Ma X Rosa, Conley Stephanie D, Kosicki Michael, Bredikhin Danila, Cui Ran, Tran Steven, Sheth Maya U, Qiu Wei-Lin, Chen Sijie, Kundu Soumya, Kang Helen Y, Amgalan Dulguun, Munger Chad J, Duan Lauren, Dang Katherine, Rubio Oriane Matthys, Kany Shinwan, Zamirpour Siavash, DePaolo John, Padmanabhan Arun, Olgin Jeffrey, Damrauer Scott, Andersson Robin, Gu Mingxia, Priest James R, Quertermous Thomas, Qiu Xiaojie, Rabinovitch Marlene, Visel Axel, Pennacchio Len, Kundaje Anshul, Glass Ian A, Gifford Casey A, Pirruccello James P, Goodyer William R, Engreitz Jesse M
Basic Science and Engineering (BASE) Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA.
Department of Genetics, Stanford University, Stanford, CA, USA.
medRxiv. 2024 Nov 22:2024.11.20.24317557. doi: 10.1101/2024.11.20.24317557.
Congenital heart defects (CHD) arise in part due to inherited genetic variants that alter genes and noncoding regulatory elements in the human genome. These variants are thought to act during fetal development to influence the formation of different heart structures. However, identifying the genes, pathways, and cell types that mediate these effects has been challenging due to the immense diversity of cell types involved in heart development as well as the superimposed complexities of interpreting noncoding sequences. As such, understanding the molecular functions of both noncoding and coding variants remains paramount to our fundamental understanding of cardiac development and CHD. Here, we created a gene regulation map of the healthy human fetal heart across developmental time, and applied it to interpret the functions of variants associated with CHD and quantitative cardiac traits. We collected single-cell multiomic data from 734,000 single cells sampled from 41 fetal hearts spanning post-conception weeks 6 to 22, enabling the construction of gene regulation maps in 90 cardiac cell types and states, including rare populations of cardiac conduction cells. Through an unbiased analysis of all 90 cell types, we find that both rare coding variants associated with CHD and common noncoding variants associated with valve traits converge to affect valvular interstitial cells (VICs). VICs are enriched for high expression of known CHD genes previously identified through mapping of rare coding variants. Eight CHD genes, as well as other genes in similar molecular pathways, are linked to common noncoding variants associated with other valve diseases or traits via enhancers in VICs. In addition, certain common noncoding variants impact enhancers with activities highly specific to particular subanatomic structures in the heart, illuminating how such variants can impact specific aspects of heart structure and function. Together, these results implicate new enhancers, genes, and cell types in the genetic etiology of CHD, identify molecular convergence of common noncoding and rare coding variants on VICs, and suggest a more expansive view of the cell types instrumental in genetic risk for CHD, beyond the working cardiomyocyte. This regulatory map of the human fetal heart will provide a foundational resource for understanding cardiac development, interpreting genetic variants associated with heart disease, and discovering targets for cell-type specific therapies.
先天性心脏病（CHD）部分源于遗传变异，这些变异会改变人类基因组中的基因和非编码调控元件。这些变异被认为在胎儿发育过程中发挥作用，影响不同心脏结构的形成。然而，由于心脏发育涉及的细胞类型极其多样，以及解读非编码序列的复杂性，确定介导这些效应的基因、信号通路和细胞类型一直具有挑战性。因此，了解非编码和编码变异的分子功能对于我们从根本上理解心脏发育和先天性心脏病至关重要。在此，我们创建了一个跨越发育时间的健康人类胎儿心脏基因调控图谱，并将其应用于解读与先天性心脏病和定量心脏特征相关的变异功能。我们从41个孕龄6至22周的胎儿心脏中采集了734,000个单细胞的多组学数据，从而构建了90种心脏细胞类型和状态的基因调控图谱，包括罕见的心脏传导细胞群体。通过对所有90种细胞类型进行无偏分析，我们发现与先天性心脏病相关的罕见编码变异和与瓣膜特征相关的常见非编码变异都汇聚到影响瓣膜间质细胞（VICs）上。VICs中已知通过罕见编码变异定位而确定的先天性心脏病基因高表达。八个先天性心脏病基因以及相似分子信号通路中的其他基因，通过VICs中的增强子与与其他瓣膜疾病或特征相关的常见非编码变异相联系。此外，某些常见非编码变异会影响对心脏特定亚解剖结构具有高度特异性活性的增强子，揭示了此类变异如何影响心脏结构和功能的特定方面。总之，这些结果表明在先天性心脏病的遗传病因中存在新的增强子、基因和细胞类型，确定了常见非编码和罕见编码变异在VICs上的分子汇聚，并提出了对先天性心脏病遗传风险有重要作用的细胞类型的更广泛观点，超越了工作心肌细胞。这个人类胎儿心脏的调控图谱将为理解心脏发育、解读与心脏病相关的遗传变异以及发现细胞类型特异性治疗靶点提供基础资源。
