Network-based prioritisation and validation of regulators of vascular smooth muscle cell proliferation in disease

Abstract

Aberrant vascular smooth muscle cell (VSMC) homeostasis and proliferation characterise vascular diseases causing heart attack and stroke. Here, we elucidate molecular determinants governing VSMC proliferation by reconstructing gene regulatory networks from single-cell transcriptomics and epigenetic profiling. We detect wide-spread activation of enhancers at disease-relevant loci in proliferation-predisposed VSMCs. We compared transcriptional network rewiring between injury responsive and non-responsive VSMCs, which suggested shared transcription factors but differing target loci between VSMC states. Through in silico perturbation analysis, we identified and prioritised previously unrecognised regulators of proliferation, including RUNX1 and TIMP1. Moreover, we demonstrated that the pioneer transcription factor RUNX1 increased VSMC responsiveness and show that TIMP1 feeds back to promote VSMC proliferation through CD74-mediated STAT3 signalling. Both RUNX1 and the TIMP1-CD74 axis were expressed in human VSMCs, showing low levels in normal arteries and increased expression in disease, suggesting clinical relevance and potential as vascular disease targets.