Weldy Chad S, Kundu Soumya, Monteiro João, Gu Wenduo, Pedroza Albert J, Dalal Alex R, Worssam Matthew D, Li Daniel, Palmisano Brian, Zhao Quanyi, Sharma Disha, Nguyen Trieu, Kundu Ramendra, Fischbein Michael P, Engreitz Jesse, Kundaje Anshul B, Cheng Paul P, Quertermous Thomas
bioRxiv. 2025 May 6:2022.05.18.492517. doi: 10.1101/2022.05.18.492517.
Vascular sites have distinct susceptibility to atherosclerosis and aneurysm, yet the biological underpinning of vascular site-specific disease risk is largely unknown. Vascular tissues have different developmental origins that may influence global chromatin accessibility, and understanding differential chromatin accessibility, gene expression profiles, and gene regulatory networks (GRN) on single cell resolution may give key insight into vascular site-specific disease risk. Here, we performed single cell chromatin accessibility (scATACseq) and gene expression profiling (scRNAseq) of healthy adult mouse vascular tissue from three vascular sites, 1) aortic root and ascending aorta, 2) brachiocephalic and carotid artery, and 3) descending thoracic aorta. Through a comprehensive analysis at single cell resolution, we discovered key regulatory enhancers to not only be cell type, but vascular site specific in vascular smooth muscle (SMC), fibroblasts, and endothelial cells. We identified epigenetic markers of embryonic origin with differential chromatin accessibility of key developmental transcription factors such as , , , and family members and discovered transcription factor motif accessibility to be cell type and vascular site specific. Notably, we found ascending fibroblasts to have distinct epigenomic patterns, highlighting SMAD2/3 function to suggest a differential susceptibility to TGFβ, a finding we confirmed through culture of primary adventitial fibroblasts. Finally, to understand how vascular site-specific enhancers may regulate human genetic risk for disease, we integrated genome wide association study (GWAS) data for ascending and descending aortic dimension, and through using a distinct base resolution deep learning model to predict variant effect on chromatin accessibility, ChromBPNet, to predict variant effects in SMC, Fibroblasts, and Endothelial cells within ascending aorta, carotid, and descending aorta sites of origin. We reveal that although cell type remains a primary influence on variant effects, vascular site modifies cell type transcription and highlights genomic regions that are enriched for specific TF motif footprints - including MEF2A, SMAD3, and HAND2. This work supports a paradigm that the epigenomic and transcriptomic landscape of vascular cells are cell type and vascular site-specific and that site-specific enhancers govern complex genetic drivers of disease risk.
血管部位对动脉粥样硬化和动脉瘤具有不同的易感性，然而血管部位特异性疾病风险的生物学基础在很大程度上尚不清楚。血管组织具有不同的发育起源，这可能会影响整体染色质可及性，而在单细胞分辨率下了解差异染色质可及性、基因表达谱和基因调控网络（GRN）可能会为血管部位特异性疾病风险提供关键见解。在这里，我们对来自三个血管部位的健康成年小鼠血管组织进行了单细胞染色质可及性（scATACseq）和基因表达谱分析（scRNAseq），这三个血管部位分别是：1）主动脉根部和升主动脉，2）头臂动脉和颈动脉，3）胸降主动脉。通过在单细胞分辨率下的全面分析，我们发现关键调控增强子不仅具有细胞类型特异性，而且在血管平滑肌（SMC）、成纤维细胞和内皮细胞中具有血管部位特异性。我们鉴定了具有关键发育转录因子（如 、 、 及 家族成员）差异染色质可及性的胚胎起源表观遗传标记，并发现转录因子基序可及性具有细胞类型和血管部位特异性。值得注意的是，我们发现升主动脉成纤维细胞具有独特的表观基因组模式，突出了SMAD2/3的功能，提示其对TGFβ的易感性存在差异，我们通过原代外膜成纤维细胞培养证实了这一发现。最后，为了了解血管部位特异性增强子如何调节人类疾病的遗传风险，我们整合了升主动脉和降主动脉尺寸的全基因组关联研究（GWAS）数据，并通过使用一种独特的碱基分辨率深度学习模型来预测变异对染色质可及性的影响，即ChromBPNet，以预测升主动脉、颈动脉和降主动脉起源部位的SMC、成纤维细胞和内皮细胞中的变异效应。我们发现，尽管细胞类型仍然是变异效应的主要影响因素，但血管部位会改变细胞类型转录，并突出显示富含特定TF基序足迹（包括MEF2A、SMAD3和HAND2）的基因组区域。这项工作支持了一种范式，即血管细胞的表观基因组和转录组景观具有细胞类型和血管部位特异性，且部位特异性增强子控制着疾病风险的复杂遗传驱动因素。
