Lopez AA, Peinado H ) ( 2017 ). Proteomic analysis of neuroblasto- ma-derived exosomes : new insights into a metastatic signature. Proteomics 17, 23-24. ∞ Pathan M et al. ( incl. Peinado H ) ( 2017 ). A novel community driven software for functional enrichment analysis of extra- cellular vesicles data. J Extracell Vesicles 6, 1321455. Figure ( A ) Exosome ‘education ’ enhances lymph node metastasis. Low metastatic B16-F1-mCherry cells were injected intra-footpad after 10 days of exosome education ( EXO ) using exosomes derived from B16- F1-R2 cells ( melanoma model derived from lymph node metastasis ) and compared to PBS. LNs were analysed by confocal microscopy demonstrating the increase of metastasis ( in red- mCherry ) after exosome education. ( B ) Left panel - electron microscopy of Iron oxide nanoparticles ( IONPs ) conjugated with specific peptides to detect pre-metastatic niches. Right – electron microscopy of B16-F10- derived exosomes. ANNUAL REPORT 2017 54 BASIC RESEARCH BRAIN METASTASIS JUNIOR GROUP OVERVIEW Brain metastasis is the most common neurological complication of cancer. When metastatic cells reach the brain, prognosis is poor given that available therapies ( i.e. surgery and radiation ) have limited benefits for patients and the disease inevitably progresses. The rise in the number of patients with brain metastasis is partially due to the increasing number of systemic therapies that work extra-cranial but not in the brain. In this scenario, cancer cells present at this highly demanding secondary site have additional time to evolve and develop into clinically detectable lesions. In the laboratory, we study why and how cells from different cancer types ( breast cancer, lung cancer and melanoma ) are able to access the brain, survive and colonise this vital organ. We dissect the biology of these processes in vivo using experimental models in order to challenge the current status of this unmet clinical need. “ The Brain Metastasis Group is seeking to identify novel ways to target both cancer cells and the associated microenvironment in order to reduce metastatic burden in the brain.” Manuel Valiente Junior Group Leader Post-doctoral Fellow Neibla Priego SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 55 MOLECuLAR ONCOLOGy PROGRAMME | bRAIN mETASTASIS JUNIOR GROUP RESEARCH HIGHLIGHTS We have identified a cell type-specific molecular marker that is present in the brain metastasis microenvironment and absent from the normal brain. This marker is present surrounding both experimental and human metastasis, independent of the source of the primary tumour. By establishing a mouse model that is unable to activate this component of the microenvironment we have proven its pro- metastatic role, since the development of brain metastasis is significantly reduced. We have translated this finding into a novel therapeutic approach by which we can target brain metastasis by blocking discrete pro-tumorigenic populations within the heterogeneous microenvironment of brain metastasis. s Graduate Students Catia P. Domingues, Pedro García ( since October ), Lucia Zhu Technicians Laura E. Doglio ( until August ), Lourdes Osuna ( since November ), Natalia Yebra Student in Practice Wendy E. Bindeman ( since September ) ∞ PUBLICATIONS ∞ Bartolini G *, Sánchez-Alcañiz JA *, Osório C, Valiente M, García-Frigola C, Marín O ( 2017 ) Neuregulin 3 mediates cortical plate invasion and laminar al- location of GABAergic interneurons. Cell Reports 18, 1157-1170. (*) Shared authorship. ∞ Wasilewsky D, Priego N, Fustero-Torre C, Valiente M ( 2017 ). Reactive astro- cytes in brain metastasis. Frontiers in Oncology 7, 298. ∞ PATENT ∞ Valiente Cortés M, Priego Bendeck N, Bosh Barrera J ( 2017 ). Methods for pre- venting and treating brain metastasis. EP17382891.4. ∞ AWARDS AND RECOGNITION ∞ Beug Foundation’s Prize for Metastasis Research. ∞ Bristol-Myers Squibb-Melanoma Re- search Alliance ( MRA ) Young Investi- gator Award. ∞ Cátia Monteiro was awarded the Best Poster Award, CNIO Frontiers Meeting : ‘ Primary and Secondary Brain Tumours ’, Madrid, Spain. ∞ Wendy Bindeman was recipient of a Fulbright fellowship. ∞ Pedro García Gómez was awarded the La Caixa INPhINIT PhD Fellowship. Figure ( a ) Metastasis initiating cells ( MIC ) not eliminated during the initial steps of colonisation grow in the brain and induce altered molecular profiles in the microenvironment. (  b-c ) Genetic and ( d-e ) pharmacologic approaches have validated important pro-metastatic components in the microenvironment. ANNUAL REPORT 2017 56 BASIC RESEARCH METABOLISM AND CELL SIGNALLING JUNIOR GROUP OVERVIEW In the Metabolism and Cell Signalling Lab we study the interplay of nutrients, metabolism and cancer. Every cell in the organism receives signals emanating from the abundance of intracellular nutrients and from the nutritional state of the organism as a whole. Integration of cellular and systemic nutrient abundance cues is key for adequate cellular and organismal functions. Importantly, the components if these signalling cascades are functionally and genetically corrupted in disease states, such as cancer. Together with genetic mutations, environmental perturbations, such as those occurring in obesity, affect the cellular signalling cascades that control responses to nutrients and hormones. In the lab, we combine mouse genetics and cell biological tools to gain insight into the genetic and environmental corruptions of nutrient signalling cascades, aiming to conceive therapeutic interventions in the context of cancer, obesity and the process of ageing. “ Our mouse genetic approaches are beginning to reveal the intricacies of nutrient signalling in the fuelling of rapidly proliferative normal and malignant B lymphocytes.” Alejo Efeyan Junior Group Leader Staff Scientist Ana Ortega SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 57 MOLECuLAR ONCOLOGy PROGRAMME | mETAbOLISm ANd CELL SIGNALLING JUNIOR GROUP RESEARCH HIGHLIGHTS Nutrient signalling in B lymphocytes One of the most rapid proliferation bursts in mammalian cells is that of B lymphocytes upon encountering certain pathogens or antigens. This proliferation suddenly multiplies the energetic and metabolic demands of the activated cell, and accordingly, accurate nutrient signalling is key to successfully accomplish the energetically onerous rounds of growth and division. Recently, components of the Rag GTPase pathway, a key nutrient signalling pathway that enables the anabolic capacity of the cell for rapid proliferation, were found mutated in follicular lymphoma ( FL ), an incurable B lymphocyte tumour. We have generated novel strains of mice that express these mutations, explored their oncogenicity and studied the reasons for such oncogenicity. We found that these mutations both suppress cell death and enhance proliferation, leading to hyperactive B cell responses upon immunisation and accelerated lymphomagenesis ( FIGURE ). Our results open up a potential therapeutic avenue for FL. Chronic signalling of elevated nutrients mimics a diabetic state Does an excess in nutrient intake correlate with human disease states because of caloric value, or because of the signalling cascades and cellular responses that overabundant nutrients activate ? We sought to answer this question with genetically engineered mice to have a constitutively active nutrient-sensing cascade, but normal food intake. These mice express a modified form of the RagA GTPase ( RagAGTP ) that activates the mechanistic target of rapamycin complex 1, the pathway responsible for the synthesis of most anabolic reactions ( proteins, lipids and nucleotides ). The sole activation of this nutrient-signalling cascade drove elevated glucose levels in circulation, caused glucose intolerance and elevated the HOMA-IR, a parameter used to diagnose insulin resistance in patients. We are currently in the process of dissecting the contribution of each organ in these metabolic perturbations. s Graduate Students Celia de la Calle, Nerea Deleyto, Ana Belén Plata ( since September ) Technicians Camino Menéndez ( since March ) ( TS )*, Ana Sagrera ( TS )* *Titulado Superior ( Advanced Degree ) Students in Practice Álvaro Fernández ( until June ), Daniel de la Nava ( June-August ), Beatriz Fernández ( February-May ) ∞ PUBLICATIONS ∞ Zabala-Letona A et al. ( incl. Ximenez-Embun P, Castro E, Olmos D, Efeyan A, Muñoz J ) ( 2017 ). mTORC1-dependent AMD1 regu- lation sustains polyamine metabolism in prostate cancer. Nature 547, 109-113. ∞ PUBLICATIONS AT OTHER INSTITUTIONS ∞ Ersching J *, Efeyan A * et al. ( 2017 ). Germi- nal center selection and affinity maturation require dynamic regulation of mTORC1. Im- munity 46, 1045-1058. *equal contribution. ∞ Kalaitzidis D et al. ( 2017 ). Amino acid-in- sensitive mTORC1 regulation enables nu- tritional stress resilience in hematopoietic stem cells. J Clin Invest 127, 1405-1413. Figure ( A ) H&E and ( B ) quantification of activated B lymphocytes in immunised RagCmut mice. ( C ) RagCmut accelerates lymphomagenesis in genetically-prone ( VavP-Bcl2+) mice. ( D ) Hyperglycaemia in RagAGTP mice. ( E ) Glucose intolerance in RagAGTP mice. ( F ) Elevated HOMA-IR, indicative of insulin resistance in RagAGTP mice. ANNUAL REPORT 2017 58 BASIC RESEARCH CANCER CELL BIOLOGY PROGRAMME ERWIN F. WAGNER Programme Director SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 59 CANCER CELL BIOLOGy PROGRAMME The overall strategic goals of the Cancer Cell Biology Programme are to achieve a better understanding of the events leading to cancer development, progression and metastasis, and to discover molecular mechanisms that could provide a basis for novel therapies. The 5 Groups investigate how tumours grow as ‘ extrinsic organs ’; the spectrum of investigations ranges from epithelial cancers such as liver, skin and intestinal, to bone and brain tumours. The research covers aspects of tumour cell biology, ranging from tumour stem cells, tumour cell interactions with host cells/environment such as tumour-associated cells like macrophages and fibroblasts, to the role of inflammation, as well as cell adhesion, metabolism and metastasis. Powerful state-of-the-art mouse genetic models, human cellular systems, high-throughput genomic/proteomic and biochemical tools, as well as patient-derived materials, are employed. At present, these aspects are successfully covered and integrated in an interactive and collaborative spirit by the complementary research areas of the 2 Senior and 3 Junior Groups. The Senior Group, led by Francisco X. Real, studies epithelial tumours focusing mainly on pancreatic and bladder cancer. The Group employs an integrative approach to understand the molecular patho-physiology of these tumours and applies this knowledge in the clinical setting. Mirna Pérez-Moreno’s Group investigates the role of cell adhesion, inflammation and cellular signalling in normal skin physiology and cancer. Nabil Djouder’s Group aims to dissect the contribution of nutrient and growth factor signalling pathways to cancer development, and in particular to gastro-intestinal cancers. Massimo Squatrito’s Group, which is partly supported by the Seve Ballesteros Foundation ( F-SB ), studies how brain tumours, mainly glioblastomas, develop and how they respond to therapy. Finally, my own Group focuses on understanding the role of the transcription factor complex AP-1 ( Fos/Jun ) in physiological and pathological processes, with a strong focus on aspects of inflammation and cancer, e.g. in the liver, lung, skin and bone. We are investigating the role of AP-1 in inflammatory skin diseases, such as psoriasis, but also aim to molecularly define the causes of lung fibrosis. We have continued our efforts to study how the whole organism responds to a locally growing tumour in the context of a complex metabolic impairment in cancer-associated-cachexia. One of our Group Leaders Mirna Pérez-Moreno left the CNIO at the end of 2017 to accept a Professorship at the University of Copenhagen ( Denmark ). We are very thankful to Mirna for her important contributions to the Programme and we wish her the best of luck in her new position. “ Our main goal is to keep CNIO globally competitive and to ensure that CNIO remains an international institution. Members of seventeen different nationalities from 5 continents are represented in our Programme with the goal to perform top- level cancer cell biology, as well as to train students and postdocs to become the next-generation of promising scientists.” ANNUAL REPORT 2017 60 BASIC RESEARCH GENES, DEVELOPMENT AND DISEASE GROUP Erwin F. Wagner Group Leader Staff Scientists Latifa Bakiri, Nuria Gago, María Jiménez, Liliana Mellor, Özge Uluçkan SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 61 CANCER CELL BIOLOGy PROGRAMME | GENES, dEvELOPmENT ANd dISEASE GROUP OVERVIEW Our studies aim to analyse gene function in healthy and pathological conditions, e.g. in tumour development, using the mouse as a model organism but also employing patient- derived samples. Specifically, the functions of the AP-1 ( Fos/ Jun ) transcription factor complex regulating cell proliferation, differentiation and oncogenesis, as well as the cross-talk between organs are being investigated. The goal is to define molecular pathways leading to disease/cancer development and to identify novel therapeutic targets ( FIGURE ). We focus on : ɗ Elucidating a causal link between inflammation, cancer and AP-1 ( Fos/Jun ) expression, using cell type-specific, switchable genetically engineered mouse models ( GEMMs ). ɗ Developing and characterising new GEMMs for cancer and human diseases, such as bone loss, arthritis, fibrosis and psoriasis, and applying these to preclinical studies. ɗ Using multiple approaches to compare mouse models of disease to human disease and to identify therapeutically relevant targets. “ Our goal is that CNIO remains an international and competitive institution. At present, 4 out of 5 Group Leaders in our department are foreigners, one of whom is partly funded by the Seve Ballesteros Foundation. Seventeen different nationalities from 5 continents are a testament to an international science culture, all focussing on unravelling the mysteries of inflammation, metabolism and cell differentiation in cancer.” Post-Doctoral Fellows Kazuhiko Matsuoka, Álvaro Ucero Graduate Student Lucía T. Díez Visiting Graduate Student Jennifer Cascino ( Fulbright Fellow, since September ) Technicians Vanessa Bermeo, Ana Guío ( TS )* Titulado Superior ( Advanced Degree ) ANNUAL REPORT 2017 62 BASIC RESEARCH RESEARCH HIGHLIGHTS We have developed a powerful technology for switchable, reversible and tissue-specific ectopic gene expression of specific AP-1 monomers/dimers in the liver, lung, skin and bone. We use mouse and human tissue samples for large-scale studies, such as deep sequencing ( RNA-Seq, ChIP-Seq ) and mass spectrometry analyses. We evaluate possible biomarkers and therapeutic approaches in small-scale preclinical studies based on these screens. Bone development, osteosarcomas and arthritis We are studying the function of AP-1 proteins in bone development and disease using loss-( LOF ) and gain-of-function ( GOF ) mouse models. In mice, transgenic c-Fos expression leads to osteosarcomas ( OSs ). Using an inducible bone-specific Wntless ( Wls ) LOF GEMM, we found that loss of Wnt signalling delays Fos-induced OS development. Our data also demonstrate that canonical Wnt signalling is not a determining factor, while increased Wnt7b and Wnt9a suggest the involvement of non- canonical Wnt signalling. Rheumatoid ( RA ), Psoriatic ( PsA ) and Osteoarthritis ( OA ) are destructive joint pathologies linked to chronic inflammatory diseases. We are studying the function of AP-1 factors in the development of arthritis using GEMMs and experimental arthritis models. Using cell type-specific and inducible AP-1 LOF mouse models, we found that c-Fos and JunB are key regulators of surgery- and age-induced OA with distinct functions. We are also investigating how a cross-talk from skin to bone contributes to the development and progression of different types of arthritis, as well as whether inflammation generated from arthritic joints can influence disease development in adjacent and distant organs. Liver disease—metabolism, fibrosis, inflammation and cancer AP-1 proteins are important modulators of hepatic lipid metabolism as specific AP-1 dimers can either activate or repress PPARγ transcription. Therefore, fatty liver disease and obesity most likely depend on AP-1 dimer composition. In addition, ectopic expression of Fra-2, but not Fra-1-containing AP-1 dimers in hepatocytes, leads to liver dysplasia. Mechanistically, molecular analyses point to the involvement of pathways connected to human hepatocellular carcinoma ( HCC ), such as the Wnt/ β-catenin and Myc pathways. Deletion of c-Fos in hepatocytes protects from chemically- induced liver carcinogenesis, whereas additional inactivation in immune cells abrogates this effect. Ectopic c-Fos or expression of Fos-dimers lead to altered cholesterol and bile acids metabolism, inflammation, fibrosis, hepatocyte/bile duct proliferation and tumours with HCC signatures. A robust connection between c-Fos expression and the activity of the LXR/RXR pathway, an important regulator of cholesterol homeostasis, was unravelled and most likely contributes to the oncogenic function of c-Fos in hepatocytes. Figure Tet-switchable AP-1 transgenic mice were generated for ectopic expression of specific AP-1 monomers/ dimers in skin, bone, liver and lung, which are complemented by loss-of- function mouse models. Proteomics, expression profiling, RNA-sequencing and ChIP-sequencing are employed to compare mouse models of disease to human disease as well as to identify novel targets. Furthermore, we are investigating the systemic response of the mouse organism to a growing tumour in cancer cachexia. Preclinical studies are performed using different genetically engineered mouse models with compounds that target the identified molecules in order to determine the potential of translating our findings for the treatment of human disease. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 63 CANCER CELL BIOLOGy PROGRAMME | GENES, dEvELOPmENT ANd dISEASE GROUP Cancer-associated cachexia ( CAC ) We previously demonstrated that ‘ browning ’, a switch from white to brown fat, contributes to the wasting process in CAC and also documented the involvement of β-adrenergic signalling and IL-6 in this process. Using GEMMS and syngeneic transplantation models, we are dissecting the switch from a local inflammation-associated tumour to the systemic effects of CAC, with the ultimate aim to identify biomarkers and therapeutic targets. Our recent studies demonstrate a deregulation of the immune system with dramatic changes in lymphoid and myeloid populations. Ongoing studies in mice and in human samples aim to dissect the involvement of the central and peripheral nervous system, the Renin-Angiotensin-Aldosterone system, as well as the tissue-specific role of Ucp-1 during CAC development ( in collaboration with Drs. R. Senarís, Spain, M. Petruzzelli, UK, H. Watzke, M. Poglitsch, and R. Zechner, Austria ). Defining a function for AP-1 in lung disease Lung fibrotic diseases and non-small cell lung cancer ( NSCLC ) share some characteristics such as higher incidence in smokers, high morbidity and lack of effective treatments leading to high mortality. Using GEMMs we found that Fra/Ap-1 proteins contribute to both diseases. While Fra-2 is associated with a fibrosis-specific innate immune response leading to disease progression, Fra- 1 and Fra-2 promote tumour growth of K-Ras-induced NSCLC. Furthermore, Fra-2 expression is increased in lung fibrosis patient samples and correlates with poor survival in human NSCLC. Since AP-1 inhibition delayed lung fibrosis progression in preclinical models, our research focusses on deciphering the molecular mechanism and finding biomarkers and therapeutic targets downstream of AP-1. The lung fibrosis studies are conducted in collaboration with Daiichi Sankyo Company ( Japan ) and Genentech ( USA ), and the cancer studies with Mariano Barbacid’s Experimental Oncology Group and Luis Paz-Ares ’ Lung Cancer Clinical Research Unit at the CNIO. Skin cancer, inflammation and human disease Characterisation of the epidermal inflammatory disease in mice lacking JunB suggests a skin to bone cross-talk. We reported that IL-17A production in skin causes bone loss by inhibiting Wnt signalling in bone-forming osteoblasts, and showed that psoriasis patients suffer from bone loss that correlates with IL-17A levels. Epidermal-deficient JunB GEMMs also suffer from dysbiosis and chronic S. aureus colonisation, which is exacerbated in the absence of adaptive immunity. We are currently evaluating the role of the microbiota in skin inflammation using antibiotic treatments, high-throughput microbiota sequencing and are investigating the functional contribution of autophagy to controlling skin infections. Comparative analyses in GEMMs and psoriatic patient samples unravelled novel molecules for targeted therapies, such as the antimicrobial proteins ( AMPs ) S100A8/A9, Lipocalin-2 and complement C3. We have generated several GEMMs to define the role of AMPs in inflammatory skin disease with a focus on the systemic effects beyond the skin in arthritis and bone loss. Although global deletion of S100A9 in the psoriasis- like mouse model alleviated skin inflammation and psoriatic arthritis, the cellular source of S100A9, with a crucial role in disease development and progression, is still unclear. Thus, we generated a new psoriasis-like GEMM with epidermal deletion of S100A9. Preliminary data show that keratinocyte-expressed S100A9 did not affect skin or joint inflammation, but reduced psoriatic-associated local bone loss. We are evaluating the role of keratinocyte-expressing S100A9 in these events using GEMMs and in vitro cultures. Despite an important contribution in skin homeostasis and cancer, the role of epidermal stem cells ( ESCs ) in chronic inflammatory skin diseases is unclear. Using a lineage-tracking system in psoriasis-like GEMMs, we observed a differential behaviour of distinct subpopulations of epidermal cells, including keratinocytes and ESCs. RNA-sequencing revealed important changes in metabolism and extracellular matrix proteins in psoriatic-like ESCs. In vitro assays and human patient samples are being utilised to further dissect the contribution of these subpopulations to psoriasis. Finally, using GEMMs for Squamous Cell Carcinomas ( SCCs ), we aim to identify therapeutic strategies for skin cancer prevention and to treat peri-neural invasion and metastasis. s ∞ PUBLICATIONS ∞ Bakiri L, Hamacher R, Graña O, Guío-Car- rión A, Campos-Olivas R, Martinez L, Dienes HP, Thomsen MK, Hasenfuss SC, Wagner EF ( 2017 ). Liver carcinogenesis by FOS-dependent inflammation and cholesterol dysregulation. J Exp Med 214, 1387-1409. ∞ Fan F, Bashari MH, Morelli E, Tonon G, Malvestiti S, Vallet S, Jarahian M, Seck- inger A, Hose D, Bakiri L, Sun C, Hu Y, Ball CR, Glimm H, Sattler M, Goldschmidt H, Wagner EF, Tassone P, Jaeger D, Podar K ( 2017 ). The AP-1 transcription factor JunB is essential for multiple myeloma cell proliferation and drug resistance in the bone marrow microenvironment. Leukemia 31, 1570-1581. ∞ Tsujino K, Li JT, Tsukui T, Ren X, Wagner EF, Sheppard D ( 2017 ). Fra-2 negatively regulates postnatal alveolar septation by modulating myofibroblast function. Am J Physiol Lung Cell Mol Physiol 313, L878-L888. ∞ Uluçkan Ö, Wagner EF ( 2017 ). Chronic systemic inflammation originating from epithelial tissues. FEBS J 284, 505-516. ANNUAL REPORT 2017 64 BASIC RESEARCH EPITHELIAL CARCINOGENESIS GROUP Francisco X. Real Group Leader Staff Scientist Victor J. Sánchez-Arevalo ( until June ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 65 CANCER CELL BIOLOGy PROGRAMME | EPITHELIAL CARCINOGENESIS GROUP OVERVIEW We focus on the molecular pathophysiology of pancreatic ductal adenocarcinoma ( PDAC ) and urothelial carcinoma ( UC ), with a disease-oriented approach. We use patient samples, cultured cells, and genetically modified mice, giving a similar weight to the 3 model systems. Primary observations made at either of these levels are then extended through additional work. To translate the findings, we bring this knowledge to a ‘population ’ level, leveraging on information and samples from large patient cohorts. In PDAC, a main hypothesis is that cell differentiation is a potent tumour suppressor mechanism acting early during carcinogenesis. We use the excellent genetic mouse models that are available because these processes cannot be readily studied using human samples. PDAC can originate both in pancreatic progenitors and in acinar cells. Understanding the contribution of early molecular events is crucial in order to design better strategies for early tumour detection and prevention in subjects at risk. In UC, we focus on identifying new genes, using them for improved tumour taxonomy, characterising the mechanisms of action, and applying this knowledge for improved prediction of outcome and therapy. “ We exploit mouse models to assess the role of transcription factors as modulators of KRas-driven PDAC, thereby providing clues on early tumorigenesis. We use urothelial organoid cultures to study the mechanisms of action of new bladder cancer genes.” Post-Doctoral Fellows Enrique Carrillo, Irene Felipe, Eleonora Lapi, Miriam Marqués, Sumit Paliwal ( since November ) Graduate Students Isidoro Cobo, Ana M. Maldonado ( since May ), Irene Millán ( since May ), Catarina Pereira, Mónica Pérez Technicians Itxaso Bellón ( until November ) ( TS )*, Miguel Deblas ( since August ), Natalia Del Pozo, María Tania Lobato ( until June ), Alba Ruiz ( May- September ) ( TS )* *Titulado Superior ( Advanced Degree ) ANNUAL REPORT 2017 66 BASIC RESEARCH RESEARCH HIGHLIGHTS Pancreas cancer molecular pathophysiology While the genetic/genomic changes associated with PDAC have been extensively described in the last few years by the genome consortia, the precursor lesions and molecular changes that precede tumour development are less well established. We have acquired extensive evidence indicating that incomplete acinar cell differentiation is associated with a scenario of pre- inflammation or inflammation and with predisposition to PDAC development using mutant KRas-driven genetic mouse models. These studies provide the basis for the pharmacological – or genetic - manipulation of acinar differentiation as a tumour preventative strategy. One of the transcription factors we focused on is NR5A2, a member of the nuclear receptor family for which putative endogenous ligands as well as pharmacological agonists have recently been identified. Nr5a2 germline heterozygosity leads to no overt pancreatic phenotype but it is associated with a pre-inflammatory state that sensitises mice to the oncogenic effects of mutant KRas. Interestingly, Nr5a2 pancreas-specific heterozygosity − in conjunction with activation of mutant KRas in the pancreas ( KPN+/- mice ) − leads to a progressive loss of the exocrine parenchyma, development of cystic tumours with variable degrees of mucinous differentiation, dysplasia, and to adenocarcinoma ( FIGURE  1). In patients, cystic tumours have variable risks of undergoing malignant transformation and are becoming a very important clinical problem because they are being increasingly diagnosed in healthy adults thanks to improved imaging techniques. We plan to exploit this new mouse model of pancreatic cystic tumours in order to explore, in collaboration with B. Gauthier ( CABIMER, Sevilla ), whether pharmacological stimulation of Nr5a2 activity can prevent the Nr5a2 haploinsufficient phenotype in the context of both pancreatitis and cancer. Urothelial carcinoma ( UC ) genetics, biology, and clinical translation Our main goals are to refine current knowledge on the genomic landscape of UC and to apply this in the clinical setting. Through exome sequencing we identified mutations in STAG2, coding for a cohesin subunit, and in RBM10, coding for a splicing regulator, as new UC genes that are more broadly involved in human cancer. STAG2 inactivation in UC is not associated with aneuploidy, suggesting that regulation of chromatin architecture and gene expression mediate its tumour suppressor role. In collaboration with Ana Losada, we have developed a conditional Stag2 knockout strain ; the cooperation of Stag2 inactivation with other genetic alterations occurring in UC ( i.e. Pik3ca, Hras, and Tp53 ) is being analysed. RBM10 is mutated in several epithelial tumours. Its inactivation in UC is not associated with stage or grade, but it occurs mainly in tumours with urothelial differentiation. In collaboration with J. Valcárcel ( CRG, Barcelona ), we have generated a conditional Rbm10 knockout strain and are analysing the molecular mechanisms through which this gene contributes to UC development using a combination of cellular, molecular and bioinformatics approaches. These studies are complemented with the use of normal murine urothelial organoids, for which we have established robust culture methods and have shown their ability to undergo urothelial differentiation. In addition, we are expanding these studies to human bladder cancers in order to develop precision medicine strategies. Within the context of a project funded by the AECC, we have analysed whether UC molecular taxonomy is able to predict response to neoadjuvant chemotherapy ( NAC ). Patients with tumours having a Basal/Squamous ( BASQ )-like phenotype ∞ PUBLICATIONS ∞ Choi W, Ochoa A, McConkey DJ, Aine M, Höglund M, Kim WY, Real FX, Kiltie AE, Milsom I, Dyrskjøt L, Lerner SP ( 2017 ). Genetic Alterations in the Molecular Sub- types of Bladder Cancer : Illustration in the Cancer Genome Atlas Dataset. Eur Urol 72, 354-365. ∞ Dyrskjot L et al. ( incl. Real FX, Malats N ) ( 2017 ). Prognostic impact of a 12-gene progression score in non-muscle invasive bladder cancer : a prospective multicenter validation study. Eur Urol 72, 461-469. ∞ Marqués M, Real FX ( 2017 ). PIcKing on FGFRs as bladder cancer therapeutic targets. Eur Urol 71, 863-865. ∞ Martinelli P, Carrillo-de Santa Pau E, Cox T, Sainz B Jr, Dusetti N5 Greenhalf W, Rinaldi L, Costello E, Ghaneh P, Malats N, Büchler M, Pajic M, Biankin AV, Iovanna J, Neoptolemos J, Real FX ( 2017 ). GATA6 regulates EMT and tumour dissemination, and is a marker of response to adjuvant chemotherapy in pancreatic cancer. Gut 66, 1665-1676. ∞ Notta F, Hahn SA, Real FX ( 2017 ). The genetic roadmap of pancreatic cancer : Still evolving. Gut 66, 2170-2178. ∞ Rosendahl J et al. ( 2017 ). Genome-wide association study identifies inversion in the CTRB1-CTRB2 locus to modify risk for alcoholic and non-alcoholic chronic pancreatitis. Gut. PMID : 28754779. ∞ Sánchez-Arévalo Lobo VJ, Fernández LC, Carrillo-de-Santa-Pau E, Richart L, Cobo I, Cendrowski J, Moreno U, del Pozo N, Megías D, Bréant B, Wright CV, Magnuson M, Real FX ( 2017 ). c-Myc down-regulation is required for pre-acinar to acinar matura- tion in the pancreas. Gut. PMID : 28159836. ∞ Gomez-Rubio P, Rosato V, Marquez M, Bosetti C, Molina-Montes E, Rava M, Piñero J, Michalski CW, Farré A, Molero X, Löhr M, Ilzarbe L, Perea J, Green- half W, O’Rorke M, Tardón A, Gress T, Barberà VM, Crnogorac-Jurcevic T, Muñoz-Bellvís L, Domínguez-Muñoz E, Gutiérrez-Sacristán A, Balsells J, Costello E, Guillén-Ponce C, Huang J, Iglesias M, Kleeff J, Kong B, Mora J, Murray L, O’Driscoll D, Peláez P, Poves I, Lawlor RT, Carrato A, Hidalgo M, Scarpa A, Sharp L, Furlong LI, Real FX, La Vecchia C, Malats N ; PanGenEU Study Investigators ( 2017 ). A systems approach identifies time-dependent associations of multi- SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 67 CANCER CELL BIOLOGy PROGRAMME | EPITHELIAL CARCINOGENESIS GROUP morbidities with pancreatic cancer risk. Ann Oncol 28, 1618-1624. ∞ van der Lelij P, Lieb S, Jude J, Witz G, Santos CP, Falkenberg K, Schlattl A, Ban J, Schwentner R, Kovar H, Real FX, Waldman T, Pearson M, Kraut N, Peters JM, Zuber J, Petronczki M ( 2017 ). Synthetic lethality within the cohesin complex in human cancer cells. eLife pii : e26980. ∞ van Kessel KE, Beukers W, Lurkin I, Ziel- van der Made A, van der Keur KA, Boor- mans JL, Dyrskjøt L, Márquez M, Ørntoft TF, Real FX, Segersten U, Malats N, Malm- ström PU, Van Criekinge W, Zwarthoff EC ( 2017 ). Validation of a DNA meth- ylation-mutation urine assay to select patients with hematuria for cystoscopy. J Urol 97, 590-595. ∞ Beukers W, van der Keur KA, Kandimalla R, Vergouwe Y, Wteyerberg EW, Boor- mans JL, Jensen JB, Lorente JA, Real FX, Segersten U, Orntoft TF, Malats N, Malmström PU, Dyrskjot L, Zwarthoff EC ( 2017 ). FGFR3, TERT and OTX1 as urinary biomarker combination for sur- veillance of bladder cancer patients in a large prospective multicenter study. J Urol 197, 1410-1418. Book Chapter ∞ Martinelli P, Real FX ( 2017 ). Animal model- ling of pancreatitis-to-cancer progression. In : “ Pancreas Cancer ”. Eds. J Neopto- lemos, R. Urrutia, MW Büchler, Abruzzese J. Springer Verlag ( In press ). ∞ AWARDS AND RECOGNITION ∞ Associate Editor, Gut. ∞ Scientific Advisory Board Member, CIT Programme, Ligue Nationale Contre le Cancer, France. ∞ Science Committee Member, Cancer Re- search UK, London, UK. Figure 1 Nr5a2 pancreatic haploinsufficiency cooperates with mutant Kras in the development of pancreatic cystic lesions. ( A ) Histological aspect of the pancreas of KPN+/- mice at 50 weeks of age, showing the replacement of the exocrine parenchyma by cystic lesions. ( B ) Quantification of the area occupied by cystic lesions in the pancreas of KPN+/+ and KPN+/- mice in relationship with age. ( C ) PAS/Alcian blue staining showing the presence of mucin-producing cells. ( D, E ) Immunohistological analysis of Ki67 and p53 in the pancreas of 50 week-old KPN+/- mice. defined by immunohistochemistry are almost 4 times more likely to achieve a pathological complete response to platinum- based NAC. These studies will guide new clinical trials including molecular stratification criteria. This work is carried out in collaboration with Núria Malats, A. Font, D. Castellano, and an extended group of Spanish uro-oncologists. s ANNUAL REPORT 2017 68 BASIC RESEARCH EPITHELIAL CELL BIOLOGY JUNIOR GROUP OVERVIEW Tumour cells evolve into a progressively complex interplay between heterogeneous tumour cells and their tissue microenvironment, which influences their proliferation and malignancy. Identifying the signalling mechanisms and cell types that sustain this complexity is one of the major goals in cancer biology. In adult skin, epithelial progenitor cells have been identified as the cell of origin of skin carcinomas. Several studies have been instrumental for defining regulatory pathways controlling their proliferation and/or differentiation. However, the identification of extrinsic factors modulating stem cell behaviour has not progressed very far to date. Using skin as a model system and employing mouse genetics and human samples, our research aims to understand how the interactions between epithelial progenitor cells, and also the interactions with their surrounding macroenvironment, sustain skin homeostasis, regeneration, and when perturbed lead to cancer. This information may provide insights for the future development of regenerative and anti-cancer therapies. Mirna Pérez-Moreno ( until December ) Junior Group Leader Post-Doctoral Fellow Silvia M. Janeiro ( until December ) Graduate Student Daniel Peña ( until December ) “ During 2017, we continued our efforts to uncover novel events controlling the behaviour of skin stem cells in order to open new insights into the mechanisms that control their regenerative characteristics, and how, when disrupted, they can lead to cancer.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 69 CANCER CELL BIOLOGy PROGRAMME | EPITHELIAL CELL bIOLOGy JUNIOR GROUP RESEARCH HIGHLIGHTS Regulation of epidermal progenitor cells self-renewal and differentiation We have continued to explore how tissues acquire an adequate control of cell division and differentiation. In particular, using mouse epidermal development as a model system, we investigated the contributions of mitotic and cytoskeletal proteins in the regulation of skin progenitor’s self-renewal through oriented cell divisions. Contributions of stromal cells to the skin stem cell niche in homeostasis We previously identified a novel connection between macrophages and skin progenitor cells that modulates their stem cell properties and regenerative potential. We are expanding these results to decipher how other signals and cells from the stroma are connected with the skin stem cell niche and regulate skin regeneration. Contributions of stromal cues in cancer stem cell maintenance and tumour progression The formation of tumours and their progression to malignancy undoubtedly involves the contributions of the tumour macroenvironment. Identifying the signalling mechanisms and cell types that contribute to tumour initiation and progression to malignancy is instrumental for detecting potential targets for clinical applications in order to eradicate tumours. The macroenvironment of many tumours is rich in cytokines, chemokines, and inflammatory enzymes. During 2017, we continued to explore the role of diverse cell-derived soluble mediators in modulating proliferation, migration and survival of skin cancer stem cells. In addition, we focused our efforts on dissecting the contributions of immune cells towards the cancer stem cell niche in tumour initiation and development. We are employing conditional loss- and gain-of-function studies in genetically modified mice in order to demonstrate the role of specific cell types and their derived soluble mediators in tumorigenesis ; this may provide further insights for the potential development of immunotherapeutic approaches. s Figure (  A ) Mouse Keratinocytes expressing mKO2-hCtd1 ( G1 ) and mAGhGeminin ( S/G2/M phase ). Scale bar 50 µm. (  B ) FISH analysis for chromosomes 11 and 12 in newborn mouse skin. Scale bar 10 µm. ∞ PUBLICATIONS ∞ Shahbazi MN, Peña-Jimenez D, Anto- nucci F, Drosten M, Perez-Moreno M ( 2017 ). Clasp2 ensures mitotic fidelity and prevents differentiation of epidermal keratinocytes. Journal of Cell Science 130, 683-688. ∞ Fontenete S, Pena-Jimenez D, and Perez-Moreno M ( 2017 ). Heterocellular cadherin connections : coordinating ad- hesive cues in homeostasis and cancer. F1000 Research 6, 1010. ∞ Fontenete S, Leite M, Figueiredo C, Cos P, Azevedo NF ( 2017 ). Detection of Hel- icobacter pylori in the Gastric Mucosa by Fluorescence in vivo Hybridization. Methods Mol Biol 1616, 137-146. ∞ AWARDS AND RECOGNITION ∞ Ambassador of the American Society for Cell Biology, ASCB, USA. A B ANNUAL REPORT 2017 70 BASIC RESEARCH GROWTH FACTORS, NUTRIENTS AND CANCER JUNIOR GROUP OVERVIEW Research conducted over the last decade has focused mainly on understanding the functions and the role of newly discovered mutated genes in the development of various diseases, including cancer. Exposure to environmental factors through the regulation and expression of virulent eukaryotic proteins is an often ignored permanent challenge for an organism. Therefore, our laboratory devotes effort towards understanding the molecular mechanisms linking environmental stresses to disease pathogenesis. Based on the integration of experimental mouse models combined with the use of human data and nanotechnology, we aim to provide a comprehensive study for a rational approach towards the development of novel mechanism-based diagnostics and therapeutics to detect, prevent and treat diseases. “ Our research directive is to understand mechanisms of diseases by using newly generated mouse models that recapitulate pathological features of human syndromes in order to guide early diagnosis and treatment.” Nabil Djouder Junior Group Leader Post-Doctoral Fellows Hugo Bernard, Sebastián Thompson ( since February ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 71 CANCER CELL BIOLOGy PROGRAMME | GROwTH FACTORS, NUTRIENTS ANd CANCER JUNIOR GROUP RESEARCH HIGHLIGHTS Pathogenic factors such as poor diets ( under-nutrition or micronutrient deficiencies ), nutrient overload, alcohol consumption, high-fat and low-fibre diets, ionising radiations, bacteria, virus infection, etc., are risk factors for diseases. How these environmental factors can alter the host’s eukaryotic epithelial cells to cause various pathologies, potentially progressing to cancer, remains largely unknown. Finding new genes affected by environmental stressors, and understanding their functions and role in disease development, may pave the basis of future therapies. Therefore, we specifically focus on the identification of likely causal links between environmental stresses and pathologies, potentially progressing to cancer, and their diagnostics and treatment ( theranostics ) through the use of nanotechnology. Molecular chaperones are essential to engage protective mechanisms to ensure cellular and protein homeostasis caused by injurious environmental stimuli. Unconventional prefoldin RPB5 interactor ( URI ) is a co-chaperone whose expression is modulated by various pathogenic environmental factors. Using URI mouse models generated in our laboratory, combined with various genetic murine models and cutting-edge technologies, we are studying diseases predominantly associated with the gastrointestinal tract ( FIGURE ). s Graduate Students Marta Brandt ( until May ), Almudena Chaves, Sergio de la Rosa ( since March ) ( PEJ ) *, Amanda Garrido, Tatiana Grazioso, Ana Teijeiro Technician Eva Martínez ( PEJ ) * *Plan de Empleo Joven ( Youth Employment Plan ) ∞ PUBLICATIONS ∞ Tummala KS, Brandt M, Teijeiro A, Graña O, Schwabe RF, Perna C and Djouder N ( 2017 ). Hepatocellular carcinomas origi- nate predominantly from hepatocytes and benign lesions from hepatic progenitor cells. Cell Reports 19, 584-600. ∞ Garrido A, Djouder N ( 2017 ) NAD+ deficits in age-related diseases and cancer ( 2017 ). Trends Cancer 3, 593-610. ∞ Teijeiro A, Djouder N ( 2017 ). Nicotinamide riboside or IL-17A signaling blockers to prevent liver disorders. Oncoscience 4, 1-2. Figure Representation of our research directive. Our laboratory is mainly interested in understanding how pathogenic environmental factors lead to diseases associated with the gastrointestinal tract. Environmental stress modulates URI expression which may have buffering activities to maintain cellular homeostasis. ANNUAL REPORT 2017 72 BASIC RESEARCH SEVE BALLESTEROS FOUNDATION-CNIO BRAIN TUMOUR JUNIOR GROUP OVERVIEW A decade of studies has underlined the complexity of the genetic events that characterise the genomic landscapes of common forms of human cancer, including gliomas. While a few cancer genes are mutated at high frequencies (>20%), the greatest number of cancer genes in most patients appear at intermediate frequencies ( 2–20%) or lower. Strikingly, the functional significance of the vast majority of these alterations still remains elusive. A current high priority in glioma research is to functionally validate candidate genetic alterations in order to distinguish those that are significant for cancer progression and treatment response. In our laboratory, we use a combination of genomic analyses, mouse models and primary tumour cell cultures, with the main goal of identifying the molecular mechanisms that could provide the basis for novel treatments for glioma patients. “ The main focus of our Group is to uncover the genetic alterations present in glioma patients that are responsible for the aggressiveness and the poor treatment response of these tumours.” Massimo Squatrito Junior Group Leader Staff Scientists Bárbara Oldrini, Alberto J. Schuhmacher ( until June ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 73 CANCER CELL BIOLOGy PROGRAMME | SEvE bALLESTEROS FOUNdATION-CNIO bRAIN TUmOUR JUNIOR GROUP RESEARCH HIGHLIGHTS Precision glioma mouse models It has gradually been established that the vast majority of human tumours are extraordinarily heterogeneous at a genetic level. To accurately recapitulate this complexity, it is now evident that in vivo animal models of cancer will need to recreate not just a handful of simple genetic alterations, but possibly dozens and increasingly intricate. In our laboratory, by combining the RCAS/TVA and CRISPR/Cas9 systems, we have developed novel mouse models for in vivo somatic genome editing that allow the targeting of specific cell types with definite genetic alterations in order to generate precision tumour models. We have shown that somatic deletion in neural stem cells ( NSCs ) of a variety of known tumour suppressor genes ( Trp53, Cdkn2a and Pten ), in combination with the expression of an oncogene driver, leads to glioblastoma ( GBM ) formation. Using this approach, we are currently performing in vivo guide RNA ( gRNA ) screenings to identify novel tumour suppressor genes that contribute to gliomagenesis. Gene fusions have been documented as cancer-drivers for more than three decades, providing valuable insights into the tumorigenesis process. The occurrence and importance of gene fusions in glioma has been appreciated only recently − largely due to high-throughput technologies − and gene fusions have been indicated as one of the major genomic abnormalities in GBM. By simultaneous delivery of pairs of gRNAs we generated different gene fusions, either by chromosomal deletion ( Bcan-Ntrk1 ) or by chromosomal translocation ( Myb-Qk ), and we have shown that they have transforming potential in vitro and in vivo. Lastly, using homology-directed-repair ( HDR ), we also produced tumours carrying the BRAF V600E mutation, frequently identified in a variety of subtypes of gliomas. In summary, we have developed an extremely powerful and versatile mouse model for in vivo somatic genome editing, which will elicit the generation of more accurate cancer models particularly appropriate for pre-clinical testing. s Graduate Students Carolina Almeida, Alvaro Curiel, Veronica Matía Technician Claudia S. Troncone ( until October ) ∞ PUBLICATIONS ∞ Bejarano L, Schuhmacher AJ, Méndez-Per- tuz M, Megías M, Blanco-Aparicio C, Martínez S, Pastor J, Squatrito M, Blasco MA ( 2017 ). Inhibition of Trf1 telomere protein impairs tumor initiation and pro- gression in glioblastoma multiform mouse models and patient-derived xenografts. Cancer Cell 32, 590-607. ∞ Wang Q, Hu B, Hu X, Kim H, Squatrito M, Scarpace L, deCarvalho AC, Lyu S, Li P, Li Y, Barthel F, Cho HJ, Lin YH, Satani N, Martinez-Ledesma E, Zheng S, Chang E, Sauvé CG, Olar A, Lan ZD, Finocchiaro G, Phillips JJ, Berger MS, Gabrusiewicz KR, Wang G, Eskilsson E, Hu J, Mikkels- en T, DePinho RA, Muller F, Heimberger AB, Sulman EP, Nam DH, Verhaak RGW ( 2017 ). Tumor evolution of glioma intrinsic gene expression subtype associates with immunological changes in the microenvi- ronment. Cancer Cell 32, 42-56. ∞ Oldrini B, Hsieh WY, Erdjument-Bromage H, Codega P, Carro MS, Curiel-García A, Campos C, Pourmaleki M, Grommes C, Vivanco I, Rohle D, Bielski CM, Taylor BS,Hollmann TJ, Rosenblum M, Tempst P, Blenis J, Squatrito M, Mellinghoff IK ( 2017 ). EGFR feedback-inhibition by Ran-binding protein 6 is disrupted in cancer. Nat Communications 8, 2035. ∞ Pudelko L, Rouhi P, Sanjiv K, Gad H, Hö- glund A, Squatrito M, Schuhmacher AJ, Hägerstrand D, Warpman Berglund U, Helleday T, Bräutigam L ( 2017 ). Glioblas- toma and glioblastoma stem cells are de- pendent on functional MTH1. Oncotarget 8, 84671-84684. ∞ Bowman R, Wang Q, Carro A, Verhaak RGW, Squatrito M ( 2017 ). GlioVis data portal for visualization and analysis of brain tumor expression datasets. Neu- ro-Oncology 19, 139-141. Book chapter ∞ Schuhmacher AJ, Squatrito M ( 2017 ). An- imal Models in Glioblastoma : Use in Biolo- gy and Developing Therapeutic Strategies. In : Somasundaram K. ( eds ). Advances in Biology and Treatment of Glioblastoma. Current Cancer Research. Springer, Cham. DOI : https ://doi.org/10.1007/978-3-319- 56820-1_9. Figure Bcan-Ntrk1 gene fusion drives high-grade glioma formation. (  a ) RCAS-gRNA-pair vector expressing the Bcan and Ntrk1 gRNAs. ( b ) Schematic representation of the Bcan and Ntrk1 gene loci and the Bcan-Ntrk1 gene fusion. ( c ) PCRs were performed with the specified primers on genomic DNA extracted from the Bcan-Ntrk1 expressing cells. ( d ) Characterisation of the Bcan-Ntrk1-induced tumours. ANNUAL REPORT 2017 74 BASIC RESEARCH STRUCTURAL BIOLOGY PROGRAMME ÓSCAR LLORCA ( since July ) Programme Director SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 75 STRuCTuRAL BIOLOGy PROGRAMME Programme’s research areas and strategic goals The main goal of the Structural Biology Programme is to use structural information to provide mechanistic understanding at the molecular level of how proteins and macromolecular complexes related to cancer function and, ultimately, to use the new mechanistic insights to help guide future drug design. Collaborations and synergies with other Programmes within the CNIO and the combination of different methodologies are essential to achieve these aims. 2017 has been a year of change for the Programme. The Groups headed by Alfonso Valencia and Santiago Ramón-Maiques have moved to different institutions, and the National Bioinformatics Institute Unit, headed by Salvador Capella, also left the CNIO during 2017. Alfonso Valencia, who led the Programme until February, was also responsible for the Structural Computational Biology Group, contributing, among other aspects, to large-scale genome projects. During Alfonso Valencia’s directorship of the Programme several organisational changes took place ; in 2016, he managed the selection of candidates for two Junior Group Leader positions, the reorganisation of the Bioinformatics Unit, and the installation of a new cluster, acquired in 2016 but installed during 2017. During their stay at CNIO, Santiago Ramon’s Group ( Structural Bases of Genome Integrity Group ) helped to advance our understanding of genome integrity ; they focused mainly on the structure and function of CAD, a key component in the metabolism of pyrimidines. We are very thankful to all the above mentioned Groups for their dedication and their contribution to the high-level science conducted at the CNIO. We wish them all the best in their new ventures. Currently, the Programme has several Core Units : Spectroscopy and NMR, Electron Microscopy ( EM ), Bioinformatics, Crystallography and Protein Engineering, and Biological Text Mining. These Units provide access, maintenance and expertise for technologies in Structural Biology and Bioinformatics. Units are an essential element for the Programme and their activities are vital to facilitate the access to Structural methods for non-experts. During 2017, three new groups joined the Structural Biology Programme ; it now counts three Junior and one Senior Research Groups. The Junior Groups headed by Daniel Lietha and Iván Plaza Menacho, work on structural and mechanistic aspects in cancer cell signalling and protein kinases, with emphasis on the search for new inhibitors. The Junior Group headed by Rafael Fernández-Leiro, and the Senior Group, led by Óscar Llorca, work on genome instability and DNA repair pathways. Frontier Structural Biology in cancer requires a strong technical component in cryo-electron microscopy ( cryo- EM ). Incorporating the so-called ‘resolution revolution’ in cryo-EM − now capable of observing macromolecules at high resolution − is the Programme’s main strategic goal for 2017 and 2018. The Programme has recruited two experts in cryo-EM, Rafael Fernández-Leiro and Óscar Llorca, who are working together with the EM Unit to set up an upgraded facility for high- resolution cryo-EM. A new electron microscope with a direct electron detector suitable for high-resolution studies of proteins and complexes is now being acquired. The synergy of cryo-EM with other Structural Biology technologies already in place in the Programme will facilitate the exploitation of the molecular and structural understanding of biological mechanisms for its application in drug design/discovery. Summary of milestones & major achievements of the Programme during 2017 During 2017, Moreno-Morcillo and colleagues from Santiago Ramón’s Group provided clues to the assembly of the multifunctional protein CAD in the July issue of the journal Structure. Le Coq and colleagues from Daniel Lietha’s Group published in the August issue of eLife, new crystal structures of SH2-containing-inositol- 5-phosphatases, proteins that play important roles in regulating the PI3K/Akt pathway in physiology and disease. Iván Plaza Menacho, Rafael Fernández-Leiro and Óscar Llorca joined the Programme in 2017. We live in exciting times at the Structural Biology Programme ; news groups have been recruited and the cryo-electron microscopy equipment is being upgraded. The prospect of using images of single molecules to obtain high-resolution information of complexes will become a reality at CNIO. “ In 2017, we solved several structures of proteins involved in cancer. The implementation of Cryo-EM will place us at the forefront of structural studies and drug discovery to fight against cancer. ” ANNUAL REPORT 2017 76 BASIC RESEARCH MACROMOLECULAR COMPLEXES IN DNA DAMAGE RESPONSE GROUP Óscar Llorca ( since July ) Group Leader Staff Scientists Javier Coloma ( since December ), Andrés López ( since December ), Ángel Rivera ( since December ), Marina Serna ( since November ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 77 STRuCTuRAL BIOLOGy PROGRAMME | mACROmOLECULAR COmPLExES IN dNA dAmAGE RESPONSE GROUP OVERVIEW Avoiding cancer requires active DNA repair mechanisms. In addition, tumour progression needs down-regulation of the cell response to DNA damage. Large and dynamic macromolecular complexes perform many of the activities of the DNA damage response. We cannot fully understand these biological reactions without understanding the structure of the participating molecules and how they interact. Our aim is to study the structural architecture of these large complexes and understand how they function. We are interested in several processes of relevance in cancer, including DNA repair, DNA damage signalling, DNA replication, and RNA quality surveillance mechanisms. We use cryo-Electron Microscopy ( cryo-EM ) as our main structural technique. Cryo-EM methods are revolutionising Biology and they are at the frontier of drug discovery. We can now explore the structure of complexes at close-to-atomic resolution by observing individual molecules in the electron microscope. “ We use cryo-EM to provide new mechanistic insights of how Hsp90 assists in the maturation of the phosphatidylinositol-3-kinase- like kinases ( PIKKs ), relevant for targeted cancer therapy.” Visiting Post-Doctoral Fellow Hugo Muñoz ( since August ) Visiting Graduate Student Carlos Fernández ( since September ) Visiting Master Student Adrián Del Rincón ( since September ) ANNUAL REPORT 2017 78 BASIC RESEARCH RESEARCH HIGHLIGHTS Hsp90-dependent maturation of phosphatidylinositol- 3-kinase-like kinases ( PIKKs ) The family of phosphatidylinositol-3-kinase-like kinases ( PIKKs ) comprises several proteins, including ATM, ATR, DNA-PKcs and mTOR, considered important molecular targets for cancer therapy. It has recently been appreciated that the assembly and maturation of active and functional PIKK complexes requires Hsp90 and a dedicated co-chaperone, the R2TP complex. Interestingly, the R2TP and Hsp90-mediated maturation of PIKKs is a regulated process in the cell, opening up an opportunity to inhibit PIKKs by interfering with their maturation. With that final goal in mind, we have started to address the structural and mechanistic understanding of human R2TP. The comparison between human and yeast R2TP complexes offers some relevant clues about the function of this complex, and in 2017, we reported the structural architecture of R2TP from yeast ( Rivera-Calzada et al., Structure 2017 ). This work was performed in collaboration with Laurence H. Pearl ( Genome Damage and Stability Centre, University of Sussex, UK ). R2TP is one of the most complex of the various Hsp90 co-chaperones identified so far : being a multi-protein complex itself, and possessing components ( RUVBL1/Rvb1 and RUVBL2/ Rvb2 in humans/yeast ) that like Hsp90 possess inherent ATPase activity of their own. We have described the architecture and catalytic properties of the yeast R2TP complex using a combination of cryo-electron microscopy, structural mass spectrometry, and biochemistry. Our data provide structural and mechanistic insights of how R2TP couples an Hsp90 dimer to a PIKK kinase ( FIGURE ). The structural and functional characterisation of the human R2TP complex is now underway, revealing an unsuspected structural and functional complexity compared to the simpler yeast model. Electron microscopy as a tool to help understanding human diseases as well as contributing to the development of new potential therapies As part of our collaboration with the Santiago Rodriguez de Córdoba’s group at the Centro de Investigaciones Biológicas ( CIB ), we used electron microscopy ( EM ) methods to contribute to the understanding of how several mutations identified in patients can cause diseases linked to the complement system, a component of innate immunity. For this, we analysed the structure of components of the complement system using EM. In addition, electron microscopy was used as part of an extensive characterisation of several monoclonal antibodies with potential therapeutic and diagnostic applications in diseases related to mutations and polymorphisms in proteins of the complement system ( Subias Hidalgo et al., Eur J Immunol 2017 ). The EM structures of each antibody bound to its target protein allowed the identification of the epitopes in the 3D structure of the target. Also, these structures provided models to explain the functional properties of the antibodies as defined by Rodriguez de Córdoba’s group. These works highlight the potential of synergising methods of structural biology with genetic, functional and clinical studies, in order to understand and cure diseases. s ∞ PUBLICATIONS ∞ Huecas S, Ramirez-Aportela E, Vergoños A, Nuñez-Ramirez R, Llorca O, Diaz JF, Juan-Rodríguez J, Oliva MA, Castellen P, Andreu JM ( 2017 ). Self-Organization of FtsZ Polymers in Solution Reveals Spacer Role of the Disordered C-Terminal Tail. Biophysical J 113, 1831-1844. ∞ PUBLICATIONS AT OTHER INSTITUTIONS ∞ Rivera-Calzada A, Mohinder P, Muñoz-Her- nandez H, Luque-Ortega JR, Gil-Carton D, Degliesposti G, Skehel JM, Prodromou C, Pearl LH and Llorca O ( 2017 ). The structure of the R2TP complex defines a platform for recruiting diverse client pro- teins to the HSP90 molecular chaperone system. Structure 25, 1145-1152. ∞ Subías Hidalgo M, Yébenes H, Rodríguez-Gallego C, Martín-Ambrosio A, Domínguez M, Tortajada A, Rodríguez de Córdoba S, Llorca O ( 2017 ). Functional and structural characterization of four mouse monoclonal antibodies to comple- ment C3 with potential therapeutic and diagnostic applications. Eur J Immunol 47, 504-515. ∞ Fuentes-Pérez ME, Núñez-Ramírez R, Martín-González A, Juan-Rodríguez D, Llorca O, Moreno-Herrero F, Oliva MA ( 2017 ). TubZ filament assembly dynam- ics requires the flexible C-terminal tail. Sci Rep 7, 43342. ∞ López-Perrote A, Harrison RE, Subías M, Alcorlo M, Rodríguez de Córdoba S, Morikis D, Llorca O ( 2017 ). Ionic tethering contributes to the conformational stability and function of complement C3b. Mol Immunol 85, 137-147. Book Chapter ∞ Fernandez-Rodriguez C, Llorca O, Marti- no F ( 2017 ). Transmission Cryo-electron Microscopy in Drug Discovery : In : Bio- physical Techniques in Drug Discovery. Publisher : Royal Society of Biochemistry. DOI : 10.1039/9781788010016. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 79 STRuCTuRAL BIOLOGy PROGRAMME | mACROmOLECULAR COmPLExES IN dNA dAmAGE RESPONSE GROUP Figure Structure of the yeast R2TP complex. Top ( A ) and tilted ( B ) views of the R2TP complex obtained using cryo- EM. Scale bar represents 10 nm. ( C ) Model of the Hsp90 and R2TP-mediated assembly of the PIKK family of kinases, based on the findings by Rivera-Calzada et al. ( 2017 ). R2TP functions as a platform that brings Hsp90 and the client proteins in proximity, allowing Hsp90 action on the PIKKs. The role of ATP hydrolysis by Hsp90 and the Rvb1- Rvb2 ATPases is not yet understood, but we find that R2TP assembly activates ATP hydrolysis by Rvb1-Rvb2. ANNUAL REPORT 2017 80 BASIC RESEARCH OVERVIEW Our Group studies regulatory mechanisms of key signalling switches controlling growth and adhesion signals. Such signals regulate important cellular processes such as proliferation, adhesion and survival. We use structural techniques, such as X-ray crystallography and electron microscopy, in combination with biochemical and functional studies to understand these mechanisms at atomic detail and to rationalise how oncogenic events result in their deregulation. The structural understanding allows us to design potential anti-cancer therapeutics that interfere with oncogenic deregulation. We focus on growth and adhesion signalling systems that interact and are regulated by specific lipids in the plasma membrane. Specifically, we pursue two main questions : ( i ) how are adhesion signals in focal adhesion complexes triggered by membrane interactions of Focal Adhesion Kinase ? and ( ii ) how are cellular growth signals regulated by changes in phosphatidylinositol ( 3,4,5 )-trisphosphate ( PIP3 ) levels affecting signalling of the Akt pathway ? CELL SIGNALLING AND ADHESION JUNIOR GROUP Daniel Lietha Junior Group Leader Post-Doctoral Fellows Iván Acebrón, Johanne Le Coq “ We identify detailed structural and mechanistic insights in order to understand how growth and adhesion signals are triggered to cause tumour invasion, and we use this information for high-specificity drug design.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 81 STRuCTuRAL BIOLOGy PROGRAMME | CELL SIGNALLING ANd AdHESION JUNIOR GROUP RESEARCH HIGHLIGHTS We discovered that Focal Adhesion Kinase ( FAK ) interacts with PIP2 lipids at cell adhesion sites and that this induces formation of large FAK oligomers on the membrane. This triggers conformational changes in FAK resulting in FAK autophosphorylation, Src recruitment and, in turn, full FAK activation via phosphorylation by Src. Currently, we are studying the atomic architecture of FAK oligomers bound to lipid membranes by electron microscopy, and are investigating how force, induced at focal adhesion sites by actomyosin contraction, induces changes to these structures to activate focal adhesion signalling. We utilise these mechanistic insights to discover highly specific allosteric FAK inhibitors. We employ experimental and virtual screening using fragment based approaches to identify allosteric ligands, and then use a structure based approach to develop these fragments into inhibitory lead compounds. SH2-domain-containing inositol 5-phosphatases ( SHIP ) remove the 5-phosphate from PIP3 and thereby, like PTEN, negatively regulate PIP3 levels in the plasma membrane. Despite their importance, little is known about the mechanisms of SHIP regulation. We solved a crystal structure containing the catalytic and C2 domains of SHIP2, showing an extensive interface between the two domains. We have shown that the C2 domain of SHIP2 binds phosphatidylserine ( PtdSer ), which positions the active site towards its membrane substrate for increased catalytic efficiency ( FIGURE ). In addition, although the C2 domain interacts far from the active site, we have found that the C2 allosterically induces strong catalytic activation of SHIP2. We employed molecular dynamics simulations to guide a mutagenesis study that has identified distinct allosteric signalling pathways emanating from hydrophobic or polar interdomain interactions, which differentially affect lipid chain or head group regions of the substrate. In addition, through cell biology experiments, we have confirmed that mutations at the domain interface affect downstream signalling to Akt. s Graduate Students Marta Acebrón, José Vicente Velázquez Technician Pilar Redondo ∞ PUBLICATIONS ∞ Le Coq J, Camacho-Artacho M, Velázquez JV, Santiveri CM, Gallego LH, Campos-Oli- vas R, Dölker N, Lietha D ( 2017 ). Structural basis for interdomain communication in SHIP2 providing high phosphatase activ- ity. Elife 6, e26640. ∞ Dao P, Lietha D, Etheve-Quelquejeu M, Garbay C, Chen H ( 2017 ). Synthesis of novel 1,2,4-triazine scaffold as FAK in- hibitors with antitumor activity. Bioorg Med Chem Lett 27, 1727-1730. Figure ( A ) The C2 boosts catalytic activity in SHIP2 : i ) by binding to PtdSer membrane lipids and positioning the active site for efficient PIP3 attack and ii ) providing allosteric signals (“ H-path ”/“ P-path ”) to affect binding to hydrophobic or polar regions in PIP3. ( B ) Activity assays show that the C2 domain and PtdSer enhance SHIP2 activity for PIP3 in membranes. ANNUAL REPORT 2017 82 BASIC RESEARCH STRUCTURAL BASES OF GENOME INTEGRITY JUNIOR GROUP OVERVIEW Safeguarding genome integrity is essential for correct cell functioning and to prevent cancer. Our Group is interested in having a good understanding of central cellular processes affecting the integrity of the genome, such as the metabolism of nucleotides, replication, recombination and repair of DNA, and the maintenance and recognition of chromatin architecture. These tasks are performed by proteins and other macromolecular components that associate to form complex and fascinating cellular machines. We combine protein engineering, X-ray crystallography, single-particle electron microscopy, together with biochemical and functional studies, in order to understand the structure and function of these macromolecular complexes at the atomic level. This knowledge should guide us in the design of compounds to modulate the activity of these machines, providing new opportunities and strategies for fighting tumours. “ We provided new insight into the architecture of CAD, the antitumoural target initiating and controlling de novo biosynthesis of pyrimidines. We proved that CAD is a dimer of trimers and that the DHO and ATC domains form the central supporting framework of the 1.5 MDa CAD particles.” Santiago Ramón-Maiques ( until February ) Junior Group Leader Post-Doctoral Fellow Maria Dolores Moreno SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 83 STRuCTuRAL BIOLOGy PROGRAMME | STRUCTURAL bASES OF GENOmE INTEGRITy JUNIOR GROUP RESEARCH HIGHLIGHTS The metabolism of cancer cells is characterised by an increased rate of de novo synthesis of pyrimidines, which fuel DNA and RNA synthesis during rapid cell growth. In animals, the de novo pathway is initiated and controlled by CAD, a multi-functional protein with four enzymatic domains : glutaminase ( GLN ), carbamoyl phosphate synthetase ( CPS ), aspartate transcarbamoylase ( ATC ) and dihydroorotase ( DHO ). Recent reports that CAD up-regulation is modulated by phosphorylation during cell growth and proliferation, and the finding of the first CAD-deficits in children with glycosylation problems, developmental delays or epilepsy, have raised the interest in this protein for therapeutic intervention. Over the past few years, we determined the structures of the DHO and ATC domains of human CAD, revealing the first atomic glimpse of a complex machinery. However, CAD forms ~1.5 MDa hexamers and to understand the functioning of this mega-enzyme we need to explain how the DHO and ATC domains assemble together and interact with the other enzymatic domains. Now, we show that a region of CAD, spanning the DHO and ATC domains including the long linker holding the mTORC1 phosphorylation site, self-associates into a ~500 kDa complex. We prove that this sub-complex is a dimer of trimers and that it is conserved in the CAD-like from fungi, which has an inactive DHO-like domain. We solved the crystal structures of the ATC and inactive DHO-like domains of the fungus Chaetomium thermophilum, thereby showing the similarity with the human CAD homologues. Based on the conserved structural features, we proposed a model for the architecture of CAD, in which the DHO-ATC complex is the central element of the particle. The model helps to explain the intricate functioning of CAD, such as the channelling of metabolites and the communication of conformational changes between domains. This knowledge has enabled us to map clinical mutations to the structural domains, in turn helping us to understand the molecular bases of the first diagnosed CAD diseases. s Graduate Student Francisco Del Caño Technician Araceli Grande ( until August ) ( TS )* *Titulado Superior ( Advanced Degree ) ∞ PUBLICATION ∞ Moreno-Morcillo M, Grande-García A, Ruiz-Ramos A, Del Caño-Ochoa F, Boskovic J, Ramón-Maiques S ( 2017 ). Structural insight into the core of CAD, the multifunctional protein leading de novo pyrimidine biosynthesis. Structure 25, 912-923. Figure (  A ) Crystal structure of the dimeric inactive DHO domain of Chaetomium thermophilum CAD-like protein. ( B ) SEC-MALS analysis of DHO-ATC mutants proves that CAD assembles as a dimer of trimers. ( C ) Model of the central core of the CAD particle, with two ATC trimers ( in blue ) joined by three DHO dimers ( in pink ). ANNUAL REPORT 2017 84 BASIC RESEARCH KINASES, PROTEIN PHOSPHORYLATION AND CANCER JUNIOR GROUP OVERVIEW Our research focuses on the structural and molecular understanding of protein kinase function. How protein kinases are activated and regulated by postranslational modifications and allosteric inputs, and how they assemble into macromolecular protein complexes to transmit signals inside the cell. With a special emphasis on how these mechanisms are corrupted in cancer due to oncogenic mutations and other oncogenic insults ( inflammation, DNA-damage, acquired drug resistance ). Crucially, such atomic and molecular information can be translated into the design and development of more potent and specific protein kinase inhibitors leading eventually to more effective drugs for the treatment of cancer patients. “ Going beyond the boundaries of the current understanding of protein kinase function : from structure to targeted therapies in cancer.” Iván Plaza Menacho ( since May ) Junior Group Leader Post-Doctoral Fellow Pablo Soriano ( since December ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 85 STRuCTuRAL BIOLOGy PROGRAMME | KINASES, PROTEIN PHOSPHORyLATION ANd CANCER JUNIOR GROUP RESEARCH HIGHLIGHTS Our main scientific goal is to understand the mechanisms of protein kinase function, regulation and signalling at the atomic and molecular level, and how these mechanisms are corrupted in cancer and disease. In summary, our achievements during 2017 relate to : ɗ RET functions as a dual-specificity kinase acting as a multi- phospho site substrate-signalling platform. We have showed, for the first time, the intrinsic RET dual-specificity kinase activity. ɗ The allosteric regulation of RET catalytic domain activity by juxtamembrane elements and structure-function identification of a PIF-like pocket on RET. This is the first study revealing mechanisms of allosteric control by flanking elements on RET kinase activation and signalling with important drug- discovery implications. s ∞ PUBLICATIONS ∞ Radaelli S, Plaza-Menacho I, Mologni L ( 2017 ). Novel targeted Therapeutics for MEN2. Endocr Relat Cancer 25, T53-T68. ∞ Plaza-Menacho I ( 2017 ). Structure and function of RET in multiple endocrine neoplasia type 2. Endocr Relat Cancer 25, T79-T90. ∞ PUBLICATIONS AT OTHER INSTITUTIONS ∞ Plaza-Menacho I,*$, Barnouin K, Barry R, Borg A, Orme M, Chauhan R, Mouilleron S, Martinez-Torres J, Meier P, McDonald N * ( 2016 ). RET functions as a dual-specificity kinase that requires allosteric inputs from juxtamembrane elements. Cell Reports 17, 3319-3332. *Corresponding author $ lead contact. ∞ Dubey BN, Lori C, Ozaki S, Fucile G, Pla- za-Menacho I, Jenal U, Schirmer T ( 2016 ). Cyclic di-GMP mediates a histidine ki- nase/phosphatase switch by noncova- lent domain cross-linking. Science Adv 2, e1600823. ∞ AWARDS AND RECOGNITION ∞ Marie Curie Fellow and Experienced Re- searcher. ∞ Ramon y Cajal Fellow. F i g u r e   C r y s t a l l o g r a p h i c identification of an unexpected activation-loop phospho-S909 reveals Intrinsic RET dual-specificity activity. ( Left ) Cartoon representation of phosphorylated RET JM-KD crystal structure. ( Right ) WB analyses using a specific antibody against RET phospho-S909 epitope ( pSQG ). Students in Practice Paula Casas ( since January, Universidad de Alcalá de Henares ), Nicolás Cuesta ( since September, Universidad de Salamanca ), Alba Morán ( since October, Universidad Autónoma ) ANNUAL REPORT 2017 86 BASIC RESEARCH GENOME INTEGRITY AND STRUCTURAL BIOLOGY JUNIOR GROUP OVERVIEW Safeguarding the genetic information is essential to all forms of life. Two key cellular processes keep it free from errors : DNA replication and repair. Importantly, when either of these processes don’t work properly genetic information may be damaged or lost. This has deleterious effects, ultimately leading to disease. Deregulation and malfunction of the protein machinery that safeguards our genome are a hallmark of cancer, but it still remains unclear how this happens at the molecular level. “ The devil is in the detail ”, and our aim is to understand to the highest level of detail exactly what goes wrong with these molecular machines, and when, so that we can act on it to correct it as well as to prevent it from happening. These macromolecules are like real-life machines with intricate mechanisms that enable them to perform their activities. To understand how they work, we use cryo-electron microscopy and biochemistry in an integrative approach. Beyond fundamental research, this structural information provides the necessary details for drug development. Rafael Fernández Leiro ( since September ) Junior Group Leader Technician Araceli Grande ( since September ) ( TS )* *Titulado Superior ( Advanced Degree ) “ Our aim is to understand to the highest level of detail what goes wrong with the protein machinery that protects our genome, and when, so that we can act on it to correct it as well as to prevent it from happening.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 87 STRuCTuRAL BIOLOGy PROGRAMME | GENOmE INTEGRITy ANd STRUCTURAL bIOLOGy JUNIOR GROUP RESEARCH HIGHLIGHTS Mismatch repair DNA mismatch repair ( MMR ) is critical for genome stability. The DNA mismatch repair machinery loads onto newly synthesised DNA and searches for mismatches. The recognition of an error in DNA by the MutS protein leads to an ATP-dependent conformational change that transfers MutS into a sliding clamp state. Only this MutS state is able to activate the MutL ATPase that in turn promotes the cleavage of the DNA for repair. These protein complexes are extremely dynamic and flexible and many steps of the cycle have remained elusive to structural analysis. Using cryo-EM we capture multiple functional steps and we can now study the conformational changes that these proteins undergo in order to recognise the mismatch and license downstream events that lead to repair. These studies started during my postdoctoral research and will be continued at the CNIO in collaboration with Titia Sixma ( Netherlands Cancer Research Institute ) and Meindert Lamers ( Leiden University ). DNA replication and repair—focus on mitochondria Eukaryotic cells have two genomes : nuclear and mitochondrial. However, how the integrity of the mitochondrial genome is maintained through the equilibrium between DNA replication, repair and degradation, and organelle dynamics still remains unclear. We are interested in understanding these pathways because of their implications on ageing and disease, and in particular their relationship to cancer. Cryo-electron microscopy ( cryo-EM ) Important recent technological developments in microscopes, detectors and image processing tools have significantly improved the resolution of cryo-EM, enabling the structural analysis of many elusive macromolecules to an unprecedented level of detail. We are upgrading our cryo-EM facility and will have state- of-the-art equipment. Combined with many other approaches already established at CNIO, we use cryo-EM to study diverse macromolecular complexes involved in cancer. s ∞ PUBLICATIONS AT OTHER INSTITUTIONS ∞ Fernández-Leiro R, Conrad J, Yang JC, Freund SM, Scheres SH, Lamers MH ( 2017 ). Self-correcting mismatches during high-fidelity DNA replication. Nat Struct Mol Biol 24, 140–143. ∞ Vizoso-Vázquez A, Lamas-Maceiras M, Fernández-Leiro R, Rico-Díaz A, Becerra M, Cerdán ME ( 2017 ). Dual function of Ixr1 in transcriptional regulation and recognition of cisplatin-DNA adducts is caused by differential binding through its two HMG-boxes. Biochim Biophys Acta - Gene Regul Mech 1860, 256–269. ∞ Fernandez-Leiro R, Scheres SHW ( 2017 ). A pipeline approach to sin- gle-particle processing in RELION. Acta Crystallogr D Struct Biol 73, 496–502. Figure Adapted from work “ Self- correcting mismatches during high- fidelity DNA replication ” published in Nat Struct Mol Biol in 2017, studying the mechanism of DNA proofreading to illustrate our workflow : ( a ) cryo- EM micrograph, ( b ) 2D averages, ( c ) 3D reconstruction and analysis combined with ( d ) biochemistry. ANNUAL REPORT 2017 88 BASIC RESEARCH SPECTROSCOPY AND NUCLEAR MAGNETIC RESONANCE UNIT OVERVIEW The Unit brings together the technical and scientific management of Nuclear Magnetic Resonance ( NMR ) Spectroscopy and the molecular biophysics instrumentation available at the Structural Biology Programme. It provides CNIO researchers with equipment and technical support in regards to a variety of techniques used for biophysical studies of molecules involved in cancer. This includes the application of NMR to the in vitro characterisation of the structure and dynamics of biomolecules ( proteins in particular ) and their interactions with other biopolymers, as well as with small molecules that could represent initial hits in the drug discovery process or research compounds for biophysical and functional studies. Furthermore, we use NMR to characterise the metabolic profiles of biofluids, cell growth media and cell and tissue extracts from both animal models of cancer and human samples. “ In 2017, we quantified interactions of proteins with lipids and small molecule inhibitors, thus contributing to the understanding of the molecular bases of allosteric activation of enzymes, as well as structure-activity relationships for synthetic enzyme inhibitors.” Ramón Campos-Olivas Unit Head Technician Clara M. Santiveri ( TS )* *Titulado Superior ( Advanced Degree ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 89 STRuCTuRAL BIOLOGy PROGRAMME | SPECTROSCOPy ANd NUCLEAR mAGNETIC RESONANCE UNIT RESEARCH HIGHLIGHTS Our Core Unit incorporates a broad range of instrumentation for the biophysical characterisation of biomolecules and their interactions, including spectrophotometers, a fluorimeter, isothermal titration and differential scanning calorimeters, a circular dichrograph, dynamic and multi-angle static light scattering apparatuses, and a surface plasmon resonance ( SPR ) instrument. Research groups mostly from, but not limited to, the Structural Biology Programme extensively used these technologies throughout 2017. For example, in collaboration with the Cell Signalling and Adhesion Group, we conducted quantitative binding measurements using SPR ( FIGURE ) to establish that both the phosphatase and C2 domains of the human SHIP2 protein bind phosphatidylserine ( PS ) lipids, thereby most likely helping to position the active site towards its substrate. SH2-containing-inositol-5-phosphatases ( SHIPs ) dephosphorylate the 5-phosphate of phosphatidylinositol-3,4,5- trisphosphate ( PI( 3,4,5 )P3 ) and play important roles in regulating the PI3K/Akt pathway in physiology and disease. The Unit hosts a 700 MHz NMR spectrometer that is well equipped with probes, and a sample changer for running up to 120 samples automatically. This provides the required throughput for the screening of small molecule protein binders ( together with the CNIO’s Structural Biology and Experimental Therapeutics -ETP- Programmes ), as well as for metabonomics measurements that, this year, were performed in collaboration with the CNIO- Lilly Cell Signalling Therapies Section ( from the ETP ), as well as the Genes, Development and Disease and the Growth Factors, Nutrients and Cancer Groups ( from the Cancer Cell Biology Programme ). Collectively, with these and other groups, we implemented sample preparation protocols and developed spectroscopic and analytical tools to characterise the metabolites present in different biological samples. s ∞ PUBLICATIONS ∞ Bakiri L, Hamacher R, Graña O, Guío-Car- rión A, Campos-Olivas R, Martinez L, Dienes HP, Thomsen MK, Hasenfuss SC, Wagner EF ( 2017 ). Liver carcinogenesis by FOS-dependent inflammation and cholesterol dysregulation. J Exp Med 214, 1387-1409. ∞ San José-Enériz E, Agirre X, Rabal O, Vi- las-Zornoza A, Sanchez-Arias JA, Miranda E, Ugarte A, Roa S, Paiva B, Estella-Her- moso de Mendoza A, Alvarez RM, Casares N, Segura V, Martín-Subero JI, Ogi FX, Soule P, Santiveri CM, Campos-Olivas R, Castellano G, de Barrena MGF, Rod- riguez-Madoz JR, García-Barchino MJ, Lasarte JJ, Avila MA, Martinez-Climent JA, Oyarzabal J, Prosper F ( 2017 ). Discovery of first-in-class reversible dual small mol- ecule inhibitors against G9a and DNMTs in hematological malignancies. Nat Commun 8, 15424. ∞ Franco-Echevarría E, González-Polo N, Zorrilla S, Martínez-Lumbreras S, Santiveri CM, Campos-Olivas R, Sánchez M, Calvo O, González B, Pérez-Cañadillas JM ( 2017 ). The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition. Nucleic Acids Res 45, 10293-10305. ∞ Le Coq J, Camacho-Artacho M, Velázquez JV, Santiveri CM, Gallego LH, Campos-Oli- vas R, Dölker N, Lietha D ( 2017 ). Structural basis for interdomain communication in SHIP2 providing high phosphatase activ- ity. Elife 6, e26640. Book Chapter ∞ Santiveri CM, López-Méndez B, Huecas S, Alfonso C, Luque-Ortega, JR, Cam- pos-Olivas R ( 2017 ). A biophysical toolkit for molecular interactions. In : eLS. John Wiley & Sons Ltd, Chichester. DOI : 10.1002/9780470015902.a0027015. Figure SHIP2 Ptase domain ( A ) and Ptase-C2 domains ( B ) binding to PS by SPR. Sensorgrams show the difference in response between the active cell coated with 30% PS vesicles and the reference cell containing Pcholine ( PC ) vesicles. (  C ) SPR response units ( RU ) at 10 s ( dashed line in A and B ) as a function of concentration indicate stronger binding for Ptase-C2. ( D ) Calcium dependency of the SHIP2-PS interaction. Relative SPR responses at 5 µM protein were recorded as in C, but in presence or absence of 0.5 mM CaCl2. ANNUAL REPORT 2017 90 BASIC RESEARCH BIOINFORMATICS UNIT OVERVIEW Bioinformatics is a key discipline for understanding the cancer genome and for the future of cancer therapeutics. Bioinformatics- based approaches have the ability to transform the huge amount of biological data into comprehensive models that provide an in-depth understanding of cancer disease and the complex relationships among genotype and phenotype that are needed to identify cancer driver molecular alterations and new therapeutic targets. The CNIO Bioinformatics Unit ( BU ) has several goals : ɗ To develop new computational methodologies and bioinformatics tools to enable the integration of biological and clinical data. ɗ To achieve genome analysis in cancer patients ’ data to identify new biomarkers and mechanisms of drug response. ɗ To provide bioinformatics support with data analysis and interpretation using computational and statistical methods. ɗ To maintain the scientific computing facilities at the CNIO and to provide training in bioinformatics tools and methods. Fátima Al-Shahrour Unit Head Post-Doctoral Fellow Hector Tejero “ PanDrugs is a feasible method to identify actionable molecular alterations and to prioritise drugs that facilitate the interpretation of the genomic landscape and clinical decision-making in cancer patients.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 91 STRuCTuRAL BIOLOGy PROGRAMME | bIOINFORmATICS UNIT RESEARCH HIGHLIGHTS In 2017, the CNIO Bioinformatics Unit published 24 peer- reviewed articles ( the full list is available on our web site http :// bioinformatics.cnio.es/) as a result of our ongoing research projects and scientific collaborations with CNIO Research Groups and other national and international research institutions. During this year, we developed several bioinformatics tools for the analysis of next-generation sequencing data in collaboration with the SING group ( University of Vigo ): RubioSeq+ for DNA- Seq analysis ( Rubio-Camarillo et al. 2017 ), nextpresso for RNA-Seq analysis ( Graña et al. 2017 ), and bicycle for bisulfite- seq analysis ( Graña et al. 2017 ). Remarkably, the RUbioSeq+ ( http ://rubioseq.bioinfo.cnio.es/) tool supports an interactive graphical user interface ( GUI ) that facilitates its usage for biomedical translational researchers who lack computational or bioinformatics skills. Also, our Group focuses on gaining a better understanding of the impact of cancer genomics on the making of clinical decisions. To this aim, we have developed two methodologies to guide the selection of therapies, propose sequential treatments and drug repositioning : PanDrugs ( http ://pandrugs.bioinfo.cnio.es ) and SATIE ( http ://satie.bioinfo.cnio.es ). All our tools are freely available and have been applied in different genomic studies undertaken in numerous scientific collaborations, such as : the study of the pre-metastatic activity of midkine in cancer ( Olmeda D et al., 2017 ), the identification of a novel oncogenic Braf kinase-inactive mutation ( Nieto, P et al., 2017 ), and also the prediction of drug response in pancreatic cancer patient-derived xenograft mouse models using transcriptomics data ( Rajeshkuma NV et al., 2017 ). Many more bioinformatics analyses were performed together with other CNIO groups, such as : the development of a targeted sequencing assay for Pheochromocytoma and Paraganglioma diagnostics ( Currás-Freixes et al., 2017 ) and the study of NUP98- HOXA9 fusion in leukaemia ( Rio-Machin A et al., 2017 ), among others. s ∞ SELECTED PUBLICATIONS * ∞ Gómez-López G, Dopazo J, Cigudosa JC, Valencia A, Al-Shahrour F ( 2017 ). Preci- sion medicine needs pioneering clinical bioinformaticians. Brief Bioinform. PMID : 29077790. ∞ Graña O, López-Fernández H, Fdez-Rive- rola F, González Pisano D, Glez-Peña D ( 2017 ). bicycle : a bioinformatics pipeline to analyze bisulfite sequencing data. Bi- oinformatics. PMID : 29211825. ∞ Perales-Patón J, Piñeiro-Yañez E, Tejero H, López-Casas PP, Hidalgo M, Gómez- López G, Al-Shahrour F ( 2017 ). Pancreas cancer precision treatment using avatar mice from a Bioinformatics Perspective. Public Health Genomics 20, 81-91. ∞ Rubio-Camarillo M, López-Fernández H, Gómez-López G, Carro Á, Fernández JM, Torre CF, Fdez-Riverola F, Glez-Peña D ( 2017 ). RUbioSeq+: A multiplatform appli- cation that executes parallelized pipelines to analyse next-generation sequencing data. Comput Methods Programs Biomed 138, 73-81. ∞ Graña O, Rubio-Camarillo M, Fdez-Rive- rola F, Pisano DG, Glez-Peña D ( 2017 ). Nextpresso : next generation sequencing expression analysis pipeline. Curr Bio- inform. DOI 10.2174/1574893612666170 810153850. ∞ Andrés-León E, Gómez-López G, Pisano DG ( 2017 ). Prediction of miRNA-mRNA Interactions Using miRGate. Methods Mol Biol 1580, 225-237. *please see BU’s web site for a list of all publications. Figure PanDrugs score calculation. ( a ) Gene Score ( GScore ) uses the biological and clinical impact of mutations, their frequency, relevance and vulnerability in cancer. Drug indication, gene-drug association and number are used to calculate Drug score ( DScore ). (  b ) ‘Best therapeutic candidates’ are based on the accumulated and weighted scoring of GScore and DScore. Graduate Students Guillermo Martín-Serrano ( since February ), Javier Perales, Kevin Troulé Technicians Andrés Cañada ( TS ) *, Ángel Carro ( until January ) ( TS ) *, Coral Fustero ( PEJ-L ) **, Gonzalo Gómez ( TS ) *, Osvaldo Graña ( TS ) *, Elena Piñeiro ( TS ) *, Miriam Rubio ( until April ) ( TS ) * *Titulado Superior ( Advanced Degree ) **Plan de Empleo Joven-Licenciado ( Youth Employment Plan-Graduate ) ( until November ) ANNUAL REPORT 2017 92 BASIC RESEARCH ELECTRON MICROSCOPY UNIT OVERVIEW The Electron Microscopy ( EM ) Unit is a research laboratory as well as a central core facility. It is available to CNIO researchers and the wider research community, providing access to Transmission Electron Microscopy and supplying expertise in EM image analysis. Our Unit offers standard specimen preparation techniques for proteins, protein complexes and vesicles, data collection and data processing services that are tailored to meet the particular needs of the users. We also give training to regular users on the use of our equipment and provide further guidance regarding specimen preparation. “ We have made a step forward in our understanding of de novo synthesis of pyrimidines by providing fundamental information about the internal structural organisation of the multifunctional protein CAD.” Jasminka Boskovic Unit Head Technician Carlos Rodríguez ( PEJ-L )* *Plan de Empleo Joven-Licenciado ( Youth Employment Plan-Graduate ) ( until December ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 93 STRuCTuRAL BIOLOGy PROGRAMME | ELECTRON mICROSCOPy UNIT RESEARCH HIGHLIGHTS The Electron Microscopy Unit is a research facility that assists with different biological scientific projects ranging from the macromolecular to the cellular level. The EM Unit’s scope of work includes sample preparation protocols, negative staining, cryo-EM, and data collection methods, as well as 2D and 3D data processing. In collaboration with CNIO’s Structural Bases of Genome Integrity Group ( Structural Biology Programme ), we carried out negative staining electron microscopy to gain insight into the molecular architecture of DHO-ATC hexamers. The EM analysis clearly indicated that despite crosslinking, the particle presents a structural flexibility that prevents the determination of a complete 3D model. A combination of structural and biophysical studies enabled us to propose a model that sets the DHO and ATC complex as the central element in the architecture of multifunctional protein CAD. Our model suggests that CAD is more than the sum of its parts, and that the detailed study of the pieces will give limited information in comparison with the complexity that would be revealed by the structural determination of the full-length particle. We continued our collaboration with Dr. Iván Ventoso, from the Centro de Biología Molecular ‘ Severo Ochoa ’ ( CSIC-UAM ) and the Departamento de Biología Molecular, Universidad Autónoma de Madrid ( UAM ). The EM Unit participated in the study of the topology and dynamics of the scanning ribosomal 43S pre- initiation complex ( PIC ). Our data supports a model where the eIF4F complex works at the leading edge of the scanning PIC, rather than acting as a simple clamp to prevent backsliding as previously suggested. We have advanced in our understanding of PI( 4,5 )P2-mediated induction of Focal Adhesion Kinase ( FAK ) clustering at the cell membrane by applying 2D electron crystallography. This work is the continuation of our collaboration with CNIO’s Cell Signalling and Adhesion Group ( Structural Biology Programme ). s Figure (  A  ) Se lected 2D projections filtered to 25 Å of a DHO-ATC model formed by the association of two ATC trimers and three DHO dimers. (  B ) Representative class averages of crosslinked and negatively stained ctDHOlike-ATC particles. ∞ PUBLICATION ∞ Moreno-Morcillo M, Grande-García A, Ruiz-Ramos A, Del Caño-Ochoa F, Boskovic J, Ramón-Maiques S ( 2017 ). Structural insight into the core of CAD, the multifunctional protein leading de novo pyrimidine biosynthesis. Structure 25, 912-923. ANNUAL REPORT 2017 94 BASIC RESEARCH CRYSTALLOGRAPHY AND PROTEIN ENGINEERING UNIT OVERVIEW The Crystallography and Protein Engineering Unit ( XTPEUnit ) is a central core facility as well as a research laboratory ; its main goal is to fulfil the requests of research groups at the CNIO and outside our Centre, by providing on-demand services at different levels. These services range from the production of recombinant proteins for different types of biochemical/biophysical assays and monoclonal antibody production, to macromolecular structural determination at low resolution by small-angle X-ray scattering ( SAXS ), or at high resolution by X-ray crystallography. The latter includes co-crystallisation in the presence of inhibitors, during the guided drug design process. “ Our Unit is fully committed to spreading the use of the advanced technologies used in Structural Biology, and to show how beneficial the information provided by protein images given at high-resolution is in understanding the biology of cancer.” Inés Muñoz Unit Head Staff Scientist Jorge L. Martínez SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 95 STRuCTuRAL BIOLOGy PROGRAMME | CRySTALLOGRAPHy ANd PROTEIN ENGINEERING UNIT RESEARCH HIGHLIGHTS This year, we worked closely with the Experimental Therapeutics Programme on several projects based on the production of proteins such as full-length human MASTL that enable new biochemical experiments. Other projects were directly focused on structural characterisation by X-ray crystallography in support of drug discovery projects, as was the case of the human proteins MASTL kinase-domain, HASPIN and CDK8/CyclinC complex in which the proteins were crystallised in the presence of compounds developed at the Medicinal Chemistry Section ( FIGURE ). Especially relevant was our continuous work on the production of proteins for the generation of antibodies by the Monoclonal Antibody Unit ( Biotechnology Programme ). During 2017, this smooth collaboration has led to the production of several cancer-involved proteins such as mouse PD1, PD-L2 and HAS1, and human IL11 and NOMO1, among others. The Unit also undertakes several internal collaborations with other CNIO Groups. Especially noteworthy are the ones established with the Telomeres and Telomerase Group, the Gastrointestinal Cancer Clinical Research Unit, the Melanoma Group, and the Experimental Oncology Group. Additionally, the Unit maintains external collaborations with groups at the Physical Chemistry Department ( University of Granada ), the Environmental Biology Department ( CIB-CSIC ), the Department of Biomedicine ( University of Bergen, Norway ), the Department of Crystallography and Structural Biology ( Instituto de Quimica- Fisica Rocasolano, CSIC ), and the Department of Molecular Engineering ( Åarhus University, Denmark ). Along 2017, the Unit also sustained its own scientific projects. We continued to characterise the role of ephrinB2 in different pathologies by carrying out a further structural characterisation of the blocking single-chain antibodies, which we developed at our Unit by using a combination of X-ray crystallography and SAXS ( FIGURE ). We have also initiated a drug-discovery project targeting the function of the Mdm2-MdmX E3 complex, in collaboration with the Pharmacology and Therapeutics Department at the Roswell Park Cancer Institute ( Buffalo, USA ). s Graduate Student Silvia L. Gomes Technicians Daniel Calvo ( PEJ-L ) *, Miguel A. Navarro ( since February ) ( PEJ-L ) *, Álvaro Otero ( until November ) ( PEJ-L ) *, Federico Ruiz ( since June ) ( TS ) **, Alicia Virseda ( until November ) ( PEJ-L ) * *Plan de Empleo Joven-Licenciado ( Youth Employment Plan-Graduate ) **Titulado Superior ( Advanced Degree ) ∞ PUBLICATIONS ∞ Olmeda D, Cerezo-Wallis D, Riveiro-Falk- enbach E, Pennacchi PC, Contreras-Alcal- de M, Ibarz N, Cifdaloz M, Catena X, Calvo TG, Cañón E, Alonso-Curbelo D, Suarez J, Osterloh L, Graña O, Mulero F, Megías D, Cañamero M, Martínez-Torrecuadrada JL, Mondal C, Di Martino J, Lora D, Mar- tinez-Corral I, Bravo-Cordero JJ, Muñoz J, Puig S, Ortiz-Romero P, Rodriguez-Peralto JL, Ortega S, Soengas MS. ( 2017 ) Whole- body imaging of lymphovascular niches identifies pre-metastatic roles of midkine. Nature 546,676-680. ∞ Méndez-Pertuz M, Martínez P, Blanco C, Gómez-Casero E, García AB, Martínez-Tor- recuadrada J, Palafox M, Cortés J, Serra V, Pastor J, Blasco MA. ( 2017 ). Modulation of telomere protection by the PI3K/AKT pathway. Nat Commun 8, 1278. ∞ Muñoz IG, Morel B, Medina-Carmona E, Pey AL ( 2017 ). A mechanism for cancer-associ- ated inactivation of NQO1 due to P187S and its reactivation by the consensus mutation H80R. FEBS Lett 591, 2826-2835. ∞ Garaulet G, Lazcano JJ, Alarcón H, de Frutos S, Martínez-Torrecuadrada JL, Rod- riguez A, ( 2017 ). Display of the albumin binding domain in the envelope improves lentiviral vector bioavailability. Hum Gene Ther Methods 28, 340-351. Book ∞ Chaudhuri B, Muñoz IG, Qian S, Urban VS ( 2017 ). Biological Small Angle Scattering : Techniques, Strategies and Tips, Advances in Experimental Medicine and Biology 1009. Springer Nature. ISBN 978-981-10-6037-3. ∞ AWARDS AND RECOGNITION ∞ Member of the Board of Directors, Asoci- ación de Usuarios de Sincrotrón de España. Figure ( a ) Ribbon representation of the X-ray structure of CDK8/CyclinC in complex with the drug ETP-50775. The coloured omit map belongs to the electron density of the bound compound ( synthesised at CNIO’s Medicinal Chemistry Section ). ( b, c, and d ) Protein crystals corresponding to the single-chain antibodies B11 and 2B1, and the complex of the human extracellular domain of ephrinB2 with 2B1. ANNUAL REPORT 2017 96 BASIC RESEARCH BIOLOGICAL TEXT MINING UNIT OVERVIEW CNIO and the State Secretariat for Telecommunications and the Information Society ( SETSI ) are collaborating on the identification and development of Text and Data mining resources to transform the growing amount of key health information hidden in electronic health records, scholarly communications, patents or social media into structured data of practical utility in the clinic, as well as for basic biomedical research. The integration of results from clinical and biomedical text mining systems with bioinformatics infrastructures is critical to empower precision medicine approaches that enable a more comprehensive and systematic understanding of the molecular characteristics of cancer patients. Our Unit is funded through an ‘ encomienda ’ between the SETSI and CNIO as part of the 90 million Euro Strategic National Plan for the Advancement of Language Technologies. The mission of the Unit is to characterise the state-of-the-art of clinical text mining systems, provide assistance to adapt and apply clinical text mining components to various use cases and to generate key resources including components, annotated data and evaluation infrastructures. Martin Krallinger Unit Head Staff Scientists José Antonio López ( since August ), Marta Villegas ( since July ) “ Clinical text and data mining is a key technology to understand health-related big data and to empower precision medicine approaches for cancer treatment.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 97 STRuCTuRAL BIOLOGy PROGRAMME | bIOLOGICAL TExT mINING UNIT RESEARCH HIGHLIGHTS The Biological Text Mining Unit began its journey in January 2017, with the aim of providing consultancy, guidance and technical assistance for cognitive computing and text-mining technologies applied to clinical and biomedical documents of relevance, particularly to precision medicine approaches. The Unit has been focusing on fostering collaborative efforts to address the needs faced by healthcare providers ( Hospital Virgen del Rocio or Hospital XII de Octubre ), Spanish national health-related agencies ( the Spanish Medical Agency, the Spanish National Library of Health or the Spanish Royal Medical Academy ) and artificial intelligence and language technologies academic research groups. Clinical text mining represents a strategic innovative research area with considerable potential to leverage uptake of cognitive computing and big data text analytics in health. To cover integration and discoverability aspects of existing resources, we have examined the design requirements, annotation formats and standards for interoperability of biomedical language technology infrastructures, and have constructed a registry of language processing components and a medical document repository. The Unit has coordinated community assessment evaluation challenges ( BioCreative and IberEval ) with the aim to benchmark existing tools, to determine cutting edge computational strategies and to enable the development of statistical machine learning models by providing access to Gold Standard annotated training datasets through an evaluation platform. These community assessments included tasks related to the technical evaluation of systems for the automatic recognition of mentions of biomedical named entities in running text ( genes, proteins, chemical compounds/drugs, cell lines, diseases, anatomic terms and mutations ) or the automatic extraction of drug-target associations. Moreover, we have applied text mining methodologies to concrete use cases, including the implementation of semantic search engines for toxicology and for cancer or the use for disease and gene concepts recognition to assist in the discovery of inverse comorbidities between cancer and neurodegenerative diseases. s Technicians Diana De La Iglesia, Aitor González ( TS )*( since July ), Ander Intxaurrondo ( TS )* ( since February ), Jesús Santamaría ( TS )* ( since March ), Santiago de la Peña ( TS )* ( until June ) *Titulado Superior ( Advanced Degree ) ∞ PUBLICATIONS ∞ Krallinger M, Rabal O, Lourenço A, Oyarza- bal J, Valencia A. ( 2017 ). Information Retrieval and Text Mining Technologies for Chemistry. Chem Rev 117, 7673-7761. ∞ Cañada A, Capella-Gutierrez S, Rabal O, Oyarzabal J, Valencia A, Krallinger M ( 2017 ). LimTox : a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes. Nucleic Acids Res 45, w484-w489. ∞ Sánchez-Valle J, Tejero H, Ibáñez K, Portero JL, Krallinger M, Al-Shahrour F, Tabarés-Seisdedos R, Baudot A, Valen- cia A ( 2017 ). A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s disease, Glioblas- toma and Lung cancer. Sci Rep 7, 4474. Figure Text mining search engine LimTox for chemical entities and genes. ANNUAL REPORT 2017 98 BASIC RESEARCH STRUCTURAL COMPUTATIONAL BIOLOGY GROUP OVERVIEW The main interest of our Group is the study of the molecular bases of cancer by bringing an evolutionary perspective to the study of the interplay between genomics and epigenomics in tumour progression. Our research is largely carried out in the context of large-scale genome projects, in which we develop new computational methods for the study of genome-cancer relationships. In this general scenario, the strategic goals of the Structural Computational Biology Group are to : ɗ Develop new ideas, methods and software platforms for the extraction, integration and representation of cancer data, including the analysis of molecular, genomic, epigenomic and phenotypic information in collaboration with large-scale genome projects. ɗ Include new technologies for data and text mining, together with Machine Learning methods, in our cancer genome analysis framework. ɗ Analyse the function, structure and specific interactions of cancer- related proteins. s Alfonso Valencia ( until February ) Group Leader Staff Scientists Andrea Nicole Dölker ( until June ), Vera Pancaldi ( until May ), Michael Tress Graduate Students Maria Rigau ( until July ), Juan Rodríguez ( until June ), Jon Sánchez Technicians Miguel Madrid ( until June ) ( TS )*, Filipe N. Were ( until March ) ( TS )* *Titulado Superior ( Advanced Degree ) ∞ PUBLICATIONS ∞ Krallinger M, Rabal O, Lourenço A, Oyarza- bal J, Valencia A ( 2017 ). Information re- trieval and text mining technologies for chemistry. Chem Rev 117, 7673-7761. ∞ Porta-Pardo E, Kamburov A, Tamborero D, Pons T, Grases D, Valencia A, Lopez-Bigas N, Getz G, Godzik A. ( 2017 ). Comparison of algorithms for the detection of cancer drivers at subgene resolution. Nat Meth- ods 14, 782-788. ∞ Tress ML, Abascal F, Valencia A ( 2017 ). Alternative splicing may not be the key to proteome complexity. Trends Biochem Sci 42, 98-110. ∞ Tress ML, Abascal F, Valencia A ( 2017 ). Most alternative isoforms are not func- tionally important. Trends Biochem Sci 42, 408-410. ∞ Cañada A, Capella-Gutierrez S, Rabal O, Oyarzabal J, Valencia A, Krallinger M ( 2017 ). LimTox : a web tool for ap- plied text mining of adverse event and toxicity associations of compounds, drugs and genes. Nucleic Acids Res 45, w484-w489. ∞ Rodriguez JM, Rodriguez-Rivas J, Di Do- menico T, Vázquez J, Valencia A, Tress ML ( 2017 ). APPRIS 2017 : principal isoforms for multiple gene sets. Nucleic Acids Res. PMID : 29069475. ∞ Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valen- cia A ( 2017 ). Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Res 45, 9244-9259. ∞ Frenkel-Morgenstern M, Gorohovski A, Tagore S, Sekar V, Vazquez M, Valencia A. ( 2017 ). ChiPPI : a novel method for mapping chimeric protein-protein inter- actions uncovers selection principles of protein fusion events in cancer. Nucleic Acids Res 45, 7094-7105. ∞ Ecker S et al. ( incl. Valencia A ) ( 2017 ). Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types. Genome Biol 18, 18. ∞ Piccolo P et al. ( incl. Valencia A ) ( 2017 ). MIB2 variants altering NOTCH signalling result in left ventricle hypertrabeculation/ non-compaction and are associated with Ménétrier-like gastropathy. Hum Mol Gen- et 26, 33-43. ∞ Vargas-Parra GM, González-Acosta M, Thompson BA, Gómez C, Fernández A, Dá- maso E, Pons T, Morak M, Del Valle J, Iglesias S, Velasco À, Solanes A, Sanjuan X, Padilla N, de la Cruz X, Valencia A, Holinski-Feder E, Brunet J, Feliubadaló L, Lázaro C, Navarro M, Pineda M, Capellá G ( 2017 ). Elucidating the molecular basis of MSH2-deficient tumors by combined germline and somatic analysis. Int J Cancer 141, 1365-1380. ∞ Flobak Å, Vazquez M, Lægreid A, Valencia A ( 2017 ). CImbinator : a web-based tool for drug synergy analysis in small- and large-scale datasets. Bioinformatics 33, 2410-2412. ∞ Catalá-López F, Hutton B, Driver JA, Page MJ, Ridao M, Valderas JM, Alon- so-Arroyo A, Forés-Martos J, Martínez S, Gènova-Maleras R, Macías-Saint-Gerons D, Crespo-Facorro B, Vieta E, Valencia A, Tabarés-Seisdedos R ( 2017 ). Cancer and central nervous system disorders : proto- col for an umbrella review of systematic reviews and updated meta-analyses of observational studies. Syst Rev 6, 69. ∞ Catalá-López F, Hutton B, Driver JA, Ridao M, Valderas JM, Gènova-Maleras R, Forés-Martos J, Alonso-Arroyo A, Saint-Gerons DM, Vieta E, Valencia A, Tabarés-Seisdedos R. ( 2017 ). Anorexia nervosa and cancer : a protocol for a systematic review and meta-analysis of observational studies. Syst Rev 6, 137. ∞ Catalá-López F, Hutton B, Page MJ, Ridao M, Driver JA, Alonso-Arroyo A, Forés-Martos J, Macías Saint-Gerons D, Vieta E, Valencia A, Tabarés-Seisde- dos R ( 2017 ). Risk of mortality among children, adolescents, and adults with autism spectrum disorder or attention deficit hyperactivity disorder and their first-degree relatives : a protocol for a systematic review and meta-analysis of observational studies. Syst Rev 6, 189. ∞ Sánchez-Valle J, Tejero H, Ibáñez K, Portero JL, Krallinger M, Al-Shahrour F, Tabarés-Seisdedos R, Baudot A, Valen- cia A ( 2017 ). A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s disease, glioblas- toma and lung cancer. Sci Rep 7, 4474. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 99 STRuCTuRAL BIOLOGy PROGRAMME | NATIONAL bIOINFORmATICS INSTITUTE UNIT NATIONAL BIOINFORMATICS INSTITUTE UNIT OVERVIEW The Spanish National Bioinformatics Institute ( Instituto Nacional de Bioinformática, INB ) is a component of the National Infrastructure of Biomolecular and Bioinformatics Resources Platform ( Plataforma en Red de Recursos Biomoleculares y Bioinformáticos, PRB2 ) of the Spanish National Institute of Health Carlos III ( Instituto de Salud Carlos III, ISCIII ). The INB is the Spanish Node of ELIXIR, the permanent European Infrastructure for Life Sciences. The INB is composed of 10 working nodes distributed across 9 different research centres. The INB Unit at the CNIO undertakes the coordination of the institute. As the coordination node, the goals of the INB Unit are to : ɗ Coordinate the Spanish participation in ELIXIR. Promote the implementation and adoption of ELIXIR guidelines among the Spanish bioinformatics community. ɗ Design, promote and ensure the execution of the INB’s scientific-technical and training programmes, undertaken with the support of all nodes. ɗ Promote the collaboration between INB nodes and third parties, including research consortia, other research infrastructures, small and medium enterprises ( SMEs ), and the industry. The main difference between the INB Unit and other Programme Units is that its activities are not restricted to the CNIO Groups alone. Moreover, the INB Unit is entirely funded by external agencies ; namely, the ISCIII at the national level and ELIXIR at the European level. s Salvador J. Capella Gutierrez ( until June ) Unit Head Technicians Andrés Cañada ( until June ) ( TS ) *, José M. Fernández ( until June ) ( TS ) *, José M. Rodríguez ( until June ) ( TS ) * *Titulado Superior ( Advanced Degree ) ∞ PUBLICATIONS ∞ Cañada A, Capella-Gutierrez S, Rabal O, Oyarzabal J, Valencia A, Krallinger M ( 2017 ). LimTox : a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes. Nucleic Acids Res 45, W484-489. ∞ Jiménez RC et al. ( incl. Capella-Gutierrez S ) ( 2017 ). Four simple recommendations to encourage best practices in research software. F1000Res 13, 6. ANNUAL REPORT 2016 100 Translational Research SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 101 Human Cancer Genetics Programme 102 Human Genetics Group 104 Hereditary Endocrine Cancer Group 108 Genetic and Molecular Epidemiology Group 112 Familial Cancer Clinical Unit 116 Molecular Cytogenetics and Genome Editing Unit 118 Human Genotyping-CEGEN Unit 120 Clinical Research Programme 122 Breast Cancer Junior Clinical Research Unit 124 Prostate Cancer Junior Clinical Research Unit 126 Molecular Diagnostics Unit 128 H12O-CNIO Haematological Malignancies Clinical Research Unit 130 H12O-CNIO Lung Cancer Clinical Research Unit 134 Biobank 138 ANNUAL REPORT 2017 102 TRANSLATIONAL RESEARCH HUMAN CANCER GENETICS PROGRAMME JAVIER BENÍTEZ Director SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 103 HuMAN CANCER GENETICS PROGRAMME | The Human Cancer Genetics Programme ( HCGP ) is a translational research programme working on areas related to genetics, genomics, pharmacogenetics, molecular cytogenetics and the environmental bases of human cancer. The HCGP works in close collaboration with the clinical community. Three Research Groups and three Units currently form the HCGP. The Human Genetics Group, led by Javier Benítez, focuses on contributing to the understanding of the genetic bases of some hereditary tumours, mainly breast cancer. Mercedes Robledo leads the Hereditary Endocrine Cancer Group that aims to identify new major susceptibility genes related to hereditary endocrine tumours as well as to define markers associated with differences in anticancer drug response and toxicity. Both Groups are also involved in the search for low susceptibility alleles that explain sporadic cancers. The Genetics and Molecular Epidemiology Group, led by Núria Malats, works not only from a genetic but also from a non-genetic point of view. She analyses exogenous factors that contribute to explain, together with genetic factors ( low susceptibility alleles ), the susceptibility to pancreatic and bladder cancer. The Genotyping Unit, headed by Anna González- Neira, supports our three research groups from a technical point of view, and provides support to other groups from the CNIO as well as to external users. They also work in pharmacogenetics in the framework of their own line of research. The new Molecular Cytogenetics and Genome Editing Unit, coordinated by Sandra Rodríguez-Perales, contributes to this provision of support with classical and molecular cytogenetics techniques and with new genome editing technologies. In addition, her research is focused on the design of human stem cell models carrying cytogenetic alterations. Finally, the Familial Cancer Unit coordinates the clinical part of the Programme through the CNIO Familial Cancer Consultancy, which is located at the Hospital de Fuenlabrada. Miguel Urioste is responsible for these activities and leads a research line focused on hereditary colorectal cancer. The Programme collaborates closely with the clinical community, not only to foster cooperation in genetic diagnosis but also to promote training and education. This year the Familial Cancer Consultancy attended around 500 consultancies, performed 1,350 genetic diagnosis and carried out more than 1100 cytogenetic studies. In addition, the Programme’s Groups have hosted 9 resident physicians from different Spanish hospitals for 3-month periods. We also offer professionals from different international research centres the opportunity to join us, either as visitors or for training visits consisting of short-term stays of 1-3 months ( a total of 6 international and 2 national visitors were hosted in 2017 ). In terms of education, 1 foreign and 9 national Master’s students and 10 national and 2 international PhD students have worked on their research projects, 6 of whom have already successfully defended their thesis. Finally, one of the main objectives of the Programme is to establish research collaborations with national and international groups ; this is well demonstrated by our publication record as well as the key roles held by several of the Programme’s members in consortia and international projects. Currently, we collaborate with 13 international Consortia that are representative of the main types of tumours that we focus on. In addition, we participate in 4 international projects from Europe and North America. Milestones and major achievements of the Programme in 2017 include : ( 1 ) Mercedes Robledo : the identification of the high susceptibility gene GOT2 as being responsible for a percentage of familial pheochromocytoma; ( 2 ) Javier Benítez : the identification of the high susceptibility gene PTHR1 as being responsible for familial neuroendocrine tumours; ( 3 ) Anna González-Neira : the identification of GPR35 as a new susceptibility gene for anthracycline -induced cardiotoxicity; ( 4 ) Sandra Rodríguez : new Head of the Molecular Cytogenetics and Genome Editing Unit; ( 5 ) Núria Malats, Board Member of the International Pancreatic Cancer Case-Control Consortium ( PanC4 ); ( 6 ) Mercedes Robledo, Member of the Organiser Committee of the ‘International Symposium on Pheochromocytoma and Paraganglioma ’, Sydney, Australia, ( 7 ) Núria Malats, Co-organiser of ‘The Barcelona Debates on the Human Microbiome : From Microbes to Medicines ’, CosmoCaixa Barcelona, Spain. “ Once again, the challenge of summarising our research in a few sentences arises. We continue to conduct translational research with the overarching goal of improving the diagnostics, prevention and treatment of cancer. And yes, we are able to achieve this goal despite the multiple economic and administrative obstacles that we face.” ANNUAL REPORT 2017 104 TRANSLATIONAL RESEARCH HUMAN GENETICS GROUP Javier Benítez Group Leader Staff Scientist Ana Osorio SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 105 HuMAN CANCER GENETICS PROGRAMME | HUmAN GENETICS GROUP OVERVIEW For several years, the Human Genetics Group has been working on the understanding of the genetic bases of familial cancer, especially breast cancer. We continue to focus on this activity but have now extended it to include the discovery of new high susceptibility genes that explain families with rare tumours, as well as low susceptibility alleles that can help us to understand the genetic bases of cancer. In addition, we want to define the role of glycosylase genes involved in the base excision DNA repair pathway ( BER ) across the different phases of the cell cycle, and to explore new alternative treatments based on this pathway. “ During 2017, we set up our studies and established collaborations with urologists and oncologists working in testicular cancer ; we discovered a new gene, PTHR1, that in combination with ATP4A ( digenic model ) is responsible for a new form of gastric neuroendocrine tumour. We also confirmed that up to 2% of Spanish breast cancer families are due to mutations in the ATM gene.” RESEARCH HIGHLIGHTS Deciphering the role of rare variants in breast cancer We are participating in an H2020 project funded by the EU with the main objective of clarifying the role of some rare variants and genes in breast cancer development. The study includes, in a first step, the Next Generation Sequencing ( NGS ) of 35 genes already known as candidates in a set of 40,000 breast cancer cases and 40,000 controls from more than 50 countries. In a second step, we will sequence, in the same group of samples, a new set of > 30 genes. The third step will include the selection of the best and already confirmed genes in order to build a new diagnostic gene panel ready to be used in clinical practice. Our Group is coordinating the WP2 that is comprised of Cambridge University, Lund University and our Centre as partners. We are responsible for gene selection, sample management from the different groups, library preparation, sequencing and variant calling. Breast and ovarian cancer susceptibility genes By performing whole exome sequencing ( WES ) in 4 BRCAX families, we have found a set of new candidate breast cancer genes. We have identified a deleterious mutation in the known breast cancer susceptibility gene ATM in 1 family and, by extending the study to a larger series, we have established that 2% of Spanish breast cancer families are explained by germline mutations in this gene ( Tavera et al., Br Cancer Res Treat 2017 ). In a second family, we have found a deleterious mutation in an excellent candidate gene from a family of DNA helicases that have a role in the Homologous Recombination ( HR ) DNA repair pathway. The high interest of this finding has prompted us to start a screening of the gene by targeted NGS in a series of 700 BRCAX families and 700 controls. We have found at least 3 additional deleterious mutations among the cases, suggesting that the gene could actually explain a small percentage of the BRCAX families. Other candidate genes, some of them direct interactors of BRCA1 and BRCA2, have been selected for further analysis in larger series of cases and controls in order to establish their role in the disease. Ovarian cancer families are rare. We performed WES in 5 families and identified novel missense variants in the known ovarian cancer susceptibility gene RAD51C, among other candidates. Through functional studies, we were able to determine its pathogeny and its possible involvement in ovarian cancer Post-Doctoral Fellow Oriol Calvete Graduate Students Juan Miguel Baquero, Paloma Martín, Beatriz Paumard ( until October ), Alejandra Tavera Technicians Alicia Barroso, Carlos Benítez-Buelga ( until July ) ( TS )*, Victoria Fernández ( TS ) * *Titulado Superior ( Advanced Degree ) ANNUAL REPORT 2017 106 TRANSLATIONAL RESEARCH risk. Because there are many variants in RAD51C with no clear implication in the disease, we have developed an algorithm based on different predictors that permit a good classification of RAD51C variants and their implication in ovarian families ( Gayarre et al., Br J Cancer 2017 ). Familial cancer exome project In 2015, we published the identification by NGS of a new gene, POT1, as being responsible for families with multiple tumours including cardiac angiosarcomas ( CAS ). We extended our study to a large series of families with angiosarcomas, sporadic CAS and sarcomas in order to elucidate the role of POT1 in cancer development. Our results have led us to the indication of testing for POT1 mutations in families with angiosarcomas with or without CAS ( 25% with mutations ), sporadic CAS, and cardiac sarcomas ( 10% with mutations ). ( Calvete et al., Eur J Hum Genet 2017 ). In 2015, we also published the identification of a gene, ATP4A, responsible for a recessive family with gastric neuroendocrine tumours ( Calvete et al., Hum Mol Genet 2015 ). By analysing additional families, we have identified a second gene PTHR1 that, combined with ATP4A, explains a second family based on a digenic model. Carriers of ATP4A present megaloblastic anaemia and low ferritin levels, PTHR1 carriers hypothyroidism and rheumatoid arthritis, while only those members carrying mutations in both genes develop gastric carcinoid ( FIGURE ). It also suggests the genetic heterogeneity of this disease ( Calvete et al., Gastric Cancer 2017 ). We have identified the NHEJ1 gene as being responsible for a family with a child that developed severe pancytopenia and bone marrow aplasia correlated with the presence of short telomeres ( Carrillo et al., Hum Mol Genet 2017 ). We downregulated NHEJ1 expression in 293T and CD34+cells and we found increased p21 expression, reduced telomerase activity and decreased expression of several telomerase/shelterin genes. Because the decrease in expression of telomerase/shelterin genes did not occur when we inhibited expression of other NHEJ genes mutated in SCID patients − DNA-PK, Artemis or LigaseIV − we propose that NHEJ1 is responsible for the inhibition of telomerase activity. Over the last 3 years, we have started to work with families with testicular cancer thanks to a collaboration that we established with the Spanish Germ-Cell Cancer Group and several institutions that are dedicated to the follow-up and treatment of patients with testicular cancer, for which the genetic bases are poorly known. We have already collected 21 families with at least 2 first-degree affected members who have been sequenced and analysed using bioinformatics tools ( a total of 71 exomes ). We are using different statistical and bioinformatics approaches ( family based association tests, based on Kernel and burden tests ) to identify candidate genes and variants for validation. SNPs and the BER pathway We have studied 3 genes from the BER pathway ( OGG1, NEIL2 and UNG ) containing SNPs that modify cancer risk in BRCA1/2 mutation carriers and are modifiers of Telomere Length ( TL ) ( Benítez-Buelga et al., Oncotarget, second review ; Baquero JM et al., Int J Cancer, submitted ). We want to evaluate the global effect of endogenous factors ( represented by the 3 genes ) on TL. On the other hand, this pathway seems to be an excellent model for new treatments based in OGG1 and NEIL2 inhibitors. Our collaboration with Helleday’s group ( Karolinska Institute ) will permit us to explore new drugs in specific situations ( BRCA carriers ) and in different types of tumours ( breast and ovarian ). s ∞ PUBLICATIONS ∞ Michailidou K et al. ( incl. Benitez J ) ( 2017 ). Association analysis identifies 65 new breast cancer risk loci. Nature 551, 92-94. ∞ Day FR, et al. ( incl. Benitez J ) ( 2017 ). Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk. Nat Genet 49, 834-841. ∞ Milne RL et al. ( incl. Benitez J ) ( 2017 ). Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer. Nat Genet 49, 1767-1778. ∞ Phelan CM, Kuchenbaecker KB et al. ( incl. Garcia MJ, Osorio A, Benitez J ) ( 2017 ). Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer. Nat Genet 49, 680-691. ∞ Lecarpentier J et al. ( incl. Osorio A ) ( 2017 ). Prediction of breast and prostate cancer risks in male BRCA1 and BRCA2 mutation carriers using polygenic risk scores. J Clin Oncol 35, 2240-2250. ∞ Ovarian Tumor Tissue Analysis ( OTTA ) Consortium et al. ( incl. Osorio A, Benítez J ) ( 2017 ). Dose-response association of CD8+ tumor-infiltrating lymphocytes and survival time in high-grade serous ovarian cancer. JAMA Oncol 3, e173290. ∞ Kuchenbaecker KB et al. ( incl. Osorio A, Benítez J ) ( 2017 ). Evaluation of polygenic risk scores for breast and ovarian can- cer risk prediction in BRCA1 and BRCA2 mutation carriers. J Natl Cancer Inst 109. ∞ Shimelis H et al. ( incl. Benitez J, Osorio A ) ( 2017 ). BRCA2 hypomorphic missense variants confer moderate risks of breast cancer. Cancer Res 77, 2789-2799. ∞ Catucci I et al. ( incl. Benitez J, Osorio A ) ( 2017 ).). Individuals with FANCM bial- lelic mutations do not develop Fanconi anemia, but show risk for breast cancer, chemotherapy toxicity and may display chromosome fragility. Genet Med. PMID : 28837162. ∞ Carrillo J, Calvete O, Pintado-Berninches L, Manguan-García C, Sevilla Navarro J, Arias-Salgado EG, Sastre L, Guenechea G, López Granados E, de Villartay JP, Revy P, Benitez J, Perona R ( 2017 ). Mutations in XLF/NHEJ1/Cernunnos gene results in downregulation of telomerase genes expression and telomere shortening. Hum Mol Genet 26, 1900-1914. ∞ Hamdi Y et al. ( incl. Osorio A, Benítez J ) ( 2017 ). Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression : identification of a modifier of breast cancer risk at locus 11q22.3. Breast Cancer Res 161, 117-134. ∞ Gayarre J, Martín-Gimeno P, Osorio A, Paumard B, Barroso A, Fernández V, de SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 107 HuMAN CANCER GENETICS PROGRAMME | HUmAN GENETICS GROUP la Hoya M, Rojo A, Caldés T, Palacios J, Urioste M, Benítez J, García MJ ( 2017 ). Characterisation of the novel deleterious RAD51C p.Arg312Trp variant and priori- tisation criteria for functional analysis of RAD51C missense changes. Br J Cancer 117, 1048-1062. ∞ Benítez-Buelga C, Baquero JM, Vacklova T, Fernández V, Martín P, Inglada-Perez L, Urioste M, Osorio A, Benítez J ( 2017 ). Genetic variation in the NEIL2 DNA gly- cosylase gene is associated with oxidative DNA damage in BRCA2 mutation carriers. Oncotarget 8, 114626-114636. ∞ Glubb DM et al. ( incl. Benitez J ) ( 2017 ). Analyses of germline variants associated with ovarian cancer survival identify func- tional candidates at the 1q22 and 19p12 outcome loci. Oncotarget 8, 6470-64684. ∞ Calvete O, Garcia-Pavia P, Domínguez F, Bougeard G, Kunze K, Braeuninger A, Teule A, Lasa A, Ramón Y Cajal T, Llort G, Fernández V, Lázaro C, Urioste M, Benitez J ( 2017 ). The wide spectrum of POT1 gene variants correlates with multiple cancer types. Eur J Hum Genet 25, 1278-12781. ∞ Walker LC et al. ( incl. Benitez J ) ( 2017 ). Evaluation of copy-number variants as modifiers of breast and ovarian cancer risk for BRCA1 pathogenic variant carriers. Eur J Hum Genet 25, 432-438. ∞ Brouckaert O et al. ( incl. Benitez J, González-Neira A ) ( 2017 ). Reproductive profiles and risk of breast cancer sub- types : a multi-center case-only study. Breast Cancer Res 19, 119. ∞ Tavera-Tapia A, Pérez-Cabornero L, Macías JA, Ceballos MI, Roncador G, de la Hoya M, Barroso A, Felipe-Ponce V, Serrano-Blanch R, Hinojo C, Miramar-Gallart MD, Urioste M, Caldés T, Santillan-Garzón S, Benitez J, Osorio A ( 2017 ). Almost 2% of Spanish breast cancer families are associated to germline pathogenic mutations in the ATM gene. Breast Cancer Res Treat 161, 597-604. ∞ Calvete O, Herraiz M, Reyes J, Patiño A, Benitez J ( 2017 ). A cumulative effect involving malfunction of the PTH1R and ATP4A genes explains a familial gastric neuroendocrine tumor with hypothy- roidism and arthritis. Gastric Cancer 20, 998-1003. ∞ Ruiz-Pinto S, Pita G, Patiño-García A, Alonso J, Pérez-Martínez A, Cartón AJ, Gutiérrez-Larraya F, Alonso MR, Barnes DR, Dennis J, Michailidou K, Gómez-San- tos C, Thompson DJ, Easton DF, Benítez J, González-Neira A ( 2017 ). Exome array analysis identifies GPR35 as a novel sus- ceptibility gene for anthracycline-induced cardiotoxicity in childhood cancer. Phar- macogenet Genomics 27, 445-453. Figure Pedigree of the family with gastric carcinoid with mutations in ATP4A and PTHR1. Only members carrying mutations in both genes develop gastric carcinoid ( II-6, II-7 ; II-8 ), while members with mutations in ATP4A or PTHR1 genes present different symptoms. ANNUAL REPORT 2017 108 TRANSLATIONAL RESEARCH HEREDITARY ENDOCRINE CANCER GROUP Mercedes Robledo Group Leader Staff Scientists Alberto Cascón, Cristina Rodríguez SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 109 HuMAN CANCER GENETICS PROGRAMME | HEREdITARy ENdOCRINE CANCER GROUP OVERVIEW Our Group is mainly interested in identifying genetic risk factors involved in endocrine tumour susceptibility. Through a comprehensive analysis of tumour genomic features we have been able to propose diagnostic and prognostic markers to identify altered pathways that could be therapeutically targeted, and to identify new major susceptibility genes. We are also interested in defining markers associated with differences in anticancer drug response and toxicity. We are applying targeted and whole-exome next-generation sequencing to a large series of clinically well-characterised patients. The aim is to identify new therapeutic approaches to personalise cancer treatment. These efforts will collectively improve the diagnosis, prognosis and treatment of patients. “ We identified new susceptibility genes for paraganglioma, established clinical features related to MDH2 disruption, and discovered predictive biomarkers of mTOR inhibitor response.” Post-Doctoral Fellow Cristina Montero Graduate Students Bruna Calsina, María Curras ( until January ), Lucía Inglada, Laura Remacha, Juan M. Roldán, María Santos ( since February ) Technicians Rocío Letón, Rafael Torres ( until September )( TS )* *Titulado Superior ( Advanced Degree ) ANNUAL REPORT 2017 110 TRANSLATIONAL RESEARCH RESEARCH HIGHLIGHTS New mutation in a Krebs cycle-related gene in pheochromocytoma ( PCC ) or paraganglioma ( PGL ) Mutations in Krebs cycle genes are frequently found in patients with PCC/PGL. Disruption of SDH, FH or MDH2 enzymatic activities leads to the accumulation of specific metabolites, which give rise to epigenetic changes in the genome that cause a characteristic hypermethylated phenotype. Tumours showing this phenotype, but no alterations in the known predisposing genes, could harbour mutations in other Krebs cycle genes. We used downregulation and methylation of RBP1, as a marker of a hypermethylation phenotype, to select PCCs and PGLs for targeted exome sequencing of a panel of Krebs cycle-related genes. Methylation profiling, metabolite assessment and additional analyses were also performed in selected cases. Following this rationale, a germline GOT2 variant, c.357A>T, was found in a patient with multiple tumours and metastasis. The presence of this variant was associated with higher tumour mRNA and protein expression levels, increased GOT2 enzymatic activity in lymphoblastic cells, and altered metabolite ratios both in tumours and in GOT2 knockdown HeLa cells transfected with the variant. Thus, we propose GOT2 as a new susceptibility gene related to metastatic PGL. This study further attests to the relevance of the Krebs cycle in the development of these tumours, and points to this central metabolic pathway as being targetable in metastatic PCC/PGL patients. MDH2 mutations in pheochromocytoma and paraganglioma MDH2 has recently been proposed by our Group as a novel PCC/ PGL susceptibility gene. We aimed to determine the prevalence of MDH2 mutations among PPGL patients and to establish the associated phenotype. Through a worldwide network we recruited close to 800 PCC/PGL patients. In this study we needed to implement a multidisciplinary approach with up to five functional assays and twenty in silico predictions ( FIGURE ), including MDH2 enzymatic activity and affinity, an immunofluorescence assay to evaluate MDH2 localisation, and a molecular dynamics ( MD ) simulation approach to examine the potential protein structure changes of the most controversial variants. With this initiative we were able to ascertain the prevalence of MDH2 mutations in PPGL in less than 1% and to highlight the importance of including this gene in the routine genetic screening of the disease, especially in metastatic, noradrenergic-secreting, multiple tumours and in young patients. Novel CNVs in pharmacogenes and mTOR pathway mutations to predict outcomes in cancer therapies Personalised cancer treatment is of enormous clinical and social relevance since it can lead to safer and more efficient therapies. This year we focused on : i ) understanding the effect of copy number variants ( CNVs ) on adverse drug reactions ( ADRs ); and ii ) discovering biomarkers predictive of mTOR inhibitor response. ADRs cause around 6.5% of admissions to hospitals, accounting for 5-10% of the annual hospital costs. Genetic factors are responsible for many ADRs and these could be prevented by genetic tests. We performed the first systematic assessment of the CNV landscape in pharmacogenes by integrating data from 2,504 whole genomes and 59,898 exomes. We described novel exonic deletions and duplications in 97% of the genes analysed. Novel deletion frequencies ranged from singletons ∞ PUBLICATIONS ∞ Phelan CM et al. ( incl. Benitez J, Rodriguez- Antona C ) ( 2017 ). Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer. Nat Genet 49, 680-691. ∞ NGS in PPGL ( NGSnPPGL ) Study Group, Toledo RA, Burnichon N, Cascon A, Benn DE, Bayley JP, Welander J, Tops CM, Firth H, Dwight T, Ercolino T, Mannelli M, Opocher G, Clifton-Bligh R, Gimm O, Maher ER, Ro- bledo M, Gimenez-Roqueplo AP, Dahia PL ( 2017 ). Consensus Statement on next-gen- eration-sequencing-based diagnostic test- ing of hereditary phaeochromocytomas and paragangliomas. Nat Rev Endocrinol 13, 233-247. ∞ Apellániz-Ruiz M, Tejero H, Inglada-Pérez L, Sánchez-Barroso L, Gutiérrez-Gutiérrez G, Calvo I, Castelo B, Redondo A, García- Donás J, Romero-Laorden N, Sereno M, Merino M, Currás-Freixes M, Montero-Conde C, Mancikova V, Åvall-Lundqvist E, Green H, Al-Shahrour F, Cascón A, Robledo M, Rodríguez-Antona C ( 2017 ). Targeted se- quencing reveals low-frequency variants in EPHA genes as markers of paclitaxel-in- duced peripheral neuropathy. Clin Cancer Res 23, 1227-1235. ∞ Roldan-Romero JM, Rodríguez-Moreno JF, García-Donás J, Rodríguez-Antona C ( 2017 ). mTOR pathway mutations and response to rapalogs in RCC-Letter. Clin Cancer Res 23, 5320. ∞ Mancikova V, Montero-Conde C, Perales-Pa- ton J, Fernandez A, Santacana M, Jodkows- ka K, Inglada-Pérez L, Castelblanco E, Bor- rego S, Encinas M, Matias-Guiu X, Fraga M, Robledo M ( 2017 ). Multilayer OMIC data in medullary thyroid carcinoma identifies the STAT3 pathway as a potential therapeutic target in RET( M918T ) tumors. Clin Cancer Res 23, 1334-1345. ∞ Remacha L, Comino-Méndez I, Richter S, Contreras L, Currás-Freixes M, Pita G, Letón R, Galarreta A, Torres-Pérez R, Honrado E, Jiménez S, Maestre L, Moran S, Esteller M, Satrústegui J, Eisenhofer G, Robledo M, Cascón A ( 2017 ). Targeted exome sequenc- ing of Krebs cycle genes reveals candidate cancer-predisposing mutations in pheo- chromocytomas and paragangliomas. Clin Cancer Res 23, 6315-6324. ∞ Pamporaki C, Hamplova B, Peitzsch M, Prejbisz A, Beuschlein F, Timmers HJLM, Fassnacht M, Klink B, Lodish M, Stratakis CA, Huebner A, Fliedner S, Robledo M, Sinnott RO, Januszewicz A, Pacak K, Eisenhofer G ( 2017 ). Characteristics of pediatric vs adult pheochromocytomas and paragangliomas. J Clin Endocrinol Metab 102, 1122-1132. ∞ Liu X, Swen JJ, Boven E, Castellano D, Gel- derblom H, Mathijssen RH, Rodríguez-An- tona C, García-Donas J, Rini BI, Guchelaar HJ. ( 2017 ) Meta-analysis on the association of VEGFR1 genetic variants with sunitinib outcome in metastatic renal cell carcinoma patients. Oncotarget 8, 1204-1212. ∞ Currás-Freixes M, Piñeiro-Yañez E, Monte- ro-Conde C, Apellániz-Ruiz M, Calsina B, Mancikova V, Remacha L, Richter S, Ercolino T, Rogowski-Lehmann N, Deutschbein T, Calatayud M, Guadalix S, Álvarez-Escolá C, Lamas C, Aller J, Sastre-Marcos J, Lázaro C, Galofré JC, Patiño-García A, Meoro-Avilés A, Balmaña-Gelpi J, De Miguel-Novoa P, Balbín M, Matías-Guiu X, Letón R, Ingla- da-Pérez L, Torres-Pérez R, Roldán-Rome- ro JM, Rodríguez-Antona C, Fliedner SMJ, Opocher G, Pacak K, Korpershoek E, de Krijger RR, Vroonen L, Mannelli M, Fassnacht M, Beuschlein F, Eisenhofer G, Cascón A, Al-Shahrour F, Robledo M ( 2017 ). PheoSeq : SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 111 HuMAN CANCER GENETICS PROGRAMME | HEREdITARy ENdOCRINE CANCER GROUP a targeted next-generation sequencing assay for pheochromocytoma and paragan- glioma diagnostics. J Mol Diagn 19, 575-588. ∞ Alegría-Landa V, Jo-Velasco M, Robledo M, Requena L ( 2017 ). Dermal hyperneury and multiple sclerotic fibromas in multiple endocrine neoplasia type 2A syndrome. JAMA Dermatol 153, 1298-1301. ∞ Oudijk L, Papathomas T, de Krijger R, Kor- pershoek E, Gimenez-Roqueplo AP, Favier J, Canu L, Mannelli M, Rapa I, Currás-Freixes M, Robledo M, Smid M, Papotti M, Volante M ( 2017 ). mTORC1 complex is significantly over-activated in SDHX-mutated paragan- gliomas. Neuroendocrinology 105, 384-393. ∞ Rodríguez-Moreno JF, Apellaniz-Ruiz M, Roldan-Romero JM, Durán I, Beltrán L, Montero-Conde C, Cascón A, Robledo M, García-Donas J, Rodríguez-Antona C ( 2017 ). Exceptional response to temsirolimus in a metastatic clear cell renal cell carcinoma with an early novel MTOR-activating muta- tion. J Natl Compr Canc Netw. 15, 1310-1315. ∞ Diekstra MH, Belaustegui A, Swen JJ, Boven E, Castellano D, Gelderblom H, Mathijssen RH, García-Donas J, Rodríguez-Antona C, Rini BI, Guchelaar HJ ( 2017 ). Sunitinib in- duced hypertension in CYP3A4 rs4646437 A-allele carriers with metastatic renal cell carcinoma. Pharmacogenomics J 17, 42-46. ∞ Castelblanco E, Zafon C, Maravall J, Gallel P, Martinez M, Capel I, Bella MR, Halperin I, Temprana J, Iglesias C, Puig-Domingo M, Robledo M, Matias-Guiu X, Mauricio D ( 2017 ). APLP2, RRM2, and PRC1 : new putative markers for the differential diag- nosis of thyroid follicular lesions. Thyroid 27, 59-66. ∞ Pascual T, Apellániz-Ruiz M, Pernaut C, Cueto-Felgueroso C, Villalba P, Álvarez C, Manso L, Inglada-Pérez L, Robledo M, Rodríguez-Antona C, Ciruelos E ( 2017 ). Polymorphisms associated with everolimus pharmacokinetics, toxicity and survival in metastatic breast cancer. PLoS One 12, e0180192. ∞ Apellániz-Ruiz M, Diekstra MH, Roldán JM, Boven E, Castellano D, Gelderblom H, Mathijssen RHJ, Swen JJ, Böhringer S, García-Donás J, Rini BI, Guchelaar HJ, Rodríguez-Antona C ( 2017 ). Evaluation of KDR rs34231037 as a predictor of sunitinib efficacy in patients with metastatic renal cell carcinoma. Pharmacogenet Genomics 27, 227-231. ∞ Sereno M, Gutiérrez-Gutiérrez G, Rubio JM, Apellániz-Ruiz M, Sánchez-Barroso L, Casa- do E, Falagan S, López-Gómez M, Merino M, Gómez-Raposo C, Rodriguez-Salas N, Tébar FZ, Rodríguez-Antona C ( 2017 ). Genetic polymorphisms of SCN9A are associated with oxaliplatin-induced neuropathy. BMC Cancer 17, 63. ∞ van der Zanden LFM, Vermeulen SH, Oskars- dottir A, Maurits JSF, Diekstra MHM, Ambert V, Cambon-Thomsen A, Castellano D, Fritsch A, Garcia Donas J, Guarch Troyas R, Guche- laar HJ, Hartmann A, Hulsbergen-van de Kaa C, Jaehde U, Junker K, Martinez-Cardus A, Masson G, Oosterwijk-Wakka J, Radu MT, Rafnar T, Rodriguez-Antona C, Roessler M, Ruijtenbeek R, Stefansson K, Warren A, Wes- sels L, Eisen T, Kiemeney LALM, Oosterwijk E ( 2017 ). Description of the EuroTARGET cohort : A European collaborative project on TArgeted therapy in renal cell cancer-GE- netic-and tumor-related biomarkers for response and toxicity. Urol Oncol 35, 529. ∞ Eisenhofer G, Klink B, Richter S, Lenders JW, Robledo M ( 2017 ). Metabologenomics of phaeochromocytoma and paraganglioma : an integrated approach for personalised bi- ochemical and genetic testing. Clin Biochem Rev 38, 69-100. Figure Mapping of MDH2 mutations onto the crystal structure ( PDB ID : 2DFD ). In red, missense variants found in our study ; in blue, amino-acid changes in neighbouring positions ( d£5Å ) in other types of cancers reported in COSMIC v80. up to 1%, and accounted for >5% of all loss-of-function alleles in 42% of studied genes. Thus, CNVs are an additional source of pharmacogenetic variability with important implications for drug response and personalised therapy. Regarding mTOR inhibitors, by next generation sequencing ( NGS ) on tumour tissues, we found that those patients with somatic mutations directly activating the pathway ( in MTOR, TSC1, TSC2 ) had improved responses. Furthermore, multiregion NGS allowed us to determine that when these mutations were acquired early on during tumour development they resulted in extraordinary responses to these drugs. s ANNUAL REPORT 2017 112 TRANSLATIONAL RESEARCH GENETIC AND MOLECULAR EPIDEMIOLOGY GROUP Núria Malats Group Leader Staff Scientist M. Evangelina López de Maturana Post-Doctoral Fellows Paulina Gómez, M. Esther Molina SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 113 HuMAN CANCER GENETICS PROGRAMME | GENETIC ANd mOLECULAR EPIdEmIOLOGy GROUP OVERVIEW The scope of the research carried out by the Genetics and Molecular Epidemiology Group ( GMEG ) ranges from the identification of aetiological agents and mechanisms to the translation of the findings into the clinical and Public Health domains, focusing on bladder, pancreatic, and breast cancers. We employ a wide variety of biomarkers to better characterise exposures, genetic susceptibility patterns, and cancer outcomes. Omics data provide a unique opportunity in this regard and the Group explores its integration in epidemiological studies. The strategic goals of the Group are to : ɗ Identify non-genetic and genetic factors, as well as their interactions, associated with cancer development and progression and with its molecular/omics subphenotypes. ɗ Develop and apply statistical/informatics tools to model the risk, prediction, and clinical course of patients with cancer by integrating epidemiologic with omics information. ɗ Assess clinical and public health strategies for cancer control using current genomic tests and data. “ We have contributed to the characterisation of pancreatic cancer aetiology by identifying both risk and protective factors that mainly point to the role of the immunological status in pancreatic carcinogenesis.” Graduate Student Sara Domínguez Technicians Ana Alfaro ( until October ), Lola Alonso ( TS )*, Lidia Estudillo ( until October ), Mirari Márquez ( TS )*, Marta Rava ( until October ) ( TS ) *, Rebeca Sánchez ( until October ) *Titulado Superior ( Advanced Degree ) Students in Practice Ashraf Abdelghany ( June-Aug. Al-Azhar University ), Alba M. Fernández del Pozo ( since Sept., Hospital 12 de Octubre ), Teresa Velasco Martínez ( March-June, Centro Docente IES Mirasierra ), Noelia Rodríguez Martín ( Feb.-Sept., Universidad Complutense de Madrid ) Visiting Scientists Chiaka L. Anumudu ( since Aug., University of Ibadan ), Isabel A. Martín ( since Sept., Universidad CEU San Pablo ), Olga Martínez ( Aug.-Sept., Hospital Ramón y Cajal ), Jesús López ( since Sept., Common Management Solutions ) ANNUAL REPORT 2017 114 TRANSLATIONAL RESEARCH RESEARCH HIGHLIGHTS Research findings During 2017, the Group centred its research on pancreatic and bladder cancers. Regarding pancreatic cancer ( PC ), we have completed several analyses using the resources from the PanGenEU Study. In this regard, we reported that specific multimorbidities aggregate and associate with PC risk in a time-dependent manner. A common genetic basis between these conditions and PC was observed through a bioinformatics analysis ( FIGURE 1 ). The common genetic basis between these conditions and PC pointed to a mechanistic link between these diseases. Using the same population and applying both a case- control and a reconstructed cohort approach, we confirmed that family history of any cancer, of PC or diabetes, conferred a higher risk of PC and also that smoking notably increased the PC risk associated with family history of PC. Furthermore, we actively participated in an international large-scale investigation that identified important disparities on PC resection practice within and between countries. It also evidenced that most PC patients remain untreated through resection, although resection was associated with better survival, highlighting pivotal potentially modifiable areas in PC clinical practice. Regarding bladder cancer ( BC ), GMEG assessed the complex interrelationships between asthma and BC in the Spanish Bladder Cancer/EPICURO Study population. This study corroborated the notion that asthma was associated with a reduced risk of cancer, especially among aggressive tumours pointing to the relationship between immune response mechanisms and bladder carcinogenesis. The Group also participated in the discovery and validation of both urine and tumour prognostic marker combination in a large European study of non-muscle invasive BC. Whole transcriptome expression profiling of 476 tumours from the same European-based study enabled the further characterisation of bladder cancer subtypes. GMEG also performed a review of the genetic susceptibility to BC risk and progression based on GWAS. Most of the variants were common and conferred small risk and, therefore, they were not clinically actionable at the individual level. Methodological contributions Integrative analytic approaches considering different regulatory levels ( i.e., host and tumour ) are still scarce. To model this multilevel structure, we proposed to apply our previously described Global-LASSO method and compared it with other approaches to integrate genomic, epigenomic, and transcriptomic data from tumour tissue with blood germline genotypes from 181 individuals with bladder cancer included in the TCGA Consortium ( FIGURE 2 ). Global-LASSO performed better than the other methods. GMEG also developed the ‘DoriTool ’ that, to our knowledge, is the most complete bioinformatics tool offering functional ‘ in silico ’ annotation of variants previously associated with a trait of interest, shedding light on the underlying biology and thereby helping the researchers in the interpretation and discussion of the results. Translational activities A critical review of both PC host- and tumour-based markers evidenced the poorly transferred knowledge into the patient management domain. International and multidisciplinary strategies to identify new markers and properly validate the promising ones are urgently needed in order to implement cost- efficient primary and secondary prevention interventions in PC. During 2017, we organised a Multistakeholder Brainstorming Meeting on European PC research in Brussels under the auspices of the EUPancreas COST Action ( BM1204 ) and the Pancreatic Cancer Europe ( EPC ) multistakeholder platform. A report pinpointing the gaps and challenges identified by the researchers and stakeholders attending the meeting were distributed, and recommendations were made for future European activity on PC research. s Figure 1 Genetic system for multimorbidity patterns and pancreatic cancer. Association between pancreatic cancer and medical conditions of the detected multimorbidity patterns based on the number of shared genes. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 115 HuMAN CANCER GENETICS PROGRAMME | GENETIC ANd mOLECULAR EPIdEmIOLOGy GROUP ∞ PUBLICATIONS ∞ Dyrskjøt L et al. ( incl. Real EX, Malats N ) ( 2017 ). Prognostic impact of a 12-gene progression score in non-muscle invasive bladder cancer : a prospective multicenter validation study. Eur Urol 72, 461-469. ∞ Huang L et al. ( incl. Malats ) ( 2017 ). Surgical resection for pancreatic cancer patients in Europe and the US. An inter- national large-scale study. Gut. PMID : 29158237. ∞ Gómez-Rubio P, Zock JP, Rava M, Marquez M, Sharp L, Hidalgo M, Carrato A, Ilzarbe L, Michalski C, Molero X, Farré A, Perea J, Greenhalf W, O’Rorke M, Tardón A, Gress T, Barberà V, Crnogorac-Jurcevic T, Domínguez-Muñoz E, Muñoz-Bellvís L, Alvarez-Urturi C, Balcells J, Barneo L, Costello E, Guillén-Ponce C, Kleeff J, Kong B, Lawlor R, Löhr M, Mora J, Murray L, O’Driscoll D, Peláez P, Poves I, Scarpa A, Real FX, Malats N ; PanGenEU Study Inves- tigators ( 2017 ). Reduced risk of pancreatic cancer associated with asthma and nasal allergies. Gut 66, 314-322. ∞ Rosendahl J et al. ( incl. Malats N ) ( 2017 ). Genome-wide association study identifies inversion in the CTRB1-CTRB2 locus to modify risk for alcoholic and non-alcoholic chronic pancreatitis. Gut. PMID : 28754779. ∞ Gómez-Rubio P, Rosato V, Marquez M, Bo- setti C, Molina-Montes M, Rava M, Michal- ski CW, Farré A, Molero X, Löhr M, Ilzarbe L, Perea J, Greenhalf W, O’Rorke M, Tardón A, Gress T, Barberà VM, Crnogorac-Jurcevic T, Muñoz-Bellvís L, Domínguez-Muñoz E, Balsells J, Costello E, Guillén-Ponce C, Huang J, Iglesias M, Kleeff J, Kong B, Mora J, Murray L, O’Driscoll D, Peláez P, Poves I, Lawlor RT, Carrato A, Hidalgo M, Scarpa A, Sharp L, Real FX, La Vecchia C, Malats N, on behalf of the PanGenEU Study In- vestigators ( 2017 ). A systems approach identifies time-dependent associations of multimorbidities with pancreatic cancer risk. Ann Oncol 28, 1618-1624. ∞ Molina-Montes E, Sánchez MJ, Buckland G, Bueno-de-Mesquita HB, Weiderpass E, Amiano P, Wark PA, Kühn T, Katzke V, Huerta JM, Ardanaz E, Quirós JR, Affret A, His M, Boutron-Ruault MC, Peeters PH, Ye W, Sund M, Boeing H, Iqbal K, Ohlsson B, Sonestedt E, Tjønneland A, Petersen KE, Travis RC, Skeie G, Agnoli C, Panico S, Palli D, Tumino R, Sacerdote C, Freisling H, Huybrechts I, Overvad K, Trichopoulou A, Bamia C, Vasilopoulou E, Wareham N, Khaw KT, Cross AJ, Ward HA, Riboli E, Duell EJ ( 2017 ). Mediterranean diet and risk of pancreatic cancer in the European Prospective Investigation into Cancer and Nutrition cohort. Br J Cancer 116, 811-820. ∞ Selinski S et al. ( incl. Malats N, Real FX ) ( 2017 ). Identification and replication of the interplay of four genetic high risk variants for urinary bladder cancer. Carcinogenesis 38, 1167-1179. ∞ Bertelsen RJ, Rava M, Carsin AE, Accordini S, Benediktsdóttir B, Dratva J, Franklin KA, Heinrich J, Holm M, Janson C, Johannessen A, Jarvis DL, Jogi R, Leynaert B, Norback D, Omenaas ER, Raherison C, Sánchez-Ramos JL, Schlünssen V, Sigsgaard T, Dharmage SC, Svanes C ( 2017 ). Clinical markers of asthma and IgE assessed in parents before conception predict asthma and hayfever in the offspring. Clin Exp Allergy 47, 627-638. ∞ Duriez E, Masselon CD, Mesmin C, Court M, Demeure K, Allory Y, Malats N, Matondo M, Radvanyi F, Garin J, Domon B ( 2017 ). Large-scale SRM screen of urothelial blad- der cancer candidate biomarkers in urine. J Proteome Res 6, 1617-1631. ∞ Akiki Z, Rava M, Diaz Gil O, Pin I, le Moual N, Siroux V, Guerra S, Chamat S, Matran R, Fitó M, Salameh P, Nadif R ( 2017 ). Serum cytokine profiles as predictors of asthma control in adults from the EGEA study. Respir Med 125, 57-64. ∞ Pineda S, Van Steen K, Malats N ( 2017 ). Integrative eQTL – analysis of omics data generated in tumor tissue and blood sam- ples in individuals with bladder cancer. Genet Epidemiol 41, 567-573. ∞ Malats N, Katsila T, Patrinos GP ( 2017 ). Cancer genomics and public health. Public Health Genomics 20, 67-69. ∞ Malats N, Molina-Montes E, La Vecchia C ( 2017 ). Genomics in primary and second- ary prevention of pancreatic cancer. Public Health Genomics 20, 92-99. ∞ Martin MA, Alonso MD, Madrid M, López de Maturana E, Malats N ( 2017 ). DoriTool : A bioinformatics integrative tool for post-as- sociation functional annotation. Public Health Genomics 20, 126-135. ∞ Rava M, Ahmed I, Kogevinas M, Le Moual N, Bouzigon E, Curjuric I, Dizier MH, Dumas O, Gonzalez JR, Imboden M, Mehta AJ, Tubert-Bitter P, Zock JP, Jarvis D, Probst- Hensch NM, Demenais F, Nadif R ( 2017 ). Genes Interacting with Occupational Ex- posures to Low Molecular Weight Agents and Irritants on Adult-Onset Asthma in Three European Studies. Environ Health Perspect 125, 207-214. Book Chapter ∞ López de Maturana E, Malats N ( 2017 ). Genetic testing, genetic variation and genetic susceptibility. In : Hyeon Ku J, ed. Bladder Cancer, Elsevier. ∞ AWARDS AND RECOGNITION ∞ Board Member, Pancreas Cancer Case-Control Consortium ( PanC4 ) In- ternational Consortium. ∞ Chair, Research Work Stream, Pancreatic Cancer Europe ( http ://www.pancreatic- cancereurope.eu/work-streams/research ). Figure 2 Global-LASSO, 2SR-MLR, and 2SR-LASSO models applied to assess the association between the germline SNPs ( host omics ) and gene expression levels ( tumour omics ) adjusting for SNPs and CpGs. ANNUAL REPORT 2017 116 TRANSLATIONAL RESEARCH FAMILIAL CANCER CLINICAL UNIT ( FCCU ) OVERVIEW Approximately 1 to 2% of the U.S. population harbours a genetic mutation in well-known genes that confer predisposition to cancer. Carriers of such genetic mutations could benefit from established preventive strategies. For example, more than half a million individuals in the U.S. harbour a pathogenic mutation in a Lynch syndrome gene that confers a high risk of colorectal cancer, a tumour readily preventable through annual colonoscopy. Like Lynch syndrome-related genes, there exist a few dozen of such cancer predisposition genes that could be candidates for carefully focused targeted sequencing, including those responsible for hereditary breast and ovarian cancer syndrome, familial adenomatous polyposis, and hereditary endocrinopathies. Identifying the individuals who have a high risk of developing cancer over time and implementing prevention or early intervention strategies could improve population health. “ It is more important to know the person who has a disease, than the disease the person has ” ( Hippocrates’ aphorism ). Advances in genetic and genomic tools are transforming medical practice and are contributing to the elucidation of the genetic basis of cancer predisposition. It is now easier to identify individuals with a moderate to high risk of developing cancer. However, the use of these new genetic technologies in a clinical setting requires the expertise of genetically educated professionals. The FCCU is committed to spreading the role of genetics in medicine ; it takes part in educational initiatives that aid the implementation of genetic and genomic technologies in the clinical setting. Miguel Urioste Clinical Unit Head Graduate Student Laura Pena Technicians Maika González, Fátima Mercadillo SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 117 HuMAN CANCER GENETICS PROGRAMME | FAmILIAL CANCER CLINICAL UNIT ( FCCU ) EDUCATIONAL, CLINICAL, DIAGNOSTIC AND RESEARCH HIGHLIGHTS The FCCU maintains its engagement to enhance the comprehensive understanding of the principles of genetics in a clinical scenario. We maintain a narrow relationship with almost all of the professionals involved in hereditary cancer care in our country, as well as with SEOM and AEGH. We actively participate in general genetics courses, cancer susceptibility classes, seminars targeted at different clinical disciplines, etc., in hospitals from all over Spain, medical schools and other centres. The Cancer Genetics Consultancy in the Fuenlabrada University Hospital ( HUF ) enables us to offer a more integrated model of instruction, training future health-care providers through rotations in the Consultancy, and inviting them to participate in clinical sessions provided by the CNIO Human Genetics Programme and conducted by HUF’s Hereditary Cancer Clinical Committee. We have also continued the relationship with certain patient associations in order to circulate basic knowledge regarding cancer predisposition. We regularly participate in the annual meetings of different associations and have also initiated specific research collaborations with some of them. Our clinical and diagnostic activities this year can be summarised as follows : 506 patients visited our consultancy at HUF ( 24.02% increase over 2016 ), and 428 genetic diagnostic studies were performed in the FCCU laboratory ( 21.59% increase ). We are also currently working with a recently reviewed multigene panel that includes more than 90 cancer predisposition genes. The FCCU actively contributes to the research on less frequent cancer predisposition syndromes. The PTEN hamartoma tumour syndrome ( PHTS ) collectively refers to several rare diseases with overlapping clinical features, a germline cause and an increased predisposition to various cancer types. Our study presents a series of 144 individuals of Spanish origin with PHTS in whom we interrogate the mutational and clinical spectra. Comparisons with respect to other population studies are discussed and guidelines for PHTS patient management are suggested. This is the largest study in Spanish PHTS patients. Our results are in agreement with previously published works in other populations, with a few exceptions such as a higher frequency of mutations in exon 1 ( FIGURE ). Finally, we discuss the usefulness of the diagnostic criteria established for this disease, based on our findings in the PTEN+ vs the PTEN- cohorts. A manuscript reporting all this information in detail is ready for submission. We are also working with the PTEN Research Foundation ( UK ) in order to increase awareness and diagnosis of PHTS and to build professional networks that facilitate advances in the understanding of the disease. Our research in colorectal cancer ( CRC ) has continued to focus on early-onset forms of CRC ( EOCRC ). We have identified a recurrent deletion of 16p13.12-p13.11 chromosomal region in EOCRC. This deletion was associated with a better prognosis. The NOMO1 gene is located in this chromosomal region, and we also observed homozygous deletion of this gene mainly associated with EOCRC, and particularly with microsatellite stable subtypes. Our findings may serve as a starting point for further studies to confirm the potential carcinogenic value of this 16p13.12-p13.11 deletion, which would place NOMO1 in a suitable position as a potential therapeutic target for EOCRC treatment. s ∞ PUBLICATIONS ∞ Gayarre J, Martín-Gimeno P, Osorio A, Paumard B, Barroso A, Fernández V, de la Hoya M, Rojo A, Caldés T, Palacios J, Urioste M, Benítez J, García MJ ( 2017 ). Characterisation of the novel deleterious RAD51C p.Arg312Trp variant and priori- tisation criteria for functional analysis of RAD51C missense changes. Br J Cancer 117, 1048-1062. ∞ Benítez-Buelga C, Baquero JM, Vacklova T, Fernández V, Martín P, Inglada-Perez L, Urioste M, Osorio A, Benítez J ( 2017 ). Genetic variation in the NEIL2 DNA gly- cosylase gene is associated with oxidative DNA damage in BRCA2 mutation carriers. Oncotarget 8, 114626-114636. ∞ Perea J, García JL, Pérez J, Rueda D, Arriba M, Rodríguez Y, Urioste M, González-Sarmiento R ( 2017 ). NOMO-1 gene is deleted in early-onset colorectal cancer. Oncotarget 8, 24429-24436. ∞ Calvete O, Garcia-Pavia P, Domínguez F, Bougeard G, Kunze K, Braeuninger A, Teule A, Lasa A, Ramón Y Cajal T, Llort G, Fernández V, Lázaro C, Urioste M, Benitez J ( 2017 ). The wide spectrum of POT1 gene variants correlates with multiple cancer types. Eur J Hum Genet 25, 1278-1281. ∞ Tavera-Tapia A, Pérez-Cabornero L, Macías JA, Ceballos MI, Roncador G, de la Hoya M, Barroso A, Felipe-Ponce V, Serrano-Blanch R, Hinojo C, Miramar-Gallart MD, Urioste M, Caldés T, Santillan-Garzón S, Benitez J, Osorio A ( 2017 ). Almost 2% of Spanish breast cancer families are associated to germline pathogenic mutations in the ATM gene. Breast Cancer Res Treat 161, 597-604. Figure Spectrum of PTEN mutations in our PHTS cohort. ( A ) Distribution and molecular consequence of point mutations. (  B ) Genetic regions affected in the 7 large deletions. ANNUAL REPORT 2017 118 TRANSLATIONAL RESEARCH MOLECULAR CYTOGENETICS AND GENOME EDITING UNIT OVERVIEW Chromosomal rearrangements are very common events involved in the initiation and development of several solid and many haematological neoplasias. The research activity of the Molecular Cytogenetics and Genome Editing Unit covers the main topics related to human cancer cytogenetics and genome engineering : from classical cytogenetics techniques to new genome engineering tools, including the CRISPR-Cas9 system. We are focusing on the implementation and development of new technologies to enhance the knowledge about the ( cyto )genetics of tumours and to discover new potential therapeutic targets. With the combined usage of CRISPR-Cas9 genome editing and cellular technologies, we are creating human in vitro models that recapitulate chromosomal, genetic and epigenetic cancer alterations. The members of the Unit also participate in collaborative projects with clinical and basic science investigators across the CNIO and other Institutes. “ We have applied genome engineering approaches for cancer modelling, reproducing chromosome rearrangements and gene alterations. We provide access to the latest Cytogenetic and CRISPR technologies.” Sandra Rodríguez Unit Head Post-Doctoral Fellow Raúl Torres ( until November ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 119 HuMAN CANCER GENETICS PROGRAMME | mOLECULAR CyTOGENETICS ANd GENOmE EdITING UNIT RESEARCH HIGHLIGHTS Optimising CRISPR-Cas9 to model cancer aberrations in human stem cells Efficient methodologies for recreating cancer-associated chromosome translocations are in high demand as tools for investigating how such events initiate cancer. The CRISPR- Cas9 system has been used to recreate the genetics of these complex rearrangements at native loci while maintaining the architecture and regulatory elements. However, the CRISPR system remains inefficient for gene editing in human stem cells. We have optimised new strategies to enhance the efficiency of CRISPR-mediated translocation induction in human stem cells, including mesenchymal and induced pluripotent stem cells. We found that the generation of targeted translocation is significantly increased when using a combination of ribonucleoprotein complexes ( Cas9 protein+sgRNA ) and ssODNs. The CRISPR- Cas9-mediated generation of targeted translocations in human stem cells opens up new avenues to model cancer. Technological and translational activities We provide state-of-the-art Molecular Cytogenetic and Genome Editing services. The Unit makes available various techniques, which may provide more sensitive and accurate tools to analyse cancer cells, to research groups ; these techniques include RNA-FISH, chromosome stability studies based on a combined array CGH-FISH approach, or the use of CRISPR libraries to perform high-throughput functional analysis. For gene editing experiments, we have set up a specific PCR-based FISH analysis to detect the genome integration site of small constructs including LV particles. In 2017, we carried out over 1,500 assays for experimental and clinically-oriented projects. s Technicians M. Carmen Carralero ( until May ), M. Carmen Martín, Marta Martínez- Lage ( TS )*, Francisco J. Moya ( until October ) ( TS ) * *Titulado Superior ( Advanced Degree ) ∞ PUBLICATIONS ∞ Rio-Machin A, Gómez-López G, Muñoz J, Garcia-Martinez F, Maiques-Diaz A, Alva- rez S, Salgado RN, Shrestha M, Torres-Ruiz R, Haferlach C, Larráyoz MJ, Calasanz MJ, Fitzgibbon J, Cigudosa JC ( 2017 ). The molecular pathogenesis of the NUP98- HOXA9 fusion protein in acute myeloid leukemia. Leukemia 31, 2000-2005. ∞ Diez B, Genovese P, Roman-Rodriguez FJ, Alvarez L, Schiroli G, Ugalde L, Rodri- guez-Perales S, Sevilla J, Diaz de Heredia C, Holmes MC, Lombardo A, Naldini L, Bueren JA, Rio P ( 2017 ). Therapeutic gene editing in CD34+ hematopoietic progeni- tors from Fanconi anemia patients. EMBO Mol Med 9, 1574-1588. ∞ Torres-Ruiz R, Martinez-Lage M, Mar- tin MC, Garcia A, Bueno C, Castaño J, Ramirez JC, Menendez P, Cigudosa JC, Rodriguez-Perales S ( 2017 ). Efficient rec- reation of t( 11 ;22 ) EWSR1-FLI1+ in human stem cells using CRISPR/Cas9. Stem Cell Rep 8, 1408-1420. ∞ Torres-Ruiz R, Rodriguez-Perales S, Bueno C, Menendez P ( 2017 ). Modeling mixed-lineage-rearranged leukemia initi- ation in CD34+ cells : a “ CRISPR ” solution. Haematologica 102, 1467-1468. ∞ Castaño J, Bueno C, Jiménez-Delgado S, Roca-Ho H, Fraga MF, Fernandez AF, Na- kanishi M, Torres-Ruiz R, Rodríguez-Per- ales S, Menéndez P ( 2017 ). Generation and characterization of a human iPSC cell line expressing inducible Cas9 in the “ safe harbor ” AAVS1 locus. Stem Cell Res 21, 137-140. ∞ Torres-Ruiz R, Rodriguez-Perales S ( 2017 ). CRISPR-Cas9 technology : applications and human disease modelling. Brief Funct Genomics 16, 4-12. ∞ Martinez-Lage M, Torres-Ruiz R, Rod- riguez-Perales S ( 2017 ). CRISPR/Cas9 Technology : Applications and Human Disease Modeling. Prog Mol Biol Transl Sci 152, 23-48. Book chapter ∞ Rodriguez-Perales S, Martinez-Lage M, Torres-Ruiz R ( 2017 ). “ Modeling Cancer Using CRISPR-Cas9 Technology ”. pp. 905- 924. Animal models for the Study of Hu- man Disease, Michael Conn ( ed ). Elsevier. ISBN : 978-0-12-415894-8. Figure Overview of CRISPR- Cas9 applications. CRISPR/Cas9 technology can be used for gene and chromosome editing, transcriptional regulation and epigenetic regulation, among others. Abbreviation : NHEJ, non-homologous end joining ; sgRNA, single guide RNA ; HDR, homologous directed repair ; dCas9, dead Cas9. ANNUAL REPORT 2017 120 TRANSLATIONAL RESEARCH HUMAN GENOTYPING- CEGEN UNIT OVERVIEW The most abundant types of genetic variation are single nucleotide variants ( SNVs ) and copy number variants ( CNVs ). Association studies involving the large-scale analysis of both SNVs and CNVs in thousands of patients can help to identify genes underlying complex diseases such cancer and drug responses. In this Unit we implement different high-throughput and cost-effective methods to measure from one to millions of SNVs and CNVs. In addition, epigenetic studies using whole-genome methylation arrays are performed in this Unit. Complementarily, research focused on the identification of predictive biomarkers for precision medicine is also undertaken. “ Our goal is to advance in our understanding of patient responses to treatment in order to personalise cancer patient care.” Anna González Neira Unit Head Graduate Student Sara Ruiz ( until April ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 121 HuMAN CANCER GENETICS PROGRAMME | HUmAN GENOTyPING-CEGEN UNIT RESEARCH HIGHLIGHTS Two novel genes associated with anthracycline-induced cardiotoxicity Anthracycline chemotherapeutic agents are widely used in the treatment of breast cancer ; however, chronic anthracycline- induced cardiotoxicity ( AIC ) is a serious long-term complication leading to substantial morbidity. Our aim was to identify new genes influencing the susceptibility to AIC. We studied the association of variants on the Illumina HumanExome BeadChip array in cancer anthracycline-treated patients. Through gene- based tests ( SKAT-O ), which have greater statistical power to detect association with rare variation and that can evaluate the cumulative effect of multiple genetic variants, we identified novel significant associations for 2 genes : the first one, ETFB ( electron transfer flavoprotein beta subunit ) is involved in mitochondrial β-oxidation and ATP production ( Ruiz Pinto et al., Breast Cancer Res Treat 2017 ), and the second one, GPR35 ( G protein-coupled receptor 35 ), is a gene with potential roles in cardiac physiology and pathology ( Ruiz Pinto et al., Pharmacogenet Genomics 2017 ). Further functional studies are currently being undertaken. Genetic Factors underlying the risk of alopecia in patients treated with chemotherapy Alopecia is a common toxicity of anticancer drugs and is considered by patients as being the second worst physical side-effect of chemotherapy, after nausea and vomiting. Alopecia associated with conventional doses of chemotherapy has traditionally been considered to be reversible in all cases upon cessation of therapy. However, the observation of some cases of alopecia that persists several years after the end of adjuvant chemotherapy has prompted us to identify genetic factors associated with the appearance of this toxicity in a cohort of cancer patients. We performed a GWAS ( Genome Wide Association Study ) involving patients suffering from this adverse drug reaction and patients without the toxicity ; both were treated with the same drug and dose. We found several significant loci ( P value <10- 6 ) associated with the risk of developing alopecia. Currently we are replicating the most significant hits in an independent cohort of patients. Identification of genetic variants associated with docetaxel and anthracycline efficacy Docetaxel and anthracycline are widely used in the treatment of breast cancer, although the benefit is limited to only a small proportion of patients, and preoperative biomarkers predictive of clinical outcome remain lacking. We carried out a pharmacogenetic study in 181 patients with locally advanced breast cancer who were previously enrolled in a phase 2 randomised clinical trial ( NCT00123929 ); a trial in which patients were randomly assigned to receive doxorubicin ( anthracycline ) or docetaxel ( taxane ) in neoadjuvant therapy. We assessed whether genetic variants in 15 key transport or metabolism genes relevant to doxorubicin and docetaxel drugs could play a role as predictive biomarkers. We identified a genetic variant located in the promoter of ABCC2, as the strongest association with tumour response observed in patients treated with doxorubicin ( P=0.009 ). We also identified a significant association for an intronic variant located in CYP1B1 associated with docetaxel tumour response ( P=2.15x10-4 ). Our integrated pathway-based approach enables the revealing of promising genetic biomarkers for treatment outcome in breast cancer patients ( submitted for publication ). s Technicians Charo Alonso, Núria Álvarez, Belén Herráez, Rocío Nuñez ( TS )*, Guillermo Pita ( TS ) * *Titulado Superior ( Advanced Degree ) Student in Practice María Rodrigo ( since July, Universidad Complutense de Madrid ) ∞ PUBLICATIONS ∞ Michailidou K et al. ( incl. Benítez J, González-Neira A ) ( 2017 ). Association analysis identifies 65 new breast cancer risk loci. Nature 551, 92-94. ∞ Milne RL et al. (  incl. Benítez J, González-Neira A ) ( 2017 ). Identifica- tion of ten variants associated with risk of estrogen-receptor-negative breast cancer. Nat Genet 49, 1767-1778. ∞ Ruiz-Pinto S et al. ( incl. Pita G, Benítez J, González-Neira A ) ( 2017 ). Exome array analysis identifies ETFB as a novel susceptibility gene for anthracycline-in- duced cardiotoxicity in cancer patients. Breast Cancer Res Treat. PMID : 28913729. ∞ Brouckaert O et al. ( incl. Benítez J, González-Neira A ) ( 2017 ). Reproductive profiles and risk of breast cancer sub- types : a multi-center case-only study. Breast Cancer Res 19, 119. ∞ Ruiz-Pinto S et al. ( incl. González-Neira A ) ( 2017 ). Exome array analysis identi- fies GPR35 as a novel susceptibility gene for anthracycline-induced cardiotoxicity in childhood cancer. Pharmacogenet Genomics 27, 445-453. ∞ Veganzones S, de la Orden V, Requejo L, Mediero B, González ML, Del Prado N, Rodríguez García C, Gutiérrez-González R, Pérez-Zamarrón A, Martínez A, Maes- tro ML, Zimman HM, González-Neira A, Vaquero J, Rodríguez-Boto G ( 2017 ). Genetic alterations of IDH1 and Vegf in brain tumors. Brain Behav 7, e00718. ANNUAL REPORT 2017 122 TRANSLATIONAL RESEARCH CLINICAL RESEARCH PROGRAMME MIGUEL QUINTELA-FANDINO Acting Programme Director SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 123 CLINICAL RESEARCH PROGRAMME The Clinical Research Programme has 2 main aims : 1 ) to translate preclinical research into novel clinical care standards ; and 2 ) to address novel clinical oncology challenges with preclinical research. The specific areas of work include : 1 ) development of novel agents ; 2 ) study of the mechanisms of action of novel compounds and tackling drug resistance ; and 3 ), moving forward in the field of biomarkers, functional taxonomy and precision medicine. Currently, the Programme is composed of 4 Clinical Research Units, 1 supporting Unit and clinical trials Management. The Breast Cancer Clinical Research Unit, headed by Miguel Quintela- Fandino, has successfully translated its preclinical research in angiogenesis into two novel independent clinical trials. The effects of targeting immune reprogramming in response to hypoxia-inducing antiangiogenics and mitochondrial metabolism in response to hypoxia-correcting antiangiogenics are being tested prospectively in 2 ongoing trials launched in 10 hospitals of the Spanish National Healthcare System. The Prostate Cancer Clinical Research Unit, under the supervision of David Olmos, has completed its biobanking collection of >17000 samples that will allow the defining of biomarkers of activity and resistance against the main agents used in the management of advanced prostate cancer. They have also gathered a large patient cohort that will determine, for the first time, novel genetic markers associated to inherited prostate cancer in the European population. The Lung Cancer Clinical Research Unit, led by Luis Paz-Ares, has significantly contributed to the discovery of biomarkers that will impact the selection tools for targeted therapies in advanced lung cancer. They have also led several practice-changing international clinical trials. Finally, the Haematological Malignancies Clinical Research Unit, headed by Joaquín Martínez-López, has developed novel tools for the diagnosis and surveillance of the clinical course of different haematological malignancies. Regarding drug development, a novel role for the MEK pathway during drug resistance in acute myeloid leukaemia has been elucidated. An exciting novel line of research based on the ex vivo expansion of natural killer cells is currently ongoing. “ The Clinical Research Programme aims to improve cancer care by developing novel agents and personalising therapeutic approaches on the basis of biomarkers.” The Molecular Diagnostics Unit and Clinical Trials Management, provide support to the Programme in different areas. The Molecular Diagnostics Unit, led by Luis Lombardía, executes a variety of molecular tests that serve the purpose of screening patient candidates for CNIO clinical trials. The latter, led by Antonio López, takes care of the operational procedures of multi-centric clinical trials, including tasks such as site selection, protocol development or regulatory and legal affairs oversight. During 2017, the Programme established novel alliances with ‘big pharma ’ including companies such as AstraZeneca or Bayer AG that support our current research ; this reflects the level of interest that our activities raise in the drug development field. The number of CNIO-sponsored/led trials has increased to 9 and the collaborating hospitals to over 60. ANNUAL REPORT 2017 124 TRANSLATIONAL RESEARCH BREAST CANCER JUNIOR CLINICAL RESEARCH UNIT OVERVIEW The Breast Cancer Clinical Research Unit ( BCCRU ) focuses on the translational interface of therapeutic development. Breast cancer is a heterogeneous disease, and thus, there are large inter-patient variations in terms of disease course, prognosis, relapse and resistance to conventional or targeted therapeutics. Our activities are directed towards personalised treatment, and range from preclinical models to the sponsoring of multicentric clinical trials. Specifically, our research areas are : ɗ Discovery of new targets for breast cancer prevention : role of fatty acid synthase ( FASN ). ɗ Breast cancer functional taxonomy : by using a systems biology approach, we are clustering the disease into subtypes defined by biologic features that constitute therapeutic targets. “ In 2017, the Breast Cancer Group has confirmed the role of FASN as a therapeutic target for the prevention of epithelial cancer development and has launched 2 clinical trials aimed at assessing the adaptive mechanisms of escape from antiangiogenic therapy.” ɗ Study of the mechanisms of resistance against targeted therapies. ɗ Conduct investigator- initiated clinical trials. Miguel Quintela-Fandino Clinical Research Unit Head Staff Scientists María José Bueno, Silvana A. Mouron SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 125 CLINICAL RESEARCH PROGRAMME | bREAST CANCER JUNIOR CLINICAL RESEARCH UNIT RESEARCH HIGHLIGHTS Our studies about fatty acid synthase ( FASN ) have finally revealed a role for this molecule as a therapeutic target for preventing the development of epithelial cancers. FASN, an enzyme expressed at almost undetectable levels in adult tissues, elicits the metabolic impulse that cells undergoing the transformation process require to complete the transition from organised 2D-growth to de-organised, anchorage-independent 3D-growth. FASN inhibitors are well tolerated and have proven to abrogate the development of breast and lung cancers driven by oncogenes such as Pi3K, K-RAS or HER2. These findings set the grounds for future clinical interventions. On the clinical side of our activities, in 2017, we launched 2 independent clinical trials addressing the adaptive mechanisms of escape against chronic exposure to antiangiogenics that our laboratory tackled between 2012 and 2016 ; the results were published last year. In one of the trials, CNIO-BR-008, we are exploring the concept of hypoxia-induced immunodepression. In a number of patients, instead of vascular normalisation, antiangiogenics deteriorate the vascular network, an occurrence associated with increased PD-L1 and kynurenine signalling ; these patients can be detected by 18F-Misonidazole PET. In this trial we are exploring the therapeutic effect of adding MEDI-4736 ( an anti-PD-L1 monoclonal antibody ) to bevacizumab in breast cancer patients who experience disease progression while in treatment with bevacizumab monotherapy, stratified by Miso- PET response. In the second trial, CNIO-BR-009, we are exploring the synergy between the mitochondrial inhibitor ME-344 and bevacizumab in patients who experience the opposite adaptive mechanism – vascular normalisation followed by mito-switch, detected by Miso-PET. s Clinical Research Fellow Juan V. Apala Graduate Students Sara Fernández, Gonzalo Pérez ( until November ) Technicians Verónica Jiménez, José Francisco López ( until June ) ( TS )*, Esperanza Martín ( until April ) *Titulado Superior ( Advanced Degree ) ∞ PUBLICATIONS ∞ Álvarez-Fernández M, Sanz-Flores M, Sanz-Castillo B, Salazar-Roa M, Partida D, Zapatero-Solana E, Ali HR, Manchado E, Lowe S, VanArsdale T, Shields D, Cal- das C, Quintela-Fandino M, Malumbres M ( 2017 ). Therapeutic relevance of the PP2A-B55 inhibitory kinase MASTL/ Greatwall in breast cancer. Cell Death Differ. PMID : 29229993. ∞ Mateo F et al. ( incl. Quintela-Fandino M ) ( 2017 ). Stem cell-like transcriptional reprogramming mediates metastatic re- sistance to mTOR inhibition. Oncogene 36, 2737-2749. ∞ Bueno MJ, Mouron S, Quintela-Fandino M ( 2017 ). Personalising and targeting antiangiogenic resistance : a complex and multifactorial approach. Br J Cancer 116, 1119-1125. ∞ Quintela-Fandino M, Soberon N, Lluch A, Manso L, Calvo I, Cortes J, Moreno-Antón F, Gil-Gil M, Martinez-Jánez N, Gonza- lez-Martin A, Adrover E, de Andres R, Viñas G, Llombart-Cussac A, Alba E, Mouron S, Guerra J, Bermejo B, Zamora E, García-Saenz JA, Simon SP, Carrasco E, Escudero MJ, Campo R, Colomer R, Blasco MA ( 2017 ). Critically short telomeres and toxicity of chemotherapy in early breast cancer. Oncotarget 8, 21472-21842. Figure Impaired ability to transform in absence of FASN : the upper-left panel shows a tumour arising in the breast epithelium of a wild-type PyMT mouse, stained for FASN. The upper-right corresponds to a FASN KO animal, where the KO is incomplete. It can be appreciated how only the FASN-positive areas are able to form tumours, whereas only minor proliferations that are unable to break the basal membrane are observed in the FASN-negative areas. Below, examples of anchorage- independent 3D growth of PyMT cells, positive ( left ) or negative for FASN. ANNUAL REPORT 2017 126 TRANSLATIONAL RESEARCH PROSTATE CANCER JUNIOR CLINICAL RESEARCH UNIT OVERVIEW Prostate cancer ( PrCa ) is one of the most heritable human cancers, as almost 60% of the PrCa risk is attributable to genetic factors. Inherited mutations in several genes involved in DNA damage response and repair ( DDR ) have been reported to predispose men to prostate cancer ; this includes mutations in BRCA2, the genetic event known to confer the greatest risk of the disease. Recent studies have revealed that germline deleterious mutations in DDR genes are present in 8-12% of patients with metastatic PrCa, mutations in BRCA2 being the most prevalent ones. Our Group has previously established that these mutations are an independent prognostic factor for the disease. These observations have come full-circle with the development of Poly ( ADP-ribose ) polymerase inhibitors to treat advanced prostate cancer. Due to the high prevalence of DDR germline mutations and the implications for the patients and their families, clinical guidelines have recently been updated to recommend genetic screening to all patients with metastatic PrCa. In consequence, the number of mutation carriers is likely to grow over the next few years, whilst the most appropriate treatment and management still remains unknown. This year our Unit’s research has focussed on gaining a better understanding of the clinical implications of BRCA2 and other DDR defects ; the molecular characterisation of these tumours and the identification of biomarkers can enable us to predict the benefit derived from currently available therapies. David Olmos Junior Clinical Research Unit Head Clinical Investigator Elena Castro Clinical Research Fellow Nuria Romero, Rebeca Lozano Graduate Students Ylenia Cendón, Lorena Magraner, Paz Nombela SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 127 CLINICAL RESEARCH PROGRAMME | PROSTATE CANCER JUNIOR CLINICAL RESEARCH UNIT RESEARCH HIGHLIGHTS PROREPAIR study. PROREPAIR-B ( Castro et al., Abstract LBA32, ESMO 2017 ) is the first prospective study to address the prevalence of germline DNA damage response genes, deleterious mutations and their impact on clinical outcomes following conventional treatments for metastatic prostate cancer. The study included 419 mCRPC patients. BRCA2 ( 3.3%), ATM ( 1.9%) and BRCA1 ( 0.9%) were the most commonly mutated genes. Pathogenic variants in all of the 107 analysed genes were identified in 15% of patients. Carriers and non-carriers presented similar characteristics at baseline, but carriers, particularly BRCA2 carriers, progressed earlier and lived shorter lives than non- carriers despite the administered treatments. This is a prospective multicentre cohort study involving 38 Spanish centres within the PROCURE network ( see below ). SWITCH Phase II study. In 2017, we also presented the final results of the SWITCH study ; a multicentre, single arm, open label, single-stage, phase II study. Clinically stable mCRPC patients who had PSA and/or limited radiographic progression after at least 12-weeks on Abiraterone plus prednisone, switched to Abiraterone plus dexamethasone. PSA50 response rate was 34.6%, Median time to biochemical and radiological progression were 5.3 and 11.8 months, respectively. Patients with AR gain detected in plasma ctDNA did not respond to the switch, while patients with AR normal status benefitted the most. The change of prednisone to dexamethasone in clinically stable patients progressing to Abiraterone plus prednisone could revert some resistances and induce durable responses in advanced prostate cancer. PROCURE biomarkers platform. This network, started by our Group in 2013, involves 63 participating oncology departments across Spain. Over 900 patients have been enrolled in the 5 currently active prospective studies ( PROREPAIR, PROSTAC, PROSABI, PROSENZA, PRORADIUM ). This network has attracted international attention and partners from Italy ( MEET- URO group ) and Australia ( Peter McCallum Cancer Centre ) have joined us this year. s Technician Vanessa Cañadilla Student in practice Isabel Santos ( July-November ) Visiting scientists Teresa Garcés ( Instituto de Investigación Biomédica de Málaga ), Gala Grau ( Instituto de Investigación Biomédica de Málaga ), Ana M. Gutiérrez ( Hospital Universitario de Móstoles, Madrid ), Fernando López ( Hospital Ramón y Cajal, Madrid ), Maria I. Pacheco ( Instituto de Investigación Biomédica de Málaga ), Leticia Rivera ( Instituto de Investigación Biomédica de Málaga ), Benjamín Olmos ( since October ) ( Hospital Universitario Virgen de la Victoria, Málaga ) ∞ PUBLICATIONS ∞ Zabala-Letona A et al. ( incl. Castro E, Olmos D, Efeyan A, Muñoz J ) ( 2017 ). mTORC1-dependent AMD1 regulation sustains polyamine metabolism in pros- tate cancer. Nature 547, 109-113. ∞ Mateo J et al. ( incl. Castro E, Olmos D ) ( 2017 ). DNA repair in prostate cancer : biology and clinical Implications. Eur Urol 71, 417-425. ∞ Romero-Laorden N, Piñeiro-Yañez E, Gutierrez-Pecharroman A, Pacheco MI, Calvo E, Al-Shahrour F, Castro E, Olmos D ( 2017 ). Somatic BRCA2 bi-allelic loss in the primary prostate cancer was associated to objective response to PARPi in a sporadic CRPC patient. Ann Oncol 28, 1158-1159. ∞ Banerjee S et al. ( incl. Olmos D ) ( 2017 ). Professional burnout in European young oncologists : results of the European Soci- ety for Medical Oncology ( ESMO ) young oncologists committee burnout survey. Ann Oncol 28, 1590-1596. ∞ García JL et al. ( incl. Olmos D ) ( 2017 ). A novel capillary nano-immunoassay for assessing androgen receptor splice variant 7 in plasma. Correlation with CD133 anti- gen expression in circulating tumor cells. A pilot study in prostate cancer patients. Clin Transl Oncol 19, 1350-1357. ∞ Rodriguez-Vida A et al. ( incl. Olmos D ) ( 2017 ). Selection and monitoring of pa- tients with metastatic castration-resist- ant prostate cancer for treatment with radium-223. Clin Transl Oncol. PMID : 29098556. ∞ Moynihan C et al. ( incl. Castro E ) ( 2017 ). Ambiguity in a masculine world : being a BRCA1/2 mutation carrier and a man with prostate cancer. Psycho-Oncol 26, 1987-1993. ∞ Heinrich D et al. ( incl. Olmos D ) ( 2017 ). The contemporary use of radium-223 in metastatic castration-resistant prostate cancer. Clin Genitourin Cancer. PMID : 29079165. ∞ Romero-Laorden N, Castro E ( 2017 ). In- herited mutations in DNA repair genes and cancer risk. Curr Prob Cancer 41, 251-264. ∞ AWARDS AND RECOGNITION ∞ Scientific Committee Member, 2017 ESMO Congress, Madrid, Spain. ∞ Faculty Board Member, 2017 EORTC-EC- CO-AACR-ESMO Methods in Clinical Can- cer Research Workshop, Netherlands. ∞ Elena Castro: awarded the 2017 Stew- art-Rahr Young Investigator Award (Pros- tate Cancer Foundation, USA); Faculty, ESMO Preceptorships in Prostate Cancer. ∞ Nuria Romero received an “ ESMO 2017 Merit Award ”, ESMO Congress, Spain. ∞ Rebeca Lozano was awarded: ‘ Best Com- munication ’ Award, 4th Androgen Project Meeting in Prostate Cancer; ‘ Best Poster ’ Award, SEOM annual Meeting, Spain. Figure The pie chart illustrates the gene distribution of the 72 pathogenic variants in DNA Damage Repair genes found in 68 mCRPC patients out of 419 included in the PROREPAIR-B study. ANNUAL REPORT 2017 128 TRANSLATIONAL RESEARCH MOLECULAR DIAGNOSTICS UNIT OVERVIEW The activity of the Molecular Diagnostics Unit ( MDU ) is primarily focused on providing an abundant assortment of molecular assays to clinicians working in hospitals of the Spanish National Health System ; our aim is to support the management of their patients with different cancers. Occasionally, MDU also provides support, with its technical expertise and logistics, to CNIO’s Clinical Research Units and Research Groups. Furthermore, in order to keep our catalogue updated, our efforts are persistently geared towards strengthening, upgrading and reducing the turnaround times and costs of the assays that are currently available. Also, with the aim of further expanding our end users portfolio, we are tasked with implementing and offering new molecular tests based on the latest discoveries in the field and/or the needs of clinicians or researchers. Finally, a crucial part of our mission is to host professionals and students who aspire to be instructed in this area. Luis Lombardía Unit Head Technician Diana Romero “ In comparison to 2016, MDU has seen a substantial increase ( around 30%) of the number of tests required by hospitals, thus contributing to a better individualised care of the patients.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 129 CLINICAL RESEARCH PROGRAMME | mOLECULAR dIAGNOSTICS UNIT RESEARCH HIGHLIGHTS During 2017, we completed the standardisation and implementation of a new assay, launched in 2016, which will enable us to detect mutations in exons 3, 6, 7, 9, 10 and 11 of the tumour suppressor gene TET2 and, therefore, enable a better prediction the prognosis of patients with myeloproliferative neoplasms. We have also expanded our catalogue with the addition of 2 new molecular diagnostic tests based on bi-directional Sanger sequencing. The first one will enable the detection of activating mutations in exons 13, 14, and 22 to 28 of the proto-oncogene ERBB2 ( Erb-B2 Receptor Tyrosine Kinase 2, aka HER2 ) in patients with breast, ovarian, colorectal, gastroesophageal and lung cancers. These oncogenic alterations can cause resistance to treatments with reversible tyrosine kinase inhibitors and, thus, promote a more aggressive and metastatic disease. Therefore, the detection of these mutations will significantly expand the range of patients that could benefit from useful targeted therapies ( FIGURE ). The other assay will enable us to detect mutations in the POLE ( Polymerase Epsilon ) gene. This gene codes for a DNA polymerase with a proofreading exonuclease activity, which thereby allows high-fidelity DNA replication to occur. Quite recently, a group of endometrial carcinomas ( EC ) − not sufficiently distinctive to allow accurate diagnosis based on routine histological staining − has been identified with a high rate of somatic missense point mutations, commonly reported at 3 hotspots in exons 9, 13 and 14 of POLE. These tumours are associated with improved progression-free-survival, which is not derived from a higher sensitivity to chemotherapy but are more likely linked to enhanced immunogenicity. Since the clinical praxis is to give adjuvant chemotherapy to most patients with EC, this test will enable us to avoid unnecessary treatments in POLE-mutated cancer patients. Additionally, as in previous years, we continue to interact with national and international standardisation groups in order to maintain a high level of quality standards in the molecular diagnostic tests provided by us. Finally, we uphold our policy of welcoming clinicians and technical specialists in order to mentor and train them in the field. s Figure Mutations in ERBB2 can produce either sensitivity ( green dashed arrows ) or resistance ( red ) in the response of patients with breast cancer to different therapies. ( RL : Receptor L ; CR : Cysteine Rich ; TM : Transmembrane ; TK : Tyrosine Kinase ; TKI : TK inhibitors ). ANNUAL REPORT 2017 130 TRANSLATIONAL RESEARCH H12O-CNIO HAEMATOLOGICAL MALIGNANCIES CLINICAL RESEARCH UNIT Joaquín Martínez-López Clinical Research Unit Head SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 131 CLINICAL RESEARCH PROGRAMME | H12O-CNIO HAEmATOLOGICAL mALIGNANCIES CLINICAL RESEARCH UNIT OVERVIEW The Haematological Malignancies Clinical Research Unit focuses on 3 main objectives : ɗ Molecular research of haematological cancers : studying of cancer induced changes at the proteomic and genomic levels. We aim to : i ) find new genomic and proteomics biomarkers for a better diagnosis of these haematological diseases ; ii ) detect new molecular alterations as predictors of response to a treatment, for example by studying minimal residual disease ; and iii ) study immune mechanisms of cancer control, with a special focus on NK cells. ɗ In vitro & in vivo research : i ) to establish the effects of new anticancer molecules in in vitro models of the disease ; ii ) to determine the mechanisms of resistance to anticancer drugs. ɗ Clinical research : translate preclinical findings to the patients through a phase I clinical trials unit. “ During this year, the Group has developed new markers and tools to provide a better diagnosis, surveillance and treatment of haematological diseases such as multiple myeloma, leukaemia and lymphoma.” Staff Scientists Rosa Ayala, Teresa Cedena, Miguel Gallardo, Inmaculada Rapado, Beatriz Sánchez-Vega Post-Doctoral Fellows Lucía Fernández, Almudena García ( since November ), María Linares, Ricardo Sánchez, Antonio Valeri Graduate Students Alicia Arenas ( until November ), Isabel Cuenca, Alejandra Leivas, M. Luz Morales, Alejandra Ortíz, Yanira Ruíz, Laura Sánchez ( since October ) Technicians Alba García ( until November ), Esther Onecha Student in Practice Sara Rodríguez Collado ( August ) ANNUAL REPORT 2017 132 TRANSLATIONAL RESEARCH RESEARCH HIGHLIGHTS During this year, our Group has developed new tools for the diagnosis and surveillance of different haematological diseases using Next Generation Sequencing ( NGS ): ɗ Targeted RNASeq for the identification of Ph-like B-acute lymphoblastic leukaemia ( ALL ). ɗ A novel NGS method for studying BCR-ABL1 protein variants in cDNA from bone marrow and cerebrospinal fluid blast cells from ALL patients. ɗ A simplified in-house deep-sequencing method to identify and quantify Minimal Residual Disease in multiple myeloma ( MM ) patients using NGS of immunoglobulin rearranged genes ( FIGURE 1 ). ɗ A specific NGS panel of different genes ( NPM1, IDH1, IDH2 or DNMT ) for evaluating relapse, drug response and Minimal Residual Disease in myeloid diseases. ∞ PUBLICATIONS ∞ Fulciniti M, Martinez-Lopez J, Senapedis W, Oliva S, Bandi RL, Amodio N, Xu Y, Szalat RL, Gulla A, Samur MK, Roccaro A, Linares M, Cea M, Baloglu E, Argueta C, Landesman Y, Shacham S, Liu S, Schenone M, Wu SL, Karger B, Prabhala R, Anderson KC, Munshi NC ( 2017 ). Functional role and therapeu- tic targeting of p21-activated kinase 4 in multiple mieloma. Blood 129, 2233-2245. ∞ Fernández L, Metais JY, Escudero A, Vela M, Valentín J, Vallcorba I, Leivas A, Torres J, Valeri A, Patiño-García A, Martínez J, Leung W, Pérez-Martínez A ( 2017 ). Mem- ory T cells expressing an NKG2D-CAR efficiently target osteosarcoma cells. Clin Cancer Res 23, 5824-5835. ∞ Jiménez C, Jara-Acevedo M, Corchete LA, Castillo D, Ordóñez GR, Sarasquete ME, Puig N, Martínez-López J, Prieto-Conde MI, García-Álvarez M, Chillón MC, Balan- zategui A, Alcoceba M, Oriol A, Rosiñol L, Palomera L, Teruel AI, Lahuerta JJ, Bladé J, Mateos MV, Orfão A, San Miguel JF, González M, Gutiérrez NC, García-Sanz R ( 2017 ). A next-generation sequencing strategy for evaluating the most common genetic abnormalities in multiple myelo- ma. J Mol Diagn 19, 99-106. ∞ Ribera J, Zamora L, Morgades M, Mallo M, Solanes N, Batlle M, Vives S, Granada I, Juncà J, Malinverni R, Genescà E, Guàrdia R, Mercadal S, Escoda L, Martinez-Lopez J, Tormo M, Esteve J, Pratcorona M, Mar- tinez-Losada C, Solé F, Feliu E, Ribera JM ; Spanish PETHEMA Group ; Spanish Soci- ety of Hematology ( 2017 ). Copy number profiling of adult relapsed B-cell precursor acute lymphoblastic leukemia reveals po- tential leukemia progression mechanisms. Gene Chromosomes Cancer 56, 812-820. ∞ PUBLICATIONS AT OTHER INSTITUTIONS ∞ Lahuerta JJ et al. ( incl. Martinez-Lopez J ) GEM ( Grupo Español de Mieloma )/ PETHEMA ( Programa para el Estudio de la Terapéutica en Hemopatías Malignas ) Cooperative Study Group ( 2017 ). Depth of response in multiple myeloma : a pooled analysis of three PETHEMA/GEM clinical trials. J Clin Oncol 35, 2900-2910. ∞ Flores-Montero J et al. ( incl. Martinez-López J ) ( 2017 ). Next generation flow ( NGF ) for highly sensitive and standardized detection Figure 1 Minimal Residual Disease detection in multiple myeloma patients using NGS. ( A ) Plot of the dynamic range, limit of quantification ( LOQ ) and limit of detection ( LOD ). ( B ) Progression- free survival ( PFS ) and overall survival ( OS ) plots according to MRD levels ( blue, negative ; red, positive ). SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 133 CLINICAL RESEARCH PROGRAMME | H12O-CNIO HAEmATOLOGICAL mALIGNANCIES CLINICAL RESEARCH UNIT of minimal residual disease in multiple my- eloma. Leukemia. PMID.28104919. ∞ Hernández-Boluda JC et al. ( incl. Martín- ez-López J ) ( 2017 ). Performance of the myelofibrosis secondary to PV and ET-prognostic model ( MYSEC-PM ) in a series of 262 patients from the Spanish registry of myelofibrosis. Leukemia. PMID : 28935991. ∞ Alvarez-Larrán A et al. ( incl. Martín- ez-López J ) ( 2017 ). Risk of thrombosis according to need of phlebotomies in pa- tients with polycythemia vera treated with hydroxyurea. Haematologica 102, 103-109. ∞ Rosiñol L et al. ( incl. Martínez-López J ) 2017. Bortezomib and thalidomide main- tenance after stem-cell transplantation for multiple myeloma : A PETHEMA/GEM trial. Leukemia 31, 1922-1927. ∞ Paiva B, Puig N, Cedena MT, de Jong BG, Ruiz Y, Rapado I, Martinez-Lopez J, Cor- don L, Alignani D, Delgado JA, van Zelm MC, Van Dongen JJ, Pascual M, Aguirre X, Prosper F, Martín-Subero JI, Vidriales MB, Gutierrez NC, Hernandez MT, Oriol A, Echeveste MA, Gonzalez Y, Johnson SK, Epstein J, Barlogie B, Morgan GJ, Orfao A, Blade J, Mateos MV, Lahuerta JJ, Miguel JF ( 2017 ).Differentiation stage of myeloma plasma cells : biological and clinical signif- icance. Leukemia 31, 382-392. ∞ Forero-Castro M et al. ( incl. Martinez J ) ( 2017 ).Mutations in TP53 and JAK2 are independent prognostic biomarkers in B-cell precursor acute lymphoblastic leu- kaemia. Br J Cancer 117, 256-265. ∞ Alvarez-Larrán A, Senín A, Fernán- dez-Rodríguez C, Pereira A, Arel- lano-Rodrigo E, Gómez M, Ferrer-Marin F, Martínez-López J, Camacho L, Colomer D, Angona A, Navarro B, Cervantes F, Bess- es C, Bellosillo B, Hernández-Boluda JC ( 2017 ).Impact of genotype on leukaemic transformation in polycythaemia vera and essential thrombocythaemia.Br J Haematol 178, 764-771. ∞ PATENT AT OTHER INSTITUTIONS ∞ Ballesteros JA, Bennet TA, Hernández P, Gómez C., Gorrochategui J, Martínez J, Robles A, Primo D ( 2017 ). Cancer-Killing t cells and uses thereof. WO/2017/178572. On the other hand, new molecular targets have been explored : ɗ The new role of PAK 4 in multiple myeloma. ɗ The control that hnRNP K exerts on proliferation and differentiation programmes in haematological malignancies such as lymphoma. ɗ The activation of the MEK/ERK1/2 pathway during drug resistance in acute myeloid leukaemia. ɗ The value of PTCH1 for predicting imatinib response in chronic myeloid leukaemia patients in chronic phase. Finally, a novel treatment strategy using autologous activated and expanded natural killer cells plus anti-myeloma drugs has been developed for multiple myeloma ; the strategy has been effective in vitro, ex vivo and in patients with relapsed or refractory myeloma ( FIGURE 2 ). Moreover, we have demonstrated that the NKG2D receptor, expressed in both natural killer cells and CD8+ T cells, NKG2D- NKG2DL could be used as an immunotherapeutic strategy against cancer ; NKG2D-4-1BB-CD3z CAR-redirected memory T cells efficiently targeted NKG2DL-expressing osteosarcoma cells in vivo and in vitro. s Figure 2 Representative flow cytometry data of lymphocyte populations from a single patient during the first cycle using autologous activated and expanded natural killer cells plus anti-myeloma drugs. ANNUAL REPORT 2017 134 TRANSLATIONAL RESEARCH H12O-CNIO LUNG CANCER CLINICAL RESEARCH UNIT Luis G. Paz-Ares Clinical Research Unit Head Staff Scientists Teresa Argullo, Irene Ferrer, Rocio García, Eva M. Garrido ( since March ), Sonia Molina, Santiago Ponce, M. Carmen Riesco ( since February ), Jon Zugazagoitia ( until September ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 135 CLINICAL RESEARCH PROGRAMME | H12O-CNIO LUNG CANCER CLINICAL RESEARCH UNIT OVERVIEW Lung cancer is the most frequent cause of cancer-related deaths worldwide. Our Unit is dedicated to the study of lung cancer, combining basic research studies with other more clinically oriented research studies, closer to solving the problems of lung cancer patients. The two main research areas of our Unit include : the identification of new molecular biomarkers that can be used in the clinic for diagnostic, prognostic and predictive purposes ; and the development of novel treatment strategies that include targeted therapies and immunotherapeutics. For example, we have elucidated the molecular determinants of the oncogenicity of FGFRs, and have discovered biomarkers to monitor the efficacy of FGFR inhibitors in lung cancer. On the other hand, we have developed a patient-derived xenograft ( PDX ) platform of non-small-cell lung cancers to test new therapeutic strategies. Finally, our Unit has extensive experience in bringing new drugs to the clinic ( phase I trials ), as well as in conducting practice-changing phase II/III trials in the fields of precision oncology and immuno-oncology. “ We have significantly contributed to the discovery of biomarkers that will impact the current selection for targeted therapies ( e.g. FGFR inhibitors ). We have led randomised clinical trials with biological therapies and immunotherapy in lung cancer that have resulted in treatment changes in clinical practice ( e.g. Durvalumab in stage III NSCLC or Afatinib in EGFR mutated NSCLC ).” Post-Doctoral Fellows Pablo Gella ( since March ), María Pedraza ( since February ), Beatriz Soldevilla Graduate Students Carlos Carretero ( since April ), Santiago García ( since November ), Ángela Marrugal, Cristina Ojeda ( since February ), Laura Ojeda, Álvaro Quintanal, Javier Ramos ( since March ), Patricia Yagüe Technicians M. José Durán, Laura García, Beatriz Gil, Rocío Suárez ANNUAL REPORT 2017 136 TRANSLATIONAL RESEARCH RESEARCH HIGHLIGHTS Biomarker discovery and implementation Our Group has deciphered the biological role of FGFR1 and FGFR4 in non-small cell lung cancer ( NSCLC ) and has developed new biomarkers with predictive roles for anti-FGFR therapy in NSCLC. The data show that the determination of FGFR1/4 gene amplification or expression alone is not sufficient to predict the efficacy of anti- FGFR therapy, but that a complementary determination of a biomarker expression may further optimise patient selection for this therapeutic strategy ( manuscripts and patent applications have been submitted ). Currently, the Group is : validating the results on a series of well-characterised PDX models ; generating an antibody against the new biomarker in order to develop a diagnostic kit ; carrying out the technical validation of the biomarker ; and submitting a phase II trial proposal with an FGFR inhibitor in NSCLC patients with high expression of this biomarker. The Group has also validated an NGS-based algorithm for the determination of genomic aberrations − in tumour tissue as well as in cfDNA − that could be used to guide treatment in clinical practice. Early clinical trials Our Group has significantly expanded its activity of testing new molecules and combinations in solid tumours, particularly in the area of immune-based approaches, and has participated in more than 25 projects in this area of research in 2017. Recently, we provided key delivery and feasibility data supporting the use of IV infusion of enadenotucirev ( or therapeutic transgene- bearing derivatives of it ) in clinical trials across a range of epithelial tumours, including the ongoing combination study of enadenotucirev with the checkpoint inhibitor nivolumab. This phase I study also provided insights into the potential immune- stimulating properties of enadenotucirev ( R Garcia-Carbonero et al., J Immunother Cancer 2017 ). Encouraging data on the novel combination of pembrolizumab plus ramucirumab in the cohort of non-small-cell lung cancer were updated at ASCO 2017, showing a response rate of 35 % and 9.7-months of progression-free survival in pretreated patients. Finally, data of a first-in-human trial with a novel T-cell bispecific antibody targeting carcinoembryonic antigen expressed on tumour cells and CD3 on T-cells, with or without atezolizumab, was communicated on at the ASCO annual meeting. Figure ( A ) The anti PD-L1 mAb Durvalumab blocks PD-L1 binding to PD-1 and CD80. ( B ) Results of the randomised clinical trial PACIFIC, showing an improvement in progression-free survival ( PFS ) ( HR 0.52 ; p<0.0001 ) in stage III Non-Small-Cell Lung Cancer ( NSCLC ) patients treated with Durvalumab ( vs placebo ) after chemoradiotherapy. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 137 CLINICAL RESEARCH PROGRAMME | H12O-CNIO LUNG CANCER CLINICAL RESEARCH UNIT Changing standard-of-care treatments in clinical practice The Lung Cancer Clinical Research Unit has led and has actively contributed to phase III trials whose results have had a significant impact on the clinical practice in the context of EGFR mutated ( L Paz-Ares et al., Ann Oncol 2017 ), ALK translocated ( Soria JC et al., NEJM 2017 ) or unselected ( Carbone D et al., NEJM 2017 ) stage IV lung cancer. More recently, Luis Paz-Ares communicated, at the ESMO 2017 Congress, the results of a Phase III trial showing a profound reduction in disease progression for stage III NSCLC patients treated with the anti PD-L1 agent Durvalumab following chemoradiation. s ∞ PUBLICATIONS ∞ Antonia SJ et al. ( incl. Paz-Ares L ); PA- CIFIC Investigators ( 2017 ). Durvalumab after chemoradiotherapy in stage III non- small-cell lung cancer. N Engl J Med 377, 1919-1929. ∞ Carbone DP et al. ( incl. Paz-Ares L ); CheckMate 026 Investigators ( 2017 ). First- line Nivolumab in stage IV or recurrent non-small-cell lung cancer. N Engl J Med 376, 2415-2426. ∞ Hirsch FR, Scagliotti GV, Mulshine JL, Kwon R, Curran WJ Jr, Wu YL, Paz-Ares L ( 2017 ). Lung cancer : current therapies and new targeted treatments. Lancet 389, 299-311. ∞ Soria JC et al. ( incl. Paz-Ares L ) ( 2017 ). First-line ceritinib versus platinum-based chemotherapy in advanced ALK-rear- ranged non-small-cell lung cancer ( AS- CEND-4 ): a randomised, open-label, phase 3 study. Lancet 389, 917-929. ∞ Peters S et al. ( incl. Paz-Ares L ) ( 2017 ). Phase II trial of Atezolizumab as first-line or subsequent therapy for patients with programmed death-ligand 1-selected advanced non-small-cell lung cancer ( BIRCH ). J Clin Oncol 35, 2781-2789. ∞ Spigel DR, Edelman MJ, O’Byrne K, Paz- Ares L, Mocci S, Phan S, Shames DS, Smith D, Yu W, Paton VE, Mok T ( 2017 ). Results From the phase III randomized trial of Onartuzumab plus Erlotinib versus Erlo- tinib in previously treated stage IIIB or IV non-small-cell lung cancer : METLung. J Clin Oncol 35, 412-420. ∞ Zugazagoitia J, Molina-Pinelo S, Lopez-Ri- os F, Paz-Ares L ( 2017 ). Biological ther- apies in nonsmall cell lung cancer. Eur Respir J 49, pii : 1601520. ∞ Paz-Ares L, Tan EH, O’Byrne K, Zhang L, Hirsh V, Boyer M, Yang JC, Mok T, Lee KH, Lu S, Shi Y, Lee DH, Laskin J, Kim DW, Lau- rie SA, Kölbeck K, Fan J, Dodd N, Märten A, Park K ( 2017 ). Afatinib versus gefitinib in patients with EGFR mutation-positive advanced non-small-cell lung cancer : overall survival data from the phase IIb LUX-Lung 7 trial. Ann Oncol 28, 270-277. ∞ Wehler T, Thomas M, Schumann C, Bosch-Barrera J, Viñolas Segarra N, Dickgreber NJ, Dalhoff K, Sebastian M, Corral Jaime J, Alonso M, Hynes SM, Lin J, Hurt K, Bence Lin A, Calvo E, Paz-Ares L ( 2017 ). A randomized, phase 2 evaluation of the CHK1 inhibitor, LY2603618, admin- istered in combination with pemetrexed and cisplatin in patients with advanced nonsquamous non-small cell lung cancer. Lung Cancer 108, 212-216. ∞ Martínez-Pérez J, Lopez-Calderero I, Saez C, Benavent M, Limon ML, Gonzalez-Ex- posito R, Soldevilla B, Riesco-Martínez MC, Salamanca J, Carnero A, Garcia-Carbonero R ( 2017 ). Prognostic relevance of Src ac- tivation in stage II-III colon cáncer. Hum Pathol 67, 119-125. ∞ Glisson B et al. ( incl. Paz-Ares L ) ( 2017 ). A randomized, placebo-controlled, phase 1b/2 study of rilotumumab or ganitum- ab in combination with platinum-based chemotherapy as first-Line treatment for extensive-stage small-cell lung cancer. Clin Lung Cancer 18, 615-625. ∞ Quintanal-Villalonga Á, Carranza-Carranza A, Meléndez R, Ferrer I, Molina-Pinelo S, Paz-Ares L ( 2017 ). Prognostic role of the FG- FR4-388Arg variant in lung squamous-cell carcinoma patients with lymph node in- volvement. Clin Lung Cancer 18, 667-674. ∞ Paz-Ares LG, Zimmermann A, Ciuleanu T, Bunn PA, Antonio BS, Denne J, Iturria N, John W, Scagliotti GV( 2017 ). Meta-analy- sis examining impact of age on overall sur- vival with pemetrexed for the treatment of advanced non-squamous non-small cell lung cancer. Lung Cancer 104, 45-51. ∞ Socinski MA, Kaye FJ, Spigel DR, Kudrik FJ, Ponce S, Ellis PM, Majem M, Lorigan P, Gandhi L, Gutierrez ME, Nepert D, Corral J, Paz Ares L ( 2017 ). Phase 1/2 Study of the CD56-targeting antibody-drug conjugate Lorvotuzumab Mertansine ( IMGN901 ) in combination with Carboplatin/Etoposide in small-cell lung cancer patients with extensive-stage disease. Clin Lung Cancer 18, 68-76. ∞ Riesco-Martinez MC, Sanchez Torre A, García-Carbonero R ( 2017 ). Safety and efficacy of nintedanib for the treatment of metastatic colorectal cancer. Expert Opin Investig Drugs 26, 1295-1305. ∞ SELECTED PUBLICATIONS AT OTHER INSTITUTIONS ∞ Kim DW et al. ( incl. Paz-Ares Rodríguez LG ) ( 2017 ). Brigatinib in patients with crizotinib-refractory anaplastic lymphoma kinase-positive non-small-cell lung can- cer : a randomized, multicenter phase II trial. J Clin Oncol 35, 2490-2498. ∞ Ganesan AP et al. ( incl. Garrido-Martin EM ) ( 2017 ). Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer. Nature Immunology 18, 940-950. ∞ Lamarca A et al. ( incl. Garcia-Carbonero R ) ( 2017 ). Design and validation of the GI- NEC score to prognosticate overall survival in patients with high-grade gastrointes- tinal neuroendocrine carcinomas. J Natl Cancer Inst 109, doi : 10.1093/jnci/djw277. ∞ García-Carbonero R, van Cutsem E, Rivera F, Jassem J, Gore I Jr, Tebbutt N, Braiteh F, Argiles G, Wainberg ZA, Funke R, An- derson M, McCall B, Stroh M, Wakshull E, Hegde P, Ye W, Chen D, Chang I, Rhee I, Hurwitz H ( 2017 ). Randomized phase II trial of Parsatuzumab ( Anti-EGFL7 ) or placebo in combination with FOLFOX and Bevacizumab for first-line metastatic colorectal cancer. Oncologist 22, 375-e30. ∞ Garcia-Carbonero R, Rinke A, Valle JW, Fazio N, Caplin M, Gorbounova V, O Connor J, Eriksson B, Sorbye H, Kulke M, Chen J, Falkerby J, Costa F, de Herder W, Lombard-Bohas C, Pavel M ( 2017 ). ENETS consensus guidelines for the standards of care in neuroendocrine neoplasms. Systemic therapy 2 : chemotherapy. An- tibes consensus conference participants. Neuroendocrinology 105, 281-294. ∞ Garcia-Carbonero R, Salazar R, Duran I, Osman-Garcia I, Paz-Ares L, Bozada JM, Boni V, Blanc C, Seymour L, Beadle J, Alvis S, Champion B, Calvo E, Fisher K ( 2017 ). Phase 1 study of intravenous administration of the chimeric adenovirus enadenotucirev in patients undergoing primary tumor resection. J Immunother Cancer 5, 71. ∞ PATENTS AT OTHER INSTITUTIONS ∞ Quintanal A, Ferrer I, Molina S, Carnero A, Paz-Ares L ( 2017 ). Combination of anti-EGFR and anti-FGFR drugs in lung cancer treatment. Spanish Patent Appli- cation 201730928. ∞ Quintanal A, Ferrer I, Molina S, Carnero A, Paz-Ares L ( 2017 ). ( 2017 ). FGFR inhibitors in lung cancer treatment. Spanish Patent Application 201730929. ∞ AWARDS AND RECOGNITION ∞ The Lilly Foundation Award for Clinical Biomedical Research 2017, Spain. ∞ Ramiro Carregal- La Rosaleda Foundation International Prize for Oncology Research 2017, Spain. ANNUAL REPORT 2017 138 TRANSLATIONAL RESEARCH BIOBANK OVERVIEW The CNIO Biobank is a cross-service platform for CNIO researchers, as well as the general scientific community, and is geared towards the promotion of biomedical research in cancer and related diseases. The CNIO Biobank facilitates access to human samples for researchers, ensuring that both the acquisition and use of human samples complies with all the legal and ethical principles that protect donors ’ rights. The CNIO Biobank is a ‘ biobank for biomedical research purposes ’, as defined by the Spanish Law 14/2007 on Biomedical Research and the Royal Decree RD 1716/2011. It is therefore defined as a public, non-profit organisation that hosts several collections of human biological samples for biomedical research. The biobank is organised as a technical unit with strict criteria for quality, order and purpose, regardless of whether or not it hosts other collections of biological samples for different purposes. Samples and their associated information are managed in compliance with Spanish legislation and international recommendations ; all of this is consistent with quality criteria for sample collection and its subsequent management. The Biobank has been authorised by the Health Authorities of the Comunidad Autónoma de Madrid – in accordance with the regulation established by RD1716/2011 – and is registered in the National Registry of Biobanks with reference B.000848. Manuel M. Morente Director Technicians Nuria Ajenjo ( TS )*, Inmaculada Almenara ( until October ), M. Jesús Artiga ( TS ), Francisco De Luna ( TS ) *Titulado Superior ( Advanced Degree ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 139 CLINICAL RESEARCH PROGRAMME | bIObANK RESEARCH HIGHLIGHTS Biobanking ɗ Collection, management, manipulation and custody of human biological samples and associated documentation, in accordance with the legal framework for biobanking. ɗ Transfer of samples and clinical biomedical information to research projects, under the approval of the corresponding scientific and ethical committees. Management of other collections ɗ Custody service of collections of biological samples and/or information related to biomedical research as promoted by the CNIO or other external research groups. ɗ Coordination of sample collections in multicentre studies. ɗ Processing of products derived from human samples for research ( tissue arrays, DNA, RNA, etc.). ɗ High-resolution slide scanning. ɗ Researchers who want to deposit their collections at the CNIO-Biobank facilities, or who wish to request samples, must sign an MTA ( Material Transfer Agreement ) that specifies the terms and conditions under which the Biobank can take the samples and data into custody, or transfer samples to researchers. Ethico-legal advice for CNIO researchers regarding the use of human samples in biomedical research ɗ Technical, scientific and ethical advice regarding the collection, storage and management of human samples used for biomedical research, as well as in regards to the creation and management of new collections that are beyond the Biobank’s scope. Other services ɗ Collaboration with CNIO researchers in human pathology. ɗ Collaboration in diagnostic activities as specialists in human pathology. During 2017, the CNIO-Biobank has supported 10 tissue requests from scientific research projects, independently of other services, corresponding to 650 cases distributed in 16 transferred tissue microarrays. Additionally, as the Spanish National Biobank Network Coordination Office, we have managed 30 tissue requests for scientific research projects of high complexity, plus 11 other requests for sample availability and/or documental support. We have also collaborated with the Familial Cancer Unit of the CNIO’s Human Cancer Genetics Programme in the acquisition of 49 clinical cases, as well as in the analysis and diagnosis of 64 new cases. The mean impact factor of the 6 published articles in 2017, for which our Unit provided support, was 9.618. The CNIO Biobank participates in and coordinates the Spanish National Biobank Network. This nationwide platform of services integrates 52 institutions ( www.redbiobancos.es ) and is an initiative of the Instituto de Salud Carlos III ( ISCIII ). Finally, the Unit has spearheaded many activities in the national and international biobanking scene through its participation and leadership in numerous forums, working groups and national and international scientific societies. These include the European, Middle Eastern and African Society for Biopreservation and Biobanking ( ESBB ), the International Society for Biological and Environmental Repositories ( ISBER ), international think tanks such as the Marble Arch International Working Group on Clinical Biobanking, BC-Net IARC-WHO/NCI initiative, and others. s ∞ PUBLICATION ∞ Doucet M, Becker KF, Björkman J, Bonnet J, Clément B, Daidone MG, Duyckaerts C, Erb G, Haslacher H, Hofman P, Huppertz B, Junot C, Lundeberg J, Metspalu A, Lavitrano M, Litton JE, Moore HM, Mor- ente M, Naimi BY, Oelmueller U, Ollier B, Parodi B, Ruan L, Stanta G, Turano P, Vaught J, Watson P, Wichmann HE, Yuille M, Zaomi M, Zatloukal K, Dagher G ( 2017 ). Quality matters : 2016 annual conference of the National Infrastructures for Biobanking. Biopreserv Biobank 15, 270-276. ∞ AWARDS AND RECOGNITION ∞ Member, Evaluation Panel ‘ Cohorts Programme ’, Agence Nationale de la Recherche ( ANR ), France. ∞ Member, Nominating Committee, the Euro- pean, Middle Eastern & African Society for Biopreservation and Biobanking ( ESBB ). ∞ Member, Scientific and Organising Com- mittee, VIII Congreso Nacional de Bioban- cos, Cartagena. ∞ Course Director, ‘ Forum de Biobancos pediátricos ’, Hospital Universitari Sant Joan de Déu ( Barcelona ) & Universitat de Barcelona. Figure Formalin-Fixed Paraffin-Embedded ( FFPE ) archives. ANNUAL REPORT 2017 140 Innovation SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 141 Biotechnology Programme 144 Genomics Core Unit 146 Transgenic Mice Core Unit 148 Monoclonal Antibodies Core Unit 150 Molecular Imaging Core Unit 152 Flow Cytometry Core Unit 154 Confocal Microscopy Core Unit 156 Proteomics Core Unit 158 Histopathology Core Unit 160 Animal Facility 162 Experimental Therapeutics Programme 164 Medicinal Chemistry Section 166 Biology Section 170 CNIO - Lilly Cell Signalling Therapies Section 174 CNIO - Lilly Epigenetics Section 176 Technology Transfer and Valorisation Office 178 ANNUAL REPORT 2017 142 ÓSCAR FERNÁNDEZ-CAPETILLO Director of Innovation SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 143 “ Innovation has become an intrinsic part of the CNIO culture. Besides from academic publications, our scientists are also actively involved in translating their discoveries back into society.” The so-called ‘Translational Research ’ only grows on the shoulders of excellent discoveries. At CNIO, our scientists cover a wide spectrum of topics related to cancer research ; these include computational and structural biology, drug development, molecular and cellular biology, animal models, human genetics and clinical groups that are in close contact with cancer patients. Each of these activities can lead to know-how and/or goods that could be of interest beyond the boundaries of academic research, and it is the job of the Direction of Innovation to help our scientists in this transition. These exercises are not only necessary to translate our discoveries, but they also return back to the CNIO in the form of royalties that help the CNIO, its groups and the inventors themselves. Examples of these activities in 2017 include an Agreement with PharmaMar to provide CNIO scientists access to a library of their natural compounds for usage in our Drug Screening projects ; the licensing of Nicotinamide Riboside to Stemtek Therapeutics for its development as a cancer preventive and/or therapeutic agent, based on discoveries from the Group of Nabil Djouder ; the creation of Senolytic Therapeutics, a company oriented towards the elimination of senescent cells, based on work from Manuel Serrano ; and the first clinical trial in which cancer patients have been treated with a therapy developed at CNIO by Marisol Soengas’ Group. Besides from these achievements, we also kept a healthy level of activity in other areas related to Innovation, such as in establishing contracts with the Industry for the co-development of cancer-related projects, or in the licensing of antibodies that continues to be an important source of funding for CNIO. ANNUAL REPORT 2017 144 INNOVATION BIOTECHNOLOGY PROGRAMME FERNANDO PELÁEZ Programme Director SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 145 BIOTECHNOLOGy PROGRAMME The main mission of the Biotechnology Programme is to provide expert technical support and advice to CNIO Research Groups in a number of disciplines and technologies widely used in biomedical research, as well as to implement and develop state-of-the-art biotechnological tools and reagents for cancer research. The Programme is currently composed of nine Core Units covering major areas in Biotechnology, namely Genomics, Proteomics, Monoclonal Antibodies, Histopathology, Flow Cytometry, Confocal Microscopy, Molecular Imaging and Transgenic Mice, as well as an Animal Facility. Although the Core Units mainly focus on meeting the internal demand and collaborating with the CNIO Research Groups, they also provide support and collaborate with groups from other public institutions, as well as with private companies. Faithful to its mission, a number of different technological innovations have been explored or implemented by the Programme’s Core Units during the past year, often in collaboration with CNIO Groups. This year, the CNIO made a significant investment in upgrading the mass spectrometry ( MS ) technology available at the Proteomics Unit ; the Centre acquired two modern MS instruments that will facilitate the performance of proteomics studies by improving sensitivity and throughput. A significant proportion of the activities run by our Core Units are related to animal models. In line with our commitment to maintaining the highest possible standards related to animal research issues, the CNIO has this year joined the ‘Agreement on Openness on Animal Research ’ promoted by the Federation of Scientific Societies in Spain ( COSCE ) that was launched in September 2016. An institutional statement on the use of research animals is available on the CNIO website. This year, the Programme and its Core Units were actively involved in several networking activities. Two of us were elected as members of the Executive Committee of the Core Technologies for Life Sciences ( CTLS ), a new scientific association aiming to create a network of scientists working at core facilities in Europe with the goal of addressing issues that are common to these facilities. In addition, the Unit Heads were very active in participating in other networks and scientific societies from their corresponding fields. Also, as an indication of our high commitment to training, education and outreach, the Programme has been deeply involved with the organisation of courses, workshops, visits from students, and specialised meetings. We collaborated with the ‘ CNIO and the city ’ project, organised by the Communications Department with funding from the FECYT ( Fundación Española para la Ciencia y la Tecnología ), organising a course for secondary school teachers that was highly successful and will be run again next year. Moreover, members of our staff participated in an increasing number of Masters and other training activities hosted at the CNIO and elsewhere. This year, the Core Units were particularly active in attracting funding from external sources through activities related to innovation, including several contracts and agreements with private companies and public institutions, based on the technologies mastered by several of our Core Units. Also, the royalties derived from the sales of the antibodies produced by the Monoclonal Antibodies Unit have grown by about 5% over the previous year, reaching a new historical maximum. Last but not least, 2017 has again been a very productive year, scientifically, for the Programme. The contribution of the Units to the overall scientific performance of the CNIO is reflected in about 20 publications, many of them appearing in top journals. “ The access to cutting-edge technologies and associated expertise is nowadays essential for accomplishing the ambitious goals dictated by our mission of performing biomedical research of excellence.” ANNUAL REPORT 2017 146 INNOVATION GENOMICS CORE UNIT OVERVIEW The Genomics Unit was established in 2000 for the purpose of providing the cutting-edge technology and services required by the CNIO research community. With the capacity to even interrogate whole genomes in a single assay, technologies such as high-density DNA microarrays and next-generation sequencing ( NGS ) reveal the genetic diversity of cancer and help to dissect molecular processes. Structural features, such as mutation repertoires, DNA-binding of protein factors, variations in chromatin structure/folding, as well as functional states such as transcriptomic profiles and changes ( mRNA, miRNA ) are being elucidated with these technologies in order to uncover basic mechanisms, therapeutic targets and prognostic biomarkers. We offer a broad range of products and services, including microarray whole genome gene expression, array comparative genomic hybridisation ( aCGH ), NGS library preparation for exome sequencing, ChIPseq and RNAseq analysis, transgenic mouse genotyping, human cell line authentication and capillary DNA sequencing. Orlando Domínguez Core Unit Head Technicians Purificación Arribas, Antonio Íñigo ( since May ), Guadalupe Luengo, “ The Genomics Unit, with its genetic and genomic services, contributes to the understanding of the molecular processes of cancer by helping CNIO scientists in a large number of basic and applied research projects.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 147 BIOTECHNOLOGy PROGRAMME | GENOmICS CORE UNIT RESEARCH HIGHLIGHTS The Genomics Unit contributes to the advancement of research projects conducted by multiple CNIO Research Groups. We provide services at 2 levels of complexity. The genomic wide level is addressed by both deep-sequencing ( NGS ) and microarray technologies. NGS permits a variety of applications, such as whole genome or whole exome tumour sequencing, transcriptome analyses by RNAseq, or location of interacting protein factors on chromosomal DNA by ChIPseq. On the other hand, DNA microarray technology is a powerful platform for transcriptome determinations or for the detection of chromosomal copy number aberrations. Its use, however, has diminished over the last few years in favour of NGS. This year, the demand for NGS services has been stable and the number of samples processed has been similar to those processed in 2016. At the single locus level other services are provided. A traditional DNA capillary sequencing service, based on a 3730xl DNA Analyzer from Applied Biosystems, is being used to find and confirm mutations in candidate genes, or for the verification of cloned genes or inserts. The Unit also provides a transgenic mouse genotyping service, based on allele- specific quantitative PCR for a quick and efficient turnaround time. The catalogue of available tests for genetic modifications has expanded, upon demand, from 30 to close to 90 in 2017. The genotyping service has seen an increase in demand in 2017 that nearly doubled that of former years. An extended contribution, in the framework of a collaborator’s project, has led to a report being published with the co-authorship of some of the Unit’s members. A novel NGS analysis pipeline that facilitates forward genetic screenings on haploid mammalian cell lines has been described. The new RNA sequencing-based method, named TrapSeq, maps insertions that lead to productive trapping by recognising chimeric mRNAs containing gene-trap sequences spliced to an exon. The method provides a fast and cost-effective way that, not only identifies the insertion site but also, reveals its impact on the expression of the trapped gene ( Mayor-Ruiz et al.). s Figure This Unit is often requested to determine the insertion site of transgenes. Here, the gene coding for Cdc6, a key protein for DNA replication previously thought to have oncogenic potential, was inserted into the mouse genome to study the effect of its deregulated function in mammalian tissues ( Búa S et al., Cell Cycle, 2015 ). The transgene was found to be inserted into an endogenous gene, as it often happens ; in this case, the Sec22a locus. Jorge Monsech, Ana Belén Moreno ( until November ) ( PEJ )*, M. Concepción Rodríguez ( since May ), Ángeles Rubio, Delfina Sanguino *Plan de Empleo Joven ( Youth Employment Plan ) ∞ PUBLICATION ∞ Mayor-Ruiz C, Dominguez O, Fernan- dez-Capetillo O ( 2017 ). TrapSeq : an RNA sequencing-based pipeline for the identi- fication of gene-trap insertions in mam- malian cells. J Mol Biol 429, 2780-2789. ANNUAL REPORT 2017 148 INNOVATION Sagrario Ortega Core Unit Head Graduate Student Aleida Pujol Technicians Estefania Ayala, M. Carmen Gómez, Jaime A. Muñoz ( TS )*, Lucía M. OVERVIEW The laboratory mouse is the experimental model of choice for genetic studies and preclinical drug development in cancer. The Transgenic Mice Unit is dedicated to the genetic edition of the mouse germ line and to the generation of genetically modified mouse strains. Hundreds of mouse genes have been specifically modified at our Unit. In many cases, these modifications reproduce the genetic alterations found in human cancers and are introduced in the mouse to generate preclinical models of the disease, thereby contributing to the development of more efficient targeted therapies. In other instances, genetically modified mice are created for testing hypothesis in vivo, in a physiological context, with the aim of gaining new insight into the molecular mechanisms responsible for converting a normal cell into a malignant cell or for making a tumour grow and expand and subsequently invade other organs and become deadly. Cancer is an extremely complex disease that cannot be sufficiently studied in a tissue culture plate. The generation of genetically modified mice is one of the basic pillars on which cancer research at the CNIO is based. TRANSGENIC MICE CORE UNIT “ A reporter mouse model, designed and created by the Transgenic Mice Unit to visualise tumour lymphangiogenesis by whole body imaging, has been crucial for elucidating mechanisms of melanoma dissemination and metastasis : Nature 546, 676 ( 2017 ).” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 149 BIOTECHNOLOGy PROGRAMME | TRANSGENIC mICE CORE UNIT RESEARCH HIGHLIGHTS The Transgenic Mice Unit has designed and created several mouse models to study the lymphatic system and its implication in tumour dissemination and metastasis. One of these models is a reporter strain in which the process of lymphatic vessel growth, or lymphangiogenesis, can be monitored, in vivo, by whole body imaging. In this knockin mouse model the fluorescent/ luminescent EGFP-Luciferase fusion reporter is expressed under the endogenous transcriptional control of the Vegfr3 gene, a classical marker expressed predominantly, and almost exclusively, in lymphatic endothelium. This genetically modified strain enables tracing and quantification of lymphangiogenesis associated to tumour growth and dissemination. The response of the lymph nodes and lymphatic vessels to metastatic tumours that spread mostly through the lymphatic network leads to an activation of Vegfr3 that can be monitored in vivo in this strain ( Martínez-Corral, Olmeda et al., Proc Natl Acad Sci USA 17, 2012 ). We have developed this reporter strain both in an immune- competent C57Bl6 background and also in an immune-suppressed nude background. The nude background allows the generation of xenograft models in combination with our lymphoreporter knockin allele. In collaboration with the group of Marisol Soengas at the CNIO, our lymphoreporter mouse model has been applied to study mechanisms of melanoma metastasis leading to the discovery of Midkine as a novel potential therapeutic target for melanoma ( Olmeda et al., Nature 546, 2017 ). Our reporter mouse model is a powerful tool for studying lymphatic vessels in physiological and pathological contexts and, combined with different mouse models of cancer such as genetically modified strains, xenograft models, etc., constitutes a unique platform for drug discovery and preclinical assays, not only in cancer and metastasis but also in many other areas such as inflammation or cardiovascular diseases ( FIGURE ). s Pérez De Ayala ( until November ) ( PEJ-L ) **, Patricia Prieto ( TS ) *, Pierfrancesco Vargiu ( TS ) * *Titulado Superior ( Advanced Degree ) **Plan de Empleo Joven-Licenciado ( Youth Employment Plan-Graduate ) Figure Imaging of lymphatic vessels and lymphangiogenesis in the Vegfr3_GFPLuc reporter mouse. (  A ) Schematic representation of the Vegfr3_EGFPLuc reporter allele. ( B ) Skin lymphatic vessels in an E13.5 embryo ( GFP direct fluorescence emission ). ( C, D and E ) Bioluminescence imaging of tumour-, inflammation- and wound healing- induced lymphangiogenesis, respectively. ∞ PUBLICATIONS ∞ Olmeda D, Cerezo-Wallis D, Riveiro-Falk- enbach E, Pennacchi PC, Contreras-Alcal- de M, Ibarz N, Cifdaloz M, Catena X, Calvo TG, Cañón E, Alonso-Curbelo D, Suarez J, Osterloh L, Graña O, Mulero F, Megías D, Cañamero M, Martínez-Torrecuadrada JL, Mondal C, Di Martino J, Lora D, Mar- tinez-Corral I, Bravo-Cordero JJ, Muñoz J, Puig S, Ortiz-Romero P, Rodriguez-Peralto JL, Ortega S, Soengas MS ( 2017 ). Whole- body imaging of lymphovascular niches identifies pre-metastatic roles of midkine. Nature 546, 676-680. ∞ Olbrich T, Mayor-Ruiz C, Vega-Sendino M, Gomez C, Ortega S, Ruiz S, Fernan- dez-Capetillo O ( 2017 ). A p53-dependent response limits the viability of mammalian haploid cells. Proc Natl Acad Sci USA 114, 9367-9372. ∞ Muñoz S, Búa S, Rodríguez-Acebes S, Megías D, Ortega S, de Martino A, Méndez J ( 2017 ). In vivo DNA re-replication elicits lethal tissue dysplasias. Cell Rep 19, 928-938. ∞ Chirivella L, Kirstein M, Ferrón SR, Domin- go-Muelas A, Durupt FC, Acosta-Uman- zor C, Cano-Jaimez M, Pérez-Sánchez F, Barbacid M, Ortega S, Burks DJ, Fariñas I ( 2017 ). Cyclin-dependent kinase 4 reg- ulates adult neural stem cell proliferation and differentiation in response to insulin. Stem Cells 35, 2403-2416. ANNUAL REPORT 2017 150 INNOVATION MONOCLONAL ANTIBODIES CORE UNIT OVERVIEW Due to their high specificity and selectivity, monoclonal antibodies ( mAbs ) are exquisite tools that enable researchers to address basic questions in biology ; they are currently one of the most important classes of reagents used in biomedicine. The Monoclonal Antibodies Unit provides CNIO Research Groups with an “ à la carte ” generation of mAbs. We are highly specialised in the production of mouse and rat monoclonal antibodies. The Unit also offers mAb characterisation and validation, medium- scale mAb production and a service of Mycoplasma testing for the cell culture facility. Giovanna Roncador Core Unit Head Technicians Álvaro García ( until November ) ( PEJ ) *, Sherezade Jiménez ( until September ), Lorena Maestre ( TS ) **, Ana I. Reyes ( until October ) *Plan de Empleo Joven ( Youth Employment Plan ) **Titulado Superior ( Advanced Degree ) “ The Unit is highly specialised in mAbs production and characterisation, providing CNIO researchers with reliable and well- validated reagents that give added value to their research projects.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 151 BIOTECHNOLOGy PROGRAMME | mONOCLONAL ANTIbOdIES CORE UNIT RESEARCH HIGHLIGHTS During the last 17 years, the Monoclonal Antibodies Unit has generated a large number of mAbs against more than 135 different antigens, mostly targeting molecules for which mAbs are not commercially available. Many of those mAbs have been licensed to external companies, generating royalties that represent an important source of revenue for the CNIO. Each year we prepare and update a detailed CNIO mAbs catalogue, which contains the datasheets of more than 80 thoroughly validated high-quality mAbs ( accessible at http ://www.cnio. es/ing/servicios/anticuerpos/default.aspx ). Research activities In collaboration with Dr Miguel Ángel Piris, Associate Medical Chief of the Pathology Service at the Fundación Jiménez Díaz, we have produced and characterised a new monoclonal antibody against the TOX protein. TOX ( Thymocyte Selection-Associated High- Mobility Group box ) is a member of the family of HMG box proteins and is involved in the regulation of gene expression. This protein is present in many subsets of immune cells, suggesting that it plays significant roles in the immune system, including the development of CD4 T cells and NK cells, as well as lymph node organogenesis. We have investigated the expression of TOX in normal and neoplastic lymphoid tissue using a novel murine monoclonal antibody. Using immunohistochemistry techniques, we found that the TOX mAb may help in the identification of neoplastic B and T cells and may be used to achieve a better understanding of the pathogenic role of TOX in inflammatory and malignant diseases. EuroMAbNet and its commitment with Ab validation In 2008, in collaboration with Oxford University, we founded EuroMAbNet ( www.euromabnet.com ), a non-profit organisation that includes internationally distinguished multidisciplinary academic laboratories focused on the generation and validation of mAbs. The use of poorly characterised reagents is of major concern to the scientific community because of the perpetuation of serious scientific misconceptions that inevitably compromise the advancement of science. To help address mAbs unreliability, EuroMAbNet is strongly committed to improving the education and training of junior scientists. For this reason, we organise annual Antibody Validation Workshops ( https ://www. euromabnet.com/meeting/) to provide practical guidelines about the main principles underlying antibody validation ( https ://www. euromabnet.com/guidelines/). These workshops outline the problems generated by the use of poorly validated reagents and are designed to educate researchers, helping them to minimise the purchase of ineffective Abs, understand when additional validation is necessary, and to have an understanding of the information needed when publishing antibody-based data. s ∞ PUBLICATIONS ∞ Manso R, Roncador G, Montes-Moreno S, Rojo F, Pérez-Sáenz MÁ, Mollejo M, Menárguez J, Carvajal N, García-Cosio M, Llamas P, Piris MA, Rodríguez-Pinilla SM ( 2017 ). p-MAPK1 expression associated with poor prognosis in angioimmuno- blastic T-cell lymphoma patients. Br J Haematol 176, 661-664. ∞ Tavera-Tapia A, Pérez-Cabornero L, Macías JA, Ceballos MI, Roncador G, de la Hoya M, Barroso A, Felipe-Ponce V, Serrano-Blanch R, Hinojo C, Miramar-Gallart MD, Urioste M, Caldés T, Santillan-Garzón S, Benitez J, Osorio A ( 2017 ). Almost 2% of Spanish breast cancer families are associated to germline pathogenic mutations in the ATM gene. Breast Cancer Res Treat 161, 597-604. ∞ Carreras J, Kikuti YY, Beà S, Miyaoka M, Hiraiwa S, Ikoma H, Nagao R, Tomita S, Martin-Garcia D, Salaverria I, Sato A, Ichiki A, Roncador G, Garcia JF, Ando K, Campo E, Nakamura N ( 2017 ). Clinicopathological characteristics and genomic profile of primary sinonasal tract diffuse large B cell lymphoma ( DLBCL ) reveals gain at 1q31 and RGS1 encoding protein ; high RGS1 immunohistochemical expression associates with poor overall survival in DLBCL not otherwise specified ( NOS ). Histopathology 70, 595-621. ∞ Kunder CA, Roncador G, Advani RH, Gual- co G, Bacchi CE, Sabile JM, Lossos IS, Nie K, Tibshirani RJ, Green MR, Alizadeh AA, Natkunam Y ( 2017 ). KLHL6 is preferen- tially expressed in germinal center-derived B-cell lymphomas. Am J Clin Pathol 148, 465-476. Figure Immunohistochemistry of several mAbs produced in the Monoclonal antibodies Unit. ANNUAL REPORT 2017 152 INNOVATION MOLECULAR IMAGING CORE UNIT OVERVIEW Molecular Imaging ( MI ) enables the visualisation of cellular function and the follow-up of molecular processes in living organisms without perturbing them. Molecular imaging offers significant advantages to the scientist over traditional research paradigms. While traditional studies of tumour response to a therapeutic agent involve a large cohort of animals analysed at multiple time points, molecular imaging allows characterisation of tumour development and response to a therapy within the same small set of animals imaged longitudinally at multiple time points, thereby reducing the number of mice and also increasing the statistical power of the study because each animal serves as its own control. Other advantages of molecular imaging procedures include the ability to interrogate the whole body, and to visualise the molecular target of interest in 3-dimensional space. Finally, Molecular Imaging is becoming a key bridging technology for the translation of experimental preclinical findings into the clinical environment. Francisca Mulero Core Unit Head Technicians Tatiana Álvarez, Guillermo Garaulet ( TS )*, Silvia Leal, Cristina Penalba ( PEJ-L ) **, Elka Jesarela San Martín, Gloria Visdominé “ Molecular imaging is rapidly growing, has tremendous potential to elucidate biological processes and pathways, and is able to translate scientific discoveries into the clinical setting.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 153 BIOTECHNOLOGy PROGRAMME | mOLECULAR ImAGING CORE UNIT RESEARCH HIGHLIGHTS The Molecular Imaging Unit provides CNIO researchers with state-of-the-art molecular imaging equipment and human resources in order to guarantee the highest quality studies, to develop and update protocols and imaging techniques that serve to optimise visualisation of tumours in both the preclinical and clinical fields, and also to assess and advise researchers on the best-suited imaging modality for their research projects. We continue to test and incorporate new applications to the ImmunoPET strategy, combining the high specificity of antibodies with the high sensitivity of PET imaging ; this year, we focused on the detection of pancreatic ductal adenocarcinoma ( PDAC ). In addition to conducting all the conventional tumour models follow-up − via different techniques such as Positron Emission Tomography-Computed Tomography ( PET-CT ), CT, and ultrasound imaging – we, this year, also contributed to the characterisation of metabolic models, in collaboration with the Growth Factors, Nutrients and Cancer Group. Using PET-CT, we determined the distribution of brown adipose tissue ( BAT ) and white adipose tissue ( WAT ) on body composition in mice, taking advantage of the  18F-FDG avidity of high metabolic tissues and using the CT to discriminate different densities between WAT and BAT ( FIGURE ). We are actively involved with the mVision Foundation − created by the international consortium devoted to imaging research ‘ m+visión ’, led by MIT ( The Massachusetts Institute of Technology ) and the Comunidad de Madrid – in order to further develop the techniques that were already put in place by the Programme. The Unit also participates in projects with national companies and research groups in order to test and develop new probes for ImmunoPET. s *Titulado Superior ( Advanced Degree ) **Plan de Empleo Joven-Licenciado ( Youth Employment Plan-Graduate ) ( until December ) ∞ PUBLICATIONS ∞ Olmeda D, Cerezo-Wallis D, Riveiro-Falk- enbach E, Pennacchi PC, Contreras-Alcal- de M, Ibarz N, Cifdaloz M, Catena X, Calvo TG, Cañón E, Alonso-Curbelo D, Suarez J, Osterloh L, Graña O, Mulero F, Megías D, Cañamero M, Martínez-Torrecuadrada JL, Mondal C, Di Martino J, Lora D, Mar- tinez-Corral I, Bravo-Cordero JJ, Muñoz J, Puig S, Ortiz-Romero P, Rodriguez-Peralto JL, Ortega S, Soengas MS ( 2017 ). Whole- body imaging of lymphovascular niches identifies pre-metastatic roles of midkine. Nature 546, 676-680. ∞ de Cárcer G, Wachowicz P, Martínez-Martín- ez S, Oller J, Méndez-Barbero N, Escobar B, González-Loyola A, Takaki T, El Bakkali A, Cámara JA, Jiménez-Borreguero LJ, Bustelo XR, Cañamero M, Mulero F, de Los Ángeles Sevilla M, Montero MJ, Redondo JM, Malumbres M ( 2017 ). Plk1 regulates contraction of postmitotic smooth muscle cells and is required for vascular homeo- stasis. Nat Med 23, 964-974. ∞ Mancheño-Corvo P, Lopez-Santalla M, Menta R, DelaRosa O, Mulero F, Del Rio B, Ramirez C, Büscher D, Bueren JA, Lopez-Belmonte J, Dalemans W, Garin MI, Lombardo E ( 2017 ). Intralymphatic administration of adipose mesenchymal stem cells reduces the se- verity of collagen-induced experimental arthritis. Front Immunol 8, 462. ∞ López-Herradón A, Fujikawa R, Gómez- Marín M, Stedile-Lovatel JP, Mulero F, Ar- dura JA, Ruiz P, Muñoz I, Esbrit P, Mahíl- lo-Fernández I, Ortega-de Mues A ( 2017 ). Impact of chiropractic manipulation on bone and skeletal muscle of ovariecto- mized rats. Calcif Tissue Int 101, 519-529. Book chapter ∞ Shaikh FA, Mulero F, Mohiuddin SA ( 2017 ). Molecular imaging in genomic medicine. In : eLS. John Wiley & Sons, Ltd : Chichester. DOI : 10.1002/9780470015902.a0027219. ∞ AWARDS AND RECOGNITION ∞ Advisory Board Chair, Fundación mVi- sion, Spain. ∞ Member of Spanish PET Group, Spanish Society of Nuclear Medicine and Molecular Imaging ( SEMNIM ). ∞ Project evaluator of the Junta de Andalu- cia, Investigación, Desarrollo e Innovación Biomédica y en Ciencias de la Salud, Spain. Figure Coronal and sagittal projections of PET-CT scans representing  18F-FDG uptake due to higher metabolism in BAT compared to WAT in perigonadal and inguinal fat pads. The square in the middle panel shows the 3D rendering of abdominal WAT ( green, inguinal fat ; purple, perigonadal fat ). ANNUAL REPORT 2017 154 INNOVATION FLOW CYTOMETRY CORE UNIT OVERVIEW Flow Cytometry is a very useful tool in the oncology field. It enables multiparametric analysis for the identification, quantification and isolation of defined subpopulations of cells, based on the levels of expression of fluorescent markers and their relation to each other. Our aim is to provide CNIO groups with the necessary technical and scientific advice regarding the use of flow cytometric technologies, collaborating with them in the design, acquisition, data analysis and interpretation. We count with 4 analysers and 3 high-speed cell sorters, containing different configurations of lasers and detectors, to cater for all our users ’ needs. We also have an automated magnetic bead separation system ( AutoMACS ) and 2 automated cell counters. Analysers are available to users upon appropriate training and cell sorters are operated by the Unit staff. Our sorters can separate up to 4- or 6- defined populations at a time, including single cell cloning. We can accept human samples to be sorted according to Biosafety regulations. Lola Martínez Core Unit Head Technicians Ultan P. Cronin ( TS )*, Elena Garrido ( until June ) ( TS )*, Tania López ( PEJ-L )**, Miguel Ángel Sánchez ( TS )* *Titulado Superior ( Advanced Degree ) **Plan de Empleo Joven-Licenciado ( Youth Employment Plan-Graduate ) ( until December ) “ In order to understand cancer, it is becoming increasingly relevant to have information at the single cell level. At the Unit we are able to sort one single cell into 96 or 384 PCR plates for further genomic studies.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 155 BIOTECHNOLOGy PROGRAMME | FLOw CyTOmETRy CORE UNIT RESEARCH HIGHLIGHTS We provide state-of-the-art equipment and software packages in flow cytometry and collaborate with CNIO investigators in setting up and optimising flow cytometry techniques of their interest. Some of the applications developed and validated at our Unit are : ɗ Cell proliferation studies ( CFSE, Cell Trace Violet, BrdU or EdU, DNA content, etc.). ɗ Apoptosis studies ( Annexin V, Mitochondrial Membrane Potential, Caspase 3, etc.). ɗ Multicolour Immunophenotyping panels ( B and T cell development, Tregs, Inflammation, etc.). ɗ Functional Assays ( side population detection, Ca 2+ flux, intracellular pH, etc.). ɗ Cytometric Bead Arrays to measure several cytokines from cell extracts and plasma. ɗ Platelet studies. ɗ Extracellular vesicle detection ( microvesicles and exosomes ). ɗ Single cell sorting for RNA sequencing. We have further developed our multicolour panels for the characterisation of the immune response by incorporating the new generation of Brilliant UV dyes from samples of haematopoietic tissues, pancreas, skin, liver, lung, as well as different tumour types. Modifications in our analytical and cell sorters have also been implemented to allow for this. These panels can still be combined with the detection of proliferation and cell death. In terms of our cell sorting capabilities, we included, at the end of the year, a MoFlo ASTRIOS in our portfolio of cell sorters. This cell sorter is equipped with 4 laser lines and 15 fluorescent detectors that enable the isolation of up to 6 different populations simultaneously. The optical configuration in the ASTRIOS will enable the usage of the new generation of Brilliant UV dyes. We also introduced, as part of our routine work, a successful calibration method for single cell deposition into 384 PCR plates. Throughout the year, we have also undertook lots of instrument testing in order to better characterise exosomes and microvesicles. s Figure Schematics Index sorting Figure. Panel (  A ) typical gating strategy of a primary sample stained with a combination of surface markers. Panel ( B ) index cell sorting schematics, a single file is generated for each sorted well so that information is retained regarding the cell sorted into the well ; heat maps based on the expression levels of the marker of interest can be generated. ∞ PUBLICATIONS ∞ Bakiri L, Hamacher R, Graña O, Guío-Car- rión A, Campos-Olivas R, Martínez L, Dienes HP, Thomsen MK, Hasenfuss SC, Wagner EF ( 2017 ). Liver carcinogenesis by FOS-dependent inflammation and cholesterol dysregulation. J Exp Med 214, 1387-1409. ∞ Sánchez-Luengo MA, Rovira M, Serrano M, Fernández-Marcos PJ, Martínez L ( 2017 ). Analysis of the advantages of cis reporters in optimized FACS-Gal. Cytometry A 91, 721-729. ∞ AWARDS AND RECOGNITION ∞ 2017 International Visitors Leadership Pro- gramme “ Hidden No More : Empowering Women Leaders in STEM ”, recognising women global leaders. US Department of State. ∞ Tania López Briones received the “ Best Student Poster Award ”, XV Congress of the Iberian Cytometry Society, Lisbon ( May 2017 ): How to reliably choose set- tings for optimal resolution in a multicolour flow experiment. ANNUAL REPORT 2017 156 INNOVATION CONFOCAL MICROSCOPY CORE UNIT OVERVIEW Optical microscopy has traditionally been an indispensable tool in cell biology studies. In fact, one of the main challenges in oncology research is the study of specific markers, expression patterns or individual cells in the tumour environment. The Confocal Microscopy Unit provides the CNIO Research Groups with all the standard methodologies as well as the latest advances in microscopy, offering access to state-of-the-art equipment and software packages related to confocal microscopy, including technical and scientific advice and support to the CNIO scientists. The Unit is also actively involved in developing, testing and implementing new microscopy technologies, tools and imaging applications that could be of interest to the Research Groups at the CNIO. Training activities are also an essential component of our mission. “ The Confocal Microscopy Unit is fully committed to the dissemination of advanced microscopy methodologies that are useful for cancer research and society at large ; we have organised courses, talks and visits, always with the aim of increasing our understanding of cell biology and the disorders of cells that lead to cancer.” Diego Megías Core Unit Head Technicians Jesús Gómez ( PEJ-L )*, Gadea Mata ( since November ) ( TS ) **, Manuel Pérez ( TS ) ** *Plan de Empleo Joven-Licenciado ( Youth Employment Plan-Graduate ) ( until December ) **Titulado Superior ( Advanced Degree ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 157 BIOTECHNOLOGy PROGRAMME | CONFOCAL mICROSCOPy CORE UNIT RESEARCH HIGHLIGHTS The Confocal Microscopy Unit is equipped with 3 laser scanning confocal systems ( Leica SP5 ) that incorporate UV and multiphoton excitation, as well as a white light laser and Hybrid Detection ; and 2 wide field systems ( a Deltavision 4D deconvolution station and a Leica DMRI6000 system, equipped with microinjection and microfluidics control ). All the microscopes are automated and equipped with incubators for live cell imaging. In addition, the Unit has implemented the use of high throughput technologies applied to confocal microscopy using two different systems : ɗ An Opera ( Perkin Elmer ) High Content Screening ( HCS ) system, which allows running HCS experiments on fixed and live cells in multiwell plates, and enables the monitoring of cell dynamics ( translocation, cell division, etc.) through the use of fluorescence. ɗ A Matrix Screening Application integrated into the SP5 confocal systems, enabling high throughput feeding of the instrument, not only in multiwell plates but also in tissue sections. These advances enable us to increase the level of information obtained from a sample as well as carry out the automated screening of cell behaviour under different treatments. The Confocal Microscopy Unit continues to dedicate significant efforts towards the development and implantation of High Content Screening technology at CNIO ; during this year, we carried out several medium size screenings with up to 5,000 compounds. In order to boost the output of our results, we reinforced our image and data analysis capabilities by hiring a dedicated person, thereby giving us the possibility of establishing more advanced routines. The Unit is promoting and helping with the latest sample preparation protocol development, bringing knowledge in tissue clearing as well as in expansion microscopy. Moreover, Microfluidics, used for live cell assays in perfusion chambers, has also experienced a great increase in performance and demand. The field of intra-vital microscopy is already available and we are now running several projects for studies of metastasis and skin alterations. s ∞ PUBLICATIONS ∞ Olmeda D, Cerezo-Wallis D, Riveiro-Falk- enbach E, Pennacchi PC, Contreras-Alcal- de M, Ibarz N, Cifdaloz M, Catena X, Calvo TG, Cañón E, Alonso-Curbelo D, Suarez J, Osterloh L, Graña O, Mulero F, Megías D, Cañamero M, Martínez-Torrecuadrada JL, Mondal C, Di Martino J, Lora D, Mar- tinez-Corral I, Bravo-Cordero JJ, Muñoz J, Puig S, Ortiz-Romero P, Rodriguez-Peralto JL, Ortega S, Soengas MS ( 2017 ). Whole- body imaging of lymphovascular niches identifies pre-metastatic roles of midkine. Nature 546, 676-680. ∞ Bejarano L, Schuhmacher AJ, Méndez-Per- tuz M, Megías M, Blanco-Aparicio C, Martínez S, Pastor J, Squatrito M, Blasco MA ( 2017 ). Inhibition of Trf1 telomere protein impairs tumor initiation and pro- gression in glioblastoma multiform mouse models and patient-derived xenografts. Cancer Cell 32, 590-607. ∞ Sánchez-Arévalo Lobo VJ, Fernández LC, Carrillo-de-Santa-Pau E, Richart L, Cobo I, Cendrowski J, Moreno U, Del Pozo N, Megías D, Bréant B, Wright CV, Magnuson M, Real FX. ( 2017 ). c-Myc downregulation is required for preacinar to acinar matu- ration and pancreatic homeostasis. Gut. PMID : 28159836. ∞ Cifdaloz M, Osterloh L, Graña O, Rivei- ro-Falkenbach E, Ximénez-Embún P, Muñoz J, Tejedo C, Calvo TG, Karras P, Olmeda D, Miñana B, Gómez-López G, Cañon E, Eyras E, Guo H, Kappes F, Or- tiz-Romero PL, Rodríguez-Peralto JL, Megías D, Valcárcel J, Soengas MS. ( 2017 ). Systems analysis identifies melanoma-en- riched pro-oncogenic networks controlled by the RNA binding protein CELF1. Nat Commun 8, 2249. ∞ Muñoz S, Búa S, Rodríguez-Acebes S, Megías D, Ortega S, de Martino A, Mén- dez J ( 2017 ). In Vivo DNA re-replication elicits lethal tissue dysplasias. Cell Rep 19, 928-938. ∞ Marión RM, López de Silanes I, Mosteiro L, Gamache B, Abad M, Guerra C, Megías D, Serrano M, Blasco MA. ( 2017 ). Common telomere changes during in vivo repro- gramming and early stages of tumorigen- esis. Stem Cell Rep 8, 460-475. ∞ Martín-Sánchez E, Mendaza S, Ulazia-Gar- mendia A, Monreal-Santesteban I, Blan- co-Luquin I, Córdoba A, Vicente-García F, Pérez-Janices N, Escors D, Megías D, López-Serra P, Esteller M, Illarramendi JJ, Guerrero-Setas D ( 2017 ). CHL1 hy- permethylation as a potential biomarker of poor prognosis in breast cancer. On- cotarget 8, 15789-15801. ∞ Amelian A, Wasilewska K, Megias D, Winn- icka K ( 2017 ). Application of standard cell cultures and 3D in vitro tissue models as an effective tool in drug design and development. Pharmacol Rep 69, 861-870. ∞ PATENT ∞ Postigo P.A. and Megías Vázquez D. ( 2017 ). Uso de un material para la fab- ricación de un cubreobjetos, un portam- uestras o un recipiente de cultivo celular. PCT/ES2017/070645. Figure The ‘  hidden bladder skeleton ’ image has been awarded in the Scientific International Immunofluorescence Contest from Abcam Company ( Catarina Santos, CNIO Epithelial Carcinogenesis Group ). ANNUAL REPORT 2017 158 INNOVATION PROTEOMICS CORE UNIT OVERVIEW Proteins are the molecular effectors of cells and catalyse almost all biological processes. The levels of protein abundance, together with their modification states and interactions, adapt dynamically to external or internal ( genetic ) stimuli and thus define the cell’s functional state and determine its phenotype. Mass spectrometry- based proteomics is the most powerful tool to study the proteome, providing fundamental information of basic biology. In addition, recent improvements in sensitivity and throughput now allow the analysis of larger cohorts of samples including biopsies, thus fully integrating proteomics into the clinical research toolbox. All these efforts have led to the provision of new insights into the molecular mechanisms underlying cancer development as well as the identification of novel biomarkers. “ The possibility to identify and profile secreted proteins, even in the exosomes, with mass spectrometry, enables the identification of novel biomarkers.” Javier Muñoz Core Unit Head Graduate Student Ana Martínez SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 159 BIOTECHNOLOGy PROGRAMME | PROTEOmICS CORE UNIT RESEARCH HIGHLIGHTS In 2017, the Unit introduced a new immuno-purification approach to profile lysine acetylation in cells and tissues ( Martinez-Val et al.). This method is being used to study the effects of several inhibitors against deacetylases and their effect in cancer. Furthermore, in collaboration with the Brain Metastasis Group, we are exploring ultra-sensitive proteomic strategies to analyse metastatic brain lesions obtained from micro-dissected tissues. In addition, we have conducted a large phosphoproteomic analysis to identify possible genes involved in certain platelet activation defects ( in collaboration with the Cell Division and Cancer Group ). Together with the Tumour Suppression Group, we are dissecting at the molecular level the transition of primed embryonic stem cells ( ESCs ) into the ground-state of pluripotency. The results of this project show that targeting the transcriptional regulator Mediator, shifts ESCs towards a state that significantly resembles that of naïve ESCs. On a different note, a lot of the evidence shows that the proteins secreted into the extracellular space, or even encapsulated in micro-vesicles such as exosomes, have important organotropic effects in cancer and most importantly in metastasis. Bearing this in mind, we are mining the secretomes of different types of samples in order to identify potential new biomarkers and molecular targets. Indeed, in collaboration with the Melanoma Group, we have identified the protein Midkine as a systemic inducer of neo-lymphangiogenesis, which defines the prognosis of melanoma patients ( Olmeda et al.). Finally, in collaboration with the Technical University of Dresden, we are performing several proteomic analyses on stomach organoids carrying different sets of cancer-inducing mutations in order to study their applicability as a novel platform for drug screening. s Technicians Fernando García ( TS ) *, Nuria Ibarz ( until October ) ( TS ) *, Ailyn Martínez ( until December ), M. Isabel Ruppen ( until June ) ( TS ) *, Pilar Ximénez de Embún ( TS ) *, Eduardo Zarzuela ( PEJ-L ) ** *Titulado Superior ( Advanced Degree ) **Plan de Empleo Joven-Licenciado ( Youth Employment Plan-Graduate ) ( until December ) ∞ PUBLICATIONS ∞ Zabala-Letona A et al. ( incl. Ximenez-Em- bun P, Castro E, Olmos D, Efeyan A, Muñoz J ) ( 2017 ). mTORC1-dependent AMD1 reg- ulation sustains polyamine metabolism in prostate cancer. Nature 547, 109-113. ∞ Olmeda D, Cerezo-Wallis D, Riveiro-Falk- enbach E, Pennacchi PC, Contreras-Alcal- de M, Ibarz N, Cifdaloz M, Catena X, Calvo TG, Cañón E, Alonso-Curbelo D, Suarez J, Osterloh L, Graña O, Mulero F, Megías D, Cañamero M, Martínez-Torrecuadrada JL, Mondal C, Di Martino J, Lora D, Mar- tinez-Corral I, Bravo-Cordero JJ, Muñoz J, Puig S, Ortiz-Romero P, Rodriguez-Peralto JL, Ortega S, Soengas MS ( 2017 ). Whole- body imaging of lymphovascular niches identifies pre-metastatic roles of midkine. Nature 546, 676-680. ∞ Rio-Machin A, Gómez-López G, Muñoz J, Garcia-Martinez F, Maiques-Diaz A, Alva- rez S, Salgado RN, Shrestha M, Torres-Ruiz R, Haferlach C, Larráyoz MJ, Calasanz MJ, Fitzgibbon J, Cigudosa JC ( 2017 ). The molecular pathogenesis of the NUP98- HOXA9 fusion protein in acute myeloid leukemia. Leukemia. 31, 2000-2005. ∞ Martinez-Val A, Garcia F, Ximénez-Embún P, Martínez Teresa-Calleja A, Ibarz N, Rup- pen I, Munoz J ( 2017 ). Urea artifacts in- terfere with immuno-purification of lysine acetylation. J Proteome Res 16, 1061-1068. ∞ Vialas V et al. ( incl. Ruppen I, Muñoz J ) ( 2017 ). A multicentric study to evalu- ate the use of relative retention times in targeted proteomics. J Proteomics 152, 138-149. Figure Secretome analysis by mass spectrometry. Serum- free conditioned media from different biological conditions ( cell lines, treatments, tissues…) can be collected and concentrated in micro-filters. Secreted proteins are then trypsin-digested and analysed by high-resolution liquid chromatography-tandem mass spectrometry ( LC-MS/MS ). Proteins are identified and quantified by means of a label- free strategy in order to obtain the profiles of secretomes across the biological conditions under study. ANNUAL REPORT 2017 160 INNOVATION HISTOPATHOLOGY CORE UNIT OVERVIEW Pathology is devoted to the study of the structural, biochemical and functional changes in cells, tissues and organs that underlie disease. By using molecular, immunological and morphological techniques, pathology aims to serve as the bridge between basic science and clinical medicine. The Histopathology Unit offers assistance and expertise through a full range of services covering from paraffin embedding and tissue sections to histochemical stains, research and diagnostic immunohistochemistry ( IHC ) testing, antibody validation, and in situ hybridisation ( ISH ), as well as the construction of tissue microarrays. Furthermore, the Unit offers other added-value services – for which assistance is provided by a team of highly specialised technicians − such as : laser-capture microdissection ; slide digitalisation for bright-field, polarisation light and fluorescence ; image analysis ; and quantification. The Unit collaborates with researchers at any stage of their scientific career in the histological characterisation of phenotypically relevant animal models of disease, thus providing them with the pathology expertise required for the success of their projects. Vacant Core Unit Head Technicians Nuria Cabrera, María Gómez, Patricia González, Gabino Hernández, Verónica Neva ( PEJ )*, Vanessa Pizarro ( since February ), Paula Tejedor ( until February ), Irene Roda, Maria Udriste ( until May ), Zaira Vega *Plan de Empleo Joven ( Youth Employment Plan ) ( until December ) “ The availability of diverse automated platforms for the performance of immunohistochemistry techniques is a key factor facilitating the reproducibility and high throughput of those techniques demanded by our users, and one of the indicators of excellence of the Unit.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 161 BIOTECHNOLOGy PROGRAMME | HISTOPATHOLOGy CORE UNIT RESEARCH HIGHLIGHTS In 2017, the Unit maintained the usual outstanding levels of throughput in terms of number of requests of services, which included nearly 34,000 paraffin-embedded blocks, more than 26,000 histochemical techniques, around 9,000 routine IHC techniques, and more than 6,000 requests for histological slide scanning and image analysis, in addition to a small number of other services such as tissue microarray preparation and ISH. This year, two of the technological areas mastered by the Unit were subjected to a significant upgrade and improvement. First, the laser microdissector was substantially upgraded in terms of software as well as hardware elements. The new version of the instrument now enables the selection of the areas to be dissected by colour detection, based on the selection system implemented in the AxioVision imaging software. Also, we incorporated a new platform for automated immunostaining, the Roche Discovery Ultra. This new system is able to perform IHC and ISH in an independent manner, which substantially increases its flexibility and capacity to adapt to the fluctuating needs of our customers. It also allows revealing the stains with chromogenic and fluorescent markers with up to five colours, and we have actually included several new chromogenic systems based on the peroxidase system. This has also made it possible to increase the number of immunohistochemical markers in both human and mouse tissues, particularly on samples from patient-derived xenograft ( PDX ) models. Other technological developments that took place in the Unit this year include the set-up of histological techniques on cells grown in tissue culture plates for the study of glucogen deposits using P.A.S. technique. The Unit is increasingly involved in clinical trials that require assistance regarding complex IHC techniques on human tissues ; these are conducted in collaboration with several pharmaceutical companies. Also, our commitment to training and educational activities is reflected in our participation in a number of training programmes at different levels, ranging from modules of ‘ Formación Profesional ’ for Pathology technicians to several Masters, as well as the course focusing on secondary school teachers that is organised through the ‘ CNIO & the City ’ project. Due to the great importance that our users place on quality and reproducibility, the Unit participates in several External Quality Assessment Schemes, such as NordiQC and UK NEQAS, which evaluate the quality of the staining techniques performed at the Unit and in which more than 800 laboratories participate worldwide. In 2017, our Unit incorporated a new companion diagnostic module from NordiQC focusing on PD-L1 ; this was done due to the high demand and increasing clinical importance of this marker. Overall, the Unit scored very high in all the evaluated techniques, and two of the protocols developed by the Unit were incorporated into the ‘ Best Methods section ’ of the UKNEQAS Cellular Pathology Technique. s Figure Techniques developed by the Histopathology Core Unit. ( A ) Section of mouse lung tissue stained with double immunohistochemistry using two different chromogenic systems against two markers, brown for Ki-67 and purple for CK-19. ( B ) Image of the same tissue for the automatic detection of Ki-67 positive cells for laser-microdissection. ∞ PUBLICATIONS ∞ Olmeda D, Cerezo-Wallis D, Riveiro-Falk- enbach E, Pennacchi PC, Contreras-Alcal- de M, Ibarz N, Cifdaloz M, Catena X, Calvo TG, Cañón E, Alonso-Curbelo D, Suarez J, Osterloh L, Graña O, Mulero F, Megías D, Cañamero M, Martínez-Torrecuadrada JL, Mondal C, Di Martino J, Lora D, Mar- tinez-Corral I, Bravo-Cordero JJ, Muñoz J, Puig S, Ortiz-Romero P, Rodriguez-Peralto JL, Ortega S, Soengas MS ( 2017 ). Whole- body imaging of lymphovascular niches identifies pre-metastatic roles of midkine. Nature 546, 676-680. ∞ Muñoz S, Búa S, Rodríguez-Acebes S, Megías D, Ortega S, de Martino A, Mén- dez J ( 2017 ). In vivo DNA re-replication elicits lethal tissue dysplasias. Cell Rep 19, 928-938. ANNUAL REPORT 2017 162 INNOVATION ANIMAL FACILITY “ The Animal Facility provides CNIO researchers with all the support required to work with mouse models, which are critical to understand the processes involved in tumour generation and development, as well as for the validation of new targets and therapeutic approaches.” Isabel Blanco Core Unit Head Management Vivotecnia Management & Services SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 163 BIOTECHNOLOGy PROGRAMME | ANImAL FACILITy The CNIO has a state-of-the-art Animal Facility, managed by Vivotecnia Management & Services. The Animal Facility’s primary responsibility is the supply, husbandry and quality control of laboratory animals used by the Research Programmes in their experimental protocols. The strict compliance to national, EU and international recommendations regarding the use and care of animals in research is of paramount importance to the CNIO. The high standards achieved by the CNIO with regards to the use and care of animals for experimentation have been recognised by the Association for Assessment and Accreditation of Laboratory Animal Care International ( AAALAC ), which granted us full accreditation in October 2016. AAALAC International is a private non-profit organisation that promotes the humane treatment of animals in science through voluntary accreditation and assessment programmes. Nearly 1,000 companies, universities, hospitals, government agencies and other research institutions in 44 countries have earned AAALAC accreditation, which is considered one of the top international recognitions in this field. The CNIO Animal Facility was established to assist researchers in the development and analysis of in vivo models. We are currently collaborating with as many as 28 Research Groups, Sections and Units from different Research Programmes. Our Animal Facility has the capacity to house 19,000 type IIL cages. Our mouse lines are maintained and bred in the Facility’s barrier area, which assures Specific Pathogen Free ( SPF ) health status through a comprehensive health surveillance programme. Microbiological and environmental parameters in the animal areas are constantly monitored. All mouse strains housed in the barrier are either generated within the barrier or introduced by rederivation. We also have an additional area with a capacity for 1,800 type II cages dedicated for the use of non-replicative strains of adenovirus, lentivirus and retrovirus, as well as for xenograft models. In this area, mice are housed in ventilated racks with integration of Individually Ventilated Caging ( IVC ) units in the building ventilation systems. Mice are always manipulated in Type II biosafety cabins. Daily operations and husbandry procedures are highly automated in order to safe-guard our personnel from any associated risks ; robotic devices perform the potentially hazardous tasks such as the processing of dirty bedding, the washing/filling of cages and bottles, etc. These automated systems maximise the productivity and ensure the quality standards in our washing and sterilising areas. All records concerning breeding protocols and animal inventory are computerised and stored in a web-based application accessible via the CNIO intranet. The Animal Facility currently harbours more than 40,000 mice representing more than 3,000 genetically modified mouse lines, either as live animals or as cryopreserved embryos or sperm, carrying close to 400 gene targeted alleles and more than 200 transgenic integrations. The Facility also provides access to more than 50 tool strains, including constitutive and inducible Cre strains, Flp strains, reporter strains, Tet transactivator strains and others. The Animal Facility offers the possibility of running a broad number of experimental procedures in the premises, including the use of gamma irradiation, UV light and volatile carcinogenic agents, as well as surgical procedures, some behavioural studies, a non-invasive blood pressure system, and a lab animal monitoring system ( Oxylet ) that enables measuring a number of physiological parameters for metabolic profiling and phenotyping of mouse models. Additionally, the monitoring of the mouse models through non-invasive imaging technologies is provided by the Molecular Imaging Core Unit, which has integrated all its image acquisition instruments within the Animal Facility. Likewise, the work of the Transgenic Mice Unit is performed in a laboratory inside the SPF barrier. Finally, the necropsy laboratory is equipped with instruments for the haematological and biochemical analysis of blood and urine, which complement the pathology and clinical diagnostics. In addition to mice, the Animal Facility hosts over 100 specimens of the frog Xenopus laevis, which are used to obtain eggs for chromosome dynamics studies. Also, in 2017, we introduced a small rat colony for a project involving the generation of monoclonal antibodies directed against mouse antigens, as new tools for cancer research. All the work carried out by the Animal Facility complies with both national and EU legislation –Spanish Royal Decree RD53/2013 and EU Directive 2010/63/UE– for the protection of animals used for research experimentation and other scientific purposes. Experimental procedures and projects are reviewed and evaluated by the Research Ethics and Animal Welfare Committee of the Instituto de Salud Carlos III, as well as by the Institutional Animal Care and Use Committee ( IACUC ). The Orden ECC/566/2015 stipulates that all animal procedures are to be carried out by qualified people in the possession of the corresponding accreditation as issued by the competent authority. The Animal Facility offers CNIO’s new staff a short course focused on the training of personnel performing work with laboratory animals ; this is complementary to the online courses that are a requisite to gain access to the facility. In line with our commitment to maintaining the highest possible standards related to animal research issues, the CNIO has joined the Agreement on Openness on Animal Research, promoted by the Federation of Scientific Societies in Spain ( COSCE ) in collaboration with the European Animal Research Association ( EARA ), which was launched on September 2016. An institutional statement on the use of research animals can be consulted on the CNIO website. s ANNUAL REPORT 2017 164 INNOVATION EXPERIMENTAL THERAPEUTICS PROGRAMME JOAQUÍN PASTOR Programme Director “ The number, diversity and results of collaborations established by basic researchers with the Experimental Therapeutics Programme are positive indicators of its integration and added value to CNIO’s Chemical-Biology and Drug Discovery activities.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 165 ExPERIMENTAL THERAPEuTICS PROGRAMME The Experimental Therapeutics Programme ( ETP ) serves as a bridge between basic research results in cancer biology ( i.e. novel therapeutic targets and hypothesis ) and the development of potential antitumour drugs. This is achieved through the application of early drug discovery phases in order to obtain advanced compounds ready for in vivo Proof of Concept ( PoC ) studies. These molecules are subject to standard in vivo characterisation by our Group as well as more detailed studies at the basic research labs where the therapeutic target emerged. The best candidates obtained by applying this operating model are then ready for clinical development in partnership with pharmaceutical companies. ETP also helps in the validation of innovative targets by providing high quality chemical probes to the basic research laboratories. Moreover, we participate in the identification of novel targets ( for projects based on phenotypic screenings ) by using our expertise in target deconvolution phases, including the development of affinity probes. Currently, the most advanced targeted project is dedicated to CDK8 inhibitors. In this project, we have selected our first leads, ETP-27 and ETP-93, which have yielded positive results in efficacy studies in haematological cancer xenograft models after oral administration. Interestingly, our chemical series displays dual CDK8/Haspin or specific CDK8 activities depending on the substitution pattern. ETP-18 represents a highly selective CDK8 inhibitor, which is undergoing pharmacokinetic ( PK ) studies. Other targeted projects dedicated to the kinases Haspin and Mastl ( in collaboration with Marcos Malumbres, CNIO Cell Division and Cancer Group ) are focused on the discovery and generation, for the first time, of specific chemical probes to interrogate their therapeutic potential. During 2017, we generated a chemical series of Haspin inhibitors by application of structure-based design strategies. Compound ETP-949 proved to be a low nanomolar and highly specific inhibitor after profiling against more than 450 kinase targets. These compounds will serve as important tools to study the therapeutic potential of the pharmacological inhibition of this mitotic and epigenetic kinase. We have continued with the exploration of several previously identified families of Mastl inhibitors ; we have now generated a preliminary SAR ( Structure Activity Relationship ) and have improved their potency up to a low nanomolar range. Currently, we are working to control their selectivity. On the other hand, we are collaborating with the CNIO Telomeres and Telomerase Group ( Maria Blasco ) in the development of TRF1 target for cancer therapy ; in this context, we have contributed to the discovery of novel TRF1 inhibitors. During 2017, ETP has helped to decipher the connection of the PI3K/AKT axis as a modulator of TRF1 localisation at telomeres by using a chemical biology approach. Moreover, we have been able to identify other potential cell signalling pathways as TRF1 regulators, currently under investigation, after the screening of our ETP-library of antitumour compounds. Furthermore, we are still working on the deconvolution of the molecular mechanism of a previously identified chemical series. Interestingly, several affinity probes have been prepared and will be used for cell localisation and pull down experiments in order to shed light on the mechanism of action of these compounds. ETP has collaborated in a project dedicated to the discovery of novel targets and modulators against Cancer Stem Cells ( Manuel Serrano ). Our team previously designed and synthesised affinity probes to help in target deconvolution studies. The use of these probes has enabled the identification of a potential mechanism of action, which is currently under in vivo validation studies. Finally, we have also collaborated with other CNIO basic researchers to carry out several screening campaigns, both targeted and phenotypic. For instance, to discover novel senolytic compounds ( Manuel Serrano ), brain metastasis blockers ( Manuel Valiente ), mTOR pathway modulators with unexplored mechanisms of action ( Alejo Efeyan ), alternative Ras pathway modulators ( Óscar Fernández-Capetillo ) and treatments for malignant peripheral nerve sheath tumours ( MPNST ) ( Héctor Peinado ), bladder cancer ( Francisco Real ), and EGFR deficient mutant KRas mouse tumours ( Mariano Barbacid/Carmen Guerra ). ETP-MedChem has also contributed with the synthesis of valuable tool compounds for research in the field of lung fibrosis ( Erwin Wagner ) and cell haploidy stabilisation ( Óscar Fernández-Capetillo ). ANNUAL REPORT 2017 166 INNOVATION MEDICINAL CHEMISTRY SECTION Sonia Martínez Section Head Staff Scientists Ana Belén García, Cristina Gómez, Esther González, Ana Isabel Hernández, María Del Rosario Rico ( until September ), Sonsoles Rodríguez, Carmen Varela SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 167 ExPERIMENTAL THERAPEuTICS PROGRAMME | mEdICINAL CHEmISTRy SECTION OVERVIEW The Medicinal Chemistry Section is part of the Experimental Therapeutics Interdisciplinary Programme that is dedicated to early Drug Discovery activities in the oncology field. Medicinal Chemistry activities start with the identification of hits through high throughput screening campaigns from targeted or phenotypic assays, and lead on to further activities related to the design, synthesis and optimisation of the compounds in order to obtain novel lead compounds with in vivo activity in appropriate animal models. For hits obtained from phenotypic screenings we introduce an additional target identification step in order to decipher the mechanism of action responsible for the observed phenotype. Our Group has experience in the design and synthesis of affinity probes for target deconvolution studies. These molecules enable the detection of the cellular localisation of the target of interest through imaging techniques and enable its isolation through pull-down experiments. Additionally, as a complementary alternative, we are developing proteolysis targeting chimeras ( PROTACs ) as promoters of cellular protein degradation in order to establish their applicability across diverse drug discovery projects. “ We developed first generation HASPIN-selective inhibitors as chemical probes through the application of structure-based design strategies in order to determine the therapeutic potential of the pharmacological inhibition of this mitotic and epigenetic kinase.” Graduate Student Francisco J. García Technicians Ivan Arribas ( PEJ-L )*, Carmen Fernández ( PEJ-L )*, Sandra Sanz ( until November ) ( PEJ ) ** *Plan de Empleo Joven-Licenciado ( Youth Employment Plan-Graduate ) ( until December ) **Plan de Empleo Joven ( Youth Employment Plan ) ( until December ) ANNUAL REPORT 2017 168 INNOVATION RESEARCH HIGHLIGHTS Project advances in 2017 : Cyclin-dependent protein kinase 8 inhibitors ( CDK8i ) project During 2017, we were involved in the optimisation of ETP-27 ; a lead compound identified and developed in our programme, with demonstrated in vivo proof-of-concept in the acute myeloid leukaemia model, MOLM-13 xenograft. Fine tuning optimisation has been done and we have identified ETP-93, an orally bioavailable compound with longer half-life than ETP-27. ETP-93 showed oral levels in both plasma and tumour, biomarker modulation ( pSTAT1 ) up to 8 hours after oral administration in PK/PD studies, and a significant tumour growth inhibition of 50% in a 10 day short-term study at 50 mpk P.O. in MOLM-13. The compound is rather selective ( S( 35 ): 0.08 ) in a 468 kinase panel ( KINOMEscanTM platform ) and only 1 main off-target has been identified. Currently, we are evaluating the positive contribution of this activity to the antiproliferative profile of the compound. Additionally, in this series we have identified very selective CDK8 inhibitors with good in vivo PK, for example ETP-18, which has been selected for further in vivo efficacy studies. Microtubule-associated serine/threonine protein kinase-like ( MASTL ) inhibitors Two different hits were identified from an HTS campaign with active full length human MASTL protein. About 100 analogues have been synthesised around them to establish Structure- Activity-Relationships ( SAR ), identifying compounds in the single digit nanomolar range from both chemical series. Selected compounds have been profiled in a small set of kinases to determine their selectivity and we have identified some main off-targets in the compounds. Currently, we are focussing our efforts on trying to obtain high quality selective chemical probes that will be used in pharmacological inhibition studies to decipher the whole therapeutic potential of MASTL. HASPIN inhibitors During the exploration of 2 chemical series we were able to obtain very potent biochemical and cellular low nanomolar haspin inhibitors, while removing the off-target activities present in the original hits. After the synthesis of about 90 compounds, we profiled the selectivity of 2 representative molecules from each chemical series, ETP-949 and ETP-885, in a 468 kinase panel ( KINOMEscanTM ) obtaining a high level of selectivity for both of them ( S( 35 ) of 0.025 and 0.007 ). Currently, one of these chemical series is under in vivo characterisation with the aim of identifying a high quality Haspin inhibitor for pharmacological target validation studies. Additionally, a third chemical series was generated in 2017, including intellectual property in the design. Inhibition of Cancer Stem Cell ( CSC ) proliferation This project is undertaken in collaboration with the CNIO Tumour Suppression Group. After the identification of compounds able to modulate CSC proliferation, stemness and, at sublethal doses, inhibit the tumour initiating capacity of pancreatic CSCs, we generated affinity probes by introducing a minimalist linker, retaining the activity ; these probes were used in deconvolution studies in 2017. The presence of the minimalist linker increased the efficiency of these studies by enabling the formation of a covalent linkage with the binding proteins after photo-irradiation treatment. Additionally, we have scaled up the hit compound to evaluate its in vivo pharmacokinetic properties. Telomeric repeat binding factor 1 ( TRF1 ) inhibitors This is a collaborative project undertaken with the CNIO Telomeres and Telomerase Group. During 2017, we focused on the synthesis of different affinity probes of hit compound ETP-946 in order to identify the putative molecular target responsible for the observed TRF1 modulation. Among them, the ETP-455 affinity probe showed similar TRF1 modulation to the hit compound and was selected for deconvolution studies. ETP-455 contains a reversible linker with a terminal alkyne reactive group that helps in cell localisation and pull down experiments by using a click chemistry reaction with functionalised ( azide reactive group ) fluorophores and/or biotinylated derivatives. Preliminary cell localisation experiments using imaging techniques have been performed, demonstrating a rather specific localisation of the chemical probe that can be removed by competition with ETP-946. s SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 169 ExPERIMENTAL THERAPEuTICS PROGRAMME | mEdICINAL CHEmISTRy SECTION ∞ PUBLICATIONS ∞ Bejarano L, Schuhmacher AJ, Méndez M, Megías D, Blanco-Aparicio C, Martínez S, Pastor J, Squatrito M, Blasco MA ( 2017 ). Inhibition of TRF1 telomere protein im- pairs tumor initiation and progression in glioblastoma multiforme mouse models and in patient-derived xenografts. Cancer Cell 32, 590-607. ∞ Méndez-Pertuz M, Martínez P, Blanco-Apa- ricio C, Gómez-Casero E, Belen García A, Martínez-Torrecuadrada J, Palafox M, Cortés J, Serra V, Pastor J, Blasco MA ( 2017 ). Modulation of telomere protection by the PI3K/AKT pathway. Nat Commun 8, 1278. ∞ Martínez González S, Hernández AI, Ál- varez RM, Rodríguez A, Ramos-Lima F, Bischoff JR, Albarrán MI, Cebriá A, Hernán- dez-Encinas E, García-Arocha J, Cebrián D, Blanco-Aparicio C, Pastor J ( 2017 ). Iden- tification of novel PI3K inhibitors through a scaffold hopping strategy. Bioorg Med Chem Lett 27, 4794-4799. ∞ Martínez González S, Rodríguez-Arísteg- ui S, Hernández AI, Varela C, González Cantalapiedra E, Álvarez RM, Rodríguez Hergueta A, Bischoff JR, Albarrán MI, Cebriá A, Cendón E, Cebrián D, Alfonso P, Pastor J ( 2017 ). Generation of tricyclic imidazo[ 1,2-a ]pyrazines as novel PI3K in- hibitors by application of a conformational restriction strategy. Bioorg Med Chem Lett 27, 2536-2543. ∞ PATENT ∞ Pastor Fernández J, Martínez González S, Blanco Aparicio C, Hernández Higueras AI, Gómez de la Oliva CA, Rivero Buceta V, Riesco Fagundo RC ( 2017 ). Preparation of tricyclic pyrolopyranopyridines as pro- tein kinase inhibitors. WO2017033019A1 20170302. Figure Selectivity profile of 2 HASPIN inhibitors from different chemical series tested in a 468 kinase panel ( KINOMEscanTM ). The selectivity score of the compound S( 35 ) is indicated in the figure. Kinases that are found to bind are marked with red circles ( blue circle for HASPIN kinase )-whereas larger circles indicate higher binding affinity. ANNUAL REPORT 2017 170 INNOVATION BIOLOGY SECTION Carmen BlancoSection Leader Post-Doctoral FellowElena Hernández SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 171 ExPERIMENTAL THERAPEuTICS PROGRAMME | bIOLOGy SECTION OVERVIEW In the Experimental Therapeutics Programme, we are working on both targeted and phenotypic-based drug discovery projects as well as on exploratory screening projects carried out in collaboration with other CNIO Groups. Furthermore, we conduct screenings with an ETP-antitumour library in order to identify potential new treatments in tumour types or metastatic settings for which there is an unmet medical need regarding new therapies. On the other hand, this library is used to identify novel signalling pathways that modulate a target responsible for an interesting phenotype. The newly identified signalling pathways are validated by using a chemical-biology approach, through which a set of inhibitors for the target, with quite dissimilar structures, are interrogated against the expected phenotype. In order to reach a conclusion, we establish correlations between cellular modulation of the target/pathway and the desired phenotype. Finally, the CNIO Group that develops the screening also performs all the biological validation required to confirm the new hypothesis. “ In collaboration with the CNIO Telomeres and Telomerase Group, we have identified new signalling pathways that modulate the levels of TRF1 at telomeres. Using a chemical-biology approach, we have contributed to the elucidation that the PI3K/AKT pathway regulates TRF1.” Technicians M. Isabel Albarrán ( TS ) *, Adrián Amezquita ( until November ) ( PEJ ) **, Antonio Cebriá ( TS ) *, Jennifer García ( PEJ ) **, Elena Gómez-Casero ( TS ) *, Javier Klett ( TS ) *, M. Carmen Rodríguez De Miguel ( TS ) * *Titulado Superior ( Advanced Degree ) **Plan de Empleo Joven ( Youth Employment Plan ) ( until December ) Visiting Scientist Ann Louw ( January-June, University of Stellenbosch, South Africa ) ANNUAL REPORT 2017 172 INNOVATION RESEARCH HIGHLIGHTS During 2017, our Section was involved in several projects : Cyclin-dependent kinase 8 ( CDK8 ) We characterised ETP-93, a second improved dual lead compound, and ETP-18, a nanomolar selective CDK8/CDK19 inhibitor, as it was described in the Medicinal Chemistry Section. Microtubule-associated serine/threonine protein kinase-like ( MASTL ) and HASPIN These projects are undertaken in collaboration with the CNIO Cell Division and Cancer Group. For MASTL, we tested 98 new compounds in our biochemical assay with active human full length MASTL protein. We identified low nanomolar inhibitors that were profiled in a small internal kinase panel, revealing off-targets that were removed. The more potent and selective inhibitors are under cellular characterisation. For HASPIN, we tested in a biochemical assay 90 compounds belonging to 3 different chemical series. Active compounds were also profiled in the small internal kinase panel. Cellular inhibition of phosphorylation of H3T3 was evaluated for those inhibitors with a biochemical IC50 below 100nM. We identified nanomolar biochemical and cellular HASPIN inhibitors and representative molecules for two chemical series that have been profiled in a panel of 468 kinases ( KinomeScan ), thereby obtaining a high level of selectivity for both of them ( S( 35 ) of 0.025 and 0.007 ). These compounds are under further cellular evaluation and in vivo PK. Figure ETP- libraries and their potential outcome after screening. ETP has 4 different collections of diverse origin covering chemically diverse small molecules, drugs that are approved or in clinical trials for cancer treatment or for other illnesses, as well as natural products. The outcome of a targeted or phenotypic screening using one of these libraries could enable the discovery of new drugs for a specific target, the identification of new targets associated with a phenotype, or a more translational result such as the postulation of new clinical trials for unmet medical needs. Moreover the screening of the PharmaMar library could trigger a collaboration to further develop results. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 173 ExPERIMENTAL THERAPEuTICS PROGRAMME | bIOLOGy SECTION Telomeric repeat binding factor 1 ( TRF1 ) This project is carried out in collaboration with the CNIO Telomeres and Telomerase Group. A phenotypic assay to measure the association of TRF1 to telomeres was used to test 44 compounds, which include ETP-946 analogues and its corresponding chemical probes. Moreover, we used one of these chemical probes, ETP-455, to perform cellular localisation assays of the putative target of ETP-946. This information has been used to design pull-down experiments that are currently ongoing. Furthermore, we have tested the ETP-antitumour library to identify new signalling pathways that modulate TRF1. We are validating these new pathways by using a chemical-biology approach that we previously applied to uncover that the PI3K/ AKT pathway regulates TRF1. Cancer stem cells ( CSC ) and screening to identify new senolytic drugs These projects are carried out in collaboration with the CNIO Tumour Suppression Group. For the CSC project, we collaborated on the pharmacokinetic characterisation of the most interesting identified hit, as well as in the in vivo validation studies. For the new senolytics screening project, ETP-Biology provided support for testing and analysing the ETP-antitumour and ETP-5K libraries in an assay that compares the viability of tumour cells and senescent cells. After validation of the hits identified by single point and the testing of analogues, four hits were selected for further characterisation. Brain metastasis screening The CNIO Brain Metastasis Group developed an ex vivo assay to search for drugs that kill human brain metastasis in mice. One class of drugs identified in the screening was further characterised ; we contributed to the experimental design and the analysis of tumour levels in PK/PD experiments in order to help design the administration schedule for the efficacy study performed by our collaborators. Screening to identify new Ras modulators The CNIO Genomic Instability Group has developed an assay to search for drugs that modulate the Ras pathway. ETP-Biology has provided support in running the experiments with both the ETP-800 and ETP-5K libraries and by testing the analogues. Two interesting hits were identified and we performed their ADME profiles ; they are currently under pharmacokinetic characterisation and will eventually progress to in vivo PoC studies. Screening to identify New mTOR modulators The CNIO Metabolism and Cell Signalling Group developed an innovative assay to search for drugs that modulate the mTOR pathway. ETP-Biology provided support in running the experiments with both the ETP-800 and ETP-5K libraries. The identified hits are under further characterisation. Collaborations with other CNIO Groups ETP-Biology has provided support by testing and analysing the ETP-antitumour library, either alone or in combination, in order to identify : i ) novel treatments or combinations in MPNST cell lines in collaboration with the Microenvironment and Metastasis Group ; ii ) novel treatments or combinations in bladder cancer cell lines in collaboration with the Epithelial Carcinogenesis Group ; iii ) novel treatments or combinations in brain cancer cell lines in collaboration with the Brain Tumour Group ; and iv ) novel treatments of KRas mutant NSCLC mouse cell lines with and without EGFR in collaboration with the Experimental Oncology Group. s ∞ PUBLICATIONS ∞ Bejarano L, Schuhmacher AJ, Méndez M, Megías D, Blanco-Aparicio C, Martínez S, Pastor J, Squatrito M, Blasco MA ( 2017 ). Inhibition of TRF1 telomere protein im- pairs tumor initiation and progression in glioblastoma multiforme mouse models and in patient-derived xenografts. Cancer Cell 32, 590-607. ∞ Méndez-Pertuz M, Martínez P, Blanco-Apa- ricio C, Gómez-Casero E, Belen García A, Martínez-Torrecuadrada J, Palafox M, Cortés J, Serra V, Pastor J, Blasco MA ( 2017 ). Modulation of telomere protection by the PI3K/AKT pathway. Nat Commun 8, 1278. ∞ Jiménez-García MP, Lucena-Cacace A, Robles-Frías MJ, Ferrer I, Narlik-Gras- sow M, Blanco-Aparicio C, Carnero A ( 2017 ). Inflammation and stem markers association to PIM1/PIM2 kinase-induced tumors in breast and uterus. Oncotarget 8, 58872-58886. ∞ Martínez González S, Hernández AI, Ál- varez RM, Rodríguez A, Ramos-Lima F, Bischoff JR, Albarrán MI, Cebriá A, Hernán- dez-Encinas E, García-Arocha J, Cebrián D, Blanco-Aparicio C, Pastor J ( 2017 ). Iden- tification of novel PI3K inhibitors through a scaffold hopping strategy. Bioorg Med Chem Lett 27, 4794-4799. ∞ Martínez González S, Rodríguez-Arísteg- ui S, Hernández AI, Varela C, González Cantalapiedra E, Álvarez RM, Rodríguez Hergueta A, Bischoff JR, Albarrán MI, Cebriá A, Cendón E, Cebrián D, Alfonso P, Pastor J ( 2017 ). Generation of tricyclic imidazo[ 1,2-a ]pyrazines as novel PI3K in- hibitors by application of a conformational restriction strategy. Bioorg Med Chem Lett 27, 2536-2543. ∞ PATENT ∞ Pastor Fernández J, Martínez González S, Blanco Aparicio C, Hernández Higueras AI, Gómez de la Oliva CA, Rivero Buceta V, Riesco Fagundo RC ( 2017 ). Preparation of tricyclic pyrolopyranopyridines as pro- tein kinase inhibitors. WO2017033019A1 20170302. ANNUAL REPORT 2017 174 INNOVATION CNIO - LILLY CELL SIGNALLING THERAPIES SECTION SCOPE OF THE ELI LILLy - CNIO PARTNERSHIP Eli Lilly and CNIO are collaborating on the identification and validation of novel targets in cancer immuno-metabolism. Our Section is funded through a research contract with Eli Lilly and focuses on the identification of small molecular weight molecules that regulate the metabolism of malignant cells, with the objective of killing them, either directly, acting synergistically with other anti-tumour agents, or activating the anti-tumour immune response. Exploring how to better target these mechanisms would lead to better and more efficient therapeutic options. A combination of in vitro and in vivo approaches is being utilized to obtain a complete understanding of the metabolic reprogramming regulated by oncogenes like RAS, as well as the characterisation of the metabolic status of tumours. For this purpose, we have developed a series of biochemical and cell-based assays exploiting advanced techniques such as extracellular flux analysis ( Seahorse technology ), NMR and metabolomics. Finally, each target goes through an in vivo validation process using xenografts, allografts and mouse models developed at the CNIO that includes the use of non-invasive in vivo imaging technologies, as well as the immune histochemical characterisation of tumours for different metabolic, immune and tumour-specific markers. The final step is the validation in human samples from healthy donors or patients using PBMCs or tumour tissue arrays. Susana Velasco Section Head Staff Scientists Ana Cerezo, Juan Manuel Funes, Eva P. Lospitao, Gloria Martínez Del Hoyo Technicians Laura Diezma, Tamara Mondejar ( TS )*, Sandra Peregrina ( TS )*, Estela Casas López *Titulado Superior ( Advanced Degree ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 175 ExPERIMENTAL THERAPEuTICS PROGRAMME | CNIO - LILLy CELL SIGNALLING THERAPIES SECTION SCIENTIFIC CONTEXT The observation of an altered metabolic state in cancer cells dates back to the early 20th century when Otto Warburg observed that cancer cells preferentially utilise glycolysis over oxidative phosphorylation for growth, even in the presence of normal oxygen levels ( Warburg 1956 ), a phenomenon known as the ‘Warburg effect ’. Warburg argued that, ‘this altered metabolic state was the underlying cause for cancer ’. The molecular mechanisms driving an altered tumour metabolism have only recently begun to be understood as a result of large-scale genomic sequencing as well as advances in metabolomic profiling technologies. Recent studies have shown that many oncogenes, including MYC and RAS, impart an altered metabolic phenotype in cancer cells through the regulation of genes involved in central metabolic pathways such as glycolysis, fatty acid metabolism, oxidative phosphorylation, nucleotide synthesis and the one carbon pool ( reviewed by Gilmour & Velasco, 2017 ). Cellular metabolism is a fine tuned process ; tumours rely heavily on specific metabolic pathways to obtain their energy while using other pathways to grow in order to give tumour cells a growth advantage. This situation may leave tumour cells in a frail position under certain treatments or circumstances, while normal cells may be able to compensate and survive. Furthermore, the high requirements of nutrients and other soluble factors, and the release of metabolites with immunosuppressive properties, together with the hypoxic conditions found in tumours creates a ‘non-friendly ’ microenvironment for an anti-tumour immune surveillance, while facilitating the growth of other tumour- promoting cells such as stromal and myeloid cells ( FIGURE ). Thus, the mechanistic understanding of cancer metabolism has led to renewed interest in developing therapeutics that target key enzymes involved in this process. Checkpoint-blockade immunotherapy has been one of the most exciting advances made in cancer treatment in recent years. Metabolic interplay in the local microenvironment can mediate T cell differentiation and function. ‘ Checkpoint-blockade ’ antibodies can also influence cellular metabolism. Finally, recent clinical trials have shown that combination immunotherapy based on immune checkpoints blockade and other oncology therapies, provides even higher response rates than either approach alone. s Figure Targeting cancer metabolic immune suppression. (  A ) T cells remain in the periphery of tumours staying away from internal areas. An immune histochemical analysis of CD3 positive T cells in a K-RasG 12/ p53-/- lung adenocarcinoma is shown. Tumour cells produce a battery of immunosuppressive metabolites such as lactic acid, kynurenine or adenosine that result in an anergic T cell phenotype, while consuming key metabolites such as glucose or tryptophan necessary for a proper T effector ( Teff ) cell activity. As a result, T cells are incapable of mounting an effective anti-tumour immune response. (  B ) Metabolic regulation of the tumour and/or tumour microenvironment would diminish the production of immune suppressive metabolites and increase the levels of metabolites such as glucose, or tryptophan necessary for a proper immune T cell response. Teff cells would be able to invade and attack the tumour, destroying it. The image depicts a virtual anti-tumour T cell response in the same lung adenocarcinoma. ∞ PUBLICATION ∞ Gilmour R, Velasco S. ( 2017 ). Back to the Future : Therapeutic targeting of cancer cell metabolism. SLAS Discov 22, 333-337. ANNUAL REPORT 2017 176 INNOVATION CNIO - LILLY EPIGENETICS SECTION “ Our goal is to identify epigenetic events that contribute to tumourigenesis and that might be susceptible to modulation by therapeutic agents.” María José Barrero Section Head Staff Scientist Sergio Ruíz Technicians Verónica García ( TS )*, Ana González ( since October ), Jacinto Sarmentero ( TS ) * *Titulado Superior ( Advanced Degree ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 177 ExPERIMENTAL THERAPEuTICS PROGRAMME | CNIO - LILLy EPIGENETICS SECTION SCOPE OF THE CNIO - ELI LILLy PARTNERSHIP Eli Lilly and CNIO are collaborating on the identification and validation of novel targets in cancer epigenetics. Our Section is funded through a research contract with Eli Lilly and focuses on the identification of small molecular weight molecules able to modulate the epigenome of malignant cells and ultimately block the growth and spread of tumours. Potential targets are being validated in vitro and in vivo using animal models developed at the CNIO. Furthermore, we are currently setting up biochemical and cell-based assays with the aim of understanding the mechanism of action of such targets at the molecular level ( FIGURE ). SCIENTIFIC CONTEXT Recent studies have shown that the alterations that take place in cancer cells not only occur at the DNA sequence but also at the level of the epigenome. Eukaryotic DNA is wrapped around histone proteins to constitute chromatin, which plays fundamental structural and regulatory roles. The epigenome consists of chemical changes in both DNA and histones that can be inherited through cell division and are controlled by the action of a large set of epigenetic regulators that possess enzymatic activity. Ultimately, DNA and histone modifications control the level of chromatin condensation, which in turn regulates the accessibility of transcription factors to the chromatin and, therefore, gene expression. During the past few years several studies, including our own, have suggested that the deregulation of the chromatin-modifying machineries can lead to aberrant gene expression causing cancer and other human diseases. The epigenome is regulated in a highly dynamic fashion by the coordinated action of regulators able to write, erase and read histone and DNA modifications. Thus, contrary to genetic mutations, epigenetic aberrations can be reversed through the targeting of the appropriate epigenetic regulators. Indeed, drugs targeting DNA methyltransferases and histone deacetylases have successfully demonstrated anticancer properties and are currently used in the clinic. Therefore, identifying the molecular function of critical epigenetic regulators and their complex relationship with the cancer epigenome ( FIGURE ), as well as the development of small molecular inhibitors of their activities holds great promise for the therapeutics of cancer. s ∞ PUBLICATION ∞ Barrero MJ ( 2017 ). Epigenetic Strategies to Boost Cancer Immunotherapies. Int J Mol Sci 18, 1108. Figure In vivo and in vitro strategies for target validation. ANNUAL REPORT 2017 178 INNOVATION TECHNOLOGY TRANSFER AND VALORISATION OFFICE Anabel Sanz Director Technology Transfer Manager M. Cruz Marín SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 179 TECHNOLOGy TRANSFER AND VALORISATION OFFICE At the CNIO, the best science is coupled with the desire to make a true impact through our research efforts, all for the benefit of cancer patients and the health system. The Technology Transfer and Valorisation Office ( TTVO ) contributes to these endeavours by ensuring appropriate intellectual protection and by fuelling the technologies that arise from our research into companies and entrepreneurs that can develop them further and thereby impact society. The TTVO carries out the all-round management and follow-up of all aspects − including relationships with stakeholders − in order to ensure the appropriate intellectual property protection and commercial viability of the research results generated by CNIO’s scientist. Additionally, the Office proactively follows up on the progress of scientific activity at the CNIO in order to identify projects with high transfer potential. The TTVO plays a managerial and advisory role throughout the entire process, whereby it safeguards the efficient use of the patent system, identifies appropriate commercial partners for a timely development of technologies, negotiates licenses, monitors the activities of licensees regarding the achievement of milestones, and oversees the payment of royalty fees. Other activities include : 1 ) working with researchers to enable them to exchange ideas, research results and materials with other researches from both academic and/or commercial entities ; and 2 ) negotiating complex intellectual property terms related to sponsored research or strategic engagements with companies. The TTVO Office managed 305 agreements related to research results and CNIO’s intellectual property in 2017. About two thirds of these were of an international nature. We provide advice and guidance to researchers wishing to valorise their research results in order to make them more attractive to companies willing to develop technological, diagnostic and therapeutic solutions. In 2017, 16 valorisation projects were monitored. Valorisation of CNIO’s research results through alliances with industry remains a priority. The Technology Transfer Office offers support to CNIO researches to leverage on public-private partnerships for valorisation purposes. In 2017, CNIO scientists, in collaboration with local industrial leaders, presented 5 innovative projects under the framework of private-public partnership funding schemes, such as the national Retos Colaboración programme. The inventions of CNIO scientists that have the potential to be transferred to the market are protected through patents. The CNIO’s patent portfolio is composed of 30 families, 5 of which are novel inventions brought about in 2017 ; these cover a wide range of applications such as novel targets, tissue regeneration, nano- systems to deliver cancer drugs to the tumour site, and methods to treat metastasis in the brain. Licensed patents are managed by our licensees and the rest is managed by the TTVO. Patents and unpatented research tools are licensed to increase their availability to the scientific community, as well as to create opportunities for our business partners and to provide a financial return on public investment. In 2017, CNIO entered into 7 new licence agreements with commercial partners for the exploitation of research results and tools. The royalty fees collected from licenses in 2017 exceeded 550,000 euros. This income reverts back to CNIO research activities as well as to the inventors themselves. A total of 52 inventors, well above 10% of CNIO’s researchers, have contributed towards and benefited from this achievement. In 2017, a remarkable step was taken under the leadership of Manuel Serrano ; namely, the start-up of a new company based on his research in the field of senescence, which has applications in cancer treatment and other diseases such as pulmonary fibrosis. Fostering an innovation culture among our scientists is one of our priorities. With the support of Fundación Banco Santander, we uphold our collaboration with the prestigious IE Business School, through which many of our investigators − 3 new ones in 2017 − have already obtained training in market-oriented innovation strategies. All the above mentioned achievements stand testament to the excellence and hard work of the CNIO scientists and to CNIO’s unwavering encouragement of innovation and technology transfer activities. “ We work closely with the CNIO faculty and researchers in order to understand how their ideas might be useful to patients as well as to ensure that all matters related to intellectual property protection and commercialisation are taken care of.” Technician Rocío Manzano ( PEJ-L )* *Plan de Empleo Joven- Licenciado ( Youth Employment Plan-Graduate ) ( until December ) ANNUAL REPORT 2017 180 Communication SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 181 Communications 182 Press Clippings 184 2017 Social Network Data 187 Invited Guest Speakers 188 Social Events 189 CNIO & The City 190 ANNUAL REPORT 2017 182 COMMuNICATION COMMUNICATIONS NURIA NORIEGA Head of Communications Communications Officer Cristina de Martos ( TS )* Science Outreach Officer Pablo Camacho ( since May ) ( TS )* *Titulado Superior ( Advanced Degree ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 183 COMMuNICATIONS The Communications Department takes the Centre’s activities beyond its doors in a truthful, accurate, and at the same time, attractive manner. Through different channels, we aim to draw the attention of the media and society in general towards the endeavours and achievements of the Centre’s researchers. Over the course of this past year, their advancements and discoveries have been well received and have attracted broad media coverage, with over 2,300 appearances in the press ( online and on paper ), and appearances on radio and TV, which represent an increase of 63% compared to the previous year. In an increasingly competitive news environment, in which the specific weight of scientific news stories has declined in recent years, several of our articles have been in the forefront of Spain’s most prominent media channels and international media outlets such as the BBC and Der Standard, among others. The paper about the visualisation of melanoma metastasis written by Marisol Soengas and David Olmeda and published in Nature journal in June, and more recently, the article about a new strategy to halt glioblastoma growth, published in Cancer Cell by Maria A. Blasco and Leire Bejarano, have generated extensive attention. Both articles appeared on the front pages of several printed and digital publications, as well as on radio and television. But these were not the only ones to be publicly commended. Other stories also captured the public’s attention, such as the research led by Nabil Djouder and Marta Brandt that was published at the end of the year in Cell Metabolism, or the award granted by the American Prostate Cancer Foundation to Elena Castro, which broke records in terms of social media traffic and reach. These spotlighted accomplishments represent valuable tools when it comes to achieving our goal of reaching out to a broader audience. With a community of over 13,000 followers on Twitter and over 34,000 on Facebook, we have a great platform of communication that we seek to make full use of in order to ascertain the concerns and interests of society. This will help us to establish an enriching dialogue that will ultimately highlight and spread the idea that research in general and cancer research in particular have an intrinsic value that is essential for the betterment of society. To this end, the Communications Department also drives and supports other initiatives developed by the Centre that pursue the dissemination of scientific knowledge, education, and the fostering of scientific values. In this regard, the Communications Department established an agreement with the TV & Media Group Atresmedia, one of the leading media groups in Spain, and the AXA Foundation to promote medical and scientific research on the occasion of World Cancer Research Day. Through this agreement, the event ‘ Present and Future of Cancer Research ’ took place at El Matadero – one of the most vibrant and cultural venues in Madrid – with Nobel Prize-winner Harald zur Hausen as guest of honour, and with the participation of CNIO’s Director Maria A. Blasco, Ángela Nieto from the Institute of Neurosciences ( CSIC-UMH ), and Pilar Garrido, Chief Oncologist at the Hospital Ramón y Cajal. The event, hosted by the well-known journalist of laSexta TV Mamen Mendizabal, served to communicate the message : research is key in the prevention and fight against cancer. Following this spirit, the CNIO participated in the ”la Caixa ” Banking Foundation publicity campaign that revolved around the unique concept of ‘ Crucial people ’, the objective of which was to give a voice to outstanding people. This homage to remarkable individuals was covered by the written press, TV, radio, cinemas and digital media in order to promote the role of research and the importance of supporting research for society. Last but not least, during 2017, the CNIO joined the Google Ad Grants for registered non-profit organisations that share Google’s philosophy of community service to help the world in areas such as science and technology, education, health, etc. Google Ad Grants is an advertising programme that offers free online positioning through the tool Google AdWords for non- profit organisations. The CNIO Friends initiative to raise funds for cancer research was again greatly successful in 2017. Beyond other activities, the CNIO brought out the book Excelentes, which presents artistic photographs and personal stories by some of the most influential people who have visited the Centre in recent years like Nobel laureates Elizabeth Blackburn and Paul Nurse, the physicist Ignacio Cirac, or the palaeontologist Juan Luis Arsuaga. The funds collected through this book, on sale at stores such as El Corte Inglés, VIPS and the CNIO store, go directly towards the CNIO Friends initiative ; these results motivate us even more to keep working on the important cause of cancer research. “ Communication is a key factor for ensuring the success of Research & Development activities that, in turn, play an essential role in the advancement of society.” ANNUAL REPORT 2017 184 COMMuNICATION PRESS CLIPPINGS 1 ABC, January 30, 2017 2 Telemadrid informativos, February 4, 2017 3 La Sexta Noche, La Sexta, February 18, 2017 4 El Global, March 27, 2017 5 QUO, April, 2017 6 Gaceta Médica, April 3, 2017 7 Diario Médico, April 10, 2017 8 El Mundo, May 6, 2017 9 El Correo, May 16, 2017 1 4 5 8 6 7 3 9 2 SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 185 COMMuNICATIONS 10 Heraldo, May 23, 2017 11 Especial informativo Antena 3, May 24, 2017 12 El Mundo, June 5, 2017 13 La 1 noticias, TVE, June 29, 2017 14 La Razón ( front page ), June 29, 2017 15 El Mundo, July 11, 2017 16 Diario Médico, July 21, 2017 17 El Progreso, July 31, 2017 18 BBC, September, 2017 19 La Razón, September 23, 2017 10 11 13 12 14 15 16 17 18 19 ANNUAL REPORT 2017 186 COMMuNICATION 20 Más vale tarde, La Sexta, September 25, 2017 21 La Razón, November 14, 2017 22 SINC, November 24, 2017 23 El País Retina, El País, November 25, 2017 24 La 1 noticias, TVE, November 27, 2017 25 La Opinión, December 5, 2017 26 Buenos días Madrid, Telemadrid, December 18, 2017 27 Diario Médico, December 22, 2017 21 20 22 26 24 23 26 27 25 SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 187 COMMuNICATIONS 2017 SOCIAL NETWORK DATA FACEBOOK +311 FOLLOWERS 34.197 LINKEDIN +779 FOLLOWERS 4.937 yOuTuBE +86 FOLLOWERS 414 TWITTER CNIO +1.555 FOLLOWERS 12.946 TWITTER CNIO & THE CITy +233 FOLLOWERS 311 TWITTER CNIO FRIENDS +117 FOLLOWERS 723 FOLLOWERS UNTIL DECEMBER 2017FOLLOWERS IN JANUARY 2017 FACEBOOK DATA PER POST COMMENTS REACH LINK CLICKS SHARED LIKES 187,63 41,62 4,43 5.716,18 93,15 TWITTER CNIO DATA PER TWEET ANSWERS REACH LINK CLICKS RETWEETS LIKES 6,74 5,43 0,32 2.154,53 8,17 LINKEDIN DATA PER POST CLICKS INTERACTIONS REACH 4.245,8 31,95 49,54 YOUTUBE GENERAL DATA VIEWS IN 2017 LIKES SHARED UPLOADED IN 2017 UPLOADED VIDEOS 88 8 21.028 172 367 ANNUAL REPORT 2017 188 COMMuNICATION INVITED GuEST SPEAKERS ( Distinguished Seminar Series ) Elaine Fuchs, January 13, 2017 Kari Alitalo, April 28, 2017 Vera Gorbunova, May 5, 2017 Paola Scaffidi, October 6, 2017 Peter Carmeliet, October 20, 2017 SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 189 COMMuNICATIONS SOCIAL EVENTS On occasion of International Women’s Day, a performance of ‘ A Room of One’s Own ’, a stage adaptation of Virginia Woolf’s essay was given. The performance was directed by María Ruiz and starred Clara Sanchís. It was promoted by the CNIO’s Women in Science Office ( WISE ). March 7, 2017. On the occasion of World Cancer Research Day, the CNIO organised the event ‘ Present and Future of Cancer Research ’ together with Atresmedia Corporation and AXA Foundation. Attendees enjoyed an inspiring talk by Harald zur Hausen, winner of the Nobel Prize in Medicine in 2008, plus a panel discussion with Prof. zur Hausen, CNIO Director Maria A. Blasco, Ángela Nieto ( Institute of Neurosciences, CSIC-UMH ) and Pilar Garrido ( Hospital Ramón y Cajal ). September 25, 2017. The CNIO celebrated its traditional Lab Day by recognising the work of its researchers, especially the youngest ones. Organised by the Dean’s Office for Academic Affairs, it was a day to enjoy the spirit of team building, and especially, of being proud to belong to the CNIO community. December 18, 2017. In 2017, the CNIO once again participated in the European Researchers ’ Night, which is funded by the EU Framework Programme for Research & Innovation, and Horizon 2020 - Marie Sklodowska- Curie actions. More than 60 CNIO volunteers and 240 visitors attended the event aimed at raising awareness about science and promoting scientific culture in society. September 29, 2017. Carmen Vela, Secretary of State for Research, Development and Innovation, as well as President of the Board of the CNIO ; Maria A. Blasco, CNIO’s Director ; and José María Fernández Sousa-Faro, Chairman of PharmaMar, signed an agreement for the implementation of new screening tests to characterise potential anti-tumour compounds of marine origin. March 17, 2017. ANNUAL REPORT 2017 190 COMMuNICATION CNIO & THE CITY CAROLINA POLA Director of International Affairs Communications Officer Cristina de Martos ( TS )* Science Outreach Officer Pablo Camacho ( since May ) ( TS )* *Titulado Superior ( Advanced Degree ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 191 CNIO & THE CITy In 2017, the Spanish National Cancer Research Centre launched a new mission to inform. A project that aims to centralise all of CNIO’s efforts in terms of bringing science and research to the general public. The CNIO & The City initiative was launched halfway through the year, forming a bridge between our laboratories, our scientists and society. Specifically, this project, jointly funded by the Spanish Foundation for Science and Technology ( FECYT ) and “ la Caixa ” Social Projects, is aimed at students, secondary schools and the further education of teachers. The objective, in addition to explaining the work that we do and conveying the importance of research for development and evolution, is to awaken a passion for science in young minds. The accessibility of research centres through outreach events, citizen science and co-creation is an aspect of growing interest and importance for European institutions, funding bodies and evaluators. It is essential that both research projects and institutions themselves consider these aspects as important in order to achieve new standards of scientific excellence in the future. The CNIO has a rich history when it comes to science outreach activities ; this ranges from its participation in European Researchers ’ Night to guided visits for secondary schools. These activities all require the commitment of the staff that take part in them and make them possible. CNIO & The City is the product of this undeniable vocation to inform and the desire to push this facet to a new level. The project, the content of which is available on the http ://cnioandthecity.cnio.es website, is divided into two main parts : FORMACNIO, devoted to teachers, and EDUCACNIO, devoted to students. Both the teachers ’ course ( held in October ) and the ‘ Laboratory immersion ’ and ‘ My first scientific project ’ ( in progress ) activities are proving hugely popular with the participants who have expressed their gratitude and enthusiasm on numerous occasions. The commitment of the researchers who participated on a voluntary basis is, without doubt, the key to the project’s success and we are hoping that this will help us to repeat the initiative in 2018. The integration of science in societal culture is a long-standing demand in Spain since the Enlightenment. This change must be led by research centres that possess the knowledge. That is our commitment, through CNIO & The City and other present and future outreach initiatives. “ Bringing science closer to society, stimulating scientific vocations and providing young people with role models are some of the Centre’s objectives and the spirit for which CNIO & The City stands.” PANTONE 344C C57 M0 Y36 K0 Negro Blanco ANNUAL REPORT 2017 192 International Affairs SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 193 ANNUAL REPORT 2017 194 INTERNATIONAL AFFAIRS INTERNATIONAL AFFAIRS CAROLINA POLA Director of International Affairs SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 195 A focus on innovation and new research alliances has been the main goal of the Department of International Affairs ( IAs ) in 2017. The start of the year strongly set the tone with the hosting of the first Innovative Medicines Initiative ( IMI ) Workshop in Oncology. This event to support the participation of CNIO and other Spanish cancer institutions in IMI, the largest European public-private initiative for drug discovery was organised in collaboration with the Spanish Centre for the Development of Industrial Technology ( CDTI ). Different actors from the Spanish oncology community gathered together at our Centre to discuss the strategy in cancer with high-rank influencers of the European programme. Putting ourselves even more firmly on the map of cancer research and innovation, the CNIO achieved an important milestone in Spain by establishing a research collaboration agreement with the largest Spanish and most international biopharmaceutical company, PharmaMar. This represents a remarkably successful case of knowledge transfer in relation to the support of innovation. In the context of furthering our international impact on public- private collaborations, we have invested efforts in expanding and consolidating our international network for innovation. The joint effort of the IAs and the Department of Innovation to actively engage collaborators in forums such as BIO-Europe 2017 in Berlin, conveys the importance of the interdepartmental work to achieve common goals. Other international networks dedicated to drug discovery, such as the Milner Therapeutics Alliance, now include the CNIO as affiliate academic institution. At the CNIO, basic discoveries and scientific creativity are at the forefront of research progress, and as such, the Centre strives to form alliances with centres of excellence that can serve as springboards for other research collaborations. In 2017, and with the invaluable support of the Ramon Areces Foundation, the 1st CNIO-Weizmann Institute of Science Joint Symposium on ‘ New Insights in Cancer Discovery ’ was launched, creating the appropriate setting for knowledge exchange. The CNIO will continue nurturing this tripartite alliance with the Weizmann Institute of Science in order to set the basis for a fruitful collaboration among scientists from both institutions. Establishing communication channels with international delegations is part of the strategy of IAs, as we can leverage their power to facilitate the creation of partnerships of value for the CNIO and represented countries. This year we established a fruitful relationship with the US Embassy in Spain, resulting in the participation of a CNIO female Head of Unit in the international programme for women leaders in STEM called “ Hidden No More ” to represent Spain in this initiative. We are tapping other embassies to forge new partnerships and to develop new projects that can add value to the scientific community in an international context. Last but not least, we believe that having a strong impact abroad is just as important as being influential in networks that are composed of Spanish Research Centres of Excellence ; in this light, the Severo Ochoa and Maria de Maetzu alliance ( SOMMa ) was recently launched to promote their members internationally and to further boost the high-profile reputation for the institutions. The CNIO is actively participating, through the IAs, as leader of the ‘ work package of Outreach ’. The goals shared by the alliance and our Centre are framed within the European ‘ Responsible Research & Innovation ’ ( RRI ) concept, which continues to guide the institutional strategy and science policy of the CNIO. “ Our international scope embraces the interests of all our different stakeholders, crucial for our development as a centre of excellence. These partnerships with both public and private entities will help us build our roadmap for the future.” ANNUAL REPORT 2017 196 CNIO Offices SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 197 Dean’s Office 198 CNIO Women in Science Office 200 ANNUAL REPORT 2017 198 CNIO OFFICES DEAN’S OFFICE MARÍA S. SOENGAS Dean for Academic Affairs Participants Mónica Álvarez, Daniela Cerezo, Marta Contreras, Guillermo de Cárcer, Ana Losada, Jorge Martínez, David Olmeda, Francisco Real, Mercedes Robledo, Manuel Valiente The CNIO is recognised for the relevance and international projection of our Scientific Programmes. Key to this success is a solid core of undergraduate students, predoctoral and postdoctoral fellows, medical residents and a broad spectrum of visiting scientists. In fact, personnel in training constitute over 60% of the workforce in our institute. As such, the CNIO dedicates particular emphasis to career development, supported in part by highly competitive PhD and Postdoctoral Programmes. Agreements are also in place with multiple universities and medical centres, in order to ultimately bridge the gap between academic and clinical environments. Also very successful are our undergraduate summer internships, as well as diverse exchange and visitor programmes. Part of the CNIO mission is to nurture and foster the development of our scientists-in-training in order to maximise their chances of success. Likewise, we acknowledge that career options extend beyond the bench and therefore we pay special attention to the areas of public communication, management of intellectual property, and the creation of start-ups or spin offs. These activities are performed in concert with CNIO’s Training Programmes, as well as with the Innovation and Communication Offices, which are deeply committed to providing the best environment for our personnel. We are most grateful to the Fundación Jesús Serra for their continuous support to strengthen career development programmes at the CNIO. We believe that an informed society is better prepared to understand ( and if needed, face ) the diseases that constitute human cancer. Therefore, we are actively involved in knowledge dissemination. For example, over 60 CNIO PhD students and postdoctoral fellows volunteered this year took part in the fifth edition of our ‘ Meet a Scientist, Become a Scientist ’ event. This is an open doors activity that we hold as part of the Marie Sklodowska Curie European Researchers’ Night and was attended by over 250 participants of all ages, who learned about the daily life at SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 199 our centre and have the opportunity to run an experiment side by side with our researchers. A particularly inspirational event this year was our Annual CNIO Lab Day. We were fortunate to host Eduardo Oliver, a founding member of the Society of Spanish Researchers in the UK ( SRUK/CERU ), and Patricia Salama, a highly accomplished European Patent Attorney of the Elzaburu Law firm. Eduardo Oliver summarised how the efforts of a small group of postdoctoral fellows coalesced in a successful organisation that today spans multiple cities in the UK and has branches in multiple countries, including Spain. It was a pleasure to hear him explain the networking strategies that SRUK/CERU has in place for the career development of young researchers. He thus emphasised the value of seeking and cultivating the right mentors. In turn, Patricia Salama spoke about her personal voyage from working at the bench to helping scientists translate their findings into valuable intellectual property. Her tips and advice on the aspects of planning and timing public disclosure of marketable results were also very appreciated by the audience. We also had 7 outstanding talks given by CNIO trainees that covered exciting discoveries in the fields of epidemiology, epigenetics, proteomics, metastasis and drug development. Progress made in other basic and translational aspects of cancer were covered in over 60 posters, which together emphasised the breadth of research covered by our different Scientific Programmes. Another main highlight of the Lab Day was the announcement of the recipients of our ‘ Director’s List Awards ’. These are recognitions of outstanding contributions made by our personnel in 3 categories : ( 1 ) predoctoral fellows with publications of the highest scientific impact ; ( 2 ) excellence in research by postdoctoral and staff investigators ; and ( 3 ) altruistic volunteering to further the mission of the Centre related to training, scientific divulgation and outreach. 1. Awards for Excellence in Research by Predoctoral Fellows We are grateful to the Agüera-Nieto family for a generous donation in the name of their mother Antonia Nieto to support an award to acknowledge the PhD student authoring the article with the highest impact in a scientific journal. This year, the “ Antonia Nieto Award ” went to Leire Bejarano, for an impressive work in Cancer Cell on new discoveries in the field of glioblastoma, a highly lethal brain cancer. We are again moved by the commitment of the Agüera-Nieto family, their energy and suggestions for the Amigos del CNIO initiative. Additional awards in the PhD category went to Marta Brandt ( Cell Metabolism ), Metehan Cifdaloz ( Nature Communications ), Teresa Olbrich ( PNAS ) and Laura Remacha ( Clin Cancer Res ). 2. Award for Excellence in Research by Postdoctoral/ Staff Investigators The awardee was David Olmeda, for the development of animal models to visualise melanoma metastasis in vivo, and the unravelling of how these systems lead to the identification of putative markers of poor patient prognosis in this disease ( Nature ). 3. Outstanding Contribution to Outreach and Awareness The recipient was Jorge Martínez-Torrecuadrada, for his tireless efforts in the organisation of the 2017 European Researcher’s Night as well as for his numerous contributions to several open doors activities held over the years. The award was presented by Valle Salnés, the General Director of Juegaterapia. In summary, we are as proud as ever for the achievements of our vibrant community of young investigators at the CNIO. We thank all those public and private contributors that have helped support and fuel their efforts, and will make sure that the coming years will be even more successful in moving the cancer field forward in a meaningful manner for the patients. “ At the CNIO we aim high : we want to carry out the most innovative and competitive basic and translational research, and to best prepare our trainees for the future, so that they can fulfil their potential as influential leaders.” DEAN’S OFFICE ANNUAL REPORT 2017 200 CNIO OFFICES CNIO WOMEN IN SCIENCE OFFICE Lola Martínez Coordinator Members Work-Life Balance Coordinator : Marinela Méndez Seminars and Events Coordinator : Nicole Dölker ( until July ), Isabel López de Silanes ( since September ), Maria A. Blasco, Cristina de Martos, The CNIO Women in Science Office ( WISE ) was established in 2012. Our main objectives are to give visibility to women, to raise awareness regarding the importance of gender equality, to help correct imbalances in the career ladder at the CNIO community, to try to promote and support women in their professional careers, as well as to come up with ideas and policies to improve the life/work balance at the CNIO. The WISE Office is composed of CNIO volunteers from across all the areas present in the Centre including the Director. All of us share the belief that women are still underrepresented in leadership positions in science and we are committed to ensuring gender equality within the research domain. Several studies and statistics from different organisations within Spain and the European Union still display the ‘ scissors ’ graphic when it comes to gender distribution and career ladder positions. There is a clear lack of female talent in leadership positions, which, together with an average 20% salary gap between men and women, are clear indicators that there remains a lot of work to be done in terms of promoting female talent and facilitating access to areas that are still not traditionally open to women. Still today, women are underrepresented in academia. Although data from Universities here in Spain and other European countries show that the percentage of women undertaking university studies is over 50%, and the representation of women at the pre-doctoral and post-doctoral stages is similar, those percentages diminish significantly as we move up the scientific career ladder : a poor 25% of women are represented at the Principal Investigator level, and it is even lower at the levels of Department Directors and beyond. This year, once again, no women were awarded Nobel Prizes in any scientific discipline, despite the fact that there were several women nominated for their key discoveries. Sadly, the acknowledgement of women when it comes to prizes continues to be very low and, in particular, when we consider the most prestigious ones ; is there simply not enough female talent present in the scientific fields, or is it still just harder for SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 201 CNIO WOMEN IN SCIENCE OFFICE them to be recognised for their achievements ? We believe it is mainly due to the second cause and so we continue with our endeavours that take the form of a successful seminar series where we give all CNIO members and others ( including, since last year, students from different high schools in Spain ) the opportunity to listen to and meet women who embody roles and positions that are traditionally not held by women. With this initiative, it is our mission to promote scientific vocations among girls − it is worrying to see the lack of female students in the so-called STEM careers − as well as to positively change the cultural and gender stereotypes that exist among teenagers. A real change is needed, and we are convinced that it needs to come through the education of our younger generations. The Office counts with two main working groups : ɗ Life/Work Balance – aimed to promote and support initiatives to help improve the delicate balance between professional and personal life at CNIO. ɗ Seminars and Events – aimed to raise and stimulate institutional awareness of gender issues, and to provide networking opportunities to all CNIO researchers. In 2017, the WISE office seminar series continued to host several top female leaders from different areas. Some of the talks given during 2017 include : ɗ How the current design of parental leaves is hampering the professional development of women. The ‘ PLENTy of rights ’ proposal. Teresa Jurado and Mariano Nieto. PPIINA ( Spanish Platform for Equal and Non-Transferable Birth and Adoption Leaves ), Madrid, Spain. February 28. ɗ A room of one’s own. A play based on Virginia Woolf’s speech directed by María Ruiz and interpreted by Clara Sanchís, to celebrate International Women’s Day. March 7. ɗ Situation of women’s sport in Spain. Personal experience. Natalia Flores Sanz. Former Spanish National indoor football player. May 23. ɗ Leave your comfort zone and be disruptive. Katharina Miller. European lawyer and founder of 3CCompliance, Madrid, Spain. September 19. ɗ Micromachisms, the daily machismo that conditions the life of women. Ana Requena. Journalist and columnist. October 17. ɗ The future of women lies in our hands. Margarita de Cos. Head Major Donors Relations WWF Spain and CEO of RAINSOFT SL, Madrid, Spain. December 12. We also participated in several initiatives such as ‘ CNIO and The City ’, a science outreach project, co-financed by the FECYT ( Spanish Foundation for Science and Technology ) and Obra Social ”la Caixa ”, with the aim of creating closer links between society and the education system. We are also working on establishing a fruitful collaboration with ESMO ( European Society for Medical Oncology ) in order to expand their survey work on behalf of Women in the Oncology field. The Office has also participated, in a consultancy capacity, in the elaboration of a non-law proposal regarding gender ; the proposal aims to integrate the gender perspective in scientific contents as well as to increase knowledge on illnesses that mainly affect women, focusing on their causes and preventive measures. The proposal was presented to Congress during the 1st quarter of the year. This year, we are also very pleased to announce that one of our members has been selected to participate, along with 47 other women from all over the world, in the International Visitor Leadership Programme run by the U.S. State Department “ Hidden No More : Empowering Women Leaders in STEM ”. “ Here at the WISE Office, we share the views expressed by the African activist and writer Malebo Sephodi : “ we do criticise the narrative that excludes women and continually puts men in the forefront.” Let’s continue working together towards Scientific Excellence, recognising and promoting talent, leaving all gender barriers behind us.” Raquel García-Medina, Diego Megías, Francisca Mulero, Fernando Peláez, Carolina Pola, Alejandra Tavera ANNUAL REPORT 2017 202 Facts & Figures SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 203 Scientific Management 204 Competitive Funding 206 Education and Training Programmes 218 Scientific Events 224 Administration 238 Board of Trustees 238 Scientific Advisory Board 240 Management 242 CNIO Personnel 2017 244 Private Sponsors 248 ANNUAL REPORT 2017 204 FACTS & FIGuRES SCIENTIFIC MANAGEMENT ISABEL BARTHELEMY Scientific Management Director Raquel Ares, Sonia Cerdá, Almudena del Codo, M. Dolores Liébanes, Ana Merino, Juan Ramón Molina ( until June ), Mercedes Moro, Victoria López, Leyre Vergés SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 205 SCIENTIFIC MANAGEMENT | The Scientific Management Department at the CNIO is committed to assisting with the facilitation of all those key areas that help our scientists to better focus their efforts on their research. The Department encompasses various Offices : Projects and Consortia, Education and Training Programmes, Scientific Events, Scientific Publishing, and Library and Archives. The mission of the Projects’ Office is to guide the CNIO scientists through all stages related to the application and management processes of externally-funded projects, whether they be financed through either public and/or private institutions, or stem from either national or international funding bodies. The Office coordinates the internal call alerts, manages the ethical certification for projects involving animal experimentation or human samples, supports scientists with the preparation of the project proposals, manages the ongoing projects, and contacts the funding agencies to resolve any issues or deal with questions. The Training Office is the central point for training at the CNIO ; it aids the recruitment process, serves as an advocate for all fellows, provides administrative support, and creates educational and learning opportunities. It is responsible for helping PhD students, Postdoctoral scientists and post-resident MDs by announcing call alerts and providing the relevant key information ; helping foreign students with their paperwork at the foreign office ; organising the summer training call ; and, in general, in collaboration with the Personnel Department, managing student’s grants. The Events Office organises CNIO meetings, such as the CNIO−”la Caixa ” Foundation Frontiers Meetings, the Distinguished Seminars series, the external Scientific Advisory Board ( SAB ) meeting, CNIO Progress Reports, as well as Faculty retreats, among others. The Office also helps scientists by providing advice for the organisation of specific events, including science outreach events, and supervises the CNIO guided visits. The Scientific Publications Office is responsible for the preparation of institutional scientific publications, including the CNIO Annual Report, booklets of the Scientific Advisory Board meeting and those of other symposia, as well as scientific dissemination leaflets. The Office also provides support for the scientific editing of press notes and other publications of scientific divulgation to a non-specialised audience. The Library administers the electronic subscriptions of over 300 scientific journals at the CNIO and manages journal article requests for journals that the CNIO is not subscribed to. The Library also provides information regarding reference management software. “ All our efforts are dedicated towards providing our scientists with the best possible framework and to taking care of all formalities so that they, in turn, can focus on making a difference through top-notch science.” ANNUAL REPORT 2017 206 FACTS & FIGuRES COMPETITIVE FUNDING The CNIO attracts a substantial proportion of its funding from external sources. Most of this funding comes from national and international funding bodies. In 2017, researchers at the CNIO were involved in 135 projects that received extramural funding. In 2017, the CNIO actively participated in a total of 42 collaborative projects : 20 were international collaborative projects ( 3 of which are coordinated by the CNIO ) and 22 were collaborative projects at the national level ( 7 of them are coordinated by the CNIO ). The international collaborative projects were funded by institutions such as the European Commission through the 7 Framework Programme and Horizon 2020, the Interreg SUDOE Programme, the US National Institutes of Health ( NIH ), the US Department of Defense ( DoD ), the Melanoma Research Alliance, the Paradifference Foundation and the Worldwide Cancer Research. In addition to these collaborative projects, researchers at the CNIO attracted funding for projects that are carried out by individual groups. In 2017, 27 of these projects received international funding, while 66 of them received national funding ( mainly from the State Research Agency, Spanish Ministry of Economy, Industry and Competitiveness, as well as the Institute of Health Carlos III ). The international individual projects are funded by the European Commission ( 4 ERC grants and 8 Marie Curie Actions ), the Worldwide Cancer Research, the Howard Hughes Medical Institute ( HHMI ) and the European Foundation for the Study of Diabetes ( EFSD ). SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 207 SCIENTIFIC MANAGEMENT | COmPETITIvE FUNdING INTERNATIONAL GRANTS COLLAbORATIvE PROJECTS EUROPEAN COMMISSION 7TH FRAMEWORK PROGRAMME ( 2007-2013 ) COST ACTION PRINCIPAL INVESTIGATOR PROJECT TITLE Malats, Núria ( coordinator ) COST Action EU Pancreas : An integrated European platform for pancreas cancer research : from basic science to clinical and public health interventions for a rare disease ( Ref.: COST BM1204 ) EURATOM PRINCIPAL INVESTIGATOR PROJECT TITLE Serrano, Manuel ( until April 30th ) RISK-IR : Risk, Stem Cells and Tissue Kinetics-Ionising Radiation ( Ref.: 323267 ) INTEGRATED PROJECT ( IP ) PRINCIPAL INVESTIGATOR PROJECT TITLE Valencia, Alfonso ( until February 28th ) RD-CONNECT : An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research ( Ref.: 305444 ) ERA-NET ON TRANSLATIONAL CANCER RESEARCH ( TRANSCAN ) PRINCIPAL INVESTIGATOR PROJECT TITLE Malats, Núria Bio-PaC : Biomarkers of tumor recurrence in pancreatic cancer ( financed by ISCIII, Ref.: AC14/00025 ) ERA NET NEURON II : NETWORK OF EUROPEAN FUNDING FOR NEUROSCIENCE RESEARCH PRINCIPAL INVESTIGATOR PROJECT TITLE Malumbres, Marcos MicroKin : Deciphering the multifaceted pathways underlying MCPH pathogenesis in the mouse and human ( financed by MEIC, Ref.: PCIN-2015-007 ) HORIZON 2020 ( 2014-2020 ) RESEARCH INFRASTRUCTURES, INCLUDING E-INFRASTRUCTURES PRINCIPAL INVESTIGATOR PROJECT TITLE Valencia, Alfonso ( until February 28th ) ELIXIR-EXCELERATE : Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences ( Ref.: 676559 ) Valencia, Alfonso ( until February 28th ) OpenMinTeD : Mining INfrastructure for TExt and Data ( Ref.: 654021 ) MARIE SKŁODOWSKA-CURIE ACTIONS ( MSCA ) PRINCIPAL INVESTIGATOR PROJECT TITLE Soengas, María S. ITN IMMUTRAIN : Training network for the immunotherapy of cancer ( Ref.: 641549 ) ANNUAL REPORT 2017 208 FACTS & FIGuRES SOCIETAL CHALLENGE 1 : HEALTH, DEMOGRAPHIC CHANGE AND WELLBEING PRINCIPAL INVESTIGATOR PROJECT TITLE Benítez, Javier BRIDGES : Breast cancer risk after diagnostic gene sequencing ( Ref.: 634935 ) INTERREG SUDOE PROGRAMME 1 PRINCIPAL INVESTIGATOR PROJECT TITLE Valencia, Alfonso ( until February 28th ) Al-Shahrour, Fátima ( since March 1st ) ONCONET : European Network for Translational Research and Innovation in Oncology /Réseau Européen de Recherche translationnelle et d’Innovation en oncologie ( Ref.: SOE1/P1/F0082 ) MELANOMA RESEARCH ALLIANCE ( MRA ) PRINCIPAL INVESTIGATOR PROJECT TITLE Soengas, María S. ( coordinator ) Imaging and targeting dormant and pro-metastatic melanoma lesions in vivo ( Ref.: 401181 ) THE PARADIFFERENCE FOUNDATION PRINCIPAL INVESTIGATOR PROJECT TITLE Robledo, Mercedes SDHB-related metastatic paraganglioma : search for the cure US CONGRESSIONALLY DIRECTED MEDICAL RESEARCH PROGRAMS ( CDMRP )/US DEPARTMENT OF DEFENSE PRINCIPAL INVESTIGATOR PROJECT TITLE Peinado, Héctor Organ-tropic metastatic secretomes and exosomes in breast cancer ( Ref.: W81XWH-13-1-0427 ) US NATIONAL INSTITUTES OF HEALTH ( NIH ) PRINCIPAL INVESTIGATOR PROJECT TITLE Muñoz Fernández, Inés Targeting Mdm2-MdmX E3 ligase for treatment of drug- resistant lymphoma ( Ref.: R01CA208352 ) Peinado, Héctor Characterization and functional analysis of breast cancer secreted exosomes in malignant progression ( Ref.: U01CA169538 ) Peinado, Héctor Exosome-mediated transfer of c-MET to bone marrow progenitors promotes metastasis ( Ref.: R01CA169416 ) Valencia, Alfonso ( until February 28th ) Tress, Michael ( from March 1st on ) GENCODE 2 : Integrated human genome annotation : generation of a reference gene set ( Ref.: U41HG007234 ) WORLDWIDE CANCER RESEARCH ( WCR, FORMERLY AICR ) PRINCIPAL INVESTIGATOR PROJECT TITLE Malats, Núria ( coordinator ) Oral microbiotic profiles and its association with risk of pancreatic ductal adenocarcinoma ( Ref.: 15-0391 ) ELIXIR ( EUROPEAN LIFE- SCIENCE INFRASTRUCTURE FOR BIOLOGICAL INFORMATION ) PRINCIPAL INVESTIGATOR PROJECT TITLE Valencia, Alfonso ( until February 28th ) The ELIXIR Beacon project ( Ref.: ES-2015-BEACON ) Valencia, Alfonso ( until February 28th ) Genomic data management for TraiT using EGA ( Ref.: ES-2015-TRAIT ) 1. This Programme is cofunded by the European Regional Development Fund ( ERDF )  SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 209 SCIENTIFIC MANAGEMENT | COmPETITIvE FUNdING INTERNATIONAL GRANTS INdIvIdUAL PROJECTS EUROPEAN COMMISSION 7TH FRAMEWORK PROGRAMME ( 2007-2013 ) EUROPEAN RESEARCH COUNCIL ( ERC ) PRINCIPAL INVESTIGATOR PROJECT TITLE Fernández-Capetillo, Óscar ERC Consolidator Grant RSHEALTH : Investigating the causes and consequences of replication stress in mammalian health ( Ref.: 617840 ) MARIE CURIE ACTIONS ( MCA ) PRINCIPAL INVESTIGATOR PROJECT TITLE Al-Shahrour, Fátima PERSMEDOMICS : Bioinformatics and integrative genomics for a novel personalized cancer therapy ( Ref.: 334361 ) Peinado, Héctor WHRI COFUND ADIPOMET : Analyzing the crosstalk of tumor and adipose tissue during metastasis ( Ref.: 608765 WHRI-309 ) Plaza, Iván WHRI COFUND : Structure-Function studies of oncogenic RET kinase Fusions in non-small cell Lung Cancer ( NSCLC ): from structure to targeted therapy ( Ref.: 608765 WHRI-612 ) Ramón, Santiago Moreno, María WHRI COFUND CAD_FL : Revealing the functional mechanism of CAD and its potential as a therapeutic target ( Ref.: 608765 WHRI-222 ) Real Arribas, Francisco Paliwal, Sumit WHRI COFUND : NFIC as a novel regulator of pancreatic acinar differentiation and homeostasis ( Ref.: 608765 WHRI-609 ) Squatrito, Massimo GLIDD : DNA Damage Response ( DDR ) signaling in tumor formation and therapeutic resistance of gliomas ( Ref.: 618751 ) Wagner, Erwin F., Gago, Nuria WHRI COFUND STEM-PSO : Unraveling the contribution of Epidermal and Non-Epidermal Progenitor ( Ref.: 608765 WHRI-319 ) HORIZON 2020 ( 2014-2020 ) EUROPEAN RESEARCH COUNCIL ( ERC ) PRINCIPAL INVESTIGATOR PROJECT TITLE Barbacid, Mariano ERC Advanced Grant THERACAN : Novel therapeutic strategies to treat pancreatic and lung cancer ( Ref.: 695566 ) Efeyan, Alejo ERC Starting Grant NutrientSensingVivo : The Physiology of Nutrient Sensing by mTOR ( Ref.: 638891 ) Serrano, Manuel ( until April 30th ) ERC Advanced Grant CELLPASTICITY : New Frontiers in Cellular Reprogramming : Exploiting Cellular Plasticity ( Ref.: 669622 ) MARIE SKŁODOWSKA-CURIE ACTIONS ( MSCA ) PRINCIPAL INVESTIGATOR PROJECT TITLE Soengas, MarÍa S. METMEL : Long range-acting drivers of premetastatic niches in melanoma ( Ref.: 753442 ) HOWARD HUGHES MEDICAL INSTITUTE ( HHMI ) PRINCIPAL INVESTIGATOR PROJECT TITLE Fernández-Capetillo, Óscar Exploring the role of replicative stress in cancer and ageing ( Ref.: 55007417 ) ANNUAL REPORT 2017 210 FACTS & FIGuRES MELANOMA RESEARCH ALLIANCE ( MRA ) PRINCIPAL INVESTIGATOR PROJECT TITLE Soengas, María S. Prognostic and therapeutic impact of lymphovascular niches in melanoma ( Ref.: 348673 ) Valiente Cortés, Manuel Blocking melanoma brain metastasis by targeting the environment ( REF.: 498103 ) PROSTATE CANCER FOUNDATION PRINCIPAL INVESTIGATOR PROJECT TITLE Olmos, David Integration of clinical, molecular and biological characteristics to define an aggressive subtype of prostate cancer based on deficient homologous recombination Castro, Elena Prospective study of lethal prostate cancer clinical and genomic evolution in DNA repair deficient tumours WORLDWIDE CANCER RESEARCH ( WCR, FORMERLY AICR ) PRINCIPAL INVESTIGATOR PROJECT TITLE Blasco, Maria Targeting telomeres in cancer ( Ref.: 16-1177 ) Lietha, Daniel Targeting regulatory mechanisms for allosteric cancer drug discovery ( Ref.: 15-1177 ) Malumbres, Marcos New therapeutic strategies by inhibiting Mastl in breast tumors ( Ref.: 15-0278 ) Peinado, Héctor Evaluation of obesity as a novel risk factor in metastasis ( Ref.: 16-1244 ) Pérez Moreno, Mirna A. Defining the role of macrophage-derived Wnts in squamous cell carcinoma ( Ref.: 15-1219 ) Soengas, María S. Harnessing endo/exocytosis for a coordinated targeting of melanoma cells, their vasculature and the immune system ( Ref.: 15-1374) US CONGRESSIONALLY DIRECTED MEDICAL RESEARCH PROGRAMS ( CDMRP )/US DEPARTMENT OF DEFENSE PRINCIPAL INVESTIGATOR PROJECT TITLE Peinado, Héctor Role of exosomes and Endoglin in Neurofibromatosis Progression ( Ref.: W81XWH-16-1-0131 ) INTERNATIONAL HUMAN FRONTIER SCIENCE PROGRAM ORGANIZATION PRINCIPAL INVESTIGATOR PROJECT TITLE Llorca, Óscar Photochemical trap and high-resolution imaging of transient chromatin complexes from living cells ( Ref.: RGP0031/2017 ) THE COMPANY OF BIOLOGISTS ( COB ) PRINCIPAL INVESTIGATOR PROJECT TITLE Djouder, Nabil Event CNIO CFM : Molecular Chaperones in Cancer ( Ref.: EA1287 ) BEUG FOUNDATION FOR METASTASIS RESEARCH PRINCIPAL INVESTIGATOR PROJECT TITLE Valiente Cortés, Manuel Altered brain vessels as a novel target in brain metastasis SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 211 SCIENTIFIC MANAGEMENT | COmPETITIvE FUNdING NATIONAL GRANTS COLLAbORATIvE PROJECTS INSTITUTE OF HEALTH CARLOS III / INSTITUTO DE SALUD CARLOS III ( ISCIII ) SUB-PROGRAMME OF COOPERATIVE HEALTH RESEARCH THEMATIC NETWORKS/ SUBPROGRAMA DE REDES TEMÁTICAS DE INVESTIGACIÓN COOPERATIVA ( RETICS ) 2 PRINCIPAL INVESTIGATOR PROJECT TITLE Rodríguez, Sandra Red Temática de Investigación Cooperativa en Cáncer ( RTICC ) ( Group, Ref : RD12/0036/0037 ) Malats, Núria Red Temática de Investigación Cooperativa en Cáncer ( RTICC ) ( Group, Ref : RD12/0036/0050 ) SUB-PROGRAMME OF GRANTS FOR RESEARCH SUPPORT PLATFORMS IN HEALTH SCIENCES AND TECHNOLOGY/ SUBPROGRAMA DE AYUDAS PARA PLATAFORMAS DE APOYO A LA INVESTIGACIÓN EN CIENCIAS Y TECNOLOGÍAS DE LA SALUD 3 PRINCIPAL INVESTIGATOR PROJECT TITLE Benítez, Javier Plataforma de recursos biomoleculares y bioinformáticos, PRB 2 ( Group, Ref : PT13/0001/0005 ) Morente, Manuel M. ( coordinator ) Plataforma de Biobancos ( Coordination node and group, Ref : PT13/0010/0001 ) Muñoz, Javier Plataforma de recursos biomoleculares y bioinformáticos, PRB 2 ( Group, Ref : PT13/001/0010 ) Valencia, Alfonso ( until February 28th ) Plataforma de recursos biomoleculares y bioinformáticos, PRB 2 ( Group, Ref : PT13/0001/0030 ) RESEARCH PROJECTS IN HEALTH 4 PRINCIPAL INVESTIGATOR PROJECT TITLE Blasco, Maria A. Cellular aging in first episode early-onset psychosis ( Collaboration with Gregorio Marañón Hospital, Ref.: PI14/00397 ) Blasco, Maria A. Safety and efficacy of gene therapy with telomerase in acute myocardial infarction. Impact on ventricular remodeling in an experimental porcine model. ( Collaboration with Gregorio Marañón Hospital, Ref. DTS15/00095 ) Morente, Manuel ( coordinator ) Optimization of tissue samples for the development and validation of disease biomarkers : the OPTIMARK project. ( Ref.: PI16/00946 ) Olmos, David ( coordinator ) THERATLAS Project : integration of early and adaptative genetic events to establish therapeutic subgroups in Castration- Resistant Prostate Cancer ( Ref.: PI16/01565 ) 2, 3, 4. This Programme is cofunded by the European Regional Development Fund ( ERDF )  ANNUAL REPORT 2017 212 FACTS & FIGuRES STATE RESEARCH AGENCY/ AGENCIA ESTATAL DE INVESTIGACIÓN ( AEI ) MINISTRY OF ECONOMY, INDUSTRY AND COMPETITIVENESS / MINISTERIO DE ECONOMÍA, INDUSTRIA Y COMPETITIVIDAD ( MEIC ) NATIONAL PLAN FOR SCIENTIFIC AND TECHNICAL RESEARCH AND INNOVATION ( 2013-2016 ) EXCELLENCE NETWORKS/ REDES DE EXCELENCIA PRINCIPAL INVESTIGATOR PROJECT TITLE Efeyan, Alejo ( Coordinator ) METABOCANCER : crosstalk between systemic and cellular metabolism in cancer ( Ref.: SAF2016-81975-REDT ) CHALLENGES-COLLABORATION/RETOS-COLABORACIÓN 5 PRINCIPAL INVESTIGATOR PROJECT TITLE Djouder, Nabil NRCANCER : desarrollo de nueva terapia antitumoral basada en nicotinamida-ribosido ( Ref.: RTC-2016-5431-1 ) Soengas, María S. Ensayo Clínico Fase I de BO-110 : un nuevo tratamiento para melanoma avanzado y otros tumores ( Ref.: RTC-2014-2442-1 ) SPANISH ASSOCIATION AGAINST CANCER / ASOCIACIÓN ESPAÑOLA CONTRA EL CÁNCER ( AECC ) PRINCIPAL INVESTIGATOR PROJECT TITLE Barbacid, Mariano ( coordinator ) A multifaceted approach to target pancreatic cancer ( Ref.: GC16173694BARB ) Benítez, Javier Cancer and immunodeficiency in children ( Ref.: CEI14142070LOPE ) Malats, Núria Real, Francisco X. ( coordinator ) Invasive bladder cancer : towards precision medicine ( Ref.: GCB14142293REAL ) Gómez, Gonzalo Peinado, Héctor Soengas, María S. ( coordinator ) Distinct routes of metastatic dissemination in different melanoma subtypes. Implications in the validation of new tumor biomarkers and therapeutic targets ( Ref.: GCB15152978SOEN ) Valiente, Manuel Study of the molecular mechanisms involved in primary ( glioblastoma ) and secondary ( metastasis ) brain tumors to identify novel therapeutic targets and anti-cancer agents, biomarkers to select treatments and novel non-invasive methods for molecular diagnosis ( Ref.: GCTRA16015SEOA ) LA MARATÓ TV3 FOUNDATION / FUNDACIÓN LA MARATÓ TV3 PRINCIPAL INVESTIGATOR PROJECT TITLE Barbacid, Mariano Molecular analysis of Capicua, a novel tumor suppressor involved in RTK signalling and transcriptional repression ( Ref.: 20131730/31 ) Fernández-Capetillo, Óscar Exploring synthetic lethal interactions between PARP and the DNA damage response in cancer treatment ( Ref.: 20134130/31 ) Soengas, María S. Role of RNA binding proteins in melanoma progression : searching for new diagnostic markers and therapeutic targets ( Ref.: 20131430/31 ) MADRI+D FOUNDATION / FUNDACIÓN PARA EL CONOCIMIENTO MADRI+D PRINCIPAL INVESTIGATOR PROJECT TITLE Dean’s Office for Academic Affairs Soengas, María S. European Researchers ’ Night 2016-2017, organized by Madri+d Foundation and founded by European Commission, H2020 Programme ( Ref : MadridERN2016-2017, GA 721631 ) 5. This Programme is cofunded by the European Regional Development Fund ( ERDF )  SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 213 SCIENTIFIC MANAGEMENT | COmPETITIvE FUNdING NATIONAL GRANTS INdIvIdUAL PROJECTS INSTITUTE OF HEALTH CARLOS III / INSTITUTO DE SALUD CARLOS III ( ISCIII ) RESEARCH PROJECTS IN HEALTH 6 PRINCIPAL INVESTIGATOR PROJECT TITLE Benítez, Javier Biologic and genetic bases of telomere shortening in hereditary breast cancer. Searching for new high susceptibility genes in BRCAX families with short telomeres ( Ref.: PI12/00070 ) Benítez, Javier Massive sequencing contributes to decipher the genetic bases of families with rare tumors ( Ref.: PI16/00440 ) Cascón, Alberto Exome sequencing of trios, mother-father-proband, in pediatric patients with multiple pheochromocytomas/paragangliomas ( Ref.: PI12/00236 ) Cascón, Alberto Next generaton sequencing of genes directly and indirectly involved in the Krebs cycle, applied to pheochromocytomas/paragangliomas with hypermethylated phenotype ( Ref.: PI15/00783 ) Cigudosa, Juan C. ( until 31st January ) Genetic diagnostics by next-generation-sequencing in myeloid neoplasias : step towards its clinical use and characterization studies on the mutation genomic and functional pathological effects ( Ref.: PI12/00425 ) Malats, Núria Aetiology of pancreas cancer : Application of “ omics ” technologies in the assessment of risk factors ( Ref.: PI12/00815 ) Malats, Núria Building and validation of risk prediction models for pancreas cancer. The application of a multi-omics approach ( Ref.: PI15/01573 ) Molina, María Esther Dietary patterns, antioxidants and biomarkers of oxidant-antioxidant status in the EPIC-Granada and EPIC-Gipuzkoa ( European Prospective Investigation into Cancer and Nutrition ) cohort ( Ref.: PI12/00002 ) Quintela, Miguel Ángel Tumor-tolerant immune reprogramming secondary to hypoxia- inducing antiangiogenics in breast cancer : physiopathogenic mechanisms and therapeutic utility ( Ref.: PI16/00354 ) Robledo, Mercedes Prognostic profiles in endocrine tumours identified by next generation sequencing, and definition of markers with clinical utility ( Ref.: PI14/00240 ) Rodríguez, Sandra Ewing Sarcoma Model : induction of the t( 11 ;22 ) translocation in human mesenchymal stem and iPS cells by the CRISPR-Cas9 system and study of the cellular context and other secondary events role ( Ref.: PI14/01884 ) Urioste, Miguel PTEN-hamartoma tumour syndrome research : Phenotypic spectrum, associated cancers, molecular basis and search of new gene ( Ref.: PI14/00459 ) STATE RESEARCH AGENCY/ AGENCIA ESTATAL DE INVESTIGACIÓN ( AEI ) MINISTRY OF ECONOMY, INDUSTRY AND COMPETITIVENESS / MINISTERIO DE ECONOMÍA, INDUSTRIA Y COMPETITIVIDAD ( MEIC ) NATIONAL R&D&I PLAN 2008-2011 SUB-PROGRAMME FOR NON-TARGETED FUNDAMENTAL RESEARCH PROJECTS / SUBPROGRAMA DE PROYECTOS DE INVESTIGACIÓN FUNDAMENTAL NO ORIENTADA PRINCIPAL INVESTIGATOR PROJECT TITLE UluÇkan, Özge PsorTACEmiR21 : Investigating the role of microRNA21/ TIMP-3/TACE in psoriasis - evaluating the potential therapeutic implications ( Ref.: SAF2012-39670 ) 6. This Programme is cofunded by the European Regional Development Fund ( ERDF )  ANNUAL REPORT 2017 214 FACTS & FIGuRES NATIONAL PLAN FOR SCIENTIFIC AND TECHNICAL RESEARCH AND INNOVATION ( 2013-2016 ) CENTRES AND UNITS OF EXCELLENCE “ SEVERO OCHOA ” SUB-PROGRAMME/ SUBPROGRAMA DE APOYO A CENTROS Y UNIDADES DE EXCELENCIA ‘ SEVERO OCHOA ’ PRINCIPAL INVESTIGATOR PROJECT TITLE Blasco, Maria A. Centre of Excellence “ Severo Ochoa ” ( Ref.: SEV-2015-0510 ) R&D EXCELLENCE PROJECTS/ PROYECTOS DE I+D EXCELENCIA 7 PRINCIPAL INVESTIGATOR PROJECT TITLE Méndez, Juan REPLICON : Molecular mechanisms that control eukaryotic DNA replication ( Ref.: BFU2013-49153-P ) Ramón, Santiago ( until March 23rd ) CADstructure : Structural determination of the architecture of CAD, an antitumoral target that controls the biosynthesis of pyrimidines ( Ref.: BFU2013-48365-P ) Ruiz, Sergio RSHIPS : Replicative stress during somatic cell reprogramming ( Ref.: SAF2013-49147-P ) Ruiz, Sergio Role of RAS signaling in pluripotency and totipotency ( Ref.: SAF2016-80874-P ) CHALLENGES-RESEARCH/RETOS-INVESTIGACIÓN 8 PRINCIPAL INVESTIGATOR PROJECT TITLE Barbacid, Mariano PANTHER : A three prong strategy to fight pancreatic ductal adenocarcinoma ( Ref.: SAF2014-59864-R ) Blasco, Maria A. TeloHealth : Telomeres, telomerase and disease ( Ref.: SAF2013-45111-R ) Djouder, Nabil MILC : Metabolic inflammation in liver cancer ( Ref.: SAF2013-46089-R ) Djouder, Nabil URI loss in intestinal pathologies ( Ref.: SAF2016-76598-R ) Efeyan, Alejo NUTRIENTOR : Physiology of nutrient sensing and signaling by the mTOR complex 1 ( Ref.: SAF2015-67538-R ) Fernández-Capetillo, Óscar BREAKINGRAD : Exploring the limits of radioresistance in mammals ( Ref.: SAF2014-59498-R ) Lietha, Daniel Structural studies elucidating the activation mechanism of Focal Adhesion Kinase ( Ref.: BFU2016-77665-R ) Llorca, Óscar ( since July 1st ) RuvBL1-RuvBL2 ATPases in DNA/RNA surveillance and human diseases : molecular and structural mechanisms ( Ref.: SAF2014-52301-R ) Losada, Ana COHESIN : Cohesin function and regulation : a multidisciplinary approach ( Ref.: BFU2013-48481-R ) Losada, Ana Molecular mechanisms of variant cohesin function ( Ref.: BFU2016-79841-R ) Malumbres, Marcos Cyclexit : Physiological and therapeutic relevance of mitotic kinases and phosphatases ( Ref.: SAF2015-69920-R ) Méndez, Juan Ramón Control of eukaryotic DNA replication ( Ref.: BFU2016-80402-R ) Muñoz, Javier steMS : Understanding ground state pluripotency of embryonic stem cells through mass spectrometry-based proteomics ( Ref.: SAF2013-45504-R ) 7, 8. This Programme is cofunded by the European Regional Development Fund ( ERDF )  SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 215 SCIENTIFIC MANAGEMENT | COmPETITIvE FUNdING Muñoz, Javier Epigenetic modifiers in pluripotency : a proteomic analysis of non-histone protein methylation ( Ref.: SAF2016-74962-R ) Ortega, Sagrario HaploEScancer : Haploid ES cells for cancer research ( Ref.: SAF2013-44866-R ) Osorio, Ana IPAGEN : Exploring the mechanism of action of PARP inhibitors in breast and ovarian cancer patients. Identification of new genetic predictors of response ( Ref.: SAF2014-57680-R ) Peinado, Héctor METASTAXOMEs : Role of tumor-secreted exosomes in lymph node microenvironment reprogramming during metastasis ( Ref.: SAF2014-54541-R ) Pérez Moreno, Mirna A. ESSENCE : Extrinsic control of the skin stem cell niche in homeostasis and cancer ( Ref.: BFU2015-71376-R ) Ramón, Santiago ( until March 23rd ) Structure and functional characterization of CAD, an anti-tumoral target controlling the synthesis of pyrimidines ( Ref.: BFU2016-80570-R ) Real, Francisco X. TRANS-PDAC : Transcriptional control of pancreatic cancer development ( Ref.: SAF2015-70553-R ) Rodríguez, Cristina PREDICT : Identification of genetic markers and physiopathologic factors predictive of the peripheral neuropathy of paclitaxel and of other oncologic drugs : massive sequencing of candidate genes ( Ref.: SAF2015-64850-R ) Serrano, Manuel ( until April 30th ) CANCERAGE : Cancer and ageing-associated diseases : new frontiers and new strategies ( Ref.: SAF2013-48256-R ) Soengas, María S. MEL-STOP : Vesicular trafficking in melanoma progression and treatment response ( Ref.: SAF2014-56868-R ) Valencia, Alfonso ( until February 28th ) EPIC : Expression Patterns of Inverse Comorbidity ( Ref.: BFU2015-71241-R ) Valiente, Manuel ReACTIVE BrainMET : Dissecting the role of reactive astrocytes in brain metastasis ( Ref.: SAF2014-57243-R ) Wagner, Erwin F. CANPSOR : Investigating Cancer Risk in Psoriasis ( Ref.: SAF2015-70857-R ) EXPLORA PROJECTS PRINCIPAL INVESTIGATOR PROJECT TITLE Blasco, Maria A. Non canonical treatment for neurodegenerative diseases : telomerase gene therapy ( Ref.: SAF2015-72455-EXP ) NETWORKS AND SCIENTIFIC MANAGERS-EUROPE / EUROPA REDES Y GESTORES PRINCIPAL INVESTIGATOR PROJECT TITLE Blasco, Maria A. CNIO in Horizon 2020 : support for proposal preparation and project management ( Ref.: EUC2014-51617 ) YOUNG RESEARCHERS PROGRAM/ PROGRAMA JÓVENES INVESTIGADORES 9 PRINCIPAL INVESTIGATOR PROJECT TITLE Álvarez, Mónica GPGenCan : Functional relevance of Greatwall/PP2A pathway in the maintenance of genomic stability : therapeutic implications in cancer ( Ref.: SAF2014-60442-JIN ) Lecona, Emilio UBQREP : Modulation of DNA Replication by ubiquitination of chromatin proteins ( Ref.: BFU2014-55168-JIN ) 9. This Programme is cofunded by the European Regional Development Fund ( ERDF )  ANNUAL REPORT 2017 216 FACTS & FIGuRES SCIENTIFIC INFRASTRUCTURES/INFRAESTRUCTURAS CIENTÍFICO-TECNOLÓGICAS 10 PRINCIPAL INVESTIGATOR PROJECT TITLE Muñoz, Javier Sistema cromatográfico UHLPC acoplado a Espectrómetro de Masas de alta resolución para estudios de proteómica avanzada ( Ref.: CNIO15-EE-2855 ) Pisano, David G. Clúster SMP de Análisis HPC ( Ref.: CNIO15-EE-3845 ) SPANISH FOUNDATION FOR SCIENCE AND TECHNOLOGY / FUNDACIÓN ESPAÑOLA PARA LA CIENCIA Y TECNOLOGÍA ( FECYT ) PRINCIPAL INVESTIGATOR PROJECT TITLE Pola, Carolina CNIO and the City – Construyendo un Puente a la Sociedad ( Ref.: FCT-16-11115 ) SPANISH ASSOCIATION AGAINST CANCER / ASOCIACIÓN ESPAÑOLA CONTRA EL CÁNCER ( AECC ) PRINCIPAL INVESTIGATOR PROJECT TITLE Efeyan, Alejo Grant for emerging Groups : Nutrient signaling in the pathogenesis and treatment of B cell Lymphoma ( Ref.: LABAE16001EFEY ) Squatrito, Massimo Grant for emerging Groups : Novel therapeutic approaches for therapy-resistant malignant brain tumors ( Ref.: LABAE16015SQUA ) de Cárcer, Guillermo Grant for emerging Groups : Identification of new biomarkers for breast cancer : mechanisms of sensitivity and resistance to cell cycle drugs ( Ref.: LABAE16017DECÁ ) Squatrito, Massimo “ Idea Semilla ” Grant : Identification of biomarkers of tumor treating fields ( TTFields ) in glioblastoma ( Ref.: IDEAS185SQUA ) ASTRAZENECA FOUNDATION / FUNDACIÓN ASTRAZENECA PRINCIPAL INVESTIGATOR PROJECT TITLE Quintela, Miguel Ángel Reprogramación inmune en cáncer de mama preexpuesto a antiangiogénicos inductores de apoxia LEUKEMIA AND LYMPHOMA FOUNDATION / FUNDACIÓN LEUCEMIA Y LINFOMA PRINCIPAL INVESTIGATOR PROJECT TITLE Ortega, Ana “ Marcos Fernández ” Grant : Functional characterization of RagC mutations in Follicular Lymphoma pathogenesis SPANISH ASSOCIATION OF GASTROENTEROLOGY / ASOCIACIÓN ESPAÑOLA DE GASTROENTEROLOGÍA PRINCIPAL INVESTIGATOR PROJECT TITLE Molina, Mª Esther Evaluación del valor pronóstico de diabetes mellitus tipo II ( DM2 ) en pacientes con cáncer de páncreas 10. This Programme is cofunded by the European Regional Development Fund ( ERDF )  SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 217 SCIENTIFIC MANAGEMENT | COmPETITIvE FUNdING FERO FOUNDATION / FUNDACIÓN FERO PRINCIPAL INVESTIGATOR PROJECT TITLE Peinado, Héctor Liquid biopsy by nanoplasmonic detection of exosomes : predicting response to ( immuno- and radio )-therapy Valiente, Manuel Predictive biomarkers for brain metastasis in small cell lung cancer ATRESMEDIA COORPORATION / ATRESMEDIA COORPORACIÓN PRINCIPAL INVESTIGATOR PROJECT TITLE Fernández-Capetillo, Óscar Premio Constantes y Vitales en la categoría “ Joven talento en investigación biomédica ” 2015 ( A3M 2015 ) OLGA TORRES FOUNDATION / FUNDACIÓN OLGA TORRES PRINCIPAL INVESTIGATOR PROJECT TITLE Djouder, Nabil Understanding the role of growth factors and nutrients in inflammatory bowel disease and colon cancer FUNDACIÓN PROYECTO NEUROFIBROMATOSIS PRINCIPAL INVESTIGATOR PROJECT TITLE Peinado, Héctor Uso de exosomas circulantes como marcadores de progresión en neurofibromatosis y para la determinación de nuevas estrategias terapéuticas BBVA FOUNDATION / FUNDACIÓN BBVA PRINCIPAL INVESTIGATOR PROJECT TITLE Squatrito, Massimo Leonardo Grant : Precision glioma mouse models by somatic genome editing with the RCAS-CRISPR-Cas9 system Valencia, Alfonso ( until February 28th ) BIG DATA Grant PerMed : Precision Medicine from Big Data to Cognitive Computing CNIO ( Ref.: 76/2016 ) FUNDACIÓN PFIZER PRINCIPAL INVESTIGATOR PROJECT TITLE Peinado, Hector Tumour exosome integrins determine organotropic metastasis ANNUAL REPORT 2017 218 FACTS & FIGuRES EDUCATION AND TRAINING PROGRAMMES One of the principal goals of the CNIO is to increase its training capacity in order to give students and professionals the opportunity to advance their careers in the healthcare sector. During 2017, the CNIO signed several new agreements with Spanish Universities and other institutions, namely with the Universidad de Extremadura, Universidad Complutense de Madrid, Universidad Internacional de la Rioja, Fundación Banco Santander, Fundación La Caixa, FCT Puerta de Hierro and CESUR. TRAINING PROGRAMMES PARTICIPANTS IN EDUCATION AND TRAINING PROGRAMMES 2013 2014 2015 2016 2017 Training of PhD students 116 108 105 110 112 Post-doctoral training 67 55 48 51 44 Training for MDs 21 14 25 17 21 Laboratory training for MSc/BSc students 36 73 80 95 99 Laboratory training for technicians 19 21 27 26 20 TRAINING OF BSC/MSC STuDENTS The CNIO is committed to training junior scientists at the onset of their careers. To this end, the Centre has established a Programme that offers BSc and MSc students the opportunity to obtain hands-on practical laboratory experience by working on ongoing research projects in one of the CNIO groups. The CNIO offers 2 types of short-term laboratory training : An annual Summer Training Programme for undergraduate students, from any country, who are in their last years of study in the biomedical field. The Programme encompasses 8 weeks of full-time laboratory training ( 292.5 hours ). During this time, the students actively participate in research projects in one of the CNIO groups. During 2017, 7 students from 4 different countries participated in this programme. Additionally, students can apply for laboratory training throughout the academic year by directly contacting the Heads of CNIO individual Research Groups or Units. This year, 99 students participated in these programmes, of which 3 ended up joining the CNIO as pre-doctoral students. TRAINING OF PHD STuDENTS The training of PhD students in cutting-edge cancer research is of key importance to the CNIO. The Centre offers many opportunities for bright and dynamic university graduates, of all nationalities, to pursue an ambitious PhD project. To attest this, 21 students obtained their PhD degrees in 2017 and 21 others joined the CNIO in the same year. Over 21% of the 112 students working at the CNIO in 2017 were graduates from foreign universities, thus contributing to the internationalisation of the Centre. Since 2008, the Fundación “ la Caixa ” offers international fellowships to PhD students to enable them to carry out their thesis projects in biomedical research in Spanish centres of excellence. The CNIO was chosen, as one of such centres, to launch a programme for outstanding young pre-doctoral students from all over the world who have an interest in pursuing an ambitious PhD project. Since 2013, the Ministry of Economy, Industry and Competitiveness has undertaken efforts to link the “ la Caixa ”/CNIO International PhD Programme to distinguished research centres accredited as “ Severo Ochoa ” Centres of Excellence. In 2017, a new doctoral fellowship programme of “ la Caixa ” Foundation, named INPhINIT, was launched to recruit outstanding international students : 2 pre-doctoral students received one of these 3-year contracts. The Fundación “ La Caixa ” also launched a call to carry out a doctorate at Spanish universities and research centres ; CNIO was chosen as a host institution. During 2017, 1 pre-doctoral student received this fellowship. The distribution of students across the CNIO’s Research Programmes in 2017 was as follows : 53% of students worked in the SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 219 SCIENTIFIC MANAGEMENT | EdUCATION ANd TRAINING PROGRAmmES Molecular Oncology Programme, 13% in the Structural Biology Programme, 13% in the Cancer Cell Biology Programme, 10% in the Human Cancer Genetics Programme, 1% in the Experimental Therapeutics Programme, 2% in the Biotechnology Programme, and 8% in the Clinical Research Programme. FuNDING OF PHD TRAINING NO. SPANISH ORGANISATIONS 88 State Research Agency, Ministry of Economy, Industry and Competitiveness / Agencia Estatal de Investigación (AEI), Ministerio de Economía, Industria y Competitividad (MEIC) ( Predoctoral fellowships ) 39 State Research Agency, Ministry of Economy, Industry and Competitiveness / Agencia Estatal de Investigacion (AEI), Ministerio de Economía, Industria y Competitividad (MEIC) ( I+D Projects ) 9 Ministry of Education, Culture and Sport / Ministerio de Educación, Cultura y Deporte (MECD) ( Predoctoral fellowships ) 6 Institute of Health Carlos III / Instituto de Salud Carlos III (ISCIII) ( I+D Projects ) 4 ”la Caixa” Banking Foundation / Fundación Bancaria ”la Caixa” ( Predoctoral fellowships ) 17 Spanish Association Against Cancer ( AECC ) / Fundación Científica de la AECC ( I+D Projects ) 2 Community of Madrid / Comunidad de Madrid 2 Cris Foundation / Fundación Cris 3 FERO Foundation / Fundación FERO 1 CNIO 5 INTERNATIONAL ORGANISATIONS 24 European Commission Framework Programme / H2020 1 Marie Skłodowska-Curie actions of the European Commission 2 European Research Council 6 Fundação do Ministério de Ciência e Tecnologia de Portugal (FCT) 1 China Scholarship Council 2 European Foundation for the Study of Diabetes 1 Melanoma Research Alliance 1 Boehringer Ingelheim 2 Consejo Nacional de Ciencia y Tecnología ( Mexico ) 2 Howard Hughes Medical Institute 1 Pfizer 5 TOTAL 112 ANNUAL REPORT 2017 220 FACTS & FIGuRES POST-DOCTORAL TRAINING One of the CNIO’s prime objectives is to attract young researchers, who have recently obtained their PhD or MD degrees, and to offer them highly attractive research projects at the forefront of cancer research. In 2017, 44 postdoctoral fellows worked at the CNIO. Notably, more than one third of these fellows were from outside of Spain, many coming from very prestigious international institutions. In 2017, the Fundación Banco Santander signed a new annual agreement with the CNIO to continue the highly competitive fellowship programme aimed at supporting outstanding young scientists who have been trained in the UK or in the USA, and who wish to start or continue their postdoctoral training at the CNIO. One young scientist from the City University of New York ( CUNY ) was awarded the Banco Santander Foundation-CNIO Fellowship in early 2017. Thanks to the donations received through the ‘ CNIO Friends ’ platform, launched in 2017, the second call of the Postdoctoral Contract ‘ CNIO Friends ’ Programme resulted in the recruitment of 2 scientists for a 2-year period each. Also, thanks to a ‘ Juegaterapia-CNIO Friends ’ Postdoctoral Contract in 2017, one scientist was able to continue with her project related to paediatric oncology. FuNDING SOuRCES OF POST-DOCTORAL RESEARCHERS NO. SPANISH ORGANISATIONS 28 State Research Agency, Ministry of Economy, Industry and Competitiveness / Agencia Estatal de Investigación ( AEI ), Ministerio de Economía, Industria y Competitividad ( MEIC ) ( Postdoctoral Fellowships ) 3 State Research Agency, Ministry of Economy, Industry and Competitiveness / Agencia Estatal de Investigación ( AEI ), Ministerio de Economía, Industria y Competitividad ( MEIC ) ( I+D Projects ) 4 Institute of Health Carlos III / Instituto de Salud Carlos III ( ISCIII ) ( I+D Projects ) 1 Institute of Health Carlos III / Instituto de Salud Carlos III ( ISCIII ) ( Postdoctoral Fellowhips ) 2 Spanish Association Against Cancer ( AECC ) / Fundación Científica de la AECC ( Postdoctoral Fellowhips ) 3 Spanish Association Against Cancer ( AECC ) / Fundación Científica de la AECC ( I+D Projects ) 1 Community of Madrid / Comunidad de Madrid 1 Banco Santander Foundation / Fundación Banco Santander 2 La Marató TV3 Foundation/ Fundació La Marató TV3 1 Celgene 1 CNIO 9 INTERNATIONAL ORGANISATIONS 16 European Commission Framework Programme / H2020 1 European Research Council 3 Marie Skłodowska-Curie actions of the European Commission 2 Melanoma Research Alliance 1 Worldwide Cancer Research UK 5 US Department of Defense 1 Daiichi Sankyo Agreement 1 Pfizer 2 TOTAL 44 SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 221 SCIENTIFIC MANAGEMENT | EdUCATION ANd TRAINING PROGRAmmES POSTGRADuATE PROGRAMMES In addition, the CNIO – in collaboration with academic institutions across Spain – provides access to a variety of postgraduate programmes that cover the areas of Cellular & Molecular Biology, Molecular Biomedicine, Biotechnology, Biocomputing & Computational Biology, Clinical & Applied Cancer Research, Therapeutic Targets, and Molecular Oncology. Official Postgraduate Programmes in Biosciences The majority of the international postgraduate trainings offered at the CNIO are developed in collaboration with the Faculty of Medicine and Faculty of Sciences at the Autonomous University of Madrid ( UAM ). These trainings fall under 4 Official Postgraduate Programmes, namely, the Doctorate in Biosciences, Master’s in Molecular and Cell Biology, Master’s in Molecular Biomedicine, and Master’s in Biotechnology. CNIO also collaborates with the UAM, as a Partner Institution of UAM´s Doctoral School (EDUAM), and is a member of the Management Committee. Master’s Degree in Biocomputing and Computational Biology The Master’s in Bioinformática y Biología Computacional is organised together with the National School of Health of the National Institute of Health Carlos III ( Escuela Nacional de Sanidad del Instituto de Salud Carlos III, ENS-ISCiii ), and the Madrid Science Park ( Parque Científico de Madrid, PCM ). Official Master’s Degree in Clinical and Applied Cancer Research The CNIO and the CEU-San Pablo University in Madrid ( USP- CEU ) co-organise a Postgraduate Training Programme in Clinical and Applied Cancer Research : the Máster Universitario en Investigación Clínica y Aplicada en Oncología. ANNUAL REPORT 2017 222 FACTS & FIGuRES Official Master’s Degree in Therapeutic Targets, Research and Development The CNIO collaborates with the Biochemistry and Molecular Biology Department at the University of Alcalá de Henares ( UAH ) for the Máster Oficial en Dianas Terapéuticas, Investigación y Desarrollo. Master’s Degree in Molecular Oncology The main objective of this Master’s degree, organised in collaboration with the Centre for Biomedical Studies ( Centro de Estudios Biosanitarios, CEB ), is to offer training in molecular oncology with an emphasis on the latest findings in translational research that are essential for state-of-the art oncological clinical practice. Upon successful completion of the 500 hours of training, a certificate for a Master’s degree in Molecular Oncology – recognised by the European School of Oncology ( ESO ) – is awarded. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 223 SCIENTIFIC MANAGEMENT | EdUCATION ANd TRAINING PROGRAmmES LABORATORy TRAINING FOR TECHNICIANS This training programme has been developed for students in Anatomical Pathology, Clinical Diagnostic Laboratory, and Archiving/Recording ; it is organised through agreements with 19 institutions that provide secondary education for laboratory technicians in Spain. It provides students with hands-on knowledge in cellular and molecular biology techniques. The programme consists of 14 weeks ( 370-400 hours ) of laboratory training for students. Of the 20 students who participated in this programme in 2017, 2 were hired by the CNIO. TRAINING FOR MDS In line with CNIO’s commitment to bridge the ‘ bench to bedside ’ gap, the Centre offers 3 training opportunity programmes to MDs and other health care professionals. Training usually consists of a 3-month period during residency. In 2017, 24 medical residents from 18 different hospitals enjoyed the benefits of rotations within the different Groups and Units at the CNIO. ADVANCED TRAINING OF SCIENTISTS THROuGH ExTRAMuRAL PROGRAMMES During 2017, the Ramón y Cajal Programme supported 8 scientists. This special initiative, established in 2001 by the former Spanish Ministry of Science and Technology ( currently the State Research Agency of the Spanish Ministry of Economy, Industry and Competitiveness ) aims to encourage Spanish or foreign scientists working abroad to return to or relocate to Spain. Successful candidates are selected on the basis of their potential capacity to lead independent projects and groups, or to contribute successfully to the ongoing research in the existing groups. Ten other scientists were funded by similar programmes, including the Juan de la Cierva programme ( Spanish Ministry of Economy, Industry and Competitiveness, 4 contracts ); Miguel Servet ( 1 contract ) and SEOM-Río Hortega ( contract funded by the Spanish Society of Medical Oncology, 1 contract ) programmes of the Institute of Health Carlos III ; and the Spanish Association Against Cancer ( AECC, 4 contracts ). VISITING RESEARCHER PROGRAMME The Jesús Serra Foundation, part of the Catalana Occidente Group, aims to help eminent international specialists work together with CNIO researchers for a few months in order for them to expand their knowledge in areas of common interest. During 2017, Raul Rabadan, from Columbia University in New York ( USA ) was beneficiary of the Jesús Serra Foundation’s Visiting Researcher Programme. In addition, Wolfgang Weninger, from the Royal Prince Alfred Hospital of Sydney ( Australia ) was also a beneficiary. ‘ SCIENCE By WOMEN ’ PROGRAMME Thanks to this Programme, launched by the Spanish “ Fundación Mujeres por África ”, 2 African Scientists stayed at the CNIO as visiting scientists : Ann Louw, from the University of Stellenbosch in South Africa, worked in the Experimental Therapeutics Programme from January to June 2017 ; and Chiaka Anumudu, from the University of Ibadan in Nigeria, worked in the Genetic and Molecular Epidemiology Group from August 2017 to January 2018. ANNUAL REPORT 2017 224 FACTS & FIGuRES SCIENTIFIC EVENTS CNIO-”LA CAIxA ”FOuNDATION FRONTIERS MEETINGS CNIO-”la Caixa ” Foundation Frontiers Meetings are the main international conferences organised by the CNIO and ”la Caixa ” Foundation. They focus on specific, cutting-edge aspects of cancer research, thus providing a unique platform for an intensive and dynamic exchange and debate of scientific ideas. The invited speakers – 20 internationally renowned leaders in oncology – present their latest findings during 2 and a half days. Up to 100 additional participants are selected, via a widely publicised call for applications, based on their potential to make relevant contributions to the conference by presenting hot topics as posters or short talks. PRIMARy AND SECONDARy BRAIN TuMORS 19-22 FEbRUARy 2017 ORGANISERS · Massimo Squatrito, Spanish National Cancer Research Centre ( CNIO ), Madrid, Spain · Manuel Valiente, Spanish National Cancer Research Centre ( CNIO ), Madrid, Spain · Richard Gilbertson, CRUK Cambridge Institute, UK · Michael Weller, University Hospital Zurich, Switzerland SESSIONS · Primary Adult Brain Tumors ( I ) · Primary Adult Brain Tumors ( Ii ) · Secondary Adult Brain Tumors ( I ) · Secondary Adult Brain Tumors ( Ii ) · Primary And Metastatic Pediatric Tumors SPEAKERS · Suzanne Baker, Brain Tumor Research Division, St. Jude Children’s Research, Hospital, Memphis, US · Gabriele Bergers, Vesalius Research Center, Leuven, Belgium · Priscilla Brastianos, Massachusetts General Hospital, Harvard Medical School, Boston, US · Amy B. Heimberger, The University of Texas MD Anderson Cancer Center, Houston, US · Eric Holland, Nancy and Buster Alvord Brain Tumor Center, Fred Hutchinson Cancer Research Center, UW Medicine, US · Luis F. Parada, Brain Tumor Center, Albert C. Foster, MSKCC, New York, US · Stefan Pfister, DKFZ, Heidelberg, Germany · Matthias Preusser, Comprehensive Cancer Center Vienna, Medical University of Vienna, Austria · Nicola Sibson, CRUK/MRC Oxford Institute for Radiation Oncology, UK · Joan Seoane, Vall d’Hebron Institute of Oncology, Barcelona, Spain · Riccardo Soffietti, University and City of Health and Science University Hospital of Turin, Italy · Michael Taylor, The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Ontario, Canada · Roeland Verhaak, The University of Texas MD Anderson Cancer Center, The Jackson Laboratory for Genomic Medicine, US Suzanne Baker Brain Tumor Research Division, St. Jude Children s´ Research, Hospital, Memphis, US Gabriele Bergers Vesalius Research Center, Leuven, Belgium Priscilla Brastianos Massachusetts General Hospital, Harvard Medical School, Boston, US Amy B. Heimberger The University of Texas MD Anderson Cancer Center, Houston, US Eric Holland Nancy and Buster Alvord Brain Tumor Center, Fred Hutchinson Cancer Research Center, UW Medicine, US Luis F. Parada Brain Tumor Center, Albert C. Foster, MSKCC, New York, US Stefan Pfister DKFZ, Heidelberg, Germany Matthias Preusser Comprehensive Cancer Center Vienna, Medical University of Vienna, Austria Nicola Sibson CRUK/MRC Oxford Institute for Radiation Oncology, UK Joan Seoane Vall d’Hebron Institute of Oncology, Barcelona, Spain Riccardo Soffietti University and City of Health and Science University Hospital of Turin, Italy Michael Taylor The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Ontario, Canada Roeland Verhaak The University of Texas MD Anderson Cancer Center, The Jackson Laboratory for Genomic Medicine, US William A. Weiss UCSF, Helen Diller Family Comprehensive Cancer Center, San Francisco, US Wolfgang Wick DKFZ, Heidelberg, Germany Frank Winkler DKFZ, Heidelberg, Germany Massimo Squatrito Spanish National Cancer Research Centre (CNIO), Madrid, Spain Manuel Valiente Spanish National Cancer Research Centre (CNIO), Madrid, Spain Richard Gilbertson CRUK Cambridge Institute, UK Michael Weller University Hospital Zurich, Switzerland Confirmed SpeakersOrganisers PRIMARY AND SECONDARY BRAIN TUMORS Madrid 19 — 22 February 2017 Application deadline January 19th Abstract submission deadline December 19th For further information and to apply please go to www.cnio.es/events Centro Nacional de Investigaciones Oncológicas (CNIO). Melchor Fernández Almagro 3, 28029 Madrid EXCELENCIA SEVERO OCHOA 2012 - 2019 MINISTERIO DE ECONOMÍA, INDUSTRIA Y COMPETITIVIDAD CNIO - ”LA CAIXA” FOUNDATION FRONTIERS MEETINGS 2017 SPANISH NATIONAL CANCER RESEARCH CENTRE SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 225 SCIENTIFIC MANAGEMENT | SCIENTIFIC EvENTS · William A. Weiss, UCSF, Helen Diller Family Comprehensive Cancer Center, San Francisco, US · Wolfgang Wick, DKFZ, Heidelberg, Germany · Frank Winkler, DKFZ, Heidelberg, Germany In addition, 11 short talks were selected among participants ’ contributions and 49 posters were presented. MOLECULAR CHAPERONES IN CANCER 2-4 mAy 2017 ORGANISERS · Nabil Djouder, Spanish National Cancer Research Centre ( CNIO ), Madrid, Spain · Wilhelm Krek, Institute for Molecular Health Sciences, Zurich, Switzerland · Paul Workman, The Institute of Cancer Research, London, UK · Xiaohong Helena Yang, Cancer Cell, Cambridge, US SESSIONS · Protein Quality Control · Folding, Misfolding and Aggregation · Stress Mechanisms in Cancer · Chaperones in Cancer · Targeting Chaperones : Chaperonotherapy SPEAKERS · Udai Banerji, The Institute of Cancer Research, London, UK · Johannes Buchner, Technical University Munich, Germany · Bernd Bukau, Center for Molecular Biology of Heidelberg University, German Cancer Research Center ( DKFZ ), Germany · Gabriela Chiosis, Memorial Sloan Kettering Cancer Center, New York, US · Ana Maria Cuervo, Albert Einstein College of Medicine, New York, US · Erica A. Golemis, Fox Chase Cancer Center, Philadelphia, US · Mathias Heikenwälder, DKFZ - German Cancer Research Center, Heidelberg, Germany · Charalampos Kalodimos, College of Biological Sciences, University of Minnesota, St. Paul, US · Michael Karin, University of California, San Diego, US · Randal J. Kaufman, Stanford Burnham Prebys Medical Discovery Institute, San Diego, US · Oscar Llorca, Centre for Biological Research ( CIB- CSIC ), Madrid, Spain · Matthias P. Mayer, Center for Molecular Biology of Heidelberg University, Heidelberg, Germany · Shelli R. McAlpine, University of New Southwales, Sydney, Australia · Marc Mendillo, Northwestern University Feinberg School of Medicine, Chicago, US · Guillermo Montoya, Novo Nordisk Foundation Center for Protein Research, Denmark · Richard Morimoto, Northwestern University, Evanston, US · Kazuhiro Nagata, Kyoto Sangyo University, Japan · Shuichi Ohkubo, Taiho Pharmaceutical Co., Ltd., Tokio, Japan · Laurence Pearl, University of Sussex, Brighton, UK · David Pincus, Whitehead Institute for Biomedical Research, Cambridge, US · Lea Sistonen, Abo Akademi University, Finland · Patricija van Oosten-Hawle University of Leeds, UK · Cara Vaughan, School of Crystallography, Birkbeck College, London, UK · Paul Workman, The Institute of Cancer Research, London, UK In addition, 10 short talks were selected among participants ’ contributions and 18 posters were presented. Udai Banerji The Institute of Cancer Research, London, UK Johannes Buchner Technical University Munich, Germany Bernd Bukau Center for Molecular Biology of Heidelberg University, German Cancer Research Center (DKFZ), Germany Gabriela Chiosis Memorial Sloan Kettering Cancer Center, New York, USA Ana Maria Cuervo Albert Einstein College of Medicine, New York, USA Erica A. Golemis Fox Chase Cancer Center, Philadelphia, US Mathias Heikenwälder DKFZ - German Cancer Research Center, Heidelberg, Germany Charalampos Kalodimos College of Biological Sciences, University of Minnesota, St. Paul, US Michael Karin University of California, San Diego, USA Randal J. Kaufman Stanford Burnham Prebys Medical Discovery Institute, San Diego, USA Oscar Llorca Centre for Biological Research (CIB-CSIC), Madrid, Spain Matthias P. Mayer Center for Molecular Biology of Heidelberg University, Heidelberg, Germany Shelli McAlpine University of New Southwales, Sydney, Australia Marc Mendillo Northwestern University Feinberg School of Medicine, Chicago, US Guillermo Montoya Novo Nordisk Foundation Center for Protein Research, Denmark Richard Morimoto Northwestern University, Evanston, US Kazuhiro Nagata Kyoto Sangyo University, Japan Shuichi Ohkubo Taiho Pharmaceutical Co. Ltd., Tokyo, Japan Laurence Pearl University of Sussex, Brighton, UK David Pincus Whitehead Institute for Biomedical Research, Cambridge, US Lea Sistonen Abo Akademi University, Finland Patricija van Oosten-Hawle University of Leeds, UK Cara Vaughan School of Crystallography, Birkbeck College, London, UK Paul Workman The Institute of Cancer Research, London, UK Nabil Djouder Spanish National Cancer Research Centre (CNIO), Madrid, Spain Wilhelm Krek Institute for Molecular Health Sciences, Zurich, Switzerland Paul Workman The Institute of Cancer Research, London, UK Xiaohong Helena Yang Cancer Cell, Cambridge, US Confirmed SpeakersOrganisers MOLECULAR CHAPERONES IN CANCER Madrid 2 — 4 May 2017 Abstract Submission deadline 30 March, 2017 Application deadline 3 April, 2017* *Limited capacity of 130 people. CNIO reserves the right to close registration and abstract submission when we reach full capacity. For further information and to apply please go to www.cnio.es/events Centro Nacional de Investigaciones Oncológicas (CNIO). Melchor Fernández Almagro 3, 28029 Madrid EXCELENCIA SEVERO OCHOA 2012 - 2019 MINISTERIO DE ECONOMÍA, INDUSTRIA Y COMPETITIVIDAD IN MEMORY OF SUSAN LINDQUIST CNIO - ”LA CAIXA” FOUNDATION FRONTIERS MEETINGS 2017 SPANISH NATIONAL CANCER RESEARCH CENTRE ANNUAL REPORT 2017 226 FACTS & FIGuRES OTHER MEETINGS & CONFERENCES The CNIO annually hosts various international meetings and conferences. Within this category, the 6 international events were held in 2017. MEETING CNIO –CELL AND GENE THERAPY CATAPULT 30 mARCH 2017 CNIO PARTICIPANTS · Maria A. Blasco · Oscar Fernández-Capetillo · Anabel Sanz · Marcos Malumbres · Maria Salazar CELL AND GENE THERAPY CATAPULT PARTICIPANTS · Ricardo Baptista · Almira Bartolome · Sara Cebrián II SYMPOSIUM CNIO-IBIMA : PROSTATE CANCER AND OTHER GENITOURINARY TUMOURS 20-21 APRIL 2017 ORGANISERS · CNIO-IBIMA-FIMABIS SESSIONS · Germ –Cell Tumours · Renal Cancer · Bladder Cancer · What’s New in the Biology of Prostate Cancer Mts SPEAKERS · Emilio Alba, Hospital Regional Universitario and Virgen de la Victoria University Hospital, UMA – IBIMA · Isabel Hierro, Hospital Regional Universitario and Virgen de la Victoria University Hospital · Enrique González-Billalabeitia, Morales Meseguer University Hospital · Ferran Algaba, Puigvert Foundation · Emilio Julve, Hospital Regional Universitario and Virgen de la Victoria University Hospital · Christophe Massard, Gustav Roussy Institute · Francisco Javier Machuca, Hospital Regional Universitario and Virgen de la Victoria University Hospital · Ana Medina, Oncologic Center of Galicia · Álvaro Montesa, Hospital Regional Universitario and Virgen de la Victoria University Hospital · Guillermo de Velasco, 12 de Octubre University Hospital · Emilio García-Galisteo, Hospital Regional Universitario and Virgen de la Victoria University Hospital · Álvaro Montesa, Hospital Regional Universitario and Virgen de la Victoria University Hospital · Francisco Real, Spanish National Cancer Research Centre · Bernardo Herrera, Hospital Regional Universitario and SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 227 SCIENTIFIC MANAGEMENT | SCIENTIFIC EvENTS Virgen de la Victoria University Hospital · Maribel Sáez, Hospital Regional Universitario and Virgen de la Victoria University Hospital · José Antonio Medina, Hospital Regional Universitario · Mª José Requena, Reina Sofia University Hospital · Raquel Correa, Hospital Regional Universitario and Virgen de la Victoria University Hospital · Antonio Conde, Hospital Provincial of Castellón · David Hernández, Hospital Regional Universitario and Virgen de la Victoria University Hospital · José Rubio, Valencia Oncology Institute Foundation · Gerhardt Attard, The Royal Marsden NHS Foundation Trust · Elena Castro, Spanish National Cancer Research Centre · Joaquin Mateo, The Royal Marsden NHS Foundation Trust · Hishima Beltrán, Cornell University · Jose Ángel Arranz, Gregorio Marañon University Hospital · Joan Carles, Vall d’Hebron Oncology Institute · Javier Puente, Hospital Clínico San Carlos · José Menéndez Vidal, Reina Sofía University Hospital · Ignacio Durán, Virgen del Rocía University Hospital · Rosa Villatoro, Costa del Sol Hospital · David Lorente, Hospital Universitario y Politécnico de La Fe · José Luis Pérez Gracia, University of Navarra Clinic · David Olmos, Spanish National Cancer Research Centre · Emilio Alba, Hospital Regional Universitario and Virgen de la Victoria University Hospital NEW INSIGHTS IN CANCER DISCOVERy 26-27 SEPTEmbER 2017 ORGANISERS · Maria Blasco, Spanish National Cancer Research Centre ( CNIO ), Spain · Oskar Fernández-Capetillo, Spanish National Cancer Research Centre ( CNIO ), Spain · Moshe Oren, Weizmann Institute of Science, Israel · Ravid Straussman, Weizmann Institute of Science, Israel CO-ORGANISERS · Ramón Areces Foundation SPEAKERS SPANISH NATIONAL CANCER RESEARCH CENTRE, MADRID, SPAIN · Maria Blasco · Oskar Fernández-Capetillo · Manuel Valiente · Rafael Fernández Leiro · Marisol Soengas · Francisco X. Real · Marcos Malumbres · Alejo Efeyan WEIZMANN INSTITUTE OF SCIENCE, REHOVOT, ISRAEL · Moshe Oren · Ravid Straussman · Itay Tirosh · Liran Shlush · Sima Lev · Varda Rotter · Yifat Merbl · Yosef Yarden CIBERER 21 NOvEmbER 2017 Jornada de investigación cooperativa 2017. Reunión Anual Programa de Cáncer Hereditario, Enfermedades Hematológicas y Dermatológicas. Jornada de investigación cooperativa 2017. Reunión Anual Programa de Cáncer Hereditario, Enfermedades Hematológicas y Dermatológicas 21 Noviembre 2017 Salón de Actos del CNIO. Madrid 10:00-10:30 Bienvenida y recepción 10:30-10:45 Coordinador Juan Bueren. U710 CIEMAT Plan Estratégico 2018-2020 y novedades CIBERER SESIÓN 1: Objetivo IRDIRC Terapias Modera – Mercedes Robledo 10:45 -12:40 10:45-11:00 Rosario Perona. U757. IIB-CSIC Uso del GSE4 para rescate de actividad telomerasa en disqueratosis congénita. 11:00-11:10 Discusión 11:10-11:25 Guillermo Güenechea U710. CIEMAT Desarrollo de terapia génica para el tratamiento del fallo de médula ósea en disqueratosis congénita 11:25-11:35 Discusión 11:35-11:50 Marcela del Rio. U714. CIEMAT. Terapias moleculares y farmacológicas para la Epidermolisis Bullosa Distrófica Recesiva 11:50-12:00 Discusión 12:00 -12:20 Pausa café 12:20 -13:45 12:20-12:35 María Villa. U749. CBMSO Nuevas contribuciones a las neoplasias linfoblásticas T 12:35-12:45 Discusión 12:45-13:00 Jordi Surrallés. U745. UAB Nuevos genes y reposicionamiento de fármacos en anemia de Fanconi 13:00-13:10 Discusión ANNUAL REPORT 2017 228 FACTS & FIGuRES ONCO EMERGENCE FORUM 14-15 dECEmbER 2017 ORGANISERS · University Toulouse III Paul Sabatier · CNIO · Biocat · Navarrabiomed · Universidad de Coimbra SESSIONS · Liquid biopsies as Prognostic biomarkers in solid tumours, new diagnostic approaches and implication in clinical studies SPEAKERS · Patrice Denefle, Directeur de l’Institut ROCHE de Recherche et de Médicine Translationnelle · María José Serrano, Virgen de las Nieves Hospital. Pfizer. University of Granada. Centre for Genomics and Oncological Research ( GENYO ) · Atocha Romero, Puerta de Hierro University Hospital · Artur Paiva, The Coimbra Hospital and University Centre · Catherine Panabieres, LCCRH – CHU of Montpellier · Gilles Favre, The University Cancer Institute of Toulouse · Gabriel Capella, The Catalan Institute of Oncology. Bellvitge Biomedical Research Institute · Hugh Ilyne, DestiNA Genomics · Simon Perera del Rosario, Anaxomics Biotech · Eduardo Pareja, Era7 Bioinformatics · María Esther Molina, Spanish National Cancer Research Centre · Jean-Philippe Nougayrède, Digestive Health Research Institute · Sara Ramio Pujol, GoodGut · Benjamin Lelouvier, Vaiomer · Fay Betsou, IBBL ( Integrated Biobank of Luxembourg ) · Raquel Bermudo Gascón, HCB-IDIBAPS Biobank, IDIBAPS · Manuel Rodríguez Maresca, Andalusian Public Health System · Manuel Morente, Spanish National Cancer Research Centre · Taycir Skhiri, FHU OncoAge · Joaquim Pereira, Hospital Santa Maria, IMM · Maya Lauriol, Canceropôle Grand Sud-Ouest · David Olmos, Spanish National Cancer Research Centre · Henriqueta Breda, Faculty of Medicine of University of Coimbra · Eva Martinez-Balibrea, Catalan Institute of Oncology Germans Trias I Pujol Research Institute · María Tabernero, IMDEA Food Institute · Alboukadel Kassambara, Institute of Human Genetics, CNRS-UM and University hospital of Montpellier · Carlos Cano Gutiérrez, University of Granada ; Tanglegen · Francisco Caramelo, Faculty of Medicine of the University of Coimbra ; Spiral Data Lda · Fátima Al-Shahrour, Spanish National Cancer Research Centre · Joaquín Dopazo, Progreso y Salud Foundation · Sacha Beaumeunier, SeqOne · Janet Piñero, Hospital del Mar Medical Research Institute ( IMIM ); Barcelona Biomedical Research Park · Josep Ll. Gelpi, Barcelona Supercomputing Center & University of Barcelona · Lucas Jurado Fasoli, Oncodieta · Anabel Sanz, Spanish National Cancer Research Centre · Ana Catarina Mamede, ResearchTrial · Marta Soler, Biocat · Francisco Ambrósio, Faculty of Medicine of the University of Coimbra · Emmanuel Le Bouder, Eurobiomed ; Transferts METABOCANCER KICK OFF MEETING 14 dECEmbER 2017 ORGANISER · CNIO METABOCANCER NETWORK MEMBERS · Alejo Efeyan · Anna Bigas · Arkaitz Carracedo · Guadalupe Sabio · José Cuezva · Marc Claret · María Mittelbrunn · Mariona Graupera · Ruben Nogueiras · Xosé Bustelo GUEST PARTICIPANTS · Guillermo Velasco · Miguel López · Nabil Djouder · Pablo José Fernández Marcos · Roger Gomis · Toño Enríquez SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 229 SCIENTIFIC MANAGEMENT | SCIENTIFIC EvENTS TRAINING COuRSES AND WORKSHOPS The CNIO is committed to disseminating the results of state- of-the-art cancer research to the wider community, including medical professionals and junior scientists, thereby enabling them to stay abreast of recent developments in specialised techniques. This is achieved through training courses and hands- on workshops organised by CNIO scientists and technologists. INNOVATIVE MEDICINES INITIATIVE WORKSHOP ON ONCOLOGY 12 JANUARy 2017 SPEAKERS · Marta Gómez Quintanilla, IMI. CDTI · Ion Arocena, ASEBIO · Javier Urzay, FARMAINDUSTRIA · Alfonso Beltrán, FIPSE. ISCIII · Maria A. Blasco, CNIO · Pierre Meulien, IMI · Carmen Eibe, PHARMAMAR · Andrés Cervantes, Hospital Clinico Universitario de Valencia · Joaquín Arribas, CIBERONC · Alfonso Valencia, INB · Jan van de Loo, European Commission · César Hernández, AEMPS · Marta Gómez Quintanilla, Health & IMI – Horizon 2020 2ND EUROMABNET : ANTIBODY VALIDATION WORKSHOP 26 mAy 2017 ORGANISER · European Monoclonal Antibody Network EuroMAbNet SPEAKERS · Giovanna Roncador, Spanish National Cancer Research Centre · Pablo Engel, University of Barcelona · Friedrich Koch-Nolte, Institute of Immunology Hamburg · Alison Banham, University of Oxford · Vladka Čurin Šerbec, Blood Trasfusion Centre of Slovenia · Alejandra Solache, Abcam · Matt Baker, Thermo Fisher Scientific ADVANCE CELL SORTING COURSE 3-4 SEPTEmbER 2017 ORGANISERS/SPEAKERS · Rui Gardner, Head of the Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center, NY, USA · Lola Martinez, Head of the Flow Cytometry Unit, CNIO, Madrid. Spain HOW TO SUCCESSFULLY PERFORM & ANALYSE A MULTICOLOR FLOW EXPERIMENT WORKSHOP 7-8 SEPTEmbER 2017 ORGANISERS/SPEAKERS · Lola Martinez, Head of the Flow Cytometry Unit. CNIO. Madrid. Spain · Andrea Valle, Application Specialist FCS Express, DeNovo Software. Milano. Italy JOIN OUR WORKSHOP FEATURING LEICA TCS SP8 DIVE AND LEICA DMI8 S 14-16 NOvEmbER 2017 ORGANISER · LEICA Microsystems – CNIO Validated Ab Positive Negative Controls Find reliable Ab Reactivity with the antigen Identify the target antigen Specificity 2nd EuroMAbNet Antibody Validation Workshop 26th of May 2017 Spanish National Cancer Research Centre Madrid, Spain Organizer: European Monoclonal Antibody Network EuroMAbNet (www.euromabnet.com) EuroMAbNet Antibody Validation Workshop will bring together highly specialized scientists in antibody technology with PhD students and young scientists who use antibodies in their research. It will provide a set of criteria and recommendations that will help researchers to select the most effective mAbs from those available on the market and provide the strategic guidance needed to perform any essential antibody validation. This will include verifying antibody specificity, selectivity, sensitivity and reproducibility. WORKSHOP PROGRAMME MORNING SESSION 9:00 Dr. Giovanna Roncador ▫ Head of the Monoclonal Antibody Unit, CNIO, Madrid Opening remarks 9:10 Prof. Pablo Engel ▫ Immunology Unit Department of Cellular Biology and Pathology Medical School, University of Barcelona, Spain The problems arising from poor antibody validation 9:40 Prof. Friedrich Koch-Nolte ▫ Professor of Immunology and Molecular Biology, Institute of Immunology, Hamburg, Germany A basic introduction to antibodies 10:20 Prof. Alison Banham ▫ Head of the Nuffield Division of Clinical Laboratory Sciences, University of Oxford, UK How to approach an antibody project COFFEE BREAK (11:00-11:30) 11:30 Dr. Giovanna Roncador ▫ Head of the Monoclonal Antibody Unit, CNIO, Madrid Principles of antibody validation - examples showing approach to using controls, demonstrating reactivity with recombinant and endogenous target antigen, specificity and reproducibility 12:20 Prof. Vladka Čurin Šerbec ▫ Center for the Production of Diagnostic Reagents and for Research, Blood Trasfusion Centre of Slovenia Consequences of antibody validation failure: How to approach this issue with antibody suppliers and other researchers 12:40 Alejandra Solache ▫ Abcam Sponsored talk LUNCH (13:00-14:00) AFTERNOON SESSION 14:00 Sponsor Representative ▫ Cell Signalling Technology Sponsored talk 14:15 Dr. Matt Baker ▫ Director R&D and Business Development, Thermo Fisher Scientific Sponsored talk: Advanced antibody validation through specificity verification 14:30 Interactive Session "Meet the Experts I" ▫ This session will be run twice, so that attendees can participate in more than one discussion group 1. Meet the expert in immunohistochemistry 2. Meet the expert in flow cytometry 3. Meet the expert in western blotting 15:40 Interactive Session "Meet the Experts II" 1. Meet the expert in immunohistochemistry 2. Meet the expert in flow cytometry 3. Meet the expert in western blotting END OF THE MEETING (17:00) Workshop programme information: www.euromabnet.com/workshop/antibody-validation.php ANNUAL REPORT 2017 230 FACTS & FIGuRES CNIO DISTINGuISHED SEMINARS The purpose of the Distinguished Seminars Series is to invite outstanding and internationally renowned scientists to give a seminar and to meet with researchers at the CNIO. Distinguished Seminars are recurrent events that are open to the general public and are held throughout the year, usually on Fridays at noon in the CNIO Auditorium. Each Distinguished Seminar series includes world-leading scientists who address topics that are of general interest to the CNIO faculty. The idea behind this international seminar series is not simply to host outstanding cancer researchers to the CNIO, but also serves to, annually, invite 3 to 4 opinion leaders from other areas of science, technology, and literature ; the overarching goal is to enable the CNIO to present its know-how as well as its vision on contemporary and future technological, societal and cultural challenges. These ‘ out-of-the-box ’ seminars are sponsored by the ‘ Fundación Banco Sabadell ’. The breadth of expertise and topics covered creates a multidisciplinary and intellectually challenging environment that goes far beyond the frontiers of cancer research. In total, the CNIO hosted 19 distinguished speakers in 2017. Friday 28 Oct Charles Brenner University of Iowa Carver College of Medicine Iowa, US Sep—Dec 2016 Friday 21 Oct Mike Hall BiozentrumUniversity of Basel, Switzerland Friday 20 Jan Raul Mostoslavsky Massachusetts General Hospital, Harvard Medical School, Boston, US Friday 11 Nov Stig E. Bojesen Herlev Hospital, University of Copenhagen, Denmark Friday 2 Dec Celeste Simon The Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, US Friday 16 Dec Hans-Guido Wendel Memorial Sloan Kettering Cancer Center, New York, US Friday 27 Jan Benjamin L. Ebert Brigham and Women’s Hospital, Harvard Medical School, Boston, US Jan—Jun 2017 Friday 10 Feb Emmanuelle Passegue University of California, San Francisco, US Friday 17 Mar Reinhard Faessler Max Planck Institute of Biochemistry, Munich, Germany Friday 10 Mar Tom Kirkwood Institute for Cell and Molecular Biosciences, Newcastle University, UK Friday 31 Mar José Luis Sanz Autonomous University of Madrid, Spain Friday 28 Apr Kari Alitalo Institute of Biomedicine, Biomedicum Helsinki, University of Helsinki, Finland Friday 5 May Vera Gorbunova University of Rochester, NY, US Friday 19 May Oscar Marín MRC Centre for Developmental Neurobiology, King’s College London, UK Friday 24 Mar Ioannis Aifantis NYU School of Medicine, US Friday 14 Oct Francisco J. Ayala University of California, Irvine, US Friday 16 Sep Francisco J. Martínez Mojica University of Alicante, Spain Friday 13 Jan Elaine Fuchs Howard Hughes Medical Institute, The Rockefeller University, NY, US Out-of-the Box Seminars supported by www.cnio.es/eventos/seminars Melchor Fernández Almagro 3 28029 Madrid, Spain Organisers Friday 17 Feb Nuria Oliver Telefónica I+D, Barcelona, Spain Friday 7 Apr Jacob Hanna Weizmann Institute of Science, Rehovot, Israel Friday 16 Jun Guillermo Oliver Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, US Friday 6 Oct Paola Scaffidi The Francis Crick Institute, London, UK Sep—Dec 2017 Friday 29 Sep Hongtao Yu Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, US Friday 19 Jan Antoni Castells Hospital Clinic of Barcelona, Spain Friday 20 Oct Peter Carmeliet Vesalius Research Center, Leuven, Belgium Friday 6 Apr Stefan Kubicek CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria Friday 1 Dec Victor G. Corces O. Wayne Rollins Research Center, Emory University, Atlanta, US Friday 2 Feb Raúl Méndez Institute for Research in Biomedicine, Barcelona, Spain Jan—Jun 2018 Friday 23 Mar Kiyoshi Nagai MRC Laboratory of Molecular Biology, Cambrigde, UK Friday 13 Apr Arlene Sharpe Harvard Medical School, Boston, US Friday 15 Jun Roger Lo Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, US Friday 1 Jun Kun-Liang Guan Sanford Consortium for Regenerative Medicine (SCRM) The University California, San Diego, US Friday 25 May Edith Heard Curie Institute, France Friday 11 May Caetano Reis e Sousa The Francis Crick Institute, London, UK Friday 8 Jun Irina Conboy Berkeley University of California, US Friday 15 Sep David J. Kwiatkowski Brigham and Women’s Hospital, Dana-Farber/ Harvard Cancer Center, Boston, US Friday 8 Sep Timothy Rebbeck Dana Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, US Out-of-the Box Seminars supported by www.cnio.es/eventos/seminars Melchor Fernández Almagro 3 28029 Madrid, Spain Organisers Friday 16 Feb Jörg Hoheisel DKFZ German Cancer Research Center, Heidelberg, Germany 18 17 Friday 16 Mar Gudrun Schleiermacher INSERM U830, Curie Institute, Paris, France Friday 20 Apr Adrian R. Krainer St. Giles Foundation, Watson School of Biological Sciences, Cold Spring Harbor, NY, US Friday 23 Feb John Rubinstein The Hospital for Sick Children Research Institute, Toronto, Canada Friday 26 Jan Andrés Aguilera Andalusian Center for Molecular Biology and Regenerative Medicine, CABIMER, CSIC, Sevilla, Spain Friday 27 Apr Magdalena Götz Ludwig-Maximilians- University of Munich, BioMedical Center (BMC), Martinsried, Germany Monday 26 Feb Shirley Kutner Hebrew University of Jerusalem, Israel SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 231 SCIENTIFIC MANAGEMENT | SCIENTIFIC EvENTS DATE SPEAKER ORGANISATION TITLE JANUARY 13/01/2017 Elaine Fuchs Howard Hughes Medical Institute, The Rockefeller University, NY, US Stem cells in silence, action and cancer 20/01/2017 Raul Mostoslavsky Kristine and Bob Higgins MGH Research Scholar Massachusetts General Hospital Cancer Center Harvard Medical School, Boston, US Linking Epigenetics, Metabolism and Cancer : lessons from SIRT6 27/01/2017 Benjamin L. Ebert Brigham and Women’s Hospital, Boston, US The genetics of myeloid neoplasia : from clonal hematopoiesis to acute leukemia FEBRUARY 17/02/2017 Nuria Oliver DataPop Alliance, New York, US The Future of the Mobile Phone MARCH 10/03/2017 Tom Kirkwood Newcastle University Institute for Ageing, UK ; University of Copenhagen Center for Healthy Aging, Copenhagen, Denmark Why and how are we living longer ? 17/03/2017 Reinhard Faessler Max Planck Institute of Biochemistry, Munich, Germany Identification of a molecular switch that controls cell migration speed 24/03/2017 Ioannis Aifantis NYU School of Medicine, US Missing Lnks : The impact of the non- coding genome in acute leukemia 31/03/2017 José Luis Sanz Autonomous University of Madrid ( UAM ), Spain I left my heart in the Jurassic : Dinomania today APRIL 07/04/2017 Jacob ( Yaqub ) Hanna Weizmann Institute of Science, Rehovot, Israel Molecular Mechanisms for Inducing, Maintaining and Resolving Distinct States of Pluripotency 28/04/2017 Kari Alitalo Institute of Biomedicine Biomedicum Helsinki, University of Helsinki, Finland Therapeutic Potential of Vascular Growth Factors MAY 05/05/2017 Vera Gorbunova University of Rochester, New York, US Mechanisms of longevity and cancer resistance in long-lived mammals 19/05/2017 Oscar Marín New Hunt’s House King’s College, London, UK Getting excited about inhibition : molecular and functional diversity of brain interneurons JUNE 16/06/2017 Guillermo Oliver Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, US The lymphatic vasculature in the 21st century : developmental mechanisms and functional roles ANNUAL REPORT 2017 232 FACTS & FIGuRES SEPTEMBER 08/09/2017 Timothy Rebbeck Dana Farber Cancer Institute and Harvard T.H.Dana Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, US Cancer Prevention and Early Detection in the Precision Medicine Era 15/09/2017 David J. Kwiatkowski Brigham and Women’s Hospital, Dana-Farber/ Harvard Cancer Center, Boston, US The TSC/mTOR pathway in germline disorders and cancer 29/09/2017 Hongtao Yu Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, US Mitotic checkpoint regulators in chromosome segregation and insulin signaling OCTOBER 06/10/2017 Paola Scaffidi The Francis Crick Institute, London, UK Epigenetics and functional intratumor heterogeneity 20/10/2017 Peter Carmeliet Vesalius Research Center, Leuven, Belgium Angiogenesis revisited : role and ( therapeutic ) implications of endothelial metabolism DECEMBER 01/12/2017 Victor G. Corces O. Wayne Rollins Research Center, Emory University, Atlanta, US Transcription and the three-dimensional organization of the genome AD-HOC SEMINARS In addition to the CNIO Distinguished Seminar Series, the CNIO also hosts numerous ad-hoc seminars throughout the year. A total of 45 ad-hoc seminars were organised by CNIO researchers in 2017. DATE SPEAKER ORGANISATION TITLE JANUARY 17/01/2017 Karin Verspoor The University of Melbourne, Australia Application of Literature Mining for Protein Function Prediction 19/01/2017 Georg Winter CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria “-taming the beast- small molecule induced target protein degradation ” FEBRUARY 08/02/2017 Erika Pastrana Nature Communications, New York, US Publishing in the Nature journals : an insider’s view 09/02/2017 Mauricio Rojas McGowan Institute for Regenerative Medicine University of Pittsburgh Medical Center University of Pittsburgh, US Idiopathic pulmonary fibrosis as a disease of Aging 13/02/2017 Anna Bigas Hospital del Mar Medical Research Institute ,IMIM, Barcelona, Spain Notch and Wnt in normal and leukemic hematopoiesis 16/02/2017 Åsmund Flobak Norwegian University of Science and Technology, The Cancer Clinic, St Olav’s University Hospital, Trondheim, Norway Rationalizing drug combination screening for improved clinical trials and precision oncology SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 233 SCIENTIFIC MANAGEMENT | SCIENTIFIC EvENTS 16/02/2017 Jean J. Zhao Dana-Farber Cancer Institute, Harvard Medical School, Boston, US Precision Oncology : From mouse models to human therapy 16/02/2017 David Dominguez-Sola The Tisch Cancer Institute & The Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, NY, US FOXO1 and the unforseen path to lymphomagenesis 21/02/2017 Luis Martí Bonmatí and Ángel Alberich The university hospital and polyclinic La Fe, QUIBIM, Valencia, Spain Introduction to personalized quantitative Imaging Dr. Bonmatí / Radiomics Dr. Alberich 24/02/2017 Manel Cascallo VCN Biosciences, Barcelona, Spain Oncolytic adenoviruses expressing hyaluronidase : from bench to patients MARCH 06/03/2017 Sara Priego Moreno Institute of Cancer and Genomic Sciences, University of Birmingham, UK Roles of Ubiquitin and SUMO during eukaryotic chromosome replication 13/03/2017 Pere Roca- Cusachs Institute for Bioengineering of Catalonia IBE, Barcelona, Spain Sensing matrix rigidity : transducing mechanical signals from integrins to the nucleus 27/03/2017 Scott Williams University of North Carolina at Chapel Hill, US Spindle orientation in stratified epithelial development, stem cells and cancer 30/03/2017 Ricardo Baptista Gene and Cell Therapy Catapult, UK Development of cost efficient platforms for the industrial manufacture of pluripotent stem cell-derived products for cell therapy : cell expansion is the starting point APRIL 06/04/2017 María Pilar Alcolea Wellcome Trust-MRC Stem Cell Institute, University of Cambridge, UK Oesophageal stem cell plasticity ; relevance for tumour development 18/04/2017 Ana O’Loghlen Queen Mary University of London, UK The chromobox protein CBX7 as a master regulator of pluripotency and senescence 20/04/2017 Lars Fugger University of Oxford, Weatherall Institute of Molecular Medicine, Oxford, U.K. Functional genomics in autoimmune diseases 20/04/2017 Lisa Torp Jensen Aarhus University, Clinical Immunology, Aarhus, Denmark Steps towards a mouse model for celiac disease 24/04/2017 Antoni Celià- Terrassa Princeton University, Princeton, US Mechanisms regulating stem cell properties and immune interplay of tumor- and metastasis-initiating cells MAY 25/05/2017 Isabel Beerman National Institute on Aging, Baltimore, US Aging of the Hematopoietic Stem Cell Compartment 26/05/2017 Santiago Zelenay Cancer Inflammation and Immunity Cancer Research UK Manchester Institute, The University of Manchester, UK Manipulating inflammation to raise cancer immunogenicity 30/05/2017 Hana Algül Technical University München, Germany Insight into the role of non-receptor tyrosine phophatases in pancreatic cancer ANNUAL REPORT 2017 234 FACTS & FIGuRES JUNE 01/06/2017 Miguel A. Tam BioLegend, San Francisco, US Versatile tools for Magnetic Cell Separation & Antigen-Specific T-Cell ( Tetramer ) Research 06/06/2017 Víctor Pérez García Mathematical Oncology Laboratory, University of Castilla La Mancha, Ciudad Real, Spain Mathematics against cancer : Examples in Neuro-Oncology 15/06/2017 Oritz Uziel Laboratory for Telomeres and Telomerase Research, The Felsenstein Medical Research Center, Rabin Medical Center and Tel Aviv University, Israel The shuttle of cancer cells derived exosomal hTERT mRNA induces phenotypic changes in the recipient fibroblast cells JULY 10/07/2017 Ana I. Vazquez Michigan State University, US Beyond genomics, Multi-layer omics data from cancer for outcome predictions 12/07/2017 Wolfgang Weninger Centenary Institute, Camperdown. Australia Function and development of perivascular macrophages 14/07/2017 Bruno Conti The Scripps Research Institute, La Jolla, US Core Body Temperature and Aging 24/07/2017 Raul Rabadan Columbia University College of Physicians and Surgeons, New York, US Heterogeneity and Evolution of Glioblastomas 28/07/2017 Anabel Rojas González Cabimer, Andalusian Center for Molecular Biology and Regenerative Medicine, Sevilla, Spain GATA transcripction factors in pancreas development and disease 31/07/2017 Antonio García Herreros IMIM Parc de Salut Mar, Barcelona, Spain Snail, epithelial to mesenchymal transition and fibroblast activation SEPTEMBER 07/09/2017 Axel Behrens The Francis Crick Institute, London, UK Unraveling cancer cell heterogeneity 15/09/2017 Jack Welch Center for Global Health, US National Cancer Institute, Bethesda, US NCI Global Health approaches and trending topics in cancer 20/09/2017 Slyvia Knapp CeMM, Viena, Austria Regulatory role of innate immunity in homeostasis and disease OCTOBER 03/10/2017 David Gallego Ortega and Fatima Valdes Mora Kinghorn Cancer Centre at the Garvan Institute of Medical Research in Sydney, Australia Understanding the link between cancer and immune system using massively-parallel single-cell RNAseq technologies and “ Histone Variants, Epigenetics and Cancer ” 05/10/2017 Luis Arnes Columbia University Medical Center, New York, US Positionally conserved lncRNAs are necessary for the specification of pancreatic lineages in development and disease 16/10/2017 Gaetano Gargiulo Max-Delbrück Center for Molecular Medicine ( MDC ), Berlin, Germany Polycomb Control of Cell Identity and Tumor Suppression : Implications for Therapy 20/10/2017 Mario Pende The Institut Necker-Enfants Malades ( INEM ), Paris, France Growth control by mTOR/S6K and Hippo/ YAP master regulators in Tuberous Sclerosis NOVEMBER 07/11/2017 Rui Benedito CNIC, Madrid, Spain Using multispectral and combinatorial genetic mosaics to understand angiogenesis in development and disease SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 235 SCIENTIFIC MANAGEMENT | SCIENTIFIC EvENTS 24/11/2017 Stefano Stella The Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Denmark CRISPR-Cpf1, the new blade for genome manipulation 30/11/2017 Marta Shahbazi University of Cambridge, UK The making of an epithelium : a stem cell perspective DECEMBER 12/12/2017 Silvestre Vicent Cambra CIMA - University of Navarra, Spain Killing two birds with one stone : integrating gene-expression approaches to identify KRAS oncogene vulnerabilities across tumors 13/12/2017 Carson Thoreen Yale University School of Medicine, New Haven, US Translational control of cell growth by the mTOR signaling pathway 18/12/2017 Isidro Cortes Ciriano Biomedical Informatics, Harvard Medical School, US Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing 19/12/2017 Alba Gutiérrez Sacristán Universitat Pompeu Fabra, IMIM ( Hospital del Mar Medical Research Institute ), Barcelona, Spain A bioinformatics approach to the study of comorbidity CNIO-WOMEN IN SCIENCE ( WISE ) SEMINARS 10/01/2017 María Angeles Durán Sociologists. Ad Honorem Professor, Center for Human and Social Sciences ( CSIC ) Medicine, health organization and care system. The changing boundaries 31/01/2017 Belén Yuste and Sonnia L. Rivas-Caballero Rocaviva Eventos, Madrid, Spain Marie Sklodowska-Curie : Ella Misma 28/02/2017 Teresa Jurado and Mariano Nieto Navarro PPIINA ( Plataforma por Permisos Iguales e Intransferibles de Nacimiento y Adopción ), Madrid, Spain How the current design of parental leaves is hampering the professional development of women. The ‘ PLENTy of rights ’ proposal 07/03/2017 María Ruiz and Clara Sanchís María Ruiz stage director -Clara Sanchís actress “ Una habitación propia ” 25/04/2017 Ana Botella Política y ex-alcaldesa de Madrid/ Politician and ex-Mayor of Madrid Experiencias de una mujer perteneciente a la generación de españolas que nacemos cuando todavía no existe una igualdad jurídica entre mujeres y hombres 23/05/2017 Natalia Flores Sanz Ex-jugadora Selección Española Fútbol Sala/Ex player of Spanish National indoor football team. Directora programa Mujer y Deporte/Director of Woman and Sport programme del Consejo Superior de Deporte Situación del deporte femenino en España. Experiencia personal 19/09/2017 Katharina Miller Founder Partner 3CCompliance, Madrid, Spain Leave your comfort zone and be disruptive ! 17/10/2017 Ana Requena Journalist and columnist at “ El Diario ” Micromachismos, el machismo cotidiano que condiciona la vida de las mujeres 12/12/2017 Margarita de Cos Head Major Donors Relations WWF Spain and CEO of RAINSOFT SL, Madrid, Spain El futuro de la mujer en nuestras manos ANNUAL REPORT 2017 236 FACTS & FIGuRES ORGANISERS · Constantes y Vitales · Spanish National Cancer Research Centre ( CNIO ) · Fundación AXA SPEAKERS · Dr. Harald Zur Hausen · Dr. Maria A. Blasco · Dr. Ángela Nieto · Dr. Pilar Garrido RESEARCHERS ’ NIGHT 29 SEPTEmbER 2017 This year, the CNIO participated in Researchers ’ Night ; an activity aimed at bringing researchers closer to the general public and concerned families in order to give them the opportunity to learn more about what researchers do for society. Each year, more than 300 European cities participate in parallel in what is ultimately a great night for science. During the activities − promoted by the European Commission and coordinated by the Madrid Regional Government and the madri+d Foundation − a total of 240 people came to the Spanish National Cancer Research Centre ( CNIO ) to attend Researchers ’ Night ( September 29, 2017 ) to learn about cancer research. The activities were entirely organised and held thanks to the voluntary efforts of 60 researchers. The guests were provided with the opportunity to meet researchers in an interactive and entertaining way, including welcome talks and short talks, hands-on experiments, view of a virtual tour through the facilities via a video project recorded by scientists from CNIO ‘ CNIO for Kids ’, and a speed dating session with the researchers. SCIENTIFIC OuTREACH EVENTS WORLD CANCER RESEARCH DAy : ‘ PRESENT AND FuTuRE OF CANCER RESEARCH ’ ENCUENTRO EXCLUSIVO CON EL NOBEL DR HARALD ZUR HAUSEN 25 SEPTEmbER 2017 To honour World Cancer Research Day, we organised, together with AXA Foundation and Constantes y Vitales, the event entitled ‘ Present and Future of Cancer Research ’; our renowned keynote speaker was Prof. Harald zur Hausen, Nobel Prize winner in Medicine in 2008. Following the talk ( Perspectives for Prevention of Cancers and Chronic Diseases ), Prof. Harald zur Hausen joined a panel discussion on cancer research that also included : Maria A. Blasco, CNIO Director, Ángela Nieto, from the Neuroscience Institute of Alicante, and Pilar Garrido, Chief of Section of the Medical Oncology service at the Ramón y Cajal Hospital. The panel was moderated by laSexta journalist, Mamen Mendizábal. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 237 SCIENTIFIC MANAGEMENT | SCIENTIFIC EvENTS OPEN DOORS DAy : INVESTIGATING TO DISARM CANCER 6-19 NOvEmbER, 2017 The CNIO also dedicates considerable efforts to bringing science and society closer together ; one of these endeavours is its collaboration with the madri+d research network for the organisation of the Madrid Science Week ( XVII Semana de la Ciencia, 6-19 November 2017 ). In 2017, 94 people participated in the guided visit to the Centre’s facilities. GuIDED VISITS Throughout the year, the CNIO provides tailor-made opportunities to visit its installations and to learn about the essentials of cancer research. During 2017, more than 490 people participated in such guided visits ; most of them were ESO and Bachillerato student groups, but also professionals in the health sector. ANNUAL REPORT 2017 238 FACTS & FIGuRES ADMINISTRATION BOARD OF TRuSTEES ȹ Honorary President · Luis de Guindos Jurado Minister of Economy, Industry and Competitiveness Ministro de Economía, Industria y Competitividad ȹ President · Carmen Vela Olmo Secretariat of State for Research, Development and Innovation of the Spanish Ministry of Economy, Industry and Competitiveness Secretaria de Estado de Investigación, Desarrollo e Innovación del Ministerio de Economía, Industria y Competitividad ȹ Vice-President · Jesús Fernández Crespo Director of the National Institute of Health Carlos III Director del Instituto de Salud Carlos III ȹ Appointed Members · José Javier Castrodeza Sanz Secretary General for Health and Consumer Affairs of the Spanish Ministry of Health, Social Services and Equality Secretario General de Sanidad y Consumo del Ministerio de Sanidad, Servicios Sociales e Igualdad · Cristina Ysasi-Ysasmendi Pemán Director of the Department of National Affairs of the Cabinet of the Presidency of the Government Directora del Departamento de Asuntos Nacionales del Gabinete de la Presidencia del Gobierno · Margarita Blázquez Herranz Deputy Director General for Networks and Cooperative Research Centres of the National Institute of Health Carlos III Subdirectora General de Redes y Centros de Investigación Cooperativa del Instituto de Salud Carlos III · Luis Gabilondo Pujol Director General of Health of the Health Department of the Government of Navarre Director General de Salud de la Consejería de Salud del Gobierno de Navarra · Luis Ángel León Mateos Director of Health Research Planning and Promotion of the Galician Health Service ( SERGAS ) Director del Área de Planificación y Promoción de la Investigación Sanitaria del Servicio Gallego de Salud de la Xunta de Galicia ( SERGAS ) SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 239 ADMINISTRATION | bOARd OF TRUSTEES · Carlos Pesquera González Head of Cabinet of the Healthcare Counsellor of the Government of Cantabria Jefe de Gabinete de la Consejera de Sanidad del Gobierno de Cantabria · Sandra García Armesto Managing Director of the Aragon Institute of Health Sciences Directora Gerente del Instituto Aragonés de Ciencias de la Salud ȹ Elected Members · Rafael Pardo Avellaneda Director, BBVA Foundation Director de la Fundación BBVA · Jaume Giró Ribas CEO of “ la Caixa ” Banking Foundation Caixa d ’ Estalvis i Pensions de Barcelona Director General de la Fundación Bancaria Caixa d ’ Estalvis i Pensions de Barcelona, “ la Caixa ” · Ignacio Polanco Moreno Chairman, Grupo PRISA Presidente del Grupo PRISA ȹ Secretary · Margarita Blázquez Herranz Deputy Director General for Networks and Cooperative Research Centres of the National Institute of Health Carlos III Subdirectora General de Redes y Centros de Investigación Cooperativa, Instituto de Salud Carlos III ȹ Legal Advisor · Fernando Arenas Escribano Chief State’s Attorney of the Ministry of Health, Social Services and Equality Abogado del Estado Jefe en el Ministerio de Sanidad, Servicios Sociales e Igualdad * In accordance with the Spanish Transparency Legislation ( Spanish Royal Decree 451/2012, of March 5 ), the following information is hereby provided : - At the close of the financial year, the accumulated remuneration received by the Top Management of the Foundation - the CNIO’s Director plus the Managing Director - has amounted to a total of 268,287 Euros. This amount was received as base salary, seniority, as well as position salary supplements. - Members of the CNIO Board of Trustees are not remunerated. ANNUAL REPORT 2017 240 FACTS & FIGuRES SCIENTIFIC ADVISORy BOARD · Mariann Bienz, PhD, FRS, FMedSci ( Chair ) Joint Divisional Head Division of Protein and Nucleic Acid Chemistry Medical Research Council Laboratory of Molecular Biology Cambridge, United Kingdom · Lauri A. Aaltonen, MD, PhD Academy Professor Director, Genome Scale Biology Research Programme Biomedicum, University of Helsinki Helsinki, Finland · Genevieve Almouzni, PhD Director, Institut Curie Research Centre Head of Nuclear Dynamics & Genome Plasticity Unit Institut Curie, Paris, France · J. Michael Bishop, MD Chancellor Emeritus and Professor in the Dept. of Microbiology and Immunology Director of the G.W. Hooper Research Foundation University of California at San Francisco San Francisco, USA · José Costa, MD, FACP Professor of Pathology and of Orthopaedics and Rehabilitation Director of the Translational Diagnostics and the Musculoskeletal Tumor Programs Yale University School of Medicine New Haven, USA · Sara Courtneidge, PhD, DSc ( hc ) Associate Director for Translational Sciences, Knight Cancer Institute Professor, Departments of Cell, Developmental and Cancer Biology and Biomedical Engineering Oregon Health & Science University Portland, USA · John F.X. Diffley, PhD Associate Research Director The Francis Crick Institute London, United Kingdom · Stephen Frye, PhD Director, Center for Integrative Chemical Biology and Drug Discovery Fred Eshelman Distinguished Professor The University of North Carolina at Chapel Hill Chapel Hill, USA · Denise Galloway, PhD Associate Division Director, Human Biology Division at Fred Hutchinson Cancer Research Center Research Professor of Microbiology at the University of Washington Seattle, USA · Scott W. Lowe, PhD Chair, Cancer Biology and Genetics Program, SKI Chair, Geoffrey Beene Cancer Research Center Memorial Sloan-Kettering Cancer Center New York, USA · Ángela Nieto, PhD Full Professor and Head of the Developmental Neurobiology Unit Neuroscience Institute of Alicante ( CSIC-UMH ) Alicante, Spain SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 241 ADMINISTRATION | SCIENTIFIC AdvISORy bOARd · Josep Tabernero, MD PhD Director, Vall d’Hebron Institute of Oncology ( VHIO ) Head, Medical Oncology Department of Vall d’Hebron University Hospital Barcelona, Spain · Alfred Wittinghofer, PhD Emeritus Group Leader Department of Structural Biology Max Planck Institute for Molecular Physiology ( MPI ) Dortmund, Germany · Ada E. Yonath, PhD Director, the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly Martin S. and Helen Kimmel Professor of Structural Biology Weizmann Institute of Science Rehovot, Israel ANNUAL REPORT 2017 242 FACTS & FIGuRES MANAGEMENT DIRECTOR SECRETARIATE SECRETARIATE ( COMMUNICATION, INNOVATION, SCIENTIFIC MANAGEMENT ) Alcamí, María Jesús Rodríguez, M. Carmen TECHNOLOGY TRANSFER & VALORISATION OFFICE Sanz, Anabel Director Marín, M. Cruz ( Technology Transfer Manager ) Manzano, Rocío * PROJECTS & CONSORTIA EDUCATION & TRAINING PROGRAMMES SCIENTIFIC EVENTS Molina, Juan Ramón  ( until June ) Del Codo, Almudena * Moro, Mercedes Head SCIENTIFIC PUBLISHING LIBRARY & ARCHIVES Cerdá, Sonia López, Victoria DIRECTOR’S OFFICE VICE-DIRECTOR INTERNATIONAL AFFAIRS Peláez, Fernando Director Fernández-Capetillo, Óscar Pola, Carolina Director Fernández-Capetillo, Óscar Director COMMUNICATION INNOVATION SCIENTIFIC MANAGEMENT Noriega, Nuria Head De Martos, Cristina ( Communications Officer ) Camacho, Pablo ( Science Outreach Officer ) ( since May ) Barthelemy, Isabel Director Blasco, Maria A. Liébanes, M. Dolores  Head Ares, Raquel Merino, Ana Vergés, Leyre SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 243 ADMINISTRATION | mANAGEmENT MANAGING DIRECTOR SECRETARIATE Ámez, María del Mar Arroyo, Juan SAP Ferrer, Alfonso Head PURCHASING MAINTENANCE HUMAN RESOURCES PREVENTION & BIOSECURITY ECONOMIC MANAGEMENT INFORMATION TECHNOLOGIES AUDIT Pérez, José Lorenzo Head Bardají, Paz Carbonel, David Marco de la Cal, Claudia ( since March ) Cespón, Constantino Head Salido, M. Isabel Head Galindo, José Antonio García, Juan J. Fernández, José Luis Head de Miguel, Marcos García-Risco, Silvia Head Moreno, Ana María Head FINANCE & ADMINISTRATION MANAGING DIRECTOR’S OFFICE INFRASTRUCTURE MANAGEMENT EXTRAMURAL CLINICAL RESEARCH Fontaneda, Manuela Director Fernández-Vera, José Ignacio  Director ( since October ) de Dios, Luis Javier Director López, Antonio  Director ( since December ) Álamo, Pedro Head Baviano, Marta García-Andrade, Javier ( until April ) Novillo, Angélica De Luna, Almudena * Luongo, Victoria Eloina * Vacant Rodríguez, M. José Fernández, Rut * Hernando, M. Elena Doyagüez, Laura * Bertol, Narciso * Plan de Empleo Joven ( Youth Employment Plan ) ( until December ) ANNUAL REPORT 2017 244 FACTS & FIGuRES CNIO PERSONNEL 2017 GENDER DISTRIBUTION IN SENIOR ACADEMIC AND MANAGEMENT POSITIONS SCIENTIFIC DIRECTION: DIRECTORS, HEADS OF AREA MANAGEMENT: DIRECTORS, HEADS OF AREA HEADS OF UNIT/BIOBANK FEmALE 46% 6 mALE 54% 7 FEmALE 31% 4 mALE 69% 9 FEmALE 56% 10 mALE 44% 8 GROUP LEADERS, HEADS OF CLINICAL RESEARCH UNIT/SECTION FEmALE 33% 10 mALE 67% 20 365 RESEARCH 90% 121 30 30% 44 > 50 11% 132 31-40 32% 406 TOTAL CNIO PERSONNEL 41 ADMINISTRATION 10% AGE DISTRIBUTION 109 41-50 27% 141 MALE 35% 265 FEMALE 65% GENDER DISTRIBUTION SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 245 SCIENTIFIC PERSONNEL 2017 DISTRIBUTION BY PROGRAMMES EXPERIMENTAL THERAPEUTICS 8% 29 CANCER CELL BIOLOGY 11% 40 BIOTECHNOLOGY 10% 35 CLINICAL RESEARCH 18% 64 MOLECULAR ONCOLOGY 33% 119 STRUCTURAL BIOLOGY 11% 41 HUMAN CANCER GENETICS 10% 37 DISTRIBUTION BY PROFESSIONAL CATEGORY TECHNICIANS 30% 110 PRINCIPAL INVESTIGATORS 13% 48 STAFF SCIENTISTS 19% 69 GRADUATE STUDENTS 27% 100 POST-DOCTORAL FELLOWS 11% 38 GENDER DISTRIBUTION BY PROFESSIONAL CATEGORY TECHNICIANS TOTAL SCIENTIFIC PERSONNEL PRINCIPAL INVESTIGATORS FEmALE 74% 81 mALE 26% 29 FEmALE 239 mALE 126 FEmALE 38% 18 mALE 62% 30 STAFF SCIENTISTS FEmALE 74% 51mALE 26% 18 GRADUATE STUDENTS FEmALE 67% 67 mALE 33% 33 POST-DOCTORAL FELLOWS FEmALE 58% 22 mALE 42% 16 TOTAL SCIENTIFIC PERSONNEL 365 ADMINISTRATION | CNIO PERSONNEL 2017 ANNUAL REPORT 2017 246 FACTS & FIGuRES TOTAL SCIENTIFIC PERSONNEL 365 TOTAL 100% 200 TECHNICIANS 25% TECHNICIANS 56% 26 36 TOTAL 100% TOTAL 100% 101 64 DISTRIBUTION BY PROFESSIONAL CATEGORY IN: BASIC RESEARCH PRINCIPAL INVESTIGATORS 12% 23 STAFF SCIENTISTS 17% 35 GRADUATE STUDENTS 35% 69 POST-DOCTORAL FELLOWS 12% 25 TECHNICIANS 24% 48 DISTRIBUTION BY PROFESSIONAL CATEGORY IN: INNOVATION DISTRIBUTION BY PROFESSIONAL CATEGORY IN: TRANSLATIONAL RESEARCH PRINCIPAL INVESTIGATORS 12% PRINCIPAL INVESTIGATORS 20% 12 13 STAFF SCIENTISTS 23% STAFF SCIENTISTS 17% 23 11 GRADUATE STUDENTS 28% 28 POST-DOCTORAL FELLOWS 12% POST-DOCTORAL FELLOWS 2% GRADUATE STUDENTS 5% 12 1 3 SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 247 11 OTHER 33% 6 PORTUGAL 18% 9 ITALY 27% 3 AUSTRIA 9% 4 FRANCE 12% SCIENTIFIC PERSONNEL: NATIONAL ORIGIN DISTRIBUTION OF SCIENTIFIC PERSONNEL BY NATIONAL ORIGIN FOREIGN SCIENTIFIC PERSONNEL: DISTRIBUTION BY PROFESSIONAL CATEGORY TECHNICIANS 3% 3 PRINCIPAL INVESTIGATORS 15% 7 STAFF SCIENTISTS 12% 8 GRADUATE STUDENTS 20% 20 POST-DOCTORAL FELLOWS 26% 10 48 NON-SPANISH 13% TOTAL SCIENTIFIC PERSONNEL 100% TOTAL SCIENTIFIC PERSONNEL 100% 365 365 317 SPANISH 87% 33 REST OF EUROPE 9% 10 AMERICA 2.7% 5 ASIA 1.37% 317 SPANISH 87% Total foreign scientific personnel 48 Percent values represent percentages of foreign employees of the total CNIO personnel in each category ADMINISTRATION | CNIO PERSONNEL 2017 ANNUAL REPORT 2017 248 FACTS & FIGuRES PRIVATE SPONSORS “ We take this opportunity to express our thanks and appreciation to all our sponsors and donors for the generous support that we received from them in 2017. They play an inherent role in our present and future successes.” One of the Fundación ”la Caixa’s ” main goals is to support an innovative programme aimed at fostering international fellowships in order to attract the most outstanding students from the international arena to obtain their doctoral degrees at accredited ‘ Severo Ochoa ’ Centres of Excellence. In 2017, a new doctoral Fellowship Programme of “ la Caixa ” Foundation, named INPhINIT, was established with the aim of recruiting outstanding international students; in addition, a new call was launched to carry out a doctorate at Spanish universities and research centres. The Fundación ” la Caixa ” also helps finance our most prominent international conferences, the CNIO-”la Caixa ” Foundation Frontiers Meetings. Fundación CRIS is dedicated t o t h e p r o m o t i o n a n d development of research with the aim of eliminating the serious health threat of cancer. Fundación CRIS generously supports 3 research groups at the CNIO : the Prostate Cancer Clinical Research Unit ( CRU ), headed by David Olmos ; the Breast Cancer CRU, headed by Miguel Quintela ; and the H120-CNIO Haematological Malignancies CRU, led by Joaquín Martínez- López. These Groups focus on the translation of advances in cancer research into improvements in patient care. The Fundación Marcelino Botín and the Banco Santander are committed to supporting scientific research and knowledge transfer from academia to the market through science programmes ; this transfer is regarded as one of the main driving forces for Spain’s economic and social development. These 2 well-recognised organisations collaborate with the CNIO in this regard by supporting the research groups led by Manuel Serrano, Maria A. Blasco and Óscar Fernández-Capetillo. T h e F u n d a c i ó n B a n c o Santander funds the Banco Santander Foundation – CNIO Fellowships for Young Researchers. These fellowships have the aim to support highly talented and motivated young scientists who wish to pursue their postdoctoral training at the CNIO. Additionally, thanks to the support of the Fundación Banco Santander, a group of 3 young researchers received training on managerial and entrepreneurial skills, in collaboration with the IE Business School. T h e F u n d a c i ó n S e v e Ballesteros is a private not- for-profit institution focused on securing, financing and promoting research projects centred on brain tumours. Fundación Seve Ballesteros supports the Seve Ballesteros Foundation – CNIO Brain Tumour Group, headed by Massimo Squatrito, since 2012. This Group focuses on the identification of markers for brain tumours as its principal activity. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 249 PRIVATE SPONSORS T h e F u n d a c i ó n J e s ú s Serra-Catalana Occidente continues to fund the Visiting Scientists Programme that was established to support prestigious international professors for short stays at the CNIO. The recipients of the Jesús Serra Foundation’s Visiting Scientist Award in 2017 were Raul Rabadan, Professor of Systems Biology and Director of the Columbia University Center for Topology of Cancer Evolution and Heterogeneity ( USA ), and Professor Wolfgang Weninger, Head of the Department of Dermatology at the Royal Prince Alfred Hospital of Sydney ( Australia ). T h e A X A R e s e a r c h Fund  ( ARF ) − a global initiative of scientific philanthropy run by the insurance group AXA − awarded an AXA-CNIO Endowed Permanent Chair position in Molecular Oncology to Mariano Barbacid as part of its 2011 call. OTHER SPONSORS Our activities are al so supported by individual donations − citizens who wish to contribute personally to the battle against cancer − as well as via external fundraising from local associations that are equally dedicated to the battle against cancer. During 2017, our research activities and seminars were supported by : Fundación Juegaterapia, A s o c i a c i ó n p a r a l a Investigación y Formación Neoplásica ( ASIFEN ), Fundación Investigación Biomédica Hospital Universitario 12 de Octubre, Instrumentos Testo, Bristol Myers Squibb, Compañia Logística de Hidrocarburos, Fundación PFIZER, Fressia Group, ASISA Vida, Fundación Banco Sabadell, the U.S. Embassy, and the British Embassy. L a s t l y, w e e x t e n d o u r heartfelt thanks to all ‘ CNIO Friends ’ donors, sponsors and benefactors who, thanks to their generous donations to support cancer research at the CNIO, have ensured the continuation of our research endeavours throughout 2017. ANNUAL REPORT 2017 250 CNIO Friends SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 251 CNIO Friends 253 ‘ CNIO Friends ’ Postdoctoral Contracts 254 ‘ Excelentes ’: a book of portraits on ideas that drive the world 255 CNIO opens its doors to ‘ CNIO Friends ’ 256 Benefactor Friends/Sponsor Friends 258 Donations to the CNIO 259 SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 253 CNIO FRIENDS This year, once again, the ‘ CNIO Friends ’ philanthropic initiative was a source of immense gratification for our Centre. By December 2017, we had over 950 Friends ; their solidarity, support and efforts push us even further, in as far as possible, to advance with our crucial task of advancing cancer research. Thanks to all of our Friends, we were able to launch two new contracts in 2017 with the aim of attracting research talent that will enable us to commence and/or continue promising new lines of research to help us battle against cancer. One of the beneficiaries is the researcher, Carolina Maestre, from the Cell Division and Cancer Group, who will research the mechanisms of cell division in tumours. The other contract went to the scientist Sebastian Thompson, from the Growth Factors, Nutrients and Cancer Group, who will carry out research in the field of nanotechnology and its application for the treatment of the disease. In Maestre’s own words, “ I would like to thank all those who have collaborated in this initiative that is enabling me to continue my scientific career in Spain ”. Thompson spotlights the donors : “ From the donor’s point of view, seeing that the money is being used for the desired purpose is extremely enriching and necessary.” This year, we have also maintained the collaboration with Juegaterapia Foundation to foster research in childhood cancer. This alliance has enabled the researcher Irene Felipe, from the Epithelial Carcinogenesis Group, to continue her research for a second year. Felipe’s work focuses on neuroblastoma, one of the most common infancy tumours in the early years of life and the second most common tumour in children after brain tumours. In February 2017, within the framework of the ‘ CNIO Friends ’ initiative, the CNIO published the book Excelentes featuring portraits of the Centre’s most influential visitors in recent years. The visual artist Amparo Garrido took care of the artistic representations and the texts were written by the journalist Mónica G. Salomone. Its pages invite the non-specialised public into the world of scientists through some of the ideas that move the world. Ideas from molecular biologists, such as the Nobel Prize-winners, Elizabeth Blackburn, Robert Huber and Paul Nurse ; physicists, such as Ignacio Cirac, who is featured on the book cover and entices the readers to open up its pages ; the palaeontologist, Juan Luis Arsuaga... as well as experts from other fields, such as the alpinist Edurne Pasaban, and the jurist María Teresa Fernández de la Vega. The book launch presentation was held at El Corte Inglés in Preciados with Mago More as the master of ceremonies, and the participation of one of Spain’s most popular humourists, José Mota. The book can be purchased at El Corte Inglés, VIPS stores and through the CNIO website ; all generated funds go to ‘ CNIO Friends ’ initiative for cancer research. Throughout the year, we received many proposals for charity activities from anonymous citizens, town halls, etc. to support our work. This led to, for example, a thousand people turning the streets of Rojales in Alicante into a huge human wave to support cancer research during the 4th Women’s Charity Walk organised by the Town Hall. The message was also clear in Las Pedroñeras, Cuenca, whose Town Hall held the 2nd Cancer Charity Race, the profits of which also went to CNIO Friends. Many other initiatives were organised across the length and breadth of the country. For yet another year, companies have also formed part of our Friends community. In 2017, the CLH Group, a leading company for the transportation and storage of oil products in the Spanish market, renewed its commitment and support to cancer research. Instrumentos Testo, S.A. a company specialised in portable measuring tools, also joined the charity initiative through the challenge of running 25,000 Km in favour of the CNIO. These accomplishments demonstrate that there are no challenges that cannot be overcome when it comes to research. CNIO Friends ended the year with an optimistic outlook towards the future, and gave expression to this positivity with the help of two of Spain’s most popular humourists. José Mota and Mago More both allowed their image to be used in a sketch − whose release coincided with Giving Tuesday, the international day of donations − to encourage society to support and encourage our work. In the sketch, they used all of their wit to shout out the message loud and clear : “ if many of us provide a bit, we will all do a lot !” Another form of philanthropy that is progressively increasing in Spain has to do with the donation of legacies and inheritances in favour of research institutions such as the CNIO. In fact, during 2017 we were notified of the execution of 4 new legacies ( one more than the previous year ), which included deposits, accounts and other monetary assets, as well as real estate. In addition, we have received communications from several people informing us of their intention to include the CNIO in their will. We hope that this trend of favouring the research institutions of this country, and the CNIO in particular, through testamentary dispositions will increase, thereby matching what is already common practice in other countries. In summary, our Friends are an essential driving force in our efforts to find new solutions to fight cancer. Our deepest thanks to them all ! CNIO FRIENDS “ With every little helpful bit, we can achieve a lot !” ANNUAL REPORT 2017 254 CNIO FRIENDS ‘ CNIO FRIENDS ’ POSTDOCTORAL CONTRACTS The new recipients of the ‘ CNIO Friends ’ postdoctoral contracts are Carolina Maestre and Sebastian Thompson, from the Cell Division and Cancer Group and Growth Factors, Nutrients and Cancer Group, respectively. Maestre is an expert on the progression of mitosis − cell division – as a target for the development of new cancer therapeutic drugs. “ We have identified a molecule that regulates mitosis and which is involved in the survival of tumour cells during their division ; we believe that if we can manage to inhibit its function, we could attack tumour proliferation.” Thompson’s work focuses on nanoparticles as drug carriers, particularly on their increased chance of reaching tumour cells in the organism. “ Thanks to CNIO Friends, we will continue to work on finding the best way of getting as many of these nanoparticles as possible to the tumours ; this could pave the way for the application of the latest advances in nanotechnology to the treatment of cancers.” SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 255 CNIO FRIENDS ‘ EXCELENTES ’: A BOOK OF PORTRAITS ON IDEAS THAT DRIVE THE WORLD In February 2017, the CNIO published the book Excelentes, of which the sales revenues all go to the ‘ CNIO Friends ’ philanthropic initiative for cancer research. The launch of the book was wonderfully presented by Mago More, the master of ceremonies. The special event was even more momentous thanks to the participation of CNIO’s director Maria Blasco, the visual artist Amparo Garrido, the science journalist and writer of the protagonists ’ stories Monica G. Salomone, and the popular Spanish humourist José Mota, who put the icing on the cake and used his ingenuity and imagination to spread the message. ANNUAL REPORT 2017 256 CNIO FRIENDS CNIO OPENS ITS DOORS TO ‘ CNIO FRIENDS ’ One of the most exiting events hosted in 2017 was the ‘ Jornada Amigos del CNIO ’ that took place in June and welcomed our donors/CNIO Friends in order to bring them closer to CNIO’s science. Our donors spent an afternoon with us and once again demonstrated their great enthusiasm for being part of the important mission of conquering of cancer. SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 257 CNIO FRIENDS Last but not least, we would also like to extend our heartfelt thanks to all the anonymous benefactors who have donated their legacies to support cancer research at the CNIO ; in doing so they have contributed to society for generations to come. BECOME A CNIO FRIEND more RESEARCH less CANCER ANNUAL REPORT 2017 258 CNIO FRIENDS ȹ Benefactor Friends · Alfonso Agüera Nieto Santa Ana-Cartagena, Murcia · Alvaro Gil Conejo Mijas, Málaga · Andrés Sánchez Arranz Madrid, Madrid · Asociación de Afectados de Cáncer-AFECC Llerena, Badajoz · Breatel, S.L.U. Madrid, Madrid · Deltaclon, S.L. Madrid, Madrid · Dolors Bosch Güell Olot, Girona · Encarnación Fernández Pérez Madrid, Madrid · Enrique García Díaz Tomares, Sevilla · Esther Valdivia Carrión Madrid, Madrid · Fernando Pascual Carreras Madrid, Madrid · Ferrán Nácher Carull Xativa, Valencia · Francisco Javier Gállego Franco Barbastro, Huesca · Gema Rubio González Madrid, Madrid · IES “ San Vicente ” de San Vicente del Raspeig San Vicente del Raspeig, Alicante · International Road Technology Consulting S.L Parla, Madrid · Jaime Escobar Fermoselle Cadalso de los Vidrios, Madrid · Jesús Miguel Iglesias Retuerto Valladolid, Valladolid · José Limiñana Valero Alicante, Alicante · José Luis Catalá López Las Palmas de Gran Canaria, Las Palmas · Juan Félix Ortigosa Córdoba Granollers, Barcelona · Luis David Sanz Navarro Madrid, Madrid · Mercedes Cáceres Alonso Madrid, Madrid · María Dolores Díaz Almagro Sevilla, Sevilla · María Jesús Amores Molero Jábaga, Cuenca · María Rodríguez López Celada de los Calderones, Cantabria · Nemesio Carro Carro León, León BENEFACTOR FRIENDS/SPONSOR FRIENDS ȹ Sponsor Friends · Asisa Vida Seguros S.A.U. Madrid, Madrid · Asociación de Mujeres Alameda del Tormes por la Igualdad El Barco de Ávila, Ávila · Colectivo de afectados “ El árbol de la Vida ” Las Pedroñeras, Cuenca · Compañía Logística de Hidrocarburos CLH, S.A. · Freesia Group Salou, Tarragona · Fundación Juegaterapia Madrid, Madrid · Instrumentos Testo, S.A. Cabrils, Barcelona · Maria Josefa Azcona Peribañez Madrid, Madrid · Petroplast Logroño, La Rioja SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 259 CNIO FRIENDS DONATIONS TO THE CNIO 261,000€ TOTAL CNIO DONATIONS 2017 (50,000€ from the Juegaterapia Foundation) 100,000€ ATRESMEDIA 2015 100,000€ 44,000€ DONATIONS BEFORE LAuNCH OF CNIO FRIENDS 2014 10,000€ 2013 25,000€ 2012 3,000€ 2011 6,000€ * In 2017, the CNIO was notified of 4 legacies ; calculation of their value is yet to be determined. 509,000€ CNIO FRIENDS 2017 261,000€ (50,000€ from Juegaterapia) 2016 144,000€ 2015 100,000€ 2014 4,000€ 734,000€* LEGACIES 2017 4 bequests pending* 2016 361,000€ 2015 350,000€ 2014 23,000€ ANNUAL REPORT 2017 260 CREATIVE TEAM AMPARO GARRIDO PHOTOGRAPHy In order to pour the Annual Report into a more creative concept, the CNIO works closely with selected professionals in the artistic and creative sectors who ensure delivery of an end product that is attractive in more ways than one. We extend our thanks to the creative team, the visual artist Amparo Garrido, and the graphic design studio underbau whose invaluable work created the images and design that illustrate this Annual Report. A Madrid-based visual artist working with photography and video, Amparo Garrido has been represented in individual and group shows both in Spain and abroad since 1998. Her work has been honoured in several prestigious competitions. She obtained the first place in the 2001 edition of the ABC Photography Prize, and second place in the 2007 Purificación García Prize. Other honourable mentions include the Pilar Citoler and Ciudad de Palma prizes. Her work can be found in major collections, including the Museo Nacional Centro de Arte Reina Sofia in Madrid, the photographic holdings of the Madrid regional authority, the Coca-Cola Foundation, the Es Baluard Museum of Modern and Contemporary Art in Palma de Mallorca, and the ‘ Types and Trends on the Threshold of the 21st Century ’ Alcobendas Collection, among many others. Amparo’s most recent solo exhibitions in Spain were shown at the Sala Robayera de Miengo, Cantabria 2017, Galería Trinta, Santiago de Compostela 2015, and the Museo del Romanticismo, Madrid 2012. CREATIVE TEAM SPANISH NATIONAL CANCER RESEARCH CENTRE, CNIO 261 CREATIVE TEAM uNDERBAu dESIGN Underbau is a design studio that emerged in 2008 from professional designers with 15 years of experience in the field of corporate design, publishing and advertising. From the very beginning, the studio has sought to maintain its primary focus on art and culture, working together with Spanish and international bodies such as the Orquesta y Coro Nacionales de España, Instituto Cervantes and Museo Thyssen-Bornemisza. Underbau’s total- design approach puts the emphasis on coherency. To achieve that, the studio assumes full responsibility for the entire creative process, from the initial concept to the final product. Centro Nacional de Investigaciones Oncológicas (CNIO) Melchor Fernández Almagro, 3 28029 Madrid, Spain www.cnio.es Coordination Sonia Cerdá Edition Sonia Cerdá and An Devriese Direction Isabel Barthelemy Text, data and figures CNIO Faculty and Management Publication database Victoria López Photo shoot Coordination M. Carmen Rodríguez Photography Amparo Garrido Design underbau Typesetting Nicolás García Marque Prepress La Troupe This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reproduction on microfilms or in any other way, and storage in data banks. © Fundación del Sector Público Estatal Centro Nacional de Investigaciones Oncológicas Carlos III (F.S.P. CNIO), 2018 National book catalogue number M-4792-2018 ISSN 2529-9514