Coronary artery disease risk gene PRDM16 regulates smooth muscle homeostasis

Vascular smooth muscle cells (VSMCs) are the primary contractile component of blood vessels and can undergo phenotypic switching from a contractile to a synthetic phenotype in vascular diseases such as coronary artery disease (CAD) and restenosis. This process leads to decreased expression of SMC lineage genes and increased proliferative, migratory and secretory abilities that drive disease progression. Super-enhancers (SE) and lineage-specific transcription factors are believed to drive expression of genes that maintain cell identity and homeostasis. The goal of this study is to identify novel regulators of VSMC homeostasis by screening for SE-regulated transcription factors in arterial tissues.

We characterized human artery SEs by analyzing the enhancer histone mark H3K27ac ChIP-seq data of multiple arterial tissues. We unexpectedly discovered the transcription factor PRDM16, a GWAS-identified CAD risk gene with previously well-documented roles in brown adipocytes but with an unknown function in vascular disease progression, is enriched with artery-specific SEs. Further analysis of public bulk RNA-seq and scRNA-seq datasets, as well as qRT-PCR and Western blotting analysis, demonstrated that PRDM16 is highly expressed in arterial tissues and in contractile VSMCs but not in visceral SMCs, and down-regulated in phenotypically modulated VSMCs. To explore the function of Prdm16 in vivo, we generated both inducible and constitutive Prdm16 SMC-specific knockout mice and performed bulk RNA-Seq analysis of aortic tissues and left carotid artery ligation to assess neointima formation. SMC-deficiency of Prdm16 does not affect the aortic morphology at baseline but significantly alters expression of many genes involved in VSMC homeostasis and cardiovascular disease, and suppresses VSMC proliferation and neointima formation in male mice. Specifically, Prdm16 negatively regulates the expression of Tgfb2 that encodes an upstream ligand of the TGF-β signaling pathway, by suppressing its promoter activity.

Our results suggest that the CAD risk gene PRDM16 is highly expressed in VSMCs and is a novel regulator of VSMC homeostasis and neointima formation.