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Split-pool barcoding serves up an epigenomic smorgasbord 分裂池条形码提供表观基因组大杂烩
IF 31.7 1区 生物学
Nature genetics Pub Date : 2024-11-25 DOI: 10.1038/s41588-024-01980-8
Vijay Ramani
{"title":"Split-pool barcoding serves up an epigenomic smorgasbord","authors":"Vijay Ramani","doi":"10.1038/s41588-024-01980-8","DOIUrl":"10.1038/s41588-024-01980-8","url":null,"abstract":"Perez, Goronzy et al. present ChIP-DIP, which enables multiplex genomic mapping of hundreds of epitopes from a single sample. The authors apply ChIP-DIP to localize modified histones, transcription factors and other chromatin-interacting proteins at scale, in both cell lines and primary cells.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2596-2597"},"PeriodicalIF":31.7,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696619","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}
引用次数: 0
Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype 单细胞多组学分析揭示复杂核型急性髓性白血病的动态克隆进化和靶向表型
IF 31.7 1区 生物学
Nature genetics Pub Date : 2024-11-25 DOI: 10.1038/s41588-024-01999-x
Aino-Maija Leppä, Karen Grimes, Hyobin Jeong, Frank Y. Huang, Alvaro Andrades, Alexander Waclawiczek, Tobias Boch, Anna Jauch, Simon Renders, Patrick Stelmach, Carsten Müller-Tidow, Darja Karpova, Markus Sohn, Florian Grünschläger, Patrick Hasenfeld, Eva Benito Garagorri, Vera Thiel, Anna Dolnik, Bernardo Rodriguez-Martin, Lars Bullinger, Krzysztof Mrózek, Ann-Kathrin Eisfeld, Alwin Krämer, Ashley D. Sanders, Jan O. Korbel, Andreas Trumpp
{"title":"Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype","authors":"Aino-Maija Leppä, Karen Grimes, Hyobin Jeong, Frank Y. Huang, Alvaro Andrades, Alexander Waclawiczek, Tobias Boch, Anna Jauch, Simon Renders, Patrick Stelmach, Carsten Müller-Tidow, Darja Karpova, Markus Sohn, Florian Grünschläger, Patrick Hasenfeld, Eva Benito Garagorri, Vera Thiel, Anna Dolnik, Bernardo Rodriguez-Martin, Lars Bullinger, Krzysztof Mrózek, Ann-Kathrin Eisfeld, Alwin Krämer, Ashley D. Sanders, Jan O. Korbel, Andreas Trumpp","doi":"10.1038/s41588-024-01999-x","DOIUrl":"10.1038/s41588-024-01999-x","url":null,"abstract":"Chromosomal instability is a major driver of intratumoral heterogeneity (ITH), promoting tumor progression. In the present study, we combined structural variant discovery and nucleosome occupancy profiling with transcriptomic and immunophenotypic changes in single cells to study ITH in complex karyotype acute myeloid leukemia (CK-AML). We observed complex structural variant landscapes within individual cells of patients with CK-AML characterized by linear and circular breakage–fusion–bridge cycles and chromothripsis. We identified three clonal evolution patterns in diagnosis or salvage CK-AML (monoclonal, linear and branched polyclonal), with 75% harboring multiple subclones that frequently displayed ongoing karyotype remodeling. Using patient-derived xenografts, we demonstrated varied clonal evolution of leukemic stem cells (LSCs) and further dissected subclone-specific drug–response profiles to identify LSC-targeting therapies, including BCL-xL inhibition. In paired longitudinal patient samples, we further revealed genetic evolution and cell-type plasticity as mechanisms of disease progression. By dissecting dynamic genomic, phenotypic and functional complexity of CK-AML, our findings offer clinically relevant avenues for characterizing and targeting disease-driving LSCs. An integrated single-cell multiomic analysis of complex karyotype acute myeloid leukemia characterizes intratumoral heterogeneity and highlights links to therapeutic sensitivities.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2790-2803"},"PeriodicalIF":31.7,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01999-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696622","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}
引用次数: 0
Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s disease 遗传性和散发性阿尔茨海默病的空间和单核转录组分析
IF 31.7 1区 生物学
Nature genetics Pub Date : 2024-11-22 DOI: 10.1038/s41588-024-01961-x
Emily Miyoshi, Samuel Morabito, Caden M. Henningfield, Sudeshna Das, Negin Rahimzadeh, Sepideh Kiani Shabestari, Neethu Michael, Nora Emerson, Fairlie Reese, Zechuan Shi, Zhenkun Cao, Shushrruth Sai Srinivasan, Vanessa M. Scarfone, Miguel A. Arreola, Jackie Lu, Sierra Wright, Justine Silva, Kelsey Leavy, Ira T. Lott, Eric Doran, William H. Yong, Saba Shahin, Mari Perez-Rosendahl, Alzheimer’s Biomarkers Consortium–Down Syndrome (ABC–DS), Elizabeth Head, Kim N. Green, Vivek Swarup
{"title":"Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s disease","authors":"Emily Miyoshi, Samuel Morabito, Caden M. Henningfield, Sudeshna Das, Negin Rahimzadeh, Sepideh Kiani Shabestari, Neethu Michael, Nora Emerson, Fairlie Reese, Zechuan Shi, Zhenkun Cao, Shushrruth Sai Srinivasan, Vanessa M. Scarfone, Miguel A. Arreola, Jackie Lu, Sierra Wright, Justine Silva, Kelsey Leavy, Ira T. Lott, Eric Doran, William H. Yong, Saba Shahin, Mari Perez-Rosendahl, Alzheimer’s Biomarkers Consortium–Down Syndrome (ABC–DS), Elizabeth Head, Kim N. Green, Vivek Swarup","doi":"10.1038/s41588-024-01961-x","DOIUrl":"10.1038/s41588-024-01961-x","url":null,"abstract":"The pathogenesis of Alzheimer’s disease (AD) depends on environmental and heritable factors, with its molecular etiology still unclear. Here we present a spatial transcriptomic (ST) and single-nucleus transcriptomic survey of late-onset sporadic AD and AD in Down syndrome (DSAD). Studying DSAD provides an opportunity to enhance our understanding of the AD transcriptome, potentially bridging the gap between genetic mouse models and sporadic AD. We identified transcriptomic changes that may underlie cortical layer-preferential pathology accumulation. Spatial co-expression network analyses revealed transient and regionally restricted disease processes, including a glial inflammatory program dysregulated in upper cortical layers and implicated in AD genetic risk and amyloid-associated processes. Cell–cell communication analysis further contextualized this gene program in dysregulated signaling networks. Finally, we generated ST data from an amyloid AD mouse model to identify cross-species amyloid-proximal transcriptomic changes with conformational context. Spatial and single-nucleus analyses in human postmortem Alzheimer’s disease (AD) brain tissues at early and late stages from individuals with and without Down syndrome, as well as in AD mouse models, show sex and species-specific phenotypic changes.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2704-2717"},"PeriodicalIF":31.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01961-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684268","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}
引用次数: 0
Elucidating the genomic basis of rare pediatric neurological diseases in Central Asia and Transcaucasia 阐明中亚和外高加索地区罕见小儿神经系统疾病的基因组基础
IF 31.7 1区 生物学
Nature genetics Pub Date : 2024-11-22 DOI: 10.1038/s41588-024-02016-x
Rauan Kaiyrzhanov, Nazira Zharkinbekova, Ulviyya Guliyeva, Manizha Ganieva, Zaruhi Tavadyan, Tamar Gachechiladze, Kamran Salayev, Sughra Guliyeva, Mariam Isayan, Mariam Kekenadze, Biayna Sukhudyan, Ani Gevorgyan, Artsruni Hakobyan, Rima Ibadova, Nazi Tabatadze, Ekaterina Kurua, Teona Shatirishvili, Nigara Yerkhojayeva, Kairgali Koneev, Dauren Zhumakhanov, Askhat Mukushev, Altynshash Jaxybayeva, Alissa Nauryzbayeva, Maksudjon Isrofilov, Saadat Badalova, Naila Zeyniyeva, Ilaha Hajiyeva, Leyla Alakbarov, Aynur Zeynalova, Viorica Chelban, Jana Vandrovcova, Valentina Turchetti, David Murphy, Stephanie Efthymiou, Shahryar Alavi, Rahema Mohammad, Tinatin Tkemaladze, Chingiz Shashkin, Nana Nino Tatishvili, Maia Beridze, Samson G. Khachatryan, Gia Melikishvili, John Hardy, Reza Maroofian, Henry Houlden
{"title":"Elucidating the genomic basis of rare pediatric neurological diseases in Central Asia and Transcaucasia","authors":"Rauan Kaiyrzhanov, Nazira Zharkinbekova, Ulviyya Guliyeva, Manizha Ganieva, Zaruhi Tavadyan, Tamar Gachechiladze, Kamran Salayev, Sughra Guliyeva, Mariam Isayan, Mariam Kekenadze, Biayna Sukhudyan, Ani Gevorgyan, Artsruni Hakobyan, Rima Ibadova, Nazi Tabatadze, Ekaterina Kurua, Teona Shatirishvili, Nigara Yerkhojayeva, Kairgali Koneev, Dauren Zhumakhanov, Askhat Mukushev, Altynshash Jaxybayeva, Alissa Nauryzbayeva, Maksudjon Isrofilov, Saadat Badalova, Naila Zeyniyeva, Ilaha Hajiyeva, Leyla Alakbarov, Aynur Zeynalova, Viorica Chelban, Jana Vandrovcova, Valentina Turchetti, David Murphy, Stephanie Efthymiou, Shahryar Alavi, Rahema Mohammad, Tinatin Tkemaladze, Chingiz Shashkin, Nana Nino Tatishvili, Maia Beridze, Samson G. Khachatryan, Gia Melikishvili, John Hardy, Reza Maroofian, Henry Houlden","doi":"10.1038/s41588-024-02016-x","DOIUrl":"10.1038/s41588-024-02016-x","url":null,"abstract":"","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2582-2584"},"PeriodicalIF":31.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684248","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}
引用次数: 0
A lifesaving revolution delayed 拯救生命的革命被推迟
IF 31.7 1区 生物学
Nature genetics Pub Date : 2024-11-22 DOI: 10.1038/s41588-024-02013-0
Susan Weiss Liebman
{"title":"A lifesaving revolution delayed","authors":"Susan Weiss Liebman","doi":"10.1038/s41588-024-02013-0","DOIUrl":"10.1038/s41588-024-02013-0","url":null,"abstract":"A family tragedy revealed a hidden genetic mutation and transformed my work as a geneticist into a mission to increase awareness of the critical importance of genetic testing.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2579-2579"},"PeriodicalIF":31.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684247","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}
引用次数: 0
Genome-wide association analysis provides insights into the molecular etiology of dilated cardiomyopathy 全基因组关联分析深入揭示扩张型心肌病的分子病因
IF 31.7 1区 生物学
Nature genetics Pub Date : 2024-11-21 DOI: 10.1038/s41588-024-01952-y
Sean L. Zheng, Albert Henry, Douglas Cannie, Michael Lee, David Miller, Kathryn A. McGurk, Isabelle Bond, Xiao Xu, Hanane Issa, Catherine Francis, Antonio De Marvao, Pantazis I. Theotokis, Rachel J. Buchan, Doug Speed, Erik Abner, Lance Adams, Krishna G. Aragam, Johan Ärnlöv, Anna Axelsson Raja, Joshua D. Backman, John Baksi, Paul J. R. Barton, Kiran J. Biddinger, Eric Boersma, Jeffrey Brandimarto, Søren Brunak, Henning Bundgaard, David J. Carey, Philippe Charron, James P. Cook, Stuart A. Cook, Spiros Denaxas, Jean-François Deleuze, Alexander S. Doney, Perry Elliott, Christian Erikstrup, Tõnu Esko, Eric H. Farber-Eger, Chris Finan, Sophie Garnier, Jonas Ghouse, Vilmantas Giedraitis, Daniel F. Guðbjartsson, Christopher M. Haggerty, Brian P. Halliday, Anna Helgadottir, Harry Hemingway, Hans L. Hillege, Isabella Kardys, Lars Lind, Cecilia M. Lindgren, Brandon D. Lowery, Charlotte Manisty, Kenneth B. Margulies, James C. Moon, Ify R. Mordi, Michael P. Morley, Andrew D. Morris, Andrew P. Morris, Lori Morton, Mahdad Noursadeghi, Sisse R. Ostrowski, Anjali T. Owens, Colin N. A. Palmer, Antonis Pantazis, Ole B. V. Pedersen, Sanjay K. Prasad, Akshay Shekhar, Diane T. Smelser, Sundararajan Srinivasan, Kari Stefansson, Garðar Sveinbjörnsson, Petros Syrris, Mari-Liis Tammesoo, Upasana Tayal, Maris Teder-Laving, Guðmundur Thorgeirsson, Unnur Thorsteinsdottir, Vinicius Tragante, David-Alexandre Trégouët, Thomas A. Treibel, Henrik Ullum, Ana M. Valdes, Jessica van Setten, Marion van Vugt, Abirami Veluchamy, W. M. Monique Verschuren, Eric Villard, Yifan Yang, COVIDsortium, DBDS Genomic Consortium, Estonian Biobank Research Team, HERMES Consortium, Folkert W. Asselbergs, Thomas P. Cappola, Marie-Pierre Dube, Michael E. Dunn, Patrick T. Ellinor, Aroon D. Hingorani, Chim C. Lang, Nilesh J. Samani, Svati H. Shah, J. Gustav Smith, Ramachandran S. Vasan, Declan P. O’Regan, Hilma Holm, Michela Noseda, Quinn Wells, James S. Ware, R. Thomas Lumbers
{"title":"Genome-wide association analysis provides insights into the molecular etiology of dilated cardiomyopathy","authors":"Sean L. Zheng, Albert Henry, Douglas Cannie, Michael Lee, David Miller, Kathryn A. McGurk, Isabelle Bond, Xiao Xu, Hanane Issa, Catherine Francis, Antonio De Marvao, Pantazis I. Theotokis, Rachel J. Buchan, Doug Speed, Erik Abner, Lance Adams, Krishna G. Aragam, Johan Ärnlöv, Anna Axelsson Raja, Joshua D. Backman, John Baksi, Paul J. R. Barton, Kiran J. Biddinger, Eric Boersma, Jeffrey Brandimarto, Søren Brunak, Henning Bundgaard, David J. Carey, Philippe Charron, James P. Cook, Stuart A. Cook, Spiros Denaxas, Jean-François Deleuze, Alexander S. Doney, Perry Elliott, Christian Erikstrup, Tõnu Esko, Eric H. Farber-Eger, Chris Finan, Sophie Garnier, Jonas Ghouse, Vilmantas Giedraitis, Daniel F. Guðbjartsson, Christopher M. Haggerty, Brian P. Halliday, Anna Helgadottir, Harry Hemingway, Hans L. Hillege, Isabella Kardys, Lars Lind, Cecilia M. Lindgren, Brandon D. Lowery, Charlotte Manisty, Kenneth B. Margulies, James C. Moon, Ify R. Mordi, Michael P. Morley, Andrew D. Morris, Andrew P. Morris, Lori Morton, Mahdad Noursadeghi, Sisse R. Ostrowski, Anjali T. Owens, Colin N. A. Palmer, Antonis Pantazis, Ole B. V. Pedersen, Sanjay K. Prasad, Akshay Shekhar, Diane T. Smelser, Sundararajan Srinivasan, Kari Stefansson, Garðar Sveinbjörnsson, Petros Syrris, Mari-Liis Tammesoo, Upasana Tayal, Maris Teder-Laving, Guðmundur Thorgeirsson, Unnur Thorsteinsdottir, Vinicius Tragante, David-Alexandre Trégouët, Thomas A. Treibel, Henrik Ullum, Ana M. Valdes, Jessica van Setten, Marion van Vugt, Abirami Veluchamy, W. M. Monique Verschuren, Eric Villard, Yifan Yang, COVIDsortium, DBDS Genomic Consortium, Estonian Biobank Research Team, HERMES Consortium, Folkert W. Asselbergs, Thomas P. Cappola, Marie-Pierre Dube, Michael E. Dunn, Patrick T. Ellinor, Aroon D. Hingorani, Chim C. Lang, Nilesh J. Samani, Svati H. Shah, J. Gustav Smith, Ramachandran S. Vasan, Declan P. O’Regan, Hilma Holm, Michela Noseda, Quinn Wells, James S. Ware, R. Thomas Lumbers","doi":"10.1038/s41588-024-01952-y","DOIUrl":"10.1038/s41588-024-01952-y","url":null,"abstract":"Dilated cardiomyopathy (DCM) is a leading cause of heart failure and cardiac transplantation. We report a genome-wide association study and multi-trait analysis of DCM (14,256 cases) and three left ventricular traits (36,203 UK Biobank participants). We identified 80 genomic risk loci and prioritized 62 putative effector genes, including several with rare variant DCM associations (MAP3K7, NEDD4L and SSPN). Using single-nucleus transcriptomics, we identify cellular states, biological pathways, and intracellular communications that drive pathogenesis. We demonstrate that polygenic scores predict DCM in the general population and modify penetrance in carriers of rare DCM variants. Our findings may inform the design of genetic testing strategies that incorporate polygenic background. They also provide insights into the molecular etiology of DCM that may facilitate the development of targeted therapeutics. Genome-wide association analyses comprising 14,256 cases and 1,199,156 controls and incorporating correlated cardiac magnetic resonance imaging traits provide insights into the molecular etiology of dilated cardiomyopathy.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2646-2658"},"PeriodicalIF":31.7,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01952-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678340","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}
引用次数: 0
Genome-wide association study reveals mechanisms underlying dilated cardiomyopathy and myocardial resilience 全基因组关联研究揭示扩张型心肌病和心肌复原力的内在机制
IF 31.7 1区 生物学
Nature genetics Pub Date : 2024-11-21 DOI: 10.1038/s41588-024-01975-5
Sean J. Jurgens, Joel T. Rämö, Daria R. Kramarenko, Leonoor F. J. M. Wijdeveld, Jan Haas, Mark D. Chaffin, Sophie Garnier, Liam Gaziano, Lu-Chen Weng, Alex Lipov, Sean L. Zheng, Albert Henry, Jennifer E. Huffman, Saketh Challa, Frank Rühle, Carmen Diaz Verdugo, Christian Krijger Juárez, Shinwan Kany, Constance A. van Orsouw, Kiran Biddinger, Edwin Poel, Amanda L. Elliott, Xin Wang, Catherine Francis, Richard Ruan, Satoshi Koyama, Leander Beekman, Dominic S. Zimmerman, Jean-François Deleuze, Eric Villard, David-Alexandre Trégouët, Richard Isnard, FinnGen, VA Million Veteran Program, HERMES Consortium, Dorret I. Boomsma, Eco J. C. de Geus, Rafik Tadros, Yigal M. Pinto, Arthur A. M. Wilde, Jouke-Jan Hottenga, Juha Sinisalo, Teemu Niiranen, Roddy Walsh, Amand F. Schmidt, Seung Hoan Choi, Kyong-Mi Chang, Philip S. Tsao, Paul M. Matthews, James S. Ware, R. Thomas Lumbers, Saskia van der Crabben, Jari Laukkanen, Aarno Palotie, Ahmad S. Amin, Philippe Charron, Benjamin Meder, Patrick T. Ellinor, Mark Daly, Krishna G. Aragam, Connie R. Bezzina
{"title":"Genome-wide association study reveals mechanisms underlying dilated cardiomyopathy and myocardial resilience","authors":"Sean J. Jurgens, Joel T. Rämö, Daria R. Kramarenko, Leonoor F. J. M. Wijdeveld, Jan Haas, Mark D. Chaffin, Sophie Garnier, Liam Gaziano, Lu-Chen Weng, Alex Lipov, Sean L. Zheng, Albert Henry, Jennifer E. Huffman, Saketh Challa, Frank Rühle, Carmen Diaz Verdugo, Christian Krijger Juárez, Shinwan Kany, Constance A. van Orsouw, Kiran Biddinger, Edwin Poel, Amanda L. Elliott, Xin Wang, Catherine Francis, Richard Ruan, Satoshi Koyama, Leander Beekman, Dominic S. Zimmerman, Jean-François Deleuze, Eric Villard, David-Alexandre Trégouët, Richard Isnard, FinnGen, VA Million Veteran Program, HERMES Consortium, Dorret I. Boomsma, Eco J. C. de Geus, Rafik Tadros, Yigal M. Pinto, Arthur A. M. Wilde, Jouke-Jan Hottenga, Juha Sinisalo, Teemu Niiranen, Roddy Walsh, Amand F. Schmidt, Seung Hoan Choi, Kyong-Mi Chang, Philip S. Tsao, Paul M. Matthews, James S. Ware, R. Thomas Lumbers, Saskia van der Crabben, Jari Laukkanen, Aarno Palotie, Ahmad S. Amin, Philippe Charron, Benjamin Meder, Patrick T. Ellinor, Mark Daly, Krishna G. Aragam, Connie R. Bezzina","doi":"10.1038/s41588-024-01975-5","DOIUrl":"10.1038/s41588-024-01975-5","url":null,"abstract":"Dilated cardiomyopathy (DCM) is a heart muscle disease that represents an important cause of morbidity and mortality, yet causal mechanisms remain largely elusive. Here, we perform a large-scale genome-wide association study and multitrait analysis for DCM using 9,365 cases and 946,368 controls. We identify 70 genome-wide significant loci, which show broad replication in independent samples and map to 63 prioritized genes. Tissue, cell type and pathway enrichment analyses highlight the central role of the cardiomyocyte and contractile apparatus in DCM pathogenesis. Polygenic risk scores constructed from our genome-wide association study predict DCM across different ancestry groups, show differing contributions to DCM depending on rare pathogenic variant status and associate with systolic heart failure across various clinical settings. Mendelian randomization analyses reveal actionable potential causes of DCM, including higher bodyweight and higher systolic blood pressure. Our findings provide insights into the genetic architecture and mechanisms underlying DCM and myocardial function more broadly. Genome-wide association and multitrait analyses for dilated cardiomyopathy (DCM) using 9,365 cases and 946,368 controls provide insights into the mechanisms underlying DCM and myocardial resilience","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2636-2645"},"PeriodicalIF":31.7,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01975-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678341","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}
引用次数: 0
Epigenetic scars of Brca1 loss point toward breast cancer cell of origin Brca1缺失的表观遗传学疤痕指向乳腺癌起源细胞
IF 31.7 1区 生物学
Nature genetics Pub Date : 2024-11-20 DOI: 10.1038/s41588-024-02021-0
Steven M. Lewis, Camila dos Santos
{"title":"Epigenetic scars of Brca1 loss point toward breast cancer cell of origin","authors":"Steven M. Lewis, Camila dos Santos","doi":"10.1038/s41588-024-02021-0","DOIUrl":"10.1038/s41588-024-02021-0","url":null,"abstract":"The two-hit hypothesis suggests that a second mutation is necessary for cancer development in cells with a defective tumor-suppressor gene, such as BRCA1. However, a study now shows that the loss of just one Brca1 allele in mice can pre-program cells for cancer-promoting changes, indicating cancer may progress earlier than previously thought.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2594-2595"},"PeriodicalIF":31.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142673218","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}
引用次数: 0
Luminal breast epithelial cells of BRCA1 or BRCA2 mutation carriers and noncarriers harbor common breast cancer copy number alterations BRCA1 或 BRCA2 基因突变携带者和非携带者的乳腺上皮细胞均存在常见的乳腺癌拷贝数改变
IF 31.7 1区 生物学
Nature genetics Pub Date : 2024-11-20 DOI: 10.1038/s41588-024-01988-0
Marc J. Williams, Michael U. J. Oliphant, Vinci Au, Cathy Liu, Caroline Baril, Ciara O’Flanagan, Daniel Lai, Sean Beatty, Michael Van Vliet, Jacky CH Yiu, Lauren O’Connor, Walter L. Goh, Alicia Pollaci, Adam C. Weiner, Diljot Grewal, Andrew McPherson, Klarisa Norton, McKenna Moore, Vikas Prabhakar, Shailesh Agarwal, Judy E. Garber, Deborah A. Dillon, Sohrab P. Shah, Joan S. Brugge, Samuel Aparicio
{"title":"Luminal breast epithelial cells of BRCA1 or BRCA2 mutation carriers and noncarriers harbor common breast cancer copy number alterations","authors":"Marc J. Williams, Michael U. J. Oliphant, Vinci Au, Cathy Liu, Caroline Baril, Ciara O’Flanagan, Daniel Lai, Sean Beatty, Michael Van Vliet, Jacky CH Yiu, Lauren O’Connor, Walter L. Goh, Alicia Pollaci, Adam C. Weiner, Diljot Grewal, Andrew McPherson, Klarisa Norton, McKenna Moore, Vikas Prabhakar, Shailesh Agarwal, Judy E. Garber, Deborah A. Dillon, Sohrab P. Shah, Joan S. Brugge, Samuel Aparicio","doi":"10.1038/s41588-024-01988-0","DOIUrl":"10.1038/s41588-024-01988-0","url":null,"abstract":"The prevalence and nature of somatic copy number alterations (CNAs) in breast epithelium and their role in tumor initiation and evolution remain poorly understood. Using single-cell DNA sequencing (49,238 cells) of epithelium from BRCA1 and BRCA2 carriers or wild-type individuals, we identified recurrent CNAs (for example, 1q-gain and 7q, 10q, 16q and 22q-loss) that are present in a rare population of cells across almost all samples (n = 28). In BRCA1/BRCA2 carriers, these occur before loss of heterozygosity (LOH) of wild-type alleles. These CNAs, common in malignant tumors, are enriched in luminal cells but absent in basal myoepithelial cells. Allele-specific analysis of prevalent CNAs reveals that they arose by independent mutational events, consistent with convergent evolution. BRCA1/BRCA2 carriers contained a small percentage of cells with extreme aneuploidy, featuring loss of TP53, BRCA1/BRCA2 LOH and multiple breast cancer-associated CNAs. Our findings suggest that CNAs arising in normal luminal breast epithelium are precursors to clonally expanded tumor genomes. Single-cell DNA sequencing identifies recurrent copy number changes in healthy breast tissue from women with wild-type or germline BRCA1 or BRCA2 mutations.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2753-2762"},"PeriodicalIF":31.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01988-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678346","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}
引用次数: 0
A temporal cortex cell atlas highlights gene expression dynamics during human brain maturation 颞叶皮层细胞图谱突显人脑成熟过程中的基因表达动态
IF 31.7 1区 生物学
Nature genetics Pub Date : 2024-11-20 DOI: 10.1038/s41588-024-01990-6
Christina Steyn, Ruvimbo Mishi, Stephanie Fillmore, Matthijs B. Verhoog, Jessica More, Ursula K. Rohlwink, Roger Melvill, James Butler, Johannes M. N. Enslin, Muazzam Jacobs, Tatjana Sauka-Spengler, Maria Greco, Sadi Quiñones, Chris G. Dulla, Joseph V. Raimondo, Anthony Figaji, Dorit Hockman
{"title":"A temporal cortex cell atlas highlights gene expression dynamics during human brain maturation","authors":"Christina Steyn, Ruvimbo Mishi, Stephanie Fillmore, Matthijs B. Verhoog, Jessica More, Ursula K. Rohlwink, Roger Melvill, James Butler, Johannes M. N. Enslin, Muazzam Jacobs, Tatjana Sauka-Spengler, Maria Greco, Sadi Quiñones, Chris G. Dulla, Joseph V. Raimondo, Anthony Figaji, Dorit Hockman","doi":"10.1038/s41588-024-01990-6","DOIUrl":"10.1038/s41588-024-01990-6","url":null,"abstract":"The human brain undergoes protracted postnatal maturation, guided by dynamic changes in gene expression. Most studies exploring these processes have used bulk tissue analyses, which mask cell-type-specific gene expression dynamics. Here, using single-nucleus RNA sequencing on temporal lobe tissue, including samples of African ancestry, we build a joint pediatric and adult atlas of 75 cell subtypes, which we verify with spatial transcriptomics. We explore the differences between pediatric and adult cell subtypes, revealing the genes and pathways that change during brain maturation. Our results highlight excitatory neuron subtypes, including the LTK and FREM subtypes, that show elevated expression of genes associated with cognition and synaptic plasticity in pediatric tissue. The resources we present here improve our understanding of the brain during its development and contribute to global efforts to build an inclusive brain cell map. This Pediatric Cell Atlas study analyzes temporal cortex single-nucleus RNA sequencing datasets from eight diverse donors from 4 to 50 years of age, describing gene expression dynamics over the course of brain maturation.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 12","pages":"2718-2730"},"PeriodicalIF":31.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01990-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678342","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}
引用次数: 0
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