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Single-cell atlas of the transcriptome and chromatin accessibility in the human retina. 人类视网膜中转录组和染色质可及性的单细胞图谱。
IF 30.8 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2026-01-23 DOI: 10.1038/s41588-025-02454-1
Jin Li,Jun Wang,Ignacio L Ibarra,Xuesen Cheng,Malte D Luecken,Jiaxiong Lu,Aboozar Monavarfeshani,Wenjun Yan,Yiqiao Zheng,Zhen Zuo,Samantha Lynn Zayas Colborn,Berenice Sarahi Cortez,Leah A Owen,Brittney Wick,Xuan Bao,Maximilian Haeussler,Nicholas M Tran,Karthik Shekhar,Joshua R Sanes,J Timothy Stout,Shiming Chen,Yumei Li,Margaret M DeAngelis,Fabian J Theis,Rui Chen
Single-cell sequencing has revolutionized the scale and resolution of molecular profiling of tissues and organs. Here we present an integrated dual-modal reference atlas of the most accessible portion of the mammalian central nervous system, the retina. We compiled around 3.9 million cells from 125 donors of diverse ancestral backgrounds, including 8 published studies and 2.7 million unpublished data points, to create a comprehensive human retina cell atlas (HRCA) with more than 130 cell types identified. We annotated each cluster, identified marker genes and characterized cis-regulatory elements and gene regulatory networks. Our analysis uncovered differences in transcriptome, chromatin and gene regulatory networks across cell types. We modeled changes in gene expression and chromatin accessibility across age, ancestry and tissue region. This integrated atlas enhanced the fine-mapping of genome-wide association study and expression quantitative trait loci variants. Accessible through interactive browsers, this multimodal multidonor and multilab HRCA can facilitate a better understanding of retinal function and pathology.
单细胞测序彻底改变了组织和器官分子图谱的规模和分辨率。在这里,我们提出了一个综合的双峰参考地图集最容易接近的部分哺乳动物中枢神经系统,视网膜。我们收集了来自125名不同祖先背景的捐赠者的390万个细胞,包括8项已发表的研究和270万个未发表的数据点,以创建一个全面的人类视网膜细胞图谱(HRCA),其中确定了130多种细胞类型。我们对每个簇进行了注释,鉴定了标记基因,并对顺式调控元件和基因调控网络进行了表征。我们的分析揭示了不同细胞类型的转录组、染色质和基因调控网络的差异。我们模拟了基因表达和染色质可及性在不同年龄、血统和组织区域的变化。该集成图谱增强了全基因组关联研究和表达数量性状位点变异的精细定位。通过交互式浏览器访问,这种多模式、多供体和多实验室的HRCA可以促进对视网膜功能和病理的更好理解。
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引用次数: 0
Central role of glycosylation processes in human genetic susceptibility to SARS-CoV-2 infections with Omicron variants. 糖基化过程在人类对带有Omicron变体的SARS-CoV-2感染的遗传易感性中的核心作用
IF 30.8 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2026-01-22 DOI: 10.1038/s41588-025-02484-9
Frank Geller,Xiaoping Wu,Vilma Lammi,Erik Abner,Jesse Tyler Valliere,Katerina Nastou,Angus Burns,Morten Rasmussen,Niklas Worm Andersson,Liam Quinn, ,Bitten Aagaard,Karina Banasik,Sofie Bliddal,Lasse Boding,Søren Brunak,Nanna Brøns,Jonas Bybjerg-Grauholm,Lea Arregui Nordahl Christoffersen,Maria Didriksen,Khoa Manh Dinh,Christian Erikstrup,Ulla Feldt-Rasmussen,Kirsten Grønbæk,Kathrine Agergård Kaspersen,Christina Mikkelsen,Claus Henrik Nielsen,Henriette Svarre Nielsen,Susanne Dam Nielsen,Janna Nissen,Celia Burgos Sequeros,Niels Tommerup,Henrik Ullum, , ,Lampros Spiliopoulos,Peter Bager,Anders Hviid,Erik Sørensen,Ole Birger Pedersen,Jacqueline M Lane,Ria Lassaunière,Hanna M Ollila,Sisse Rye Ostrowski,Bjarke Feenstra
The host genetics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have previously been studied based on cases from the earlier waves of the pandemic in 2020 and 2021, identifying 51 genomic loci associated with infection and/or severity. SARS-CoV-2 has shown rapid sequence evolution, increasing transmissibility, particularly for Omicron variants, which raises the question of whether this affected the host genetic factors. We performed a genome-wide association study of SARS-CoV-2 infection with Omicron variants, including more than 150,000 cases from four cohorts. We identified 13 genome-wide significant loci, of which only five were previously described as associated with SARS-CoV-2 infection. The strongest signal was a single nucleotide polymorphism in an intron of ST6GAL1, a gene affecting immune development and function, connected to three other associated loci (harboring MUC1, MUC5AC and MUC16) through O-glycan biosynthesis. Our study provides robust evidence for individual genetic variation related to glycosylation, translating into susceptibility to SARS-CoV-2 infections with Omicron variants.
此前已经根据2020年和2021年早期大流行的病例研究了严重急性呼吸综合征冠状病毒2 (SARS-CoV-2)的宿主遗传学,确定了与感染和/或严重程度相关的51个基因组位点。SARS-CoV-2显示出快速的序列进化,增加了传播性,特别是对于组粒变异,这就提出了这是否影响宿主遗传因素的问题。我们对SARS-CoV-2感染与Omicron变体进行了全基因组关联研究,包括来自四个队列的15万多例病例。我们确定了13个全基因组显著位点,其中只有5个位点以前被描述为与SARS-CoV-2感染相关。最强的信号是ST6GAL1内含子的单核苷酸多态性,ST6GAL1是一种影响免疫发育和功能的基因,通过o -聚糖生物合成与其他三个相关位点(包含MUC1, MUC5AC和MUC16)相连。我们的研究为糖基化相关的个体遗传变异提供了强有力的证据,转化为对具有Omicron变体的SARS-CoV-2感染的易感性。
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引用次数: 0
Genomic evolution of pancreatic cancer at single-cell resolution. 单细胞分辨率下胰腺癌的基因组进化。
IF 29 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2026-01-22 DOI: 10.1038/s41588-025-02468-9
Haochen Zhang, Palash Sashittal, Elias-Ramzey Karnoub, Akhil Jakatdar, Shigeaki Umeda, Jungeui Hong, Anne Marie Noronha, Agustin Cardenas, Amanda Erakky, Caitlin A McIntyre, Akimasa Hayashi, Nicolas Lecomte, Marc Hilmi, Wungki Park, Nan Pang, Eileen M O'Reilly, Alice C Wei, Benjamin J Raphael, Christine A Iacobuzio-Donahue

Most evolutionary studies on pancreatic cancer rely on bulk sequencing, yet clonal evolution happens at the single-cell level. We used single-nucleus DNA sequencing to study 137,491 single nuclei from 24 pancreatic neoplasms reflecting various clinical scenarios. We found higher frequencies of somatic alterations to driver genes that bulk studies indicate; many manifest as copy number alterations and account for the majority of spatial heterogeneity. In pancreatic cancers with canonical KRAS oncogenic mutations, we found likely varied dependence on the genotype that may signify differential response to KRAS inhibition. In pancreatic cancers with germline heterozygous BRCA2 mutations, we discovered varied mechanisms and timing of inactivation of the wild-type allele that sculpted differential evolutionary trajectories. Inactivation of tumor-intrinsic response to transforming growth factor-β happens through various mechanisms, takes place after oncogenesis and coincides with invasion and metastasis, reflecting increasing selective pressure for the phenotype later in pancreatic ductal adenocarcinoma development.

大多数胰腺癌的进化研究依赖于批量测序,但克隆进化发生在单细胞水平。我们使用单核DNA测序研究了来自24个胰腺肿瘤的137,491个单核,反映了不同的临床情况。大量研究表明,我们发现驱动基因的体细胞改变频率更高;许多表现为拷贝数的改变,占空间异质性的大部分。在具有典型KRAS致癌突变的胰腺癌中,我们发现可能对基因型的不同依赖可能表明对KRAS抑制的不同反应。在具有种系杂合BRCA2突变的胰腺癌中,我们发现了野生型等位基因失活的不同机制和时间,这些机制和时间塑造了不同的进化轨迹。肿瘤对转化生长因子-β的内在反应失活通过多种机制发生,发生在肿瘤发生后,与侵袭和转移相吻合,反映了胰腺导管腺癌发展后期表型的选择压力增加。
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引用次数: 0
Multi-trait and multi-ancestry genetic analysis of comorbid lung diseases and traits improves genetic discovery and polygenic risk prediction 肺部共病和性状的多性状和多祖先遗传分析有助于基因发现和多基因风险预测
IF 30.8 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2026-01-21 DOI: 10.1038/s41588-025-02470-1
Yixuan He, Wenhan Lu, Yon Ho Jee, Mu-Yi Shih, Ying Wang, Kristin Tsuo, David C. Qian, James A. Diao, Hailiang Huang, Chirag J. Patel, Jinyoung Byun, Bogdan Pasaniuc, Elizabeth G. Atkinson, Christopher I. Amos, Yen-Chen Anne Feng, Matthew Moll, Michael H. Cho, Alicia R. Martin
While respiratory diseases such as chronic obstructive pulmonary disease (COPD) and asthma share many risk factors, most studies investigate them in isolation and in predominantly European-ancestry populations. Here, we conducted the most powerful multi-trait and multi-ancestry genetic analysis of respiratory diseases and auxiliary traits to date, identifying 25 new loci associated with lung function in individuals of East Asian ancestry. Using these results, we developed PRSxtra (cross-trait and cross-ancestry), a multi-trait and multi-ancestry polygenic risk score (PRS) approach that leverages shared components of heritable risk via pleiotropic effects. PRSxtra significantly improved the prediction of asthma, COPD and lung cancer compared to trait- and ancestry-matched PRSs in a multi-ancestry cohort from the All of Us Research Program, especially in diverse populations. Our results present a new framework for multi-trait and multi-ancestry studies of respiratory diseases to improve genetic discovery and polygenic prediction.
虽然慢性阻塞性肺疾病(COPD)和哮喘等呼吸系统疾病有许多共同的危险因素,但大多数研究都是在孤立的情况下调查的,而且主要是在欧洲血统的人群中进行的。在这里,我们对呼吸系统疾病和辅助性状进行了迄今为止最强大的多性状和多祖先遗传分析,在东亚祖先个体中确定了25个与肺功能相关的新位点。利用这些结果,我们开发了PRSxtra(交叉性状和交叉祖先),这是一种多性状和多祖先多基因风险评分(PRS)方法,通过多效性效应利用遗传风险的共享成分。在来自“我们所有人”研究项目的多祖先队列中,与性状匹配和祖先匹配的prs相比,PRSxtra显著提高了哮喘、COPD和肺癌的预测,特别是在不同人群中。我们的研究结果为呼吸系统疾病的多性状和多祖先研究提供了一个新的框架,以改善遗传发现和多基因预测。
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引用次数: 0
The polygenic, omnigenic and stratagenic models of complex disease risk. 复杂疾病风险的多基因、全基因和策略模型。
IF 30.8 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2026-01-20 DOI: 10.1038/s41588-025-02467-w
Judit García-González,Paul F O'Reilly
A key goal of human genetics research is to understand how the effects of genetic variants combine to produce the risk of complex disease. Here we discuss and contrast three conceptual models developed to explain how multigenic risk is generated. The polygenic model, derived from the century-old infinitesimal model, has been the dominant framework for understanding the genetic inheritance of complex traits. More recently, two mechanistic models have been proposed: the omnigenic model, which hypothesizes core genes with direct effects on disease and peripheral genes with regulatory, indirect effects, and what we call the 'stratagenic' model, in which the genetic risk of disease is stratified across genomic pathways of functional relevance. There are key differences in the implications of these models for research, drug development and precision medicine. Therefore, it is essential to determine which model is most accurate for each disease or whether a single model is broadly optimal across complex diseases.
人类遗传学研究的一个关键目标是了解基因变异的影响如何结合起来产生复杂疾病的风险。在这里,我们讨论并对比了三个概念模型来解释多基因风险是如何产生的。多基因模型源自已有百年历史的无限小模型,已成为理解复杂性状遗传的主要框架。最近,提出了两种机制模型:全基因模型,假设核心基因对疾病有直接影响,外周基因有调节,间接影响;我们称之为“战略”模型,其中疾病的遗传风险在功能相关的基因组途径中分层。这些模型对研究、药物开发和精准医疗的影响存在关键差异。因此,有必要确定哪种模型对每种疾病最准确,或者单一模型是否在复杂疾病中是最优的。
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引用次数: 0
Impact and correction of segmentation errors in spatial transcriptomics. 空间转录组学中分割错误的影响和纠正。
IF 30.8 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2026-01-20 DOI: 10.1038/s41588-025-02497-4
Jonathan Mitchel,Teng Gao,Viktor Petukhov,Eli Cole,Peter V Kharchenko
Spatial transcriptomics aims to elucidate how cells coordinate within tissues by connecting cellular states to their native microenvironments. Imaging-based assays are especially promising, capturing molecular and cellular features at subcellular resolution in three dimensions. Interpretation of such data, however, hinges on accurate cell segmentation. Assigning individual molecules to the correct cells remains challenging. Here we re-analyze data from multiple tissues and platforms to find that segmentation errors currently confound most downstream analysis of cellular state, including differential expression, neighbor influence and ligand-receptor interactions. The extent to which misassigned molecules impact the results can be striking, frequently dominating the results. Thus, we show that matrix factorization of local molecular neighborhoods can effectively identify and isolate such molecular admixtures, thereby reducing their impact on downstream analyses, in a manner analogous to doublet filtering in single-cell RNA sequencing. As the applications of spatial transcriptomics assays become more widespread, accounting for segmentation errors will be important for resolving molecular mechanisms of tissue biology.
空间转录组学旨在通过将细胞状态与其原生微环境联系起来,阐明细胞如何在组织内协调。基于成像的分析尤其有希望,在亚细胞分辨率下捕获分子和细胞特征。然而,这些数据的解释取决于准确的细胞分割。将单个分子分配给正确的细胞仍然具有挑战性。在这里,我们重新分析了来自多个组织和平台的数据,发现分割错误目前混淆了大多数细胞状态的下游分析,包括差异表达、邻居影响和配体-受体相互作用。错误分配的分子对结果的影响程度可能是惊人的,经常主导结果。因此,我们表明,局部分子邻域的矩阵分解可以有效地识别和分离这些分子混合物,从而减少它们对下游分析的影响,类似于单细胞RNA测序中的双重过滤。随着空间转录组学分析的应用越来越广泛,对分割错误的解释对于解决组织生物学的分子机制将是重要的。
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引用次数: 0
Engineering AI co-scientists for statistical genetics applications. 统计遗传学应用的工程人工智能合作科学家。
IF 30.8 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2026-01-20 DOI: 10.1038/s41588-025-02487-6
Bingxin Zhao
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引用次数: 0
Exploring and visualizing stratified GWAS results with PheWeb2. 利用PheWeb2对分层GWAS结果进行探索和可视化。
IF 29 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2026-01-19 DOI: 10.1038/s41588-025-02469-8
Justin Bellavance, Hongyu Xiao, Le Chang, Mehrdad Kazemi, Seyla Wickramasinghe, Alexandra J Mayhew, Parminder Raina, Peter VandeHaar, Daniel Taliun, Sarah A Gagliano Taliun
{"title":"Exploring and visualizing stratified GWAS results with PheWeb2.","authors":"Justin Bellavance, Hongyu Xiao, Le Chang, Mehrdad Kazemi, Seyla Wickramasinghe, Alexandra J Mayhew, Parminder Raina, Peter VandeHaar, Daniel Taliun, Sarah A Gagliano Taliun","doi":"10.1038/s41588-025-02469-8","DOIUrl":"https://doi.org/10.1038/s41588-025-02469-8","url":null,"abstract":"","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":" ","pages":""},"PeriodicalIF":29.0,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146003722","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
Genetic risk for delirium 精神错乱的遗传风险。
IF 29 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2026-01-13 DOI: 10.1038/s41588-025-02495-6
Kyle Vogan
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引用次数: 0
The predicament of heritable confounders. 遗传混杂的困境。
IF 29 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2026-01-13 DOI: 10.1038/s41588-025-02465-y
Na Cai, Andy Dahl, Richard Border, Aditya Gorla, Jolien Rietkerk, Joel Mefford, Noah Zaitlen, Morten Dybdahl Krebs, Andrew J Schork, Kenneth Kendler, Jonathan Flint

Identifying significant associations between genetic loci and psychiatric disorders is dependent on very large sample sizes. Methods for diagnosing diseases on this scale, such as the use of self-assessment questionnaires and data from electronic health records, incorporate heritable variation unrelated to the disease of interest into the diagnosis. Consequently, genetic mapping will identify loci unrelated to the target disease while missing some that are related, and genetic correlations cannot be used to infer the genetic relationships between diseases and between cohorts. Furthermore, shared biases between different disorders appear as shared etiology. As sample sizes grow, such confounders propagate, and findings based on their presence are replicated and extended. Here, we draw attention to the problem, make suggestions for flagging affected cohorts, and discuss future data collection and machine learning approaches to mitigate the effects of heritable confounders in psychiatric disorders.

确定基因位点和精神疾病之间的显著关联依赖于非常大的样本量。在这一范围内诊断疾病的方法,如使用自我评估问卷和电子健康记录数据,将与感兴趣的疾病无关的遗传变异纳入诊断。因此,遗传作图将确定与目标疾病无关的位点,而遗漏了一些相关的位点,并且遗传相关性不能用于推断疾病之间和群体之间的遗传关系。此外,不同疾病之间的共同偏见表现为共同的病因。随着样本量的增加,这类混杂因素会不断传播,基于它们的发现会被复制和扩展。在这里,我们提请注意这个问题,提出了标记受影响队列的建议,并讨论了未来的数据收集和机器学习方法,以减轻遗传混杂因素对精神疾病的影响。
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引用次数: 0
期刊
Nature genetics
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