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Mapping drug resistance variants in cancer, one base at a time 逐个碱基绘制癌症抗药性变异图
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-25 DOI: 10.1038/s41588-024-01976-4
DNA variants arising in the genome of cancer cells are a major cause of therapy failure, but for most variants, their effects on drug response are unknown. Base-editing screens provide a systematic approach to uncover the functions of cancer variants at scale, which might help to inform the use of precision cancer therapies.
癌细胞基因组中出现的DNA变异是治疗失败的主要原因,但大多数变异对药物反应的影响尚不清楚。碱基编辑筛选为大规模揭示癌症变异的功能提供了一种系统方法,这可能有助于为精准癌症疗法的使用提供依据。
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引用次数: 0
Systematic perturbation screens identify regulators of inflammatory macrophage states and a role for TNF mRNA m6A modification 系统扰动筛选确定炎症巨噬细胞状态的调节因子以及 TNF mRNA m6A 修饰的作用
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-23 DOI: 10.1038/s41588-024-01962-w
Simone M. Haag, Shiqi Xie, Celine Eidenschenk, Jean-Philippe Fortin, Marinella Callow, Mike Costa, Aaron Lun, Chris Cox, Sunny Z. Wu, Rachana N. Pradhan, Jaclyn Lock, Julia A. Kuhn, Loryn Holokai, Minh Thai, Emily Freund, Ariane Nissenbaum, Mary Keir, Christopher J. Bohlen, Scott Martin, Kathryn Geiger-Schuller, Hussein A. Hejase, Brian L. Yaspan, Sandra Melo Carlos, Shannon J. Turley, Aditya Murthy
Macrophages exhibit remarkable functional plasticity, a requirement for their central role in tissue homeostasis. During chronic inflammation, macrophages acquire sustained inflammatory ‘states’ that contribute to disease, but there is limited understanding of the regulatory mechanisms that drive their generation. Here we describe a systematic functional genomics approach that combines genome-wide phenotypic screening in primary murine macrophages with transcriptional and cytokine profiling of genetic perturbations in primary human macrophages to uncover regulatory circuits of inflammatory states. This process identifies regulators of five distinct states associated with key features of macrophage function. Among these regulators, loss of the N6-methyladenosine (m6A) writer components abolishes m6A modification of TNF transcripts, thereby enhancing mRNA stability and TNF production associated with multiple inflammatory pathologies. Thus, phenotypic characterization of primary murine and human macrophages describes the regulatory circuits underlying distinct inflammatory states, revealing post-transcriptional control of TNF mRNA stability as an immunosuppressive mechanism in innate immunity. Functional screens using mouse and human primary macrophages identify regulators of distinct inflammatory states, including a role for m6A mRNA modification in TNF production.
巨噬细胞具有显著的功能可塑性,这是它们在组织稳态中发挥核心作用的必要条件。在慢性炎症过程中,巨噬细胞会获得导致疾病的持续炎症 "状态",但人们对产生这种状态的调控机制了解有限。在这里,我们介绍了一种系统的功能基因组学方法,该方法将原代小鼠巨噬细胞的全基因组表型筛选与原代人类巨噬细胞基因扰动的转录和细胞因子谱分析相结合,以揭示炎症状态的调控回路。这一过程确定了与巨噬细胞功能关键特征相关的五种不同状态的调控因子。在这些调控因子中,N6-甲基腺苷(m6A)作家成分的缺失会取消 TNF 转录本的 m6A 修饰,从而增强 mRNA 的稳定性和与多种炎症病理相关的 TNF 的产生。因此,原代小鼠和人类巨噬细胞的表型特征描述了不同炎症状态背后的调控回路,揭示了转录后控制 TNF mRNA 稳定性是先天免疫中的一种免疫抑制机制。
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引用次数: 0
Publisher Correction: Rare variant analyses in 51,256 type 2 diabetes cases and 370,487 controls reveal the pathogenicity spectrum of monogenic diabetes genes 出版商更正:对51,256例2型糖尿病病例和370,487例对照组的罕见变异分析揭示了单基因糖尿病基因的致病谱
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-22 DOI: 10.1038/s41588-024-01986-2
Alicia Huerta-Chagoya, Philip Schroeder, Ravi Mandla, Jiang Li, Lowri Morris, Maheak Vora, Ahmed Alkanaq, Dorka Nagy, Lukasz Szczerbinski, Jesper G. S. Madsen, Silvia Bonàs-Guarch, Fanny Mollandin, Joanne B. Cole, Bianca Porneala, Kenneth Westerman, Josephine H. Li, Toni I. Pollin, Jose C. Florez, Anna L. Gloyn, David J. Carey, Inês Cebola, Uyenlinh L. Mirshahi, Alisa K. Manning, Aaron Leong, Miriam Udler, Josep M. Mercader
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引用次数: 0
Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon 在首届 "未确诊黑客马拉松 "的帮助下推动罕见病诊断的发展
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-21 DOI: 10.1038/s41588-024-01941-1
Angelica Maria Delgado-Vega, Helene Cederroth, Fulya Taylan, Katja Ekholm, Marlene Ek, Håkan Thonberg, Anders Jemt, Daniel Nilsson, Jesper Eisfeldt, Kristine Bilgrav Saether, Ida Höijer, Ozlem Akgun-Dogan, Yui Asano, Tahsin Stefan Barakat, Dominyka Batkovskyte, Gareth Baynam, Olaf Bodamer, Wanna Chetruengchai, Pádraic Corcoran, Madeline Couse, Daniel Danis, German Demidov, Eisuke Dohi, Mattias Erhardsson, Luis Fernandez-Luna, Toyofumi Fujiwara, Neha Garg, Roberto Giugliani, Claudia Gonzaga-Jauregui, Giedre Grigelioniene, Tudor Groza, Cecilia Gunnarsson, Anna Hammarsjö, Charles Kumi Hammond, Özden Hatirnaz Ng, Sirisha Hesketh, Dineshani Hettiarachchi, Maria Johansson Soller, Umn Ahmed Kirmani, Martin Kjellberg, Malin Kvarnung, Oleg Kvlividze, Kristina Lagerstedt-Robinson, Paul Lasko, Timo Lassmann, Lynette Y. S. Lau, Steven Laurie, Weng Khong Lim, Zhandong Liu, Mariya Lysenkova Wiklander, Prince Makay, Alassane Baneye Maiga, Carolina Maya-González, M. Stephen Meyn, Ramprasad Neethiraj, Vincenzo Nigro, Felix Nordgren, Jessica Nordlund, Sara Orrsjö, Jesper Ottosson, Ugur Ozbek, Özkan Özdemir, Clyde Partin, David A. Pearce, Raquel Peck, Annie Pedersen, Maria Pettersson, Monnat Pongpanich, Manuel Posada de la Paz, Arun Ramani, Juan Andres Romero, Vanessa I. Romero, Richard Rosenquist, Aung Min Saw, Matthew Spencer, Eva-Lena Stattin, Chalurmpon Srichomthong, Isabel Tapia-Paez, Domenica Taruscio, Julie P. Taylor, Tinatin Tkemaladze, Ian Tully, Zeynep Tümer, Wendy A. G. van Zelst-Stams, Alain Verloes, Emma Västerviga, Sailan Wang, Rachel Yang, Shinya Yamamoto, Vicente A. Yépez, Qing Zhang, Vorasuk Shotelersuk, Samuel Agyei Wiafe, Yasemin Alanay, Lorenzo D. Botto, Salman Kirmani, Aimé Lumaka, Elizabeth Emma Palmer, Ratna Dua Puri, Valtteri Wirta, Anna Lindstrand, Orion J. Buske, Mikk Cederroth, Ann Nordgren
In the first-ever Undiagnosed Hackathon, nearly 100 experts from 28 countries combined advanced phenotyping and genomic techniques for 48 hours, ultimately providing diagnoses to 40% of the previously undiagnosed families. This inspiring model demonstrates the power of multidisciplinary collaboration and patient partnership in precision diagnostics.
在首次 "未确诊黑客马拉松 "中,来自 28 个国家的近 100 名专家在 48 小时内将先进的表型和基因组技术相结合,最终为 40% 以前未确诊的家庭提供了诊断结果。这一鼓舞人心的模式展示了精准诊断中多学科合作和患者伙伴关系的力量。
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引用次数: 0
Genomic analysis of intracranial and subcortical brain volumes yields polygenic scores accounting for variation across ancestries 对颅内和皮层下脑容量的基因组分析产生了多基因分数,说明了不同血统之间的差异
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-21 DOI: 10.1038/s41588-024-01951-z
Luis M. García-Marín, Adrian I. Campos, Santiago Diaz-Torres, Jill A. Rabinowitz, Zuriel Ceja, Brittany L. Mitchell, Katrina L. Grasby, Jackson G. Thorp, Ingrid Agartz, Saud Alhusaini, David Ames, Philippe Amouyel, Ole A. Andreassen, Konstantinos Arfanakis, Alejandro Arias-Vasquez, Nicola J. Armstrong, Lavinia Athanasiu, Mark E. Bastin, Alexa S. Beiser, David A. Bennett, Joshua C. Bis, Marco P. M. Boks, Dorret I. Boomsma, Henry Brodaty, Rachel M. Brouwer, Jan K. Buitelaar, Ralph Burkhardt, Wiepke Cahn, Vince D. Calhoun, Owen T. Carmichael, Mallar Chakravarty, Qiang Chen, Christopher R. K. Ching, Sven Cichon, Benedicto Crespo-Facorro, Fabrice Crivello, Anders M. Dale, George Davey Smith, Eco J. C. de Geus, Philip L. De Jager, Greig I. de Zubicaray, Stéphanie Debette, Charles DeCarli, Chantal Depondt, Sylvane Desrivières, Srdjan Djurovic, Stefan Ehrlich, Susanne Erk, Thomas Espeseth, Guillén Fernández, Irina Filippi, Simon E. Fisher, Debra A. Fleischman, Evan Fletcher, Myriam Fornage, Andreas J. Forstner, Clyde Francks, Barbara Franke, Tian Ge, Aaron L. Goldman, Hans J. Grabe, Robert C. Green, Oliver Grimm, Nynke A. Groenewold, Oliver Gruber, Vilmundur Gudnason, Asta K. Håberg, Unn K. Haukvik, Andreas Heinz, Derrek P. Hibar, Saima Hilal, Jayandra J. Himali, Beng-Choon Ho, David F. Hoehn, Pieter J. Hoekstra, Edith Hofer, Wolfgang Hoffmann, Avram J. Holmes, Georg Homuth, Norbert Hosten, M. Kamran Ikram, Jonathan C. Ipser, Clifford R. Jack Jr, Neda Jahanshad, Erik G. Jönsson, Rene S. Kahn, Ryota Kanai, Marieke Klein, Maria J. Knol, Lenore J. Launer, Stephen M. Lawrie, Stephanie Le Hellard, Phil H. Lee, Hervé Lemaître, Shuo Li, David C. M. Liewald, Honghuang Lin, W. T. Longstreth Jr, Oscar L. Lopez, Michelle Luciano, Pauline Maillard, Andre F. Marquand, Nicholas G. Martin, Jean-Luc Martinot, Karen A. Mather, Venkata S. Mattay, Katie L. McMahon, Patrizia Mecocci, Ingrid Melle, Andreas Meyer-Lindenberg, Nazanin Mirza-Schreiber, Yuri Milaneschi, Thomas H. Mosley, Thomas W. Mühleisen, Bertram Müller-Myhsok, Susana Muñoz Maniega, Matthias Nauck, Kwangsik Nho, Wiro J. Niessen, Markus M. Nöthen, Paul A. Nyquist, Jaap Oosterlaan, Massimo Pandolfo, Tomas Paus, Zdenka Pausova, Brenda W. J. H. Penninx, G. Bruce Pike, Bruce M. Psaty, Benno Pütz, Simone Reppermund, Marcella D. Rietschel, Shannon L. Risacher, Nina Romanczuk-Seiferth, Rafael Romero-Garcia, Gennady V. Roshchupkin, Jerome I. Rotter, Perminder S. Sachdev, Philipp G. Sämann, Arvin Saremi, Muralidharan Sargurupremraj, Andrew J. Saykin, Lianne Schmaal, Helena Schmidt, Reinhold Schmidt, Peter R. Schofield, Markus Scholz, Gunter Schumann, Emanuel Schwarz, Li Shen, Jean Shin, Sanjay M. Sisodiya, Albert V. Smith, Jordan W. Smoller, Hilkka S. Soininen, Vidar M. Steen, Dan J. Stein, Jason L. Stein, Sophia I. Thomopoulos, Arthur W. Toga, Diana Tordesillas-Gutiérrez, Julian N. Trollor, Maria C. Valdes-Hernandez, Dennis van ′t Ent, Hans van Bokhoven, Dennis van der Meer, Nic J. A. van der Wee, Javier Vázquez-Bourgon, Dick J. Veltman, Meike W. Vernooij, Arno Villringer, Louis N. Vinke, Henry Völzke, Henrik Walter, Joanna M. Wardlaw, Daniel R. Weinberger, Michael W. Weiner, Wei Wen, Lars T. Westlye, Eric Westman, Tonya White, A. Veronica Witte, Christiane Wolf, Jingyun Yang, Marcel P. Zwiers, M. Arfan Ikram, Sudha Seshadri, Paul M. Thompson, Claudia L. Satizabal, Sarah E. Medland, Miguel E. Rentería
Subcortical brain structures are involved in developmental, psychiatric and neurological disorders. Here we performed genome-wide association studies meta-analyses of intracranial and nine subcortical brain volumes (brainstem, caudate nucleus, putamen, hippocampus, globus pallidus, thalamus, nucleus accumbens, amygdala and the ventral diencephalon) in 74,898 participants of European ancestry. We identified 254 independent loci associated with these brain volumes, explaining up to 35% of phenotypic variance. We observed gene expression in specific neural cell types across differentiation time points, including genes involved in intracellular signaling and brain aging-related processes. Polygenic scores for brain volumes showed predictive ability when applied to individuals of diverse ancestries. We observed causal genetic effects of brain volumes with Parkinson’s disease and attention-deficit/hyperactivity disorder. Findings implicate specific gene expression patterns in brain development and genetic variants in comorbid neuropsychiatric disorders, which could point to a brain substrate and region of action for risk genes implicated in brain diseases. Genome-wide association analyses of intracranial and nine subcortical brain volumes in 74,898 participants of European ancestry identify 254 independent loci and yield polygenic scores accounting for brain variation across ancestries.
皮层下大脑结构与发育、精神和神经系统疾病有关。在这里,我们对 74,898 名欧洲血统参与者的颅内和九个皮层下脑容量(脑干、尾状核、普鲁门、海马、球状苍白球、丘脑、伏隔核、杏仁核和腹侧间脑)进行了全基因组关联研究荟萃分析。我们确定了与这些脑容量相关的 254 个独立基因位点,解释了高达 35% 的表型变异。我们观察了不同分化时间点特定神经细胞类型的基因表达,包括参与细胞内信号转导和大脑衰老相关过程的基因。当应用于不同血统的个体时,脑容量的多基因评分显示出预测能力。我们观察到脑容量对帕金森病和注意力缺陷/多动症的因果遗传效应。研究结果揭示了大脑发育过程中的特定基因表达模式以及合并神经精神疾病的基因变异,这可能会为与脑部疾病有关的风险基因指出大脑基质和作用区域。
{"title":"Genomic analysis of intracranial and subcortical brain volumes yields polygenic scores accounting for variation across ancestries","authors":"Luis M. García-Marín, Adrian I. Campos, Santiago Diaz-Torres, Jill A. Rabinowitz, Zuriel Ceja, Brittany L. Mitchell, Katrina L. Grasby, Jackson G. Thorp, Ingrid Agartz, Saud Alhusaini, David Ames, Philippe Amouyel, Ole A. Andreassen, Konstantinos Arfanakis, Alejandro Arias-Vasquez, Nicola J. Armstrong, Lavinia Athanasiu, Mark E. Bastin, Alexa S. Beiser, David A. Bennett, Joshua C. Bis, Marco P. M. Boks, Dorret I. Boomsma, Henry Brodaty, Rachel M. Brouwer, Jan K. Buitelaar, Ralph Burkhardt, Wiepke Cahn, Vince D. Calhoun, Owen T. Carmichael, Mallar Chakravarty, Qiang Chen, Christopher R. K. Ching, Sven Cichon, Benedicto Crespo-Facorro, Fabrice Crivello, Anders M. Dale, George Davey Smith, Eco J. C. de Geus, Philip L. De Jager, Greig I. de Zubicaray, Stéphanie Debette, Charles DeCarli, Chantal Depondt, Sylvane Desrivières, Srdjan Djurovic, Stefan Ehrlich, Susanne Erk, Thomas Espeseth, Guillén Fernández, Irina Filippi, Simon E. Fisher, Debra A. Fleischman, Evan Fletcher, Myriam Fornage, Andreas J. Forstner, Clyde Francks, Barbara Franke, Tian Ge, Aaron L. Goldman, Hans J. Grabe, Robert C. Green, Oliver Grimm, Nynke A. Groenewold, Oliver Gruber, Vilmundur Gudnason, Asta K. Håberg, Unn K. Haukvik, Andreas Heinz, Derrek P. Hibar, Saima Hilal, Jayandra J. Himali, Beng-Choon Ho, David F. Hoehn, Pieter J. Hoekstra, Edith Hofer, Wolfgang Hoffmann, Avram J. Holmes, Georg Homuth, Norbert Hosten, M. Kamran Ikram, Jonathan C. Ipser, Clifford R. Jack Jr, Neda Jahanshad, Erik G. Jönsson, Rene S. Kahn, Ryota Kanai, Marieke Klein, Maria J. Knol, Lenore J. Launer, Stephen M. Lawrie, Stephanie Le Hellard, Phil H. Lee, Hervé Lemaître, Shuo Li, David C. M. Liewald, Honghuang Lin, W. T. Longstreth Jr, Oscar L. Lopez, Michelle Luciano, Pauline Maillard, Andre F. Marquand, Nicholas G. Martin, Jean-Luc Martinot, Karen A. Mather, Venkata S. Mattay, Katie L. McMahon, Patrizia Mecocci, Ingrid Melle, Andreas Meyer-Lindenberg, Nazanin Mirza-Schreiber, Yuri Milaneschi, Thomas H. Mosley, Thomas W. Mühleisen, Bertram Müller-Myhsok, Susana Muñoz Maniega, Matthias Nauck, Kwangsik Nho, Wiro J. Niessen, Markus M. Nöthen, Paul A. Nyquist, Jaap Oosterlaan, Massimo Pandolfo, Tomas Paus, Zdenka Pausova, Brenda W. J. H. Penninx, G. Bruce Pike, Bruce M. Psaty, Benno Pütz, Simone Reppermund, Marcella D. Rietschel, Shannon L. Risacher, Nina Romanczuk-Seiferth, Rafael Romero-Garcia, Gennady V. Roshchupkin, Jerome I. Rotter, Perminder S. Sachdev, Philipp G. Sämann, Arvin Saremi, Muralidharan Sargurupremraj, Andrew J. Saykin, Lianne Schmaal, Helena Schmidt, Reinhold Schmidt, Peter R. Schofield, Markus Scholz, Gunter Schumann, Emanuel Schwarz, Li Shen, Jean Shin, Sanjay M. Sisodiya, Albert V. Smith, Jordan W. Smoller, Hilkka S. Soininen, Vidar M. Steen, Dan J. Stein, Jason L. Stein, Sophia I. Thomopoulos, Arthur W. Toga, Diana Tordesillas-Gutiérrez, Julian N. Trollor, Maria C. Valdes-Hernandez, Dennis van ′t Ent, Hans van Bokhoven, Dennis van der Meer, Nic J. A. van der Wee, Javier Vázquez-Bourgon, Dick J. Veltman, Meike W. Vernooij, Arno Villringer, Louis N. Vinke, Henry Völzke, Henrik Walter, Joanna M. Wardlaw, Daniel R. Weinberger, Michael W. Weiner, Wei Wen, Lars T. Westlye, Eric Westman, Tonya White, A. Veronica Witte, Christiane Wolf, Jingyun Yang, Marcel P. Zwiers, M. Arfan Ikram, Sudha Seshadri, Paul M. Thompson, Claudia L. Satizabal, Sarah E. Medland, Miguel E. Rentería","doi":"10.1038/s41588-024-01951-z","DOIUrl":"10.1038/s41588-024-01951-z","url":null,"abstract":"Subcortical brain structures are involved in developmental, psychiatric and neurological disorders. Here we performed genome-wide association studies meta-analyses of intracranial and nine subcortical brain volumes (brainstem, caudate nucleus, putamen, hippocampus, globus pallidus, thalamus, nucleus accumbens, amygdala and the ventral diencephalon) in 74,898 participants of European ancestry. We identified 254 independent loci associated with these brain volumes, explaining up to 35% of phenotypic variance. We observed gene expression in specific neural cell types across differentiation time points, including genes involved in intracellular signaling and brain aging-related processes. Polygenic scores for brain volumes showed predictive ability when applied to individuals of diverse ancestries. We observed causal genetic effects of brain volumes with Parkinson’s disease and attention-deficit/hyperactivity disorder. Findings implicate specific gene expression patterns in brain development and genetic variants in comorbid neuropsychiatric disorders, which could point to a brain substrate and region of action for risk genes implicated in brain diseases. Genome-wide association analyses of intracranial and nine subcortical brain volumes in 74,898 participants of European ancestry identify 254 independent loci and yield polygenic scores accounting for brain variation across ancestries.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2333-2344"},"PeriodicalIF":31.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142451818","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
Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora 单倍型解析的基因组组装和重测序分析为深入了解密花松树的基因组进化和等位基因失衡提供了线索
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-20 DOI: 10.1038/s41588-024-01944-y
Min-Jeong Jang, Hye Jeong Cho, Young-Soo Park, Hye-Young Lee, Eun-Kyung Bae, Seungmee Jung, Hongshi Jin, Jongchan Woo, Eunsook Park, Seo-Jin Kim, Jin-Wook Choi, Geun Young Chae, Ji-Yoon Guk, Do Yeon Kim, Sun-Hyung Kim, Min-Jeong Kang, Hyoshin Lee, Kyeong-Seong Cheon, In Sik Kim, Yong-Min Kim, Myung-Shin Kim, Jae-Heung Ko, Kyu-Suk Kang, Doil Choi, Eung-Jun Park, Seungill Kim
Haplotype-level allelic characterization facilitates research on the functional, evolutionary and breeding-related features of extremely large and complex plant genomes. We report a 21.7-Gb chromosome-level haplotype-resolved assembly in Pinus densiflora. We found genome rearrangements involving translocations and inversions between chromosomes 1 and 3 of Pinus species and a proliferation of specific long terminal repeat (LTR) retrotransposons (LTR-RTs) in P. densiflora. Evolutionary analyses illustrated that tandem and LTR-RT-mediated duplications led to an increment of transcription factor (TF) genes in P. densiflora. The haplotype sequence comparison showed allelic imbalances, including presence–absence variations of genes (PAV genes) and their functional contributions to flowering and abiotic stress-related traits in P. densiflora. Allele-aware resequencing analysis revealed PAV gene diversity across P. densiflora accessions. Our study provides insights into key mechanisms underlying the evolution of genome structure, LTR-RTs and TFs within the Pinus lineage as well as allelic imbalances and diversity across P. densiflora. Chromosome-scale and haplotype-resolved assembly of Pinus densiflora sheds light on Pinus-specific genome enlargement. Comparison between haplotypes and resequencing of 30 wild accessions show allelic imbalance with roles in flowering regulation and stress resistance.
单倍型水平的等位基因特征有助于研究超大型复杂植物基因组的功能、进化和育种相关特征。我们报告了一个 21.7 千兆字节的染色体级等位基因组装结果。我们发现了松属植物 1 号染色体和 3 号染色体之间涉及易位和倒位的基因组重排,以及特定长末端重复(LTR)反转座子(LTR-RTs)的扩散。进化分析表明,串联和 LTR-RT 介导的复制导致了 P. densiflora 中转录因子(TF)基因的增加。单倍型序列比较显示了等位基因的不平衡,包括基因(PAV基因)的存在-不存在变异,以及它们对丹顶鹤开花和非生物胁迫相关性状的功能贡献。等位基因感知的重测序分析揭示了不同登喜路品种中 PAV 基因的多样性。我们的研究深入揭示了松科植物基因组结构、LTR-RT 和 TFs 演化的关键机制,以及等位基因的不平衡和松科植物的多样性。
{"title":"Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora","authors":"Min-Jeong Jang, Hye Jeong Cho, Young-Soo Park, Hye-Young Lee, Eun-Kyung Bae, Seungmee Jung, Hongshi Jin, Jongchan Woo, Eunsook Park, Seo-Jin Kim, Jin-Wook Choi, Geun Young Chae, Ji-Yoon Guk, Do Yeon Kim, Sun-Hyung Kim, Min-Jeong Kang, Hyoshin Lee, Kyeong-Seong Cheon, In Sik Kim, Yong-Min Kim, Myung-Shin Kim, Jae-Heung Ko, Kyu-Suk Kang, Doil Choi, Eung-Jun Park, Seungill Kim","doi":"10.1038/s41588-024-01944-y","DOIUrl":"10.1038/s41588-024-01944-y","url":null,"abstract":"Haplotype-level allelic characterization facilitates research on the functional, evolutionary and breeding-related features of extremely large and complex plant genomes. We report a 21.7-Gb chromosome-level haplotype-resolved assembly in Pinus densiflora. We found genome rearrangements involving translocations and inversions between chromosomes 1 and 3 of Pinus species and a proliferation of specific long terminal repeat (LTR) retrotransposons (LTR-RTs) in P. densiflora. Evolutionary analyses illustrated that tandem and LTR-RT-mediated duplications led to an increment of transcription factor (TF) genes in P. densiflora. The haplotype sequence comparison showed allelic imbalances, including presence–absence variations of genes (PAV genes) and their functional contributions to flowering and abiotic stress-related traits in P. densiflora. Allele-aware resequencing analysis revealed PAV gene diversity across P. densiflora accessions. Our study provides insights into key mechanisms underlying the evolution of genome structure, LTR-RTs and TFs within the Pinus lineage as well as allelic imbalances and diversity across P. densiflora. Chromosome-scale and haplotype-resolved assembly of Pinus densiflora sheds light on Pinus-specific genome enlargement. Comparison between haplotypes and resequencing of 30 wild accessions show allelic imbalance with roles in flowering regulation and stress resistance.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2551-2561"},"PeriodicalIF":31.7,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142451399","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
Base editing screens define the genetic landscape of cancer drug resistance mechanisms 碱基编辑筛选确定癌症耐药机制的基因图谱
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-18 DOI: 10.1038/s41588-024-01948-8
Matthew A. Coelho, Magdalena E. Strauss, Alex Watterson, Sarah Cooper, Shriram Bhosle, Giuditta Illuzzi, Emre Karakoc, Cansu Dinçer, Sara F. Vieira, Mamta Sharma, Marie Moullet, Daniela Conticelli, Jonas Koeppel, Katrina McCarten, Chiara M. Cattaneo, Vivien Veninga, Gabriele Picco, Leopold Parts, Josep V. Forment, Emile E. Voest, John C. Marioni, Andrew Bassett, Mathew J. Garnett
Drug resistance is a principal limitation to the long-term efficacy of cancer therapies. Cancer genome sequencing can retrospectively delineate the genetic basis of drug resistance, but this requires large numbers of post-treatment samples to nominate causal variants. Here we prospectively identify genetic mechanisms of resistance to ten oncology drugs from CRISPR base editing mutagenesis screens in four cancer cell lines using a guide RNA library predicted to install 32,476 variants in 11 cancer genes. We identify four functional classes of protein variants modulating drug sensitivity and use single-cell transcriptomics to reveal how these variants operate through distinct mechanisms, including eliciting a drug-addicted cell state. We identify variants that can be targeted with alternative inhibitors to overcome resistance and functionally validate an epidermal growth factor receptor (EGFR) variant that sensitizes lung cancer cells to EGFR inhibitors. Our variant-to-function map has implications for patient stratification, therapy combinations and drug scheduling in cancer treatment. Base editing screens of 11 cancer genes identify four functional classes of variants that collectively underpin sensitivity and resistance to ten commonly used drugs in cancer cell lines.
耐药性是癌症疗法长期疗效的主要限制因素。癌症基因组测序可以回顾性地描述耐药性的遗传基础,但这需要大量的治疗后样本来确定因果变异。在这里,我们通过 CRISPR 碱基编辑诱变筛选,在四种癌细胞系中使用引导 RNA 文库,预测在 11 个癌症基因中安装了 32,476 个变体,从而前瞻性地确定了十种肿瘤药物耐药性的遗传机制。我们确定了调节药物敏感性的四类功能性蛋白质变体,并利用单细胞转录组学揭示了这些变体如何通过不同的机制发挥作用,包括诱发药物成瘾的细胞状态。我们发现了可以用替代抑制剂克服耐药性的变体,并从功能上验证了表皮生长因子受体(EGFR)变体能使肺癌细胞对 EGFR 抑制剂敏感。我们的变体-功能图谱对癌症治疗中的患者分层、治疗组合和药物调配具有重要意义。
{"title":"Base editing screens define the genetic landscape of cancer drug resistance mechanisms","authors":"Matthew A. Coelho, Magdalena E. Strauss, Alex Watterson, Sarah Cooper, Shriram Bhosle, Giuditta Illuzzi, Emre Karakoc, Cansu Dinçer, Sara F. Vieira, Mamta Sharma, Marie Moullet, Daniela Conticelli, Jonas Koeppel, Katrina McCarten, Chiara M. Cattaneo, Vivien Veninga, Gabriele Picco, Leopold Parts, Josep V. Forment, Emile E. Voest, John C. Marioni, Andrew Bassett, Mathew J. Garnett","doi":"10.1038/s41588-024-01948-8","DOIUrl":"10.1038/s41588-024-01948-8","url":null,"abstract":"Drug resistance is a principal limitation to the long-term efficacy of cancer therapies. Cancer genome sequencing can retrospectively delineate the genetic basis of drug resistance, but this requires large numbers of post-treatment samples to nominate causal variants. Here we prospectively identify genetic mechanisms of resistance to ten oncology drugs from CRISPR base editing mutagenesis screens in four cancer cell lines using a guide RNA library predicted to install 32,476 variants in 11 cancer genes. We identify four functional classes of protein variants modulating drug sensitivity and use single-cell transcriptomics to reveal how these variants operate through distinct mechanisms, including eliciting a drug-addicted cell state. We identify variants that can be targeted with alternative inhibitors to overcome resistance and functionally validate an epidermal growth factor receptor (EGFR) variant that sensitizes lung cancer cells to EGFR inhibitors. Our variant-to-function map has implications for patient stratification, therapy combinations and drug scheduling in cancer treatment. Base editing screens of 11 cancer genes identify four functional classes of variants that collectively underpin sensitivity and resistance to ten commonly used drugs in cancer cell lines.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2479-2492"},"PeriodicalIF":31.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01948-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142448166","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 regulatory network controlling developmental boundaries and meristem fates contributed to maize domestication 控制发育边界和分生组织命运的调控网络促进了玉米的驯化
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-16 DOI: 10.1038/s41588-024-01943-z
Zhaobin Dong, Gaoyuan Hu, Qiuyue Chen, Elena A. Shemyakina, Geeyun Chau, Clinton J. Whipple, Jennifer C. Fletcher, George Chuck
During domestication, early farmers selected different vegetative and reproductive traits, but identifying the causative loci has been hampered by their epistasis and functional redundancy. Using chromatin immunoprecipitation sequencing combined with genome-wide association analysis, we uncovered a developmental regulator that controls both types of trait while acting upstream of multiple domestication loci. tasselsheath4 (tsh4) is a new maize domestication gene that establishes developmental boundaries and specifies meristem fates despite not being expressed within them. TSH4 accomplishes this by using a double-negative feedback loop that targets and represses the very same microRNAs that negatively regulate it. TSH4 functions redundantly with a pair of homologs to positively regulate a suite of domestication loci while specifying the meristem that doubled seed yield in modern maize. TSH4 has a critical role in yield gain and helped generate ideal crop plant architecture, thus explaining why it was a major domestication target. Maize transcription factor TASSELSHEATH4 establishes the leaf versus meristem cell boundary and vegetative versus floral axillary meristem fates as part of a domestication gene network.
在驯化过程中,早期农民选择了不同的无性系和生殖性状,但由于这些性状的外显性和功能冗余性,确定致病位点的工作一直受到阻碍。Tasselsheath4(tsh4)是一个新的玉米驯化基因,它能建立发育界限并指定分生组织的命运,尽管它并不在分生组织中表达。TSH4 通过双重负反馈回路来实现这一目标,该回路靶向并抑制对其进行负调控的相同 microRNA。TSH4 与一对同源物具有冗余功能,可以正向调节一系列驯化基因座,同时指定分生组织,使现代玉米的种子产量翻倍。TSH4 在增产中起着关键作用,有助于产生理想的作物植株结构,从而解释了为什么它是主要的驯化目标。
{"title":"A regulatory network controlling developmental boundaries and meristem fates contributed to maize domestication","authors":"Zhaobin Dong, Gaoyuan Hu, Qiuyue Chen, Elena A. Shemyakina, Geeyun Chau, Clinton J. Whipple, Jennifer C. Fletcher, George Chuck","doi":"10.1038/s41588-024-01943-z","DOIUrl":"10.1038/s41588-024-01943-z","url":null,"abstract":"During domestication, early farmers selected different vegetative and reproductive traits, but identifying the causative loci has been hampered by their epistasis and functional redundancy. Using chromatin immunoprecipitation sequencing combined with genome-wide association analysis, we uncovered a developmental regulator that controls both types of trait while acting upstream of multiple domestication loci. tasselsheath4 (tsh4) is a new maize domestication gene that establishes developmental boundaries and specifies meristem fates despite not being expressed within them. TSH4 accomplishes this by using a double-negative feedback loop that targets and represses the very same microRNAs that negatively regulate it. TSH4 functions redundantly with a pair of homologs to positively regulate a suite of domestication loci while specifying the meristem that doubled seed yield in modern maize. TSH4 has a critical role in yield gain and helped generate ideal crop plant architecture, thus explaining why it was a major domestication target. Maize transcription factor TASSELSHEATH4 establishes the leaf versus meristem cell boundary and vegetative versus floral axillary meristem fates as part of a domestication gene network.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2528-2537"},"PeriodicalIF":31.7,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142440225","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 genome-wide association analysis reveals new pathogenic pathways in gout 全基因组关联分析揭示了痛风的新致病途径*。
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-15 DOI: 10.1038/s41588-024-01921-5
Tanya J. Major, Riku Takei, Hirotaka Matsuo, Megan P. Leask, Nicholas A. Sumpter, Ruth K. Topless, Yuya Shirai, Wei Wang, Murray J. Cadzow, Amanda J. Phipps-Green, Zhiqiang Li, Aichang Ji, Marilyn E. Merriman, Emily Morice, Eric E. Kelley, Wen-Hua Wei, Sally P. A. McCormick, Matthew J. Bixley, Richard J. Reynolds, Kenneth G. Saag, Tayaza Fadason, Evgenia Golovina, Justin M. O’Sullivan, Lisa K. Stamp, Nicola Dalbeth, Abhishek Abhishek, Michael Doherty, Edward Roddy, Lennart T. H. Jacobsson, Meliha C. Kapetanovic, Olle Melander, Mariano Andrés, Fernando Pérez-Ruiz, Rosa J. Torres, Timothy Radstake, Timothy L. Jansen, Matthijs Janssen, Leo A. B. Joosten, Ruiqi Liu, Orsolya I. Gaal, Tania O. Crişan, Simona Rednic, Fina Kurreeman, Tom W. J. Huizinga, René Toes, Frédéric Lioté, Pascal Richette, Thomas Bardin, Hang Korng Ea, Tristan Pascart, Geraldine M. McCarthy, Laura Helbert, Blanka Stibůrková, Anne-K. Tausche, Till Uhlig, Véronique Vitart, Thibaud S. Boutin, Caroline Hayward, Philip L. Riches, Stuart H. Ralston, Archie Campbell, Thomas M. MacDonald, FAST Study Group, Akiyoshi Nakayama, Tappei Takada, Masahiro Nakatochi, Seiko Shimizu, Yusuke Kawamura, Yu Toyoda, Hirofumi Nakaoka, Ken Yamamoto, Keitaro Matsuo, Nariyoshi Shinomiya, Kimiyoshi Ichida, Japan Gout Genomics Consortium, Chaeyoung Lee, Asia Pacific Gout Consortium, Linda A. Bradbury, Matthew A. Brown, Philip C. Robinson, Russell R. C. Buchanan, Catherine L. Hill, Susan Lester, Malcolm D. Smith, Maureen Rischmueller, Hyon K. Choi, Eli A. Stahl, Jeff N. Miner, Daniel H. Solomon, Jing Cui, Kathleen M. Giacomini, Deanna J. Brackman, Eric M. Jorgenson, GlobalGout Genetics Consortium, Hongbo Liu, Katalin Susztak, 23andMe Research Team, Suyash Shringarpure, Alexander So, Yukinori Okada, Changgui Li, Yongyong Shi, Tony R. Merriman
Gout is a chronic disease that is caused by an innate immune response to deposited monosodium urate crystals in the setting of hyperuricemia. Here, we provide insights into the molecular mechanism of the poorly understood inflammatory component of gout from a genome-wide association study (GWAS) of 2.6 million people, including 120,295 people with prevalent gout. We detected 377 loci and 410 genetically independent signals (149 previously unreported loci in urate and gout). An additional 65 loci with signals in urate (from a GWAS of 630,117 individuals) but not gout were identified. A prioritization scheme identified candidate genes in the inflammatory process of gout, including genes involved in epigenetic remodeling, cell osmolarity and regulation of NOD-like receptor protein 3 (NLRP3) inflammasome activity. Mendelian randomization analysis provided evidence for a causal role of clonal hematopoiesis of indeterminate potential in gout. Our study identifies candidate genes and molecular processes in the inflammatory pathogenesis of gout suitable for follow-up studies. Genome-wide association analysis of gout and urate identifies 148 new loci, implicating biological pathways and prioritizing candidate genes involved in inflammatory processes.
痛风是一种慢性疾病,是在高尿酸血症的情况下对沉积的单钠尿酸盐结晶的先天性免疫反应引起的。在这里,我们通过一项对 260 万人(包括 120,295 名痛风患者)进行的全基因组关联研究(GWAS),深入探讨了痛风中鲜为人知的炎症成分的分子机制。我们发现了 377 个基因位点和 410 个基因独立信号(149 个以前未报道过的尿酸盐和痛风基因位点)。此外,我们还发现了 65 个在尿酸盐中有信号的位点(来自 630,117 人的 GWAS),但在痛风中没有信号。一个优先排序方案确定了痛风炎症过程中的候选基因,包括参与表观遗传重塑、细胞渗透压和 NOD 样受体蛋白 3 (NLRP3) 炎症小体活性调节的基因。孟德尔随机分析提供了证据,证明具有不确定潜能的克隆造血在痛风中起着因果作用。我们的研究确定了痛风炎症发病机制中适合后续研究的候选基因和分子过程。
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引用次数: 0
Parsing the spectrum of allelic architectures in diabetes 解析糖尿病等位基因结构谱
IF 31.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-10-14 DOI: 10.1038/s41588-024-01950-0
Yangxi Li, Constantin Polychronakos
Distinguishing ordinary diabetes from its monogenic forms has been one of the challenges in optimally managing the disease. Using high-quality imputation of rare variants and large databases, a study now defines the gray zone between the two and lays down a blueprint for objectively evaluating the related variants.
区分普通糖尿病和单基因糖尿病一直是优化糖尿病管理的挑战之一。现在,一项研究利用罕见变异的高质量归因和大型数据库,界定了两者之间的灰色地带,并为客观评估相关变异绘制了蓝图。
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引用次数: 0
期刊
Nature genetics
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