Nature Methods最新文献

{"title":"Organoids get an upgrade","authors":"Madhura Mukhopadhyay","doi":"10.1038/s41592-024-02549-3","DOIUrl":"10.1038/s41592-024-02549-3","url":null,"abstract":"Immune–organoid systems will be the next generation of in vitro models.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 12","pages":"2228-2229"},"PeriodicalIF":36.1,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789390","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":"Subcellular spatial proteomics","authors":"Rita Strack","doi":"10.1038/s41592-024-02546-6","DOIUrl":"10.1038/s41592-024-02546-6","url":null,"abstract":"Advances in multiplexed super-resolution microscopy will usher in the next era of spatial proteomics.","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":"21 12","pages":"2227-2227"},"PeriodicalIF":36.1,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789404","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 dynamics of hematopoiesis over the human lifespan.","authors":"Hojun Li, Parker Côté, Michael Kuoch, Jideofor Ezike, Katie Frenis, Anton Afanassiev, Laura Greenstreet, Mayuri Tanaka-Yano, Giuseppe Tarantino, Stephen Zhang, Jennifer Whangbo, Vincent L Butty, Enrico Moiso, Marcelo Falchetti, Kate Lu, Guinevere G Connelly, Vivian Morris, Dahai Wang, Antonia F Chen, Giada Bianchi, George Q Daley, Salil Garg, David Liu, Stella T Chou, Aviv Regev, Edroaldo Lummertz da Rocha, Geoffrey Schiebinger, R Grant Rowe","doi":"10.1038/s41592-024-02495-0","DOIUrl":"10.1038/s41592-024-02495-0","url":null,"abstract":"<p><p>Over a lifetime, hematopoietic stem cells (HSCs) adjust their lineage output to support age-aligned physiology. In model organisms, stereotypic waves of hematopoiesis have been observed corresponding to defined age-biased HSC hallmarks. However, how the properties of hematopoietic stem and progenitor cells change over the human lifespan remains unclear. To address this gap, we profiled individual transcriptome states of human hematopoietic stem and progenitor cells spanning gestation, maturation and aging. Here we define the gene expression networks dictating age-specific differentiation of HSCs and the dynamics of fate decisions and lineage priming throughout life. We additionally identifiy and functionally validate a fetal-specific HSC state with robust engraftment and multilineage capacity. Furthermore, we observe that classification of acute myeloid leukemia against defined transcriptional age states demonstrates that utilization of early life transcriptional programs associates with poor prognosis. Overall, we provide a disease-relevant framework for heterochronic orientation of stem cell ontogeny along the real time axis of the human lifespan.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785755","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":"Cell Painting: a decade of discovery and innovation in cellular imaging.","authors":"Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth, Shantanu Singh, Jordi Carreras-Puigvert, Nigel Greene, Andreas Bender, Anne E Carpenter","doi":"10.1038/s41592-024-02528-8","DOIUrl":"10.1038/s41592-024-02528-8","url":null,"abstract":"<p><p>Modern quantitative image analysis techniques have enabled high-throughput, high-content imaging experiments. Image-based profiling leverages the rich information in images to identify similarities or differences among biological samples, rather than measuring a few features, as in high-content screening. Here, we review a decade of advancements and applications of Cell Painting, a microscopy-based cell-labeling assay aiming to capture a cell's state, introduced in 2013 to optimize and standardize image-based profiling. Cell Painting's ability to capture cellular responses to various perturbations has expanded owing to improvements in the protocol, adaptations for different perturbations, and enhanced methodologies for feature extraction, quality control, and batch-effect correction. Cell Painting is a versatile tool that has been used in various applications, alone or with other -omics data, to decipher the mechanism of action of a compound, its toxicity profile, and other biological effects. Future advances will likely involve computational and experimental techniques, new publicly available datasets, and integration with other high-content data types.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785810","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":"SMR-Portal: an online platform for integrative analysis of GWAS and xQTL data to identify complex trait genes.","authors":"Yazhou Guo, Tao Xu, Jie Luo, Zhuqing Jiang, Wenhao Chen, Hui Chen, Ting Qi, Jian Yang","doi":"10.1038/s41592-024-02561-7","DOIUrl":"https://doi.org/10.1038/s41592-024-02561-7","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770663","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":"RNA-Puzzles Round V: blind predictions of 23 RNA structures.","authors":"Fan Bu, Yagoub Adam, Ryszard W Adamiak, Maciej Antczak, Belisa Rebeca H de Aquino, Nagendar Goud Badepally, Robert T Batey, Eugene F Baulin, Pawel Boinski, Michal J Boniecki, Janusz M Bujnicki, Kristy A Carpenter, Jose Chacon, Shi-Jie Chen, Wah Chiu, Pablo Cordero, Naba Krishna Das, Rhiju Das, Wayne K Dawson, Frank DiMaio, Feng Ding, Anne-Catherine Dock-Bregeon, Nikolay V Dokholyan, Ron O Dror, Stanisław Dunin-Horkawicz, Stephan Eismann, Eric Ennifar, Reza Esmaeeli, Masoud Amiri Farsani, Adrian R Ferré-D'Amaré, Caleb Geniesse, George E Ghanim, Horacio V Guzman, Iris V Hood, Lin Huang, Dharm Skandh Jain, Farhang Jaryani, Lei Jin, Astha Joshi, Masha Karelina, Jeffrey S Kieft, Wipapat Kladwang, Sebastian Kmiecik, Deepak Koirala, Markus Kollmann, Rachael C Kretsch, Mateusz Kurciński, Jun Li, Shuang Li, Marcin Magnus, BenoÎt Masquida, S Naeim Moafinejad, Arup Mondal, Sunandan Mukherjee, Thi Hoang Duong Nguyen, Grigory Nikolaev, Chandran Nithin, Grace Nye, Iswarya P N Pandaranadar Jeyeram, Alberto Perez, Phillip Pham, Joseph A Piccirilli, Smita Priyadarshini Pilla, Radosław Pluta, Simón Poblete, Almudena Ponce-Salvatierra, Mariusz Popenda, Lukasz Popenda, Fabrizio Pucci, Ramya Rangan, Angana Ray, Aiming Ren, Joanna Sarzynska, Congzhou Mike Sha, Filip Stefaniak, Zhaoming Su, Krishna C Suddala, Marta Szachniuk, Raphael Townshend, Robert J Trachman, Jian Wang, Wenkai Wang, Andrew Watkins, Tomasz K Wirecki, Yi Xiao, Peng Xiong, Yiduo Xiong, Jianyi Yang, Joseph David Yesselman, Jinwei Zhang, Yi Zhang, Zhenzhen Zhang, Yuanzhe Zhou, Tomasz Zok, Dong Zhang, Sicheng Zhang, Adriana Żyła, Eric Westhof, Zhichao Miao","doi":"10.1038/s41592-024-02543-9","DOIUrl":"10.1038/s41592-024-02543-9","url":null,"abstract":"<p><p>RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between prediction and experiment. Our analyses reveal some critical steps to be overcome to achieve good accuracy in modeling RNA structures: identification of helix-forming pairs and of non-Watson-Crick modules, correct coaxial stacking between helices and avoidance of entanglements. Three of the top four modeling groups in this round also ranked among the top four in the CASP15 contest.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770662","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":"Publisher Correction: Massively parallel single-cell sequencing of diverse microbial populations.","authors":"Freeman Lan, Jason Saba, Tyler D Ross, Zhichao Zhou, Katie Krauska, Karthik Anantharaman, Robert Landick, Ophelia S Venturelli","doi":"10.1038/s41592-024-02570-6","DOIUrl":"https://doi.org/10.1038/s41592-024-02570-6","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142755521","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":"Integrative mapping of human CD8⁺ T cells in inflammation and cancer.","authors":"Ziwei Xue, Lize Wu, Ruonan Tian, Bing Gao, Yu Zhao, Bing He, Di Sun, Bingkang Zhao, Yicheng Li, Kaixiang Zhu, Lie Wang, Jianhua Yao, Wanlu Liu, Linrong Lu","doi":"10.1038/s41592-024-02530-0","DOIUrl":"https://doi.org/10.1038/s41592-024-02530-0","url":null,"abstract":"<p><p>CD8⁺ T cells exhibit remarkable phenotypic diversity in inflammation and cancer. However, a comprehensive understanding of their clonal landscape and dynamics remains elusive. Here we introduce scAtlasVAE, a deep-learning-based model for the integration of large-scale single-cell RNA sequencing data and cross-atlas comparisons. scAtlasVAE has enabled us to construct an extensive human CD8⁺ T cell atlas, comprising 1,151,678 cells from 961 samples across 68 studies and 42 disease conditions, with paired T cell receptor information. Through incorporating information in T cell receptor clonal expansion and sharing, we have successfully established connections between distinct cell subtypes and shed light on their phenotypic and functional transitions. Notably, our approach characterizes three distinct exhausted T cell subtypes and reveals diverse transcriptome and clonal sharing patterns in autoimmune and immune-related adverse event inflammation. Furthermore, scAtlasVAE facilitates the automatic annotation of CD8⁺ T cell subtypes in query single-cell RNA sequencing datasets, enabling unbiased and scalable analyses. In conclusion, our work presents a comprehensive single-cell reference and computational framework for CD8⁺ T cell research.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142755517","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":"Human CD8⁺ T cell map with single-cell transcriptome and TCR information.","authors":"","doi":"10.1038/s41592-024-02529-7","DOIUrl":"https://doi.org/10.1038/s41592-024-02529-7","url":null,"abstract":"","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142755509","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 proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs.","authors":"Caroline Brown, Snehasish Ghosh, Rachel McAllister, Mukesh Kumar, Gerard Walker, Eric Sun, Talat Aman, Aniruddha Panda, Shailesh Kumar, Wenxue Li, Jeff Coleman, Yansheng Liu, James E Rothman, Moitrayee Bhattacharyya, Kallol Gupta","doi":"10.1038/s41592-024-02517-x","DOIUrl":"10.1038/s41592-024-02517-x","url":null,"abstract":"<p><p>The native membrane environment profoundly influences every aspect of membrane protein (MP) biology. Despite this, the most prevalent method of studying MPs uses detergents to disrupt and remove this vital membrane context, impeding our ability to decipher the local molecular context and its effect. Here we develop a membrane proteome-wide platform that enables rapid spatially resolved extraction of target MPs directly from cellular membranes into native nanodiscs that maintain the local membrane context, using a library of membrane-active polymers. We accompany this with an open-access database that quantifies the polymer-specific extraction efficiency for 2,065 unique mammalian MPs and provides the most optimized extraction condition for each. To validate, we demonstrate how this resource can enable rapid extraction and purification of target MPs from different organellar membranes with high efficiency and purity. Further, we show how the database can be extended to capture overexpressed multiprotein complexes by taking two synaptic vesicle MPs. We expect these publicly available resources to empower researchers across disciplines to efficiently capture membrane 'nano-scoops' containing a target MP and interface with structural, functional and bioanalytical approaches.</p>","PeriodicalId":18981,"journal":{"name":"Nature Methods","volume":" ","pages":""},"PeriodicalIF":36.1,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142751275","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}