Cell Research最新文献

{"title":"GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model","authors":"Xiaodong Yang, Guole Liu, Guihai Feng, Dechao Bu, Pengfei Wang, Jie Jiang, Shubai Chen, Qinmeng Yang, Hefan Miao, Yiyang Zhang, Zhenpeng Man, Zhongming Liang, Zichen Wang, Yaning Li, Zheng Li, Yana Liu, Yao Tian, Wenhao Liu, Cong Li, Ao Li, Jingxi Dong, Zhilong Hu, Chen Fang, Lina Cui, Zixu Deng, Haiping Jiang, Wentao Cui, Jiahao Zhang, Zhaohui Yang, Handong Li, Xingjian He, Liqun Zhong, Jiaheng Zhou, Zijian Wang, Qingqing Long, Ping Xu, Hongmei Wang, Zhen Meng, Xuezhi Wang, Yangang Wang, Yong Wang, Shihua Zhang, Jingtao Guo, Yi Zhao, Yuanchun Zhou, Fei Li, Jing Liu, Yiqiang Chen, Ge Yang, Xin Li","doi":"10.1038/s41422-024-01034-y","DOIUrl":"https://doi.org/10.1038/s41422-024-01034-y","url":null,"abstract":"<p>Deciphering universal gene regulatory mechanisms in diverse organisms holds great potential for advancing our knowledge of fundamental life processes and facilitating clinical applications. However, the traditional research paradigm primarily focuses on individual model organisms and does not integrate various cell types across species. Recent breakthroughs in single-cell sequencing and deep learning techniques present an unprecedented opportunity to address this challenge. In this study, we built an extensive dataset of over 120 million human and mouse single-cell transcriptomes. After data preprocessing, we obtained 101,768,420 single-cell transcriptomes and developed a knowledge-informed cross-species foundation model, named GeneCompass. During pre-training, GeneCompass effectively integrated four types of prior biological knowledge to enhance our understanding of gene regulatory mechanisms in a self-supervised manner. By fine-tuning for multiple downstream tasks, GeneCompass outperformed state-of-the-art models in diverse applications for a single species and unlocked new realms of cross-species biological investigations. We also employed GeneCompass to search for key factors associated with cell fate transition and showed that the predicted candidate genes could successfully induce the differentiation of human embryonic stem cells into the gonadal fate. Overall, GeneCompass demonstrates the advantages of using artificial intelligence technology to decipher universal gene regulatory mechanisms and shows tremendous potential for accelerating the discovery of critical cell fate regulators and candidate drug targets.</p>","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":null,"pages":null},"PeriodicalIF":44.1,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142383954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Feeling the danger: local wound signaling in plants","authors":"Lukas Hoermayer,&nbsp;Jiří Friml","doi":"10.1038/s41422-024-01035-x","DOIUrl":"10.1038/s41422-024-01035-x","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":null,"pages":null},"PeriodicalIF":28.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01035-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PCDH10 is a neuronal receptor for western equine encephalitis virus","authors":"Yan Yang,&nbsp;Li-Xin Zhao,&nbsp;Zhen-Qi Li,&nbsp;Su-Yun Wang,&nbsp;Zhi-Sheng Xu,&nbsp;Yan-Yi Wang","doi":"10.1038/s41422-024-01031-1","DOIUrl":"10.1038/s41422-024-01031-1","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":null,"pages":null},"PeriodicalIF":28.1,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01031-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142275321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"α-Synuclein amyloid fibril directly binds to LC3B and suppresses SQSTM1/p62-mediated selective autophagy","authors":"Qianhui Xu, Huilan Wang, Ruonan Yang, Youqi Tao, Ziying Wang, Shengnan Zhang, Bo Sun, Dan Li, Boxun Lu, Cong Liu","doi":"10.1038/s41422-024-01022-2","DOIUrl":"https://doi.org/10.1038/s41422-024-01022-2","url":null,"abstract":"<p>Dear Editor,</p><p>Parkinson’s disease (PD) is a progressive neurodegenerative disorder, which manifests through the abnormal accumulation of pathological amyloid fibrils composed of α-synuclein (α-syn) into Lewy bodies and the deterioration of dopaminergic neurons in the substantia nigra.^1,2,3,4 In addition to α-syn fibrillar aggregation, the disruption of selective autophagy is also tightly linked to the pathogenesis of PD.^5,6 The co-localization of LC3B, the key autophagosome protein in selective autophagy,⁷ and α-syn in the Lewy bodies of PD patients’ brains points towards a potential role of α-syn in modulating selective autophagy.⁸ Yet, the interplay between them has not been mechanistically elucidated.</p>","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":null,"pages":null},"PeriodicalIF":44.1,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142262896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AMPK-PDZD8-GLS1 axis mediates calorie restriction-induced lifespan extension","authors":"Mengqi Li,&nbsp;Yu Wang,&nbsp;Xiaoyan Wei,&nbsp;Wei-Feng Cai,&nbsp;Yan-Hui Liu,&nbsp;Jianfeng Wu,&nbsp;Yan Chen,&nbsp;Jinye Xiong,&nbsp;Li-Feng Cui,&nbsp;Mingxia Zhu,&nbsp;Cixiong Zhang,&nbsp;Liyun Lin,&nbsp;Yong Yu,&nbsp;Hai-Long Piao,&nbsp;Sheng-Cai Lin,&nbsp;Chen-Song Zhang","doi":"10.1038/s41422-024-01021-3","DOIUrl":"10.1038/s41422-024-01021-3","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":null,"pages":null},"PeriodicalIF":28.1,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01021-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142275854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Author Correction: Targeting pro-inflammatory T cells as a novel therapeutic approach to potentially resolve atherosclerosis in humans","authors":"Lin Fan,&nbsp;Junwei Liu,&nbsp;Wei Hu,&nbsp;Zexin Chen,&nbsp;Jie Lan,&nbsp;Tongtong Zhang,&nbsp;Yang Zhang,&nbsp;Xianpeng Wu,&nbsp;Zhiwei Zhong,&nbsp;Danyang Zhang,&nbsp;Jinlong Zhang,&nbsp;Rui Qin,&nbsp;Hui Chen,&nbsp;Yunfeng Zong,&nbsp;Jianmin Zhang,&nbsp;Bing Chen,&nbsp;Jun Jiang,&nbsp;Jifang Cheng,&nbsp;Jingyi Zhou,&nbsp;Zhiwei Gao,&nbsp;Zhenjie Liu,&nbsp;Ying Chai,&nbsp;Junqiang Fan,&nbsp;Pin Wu,&nbsp;Yinxuan Chen,&nbsp;Yuefeng Zhu,&nbsp;Kai Wang,&nbsp;Ying Yuan,&nbsp;Pintong Huang,&nbsp;Ying Zhang,&nbsp;Huiqin Feng,&nbsp;Kaichen Song,&nbsp;Xun Zeng,&nbsp;Wei Zhu,&nbsp;Xinyang Hu,&nbsp;Weiwei Yin,&nbsp;Wei Chen,&nbsp;Jian’an Wang","doi":"10.1038/s41422-024-01003-5","DOIUrl":"10.1038/s41422-024-01003-5","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":null,"pages":null},"PeriodicalIF":28.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01003-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142281026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lysine methylation steps into another step of the central dogma","authors":"Zuodong Zhao,&nbsp;Bing Zhu","doi":"10.1038/s41422-024-01033-z","DOIUrl":"10.1038/s41422-024-01033-z","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":null,"pages":null},"PeriodicalIF":28.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01033-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"tRNA repair: the key to thermo-sensitive male sterility in rice","authors":"Nai-Qian Dong,&nbsp;Hong-Xuan Lin","doi":"10.1038/s41422-024-01032-0","DOIUrl":"10.1038/s41422-024-01032-0","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":null,"pages":null},"PeriodicalIF":28.1,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01032-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142234503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Designing de novo D-protein binders","authors":"Haiyan Liu","doi":"10.1038/s41422-024-01029-9","DOIUrl":"https://doi.org/10.1038/s41422-024-01029-9","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":null,"pages":null},"PeriodicalIF":44.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142166293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The 1% gift to humanity: The Human Genome Project II","authors":"Weibin Liu,&nbsp;Yan Li,&nbsp;George P. Patrinos,&nbsp;Shuhua Xu,&nbsp;Meow-Keong Thong,&nbsp;Zhengming Chen,&nbsp;Francis P. Crawley,&nbsp;Liming Li,&nbsp;Perihan Elif Ekmekci,&nbsp;Radoje Drmanac,&nbsp;Weiyang Cheong,&nbsp;Robert Benamouzig,&nbsp;Quan Nguyen,&nbsp;Pavel Volchkov,&nbsp;Juergen K. V. Reichardt,&nbsp;Piero Carninci,&nbsp;Partha Majumder,&nbsp;Xin Jin,&nbsp;George Church,&nbsp;Jian Wang,&nbsp;Xun Xu","doi":"10.1038/s41422-024-01026-y","DOIUrl":"10.1038/s41422-024-01026-y","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":null,"pages":null},"PeriodicalIF":28.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01026-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142202382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}