Study / S47YSBZLH2025-10-07

Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression

Nicolas Barbera, Lily Lei, Alexia Wallace, Faruk Erin, R. Noah Perry et al.

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About this study

Genome-wide association studies (GWAS) have identified over 300 genomic loci associated with coronary artery disease (CAD) risk, but identifying functional variants remains challenging due to linkage disequilibrium. Here we show a comprehensive functional characterisation of CAD-associated variants in primary vascular smooth muscle cells (SMCs). We performed lentivirus-based massively parallel reporter assays (lentiMPRAs) on 25,892 CAD-associated variants, testing their allele-specific enhancer activity in quiescent and proliferative SMCs. We identified 122 candidate variants with enhancer activity and allelic imbalance, including 23 variants showing condition-biased and 41 showing sex-biased effects. Integrating lentiMPRA with CUT&RUN epigenome profiling and expression quantitative trait loci data, we prioritised 49 functionally relevant variants. CRISPRi experiments on 8 variants confirmed their regulatory effects on 9 variant-gene pairs: rs35976034 (MAP1S), rs4888409 (CFDP1), rs73193808 (MAP3K7CL), rs67631072 (INPP5B/FHL3), rs1651285 (SNHG18), rs17293632 (SMAD3), rs2238792 (ARVCF), and rs4627080 (NRIP3). Our results fine-map the causal variants that confer CAD risk through their effects on vascular smooth muscle cells.

Full author list & citation

Nicolas Barbera, Lily Lei, Alexia Wallace, Faruk Erin, R. Noah Perry, Hester M. den Ruijter, Mete Civelek. Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression. 2025-10-07. https://doi.org/10.1038/s44161-025-00714-1

Experiments 2

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lentiMPRA of CAD-associated SNP alleles in proliferative primary human aortic SMCs

A 200-bp allele-specific candidate regulatory sequence library was tested after lentiviral integration in primary aortic smooth muscle cells from six donors (three female and three male). Cells remained in complete smooth muscle medium containing 5% FBS for 24 hours to model the proliferative state; RNA/DNA reporter counts were analyzed with MPRAnalyze.

Integrated lentiMPRAHumanGRCh38

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E9FE6STC4

lentiMPRA of CAD-associated SNP alleles in quiescent primary human aortic SMCs

A 200-bp allele-specific candidate regulatory sequence library was tested after lentiviral integration in primary aortic smooth muscle cells from six donors (three female and three male). Cells were switched to serum-free medium for 24 hours to model the quiescent state; RNA/DNA reporter counts were analyzed with MPRAnalyze.

Integrated lentiMPRAHumanGRCh38

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Raw source data 19 files

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