DNA methylation analysis for target regions in human smooth muscle cells.

Macrophage-like cells derived from vascular smooth muscle cells (SMCs) play critical roles in atherogenesis, and TET2-mediated DNA hydroxymethylation was implicated to regulate the transdifferentiation. We examined transcriptomes and (hydroxy)methylomes of human coronary artery SMCs during cholesterol-induced transdifferentiation. A unique approach of gene ontology (GO)-centric clustering of differentially expressed genes exhaustively identified through all possible pairwise comparisons (pan-DEGs) revealed dynamic and multifaceted modulations of genes involved in extracellular matrix organization, angiogenesis, cell migration, hypoxia response, and cholesterol biosynthesis. Intriguingly, transient activation was observed for an immuno-metabolic circuit consisting of type I interferon response and cholesterol metabolism. We found neither global nor DEG-proximal change in (hydroxy)methylation. These datasets would serve as a unique resource to address the mechanisms underlying cholesterol-induced transdifferentiation of SMCs. Moreover, GO-centric clustering of pan-DEGs may provide a useful approach to interpret multifaceted transcriptomic alterations. Overall design: We conducted a series of genome and epigenome analysis, including RNA-sequencing and DNA methylation and hydroxymethylation status in human smooth muscle cells.

源自血管平滑肌细胞（vascular smooth muscle cells，SMCs）的巨噬细胞样细胞在动脉粥样硬化发生过程中发挥关键作用，而TET2介导的DNA羟甲基化被证实参与调控其转分化过程。我们在胆固醇诱导的细胞转分化过程中，对人冠状动脉平滑肌细胞的转录组及（羟）甲基组进行了检测分析。我们采用一种独特的以基因本体论（gene ontology，GO）为核心的聚类分析方法，对通过所有成对比较全面鉴定出的泛差异表达基因（pan-DEGs）进行分析，结果揭示了参与细胞外基质组织、血管生成、细胞迁移、缺氧应答及胆固醇生物合成的基因所发生的动态且多层面的调控变化。值得注意的是，由I型干扰素应答与胆固醇代谢构成的免疫代谢通路呈现出瞬时激活现象。我们未发现（羟）甲基化存在全局变化，也未观察到差异表达基因邻近区域的（羟）甲基化改变。本数据集可作为研究胆固醇诱导的平滑肌细胞转分化潜在机制的独特资源。此外，针对泛差异表达基因的基因本体论聚类分析，可为解读多层面转录组变化提供一种有效的分析思路。实验设计概述：我们对人平滑肌细胞开展了一系列基因组与表观基因组分析，包括RNA测序以及DNA甲基化和羟甲基化状态检测。