{"title":"Profiling the disordered proteome in cells using a chemical tag","authors":"Tze Cin Owyong, Shouxiang Zhang","doi":"10.1038/s41580-025-00833-4","DOIUrl":"10.1038/s41580-025-00833-4","url":null,"abstract":"In this Tools of the Trade article, Zhang and Owyong (Hong lab) discuss the development of a fluorescent probe that binds disordered proteins in situ and allows their enrichment and identification using a mass-spectrometry-based workflow.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 5","pages":"334-334"},"PeriodicalIF":81.3,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414665","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":"Regulation and function of insulin and insulin-like growth factor receptor signalling","authors":"Eunhee Choi, Cunming Duan, Xiao-chen Bai","doi":"10.1038/s41580-025-00826-3","DOIUrl":"10.1038/s41580-025-00826-3","url":null,"abstract":"Receptors of insulin and insulin-like growth factors (IGFs) are receptor tyrosine kinases whose signalling controls multiple aspects of animal physiology throughout life. In addition to regulating metabolism and growth, insulin–IGF receptor signalling has recently been linked to a variety of new, cell type-specific functions. In the last century, key questions have focused on how structural differences of insulin and IGFs affect receptor activation, and how insulin–IGF receptor signalling translates into pleiotropic biological functions. Technological advances such as cryo-electron microscopy have provided a detailed understanding of how native and engineered ligands activate insulin–IGF receptors. In this Review, we highlight recent structural and functional insights into the activation of insulin–IGF receptors, and summarize new agonists and antagonists developed for intervening in the activation of insulin–IGF receptor signalling. Furthermore, we discuss recently identified regulatory mechanisms beyond ligand–receptor interactions and functions of insulin–IGF receptor signalling in diseases. Insulin and insulin-like growth factor (IGF) signalling regulates metabolism, cell growth and proliferation and diverse cell-specific processes. This Review discusses recent structural insights into insulin–receptor and IGF–receptor binding and activation, regulation of insulin and IGF signalling and new agonists with therapeutic potential.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 7","pages":"558-580"},"PeriodicalIF":81.3,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385074","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":"Expanding the genetic code for site-specific lysine lactylation","authors":"Zhi Zong","doi":"10.1038/s41580-025-00832-5","DOIUrl":"10.1038/s41580-025-00832-5","url":null,"abstract":"In this Tools of the Trade article, Zong (Zhou lab) describes how using genetic code expansion enabled the precise incorporation of post-translational modifications such as lysine lactylation into proteins, allowing the authors to investigate their role in cellular processes.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 4","pages":"252-252"},"PeriodicalIF":81.3,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083415","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":"Unravelling the complexity of gene regulation through multiplexed protein mapping","authors":"Isabel Nadine Goronzy","doi":"10.1038/s41580-025-00830-7","DOIUrl":"10.1038/s41580-025-00830-7","url":null,"abstract":"In this Tools of the Trade article, Goronzy (Guttman lab) describes the development of ChIP-DIP, a high-throughput, split-pool barcoding method that enables genome-wide profiling of hundreds of regulatory proteins, transforming our ability to study the regulation of gene activity across cell types and biological contexts.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 4","pages":"251-251"},"PeriodicalIF":81.3,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143124317","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":"Silencing centromeres with age","authors":"Katharine H. Wrighton","doi":"10.1038/s41580-025-00829-0","DOIUrl":"10.1038/s41580-025-00829-0","url":null,"abstract":"Centromeres are silenced in aged cells by the epigenetic downregulation of centromere transcription.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 3","pages":"173-173"},"PeriodicalIF":81.3,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143072634","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":"Shaping epithelial tissues by stem cell mechanics in development and cancer","authors":"Vincent F. Fiore, Jorge Almagro, Elaine Fuchs","doi":"10.1038/s41580-024-00821-0","DOIUrl":"10.1038/s41580-024-00821-0","url":null,"abstract":"Adult stem cells balance self-renewal and differentiation to build, maintain and repair tissues. The role of signalling pathways and transcriptional networks in controlling stem cell function has been extensively studied, but there is increasing appreciation that mechanical forces also have a crucial regulatory role. Mechanical forces, signalling pathways and transcriptional networks must be coordinated across diverse length and timescales to maintain tissue homeostasis and function. Such coordination between stem cells and neighbouring cells dictates when cells divide, migrate and differentiate. Recent advances in measuring and manipulating the mechanical forces that act upon and are produced by stem cells are providing new insights into development and disease. In this Review, we discuss the mechanical forces involved when epithelial stem cells construct their microenvironment and what happens in cancer when stem cell niche mechanics are disrupted or dysregulated. As the skin has evolved to withstand the harsh mechanical pressures from the outside environment, we often use the stem cells of mammalian skin epithelium as a paradigm for adult stem cells shaping their surrounding tissues. Adult stem cells self-renew and differentiate to build, maintain and repair tissues. This Review discusses recent insights into the contribution of mechanical forces produced by epithelial stem cell activity in building surrounding tissues, and the roles of stem cell niche mechanics disruption in cancer.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 6","pages":"442-455"},"PeriodicalIF":81.3,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055052","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 centromere as a tag of self-DNA","authors":"Ruth Kroschewski","doi":"10.1038/s41580-025-00827-2","DOIUrl":"10.1038/s41580-025-00827-2","url":null,"abstract":"Intriguing findings in yeast suggested that centromeres ‘tag’ DNA as self and allow its condensation during mitosis; vice versa, if a certain DNA is condensed during mitosis, it harbours a centromere.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 3","pages":"172-172"},"PeriodicalIF":81.3,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055051","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}
Jesus M. Gomez-Salinero, David Redmond, Shahin Rafii
{"title":"Microenvironmental determinants of endothelial cell heterogeneity","authors":"Jesus M. Gomez-Salinero, David Redmond, Shahin Rafii","doi":"10.1038/s41580-024-00825-w","DOIUrl":"10.1038/s41580-024-00825-w","url":null,"abstract":"During development, endothelial cells (ECs) undergo an extraordinary specialization by which generic capillary microcirculatory networks spanning from arteries to veins transform into patterned organotypic zonated blood vessels. These capillary ECs become specialized to support the cellular and metabolic demands of each specific organ, including supplying tissue-specific angiocrine factors that orchestrate organ development, maintenance of organ-specific functions and regeneration of injured adult organs. Here, we illustrate the mechanisms by which microenvironmental signals emanating from non-vascular niche cells induce generic ECs to acquire specific inter-organ and intra-organ functional attributes. We describe how perivascular, parenchymal and immune cells dictate vascular heterogeneity and capillary zonation, and how this system is maintained through tissue-specific signalling activated by vasculogenic and angiogenic factors and deposition of matrix components. We also discuss how perturbation of organotypic vascular niche cues lead to erasure of EC signatures, contributing to the pathogenesis of disease processes. We also describe approaches that use reconstitution of tissue-specific signatures of ECs to promote regeneration of damaged organs. Endothelial cells (ECs) undergo organ-specific specialization, driven by microenvironmental cues, to form patterned vascular networks. This article discusses mechanisms driving vascular inter-organ and intra-organ EC heterogeneity, crosstalk between ECs and neighbouring cells, and the therapeutic potential of engineering ECs.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 6","pages":"476-495"},"PeriodicalIF":81.3,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049942","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}
Benjamín Cartes-Saavedra, Arijita Ghosh, György Hajnóczky
{"title":"The roles of mitochondria in global and local intracellular calcium signalling","authors":"Benjamín Cartes-Saavedra, Arijita Ghosh, György Hajnóczky","doi":"10.1038/s41580-024-00820-1","DOIUrl":"10.1038/s41580-024-00820-1","url":null,"abstract":"Activation of Ca2+ channels in Ca2+ stores in organelles and the plasma membrane generates cytoplasmic calcium ([Ca2+]c) signals that control almost every aspect of cell function, including metabolism, vesicle fusion and contraction. Mitochondria have a high capacity for Ca2+ uptake and chelation, alongside efficient Ca2+ release mechanisms. Still, mitochondria do not store Ca2+ in a prolonged manner under physiological conditions and lack the capacity to generate global [Ca2+]c signals. However, mitochondria take up Ca2+ at high local [Ca2+]c signals that originate from neighbouring organelles, and also during sustained global elevations of [Ca2+]c. Accumulated Ca2+ in the mitochondria stimulates oxidative metabolism and upon return to the cytoplasm, can produce spatially confined rises in [Ca2+]c to exert control over processes that are sensitive to Ca2+. Thus, the mitochondrial handling of [Ca2+]c is of physiological relevance. Furthermore, dysregulation of mitochondrial Ca2+ handling can contribute to debilitating diseases. We discuss the mechanisms and relevance of mitochondria in local and global calcium signals. Mitochondria rapidly take up calcium (Ca2+) from the cytoplasm and neighbouring organelles upon an increase in local and global calcium levels, thereby stimulating metabolism and regulating processes that are sensitive to Ca2+. This Review discusses mitochondrial calcium trafficking and its dysregulation in disease.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"26 6","pages":"456-475"},"PeriodicalIF":81.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044165","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}