Pub Date : 2024-10-14DOI: 10.1038/s41422-024-01039-7
Yangkyun Oh, Won-Jae Lee
While a balanced intake of macronutrients — carbohydrates, fats, and proteins — is essential for metabolic homeostasis, animals need higher protein intake during critical life stages like pregnancy. A recent paper inCellby Wu et al. introduces the novel concept of adjusting protein intake setpoints based on sex and mating status, using two opposing G protein-coupled receptor (GPCR) signaling pathways that regulate protein appetite-controlling neurons in the fruit fly,Drosophila melanogaster.
{"title":"Fine-tuning protein hunger: sex- and mating-dependent setpoint control","authors":"Yangkyun Oh, Won-Jae Lee","doi":"10.1038/s41422-024-01039-7","DOIUrl":"https://doi.org/10.1038/s41422-024-01039-7","url":null,"abstract":"<p><b>While a balanced intake of macronutrients — carbohydrates, fats, and proteins — is essential for metabolic homeostasis, animals need higher protein intake during critical life stages like pregnancy. A recent paper in</b> <b><i>Cell</i></b> <b>by Wu et al. introduces the novel concept of adjusting protein intake setpoints based on sex and mating status, using two opposing G protein-coupled receptor (GPCR) signaling pathways that regulate protein appetite-controlling neurons in the fruit fly,</b> <b><i>Drosophila melanogaster</i></b>.</p>","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"193 1","pages":""},"PeriodicalIF":44.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430543","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}
Pub Date : 2024-10-14DOI: 10.1038/s41422-024-01040-0
Benoit Viollet, Bruno Guigas
The capacity to effectively adapt metabolism to environmental demands is crucial for cell viability, proliferation, and function. Recent discoveries inCell Researchhave highlighted the role of the lysosomal pool of AMPK in promoting glutaminolysis during glucose shortage through the activation of a PDZD8-GLS1 axis.
{"title":"Fueling metabolic adaptation: lysosomal AMPK ignites glutaminolysis","authors":"Benoit Viollet, Bruno Guigas","doi":"10.1038/s41422-024-01040-0","DOIUrl":"https://doi.org/10.1038/s41422-024-01040-0","url":null,"abstract":"<p><b>The capacity to effectively adapt metabolism to environmental demands is crucial for cell viability, proliferation, and function. Recent discoveries in</b> <b><i>Cell Research</i></b> <b>have highlighted the role of the lysosomal pool of AMPK in promoting glutaminolysis during glucose shortage through the activation of a PDZD8-GLS1 axis</b>.</p>","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"229 1","pages":""},"PeriodicalIF":44.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430544","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}
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.
{"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":"13 1","pages":""},"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}
Pub Date : 2024-10-01DOI: 10.1038/s41422-024-01035-x
Lukas Hoermayer, Jiří Friml
{"title":"Feeling the danger: local wound signaling in plants","authors":"Lukas Hoermayer, 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":"34 11","pages":"761-762"},"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}
Pub Date : 2024-09-20DOI: 10.1038/s41422-024-01031-1
Yan Yang, Li-Xin Zhao, Zhen-Qi Li, Su-Yun Wang, Zhi-Sheng Xu, Yan-Yi Wang
{"title":"PCDH10 is a neuronal receptor for western equine encephalitis virus","authors":"Yan Yang, Li-Xin Zhao, Zhen-Qi Li, Su-Yun Wang, Zhi-Sheng Xu, 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":"34 11","pages":"802-805"},"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}
Pub Date : 2024-09-19DOI: 10.1038/s41422-024-01022-2
Qianhui Xu, Huilan Wang, Ruonan Yang, Youqi Tao, Ziying Wang, Shengnan Zhang, Bo Sun, Dan Li, Boxun Lu, Cong Liu
Dear Editor,
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.
{"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.<sup>1,2,3,4</sup> In addition to α-syn fibrillar aggregation, the disruption of selective autophagy is also tightly linked to the pathogenesis of PD.<sup>5,6</sup> The co-localization of LC3B, the key autophagosome protein in selective autophagy,<sup>7</sup> and α-syn in the Lewy bodies of PD patients’ brains points towards a potential role of α-syn in modulating selective autophagy.<sup>8</sup> Yet, the interplay between them has not been mechanistically elucidated.</p>","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"16 1","pages":""},"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}
Pub Date : 2024-09-17DOI: 10.1038/s41422-024-01033-z
Zuodong Zhao, Bing Zhu
{"title":"Lysine methylation steps into another step of the central dogma","authors":"Zuodong Zhao, 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":"34 11","pages":"759-760"},"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}
Pub Date : 2024-09-16DOI: 10.1038/s41422-024-01032-0
Nai-Qian Dong, Hong-Xuan Lin
{"title":"tRNA repair: the key to thermo-sensitive male sterility in rice","authors":"Nai-Qian Dong, 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":"34 11","pages":"755-756"},"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}
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