# Gene regulatory networks controlling smooth muscle phenotype and vasculardisease risk

> **NIH NIH R01** · STANFORD UNIVERSITY · 2024 · $694,555

## Abstract

Building on the extensive genome wide association studies (GWAS) of coronary artery disease (CAD), and
single cell characterization of atherosclerosis, we have shown that the smooth muscle cell (SMC) lineage
harbors much of the risk for vascular disease. Further, these data indicate that SMC can assume two disease-
related transition states linked to disease risk. We identified TCF21 as a protective CAD GWAS gene and
showed that it regulates a disease-related transition of medial SMC to a fibroblast-like phenotype, producing
cells we term “fibromyocytes” (FMC). Further, we and others have found that SMC can also transition to a
second phenotype, characterized by expression of genes known for their role in endochondral bone formation
and intimal vascular calcification. We showed in mouse genetic models that this chondrogenic process, which
gives rise to cells we term “chondromyocytes” (CMC) is actively inhibited by the CAD GWAS protective Tgfb1
signaling molecules Smad3 and Zeb2, and promoted by the CAD GWAS causal factors Pdgfd and Twist1.
Further, recent transcriptomic and epigenomic (multi-omic) single cell studies indicate that FMC and CMC are
the end products of disparate trajectories that SMC differentially traverse in the disease setting. Our central
hypothesis for this work postulates that these trajectories are specified by enhancers and key
regulatory transcription factors (TFs) that mediate the branch point directionality of transition
commitment, and that these cis- and trans-acting genetic modulators underlie the fundamental
mechanisms of CAD gene causality in the SMC lineage. Algorithms that link disease variation and disease
scRNAseq data show that disease genetic risk resides in cell state changes from SMC to FMC and SMC to
CMC, making it imperative that we investigate the enhancers, related TFs, and regulons that mediate these
phenotype transitions. Specifically, in Aim 1 we will generate and analyze a time-course of single cell multi-
omic data from a mouse atherosclerosis model to map the epigenomic and transcriptomic regulatory elements
that mediate SMC transition to the FMC and CMC trajectories. We will perform similar studies with mice
targeted for CAD associated genes that promote or inhibit disease risk, to identify differences between the cis-
and trans-acting factors, and disease-related regulons that determine the disease trajectories and directionality
of disease risk. In Aim 2 we will perform multi-omic assays on human coronary lesions of varying severity to
examine the molecular mechanisms that mediate SMC transitions in human disease. Finally, in Aim 3, we will
perform in vitro enhancer PerturbSeq in human coronary artery smooth muscle cells to validate computational
results from previous Aims, and further characterize downstream targets and gene regulatory networks of
transition enhancers and TFs. The proposed studies will identify cellular and molecular mechanisms that
mediate SMC transitions to FMC and CMC, and th...

## Key facts

- **NIH application ID:** 10954200
- **Project number:** 1R01HL171045-01A1
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** THOMAS QUERTERMOUS
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $694,555
- **Award type:** 1
- **Project period:** 2024-07-15 → 2028-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10954200

## Citation

> US National Institutes of Health, RePORTER application 10954200, Gene regulatory networks controlling smooth muscle phenotype and vasculardisease risk (1R01HL171045-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10954200. Licensed CC0.

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