Browsing by Author "Lai, Yiwei"
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Publication Cell transcriptomic atlas of the non-human primate Macaca fascicularis.(Nature Publishing Group, 2022-04) Han, Lei; Wei, Xiaoyu; Liu, Chuanyu; Volpe, Giacomo; Zhuang, Zhenkun; Zou, Xuanxuan; Wang, Zhifeng; Pan, Taotao; Yuan, Yue; Zhang, Xiao; Fan, Peng; Guo, Pengcheng; Lai, Yiwei; Lei, Ying; Liu, Xingyuan; Yu, Feng; Shangguan, Shuncheng; Lai, Guangyao; Deng, Qiuting; Liu, Ya; Wu, Liang; Shi, Quan; Yu, Hao; Huang, Yunting; Cheng, Mengnan; Xu, Jiangshan; Liu, Yang; Wang, Mingyue; Wang, Chunqing; Zhang, Yuanhang; Xie, Duo; Yang, Yunzhi; Yu, Yeya; Zheng, Huiwen; Wei, Yanrong; Huang, Fubaoqian; Lei, Junjie; Huang, Waidong; Zhu, Zhiyong; Lu, Haorong; Wang, Bo; Wei, Xiaofeng; Chen, Fengzhen; Yang, Tao; Du, Wensi; Chen, Jing; Xu, Shibo; An, Juan; Ward, Carl; Wang, Zongren; Pei, Zhong; Wong, Chi-Wai; Liu, Xiaolei; Zhang, Huafeng; Liu, Mingyuan; Qin, Baoming; Schambach, Axel; Isern, Joan; Feng, Liqiang; Liu, Yan; Guo, Xiangyu; Liu, Zhen; Sun, Qiang; Maxwell, Patrick H; Barker, Nick; Muñoz-Cánoves, Pura; Gu, Ying; Mulder, Jan; Uhlen, Mathias; Tan, Tao; Liu, Shiping; Yang, Huanming; Wang, Jian; Hou, Yong; Xu, Xun; Esteban, Miguel A; Liu, LongqiStudying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell-cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs.Publication Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration.(Nature Publishing Group, 2023-01) Moiseeva, Victoria; Cisneros, Andrés; Sica, Valentina; Deryagin, Oleg; Lai, Yiwei; Jung, Sascha; Andrés, Eva; An, Juan; Segalés, Jessica; Ortet, Laura; Lukesova, Vera; Volpe, Giacomo; Benguria, Alberto; Dopazo, Ana; Benitah, Salvador Aznar; Urano, Yasuteru; Del Sol, Antonio; Esteban, Miguel A; Ohkawa, Yasuyuki; Serrano, Antonio L; Perdiguero, Eusebio; Munoz-Canoves, Pura; Unión Europea. Comisión Europea. European Research Council (ERC); Fundación La Caixa; Fundación La Marató TV3; Ministerio de Ciencia e Innovación. Centro de Excelencia Severo Ochoa (España); Chinese Academy of Sciences; Japan Science & Technology Agency; Japan Society for the Promotion of Science (Japón)Tissue regeneration requires coordination between resident stem cells and local niche cells1,2. Here we identify that senescent cells are integral components of the skeletal muscle regenerative niche that repress regeneration at all stages of life. The technical limitation of senescent-cell scarcity3 was overcome by combining single-cell transcriptomics and a senescent-cell enrichment sorting protocol. We identified and isolated different senescent cell types from damaged muscles of young and old mice. Deeper transcriptome, chromatin and pathway analyses revealed conservation of cell identity traits as well as two universal senescence hallmarks (inflammation and fibrosis) across cell type, regeneration time and ageing. Senescent cells create an aged-like inflamed niche that mirrors inflammation associated with ageing (inflammageing4) and arrests stem cell proliferation and regeneration. Reducing the burden of senescent cells, or reducing their inflammatory secretome through CD36 neutralization, accelerates regeneration in young and old mice. By contrast, transplantation of senescent cells delays regeneration. Our results provide a technique for isolating in vivo senescent cells, define a senescence blueprint for muscle, and uncover unproductive functional interactions between senescent cells and stem cells in regenerative niches that can be overcome. As senescent cells also accumulate in human muscles, our findings open potential paths for improving muscle repair throughout life.Publication Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.(Cell Press, 2022-05-12) Chen, Ao; Liao, Sha; Cheng, Mengnan; Ma, Kailong; Wu, Liang; Lai, Yiwei; Qiu, Xiaojie; Yang, Jin; Xu, Jiangshan; Hao, Shijie; Wang, Xin; Lu, Huifang; Chen, Xi; Liu, Xing; Huang, Xin; Li, Zhao; Hong, Yan; Jiang, Yujia; Peng, Jian; Liu, Shuai; Shen, Mengzhe; Liu, Chuanyu; Li, Quanshui; Yuan, Yue; Wei, Xiaoyu; Zheng, Huiwen; Feng, Weimin; Wang, Zhifeng; Liu, Yang; Wang, Zhaohui; Yang, Yunzhi; Xiang, Haitao; Han, Lei; Qin, Baoming; Guo, Pengcheng; Lai, Guangyao; Muñoz-Cánoves, Pura; Maxwell, Patrick H; Thiery, Jean Paul; Wu, Qing-Feng; Zhao, Fuxiang; Chen, Bichao; Li, Mei; Dai, Xi; Wang, Shuai; Kuang, Haoyan; Hui, Junhou; Wang, Liqun; Fei, Ji-Feng; Wang, Ou; Wei, Xiaofeng; Lu, Haorong; Wang, Bo; Liu, Shiping; Gu, Ying; Ni, Ming; Zhang, Wenwei; Mu, Feng; Yin, Ye; Yang, Huanming; Lisby, Michael; Cornall, Richard J; Mulder, Jan; Uhlén, Mathias; Esteban, Miguel A; Li, Yuxiang; Liu, Longqi; Xu, Xun; Wang, JianSpatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.