【Nature Genetics】2025年7-8月刊论文导读
期刊介绍：
Nature Genetics 创刊于1992年，是Springer Nature旗下聚焦遗传学与基因组学的顶级月刊。该期刊覆盖人类与模式生物的遗传变异、群体遗传学、功能基因组学、表观遗传学、基因组技术与计算生物学等多学科领域，最新影响因子为31.8。本期文献导读将呈现2025年7至8月期间发表的研究亮点。
本期共发表论著47篇，其中包括其中包括生物医学相关论著23篇。
1.herapeutic strategies for fragile X syndrome and implications for other gene-silencing disorders
脆性X综合征治疗策略及其对其他基因沉默疾病的启示
以色列耶路撒冷希伯来大学西尔伯曼生命科学研究所遗传学系阿兹里埃利干细胞和基因研究中心
Fragile X syndrome (FXS) is the most prevalent gene-silencing disorder, caused by CGG-repeat expansion in the 5′-UTR of FMR1, leading to hyper-methylation and transcriptional silencing. We review human pluripotent-stem-cell-based models (ESC, iPSC, neural progenitor, organoid) that faithfully recapitulate the epigenetic switch of FMR1 from active to silent during differentiation. We highlight CRISPR-based repeat contraction, dCas9-TET1/VP192-mediated demethylation/activation, small-molecule screens and genome-wide CRISPR knockout screens that achieve ≥80 % FMR1 re-activation and FMRP restoration. We extend these lessons to repeat-expansion (FRAXE, Friedreich ataxia), X-linked (Rett, IP) and imprinting disorders (Angelman, Prader–Willi), advocating gene re-activation as a universal therapeutic paradigm while addressing specificity, delivery and off-target challenges.
脆性X综合征（FXS）是最常见的基因沉默病，由FMR1基因5′-UTR的CGG重复扩增导致高甲基化与转录沉默。该文综述了人类多能干细胞模型（ESC、iPSC、神经祖细胞、类器官）如何忠实再现FMR1由活跃到沉默的表观遗传转换。文章重点介绍了CRISPR介导的重复收缩、dCas9-TET1/VP192去甲基化/激活、小分子筛选及全基因组CRISPR敲除筛选，可实现≥80 %的FMR1再激活与FMRP恢复。研究将经验推广至重复扩增型（FRAXE、弗里德赖希共济失调）、X连锁型（Rett、IP）及印记型（天使、普-威）疾病，提出基因再激活作为通用治疗范式，并讨论特异性、递送及脱靶挑战。
2.A contextual genomic perspective on physical activity and its relationship to health, well being and illness.
身体活动的基因组情境视角及其与健康、福祉和疾病的关系
美国康涅狄格州退伍军人事务部医疗保健系统
Physical activity (PA) is one of the most fundamental traits in the animal kingdom, has pervasive health benefits, and is genetically influenced. Using data from the Million Veteran Program, we conducted genetic analyses of leisure, work and home-time PA. For leisure, we included 189,812 individuals of European ancestry (SNP-based heritability (h²) = 0.083 ± 0.005), 27,044 of African ancestry (h² = 0.034 ± 0.017) and 10,263 of Latin American ancestry (h² = 0.083 ± 0.036) in a cross-ancestry meta-analysis with UK Biobank data, identifying 70 lead variants. Leisure-time PA was genetically distinct from PA at home or work, with the latter two showing less health benefit with respect to health outcomes and lifespan. Mendelian randomization analyses showed a protective role of leisure-time PA against COVID-19 hospitalization (β = −0.067 ± 0.016; P = 2.8 × 10⁻⁵), and with other traits including cardiovascular and respiratory system diseases, metabolic traits and aging. These findings provide new insights into the biology of PA, showing specific causal health benefits of leisure-time PA.
身体活动（PA）是动物界最基本的特征之一，具有广泛的健康益处，并受遗传因素影响。作者利用“百万退伍军人计划”的数据，对休闲、工作及居家时间的身体活动进行了遗传分析。在休闲活动方面，研究纳入了189,812名欧洲裔个体（基于SNP的遗传力 h² = 0.083 ± 0.005）、27,044名非洲裔个体（h² = 0.034 ± 0.017）以及10,263名拉丁美洲裔个体（h² = 0.083 ± 0.036），与英国生物样本库的数据进行跨族裔荟萃分析，共鉴定出70个主要变异位点。从遗传角度看，休闲时间的身体活动与在家或工作中的身体活动存在显著差异，后两者在健康结果和寿命方面的益处较少。孟德尔随机化分析表明，休闲时间的身体活动对COVID-19住院具有保护作用（β = −0.067 ± 0.016；P = 2.8 × 10⁻⁵），并与心血管和呼吸系统疾病、代谢特征及衰老等其他性状相关。这些发现为身体活动的生物学机制提供了新的见解，揭示了休闲时间身体活动对健康的特定因果益处。
3.Single-cell and spatial transcriptomics reveal mechanisms of radioresistance and immune escape in recurrent nasopharyngeal carcinoma
单细胞与空间转录组学揭示复发性鼻咽癌放疗抵抗及免疫逃逸的机制
中山大学附属第五医院鼻咽癌中心
Radiotherapy resistance and immune evasion are prominent features of recurrent nasopharyngeal carcinoma (rNPC). However, their mechanisms remain incompletely understood. Here, we conducted single-cell and spatial transcriptomics analysis of 39 tumors from 24 patients to reveal the microenvironmental differences between primary and rNPC. Specific MCAM⁺ cancer-associated fibroblasts are significantly enriched in rNPC, where they promote tumor radioresistance through the collagen IV–ITGA2–FAK–AKT axis. Furthermore, we found that collagen IV suppresses the infiltration of T cells, and we identified mechanisms of immune escape in rNPC. We uncovered the presence and function of CD8⁺ZNF683⁺ cells in rNPC with lower cytotoxicity. The abundance of B cells and tertiary lymphoid structures significantly diminishes in rNPC. Finally, we confirmed that CD47–SIRPα commonly existed between myeloid and malignant cells in rNPC. This study provides an in-depth understanding of the mechanism of radioresistance and immune evasion in rNPC as well as highlighting critical preliminary targets for curing rNPC.
放疗抵抗与免疫逃逸是复发性鼻咽癌（rNPC）的显著特征，但其机制仍不清楚。该研究对24例患者的39个肿瘤进行了单细胞与空间转录组学分析，揭示了原发与复发肿瘤微环境的差异。复发性鼻咽癌中特异性富集MCAM⁺癌症相关成纤维细胞，其通过胶原IV–ITGA2–FAK–AKT轴促进肿瘤放疗抵抗。此外，研究发现胶原IV抑制T细胞浸润，并鉴定出rNPC的免疫逃逸机制。研究还揭示了CD8⁺ZNF683⁺细胞在rNPC中的存在及其低细胞毒性的功能，B细胞及三级淋巴结构的丰度在rNPC中显著下降。最后，证实CD47–SIRPα轴在rNPC的髓系细胞与恶性细胞之间普遍存在。该研究深入解析了rNPC放疗抵抗和免疫逃逸的机制，并为治愈rNPC提供了关键的前期靶点。
4.NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling
NKX2-1通过表观遗传与三维染色质重塑驱动前列腺癌神经内分泌转分化
美国佐治亚州亚特兰大埃默里大学医学院泌尿外科
A substantial amount of castration-resistant prostate cancer (CRPC) progresses into a neuroendocrine (NE) subtype, known as NEPC, which is associated with poor clinical outcomes. Here we report distinct three-dimensional chromatin architectures between NEPC and CRPC tumors, which were recapitulated by isogenic cell lines undergoing NE transformation (NET). Mechanistically, pioneer factors such as FOXA2 initiate binding at NE enhancers to mediate regional DNA demethylation and induce neural transcription factor (TF) NKX2-1 expression. NKX2-1 preferentially binds gene promoters and interacts with enhancer-bound FOXA2 through chromatin looping. NKX2-1 is highly expressed in NEPC and indispensable for NET of prostate cancer. NKX2-1/FOXA2 further recruits p300/CBP to activate NE enhancers, and pharmacological inhibition of p300/CBP effectively blunts NE gene expression and abolishes NEPC tumor growth. Taken together, our study reports a hierarchical network of TFs governed by NKX2-1 in critically regulating chromatin remodeling and driving luminal-to-NE transformation and suggests promising therapeutic approaches to mitigate NEPC.
大量去势抵抗性前列腺癌（CRPC）会进展为神经内分泌亚型（NEPC），临床预后极差。研究首次发现NEPC与CRPC肿瘤具有截然不同的三维染色质构象，并在发生神经内分泌转化（NET）的同源细胞系中复现这一特征。机制上，先驱因子FOXA2率先结合于神经内分泌增强子，介导局部DNA去甲基化并诱导神经转录因子NKX2-1的表达。NKX2-1优先结合基因启动子，并通过染色质环化与增强子上的FOXA2相互作用。NKX2-1在NEPC中高表达，对前列腺癌的NET至关重要。NKX2-1/FOXA2进一步招募p300/CBP激活神经内分泌增强子，而药理学抑制p300/CBP可有效削弱NE基因表达并抑制NEPC肿瘤生长。综上，该研究揭示了由NKX2-1主导的转录因子层级网络，该网络通过染色质重塑驱动NEPC腔面型向神经内分泌型转化，并为缓解NEPC提供了有前景的治疗策略。
5.Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk
改进的多族裔精确定位揭示调控分子性状与疾病风险的顺式调控变异
美国南加州大学凯克医学院遗传流行病学中心
Multiancestry statistical fine-mapping of cis-molecular quantitative trait loci (cis-molQTL) aims to improve the precision of distinguishing causal cis-molQTLs from tagging variants. Here we present the sum of shared single effects (SuShiE) model, which leverages linkage disequilibrium heterogeneity to improve fine-mapping precision, infer cross-ancestry effect size correlations and estimate ancestry-specific expression prediction weights. Through extensive simulations, we find that SuShiE consistently outperforms existing methods. We apply SuShiE to 36,907 molecular phenotypes including mRNA expression and protein levels from individuals of diverse ancestries in the TOPMed-MESA and GENOA studies. SuShiE fine-maps cis-molQTLs for 18.2% more genes compared with existing methods while prioritizing fewer variants and exhibiting greater functional enrichment. While SuShiE infers highly consistent cis-molQTL architectures across ancestries, it finds evidence of heterogeneity at genes with predicted loss-of-function intolerance. Lastly, using SuShiE-derived cis-molQTL effect sizes, we perform transcriptome- and proteome-wide association studies on six white blood cell-related traits in the All of Us biobank and identify 25.4% more genes compared with existing methods. Overall, SuShiE provides new insights into the cis-genetic architecture of molecular traits.
多族裔顺式分子数量性状位点（cis-molQTL）的精细定位旨在提高区分因果cis-molQTL与标签变异的精度。研究开发了“共享单效应总和”（SuShiE）模型，利用连锁不平衡的异质性提升定位精度，推断跨族裔效应大小相关性，并估计族裔特异的表达预测权重。大量模拟显示SuShiE始终优于现有方法。研究将SuShiE应用于TOPMed-MESA与GENOA研究中36,907个分子表型（包括mRNA表达与蛋白水平），涵盖多族裔个体。与现有方法相比，SuShiE可多精确定位18.2%基因的cis-molQTL，且优先筛选的变异更少、功能富集度更高。尽管SuShiE推断的cis-molQTL结构在族裔间高度一致，但在预测为不耐受功能缺失的基因中发现了异质性证据。最后，利用SuShiE推导的cis-molQTL效应值，研究在All of Us生物样本库中对六种白细胞相关性状进行转录组与蛋白质组范围关联研究，识别的基因数比现有方法增加25.4%。总体而言，SuShiE为分子性状的顺式遗传架构提供了新见解。
6.G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing
G-四链体作为启动子元件调控核小体排斥与RNA聚合酶II暂停
法国蒙彼利埃大学分子总理研究所
Despite their central role in transcription, it has been difficult to define universal sequences associated with eukaryotic promoters. Within the chromatin context, recruitment of transcriptional machinery requires promoter opening, but how DNA elements contribute to this process is unclear. Here we show that G-quadruplex (G4) secondary DNA structures are highly enriched at mammalian promoters. G4s are located at the deepest point of nucleosome exclusion at promoters and correlate with maximum promoter activity. We found that experimental G4s exclude nucleosomes in vivo and in vitro while favouring strong positioning. At model promoters, impairing G4s affected both transcriptional activity and chromatin opening. G4 destabilization also resulted in an inactive promoter state and affected the transition to effective RNA production. Finally, G4 stabilization resulted in global reduction of proximal promoter pausing. Altogether, our data introduce G4s as bona fide promoter elements allowing nucleosome exclusion and facilitating pause–release by RNA polymerase II.
尽管启动子在转录中居于核心地位，但一直难以界定与真核启动子相关的通用序列。在染色质环境中，转录机器的招募需要启动子区域开放，然而DNA元件如何参与此过程尚不清楚。研究发现G-四链体（G4）二级DNA结构在哺乳动物启动子中高度富集。G4位于启动子核小体排斥最深的位置，并与最大启动子活性相关。实验表明，G4在体内外均能排斥核小体并促进其精确定位。在模型启动子中，破坏G4会同时影响转录活性与染色质开放。G4去稳定化导致启动子失活，并阻碍有效RNA生成的过渡。反之，G4稳定化显著减少近端启动子暂停。综上，研究提出G4是公认的启动子元件，可排斥核小体并促进RNA聚合酶II的暂停-释放。
7.Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution
单细胞分辨率多层组学数据解析状态依赖的免疫特征
日本大阪大学医学研究生院统计遗传学系
Current molecular quantitative trait locus catalogs are mostly at bulk resolution and centered on Europeans. Here, we constructed an immune cell atlas with single-cell transcriptomics of >1.5 million peripheral blood mononuclear cells, host genetics, plasma proteomics and gut metagenomics from 235 Japanese persons, including patients with coronavirus disease 2019 (COVID-19) and healthy individuals. We mapped germline genetic effects on gene expression within immune cell types and across cell states. We elucidated cell type- and context-specific human leukocyte antigen (HLA) and genome-wide associations with T and B cell receptor repertoires. Colocalization using dynamic genetic regulation provided better understanding of genome-wide association signals. Differential gene and protein expression analyses depicted cell type- and context-specific effects of polygenic risks. Various somatic mutations including mosaic chromosomal alterations, loss of Y chromosome and mitochondrial DNA (mtDNA) heteroplasmy were projected into single-cell resolution. We identified immune features specific to somatically mutated cells. Overall, immune cells are dynamically regulated in a cell state-dependent manner characterized with multiomic profiles.
现有分子数量性状位点目录多为群体水平且以欧洲人群为中心。研究通过单细胞转录组学，从235名日本人（含COVID-19患者与健康人）构建了免疫细胞图谱，整合>150万外周血单核细胞、宿主遗传、血浆蛋白质组及肠道宏基因组数据。研究在免疫细胞类型及细胞状态层面绘制了胚系遗传对基因表达的效应图谱，阐明了细胞类型与情境特异的HLA及全基因组与T/B细胞受体库的关联。利用动态遗传调控共定位，更深入地理解了全基因组关联信号。差异基因与蛋白表达分析描绘了多基因风险在细胞类型与情境中的特异效应。多种体细胞突变（包括嵌合染色体改变、Y染色体丢失及线粒体DNA异质性）被映射到单细胞分辨率。研究鉴定了体细胞突变细胞特异的免疫特征。总体而言，免疫细胞以细胞状态依赖的方式受到多层组学特征的动态调控。
8.Massively parallel immunopeptidome by DNA sequencing provides insights into cancer antigen presentation
DNA测序大规模并行免疫肽组学揭示癌症抗原呈递机制
美国加利福尼亚州斯坦福斯坦福大学皮肤科
Human leukocyte antigens (HLAs) are encoded by the most polymorphic genes in the human genome. HLA class I alleles control antigen presentation for T cell recognition, which is pivotal for autoimmunity, infectious diseases and cancer. Current knowledge of HLA-bound peptides is limited, skewed and falls short of population-wide HLA binding profiles for high-value targets. Here we present ESCAPE-seq (enhanced single-chain antigen presentation sequencing), a massively parallel platform for comprehensive screening of class I HLA–peptide combinations for antigen presentation via deep DNA sequencing. ESCAPE-seq demonstrates programmability, high throughput, sensitivity and nominated viral and cancer epitopes. We simultaneously assessed over 75,000 peptide–HLA combinations, revealing broadly presented epitopes from oncogenic driver mutations and fusions across diverse HLA-A, HLA-B and HLA-C alleles that cover 90% of the human population. We further identified epitopes that are differentially presented, comparing oncogenic hotspot mutations versus wild type. ESCAPE-seq enables one-shot population-wide antigen presentation discovery, offering insights into HLA specificity and immune recognition of genomic mutations.
人类白细胞抗原（HLA）由人类基因组中最多态的基因编码。HLA I类等位基因控制抗原呈递以供T细胞识别，对自身免疫、感染性疾病及癌症至关重要。目前对HLA结合肽段的认知有限、偏向性大，且缺乏覆盖全人群的HLA结合图谱。研究提出ESCAPE-seq（增强单链抗原呈递测序），一种基于深度DNA测序的大规模并行平台，可全面筛查I类HLA-肽段组合的抗原呈递能力。ESCAPE-seq具备可编程、高通量、高灵敏度，可提名病毒与肿瘤表位的优点。研究并行评估了超过75,000种肽段–HLA组合，揭示了覆盖90%人群的HLA-A、-B、-C等位基因广泛呈递的来源于癌基因驱动突变及融合蛋白的表位。研究还鉴定了癌基因热点突变与野生型之间差异呈递的表位。ESCAPE-seq实现一次性全人群抗原呈递发现，为HLA特异性及基因组突变的免疫识别提供了深刻见解。
9.Insights into Yersinia pestis evolution through rearrangement analysis of 242 complete genomes通过242个完整基因组的重排分析洞察鼠疫耶尔森菌的进化
中国军事医学科学院病原体与生物安全国家重点实验室
Yersinia pestis, the bacterium that causes the plague, has a dynamic genome with highly conserved fragments prone to rearrangement, influencing gene function and evolution. However, understanding these patterns is limited by few complete genomes and analytical methods. We developed a dual-validation strategy to analyze 242 complete genomes of Y. pestis natural isolates from diverse phylogroups. We detected 459 rearrangements, which enhanced phylogenetic resolution and resolved the third pandemic's polytomy. Rearrangements are primarily mediated by four common insertion sequences, with IS1661 and IS100 showing the highest activity. These rearrangements are under strong positive selection, evidenced by 43 hotspots and convergent evolution in the rpsO-pnp operon, whose disruptions and reconnections altered gene expressions and temperature stress responses. We also identified unique structural alterations in human avirulent phylogroups, inactivating three genes and reordering 17 intergenic regions, some affecting virulence-related genes. This study provides a fresh perspective on Y. pestis evolution, revealing experimental targets and establishing a methodology for microbes with frequent rearrangements.
鼠疫耶尔森菌（Yersinia pestis）是鼠疫的病原体，其基因组在高度保守的片段中易发生重排，从而影响基因功能与进化。然而，受限于完整基因组数量和解析方法，对这些模式的理解仍不充分。该研究开发了一种双重验证策略，分析了来自不同系统发育群的242个自然分离株的完整基因组，共检测到459次重排事件，显著提升了系统发育分辨率并解决了第三次大流行的多歧分支问题。重排主要由四种常见插入序列介导，其中IS1661和IS100活性最高。这些重排受到强烈的正选择作用，表现为43个热点区域以及rpsO-pnp操纵子中的趋同进化，其断裂与重连改变了基因表达和温度胁迫响应。此外，研究在人类无毒系统发育群中发现独特的结构变异，导致三个基因失活并重新排列17个基因间区，其中一些影响毒力相关基因。该研究为理解鼠疫菌进化提供了新视角，揭示了实验靶点，并为频繁发生重排的微生物建立了研究方法。
10.Uncovering the multivariate genetic architecture of frailty with genomic structural equation modeling基于基因组结构方程模型揭示衰弱的多变量遗传结构
美国科罗拉多大学博尔德分校行为遗传学研究所
Frailty is a multifaceted clinical state associated with accelerated aging and adverse health outcomes. Informed etiological models of frailty hold promise for producing widespread health improvements across the aging population. Frailty is currently measured using aggregate scores, which obscure etiological pathways that are only relevant to subcomponents of frailty. Here we perform a multivariate genome-wide association study of the latent genetic architecture between 30 frailty deficits, which identifies 408 genomic risk loci. Our model includes a general factor of genetic overlap across all deficits, plus six new factors indexing a shared genetic signal across specific groups of deficits. We demonstrate the added clinical and etiological value of the six factors, including predicting frailty in external datasets, highlighting divergent genetic correlations with clinically relevant outcomes and uncovering unique underlying biology linked to aging. We show that nuanced models of frailty are key to understanding its causes and how it relates to worse health.
衰弱是一种与加速衰老和不良健康结局相关的多维临床状态。构建具备病因学依据的衰弱模型有望在整个老龄人群中实现广泛的健康改善。目前衰弱通过综合评分评估，掩盖了仅与衰弱子成分相关的病因途径。该研究对30项衰弱缺陷之间的潜在遗传结构开展多变量全基因组关联研究，鉴定出408个基因组风险位点。模型包含一个涵盖所有缺陷的遗传重叠一般因子，以及六个新因子，这些因子分别对应特定缺陷组的共享遗传信号。研究证明了这六个因子在临床和病因学上的附加价值：可在外部数据集中预测衰弱，与临床相关结局呈现不同的遗传相关性，并揭示与衰老相关的独特生物学基础。研究表明，精细的衰弱模型是理解其病因及其与更差健康关系的关键。
11.Single-nucleus chromatin accessibility profiling identifies cell types and functional variants contributing to major depression单核染色质可及性图谱鉴定与重性抑郁障碍相关的细胞类型与功能性变异
加拿大麦吉尔大学道格拉斯研究所精神病学系自杀研究小组
Genetic variants associated with major depressive disorder (MDD) are enriched in the regulatory genome. Here, we investigate gene-regulatory mechanisms underlying MDD compared to neurotypical controls by combining single-cell chromatin accessibility with gene expression in over 200,000 cells from the dorsolateral prefrontal cortex of 84 individuals. MDD-associated alterations in chromatin accessibility were prominent in deep-layer excitatory neurons characterized by transcription factor (TF) motif accessibility and binding of NR4A2, an activity-dependent TF reactive to stress. The same neurons were enriched for MDD-associated genetic variants, disrupting TF binding sites linked to genes that likely affect synaptic communication. Furthermore, a gray matter microglia cluster exhibited decreased accessibility in individuals with MDD at binding sites bound by TFs known to regulate immune homeostasis. Finally, we identified gene-regulatory effects of MDD-risk variants using sequence-based accessibility predictions, donor-specific genotypes and cell-based assays. These findings shed light on the cell types and regulatory mechanisms through which genetic variation may increase the risk of MDD.
与重性抑郁障碍（MDD）相关的遗传变异在调控基因组中富集。该研究结合单细胞染色质可及性与基因表达，对84名个体的背外侧前额叶皮层逾20万个细胞进行分析，以探究MDD相较于神经典型对照的基因调控机制。MDD相关的染色质可及性改变在深部兴奋性神经元中最为显著，这些神经元以转录因子（TF）基序可及性及应激反应性活动依赖转录因子NR4A2的结合为特征。同一神经元群体中富集了MDD相关遗传变异，这些变异破坏了与突触通讯相关基因的TF结合位点。此外，在MDD个体的灰质小胶质细胞簇中，调控免疫稳态的TF结合位点可及性降低。最后，研究利用序列可及性预测、供体特异基因型及细胞实验鉴定了MDD风险变异的基因调控效应。这些发现揭示了可能通过遗传变异增加MDD风险的细胞类型与调控机制。
12.Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states全面转录因子扰动重现成纤维细胞转录状态
美国纪念斯隆凯特琳癌症中心计算和系统生物学项目
Cell atlas projects have revealed that common cell types often comprise distinct, recurrent transcriptional states, but the function and regulation of these states remain poorly understood. Here, we show that systematic activation of transcription factors can recreate such states in vitro, providing tractable models for mechanistic and functional studies. Using a scalable CRISPR activation (CRISPRa) Perturb-seq platform, we activated 1,836 transcription factors in two cell types. CRISPRa induced gene expression within physiological ranges, with chromatin features predicting responsiveness. Comparisons with atlas datasets showed that transcription factor perturbations recapitulated key fibroblast states and identified their regulators, including KLF2 and KLF4 for a universal state present in many tissues, and PLAGL1 for a disease-associated inflammatory state. Inducing the universal state suppressed the inflammatory state, suggesting therapeutic potential. These findings position CRISPRa as a nuanced tool for perturbing differentiated cells and establish a general strategy for studying clinically relevant transcriptional states ex vivo.
细胞图谱项目表明，常见细胞类型往往包含不同且反复出现的转录状态，但其功能与调控机制仍不清楚。该研究证明，通过系统性激活转录因子可在体外重现这些状态，为机制与功能研究提供可操作模型。研究利用可扩展的CRISPR激活（CRISPRa）Perturb-seq平台，在两种细胞中激活了1,836个转录因子。CRISPRa诱导的基因表达处于生理范围内，染色质特征可预测响应性。与图谱数据比对显示，转录因子扰动重现了关键成纤维细胞状态及其调控因子，包括介导多种组织共有普遍状态的KLF2和KLF4，以及介导疾病相关炎症状态的PLAGL1。诱导普遍状态可抑制炎症状态，提示治疗潜力。这些结果确立了CRISPRa作为扰动分化细胞的精细工具，并建立了体外研究临床相关转录状态的通用策略。
13.Noncoding rare variant associations with blood traits in 166,740 UK Biobank genomes166,740例英国生物银行基因组中非编码罕见变异与血液性状的关联
瑞士洛桑洛桑大学计算生物学系
Large biobanks with whole-genome sequencing (WGS) now enable the association of noncoding rare variants with complex human traits. Given that >98 % of the genome is available for exploration, the selection of noncoding variants remains a critical yet unresolved challenge in these analyses. Here we leverage knowledge of blood gene regulation and deleteriousness scores to select noncoding variants pertinent for association with blood-related traits. Integrating WGS and 42 blood cell count and biomarker measurements for 166,740 UK Biobank samples, we perform variant collapsing tests, identifying hundreds of gene-trait associations involving noncoding variants. However, we demonstrate that most of these noncoding rare variant associations (1) reproduce associations known from previous studies and (2) are driven by linkage disequilibrium between nearby common and rare variants. This study underscores the prevailing challenges in rare variant analysis and the need for caution when interpreting noncoding rare variant association results.
拥有全基因组测序（WGS）的大型生物银行现已支持非编码罕见变异与复杂性状的关联研究。鉴于>98%的基因组可供探索，如何筛选非编码变异仍是分析中的关键且未解决的难题。该研究利用血液基因调控知识与有害性评分，筛选与血液性状相关的非编码罕见变异。整合166,740名英国生物银行样本的WGS数据及42项血细胞计数和生物标志物测量，研究开展变异折叠检验，鉴定出数百个涉及非编码变异的基因-性状关联。然而，研究证明这些非编码罕见变异关联大多（1）重复了既往已知的关联结果，且（2）由邻近常见变异与罕见变异之间的连锁不平衡驱动。该研究强调了罕见变异分析仍面临的挑战，并警示在解读非编码罕见变异关联结果时需谨慎。
14.Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas跨物种单细胞肾脏图谱中个体患者通路协调分析
美国宾夕法尼亚州费城宾夕法尼亚大学佩雷尔曼医学院医学系肾脏、电解质和高血压科
The use of single-cell RNA sequencing in clinical and translational research is limited by the challenge of identifying cell-type-specific, targetable molecular changes in individual patients and cross-species differences. Here we created an integrated single-cell kidney atlas including over 1 million cells from 140 samples, defining more than 70 conserved cell states in human and rodent models. We developed CellSpectra, a computational tool that quantifies changes in gene expression coordination across cellular functions, which we applied to kidney and lung cancer data. This tool powers our patient-level single-cell functional profiling report, which highlights cell-type-specific changes in the coordination of pathway gene expression in individuals. Our cross-species atlas facilitates the selection of a rodent model that closely reflects the cellular and pathway-level signatures observed in patient samples, advancing the application of single-cell methodologies in clinical precision medicine. Finally, using experimental models, we demonstrate how our informatics approach can be applied for the potential selection of suitable therapeutics.
单细胞RNA测序在临床与转化研究中的应用受限于难以识别个体患者中细胞类型特异、可靶向的分子变化及跨物种差异。该研究构建了整合的单细胞肾脏图谱，涵盖140份样本逾100万个细胞，定义了人和啮齿模型中70余种保守细胞状态。研究开发了计算工具CellSpectra，可量化基因表达在细胞功能中的协调性变化，并将其应用于肾脏及肺癌数据。该工具支持个体水平的单细胞功能分析报告，突出个体在通路基因表达协调方面的细胞类型特异性变化。跨物种图谱有助于选择最能反映患者样本细胞与通路特征的啮齿模型，推动单细胞方法在临床精准医学中的应用。最后，研究利用实验模型展示了该信息学方法在潜在治疗选择中的应用。
15.Tracing the evolution of single-cell 3D genomes in Kras-driven cancers追踪Kras驱动癌症单细胞三维基因组的演化
美国耶鲁大学医学院遗传学系
Although three-dimensional (3D) genome structures are altered in cancer, it remains unclear how these changes evolve and diversify during cancer progression. Leveraging genome-wide chromatin tracing to visualize 3D genome folding directly in tissues, we generated 3D genome cancer atlases of oncogenic Kras-driven mouse lung adenocarcinoma (LUAD) and pancreatic ductal adenocarcinoma. Here we define nonmonotonic, stage-specific alterations in 3D genome compaction, heterogeneity and compartmentalization as cancers progress from normal to preinvasive and ultimately to invasive tumors, discovering a potential structural bottleneck in early tumor progression. Remarkably, 3D genome architectures distinguish morphologic cancer states in single cells, despite considerable cell-to-cell heterogeneity. Analyses of genome compartmentalization changes not only showed that compartment-associated genes are more homogeneously regulated but also elucidated prognostic and dependency genes in LUAD, as well as an unexpected role for Rnf2 in 3D genome regulation. Our results highlight the power of single-cell 3D genome mapping to identify diagnostic, prognostic and therapeutic biomarkers in cancer.
尽管癌症中三维（3D）基因组结构发生改变，但这些变化在肿瘤进展过程中如何演化与多样化仍不清楚。研究利用全基因组染色质追踪技术直接在组织中可视化3D基因组折叠，构建了Kras驱动的肺癌腺癌（LUAD）与胰腺导管腺癌的3D基因组癌症图谱。研究定义了从正常→癌前→侵袭性肿瘤的进展过程中，3D基因组压缩度、异质性和区室化呈现非单调、阶段特异性的改变，并发现早期肿瘤进展中潜在的结构瓶颈。值得注意的是，尽管存在显著细胞间异质性，3D基因组构架可在单细胞水平区分形态学癌症状态。基因组区室化变化分析不仅表明区室相关基因调控更均一，还阐明了LUAD中的预后与依赖基因以及Rnf2在3D基因组调控中的意外作用。结果突显了单细胞3D基因组图谱在鉴定癌症诊断、预后及治疗生物标志物中的巨大潜力。
16.Temporal genomic dynamics shape clinical trajectory in multiple myeloma时间性基因组动态塑造多发性骨髓瘤临床轨迹
美国佛罗里达州迈阿密市迈阿密大学西尔维斯特综合癌症中心骨髓瘤研究所
Multiple myeloma evolution is characterized by the accumulation of genomic drivers over time. To unravel this timeline and its impact on clinical outcomes, we analyzed 421 whole-genome sequences from 382 patients. Using clock-like mutational signatures, we estimated a time lag of two to four decades between the initiation of events and diagnosis. We demonstrate that odd-numbered chromosome trisomies in patients with hyperdiploidy can be acquired simultaneously with other chromosomal gains (for example, 1q gain). We show that hyperdiploidy is acquired after immunoglobulin heavy chain translocation when both events co-occur. Finally, patients with early 1q gain had adverse outcomes similar to those with 1q amplification (>1 extra copy), but fared worse than those with late 1q gain. This finding underscores that the 1q gain prognostic impact depends more on the timing of acquisition than on the number of copies gained. Overall, this study contributes to a better understanding of the life history of myeloma and may have prognostic implications.
多发性骨髓瘤的演化以基因组驱动事件随时间累积为特征。为理清这一时间轴及其对临床结局的影响，研究分析了382例患者的421份全基因组序列。利用类时钟突变特征，研究估计从事件起始到确诊的时间滞后为二至四十年。研究发现，超二倍体患者中奇数号染色体三体可与其他染色体获得（如1q获得）同步发生；当两种事件共存时，超二倍体发生于免疫球蛋白重链易位之后。此外，早期1q获得患者的不良预后与1q扩增（>1额外拷贝）患者相似，但差于晚期1q获得患者。该结果强调，1q获得的预后影响更多取决于获得时机而非拷贝数量。总体而言，该研究深化了对骨髓瘤生命史的理解，并可能具有预后意义。
17.Single-cell DNA methylome and 3D genome atlas of human subcutaneous adipose tissue人类皮下脂肪组织单细胞DNA甲基组与三维基因组图谱
美国加州大学洛杉矶分校计算机科学系
The cell-type-level epigenomic landscape of human subcutaneous adipose tissue (SAT) is not well characterized. Here, we elucidate the epigenomic landscape across SAT cell types using snm3C-seq. We find that SAT CG methylation (mCG) displays pronounced hypermethylation in myeloid cells and hypomethylation in adipocytes and adipose stem and progenitor cells, driving nearly half of the 705,063 differentially methylated regions (DMRs). Moreover, TET1 and DNMT3A are identified as plausible regulators of the cell-type-level mCG profiles. Both global mCG profiles and chromosomal compartmentalization reflect SAT cell-type lineage. Notably, adipocytes display more short-range chromosomal interactions, forming complex local 3D genomic structures that regulate transcriptional functions, including adipogenesis. Furthermore, adipocyte DMRs and A compartments are enriched for abdominal obesity genome-wide association study (GWAS) variants and polygenic risk, while myeloid A compartments are enriched for inflammation. Together, we characterize the SAT single-cell-level epigenomic landscape and link GWAS variants and partitioned polygenic risk of abdominal obesity and inflammation to the SAT epigenome.
人类皮下脂肪组织（SAT）在细胞类型水平的表观基因组图谱尚未充分阐明。该研究利用snm3C-seq绘制了跨细胞类型的SAT表观基因组图谱。结果显示，SAT中CG甲基化（mCG）在髓系细胞呈显著高甲基化，在脂肪细胞及脂肪干细胞/祖细胞呈低甲基化，驱动了705,063个差异甲基化区域（DMRs）的近半数。TET1与DNMT3A被鉴定为调控细胞类型特异性mCG谱的潜在因子。全局mCG谱及染色体区室化均反映SAT细胞谱系。脂肪细胞表现出更多短程染色质互作，形成复杂的局部3D基因组结构，调控包括脂肪生成在内的转录功能。脂肪细胞DMRs与A区室富集腹型肥胖GWAS变异及多基因风险，而髓系A区室富集炎症相关变异。综上，研究刻画了SAT单细胞表观组图谱，并将腹型肥胖与炎症的GWAS变异及多基因风险关联至SAT表观组。
18.Tamoxifen induces PI3K activation in uterine cancer他莫昔芬诱导子宫癌PI3K激活
麻省理工学院和哈佛大学布罗德研究所
Mutagenic processes and clonal selection contribute to the development of therapy-associated secondary neoplasms, a known complication of cancer treatment. The association between tamoxifen therapy and secondary uterine cancers is uncommon but well established; however, the genetic mechanisms underlying tamoxifen-driven tumorigenesis remain unclear. We find that oncogenic PIK3CA mutations, common in spontaneously arising estrogen-associated de novo uterine cancer, are significantly less frequent in tamoxifen-associated tumors. In vivo, tamoxifen-induced estrogen receptor stimulation activates phosphoinositide 3-kinase (PI3K) signaling in normal mouse uterine tissue, potentially eliminating the selective benefit of PI3K-activating mutations in tamoxifen-associated uterine cancer. Together, we present a unique pathway of therapy-associated carcinogenesis in which tamoxifen-induced activation of the PI3K pathway acts as a non-genetic driver event, contributing to the multistep model of uterine carcinogenesis. While this PI3K mechanism is specific to tamoxifen-associated uterine cancer, the concept of treatment-induced signaling events may have broader applicability to other routes of tumorigenesis.
突变过程与克隆选择促使治疗相关继发性肿瘤发生——这是癌症治疗已知并发症。他莫昔芬治疗与继发性子宫癌的关联虽罕见但已确立，然而其驱动肿瘤发生的遗传机制尚不明确。研究发现，自发雌激素相关新发子宫癌中常见的致癌PIK3CA突变在他莫昔芬相关肿瘤中显著减少。体内实验显示，他莫昔芬诱导的雌激素受体刺激可在正常小鼠子宫组织中激活PI3K信号，从而可能消除PI3K激活突变在他莫昔芬相关子宫癌中的选择优势。综上，研究提出一条独特的治疗相关致癌途径：他莫昔芬诱导的PI3K通路激活作为非遗传驱动事件，参与子宫癌的多步骤发生模型。虽然该PI3K机制特异地作用于他莫昔芬相关子宫癌，但“治疗诱导信号事件”的概念或许可推广至其他肿瘤发生途径。
19.Precise modulation of BRG1 levels reveals features of mSWI/SNF dosage sensitivity精确调控BRG1水平揭示mSWI/SNF剂量敏感性特征
美国马萨诸塞州波士顿波士顿儿童医院霍华德休斯医学研究所
Mammalian switch/sucrose nonfermentable (mSWI/SNF) complex regulates chromatin accessibility and frequently shows alterations due to mutation in cancer and neurological diseases. Inadequate expression of mSWI/SNF in heterozygous mice can lead to developmental defects, indicating dosage-sensitive effects of mSWI/SNF. However, how its dosage affects function has remained unclear. Using a targeted protein degradation system, we investigated its dosage-sensitive effects by precisely controlling protein levels of BRG1, the ATPase subunit of the mSWI/SNF complex. We found that binding of BRG1 to chromatin exhibited a linear response to the BRG1 protein level. Although chromatin accessibility at most promoters and insulators was largely unaffected by BRG1 depletion, 44 % of enhancers, including 84 % of defined super-enhancers, showed reduced accessibility. Notably, half of the BRG1-regulated enhancers, particularly super-enhancers, exhibited a buffered response to BRG1 loss. Consistently, transcription exhibited a predominantly buffered response to changes in BRG1 levels. Collectively, our findings demonstrate a genomic feature-specific response to BRG1 dosage, shedding light on the dosage-sensitive effects of mSWI/SNF complex defects in cancer and other diseases.
哺乳动物SWI/SNF（mSWI/SNF）复合体调控染色质可及性，在癌症及神经系统疾病中常出现异常改变。杂合小鼠mSWI/SNF表达不足可导致发育缺陷，提示其剂量敏感性。然而剂量如何影响功能仍不清楚。研究利用靶向蛋白降解系统，精确控制mSWI/SNF核心ATP酶亚基BRG1的蛋白水平，研究其剂量效应。结果显示，BRG1与染色质的结合对蛋白水平呈线性响应。尽管BRG1缺失对绝大多数启动子及绝缘子的染色质可及性影响甚微，44%的增强子（包括84%已定义超级增强子）可及性降低。值得注意的是，半数BRG1调控的增强子（特别是超级增强子）对BRG1缺失呈现缓冲反应；转录亦主要呈缓冲响应。综上，研究揭示了基因组特征依赖性的BRG1剂量响应，为阐释mSWI/SNF复合体缺陷在癌症等疾病中的剂量敏感性提供了新见解。
20.Mutational landscape of triple-negative breast cancer in African American women非洲裔美国女性三阴性乳腺癌突变图谱
美国纽约州布法罗罗斯威尔公园综合癌症中心癌症预防和控制部
African American (AA) women have the highest incidence of triple-negative breast cancer (TNBC) among all racial groups, but are underrepresented in cancer genomic studies. In 462 AA women with TNBC, we characterized the tumor mutational landscape by whole-exome sequencing and RNA sequencing. We unveiled a high-resolution mutational portrait of TNBC in AA women reminiscent of that in Asian and non-Hispanic white women, with no evidence of associations of mutational features with African ancestry. We also made some distinctive discoveries, including an almost complete dominance of TP53 mutations, low frequency of PIK3CA mutations and mutational signature-based subtypes with etiologic and prognostic significance. These findings do not support major racial differences in TNBC biology at the level of somatic mutations. Our study contributes considerably to diversifying the knowledge base of breast cancer genomics and provides insights into the disease etiology, disparities and therapeutic vulnerability of TNBC in AA women.
非洲裔美国（AA）女性三阴性乳腺癌（TNBC）发病率居各族裔之首，但在癌症基因组研究中代表性不足。该研究对462例AA女性TNBC患者进行全外显子组及转录组测序，描绘其高分辨率突变图谱。该图谱与亚裔及非西班牙裔白人女性高度相似，未发现突变特征与非洲祖源存在关联。同时研究获得独特发现：TP53突变几乎全面主导、PIK3CA突变频率较低，以及具有病因与预后意义的突变特征亚型。研究结果不支持在体细胞突变层面存在显著的TNBC种族差异。该研究极大丰富了乳腺癌基因组多样性知识库，并为阐明AA女性TNBC的病因、差异及治疗脆弱性提供了新见解。
21.ERG-driven prostate cancer initiation is cell-context dependent and requires KMT2A and DOT1LERG驱动的前列腺癌发生依赖细胞情境并需要KMT2A与DOT1L
美国纪念斯隆凯特琳癌症中心人类肿瘤学和发病机制项目
Despite the high prevalence of ERG transcription factor translocations in prostate cancer, the mechanism of tumorigenicity remains poorly understood. Using lineage tracing, we find the tumor-initiating activity of ERG resides in a subpopulation of murine basal cells that coexpress luminal genes (Basal^lum) and not in the larger population of ERG^+ luminal cells. Upon ERG activation, Basal^lum cells give rise to highly proliferative intermediate (IM) cells with stem-like features that coexpress basal, luminal, hillock and club marker genes, before transitioning to Krt8^+ luminal cells. Transcriptomic analysis of ERG^+ human prostate cancers confirms the presence of rare ERG^+ Basal^lum cells, as well as IM cells whose presence is associated with a worse prognosis. Single-cell analysis revealed a chromatin state in ERG^+ IM cells enriched for STAT3 transcription factor binding sites and elevated expression of the KMT2A/MLL1 and DOT1L, all three of which are essential for ERG-driven tumorigenicity in vivo. In addition to providing translational opportunities, this work illustrates how single-cell approaches combined with lineage tracing can identify cancer vulnerabilities not evident from bulk analysis.
尽管ERG转录因子重排在前列腺癌中极为常见，其致瘤机制仍不清楚。通过谱系追踪，研究发现ERG的肿瘤启动活性定位于共表达腔面基因的小鼠基底细胞亚群（Basal^lum），而非占多数的ERG^+腔面细胞。ERG激活后，Basal^lum细胞先产生具有干细胞特征、共表达基底/腔面/嵴/棒状标志的高增殖中间（IM）细胞，随后转变为Krt8^+腔面细胞。ERG^+人类前列腺癌转录组分析证实存在罕见ERG^+ Basal^lum细胞及与预后不良相关的IM细胞。单细胞分析发现ERG^+ IM细胞呈现富集STAT3结合位点的染色质状态，并高表达KMT2A/MLL1与DOT1L，这三者均为ERG致瘤所必需。该研究不仅提供转化机遇，也展示了单细胞技术结合谱系追踪可发现传统分析难以识别的癌症脆弱点。
22.Cross-biobank generalizability and accuracy of electronic health record-based predictors compared to polygenic scores电子健康记录风险评分与多基因评分的跨生物库普适性与准确性比较
芬兰赫尔辛基大学分子医学研究所
Electronic health record (EHR)-based phenotype risk scores (PheRS) leverage individuals' health trajectories to estimate disease risk, similar to how polygenic scores (PGS) use genetic information. While PGS generalizability has been studied, less is known about PheRS generalizability across healthcare systems and whether PheRS are complementary to PGS. We trained elastic-net-based PheRS to predict the onset of 13 common diseases for 845,929 individuals (age = 32–70 years) from three biobank-based studies in Finland (FinnGen), the UK (UKB) and Estonia (EstB). All PheRS were statistically significantly associated with the diseases of interest and most generalized well without retraining when applied to other studies. PheRS and PGS were only moderately correlated and models including both predictors improved onset prediction compared to PGS alone for 8 of 13 diseases. Our results indicate that EHR-based risk scores can transfer well between EHRs, capture largely independent information from PGS, and provide additive benefits for disease risk prediction.
基于电子健康记录（EHR）的表型风险评分（PheRS）利用个人健康轨迹评估疾病风险，与使用遗传信息的多基因评分（PGS）相似。PGS的跨队列普适性已有研究，但PheRS在不同医疗体系间的普适性及其与PGS的互补性仍未知。研究在芬兰（FinnGen）、英国（UKB）及爱沙尼亚（EstB）三大生物银行共84.5万名32–70岁人群中训练弹性网PheRS，预测13种常见疾病的发生。所有PheRS均与目标疾病显著相关，多数无需重训练即可跨研究泛化。PheRS与PGS仅呈中等相关，联合模型在13种疾病中的8种上较单独PGS改善了发病预测。结果表明，EHR风险评分可跨体系迁移，并与PGS信息基本独立，为疾病风险预测提供加性益处。
23.Telomere attrition becomes an instrument for clonal selection in aging hematopoiesis and leukemogenesis端粒缩短成为衰老造血和白血病发生中克隆选择的工具
英国剑桥大学剑桥干细胞研究所
The mechanisms through which mutations in splicing factor genes drive clonal hematopoiesis (CH) and myeloid malignancies, and their close association with advanced age, remain poorly understood. Here we show that telomere maintenance plays an important role in this phenomenon. First by studying 454,098 UK Biobank participants, we find that, unlike most CH subtypes, splicing-factor-mutant CH is more common in those with shorter genetically predicted telomeres, as is CH with mutations in PPM1D and the TERT gene promoter. We go on to show that telomere attrition becomes an instrument for clonal selection in advanced age, with splicing factor mutations 'rescuing' HSCs from critical telomere shortening. Our findings expose the lifelong influence of telomere maintenance on hematopoiesis and identify a potential shared mechanism through which different splicing factor mutations drive leukemogenesis. Understanding the mechanistic basis of these observations can open new therapeutic avenues against splicing-factor-mutant CH and hematological or other cancers.
剪接因子基因突变如何驱动克隆造血（CH）及髓系恶性肿瘤，并与高龄密切相关，其机制仍不清楚。该研究发现端粒维护在其中扮演关键角色。首先，在454,098名英国生物银行参与者中，研究发现与大多数CH亚型不同，剪接因子突变CH在遗传预测端粒较短者中更常见，PPM1D及TERT启动子突变CH亦然。进一步研究表明，端粒缩短在衰老过程中成为克隆选择工具，剪接因子突变通过“拯救”造血干细胞免于关键端粒缩短而获得优势。研究的发现揭示了端粒维护对造血系统的终生影响，并指出不同剪接因子突变驱动白血病的潜在共同机制。深入理解这些观察的机制基础，可为针对剪接因子突变CH及血液系统或其他癌症开辟新的治疗途径。
汇报人：王静
审核：徐凡淇、吴婷婷、任建君
