华西耳鼻喉前沿学术速递——文献导读（第39期）
【Nature Genetics】2024年4-6月刊论文导读
期刊介绍：
Nature Genetics创刊于1992年，由NATURE RESEARCH出版商出版，发表最高质量的遗传学研究。它包括对人类和植物性状以及其他模式生物的遗传和功能基因组研究。目前的重点是通过扰动实验研究常见和复杂疾病的遗传基础以及基因网络的功能机制、结构和进化。在行业领域中学术影响力很大，属于国际一流期刊，影响因子指数41.307。
Volume 56 Issue 4, April 2024
在2024年4月，Nature Genetics共发表25篇文章，其中包括1篇Comment，4篇Research Highlights，1篇News & Views，4篇Research Briefings，15篇Articles。
1. Protein-altering variants at copy number-variable regions influence diverse human phenotypes
拷贝数可变区域的蛋白质改变变异影响不同的人类表型
美国马萨诸塞州波士顿布莱根妇女医院、哈佛医学院、麻省理工学院等合作发表
Abstract
Copy number variants (CNVs) are among the largest genetic variants, yet CNVs have not been effectively ascertained in most genetic association studies. Here we ascertained protein-altering CNVs from UK Biobank whole-exome sequencing data (n = 468,570) using haplotype-informed methods capable of detecting subexonic CNVs and variation within segmental duplications. Incorporating CNVs into analyses of rare variants predicted to cause gene loss of function (LOF) identified 100 associations of predicted LOF variants with 41 quantitative traits. A low-frequency partial deletion of RGL3 exon 6 conferred one of the strongest protective effects of gene LOF on hypertension risk (odds ratio = 0.86 (0.82–0.90)). Protein-coding variation in rapidly evolving gene families within segmental duplications—previously invisible to most analysis methods—generated some of the human genome’s largest contributions to variation in type 2 diabetes risk, chronotype and blood cell traits. These results illustrate the potential for new genetic insights from genomic variation that has escaped large-scale analysis to date.
摘要：
拷贝数变异（CNV）是最大的遗传变异之一，但在大多数遗传关联研究中尚未有效确定CNV。本研究利用英国生物银行全外显子组测序数据（n = 468,570），采用基于单倍型的方法来确定影响蛋白质的 CNV，这些方法能检测亚外显子区域的CNVs和段重复序列内的变异。将CNV纳入会导致基因功能丧失（LOF）的罕见变异的分析中，确定了100个预测的LOF变异与41个数量性状的关联。RGL3外显子6的低频部分缺失LOF基因被发现对高血压风险具有最强保护作用之一（OR= 0.86 （0.82–0.90））。在段重复序列中，快速进化的基因家族中的蛋白质编码变异——以前大多数分析方法都无法发现——产生了对2型糖尿病风险、生物钟类型和血细胞性状变异最大贡献的人类基因组。这些结果展示了从迄今为止尚未进行大规模分析的基因组变异中获得新的遗传见解的潜力。
2. Protein-truncating variants in BSN are associated with severe adult-onset obesity, type 2 diabetes and fatty liver disease
BSN中的蛋白质截短变体与严重的成人早发性肥胖、2型糖尿病和脂肪肝病有关
英国剑桥大学
Abstract
Obesity is a major risk factor for many common diseases and has a substantial heritable component. To identify new genetic determinants, we performed exome-sequence analyses for adult body mass index (BMI) in up to 587,027 individuals. We identified rare loss-of-function variants in two genes (BSN and APBA1) with effects substantially larger than those of well-established obesity genes such as MC4R. In contrast to most other obesity-related genes, rare variants in BSN and APBA1 were not associated with normal variation in childhood adiposity. Furthermore, BSN protein-truncating variants (PTVs) magnified the influence of common genetic variants associated with BMI, with a common variant polygenic score exhibiting an effect twice as large in BSN PTV carriers than in noncarriers. Finally, we explored the plasma proteomic signatures of BSN PTV carriers as well as the functional consequences of BSN deletion in human induced pluripotent stem cell-derived hypothalamic neurons. Collectively, our findings implicate degenerative processes in synaptic function in the etiology of adult-onset obesity.
摘要：
肥胖是许多常见疾病的主要危险因素，且具有很大的遗传成分。为了确定新的遗传决定因素，本研究对多达587,027名个体的成人体重指数（BMI）进行了外显子组序列分析。本研究在两个基因（BSN和APBA1）中发现了罕见的功能丧失变异，其影响明显大于已知肥胖基因（如MC4R）的影响。与大多数其他肥胖相关基因相比，BSN和APBA1的罕见变异与儿童肥胖的正常变异无关。此外，BSN蛋白截短变异（PTV）放大了与BMI相关的常见遗传变异的影响，常见变异多基因评分在BSN PTV携带者中表现出的影响是非携带者的两倍。最后，探讨了BSN PTV携带者的血浆蛋白质组学特征以及BSN缺失在人诱导的多能干细胞来源的下丘脑神经元中的功能后果。总的来说，本研究结果表明突触功能的退行性过程与成人发病肥胖的病因有关。
3. Comprehensive whole-genome sequence analyses provide insights into the genomic architecture of cerebral palsy
综合全基因组序列分析为脑瘫基因组结构提供见解
加拿大多伦多市荷兰布鲁尔维尤儿童康复医院、多伦多大学医学院、多伦多市病童医院等机构合作发表
Abstract
We performed whole-genome sequencing (WGS) in 327 children with cerebral palsy (CP) and their biological parents. We classified 37 of 327 (11.3%) children as having pathogenic/likely pathogenic (P/LP) variants and 58 of 327 (17.7%) as having variants of uncertain significance. Multiple classes of P/LP variants included single-nucleotide variants (SNVs)/indels (6.7%), copy number variations (3.4%) and mitochondrial mutations (1.5%). The COL4A1 gene had the most P/LP SNVs. We also analyzed two pediatric control cohorts (n = 203 trios and n = 89 sib-pair families) to provide a baseline for de novo mutation rates and genetic burden analyses, the latter of which demonstrated associations between de novo deleterious variants and genes related to the nervous system. An enrichment analysis revealed previously undescribed plausible candidate CP genes (SMOC1, KDM5B, BCL11A and CYP51A1). A multifactorial CP risk profile and substantial presence of P/LP variants combine to support WGS in the diagnostic work-up across all CP and related phenotypes.
摘要：
本研究对327名脑瘫（CP）儿童及其亲生父母进行了全基因组测序（WGS）。将327名儿童中的37名（11.3%）归类为具有致病性/可能致病性（P/LP）变异，将327名儿童中的58名（17.7%）归类为具有意义不确定的变异。多类型P/LP变异包括单核苷酸变异（SNV）/插入缺失（6.7%）、拷贝数变异（3.4%）和线粒体突变（1.5%）。COL4A1基因的P/LP SNVs最多。本研究还分析了两个儿科对照队列（n = 203个三胞胎和 n = 89个双胞胎家族），为新发突变率和遗传负荷分析提供基线数据，后者证明了新发有害变异与神经系统相关基因之间的关联。富集分析揭示了以前未描述的似是而非的候选CP基因（SMOC1、KDM5B、BCL11A和CYP51A1）。多因素CP风险概况和P/LP变体的大量存在相结合，支持WGS在所有CP和相关表型的诊断检查中。
4. Cell-type-specific and disease-associated expression quantitative trait loci in the human lung
人肺细胞类型特异性和疾病相关表达数量性状位点
美国亚利桑那州凤凰城转化基因组学研究所、澳大利亚墨尔本大学、圣文森特医学研究所等机构合作发表
Abstract
Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis. Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA sequencing of lung tissue from 66 individuals with pulmonary fibrosis and 48 unaffected donors. Using a pseudobulk approach, we mapped expression quantitative trait loci (eQTLs) across 38 cell types, observing both shared and cell-type-specific regulatory effects. Furthermore, we identified disease interaction eQTLs and demonstrated that this class of associations is more likely to be cell-type-specific and linked to cellular dysregulation in pulmonary fibrosis. Finally, we connected lung disease risk variants to their regulatory targets in disease-relevant cell types. These results indicate that cellular context determines the impact of genetic variation on gene expression and implicates context-specific eQTLs as key regulators of lung homeostasis and disease.
摘要：
常见的遗传变异对慢性肺部疾病（包括肺纤维化）具有显著风险。以细胞类型特异性和情境依赖性的方式定义基因表达的遗传控制对于理解遗传变异影响复杂性状和疾病病理生物学的机制至关重要。为此，本研究对66名肺纤维化患者和48名未受影响的供体的肺组织进行了单细胞RNA测序。使用伪批量方法，绘制了38种细胞类型的表达数量性状位点（eQTL），观察了共享和细胞类型特异性的调控作用。此外，鉴定了疾病相互作用的eQTL，并证明这类关联更有可能是细胞类型特异性的，并且与肺纤维化的细胞失调有关。最后，将肺部疾病风险变异与其在疾病相关细胞类型中的调控靶点联系起来。这些结果表明，细胞环境决定了遗传变异对基因表达的影响，并将情境特异性的eQTL视为肺稳态和疾病的关键调节因子。
5. Cell subtype-specific effects of genetic variation in the Alzheimer’s disease brain
阿尔茨海默病大脑遗传变异的细胞亚型特异性影响
美国哥伦比亚大学、麻省理工学院、哈佛大学等机构合作发表
Abstract
The relationship between genetic variation and gene expression in brain cell types and subtypes remains understudied. Here, we generated single-nucleus RNA sequencing data from the neocortex of 424 individuals of advanced age; we assessed the effect of genetic variants on RNA expression in cis (cis-expression quantitative trait loci) for seven cell types and 64 cell subtypes using 1.5 million transcriptomes. This effort identified 10,004 eGenes at the cell type level and 8,099 eGenes at the cell subtype level. Many eGenes are only detected within cell subtypes. A new variant influences APOE expression only in microglia and is associated with greater cerebral amyloid angiopathy but not Alzheimer’s disease pathology, after adjusting for APOEε4, providing mechanistic insights into both pathologies. Furthermore, only a TMEM106B variant affects the proportion of cell subtypes. Integration of these results with genome-wide association studies highlighted the targeted cell type and probable causal gene within Alzheimer’s disease, schizophrenia, educational attainment and Parkinson’s disease loci.
摘要：
脑细胞类型和亚型中遗传变异与基因表达之间的关系仍未得到充分研究。本研究从424名高龄个体的新皮层生成了单核RNA测序数据，使用150万个转录组评估了遗传变异对7种细胞类型和64种细胞亚型的顺式RNA表达的影响（顺式表达数量性状位点）。这项工作在细胞类型水平上鉴定了10,004个eGene，在细胞亚型水平上鉴定了8,099个eGene，许多eGene仅在细胞亚型中检测到。在调整APOEε4后，一种新的变体仅影响小胶质细胞中的APOE表达，并且与更大的脑淀粉样血管病相关，但与阿尔茨海默病病理学无关，从而提供了对这两种病理的机制见解。此外，只有TMEM106B变异会影响细胞亚型的比例。将这些结果与全基因组关联研究相结合，突出了阿尔茨海默病、精神分裂症、教育程度和帕金森病基因座中的靶向细胞类型和可能的致病基因。
6. Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles
来自多模态单细胞数据的组织特异性增强子-基因图谱可识别致病疾病等位基因
美国马萨诸塞州波士顿布莱根妇女医院、哈佛医学院、麻省理工学院
Abstract
Translating genome-wide association study (GWAS) loci into causal variants and genes requires accurate cell-type-specific enhancer–gene maps from disease-relevant tissues. Building enhancer–gene maps is essential but challenging with current experimental methods in primary human tissues. Here we developed a nonparametric statistical method, SCENT (single-cell enhancer target gene mapping), that models association between enhancer chromatin accessibility and gene expression in single-cell or nucleus multimodal RNA sequencing and ATAC sequencing data. We applied SCENT to 9 multimodal datasets including >120,000 single cells or nuclei and created 23 cell-type-specific enhancer–gene maps. These maps were highly enriched for causal variants in expression quantitative loci and GWAS for 1,143 diseases and traits. We identified likely causal genes for both common and rare diseases and linked somatic mutation hotspots to target genes. We demonstrate that application of SCENT to multimodal data from disease-relevant human tissue enables the scalable construction of accurate cell-type-specific enhancer–gene maps, essential for defining noncoding variant function.
摘要：
将全基因组关联研究（GWAS）位点翻译成因果变异和基因需要来自疾病相关组织的准确细胞类型特异性增强子-基因图谱。构建增强子-基因图谱是必不可少的，但对于目前在原代人体组织中的实验方法来说具有挑战性。本研究开发了一种非参数统计方法，即SCENT（单细胞增强子靶基因定位），该方法模拟了单细胞或细胞核多模态RNA测序和ATAC测序数据中增强子染色质可及性与基因表达之间的关联。本研究将SCENT应用于9个多模态数据集，包括>120,000个单细胞或细胞核，并创建了23个细胞类型特异性增强子-基因图谱。这些图谱高度富集了1,143种疾病和性状的表达数量位点和GWAS的因果变异，确定了常见病和罕见病的可能致病基因，并将体细胞突变热点与靶基因联系起来。研究结果证明，将SCENT应用于来自疾病相关人体组织的多模态数据，可以扩展构建准确的细胞类型特异性增强子-基因图谱，这对于定义非编码变异功能至关重要。
7. Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis
单细胞多组学回归模型识别功能性和疾病相关增强子，并实现染色质电位分析
美国纪念斯隆凯特琳癌症中心计算与系统生物学项目
Abstract
We present a gene-level regulatory model, single-cell ATAC + RNA linking (SCARlink), which predicts single-cell gene expression and links enhancers to target genes using multi-ome (scRNA-seq and scATAC–seq co-assay) sequencing data. The approach uses regularized Poisson regression on tile-level accessibility data to jointly model all regulatory effects at a gene locus, avoiding the limitations of pairwise gene–peak correlations and dependence on peak calling. SCARlink outperformed existing gene scoring methods for imputing gene expression from chromatin accessibility across high-coverage multi-ome datasets while giving comparable to improved performance on low-coverage datasets. Shapley value analysis on trained models identified cell-type-specific gene enhancers that are validated by promoter capture Hi-C and are 11× to 15× and 5× to 12× enriched in fine-mapped eQTLs and fine-mapped genome-wide association study (GWAS) variants, respectively. We further show that SCARlink-predicted and observed gene expression vectors provide a robust way to compute a chromatin potential vector field to enable developmental trajectory analysis.
摘要：
本研究提出了一种基因水平调控模型，单细胞ATAC + RNA连接（SCARlink），该模型使用多组（scRNA-seq和scATAC-seq共测定）测序数据预测单细胞基因表达并将增强子与靶基因连接起来。该方法对瓦片级可及性数据使用正则化泊松回归，共同模拟基因位点的所有调控效应，避免了成对基因-峰相关性和对峰调用依赖性的局限性。在高覆盖率多组数据集中，SCARlink在根据染色质可及性估算基因表达方面优于现有的基因评分方法，同时在低覆盖率数据集上提供了相当的改进性能。通过对训练模型的Shapley值分析，确定了细胞类型特异性基因增强子，这些增强子通过启动子捕获Hi-C验证，分别富集在精细定位的eQTL和精细定位的全基因组关联研究（GWAS）变体中11×至15×和5×至12×。研究进一步表明，SCARlink预测和观察到的基因表达载体提供了一种计算染色质电位载体场以实现发育轨迹分析的可靠方法。
8. Proteogenomic insights into early-onset endometrioid endometrial carcinoma: predictors for fertility-sparing therapy response
早发性子宫内膜样子宫内膜癌的蛋白质基因组学见解：保留生育能力的治疗反应的预测因素
华中科技大学同济医学院附属同济医院
Abstract
Endometrial carcinoma remains a public health concern with a growing incidence, particularly in younger women. Preserving fertility is a crucial consideration in the management of early-onset endometrioid endometrial carcinoma (EEEC), particularly in patients under 40 who maintain both reproductive desire and capacity. To illuminate the molecular characteristics of EEEC, we undertook a large-scale multi-omics study of 215 patients with endometrial carcinoma, including 81 with EEEC. We reveal an unexpected association between exposome-related mutational signature and EEEC, characterized by specific CTNNB1 and SIGLEC10 hotspot mutations and disruption of downstream pathways. Interestingly, SIGLEC10Q144K mutation in EEECs resulted in aberrant SIGLEC-10 protein expression and promoted progestin resistance by interacting with estrogen receptor alpha. We also identified potential protein biomarkers for progestin response in fertility-sparing treatment for EEEC. Collectively, our study establishes a proteogenomic resource of EEECs, uncovering the interactions between exposome and genomic susceptibilities that contribute to the development of primary prevention and early detection strategies for EEECs.
摘要：
子宫内膜癌仍然是一个公共卫生问题，尤其是在年轻女性中发病率不断增长。在治疗早发性子宫内膜样子宫内膜癌（EEEC）时，保留生育能力是一个至关重要的考虑因素，尤其对于40岁以下既有生殖欲望又有生育能力的患者。为了阐明EEEC的分子特征，本研究对215例子宫内膜癌患者进行了大规模的多组学研究，其中包括81例EEEC。结果揭示了暴露组相关突变特征与EEEC之间的意外关联，其特征是特定的CTNNB1和SIGLEC10热点突变以及下游通路的破坏。有趣的是，EEEC中的Q144K突变导致SIGLEC-10蛋白表达异常，并通过与雌激素受体α相互作用促进孕激素抵抗。本研究还确定了EEEC保留生育能力治疗中孕激素反应的潜在蛋白质生物标志物。总的来说，本研究建立了EEEC的蛋白质基因组资源，揭示了暴露组和基因组易感性之间的相互作用，这有助于制定EEEC的一级预防和早期检测策略。
9. A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast
单细胞图谱绘制成人乳房中稳态细胞转变的图谱
英国剑桥大学
Abstract
Here we use single-cell RNA sequencing to compile a human breast cell atlas assembled from 55 donors that had undergone reduction mammoplasties or risk reduction mastectomies. From more than 800,000 cells we identified 41 cell subclusters across the epithelial, immune and stromal compartments. The contribution of these different clusters varied according to the natural history of the tissue. Age, parity and germline mutations, known to modulate the risk of developing breast cancer, affected the homeostatic cellular state of the breast in different ways. We found that immune cells from BRCA1 or BRCA2 carriers had a distinct gene expression signature indicative of potential immune exhaustion, which was validated by immunohistochemistry. This suggests that immune-escape mechanisms could manifest in non-cancerous tissues very early during tumor initiation. This atlas is a rich resource that can be used to inform novel approaches for early detection and prevention of breast cancer.
摘要：
本研究使用单细胞RNA测序来编制了由55名接受过乳房缩小整形术或降低风险的乳房切除术的供体组装而成的人类乳腺细胞图谱。从超过800,000个细胞中，鉴定了上皮、免疫和基质区室的41个细胞亚簇。这些不同细胞簇的贡献根据组织的自然史而变化。已知年龄、胎次和种系突变会调节患乳腺癌的风险，它们以不同的方式影响乳房的稳态细胞状态。研究发现来自BRCA1或BRCA2携带者的免疫细胞具有独特的基因表达特征，表明潜在的免疫衰竭，这已通过免疫组化得到验证。这表明免疫逃逸机制可能在肿瘤发生期的非常早期就在非癌性组织中显现。该图谱是一个丰富的资源，可用于为早期发现和预防乳腺癌的新方法提供信息。
10. MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch
增强子的MYC活性通过表观遗传开关驱动预后转录程序
南丹麦大学、丹麦哥本哈根大学、美国麻省理工学院及哈佛大学布罗德研究所等机构合作发表
Abstract
The transcription factor MYC is overexpressed in most cancers, where it drives multiple hallmarks of cancer progression. MYC is known to promote oncogenic transcription by binding to active promoters. In addition, MYC has also been shown to invade distal enhancers when expressed at oncogenic levels, but this enhancer binding has been proposed to have low gene-regulatory potential. Here, we demonstrate that MYC directly regulates enhancer activity to promote cancer type-specific gene programs predictive of poor patient prognosis. MYC induces transcription of enhancer RNA through recruitment of RNA polymerase II (RNAPII), rather than regulating RNAPII pause-release, as is the case at promoters. This process is mediated by MYC-induced H3K9 demethylation and acetylation by GCN5, leading to enhancer-specific BRD4 recruitment through its bromodomains, which facilitates RNAPII recruitment. We propose that MYC drives prognostic cancer type-specific gene programs through induction of an enhancer-specific epigenetic switch, which can be targeted by BET and GCN5 inhibitors.
摘要：
转录因子MYC在大多数癌症中过表达，它被认为是驱动癌症进展的多种标志。已知MYC通过与活性启动子结合来促进致癌转录。此外，当在致癌水平上表达时，MYC也被证明会侵入远端增强子，但这种增强子结合被认为具有较低的基因调控潜力。本研究证明MYC可直接调节增强子活性，以促进预测患者预后不良的癌症类型特异性基因程序。MYC通过募集RNA聚合酶II（RNAPII）诱导增强子RNA的转录，而不是像启动子处调节RNAPII的暂停释放。该过程由MYC诱导的H3K9去甲基化和GCN5乙酰化介导，导致通过其溴结构域招募增强子特异性的BRD4，从而促进RNAPII的募集。本研究提出，MYC通过诱导增强子特异性的表观遗传开关，推动预后癌症类型特异性基因程序，这可以通过BET和GCN5抑制剂进行靶向。
11. Increased enhancer–promoter interactions during developmental enhancer activation in mammals
在哺乳动物发育增强子激活过程中增强子-启动子相互作用增加
美国加州大学、西班牙安达卢西亚发育生物学中心等机构合作发表
Abstract
Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer–promoter and enhancer–enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer–promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer–promoter physical proximity for developmental gene activation in mammals.
摘要：
远程增强子被认为通过物理接近与其目标启动子相互作用，但这种接近对增强子功能的重要性仍不清楚。在这里，本研究通过生成近千个具有已知体内活性的增强子高分辨率组织分辨的接触图，研究了增强子在哺乳动物发育过程中的三维（3D）构象。61%的发育增强子绕过其邻近的基因，这些基因通常以启动子CpG甲基化为标志。大多数增强子表现出组织特异性的3D构象，并且增强子-启动子和增强子-增强子相互作用在体内增强子激活后适度但持续增加。少于14%的增强子-启动子相互作用在不同组织中稳定形成；然而，这些不变的相互作用是在没有增强子的情况下形成的，可能是由相邻的CTCF结合介导。本研究结果强调了增强子-启动子物理接近对哺乳动物发育基因激活的重要性。
12. Enhancer–promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation
增强子-启动子相互作用在从细胞命运规范到组织分化的过渡中变得更具指导意义
德国海德堡欧洲分子生物学实验室（EMBL）
Abstract
To regulate expression, enhancers must come in proximity to their target gene. However, the relationship between the timing of enhancer–promoter (E–P) proximity and activity remains unclear, with examples of uncoupled, anticorrelated and correlated interactions. To assess this, we selected 600 characterized enhancers or promoters with tissue-specific activity in Drosophila embryos and performed Capture-C in FACS-purified myogenic or neurogenic cells during specification and tissue differentiation. This enabled direct comparison between E–P proximity and activity transitioning from OFF-to-ON and ON-to-OFF states across developmental conditions. This showed remarkably similar E–P topologies between specified muscle and neuronal cells, which are uncoupled from activity. During tissue differentiation, many new distal interactions emerge where changes in E–P proximity reflect changes in activity. The mode of E–P regulation therefore appears to change as embryogenesis proceeds, from largely permissive topologies during cell-fate specification to more instructive regulation during terminal tissue differentiation, when E–P proximity is coupled to activation.
摘要：
为了调节基因表达，增强子必须靠近其靶基因。然而，增强子-启动子（E-P）接近的时间与活性之间的关系仍不清楚，有解耦联、反相关和相关相互作用的例子。为了评估这一点，本研究在果蝇胚胎中选择了600种具有组织特异性活性的表征增强子或启动子，并在规范化和组织分化期间在FACS纯化的肌源性或神经源性细胞中进行了Capture-C。这使得在发育条件下，E-P接近度和从OFF-to-ON状态和ON-to-OFF状态转换的活动之间可以直接比较。这显示了特定肌肉和神经元细胞之间非常相似的E-P拓扑结构，它们与活动无关。在组织分化过程中，出现了许多新的远端相互作用，其中E-P接近度的变化反映了活性的变化。因此，随着胚胎发生的进行，E-P调节的模式似乎发生了变化，从细胞命运规范期间的宽松拓扑，到终末组织分化期间更具指导性的调节，此时E-P接近与激活相耦合。
13. The homeobox transcription factor DUXBL controls exit from totipotency
同源盒转录因子DUXBL控制从全能性细胞状态的退出
美国基因组完整性实验室、德国马克斯普朗克心肺研究所、德国法兰克福心肺研究所、广州医科大学第二附属医院等机构合作发表
Abstract
In mice, exit from the totipotent two-cell (2C) stage embryo requires silencing of the 2C-associated transcriptional program. However, the molecular mechanisms involved in this process remain poorly understood. Here we demonstrate that the 2C-specific transcription factor double homeobox protein (DUX) mediates an essential negative feedback loop by inducing the expression of DUXBL to promote this silencing. We show that DUXBL gains accessibility to DUX-bound regions specifically upon DUX expression. Furthermore, we determine that DUXBL interacts with TRIM24 and TRIM33, members of the TRIM superfamily involved in gene silencing, and colocalizes with them in nuclear foci upon DUX expression. Importantly, DUXBL overexpression impairs 2C-associated transcription, whereas Duxbl inactivation in mouse embryonic stem cells increases DUX-dependent induction of the 2C-transcriptional program. Consequently, DUXBL deficiency in embryos results in sustained expression of 2C-associated transcripts leading to early developmental arrest. Our study identifies DUXBL as an essential regulator of totipotency exit enabling the first divergence of cell fates.
摘要：
在小鼠中，从全能双细胞（2C）阶段胚胎的退出需要沉默2C相关的转录程序。然而，这一过程中涉及的分子机制仍然知之甚少。在这里，本研究证明了2C特异性转录因子双同源盒蛋白（DUX）通过诱导DUXBL的表达来促进这种沉默，从而介导一个重要的负反馈回路。结果表明，DUXBL在DUX表达式上获得了对DUX绑定区域的可访问性。此外，本研究确定了DUXBL与参与基因沉默的TRIM超家族成员TRIM24和TRIM33相互作用，并在DUX表达时与它们在核病灶中共定位。重要的是，DUXBL过表达会损害2C相关转录，而小鼠胚胎干细胞中的Duxbl失活会增加2C转录程序的DUX依赖性诱导。因此，胚胎中的DUXBL缺陷导致2C相关转录本的持续表达，从而导致早期发育停滞。本研究将DUXBL确定为全能性退出的重要调节因子，从而实现细胞命运的首次分化。
Volume 56 Issue 5, May 2024
在2024年5月，Nature Genetics共发表37篇文章，其中包括1篇Comment，4篇Research Highlights，3篇News & Views，3篇Research Briefings，2篇Perspectives，22篇Articles，2篇Amendments & Corrections。
1. Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries
利用功能基因组注释和基因组覆盖率来改善祖先内部和祖先之间复杂性状的多基因预测
澳大利亚昆士兰大学、美国哈佛大学和麻省理工学院等机构合作发表
Abstract
We develop a method, SBayesRC, that integrates genome-wide association study (GWAS) summary statistics with functional genomic annotations to improve polygenic prediction of complex traits. Our method is scalable to whole-genome variant analysis and refines signals from functional annotations by allowing them to affect both causal variant probability and causal effect distribution. We analyze 50 complex traits and diseases using ∼7 million common single-nucleotide polymorphisms (SNPs) and 96 annotations. SBayesRC improves prediction accuracy by 14% in European ancestry and up to 34% in cross-ancestry prediction compared to the baseline method SBayesR, which does not use annotations, and outperforms other methods, including LDpred2, LDpred-funct, MegaPRS, PolyPred-S and PRS-CSx. Investigation of factors affecting prediction accuracy identifies a significant interaction between SNP density and annotation information, suggesting whole-genome sequence variants with annotations may further improve prediction. Functional partitioning analysis highlights a major contribution of evolutionary constrained regions to prediction accuracy and the largest per-SNP contribution from nonsynonymous SNPs.
摘要：
本研究开发了一种名为SBayesRC的方法，该方法将全基因组关联研究（GWAS）汇总统计与功能基因组注释相结合，以改善复杂性状的多基因预测。该方法可扩展到全基因组变异分析，并通过允许功能注释影响因果变异概率和因果效应分布来细化功能注释中的信号。使用约700万个常见的单核苷酸多态性（SNP）和96个注释分析了50种复杂的性状和疾病。与不使用注释的基线方法SBayesR相比，SBayesRC将欧洲血统的预测准确率提高了14%，将跨血统预测的预测准确性提高了34%，并且优于其他方法，包括LDpred2、LDpred-funct、MegaPRS、PolyPred-S和PRS-CSx。对影响预测准确性的因素的调查确定了SNP密度和注释信息之间的显著相互作用，这表明带有注释的全基因组序列变异可能会进一步改善预测。功能分区分析突出了进化约束区域对预测准确性的主要贡献，以及非同义SNP对每个SNP的最大贡献。
2. Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits
超过100万名欧洲血统个体的全基因组分析改善了血压性状的多基因风险评分
美国国立卫生研究院精准健康研究中心、美国范德比尔特大学医学中心、伊朗伊斯法罕医科大学等机构合作发表
Abstract
Hypertension affects more than one billion people worldwide. Here we identify 113 novel loci, reporting a total of 2,103 independent genetic signals (P < 5 × 10−8) from the largest single-stage blood pressure (BP) genome-wide association study to date (n = 1,028,980 European individuals). These associations explain more than 60% of single nucleotide polymorphism-based BP heritability. Comparing top versus bottom deciles of polygenic risk scores (PRSs) reveals clinically meaningful differences in BP (16.9 mmHg systolic BP, 95% CI, 15.5–18.2 mmHg, P = 2.22 × 10−126) and more than a sevenfold higher odds of hypertension risk (odds ratio, 7.33; 95% CI, 5.54–9.70; P = 4.13 × 10−44) in an independent dataset. Adding PRS into hypertension-prediction models increased the area under the receiver operating characteristic curve (AUROC) from 0.791 (95% CI, 0.781–0.801) to 0.826 (95% CI, 0.817–0.836, ∆AUROC, 0.035, P = 1.98 × 10−34). We compare the 2,103 loci results in non-European ancestries and show significant PRS associations in a large African-American sample. Secondary analyses implicate 500 genes previously unreported for BP. Our study highlights the role of increasingly large genomic studies for precision health research.
摘要：
高血压影响着全世界超过10亿人。本研究识别了113个新位点，报告了来自迄今为止最大的单阶段血压（BP）全基因组关联研究（n = 1,028,980名欧洲个体）的总共2,103个独立遗传信号（P<5×10−8）。这些关联解释了超过60%的基于单核苷酸多态性（SNP）的BP遗传性。在独立数据集中比较多基因风险评分（PRS）的最高和最低十分位数显示血压存在临床意义的差异（收缩压16.9 mmHg，95% CI，15.5-18.2mmHg，P=2.22×10−126），高血压风险概率高出7倍以上（OR，7.33；95% CI，5.54-9.70；P=4.13×10−44）。将PRS纳入高血压预测模型后，受试者工作特征曲线下面积（AUROC）从0.791（95%CI，0.781-0.801）增加到0.826（95%CI，0.817-0.836，∆AUROC，0.035，P=1.98 ×10−34）。本研究比较了非欧洲血统的2,103个位点结果，并在大型非裔美国人样本中显示出显著的PRS关联。二次分析涉及500个以前未报道的BP基因。本研究强调了日益大规模的基因组研究在精准健康研究中的作用。
3. Genome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder
全基因组关联分析确定了95个风险位点，并提供了对创伤后应激障碍神经生物学的见解
美国加州大学圣地亚哥分校、退伍军人事务部圣地亚哥医疗保健系统等机构合作发表
Abstract
Post-traumatic stress disorder (PTSD) genetics are characterized by lower discoverability than most other psychiatric disorders. The contribution to biological understanding from previous genetic studies has thus been limited. We performed a multi-ancestry meta-analysis of genome-wide association studies across 1,222,882 individuals of European ancestry (137,136 cases) and 58,051 admixed individuals with African and Native American ancestry (13,624 cases). We identified 95 genome-wide significant loci (80 new). Convergent multi-omic approaches identified 43 potential causal genes, broadly classified as neurotransmitter and ion channel synaptic modulators (for example, GRIA1, GRM8 and CACNA1E), developmental, axon guidance and transcription factors (for example, FOXP2, EFNA5 and DCC), synaptic structure and function genes (for example, PCLO, NCAM1 and PDE4B) and endocrine or immune regulators (for example, ESR1, TRAF3 and TANK). Additional top genes influence stress, immune, fear and threat-related processes, previously hypothesized to underlie PTSD neurobiology. These findings strengthen our understanding of neurobiological systems relevant to PTSD pathophysiology, while also opening new areas for investigation.
摘要：
创伤后应激障碍 （PTSD） 遗传学的特征是发现率低于大多数其他精神疾病。因此，以前的遗传学研究对生物学理解的贡献是有限的。本研究对1,222,882名欧洲血统的个体（137,136例患者）和58,051名具有非洲和美洲血统的混合个体（13,624例患者）进行了全基因组关联研究的多祖先荟萃分析。鉴定了95个全基因组重要位点（80个新位点）。收敛的多组学方法识别了43个潜在的致病基因，大致分为神经递质和离子通道突触调节因子（例如GRIA1、GRM8和CACNA1E）、发育、轴突引导和转录因子（例如FOXP2、EFNA5和DCC）、突触结构和功能基因（例如PCLO、NCAM1和PDE4B）和内分泌或免疫调节剂（例如，ESR1、TRAF3和TANK）。其他顶级基因会影响压力、免疫、恐惧和威胁相关过程，这些过程以前被认为是创伤后应激障碍神经生物学的基础。这些发现加强了对与创伤后应激障碍病理生理学相关的神经生物学系统的理解，同时也为研究开辟了新的领域。
4. Multi-ancestry genome-wide association study of kidney cancer identifies 63 susceptibility regions
肾癌多祖先全基因组关联研究确定了63个易感区域
美国国家癌症研究所癌症流行病学和遗传学部、美国德克萨斯大学MD安德森癌症中心、国际癌症研究机构等机构合作发表
Abstract
Here, in a multi-ancestry genome-wide association study meta-analysis of kidney cancer (29,020 cases and 835,670 controls), we identified 63 susceptibility regions (50 novel) containing 108 independent risk loci. In analyses stratified by subtype, 52 regions (78 loci) were associated with clear cell renal cell carcinoma (RCC) and 6 regions (7 loci) with papillary RCC. Notably, we report a variant common in African ancestry individuals (rs7629500) in the 3′ untranslated region of VHL, nearly tripling clear cell RCC risk (odds ratio 2.72, 95% confidence interval 2.23–3.30). In cis-expression quantitative trait locus analyses, 48 variants from 34 regions point toward 83 candidate genes. Enrichment of hypoxia-inducible factor-binding sites underscores the importance of hypoxia-related mechanisms in kidney cancer. Our results advance understanding of the genetic architecture of kidney cancer, provide clues for functional investigation and enable generation of a validated polygenic risk score with an estimated area under the curve of 0.65 (0.74 including risk factors) among European ancestry individuals.
摘要：
在肾癌（29,020例病例和835,670例对照）的多种族全基因组关联研究荟萃分析中，本研究识别了63个易感区域（50个新区域），其中包含108个独立风险位点。在按亚型分层的分析中，52个区域（78个位点）与透明细胞肾细胞癌（RCC）相关，6个区域（7个位点）与乳头状RCC相关。值得注意的是，本研究报告了一个VHL 3′非翻译区中非洲血统个体中的常见变异（rs7629500），几乎是透明细胞RCC风险的三倍（OR 2.72,95%置信区间2.23-3.30）。在顺式表达数量性状位点分析中，来自34个区域的48个变异指向83个候选基因。缺氧诱导因子结合位点的富集强调了缺氧相关机制在肾癌中的重要性。本研究结果促进了对肾癌遗传结构的理解，为功能研究提供了线索，并能够生成经过验证的多基因风险评分，欧洲血统个体的估计曲线下面积为0.65（包括风险因素为0.74）。
5. Genome-wide association analyses of breast cancer in women of African ancestry identify new susceptibility loci and improve risk prediction
非洲血统女性乳腺癌的全基因组关联分析确定了新的易感位点并改进了风险预测
美国范德比尔特大学医学中心、弗吉尼亚大学医学院、国立卫生研究院国家癌症研究所等机构合作发表
Abstract
We performed genome-wide association studies of breast cancer including 18,034 cases and 22,104 controls of African ancestry. Genetic variants at 12 loci were associated with breast cancer risk (P<5×10−8), including associations of a low-frequency missense variant rs61751053 in ARHGEF38 with overall breast cancer (odds ratio (OR) = 1.48) and a common variant rs76664032 at chromosome 2q14.2 with triple-negative breast cancer (TNBC) (OR = 1.30). Approximately 15.4% of cases with TNBC carried six risk alleles in three genome-wide association study-identified TNBC risk variants, with an OR of 4.21 (95% confidence interval = 2.66–7.03) compared with those carrying fewer than two risk alleles. A polygenic risk score (PRS) showed an area under the receiver operating characteristic curve of 0.60 for the prediction of breast cancer risk, which outperformed PRS derived using data from females of European ancestry. Our study markedly increases the population diversity in genetic studies for breast cancer and demonstrates the utility of PRS for risk prediction in females of African ancestry.
摘要：
本研究对乳腺癌进行了全基因组关联研究，包括18,034例病例和22,104例非洲血统的对照。12个位点的遗传变异与乳腺癌风险相关（P<5×10−8），包括ARHGEF38低频错义变异rs61751053与整体乳腺癌的关联（比值比（OR）= 1.48） 和染色体2q14.2的常见变异rs76664032与三阴性乳腺癌（TNBC）（OR = 1.30）。大约15.4%的TNBC病例携带在三个全基因组关联研究确定的TNBC风险变异中的6个风险等位基因，与携带少于2个风险等位基因的病例相比，OR为4.21（95% CI= 2.66-7.03）。多基因风险评分（PRS）显示，用于预测乳腺癌风险的受试者工作特征曲线下面积为0.60，优于使用欧洲血统女性数据得出的PRS。本研究显著增加了乳腺癌遗传研究中的人群多样性，并证明了PRS在非洲血统女性风险预测中的实用性。
6. Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis
综合常见和罕见变异分析提供了对肝硬化遗传结构的见解
丹麦哥本哈根大学、美国宾夕法尼亚大学等机构合作发表
Abstract
We report a multi-ancestry genome-wide association study on liver cirrhosis and its associated endophenotypes, alanine aminotransferase (ALT) and γ-glutamyl transferase. Using data from 12 cohorts, including 18,265 cases with cirrhosis, 1,782,047 controls, up to 1 million individuals with liver function tests and a validation cohort of 21,689 cases and 617,729 controls, we identify and validate 14 risk associations for cirrhosis. Many variants are located near genes involved in hepatic lipid metabolism. One of these, PNPLA3 p.Ile148Met, interacts with alcohol intake, obesity and diabetes on the risk of cirrhosis and hepatocellular carcinoma (HCC). We develop a polygenic risk score that associates with the progression from cirrhosis to HCC. By focusing on prioritized genes from common variant analyses, we find that rare coding variants in GPAM associate with lower ALT, supporting GPAM as a potential target for therapeutic inhibition. In conclusion, this study provides insights into the genetic underpinnings of cirrhosis.
摘要：
本研究报告了一项关于肝硬化及其相关内表型（丙氨酸氨基转移酶（ALT）和γ-谷氨酰转移酶）的多种族全基因组关联研究。使用来自12个队列的数据，包括18,265例肝硬化病例、1,782,047例对照组、多达100万例肝功能检查个体以及21,689例病例和617,729例对照组的验证队列，识别并验证了14个肝硬化风险关联。许多变异位于参与肝脂代谢的基因附近。其中之一，PNPLA3 p.Ile148Met，与酒精摄入、肥胖和糖尿病相互作用，增加肝硬化和肝细胞癌（HCC）的风险。本研究还开发了一个与肝硬化到肝癌进展相关的多基因风险评分。通过关注来自常见变异分析的优先基因，发现GPAM中罕见的编码变异与较低的ALT相关，支持GPAM作为治疗抑制的潜在靶点。总之，这项研究为肝硬化的遗传基础提供了见解。
7. Genetic mapping across autoimmune diseases reveals shared associations and mechanisms
跨自身免疫性疾病的遗传图谱揭示了共同的关联和机制
美国耶鲁大学、加拿大多伦多大学、英国伦敦玛丽女王大学等机构合作发表
Abstract
Autoimmune and inflammatory diseases are polygenic disorders of the immune system. Many genomic loci harbor risk alleles for several diseases, but the limited resolution of genetic mapping prevents determining whether the same allele is responsible, indicating a shared underlying mechanism. Here, using a collection of 129,058 cases and controls across 6 diseases, we show that ~40% of overlapping associations are due to the same allele. We improve fine-mapping resolution for shared alleles twofold by combining cases and controls across diseases, allowing us to identify more expression quantitative trait loci driven by the shared alleles. The patterns indicate widespread sharing of pathogenic mechanisms but not a single global autoimmune mechanism. Our approach can be applied to any set of traits and is particularly valuable as sample collections become depleted.
摘要：
自身免疫性疾病和炎症性疾病是免疫系统的多基因疾病。许多基因组位点都含有多种疾病的风险等位基因，但遗传图谱的有限分辨率无法确定同一等位基因是否负责，这表明存在共同的潜在机制。在这里，使用6种疾病的129,058个病例和对照的集合，发现了～40%的重叠关联是由于相同的等位基因。本研究通过结合跨疾病的病例和对照，将共享等位基因的精细定位分辨率提高了两倍，从而能够识别更多由共享等位基因驱动的表达数量性状位点。这些模式表明致病机制广泛共享，但不是单一的整体自身免疫机制。该方法可以应用于任何一组性状，并在样本收集耗尽时特别有价值。
8. Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits
对东亚人血液甲基化数量性状位点的分析揭示了对复杂性状的祖先特异性影响
中国科学院
Abstract
Methylation quantitative trait loci (mQTLs) are essential for understanding the role of DNA methylation changes in genetic predisposition, yet they have not been fully characterized in East Asians (EAs). Here we identified mQTLs in whole blood from 3,523 Chinese individuals and replicated them in additional 1,858 Chinese individuals from two cohorts. Over 9% of mQTLs displayed specificity to EAs, facilitating the fine-mapping of EA-specific genetic associations, as shown for variants associated with height. Trans-mQTL hotspots revealed biological pathways contributing to EA-specific genetic associations, including an ERG-mediated 233 trans-mCpG network, implicated in hematopoietic cell differentiation, which likely reflects binding efficiency modulation of the ERG protein complex. More than 90% of mQTLs were shared between different blood cell lineages, with a smaller fraction of lineage-specific mQTLs displaying preferential hypomethylation in the respective lineages. Our study provides new insights into the mQTL landscape across genetic ancestries and their downstream effects on cellular processes and diseases/traits.
摘要：
甲基化数量性状位点（mQTL）对于理解DNA甲基化变化在遗传易感性中的作用至关重要，但在东亚人（EA）中尚未得到充分表征。本研究从3,523名中国人的全血中识别出了mQTL，并在两个队列的额外1,858名中国人中进行了验证。超过9%的mQTL显示出对EA的特异性，有助于EA特异性遗传关联的精细定位，如与身高相关的变异所示。Trans-mQTL热点揭示了有助于EA特异性遗传关联的生物学途径，包括ERG介导的233 trans-mCpG网络，与造血细胞分化有关，这可能反映了ERG蛋白复合物的结合效率调节。超过90%的mQTL在不同的血细胞谱系之间共享，而在各自谱系中表现出优先低甲基化的谱系特异性mQTL比例较小。本研究为跨遗传祖先的mQTL景观及其对细胞过程和疾病/性状的下游影响提供了新的见解。
9. Genetic modifiers of rare variants in monogenic developmental disorder loci
单基因发育障碍位点中罕见变异的遗传修饰因子
英国埃克塞特大学
Abstract
Rare damaging variants in a large number of genes are known to cause monogenic developmental disorders (DDs) and have also been shown to cause milder subclinical phenotypes in population cohorts. Here, we show that carrying multiple (2−5) rare damaging variants across 599 dominant DD genes has an additive adverse effect on numerous cognitive and socioeconomic traits in UK Biobank, which can be partially counterbalanced by a higher educational attainment polygenic score (EA-PGS). Phenotypic deviators from expected EA-PGS could be partly explained by the enrichment or depletion of rare DD variants. Among carriers of rare DD variants, those with a DD-related clinical diagnosis had a substantially lower EA-PGS and more severe phenotype than those without a clinical diagnosis. Our results suggest that the overall burden of both rare and common variants can modify the expressivity of a phenotype, which may then influence whether an individual reaches the threshold for clinical disease.
摘要：
已知大量基因中罕见的破坏性变异会导致单基因发育障碍（DD），并且在群体队列中也显示出引起较轻的亚临床表型。本研究表明，在599个显性DD基因中携带多个（2-5）罕见的破坏性变异对英国生物样本库中的许多认知和社会经济特征具有累加的不利影响，而这一影响可以通过更高的教育程度多基因评分（EA-PGS）部分抵消。与预期的EA-PGS的表型偏差可能部分解释为罕见DD变体的富集或耗竭。在罕见DD变异的携带者中，与没有临床诊断的患者相比，具有DD相关临床诊断的患者的EA-PGS明显较低，表型更严重。本研究结果表明，罕见和常见变异的总体负担可以改变表型的表达能力，这可能会影响个体是否达到临床疾病的阈值。
10. Functional variants in a TTTG microsatellite on 15q26.1 cause familial nonautoimmune thyroid abnormalities
15q26.1上TTTG微卫星的功能变异导致家族性非自身免疫性甲状腺异常
日本庆应义塾大学、东京国立儿童健康与发展研究所、帝都大学等机构合作发表
Abstract
Insufficient thyroid hormone production in newborns is referred to as congenital hypothyroidism. Multinodular goiter (MNG), characterized by an enlarged thyroid gland with multiple nodules, is usually seen in adults and is recognized as a separate disorder from congenital hypothyroidism. Here we performed a linkage analysis of a family with both nongoitrous congenital hypothyroidism and MNG and identified a signal at 15q26.1. Follow-up analyses with whole-genome sequencing and genetic screening in congenital hypothyroidism and MNG cohorts showed that changes in a noncoding TTTG microsatellite on 15q26.1 were frequently observed in congenital hypothyroidism (137 in 989) and MNG (3 in 33) compared with controls (3 in 38,722). Characterization of the noncoding variants with epigenomic data and in vitro experiments suggested that the microsatellite is located in a thyroid-specific transcriptional repressor, and its activity is disrupted by the variants. Collectively, we presented genetic evidence linking nongoitrous congenital hypothyroidism and MNG, providing unique insights into thyroid abnormalities.
摘要：
新生儿甲状腺激素分泌不足被称为先天性甲状腺功能减退症。多结节性甲状腺肿（MNG）的特征是甲状腺肿大伴多个结节，常见于成人，并被认为是一种独立于先天性甲状腺功能减退症的疾病。本研究对一个同时患有非甲状腺肿性先天性甲状腺功能减退症和MNG的家庭进行了连锁分析，识别出15q26.1的信号。先天性甲状腺功能减退症和MNG队列的全基因组测序和基因筛查随访分析表明，与对照组（38,722例）相比，先天性甲状腺功能减退症（989例中有137例）和MNG（33例中有3例）经常观察到15q26.1上非编码TTTG微卫星的变化。通过表观基因组数据和体外实验对非编码变异进行表征表明，该微卫星位于甲状腺特异性转录抑制因子中，其活性被变异破坏。总的来说，本研究提出了将非甲状腺肿性先天性甲状腺功能减退症与MNG联系起来的遗传证据，为甲状腺异常提供了独特的见解。
11. STR mutations on chromosome 15q cause thyrotropin resistance by activating a primate-specific enhancer of MIR7-2/MIR1179
染色体15q上的STR突变通过激活灵长类动物特异性增强子MIR7-2/MIR1179引起促甲状腺素耐药
美国密歇根大学、芝加哥大学、华盛顿大学等机构合作发表
Abstract
Thyrotropin (TSH) is the master regulator of thyroid gland growth and function. Resistance to TSH (RTSH) describes conditions with reduced sensitivity to TSH. Dominantly inherited RTSH has been linked to a locus on chromosome 15q, but its genetic basis has remained elusive. Here we show that non-coding mutations in a (TTTG)4 short tandem repeat (STR) underlie dominantly inherited RTSH in all 82 affected participants from 12 unrelated families. The STR is contained in a primate-specific Alu retrotransposon with thyroid-specific cis-regulatory chromatin features. Fiber-seq and RNA-seq studies revealed that the mutant STR activates a thyroid-specific enhancer cluster, leading to haplotype-specific upregulation of the bicistronic MIR7-2/MIR1179 locus 35 kb downstream and overexpression of its microRNA products in the participants’ thyrocytes. An imbalance in signaling pathways targeted by these micro-RNAs provides a working model for this cause of RTSH. This finding broadens our current knowledge of genetic defects altering pituitary–thyroid feedback regulation.
摘要：
促甲状腺素（TSH）是甲状腺生长和功能的主要调节因子。TSH耐药性（RTSH）是指对TSH敏感性降低的情况。显性遗传RTSH与15q染色体上的一个位点有关，但其遗传基础仍然难以捉摸。本研究表明（TTTG）4短串联重复序列（STR）中的非编码突变是来自12个无关家庭的所有82名受影响参与者的显性遗传RTSH的基础。STR包含在具有甲状腺特异性顺式调节染色质特征的灵长类动物特异性Alu逆转录转座子中。Fiber-seq和RNA-seq研究表明，突变体STR激活甲状腺特异性增强子簇，导致双反子MIR7-2/MIR1179位点下游35 kb的单倍型特异性上调，并在参与者的甲状腺细胞中过表达其microRNA产物。这些micro-RNA靶向信号通路的不平衡为RTSH的这一原因提供了工作模型。这一发现拓宽了目前对改变垂体-甲状腺反馈调节的遗传缺陷的认识。
12. Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes
肿瘤中的单细胞mtDNA动力学由核和线粒体基因组的共调控驱动
美国威尔康奈尔医学院、纪念斯隆凯特琳癌症中心
Abstract
The extent of cell-to-cell variation in tumor mitochondrial DNA (mtDNA) copy number and genotype, and the phenotypic and evolutionary consequences of such variation, are poorly characterized. Here we use amplification-free single-cell whole-genome sequencing (Direct Library Prep (DLP+)) to simultaneously assay mtDNA copy number and nuclear DNA (nuDNA) in 72,275 single cells derived from immortalized cell lines, patient-derived xenografts and primary human tumors. Cells typically contained thousands of mtDNA copies, but variation in mtDNA copy number was extensive and strongly associated with cell size. Pervasive whole-genome doubling events in nuDNA associated with stoichiometrically balanced adaptations in mtDNA copy number, implying that mtDNA-to-nuDNA ratio, rather than mtDNA copy number itself, mediated downstream phenotypes. Finally, multimodal analysis of DLP+ and single-cell RNA sequencing identified both somatic loss-of-function and germline noncoding variants in mtDNA linked to heteroplasmy-dependent changes in mtDNA copy number and mitochondrial transcription, revealing phenotypic adaptations to disrupted nuclear/mitochondrial balance.
摘要：
肿瘤线粒体DNA（mtDNA）拷贝数和基因型的细胞间变异程度，以及这种变异的表型和进化后果表征不明确。本研究使用无扩增单细胞全基因组测序（直接文库制备（DLP+））同时测定来自永生化细胞系、患者来源的异种移植物和原发性人类肿瘤的72,275个单细胞中的mtDNA拷贝数和核DNA（nuDNA）。细胞通常包含数千个mtDNA拷贝，但mtDNA拷贝数的变化很大，且与细胞大小密切相关。nuDNA中普遍存在的全基因组倍增事件与mtDNA拷贝数的化学计量平衡适应有关，这意味着mtDNA与nuDNA的比率，而不是mtDNA拷贝数本身，介导了下游表型。最后，DLP+和单细胞RNA测序的多模式分析确定了mtDNA中的体细胞功能丧失和种系非编码变异，这些变异与mtDNA拷贝数和线粒体转录的异质依赖性变化有关，揭示了对破坏的核/线粒体平衡的表型适应。
13. Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns
染色体进化筛选概括了组织特异性肿瘤非整倍体模式
美国布莱根妇女医院、哈佛医学院、马萨诸塞州总医院、霍华德休斯医学研究所合作发表
Abstract
Whole chromosome and arm-level copy number alterations occur at high frequencies in tumors, but their selective advantages, if any, are poorly understood. Here, utilizing unbiased whole chromosome genetic screens combined with in vitro evolution to generate arm- and subarm-level events, we iteratively selected the fittest karyotypes from aneuploidized human renal and mammary epithelial cells. Proliferation-based karyotype selection in these epithelial lines modeled tissue-specific tumor aneuploidy patterns in patient cohorts in the absence of driver mutations. Hi-C-based translocation mapping revealed that arm-level events usually emerged in multiples of two via centromeric translocations and occurred more frequently in tetraploids than diploids, contributing to the increased diversity in evolving tetraploid populations. Isogenic clonal lineages enabled elucidation of pro-tumorigenic mechanisms associated with common copy number alterations, revealing Notch signaling potentiation as a driver of 1q gain in breast cancer. We propose that intrinsic, tissue-specific proliferative effects underlie tumor copy number patterns in cancer.
摘要：
全染色体和手臂水平拷贝数改变在肿瘤中高频发生，但它们的选择优势尚不清楚。本研究利用无偏倚的全染色体遗传筛选与体外进化相结合来生成手臂和亚手臂水平的事件，从非整倍体化的人肾和乳腺上皮细胞中迭代选择了最合适的核型。这些上皮细胞系中基于增殖的核型中，模拟了在没有驱动突变的情况下患者队列中的组织特异性肿瘤非整倍体模式。基于Hi-C的易位映射显示，臂水平事件通常通过着丝粒易位以2的倍数出现，并且在四倍体中比二倍体更频繁地发生，有助于进化中的四倍体群体的多样性增加。同基因克隆谱系能够阐明与常见拷贝数改变相关的促肿瘤机制，揭示Notch信号增强作为乳腺癌1q增益的驱动因素。因此，本研究表明内在的、组织特异性的增殖效应是癌症中肿瘤拷贝数模式的基础。
14. Single-mitosis dissection of acute and chronic DNA mutagenesis and repair
急性和慢性DNA诱变和修复的单有丝分裂解剖
德国癌症研究中心、英国剑桥大学、英国爱丁堡大学
Abstract
How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, during single mitoses and at single-strand resolution. To distinguish between chronic (reactive oxygen species (ROS)) and acute (ultraviolet light (UV)) mutagenesis, we microfluidically separate pairs of sister cells from the first mitosis following burst UV damage. Strikingly, UV mutations manifest as sister-specific events, revealing mirror-image mutation phasing genome-wide. In contrast, ROS mutagenesis in transcribed regions is reduced strand agnostically. Successive rounds of genome replication over persisting UV damage drives multiallelic variation at CC dinucleotides. Finally, we show that mutation phasing can be resolved to single strands across the entire genome of liver tumors from F1 mice. This strategy can be broadly used to distinguish the contributions of overlapping cancer relevant mutational processes.
摘要：
慢性突变过程和间断的DNA损伤爆发如何驱动癌症基因组的进化尚不清楚。本研究展示了一种策略，可以解开和量化单细胞、单有丝分裂期间和单链分辨率下基因组进化的不同机制。为了区分慢性活性氧（ROS）和急性紫外线（UV）诱变，通过微流体技术将一对姐妹细胞从紫外线损伤后的第一次有丝分裂中分离出来。引人注目的是，UV突变表现为姐妹特异性事件，揭示了全基因组的镜像突变阶段。相反，转录区域中的ROS诱变不可知性地减少。连续几轮的基因组复制对持续的紫外线损伤驱动了CC二核苷酸的多等位基因变异。最后，结果表明突变阶段可以分解为F1小鼠肝肿瘤整个基因组中的单链。该策略可以广泛用于区分重叠癌症相关突变过程的贡献。
15. Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification
联合基因型和表型结果建模可改善碱基编辑变异效应量化
美国马萨诸塞州总医院、哈佛医学院、麻省理工学院等机构合作发表
Abstract
CRISPR base editing screens enable analysis of disease-associated variants at scale; however, variable efficiency and precision confounds the assessment of variant-induced phenotypes. Here, we provide an integrated experimental and computational pipeline that improves estimation of variant effects in base editing screens. We use a reporter construct to measure guide RNA (gRNA) editing outcomes alongside their phenotypic consequences and introduce base editor screen analysis with activity normalization (BEAN), a Bayesian network that uses per-guide editing outcomes provided by the reporter and target site chromatin accessibility to estimate variant impacts. BEAN outperforms existing tools in variant effect quantification. We use BEAN to pinpoint common regulatory variants that alter low-density lipoprotein (LDL) uptake, implicating previously unreported genes. Additionally, through saturation base editing of LDLR, we accurately quantify missense variant pathogenicity that is consistent with measurements in UK Biobank patients and identify underlying structural mechanisms. This work provides a widely applicable approach to improve the power of base editing screens for disease-associated variant characterization.
摘要：
CRISPR碱基编辑筛选能够大规模分析疾病相关变异；然而，可变的效率和精度混淆了变异诱导表型的评估。本研究提供了一个集成的实验和计算管道，可以改进对基本编辑筛选中变体效应的估计。使用报告基因构建来测量向导RNA（gRNA）编辑结果及其表型后果，并引入具有活性归一化（BEAN）的碱基编辑器筛选分析，这是一种贝叶斯网络，它使用报告基因和靶位点染色质可及性提供的每向导编辑结果来估计变异影响。BEAN在变异效应量化方面优于现有工具。使用BEAN来确定改变低密度脂蛋白（LDL）摄取的常见调控变异，涉及以前未报道的基因。此外，通过LDLR的饱和碱基编辑，准确地量化了与英国生物样本库患者的测量结果一致的错义变异致病性，并确定了潜在的结构机制。这项工作提供了一种广泛适用的方法，以提高用于疾病相关变异表征的碱基编辑筛选的能力。
16. A spatiotemporal atlas of cholestatic injury and repair in mice
小鼠胆汁淤积性损伤和修复的时空图谱
中国科学院、上海科技大学、华大基因研究院、广州医科大学附属第五医院等机构合作发表
Abstract
Cholestatic liver injuries, characterized by regional damage around the bile ductular region, lack curative therapies and cause considerable mortality. Here we generated a high-definition spatiotemporal atlas of gene expression during cholestatic injury and repair in mice by integrating spatial enhanced resolution omics sequencing and single-cell transcriptomics. Spatiotemporal analyses revealed a key role of cholangiocyte-driven signaling correlating with the periportal damage-repair response. Cholangiocytes express genes related to recruitment and differentiation of lipid-associated macrophages, which generate feedback signals enhancing ductular reaction. Moreover, cholangiocytes express high TGFβ in association with the conversion of liver progenitor-like cells into cholangiocytes during injury and the dampened proliferation of periportal hepatocytes during recovery. Notably, Atoh8 restricts hepatocyte proliferation during 3,5-diethoxycarbonyl-1,4-dihydro-collidin damage and is quickly downregulated after injury withdrawal, allowing hepatocytes to respond to growth signals. Our findings lay a keystone for in-depth studies of cellular dynamics and molecular mechanisms of cholestatic injuries, which may further develop into therapies for cholangiopathies.
摘要：
胆汁淤积性肝损伤的特征是胆管区域周围的区域损伤，缺乏治愈性治疗并导致相当大的死亡率。本研究通过整合空间增强分辨率组学测序和单细胞转录组学，生成了小鼠胆汁淤积损伤和修复过程中基因表达的高清时空图谱。时空分析揭示了胆管细胞驱动的信号传导与门静脉周围损伤修复反应相关的关键作用。胆管细胞表达与脂质相关巨噬细胞募集和分化相关的基因，这些巨噬细胞产生增强导管反应的反馈信号。此外，胆管细胞表达高TGFβ与损伤期间肝祖细胞样细胞转化为胆管细胞以及恢复期间门静脉周围肝细胞增殖的抑制有关。值得注意的是，Atoh8在3,5-二乙氧羰基-1,4-二氢对撞损伤期间限制肝细胞增殖，并在损伤退出后迅速下调，使肝细胞对生长信号做出反应。该研究结果为深入研究胆汁淤积损伤的细胞动力学和分子机制奠定了基石，这可能进一步发展成为胆管病的治疗方法。
17. A spatiotemporal atlas of mouse liver homeostasis and regeneration
小鼠肝脏稳态和再生的时空图谱
华大基因研究院、吉林大学、中国科学院、广州医科大学附属第五医院等机构合作发表
Abstract
The mechanism by which mammalian liver cell responses are coordinated during tissue homeostasis and perturbation is poorly understood, representing a major obstacle in our understanding of many diseases. This knowledge gap is caused by the difficulty involved with studying multiple cell types in different states and locations, particularly when these are transient. We have combined Stereo-seq (spatiotemporal enhanced resolution omics-sequencing) with single-cell transcriptomic profiling of 473,290 cells to generate a high-definition spatiotemporal atlas of mouse liver homeostasis and regeneration at the whole-lobe scale. Our integrative study dissects in detail the molecular gradients controlling liver cell function, systematically defining how gene networks are dynamically modulated through intercellular communication to promote regeneration. Among other important regulators, we identified the transcriptional cofactor TBL1XR1 as a rheostat linking inflammation to Wnt/β-catenin signaling for facilitating hepatocyte proliferation. Our data and analytical pipelines lay the foundation for future high-definition tissue-scale atlases of organ physiology and malfunction.
摘要：
哺乳动物肝细胞反应在组织稳态和扰动过程中协调的机制知之甚少，这是理解许多疾病的主要障碍。这种知识差距是由于研究不同状态和位置的多种细胞类型所涉及的困难造成的，特别是当这些细胞类型是瞬时的。本研究将Stereo-seq（时空增强分辨率组学测序）与473,290个细胞的单细胞转录组学分析相结合，在全叶尺度上生成了小鼠肝脏稳态和再生的高清时空图谱。综合研究详细剖析了控制肝细胞功能的分子梯度，系统地定义了基因网络如何通过细胞间通讯动态调节以促进再生。在其他重要的调节因子中，将转录辅因子TBL1XR1确定为将炎症与Wnt/β-catenin信号转导联系起来以促进肝细胞增殖的变阻器。本研究的数据和分析管道为未来器官生理学和功能障碍的高清组织规模图谱奠定了基础。
Volume 56 Issue 6, June 2024
在2024年6月，Nature Genetics共发表42篇文章，其中包括1篇Comment，4篇Research Highlights，2篇News & Views，6篇Research Briefings，1篇Review Articles，2篇Matters Arising，1篇Brief Communications，1篇Letters，19篇Articles，2篇Technical Reports，3篇Amendments & Corrections。
1. Genome-wide meta-analyses of restless legs syndrome yield insights into genetic architecture, disease biology and risk prediction
不宁腿综合征的全基因组荟萃分析有助于了解遗传结构、疾病生物学和风险预测
德国慕尼黑亥姆霍兹中心神经基因组学研究所、慕尼黑工业大学、英国剑桥大学、丹麦哥本哈根大学等机构合作发表
Abstract
Restless legs syndrome (RLS) affects up to 10% of older adults. Their healthcare is impeded by delayed diagnosis and insufficient treatment. To advance disease prediction and find new entry points for therapy, we performed meta-analyses of genome-wide association studies in 116,647 individuals with RLS (cases) and 1,546,466 controls of European ancestry. The pooled analysis increased the number of risk loci eightfold to 164, including three on chromosome X. Sex-specific meta-analyses revealed largely overlapping genetic predispositions of the sexes (rg = 0.96). Locus annotation prioritized druggable genes such as glutamate receptors 1 and 4, and Mendelian randomization indicated RLS as a causal risk factor for diabetes. Machine learning approaches combining genetic and nongenetic information performed best in risk prediction (area under the curve (AUC) = 0.82–0.91). In summary, we identified targets for drug development and repurposing, prioritized potential causal relationships between RLS and relevant comorbidities and risk factors for follow-up and provided evidence that nonlinear interactions are likely relevant to RLS risk prediction.
摘要：
不宁腿综合征（RLS）影响多达10%的老年人。他们的医疗保健因诊断延迟和治疗不足而受到阻碍。为了推进疾病预测并找到新的治疗切入点，本研究对116,647名RLS患者（病例）和1,546,466名欧洲血统的对照组进行了全基因组关联研究的荟萃分析。汇总分析将风险位点的数量增加了八倍，达到164个，其中包括X染色体上的3个。基因座注释优先考虑可成药基因，如谷氨酸受体1和4，孟德尔随机化表明RLS是糖尿病的致病危险因素。结合遗传和非遗传信息的机器学习方法在风险预测方面表现最佳（曲线下面积（AUC）= 0.82-0.91）。总之，本研究确定了药物开发和再利用的靶点，优先考虑了RLS与相关合并症和风险因素之间的潜在因果关系，并提供了非线性相互作用可能与RLS风险预测相关的证据。
2. Body mass index stratification optimizes polygenic prediction of type 2 diabetes in cross-biobank analyses
体重指数分层优化了跨生物样本库分析中2型糖尿病的多基因预测
日本大阪大学、东京大学、东北大学、虎之门医院合作发表
Abstract
Type 2 diabetes (T2D) shows heterogeneous body mass index (BMI) sensitivity. Here, we performed stratification based on BMI to optimize predictions for BMI-related diseases. We obtained BMI-stratified datasets using data from more than 195,000 individuals (nT2D = 55,284) from BioBank Japan (BBJ) and UK Biobank. T2D heritability in the low-BMI group was greater than that in the high-BMI group. Polygenic predictions of T2D toward low-BMI targets had pseudo-R2 values that were more than 22% higher than BMI-unstratified targets. Polygenic risk scores (PRSs) from low-BMI discovery outperformed PRSs from high BMI, while PRSs from BMI-unstratified discovery performed best. Pathway-specific PRSs demonstrated the biological contributions of pathogenic pathways. Low-BMI T2D cases showed higher rates of neuropathy and retinopathy. Combining BMI stratification and a method integrating cross-population effects, T2D predictions showed greater than 37% improvements over unstratified-matched-population prediction. We replicated findings in the Tohoku Medical Megabank (n = 26,000) and the second BBJ cohort (n = 33,096). Our findings suggest that target stratification based on existing traits can improve the polygenic prediction of heterogeneous diseases.
摘要：
2型糖尿病（T2D）表现出异质性体重指数（BMI）敏感性。本研究根据BMI进行了分层，以优化对BMI相关疾病的预测。使用来自日本生物银行（BBJ）和英国生物样本库的超过195,000人（nT2D = 55,284）的数据获得了BMI分层数据集。低BMI组的T2D遗传力大于高BMI组。T2D对低BMI目标的多基因预测具有伪R2值，比BMI未分层的目标高22%以上。低BMI发现的多基因风险评分（PRS）优于高BMI发现的PRS，而BMI未分层发现的PRS表现最佳。通路特异性PRS证明了致病途径的生物学贡献。低BMI T2D病例的神经病变和视网膜病变发生率更高。结合BMI分层和整合跨人群效应的方法，T2D预测结果显示比未分层匹配人群预测改善37%以上。在东北医疗大型银行（n = 26,000）和第二个BBJ队列（n = 33,096）中重复了研究结果。本研究结果表明，基于现有性状的靶向分层可以改善异质性疾病的多基因预测。
3. Cross-ancestry genome-wide association studies of brain imaging phenotypes
脑成像表型的跨祖先全基因组关联研究
中国天津医科大学总医院、中国人民武装警察部队特色医学中心、河南省人民医院、南京大学鼓楼医院等机构合作发表
Abstract
Genome-wide association studies of brain imaging phenotypes are mainly performed in European populations, but other populations are severely under-represented. Here, we conducted Chinese-alone and cross-ancestry genome-wide association studies of 3,414 brain imaging phenotypes in 7,058 Chinese Han and 33,224 white British participants. We identified 38 new associations in Chinese-alone analyses and 486 additional new associations in cross-ancestry meta-analyses at P<1.46×10−11 for discovery and P<0.05 for replication. We pooled significant autosomal associations identified by single- or cross-ancestry analyses into 6,443 independent associations, which showed uneven distribution in the genome and the phenotype subgroups. We further divided them into 44 associations with different effect sizes and 3,557 associations with similar effect sizes between ancestries. Loci of these associations were shared with 15 brain-related non-imaging traits including cognition and neuropsychiatric disorders. Our results provide a valuable catalog of genetic associations for brain imaging phenotypes in more diverse populations.
摘要：
脑成像表型的全基因组关联研究主要在欧洲人群中进行，但其他人群的代表性严重不足。本研究对7,058名中国汉族和33,224名英国白人参与者的3,414种脑成像表型进行了中国单独和跨祖先全基因组关联研究。在单独的中国人群分析中发现了38个新的关联，在跨祖先荟萃分析中发现了486个额外的新关联。将通过单祖先或交叉祖先分析确定的重要常染色体关联汇总到6,443个独立关联中，这些关联在基因组和表型亚组中分布不均匀。研究进一步将它们分为44个具有不同效应大小的关联和3,557个具有相似效应大小的关联。这些关联的位点与15个与大脑相关的非成像特征共享，包括认知和神经精神疾病。该研究结果为更多样化人群的脑成像表型提供了有价值的遗传关联目录。
4. Spatial genomic, biochemical and cellular mechanisms underlying meningioma heterogeneity and evolution
脑膜瘤异质性和进化的空间基因组、生化和细胞机制
美国约翰霍普金斯大学、加州大学旧金山分校、西北大学
Abstract
Intratumor heterogeneity underlies cancer evolution and treatment resistance, but targetable mechanisms driving intratumor heterogeneity are poorly understood. Meningiomas are the most common primary intracranial tumors and are resistant to all medical therapies, and high-grade meningiomas have significant intratumor heterogeneity. Here we use spatial approaches to identify genomic, biochemical and cellular mechanisms linking intratumor heterogeneity to the molecular, temporal and spatial evolution of high-grade meningiomas. We show that divergent intratumor gene and protein expression programs distinguish high-grade meningiomas that are otherwise grouped together by current classification systems. Analyses of matched pairs of primary and recurrent meningiomas reveal spatial expansion of subclonal copy number variants associated with treatment resistance. Multiplexed sequential immunofluorescence and deconvolution of meningioma spatial transcriptomes using cell types from single-cell RNA sequencing show decreased immune infiltration, decreased MAPK signaling, increased PI3K–AKT signaling and increased cell proliferation, which are associated with meningioma recurrence. To translate these findings to preclinical models, we use CRISPR interference and lineage tracing approaches to identify combination therapies that target intratumor heterogeneity in meningioma cell co-cultures.
摘要：
肿瘤内异质性是癌症进化和治疗耐药性的基础，但驱动瘤内异质性的靶向机制知之甚少。脑膜瘤是最常见的原发性颅内肿瘤，对所有药物治疗均有耐药性，高级别脑膜瘤具有显著的瘤内异质性。本研究使用空间方法来确定将肿瘤内异质性与高级别脑膜瘤的分子、时间和空间进化联系起来的基因组、生化和细胞机制。研究结果发现，不同的肿瘤内基因和蛋白质表达程序可以区分高级别脑膜瘤，否则这些脑膜瘤被当前的分类系统归为一类。对原发性和复发性脑膜瘤配对的分析揭示了与治疗耐药性相关的亚克隆拷贝数变异的空间扩展。使用来自单细胞RNA测序的细胞类型对脑膜瘤空间转录组进行多重连续免疫荧光和去卷积，显示免疫浸润减少、MAPK信号转导减少、PI3K-AKT信号转导增加和细胞增殖增加，这与脑膜瘤复发有关。为了将这些发现转化为临床前模型，使用CRISPR干扰和谱系追踪方法来确定针对脑膜瘤细胞共培养物中肿瘤内异质性的联合疗法。
5. Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells
造血干细胞和祖细胞嵌合结构变异的细胞类型特异性影响
德国欧洲分子生物学实验室、韩国延世大学、德国乌尔姆大学等机构合作发表
Abstract
The functional impact and cellular context of mosaic structural variants (mSVs) in normal tissues is understudied. Utilizing Strand-seq, we sequenced 1,133 single-cell genomes from 19 human donors of increasing age, and discovered the heterogeneous mSV landscapes of hematopoietic stem and progenitor cells. While mSVs are continuously acquired throughout life, expanded subclones in our cohort are confined to individuals >60. Cells already harboring mSVs are more likely to acquire additional somatic structural variants, including megabase-scale segmental aneuploidies. Capitalizing on comprehensive single-cell micrococcal nuclease digestion with sequencing reference data, we conducted high-resolution cell-typing for eight hematopoietic stem and progenitor cells. Clonally expanded mSVs disrupt normal cellular function by dysregulating diverse cellular pathways, and enriching for myeloid progenitors. Our findings underscore the contribution of mSVs to the cellular and molecular phenotypes associated with the aging hematopoietic system, and establish a foundation for deciphering the molecular links between mSVs, aging and disease susceptibility in normal tissues.
摘要：
对正常组织中嵌合结构变异（mSV）的功能影响和细胞背景研究不足。本研究利用Strand-seq，对来自19名年龄增长的人类供体的1,133个单细胞基因组进行了测序，并发现了造血干细胞和祖细胞的异质性mSV景观。虽然mSV在一生中不断获得，但本队列中的扩展亚克隆仅限于个体>60。已经携带mSV的细胞更有可能获得额外的体细胞结构变异，包括兆碱基规模的节段非整倍体。利用全面的单细胞微球菌核酸酶消化和测序参考数据，对八种造血干细胞和祖细胞进行了高分辨率细胞分型。克隆扩增的mSV通过失调多种细胞通路和富集髓系祖细胞来破坏正常的细胞功能。本研究结果强调了mSVs对与衰老造血系统相关的细胞和分子表型的贡献，并为破译mSVs与衰老和正常组织中疾病易感性之间的分子联系奠定了基础。
6. Analysis of somatic mutations in whole blood from 200,618 individuals identifies pervasive positive selection and novel drivers of clonal hematopoiesis
对200,618名个体的全血体细胞突变分析确定了克隆造血的普遍阳性选择和新驱动因素
美国卡利科生命科学有限责任公司、英国威康桑格研究所、剑桥大学
Abstract
Human aging is marked by the emergence of a tapestry of clonal expansions in dividing tissues, particularly evident in blood as clonal hematopoiesis (CH). CH, linked to cancer risk and aging-related phenotypes, often stems from somatic mutations in a set of established genes. However, the majority of clones lack known drivers. Here we infer gene-level positive selection in whole blood exomes from 200,618 individuals in UK Biobank. We identify 17 additional genes, ZBTB33, ZNF318, ZNF234, SPRED2, SH2B3, SRCAP, SIK3, SRSF1, CHEK2, CCDC115, CCL22, BAX, YLPM1, MYD88, MTA2, MAGEC3 and IGLL5, under positive selection at a population level, and validate this selection pattern in 10,837 whole genomes from single-cell-derived hematopoietic colonies. Clones with mutations in these genes grow in frequency and size with age, comparable to classical CH drivers. They correlate with heightened risk of infection, death and hematological malignancy, highlighting the significance of these additional genes in the aging process.
摘要：
人类衰老的标志是分裂组织中出现克隆扩增交织，在血液中尤其明显，如克隆造血（CH）。CH与癌症风险和衰老相关表型有关，通常源于一组已建立基因的体细胞突变。但是，大多数克隆缺乏已知的驱动程序。本研究推断了英国生物样本库中200,618名个体的全血外显子组的基因水平正选择。在群体水平的正选择下鉴定了另外17个基因，ZBTB33、ZNF318、ZNF234、SPRED2、SH2B3、SRCAP、SIK3、SRSF1、CHEK2、CCDC115、CCL22、BAX、YLPM1、MYD88、MTA2、MAGEC3和IGLL5，并在来自单细胞来源的造血菌落的10,837个全基因组中验证这种选择模式。这些基因突变的克隆随着年龄的增长而增加频率和大小，与经典的CH驱动因素相当。它们与感染、死亡和血液系统恶性肿瘤的风险增加相关，突出了这些额外基因在衰老过程中的重要性。
7. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells
顺式基因调控的系统解码定义了人T细胞中多基因共刺激受体位点的上下文依赖性控制
美国加州大学旧金山分校、斯坦福大学、麻省理工学院和哈佛大学
Abstract
Cis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T cell-mediated immunity. Tiling CRISPR interference (CRISPRi) screens in primary human T cells, both conventional and regulatory subsets, uncovered gene-, cell subset- and stimulation-specific CREs. Integration with CRISPR knockout screens and assay for transposase-accessible chromatin with sequencing (ATAC-seq) profiling identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. We then discovered a critical CCCTC-binding factor (CTCF) boundary that reinforces CRE interaction with CTLA4 while also preventing promiscuous activation of CD28. By systematically mapping CREs and associated trans regulators directly in primary human T cell subsets, this work overcomes longstanding experimental limitations to decode context-dependent gene regulatory programs in a complex, multi-gene locus critical to immune homeostasis.
摘要：
顺式调节元件（CRE）与反式调节因子相互作用以协调基因表达，但转录调控在多基因位点中的协调方式尚未通过实验定义。本研究试图表征控制相邻共刺激基因CD28、CTLA4和ICOS动态表达的CRE，这些基因编码T细胞介导的免疫调节因子。在原代人类T细胞（包括常规细胞和调节亚群）中进行平铺CRISPR干扰（CRISPRi）筛选，发现了基因、细胞亚群和刺激特异性CRE。整合CRISPR敲除筛选以及用测序(ATAC-seq)分析转座酶可及染色质测定，鉴定了影响特定CRISPRi反应元件的染色质状态以控制共刺激基因表达的反式调节因子。发现了一个关键的CCCTC结合因子（CTCF）边界，该边界加强了CRE与CTLA4的相互作用，同时还阻止了CD28的混杂激活。通过系统地将CREs和相关的反式调节因子直接定位在原代人类T细胞亚群中，这项工作克服了长期存在的实验局限性，即在对免疫稳态至关重要的复杂多基因位点中解码上下文依赖性基因调控程序。
8. Systematic epigenome editing captures the context-dependent instructive function of chromatin modifications
系统性表观基因组编辑捕获染色质修饰的上下文依赖性指导功能
欧洲分子生物学实验室（EMBL）
Abstract
Chromatin modifications are linked with regulating patterns of gene expression, but their causal role and context-dependent impact on transcription remains unresolved. Here we develop a modular epigenome editing platform that programs nine key chromatin modifications, or combinations thereof, to precise loci in living cells. We couple this with single-cell readouts to systematically quantitate the magnitude and heterogeneity of transcriptional responses elicited by each specific chromatin modification. Among these, we show that installing histone H3 lysine 4 trimethylation (H3K4me3) at promoters can causally instruct transcription by hierarchically remodeling the chromatin landscape. We further dissect how DNA sequence motifs influence the transcriptional impact of chromatin marks, identifying switch-like and attenuative effects within distinct cis contexts. Finally, we examine the interplay of combinatorial modifications, revealing that co-targeted H3K27 trimethylation (H3K27me3) and H2AK119 monoubiquitination (H2AK119ub) maximizes silencing penetrance across single cells. Our precision-perturbation strategy unveils the causal principles of how chromatin modification(s) influence transcription and dissects how quantitative responses are calibrated by contextual interactions.
摘要：
染色质修饰与基因表达的调节模式有关，但它们的因果作用和对转录的上下文依赖性影响仍未解决。本研究开发了一个模块化的表观基因组编辑平台，该平台将九个关键的染色质修饰或其组合编程为活细胞中的精确位点。将其与单细胞读数相结合，以系统地定量每个特定染色质修饰引起的转录反应的幅度和异质性。其中，研究结果表明，在启动子上安装组蛋白H3赖氨酸4三甲基化（H3K4me3） 可以通过分层重塑染色质景观来因果地指导转录。进一步剖析了DNA序列基序如何影响染色质标记的转录影响，确定了不同顺式背景下的开关样和衰减效应。最后，研究了组合修饰的相互作用，揭示了共靶向H3K27三甲基化（H3K27me3）和H2AK119单泛素化（H2AK119ub）最大限度地提高了单细胞的沉默外显率。本研究的精确扰动策略揭示了染色质修饰如何影响转录的因果原理，并剖析了定量反应如何通过上下文相互作用进行校准。
9. Comparative cofactor screens show the influence of transactivation domains and core promoters on the mechanisms of transcription
比较辅因子筛选显示了反式激活结构域和核心启动子对转录机制的影响
澳大利亚彼得·麦卡勒姆癌症中心、墨尔本大学、昆士兰大学等机构合作发表
Abstract
Eukaryotic transcription factors (TFs) activate gene expression by recruiting cofactors to promoters. However, the relationships between TFs, promoters and their associated cofactors remain poorly understood. Here we combine GAL4-transactivation assays with comparative CRISPR–Cas9 screens to identify the cofactors used by nine different TFs and core promoters in human cells. Using this dataset, we associate TFs with cofactors, classify cofactors as ubiquitous or specific and discover transcriptional co-dependencies. Through a reductionistic, comparative approach, we demonstrate that TFs do not display discrete mechanisms of activation. Instead, each TF depends on a unique combination of cofactors, which influences distinct steps in transcription. By contrast, the influence of core promoters appears relatively discrete. Different promoter classes are constrained by either initiation or pause-release, which influences their dynamic range and compatibility with cofactors. Overall, our comparative cofactor screens characterize the interplay between TFs, cofactors and core promoters, identifying general principles by which they influence transcription.
摘要：
真核转录因子（TF）通过将辅助因子募集到启动子来激活基因表达。然而，TFs、启动子及其相关辅因子之间的关系仍然知之甚少。本研究将GAL4反式激活测定与比较CRISPR-Cas9筛选相结合，以鉴定人类细胞中九种不同TF和核心启动子使用的辅助因子。使用该数据集，将TF与辅因子相关联，将辅因子分类为普遍存在或特异性，并发现转录共依赖性。通过还原论的比较方法，证明了TF不显示离散的激活机制。相反，每个TF都依赖于辅因子的独特组合，这会影响转录中的不同步骤。相比之下，核心启动子的影响似乎相对离散。不同的启动子类别受到起始或暂停释放的限制，这会影响它们的动态范围和与辅因子的相容性。总体而言，本研究的比较辅因子筛选表征了TF、辅因子和核心启动子之间的相互作用，确定了它们影响转录的一般原则。
10. Inseparable RNA binding and chromatin modification activities of a nucleosome-interacting surface in EZH2
EZH2中核小体相互作用表面不可分割的RNA结合和染色质修饰活性
澳大利亚莫纳什大学、阿德莱德大学、欧洲分子生物学实验室（EMBL）
Abstract
Polycomb repressive complex 2 (PRC2) interacts with RNA in cells, but there is no consensus on how RNA regulates PRC2 canonical functions, including chromatin modification and the maintenance of transcription programs in lineage-committed cells. We assayed two separation-of-function mutants of the PRC2 catalytic subunit EZH2, defective in RNA binding but functional in methyltransferase activity. We find that part of the RNA-binding surface of EZH2 is required for chromatin modification, yet this activity is independent of RNA. Mechanistically, the RNA-binding surface within EZH2 is required for chromatin modification in vitro and in cells, through interactions with nucleosomal DNA. Contrarily, an RNA-binding-defective mutant exhibited normal chromatin modification activity in vitro and in lineage-committed cells, accompanied by normal gene repression activity. Collectively, we show that part of the RNA-binding surface of EZH2, rather than the RNA-binding activity per se, is required for the histone methylation in vitro and in cells, through interactions with the substrate nucleosome.
摘要：
Polycomb抑制复合物2（PRC2）与细胞中的RNA相互作用，但关于RNA如何调节PRC2规范功能（包括染色质修饰和维持谱系细胞中的转录程序）尚未达成共识。本研究测定了PRC2催化亚基EZH2的两个功能分离突变体，它们在RNA结合中存在缺陷，但在甲基转移酶活性中起作用。发现EZH2的部分RNA结合表面是染色质修饰所必需的，但这种活性与RNA无关。从机制上讲，EZH2内的RNA结合表面是体外和细胞中通过与核小体DNA的相互作用进行染色质修饰所必需的。相反，RNA结合缺陷突变体在体外和谱系结合细胞中表现出正常的染色质修饰活性，并伴有正常的基因抑制活性。总的来说，本研究表明，通过与底物核小体的相互作用，EZH2的部分RNA结合表面，而不是RNA结合活性本身，是体外和细胞中组蛋白甲基化所必需的。
11. Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF
对ISWI亚基的系统评估表明NURF为CTCF创造了局部可及性
瑞士弗里德里希·米歇尔生物医学研究所、巴塞尔大学、瑞士生物信息学研究所
Abstract
Catalytic activity of the imitation switch (ISWI) family of remodelers is critical for nucleosomal organization and DNA binding of certain transcription factors, including the insulator protein CTCF. Here we define the contribution of individual subcomplexes by deriving a panel of isogenic mouse stem cell lines, each lacking one of six ISWI accessory subunits. Individual deletions of subunits of either CERF, RSF, ACF, WICH or NoRC subcomplexes only moderately affect the chromatin landscape, while removal of the NURF-specific subunit BPTF leads to a strong reduction in chromatin accessibility and SNF2H ATPase localization around CTCF sites. This affects adjacent nucleosome occupancy and CTCF binding. At a group of sites with reduced chromatin accessibility, CTCF binding persists but cohesin occupancy is reduced, resulting in decreased insulation. These results suggest that CTCF binding can be separated from its function as an insulator in nuclear organization and identify a specific role for NURF in mediating SNF2H localization and chromatin opening at bound CTCF sites.
摘要：
重塑基因的模拟开关（ISWI）家族的催化活性对于某些转录因子（包括绝缘体蛋白CTCF）的核小体组织和DNA结合至关重要。本研究通过推导一组同基因小鼠干细胞系来定义单个亚复合物的贡献，每个系都缺少六个ISWI辅助亚基中的一个。CERF、RSF、ACF、WICH或NoRC亚复合物亚基的单独缺失仅对染色质景观产生适度影响，而去除NURF特异性亚基BPTF会导致染色质可及性和CTCF位点周围SNF2H ATP酶定位的显著降低。这会影响相邻核小体的占有率和CTCF结合。在染色质可及性降低的一组位点，CTCF结合持续存在，但粘连蛋白占有率降低，导致绝缘性降低。这些结果表明，CTCF结合可以与其在核组织中作为绝缘体的功能分开，并确定NURF在介导SNF2H定位和结合CTCF位点染色质打开中的特定作用。
12. Genome folding principles uncovered in condensin-depleted mitotic chromosomes
在凝聚素耗尽的有丝分裂染色体中发现的基因组折叠原理
深圳湾实验室分子生理研究所、汕头大学、首都医科大学、华南理工大学、香港大学、美国宾夕法尼亚大学等机构合作发表
Abstract
During mitosis, condensin activity is thought to interfere with interphase chromatin structures. To investigate genome folding principles in the absence of chromatin loop extrusion, we codepleted condensin I and condensin II, which triggered mitotic chromosome compartmentalization in ways similar to that in interphase. However, two distinct euchromatic compartments, indistinguishable in interphase, emerged upon condensin loss with different interaction preferences and dependencies on H3K27ac. Constitutive heterochromatin gradually self-aggregated and cocompartmentalized with facultative heterochromatin, contrasting with their separation during interphase. Notably, some cis-regulatory element contacts became apparent even in the absence of CTCF/cohesin-mediated structures. Heterochromatin protein 1 (HP1) proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M to G1 phase in the combined absence of HP1α, HP1β and HP1γ, constitutive heterochromatin compartments are normally re-established. In sum, condensin-deficient mitotic chromosomes illuminate forces of genome compartmentalization not identified in interphase cells.
摘要：
在有丝分裂过程中，凝聚素活性被认为会干扰间期染色质结构。为了研究在没有染色质环挤出的情况下基因组折叠原理，本研究编码了凝聚素I和凝聚素II，它们以类似于间期的方式触发有丝分裂染色体区室化。然而，在凝聚素丢失时出现了两个不同的常染色体区室，在间期无法区分，具有不同的相互作用偏好和对H3K27ac的依赖性。组成型异染色质逐渐自聚集并与兼性异染色质共区室，与它们在间期的分离形成鲜明对比。值得注意的是，即使在没有CTCF/粘连蛋白介导的结构的情况下，一些顺式调节元件的接触也变得明显。异染色质蛋白1（HP1）蛋白被认为可以分裂组成型异染色质，但有丝分裂染色质中不存在，这表明，令人惊讶的是，组成型异染色质可以在没有HP1的情况下自我聚集。事实上，在HP1α、HP1β和HP1γ联合缺失的情况下，在从M期到G1期的细胞中，组成型异染色质区室通常会重新建立。总之，凝聚素缺陷的有丝分裂染色体阐明了在间期细胞中未发现的基因组区室化力量。
13. High-throughput fitness experiments reveal specific vulnerabilities of human-adapted Salmonella during stress and infection
高通量适应性实验揭示了人类适应沙门氏菌在应激和感染期间的特定脆弱性
美国斯坦福大学、波士顿学院、利物浦大学、爱尔兰都柏林圣三一学院
Abstract
Salmonella enterica is comprised of genetically distinct ‘serovars’ that together provide an intriguing model for exploring the genetic basis of pathogen evolution. Although the genomes of numerous Salmonella isolates with broad variations in host range and human disease manifestations have been sequenced, the functional links between genetic and phenotypic differences among these serovars remain poorly understood. Here, we conduct high-throughput functional genomics on both generalist (Typhimurium) and human-restricted (Typhi and Paratyphi A) Salmonella at unprecedented scale in the study of this enteric pathogen. Using a comprehensive systems biology approach, we identify gene networks with serovar-specific fitness effects across 25 host-associated stresses encountered at key stages of human infection. By experimentally perturbing these networks, we characterize previously undescribed pseudogenes in human-adapted Salmonella. Overall, this work highlights specific vulnerabilities encoded within human-restricted Salmonella that are linked to the degradation of their genomes, shedding light into the evolution of this enteric pathogen.
摘要：
肠道沙门氏菌由遗传上不同的“血清型”组成，它们共同为探索病原体进化的遗传基础提供了一个有趣的模型。尽管已经对宿主范围和人类疾病表现存在广泛差异的许多沙门氏菌分离株的基因组进行了测序，但这些血清型之间的遗传和表型差异之间的功能联系仍然知之甚少。本研究对通用型（鼠伤寒）和人类限制性（伤寒和副伤寒A）沙门氏菌进行了以前该类肠道病原体研究从未有的规模的高通量功能基因组学。使用全面的系统生物学方法，在人类感染的关键阶段遇到的25种宿主相关压力中鉴定了具有血清型特异性适应性效应的基因网络。通过实验扰动这些网络，表征了人类适应的沙门氏菌中以前未描述的假基因。总体而言，这项工作突出了人类限制性沙门氏菌中编码的特定脆弱性，这些脆弱性与其基因组的退化有关，从而揭示了这种肠道病原体的进化。
汇报人：张宇阳
导师：赵宇
编辑：
审核：宋瑶、任建君
