Tore Skotland, Kim Ekroos, Jeffrey McDonald, Robert Ahrends, Gerhard Liebisch, Kirsten Sandvig
{"title":"Pitfalls in lipid mass spectrometry of mammalian samples — a brief guide for biologists","authors":"Tore Skotland, Kim Ekroos, Jeffrey McDonald, Robert Ahrends, Gerhard Liebisch, Kirsten Sandvig","doi":"10.1038/s41580-024-00758-4","DOIUrl":"10.1038/s41580-024-00758-4","url":null,"abstract":"This Comment discusses erroneous reporting of mass spectrometry analyses of lipids in mammalian samples, and provides recommendations for how to avoid it. Publications that report mass spectrometry analyses of lipids often include lipid species that probably do not exist in the samples. Here we provide recommendations for scientists on submitting lipid data, and for reviewers, editors and readers on evaluating these data, to reduce the reporting of erroneous lipid species.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"25 10","pages":"759-760"},"PeriodicalIF":81.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141477007","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":"Polarized endoplasmic reticulum–plasma membrane contacts in cell migration","authors":"Lisa Heinke","doi":"10.1038/s41580-024-00759-3","DOIUrl":"10.1038/s41580-024-00759-3","url":null,"abstract":"In a recent study, Bong et al. identify a polarized distribution of contact sites between the endoplasmic reticulum and plasma membrane in migrating cells, whereby higher density of contacts in the back of the cells prevents the formation of additional migration fronts.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"25 8","pages":"595-595"},"PeriodicalIF":81.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141477008","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":"Harnessing the deep learning power of foundation models in single-cell omics","authors":"Qin Ma, Yi Jiang, Hao Cheng, Dong Xu","doi":"10.1038/s41580-024-00756-6","DOIUrl":"10.1038/s41580-024-00756-6","url":null,"abstract":"Foundation models hold great promise for analyzing single-cell omics data, yet various challenges remain that require further advancements. In this Comment, we discuss the progress, limitations and best practices in applying foundation models to interrogate data and improve downstream tasks in single-cell omics. This Comment discusses the progress, limitations and best practices in applying foundation models to single-cell omics data.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"25 8","pages":"593-594"},"PeriodicalIF":81.3,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141458258","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":"Identification of RNA structures and their roles in RNA functions","authors":"Xinang Cao, Yueying Zhang, Yiliang Ding, Yue Wan","doi":"10.1038/s41580-024-00748-6","DOIUrl":"10.1038/s41580-024-00748-6","url":null,"abstract":"The development of high-throughput RNA structure profiling methods in the past decade has greatly facilitated our ability to map and characterize different aspects of RNA structures transcriptome-wide in cell populations, single cells and single molecules. The resulting high-resolution data have provided insights into the static and dynamic nature of RNA structures, revealing their complexity as they perform their respective functions in the cell. In this Review, we discuss recent technical advances in the determination of RNA structures, and the roles of RNA structures in RNA biogenesis and functions, including in transcription, processing, translation, degradation, localization and RNA structure-dependent condensates. We also discuss the current understanding of how RNA structures could guide drug design for treating genetic diseases and battling pathogenic viruses, and highlight existing challenges and future directions in RNA structure research. Recently developed RNA structure profiling methods are transforming our understanding of static and dynamic facets of RNA structures at single-cell and single-molecule resolution. These data have revealed new roles for structures in RNA biogenesis and function, and guide drug design against viral RNAs and for treatment of genetic diseases.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"25 10","pages":"784-801"},"PeriodicalIF":81.3,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141453130","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 of cellular and systemic sphingolipid homeostasis","authors":"Andrew Kuo, Timothy Hla","doi":"10.1038/s41580-024-00742-y","DOIUrl":"10.1038/s41580-024-00742-y","url":null,"abstract":"One hundred and fifty years ago, Johann Thudichum described sphingolipids as unusual “Sphinx-like” lipids from the brain. Today, we know that thousands of sphingolipid molecules mediate many essential functions in embryonic development and normal physiology. In addition, sphingolipid metabolism and signalling pathways are dysregulated in a wide range of pathologies, and therapeutic agents that target sphingolipids are now used to treat several human diseases. However, our understanding of sphingolipid regulation at cellular and organismal levels and their functions in developmental, physiological and pathological settings is rudimentary. In this Review, we discuss recent advances in sphingolipid pathways in different organelles, how secreted sphingolipid mediators modulate physiology and disease, progress in sphingolipid-targeted therapeutic and diagnostic research, and the trans-cellular sphingolipid metabolic networks between microbiota and mammals. Advances in sphingolipid biology have led to a deeper understanding of mammalian physiology and may lead to progress in the management of many diseases. Sphingolipids are a heterogeneous group of lipids with important roles in membrane form and function, cell signalling, and development. This Review discusses the regulation of sphingolipid metabolism at the subcellular and organismal levels and explores the therapeutic potential of targeting sphingolipids in human diseases.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"25 10","pages":"802-821"},"PeriodicalIF":81.3,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141334424","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}
Navin Gopaldass, Kai-En Chen, Brett Collins, Andreas Mayer
{"title":"Assembly and fission of tubular carriers mediating protein sorting in endosomes","authors":"Navin Gopaldass, Kai-En Chen, Brett Collins, Andreas Mayer","doi":"10.1038/s41580-024-00746-8","DOIUrl":"10.1038/s41580-024-00746-8","url":null,"abstract":"Endosomes are central protein-sorting stations at the crossroads of numerous membrane trafficking pathways in all eukaryotes. They have a key role in protein homeostasis and cellular signalling and are involved in the pathogenesis of numerous diseases. Endosome-associated protein assemblies or coats collect transmembrane cargo proteins and concentrate them into retrieval domains. These domains can extend into tubular carriers, which then pinch off from the endosomal membrane and deliver the cargoes to appropriate subcellular compartments. Here we discuss novel insights into the structure of a number of tubular membrane coats that mediate the recruitment of cargoes into these carriers, focusing on sorting nexin-based coats such as Retromer, Commander and ESCPE-1. We summarize current and emerging views of how selective tubular endosomal carriers form and detach from endosomes by fission, highlighting structural aspects, conceptual challenges and open questions. Endosomes function as sorting stations that segregate cargo proteins into endosomal carriers, enabling their distribution to subcellular target compartments. Increasingly detailed structural insights have revealed how proteins, such as sorting nexins, assemble on endosomal membranes to form a coat that facilitates the formation and detachment of tubular carriers.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"25 10","pages":"765-783"},"PeriodicalIF":81.3,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141334422","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":"A histone code controls positional identity in limb regeneration","authors":"Lisa Heinke","doi":"10.1038/s41580-024-00751-x","DOIUrl":"10.1038/s41580-024-00751-x","url":null,"abstract":"Kawaguchi et al. identify a chromatin code based on repressive histone 3 lysine 27 trimethylation (H3K27me3) that serves as a segment-specific positional marker in connective tissue cells of axolotls, enabling correct patterning during limb regeneration.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"25 7","pages":"514-514"},"PeriodicalIF":81.3,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141298932","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 phosphoinositide PI5P inhibits the Hippo pathway effector YAP","authors":"Kim Baumann","doi":"10.1038/s41580-024-00750-y","DOIUrl":"10.1038/s41580-024-00750-y","url":null,"abstract":"This study uncovered a link between PI5P, PI5P4Ks and the Hippo pathway, whereby PI5P reinforces the inhibition of YAP, the effector of the Hippo pathway.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"25 7","pages":"513-513"},"PeriodicalIF":81.3,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141298985","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}