primary human smooth muscle cells  (PromoCell)

Journal: bioRxiv

Article Title: The 9p21.3 Coronary Artery Disease Risk Locus Modulates Vascular Cell-State Transitions via Enhancer-Driven Regulation of MTAP

doi: 10.1101/2025.11.18.689066

Figure Lengend Snippet: The 9p21.3 coronary artery disease (CAD) locus maps to an enhancer dense region in CAD-relevant cell types. (A) Manhattan plot showing Phenome-wide association (PheWAS) of 9p21.3 locus (tagged by rs4977574) to multiple disease traits in FinnGen data freeze 13 (DF13). Each triangle represents a phenotype association at 9p21.3 locus and different triangle colors represent various classification of phenotypes. Direction of the triangle indicates increased directionality of association. Increased risk is indicated by an upward triangle and reduced risk is indicated by a downward facing triangle. (B) Schematic depicting an extensive vascular cell wall profiling at baseline and in response to CAD-relevant stimulatory condition. (C) Chromatin state and epigenetic landscape of 9p21.3 CAD haplotype spanning ∼ 50-kb DNA sequence within the 3’ region of long non-coding RNA CDKN2B-AS1 ( ANRIL ). Also depicted are all 50 CAD associated SNPs (r 2 > 0.8), tagged by rs4977573 and credible set variants from FinnGen and UKBB finemapping efforts. (D-E) Dot plots showing enrichment for CAD heritability at baseline and in response to CAD-relevant stimulatory conditions, including Inflammatory (IL-1α and IL-6 & TNF-α) vascular fibroblast and smooth muscle cells. Solid dark lines around each dot represent significance at a threshold of -log 10 (adjusted P-value) ≥ 3.35. (F-G) Dot plots showing the impact of CAD-relevant stimulatory conditions on enhancer activities (proxy of H3K27ac) at 9p21.3 locus in vascular fibroblast and smooth muscle cells. Fold changes are indicated as Red (increased fold change) or Blue (Reduced fold change) and solid dark lines around each dot represent significance at a threshold of -log 10 (FDR) ≥ 1.3.

Article Snippet: We utilized human vascular fibroblasts (Cell Systems, ACBRI 5118) and primary human coronary artery smooth muscle cells (ATCC; PCS-100-021).

Techniques: Sequencing

Journal: bioRxiv

Article Title: The 9p21.3 Coronary Artery Disease Risk Locus Modulates Vascular Cell-State Transitions via Enhancer-Driven Regulation of MTAP

doi: 10.1101/2025.11.18.689066

Figure Lengend Snippet: Characterization of 9p21.3 enhancers and identification of cell-types mediating risk for CAD (A-D) Plots showing super enhancers (blue), enhancers (red), and enhancers within 9p21.3 haplotype (green). (E-G) Dot plots showing enrichment for CAD heritability at baseline and in response to CAD-relevant stimulatory conditions, including Inflammatory (IL-1α and IL-6 & TNF-α) atrial derived fibroblast, coronary artery derived endothelial cells, and adipose derived pericytes. Solid dark lines around each dot represent significance at a threshold of -log 10 (adjusted P-value) ≥ 3.35. (H-I) Dot plots showing the impact of CAD-relevant stimulatory conditions on enhancer activities (proxy of H3K27ac) at 9p21.3 locus in endothelial cells and pericytes. Fold changes are indicated as Red (increased fold change) or Blue (Reduced fold change) and solid dark lines around each dot represent significance at a threshold of -log 10 (FDR) ≥ 1.3. (J) T-statistic versus absolute t-statistic (y-axis) for gene expression across five primary human vascular cell types under basal conditions. Differentially expressed genes, representing the top 10% by absolute t-statistic, are highlighted in red; all other genes are in blue. The dashed line indicates a high absolute t-statistic threshold.

Article Snippet: We utilized human vascular fibroblasts (Cell Systems, ACBRI 5118) and primary human coronary artery smooth muscle cells (ATCC; PCS-100-021).

Techniques: Derivative Assay, Gene Expression

Journal: bioRxiv

Article Title: The 9p21.3 Coronary Artery Disease Risk Locus Modulates Vascular Cell-State Transitions via Enhancer-Driven Regulation of MTAP

doi: 10.1101/2025.11.18.689066

Figure Lengend Snippet: The 9p21.3 locus contains multiple functional vascular cell enhancers regulating cis-expressing genes. (A) Contact matrix (at 5000 bp resolution) from Micro-C 1 analysis of the H1 human embryonic stem cell (h1-ESC) spanning 1 Mb around 9p21.3 CAD haplotype (indicated as a blue rectangle). (B) Schematic showing experimental workflow to identify all functional non-coding 9p21.3 elements by CRISPR interference (CRISPRi) paired with Multiplex Analysis of Cells (MAC-seq) sequencing readout collectively referred to as CRISPRi-MAC-seq. (C) Donut plot showing the proportion of control, TSS-targeting, enhancer-targeting, and SNP-targeting guides (n=417 total guides) in our densely-tiled 9p21.3 library. (C) Box plots showing TSS repression efficiency via assessing normalized MTAP expression in vascular fibroblasts and smooth muscle cells treated with lentivirus containing transcriptional start site (TSS) guides for MTAP (n=4) compared to non-targeting control (n=13). Significance was determined using a two-tailed t-test, with a significance threshold of P-value<0.05. (E-F) Plot shows a sliding window approach that aggregates sgRNA transcriptional effects across a subset of the 9p21.3 annotated enhancers, including E4, E5, E8 and E9 in vascular fibroblast and smooth muscle cells. To assign significance to observed data relative to the permutation background, a permutation z-score was calculated. A significance level of z-score<-1.96 was used to identify significantly repressed regions – illustrated as red points on the sliding window plots.

Article Snippet: We utilized human vascular fibroblasts (Cell Systems, ACBRI 5118) and primary human coronary artery smooth muscle cells (ATCC; PCS-100-021).

Techniques: Functional Assay, Expressing, CRISPR, Multiplex Assay, Sequencing, Control, Two Tailed Test

Journal: bioRxiv

Article Title: The 9p21.3 Coronary Artery Disease Risk Locus Modulates Vascular Cell-State Transitions via Enhancer-Driven Regulation of MTAP

doi: 10.1101/2025.11.18.689066

Figure Lengend Snippet: Convergent genomics evidence points to MTAP as the primary 9p21.3 CAD effector gene in vascular fibroblast and smooth muscle cells. (A) Density plot of Gnocchi scores across the genome. Windows overlapping coding regions (red color) compared to windows overlapping 9p21.3 non-coding regions (blue color). (B) Distribution of CAD/T2D variants in constraint regions spanning ∼120-kb region on the P-arm of chromosome 9. Overlaid on this plot is enhancer annotation for 9p21.3 locus along with constraint blocks and constraint variants flanking or overlapping enhancer region. (C) Dot plots showing fine-mapped variants associated with a combined trait for coronary revascularization, including coronary artery bypass grafting (CABG) and percutaneous coronary intervention (ANGIO) using data from large-scale population efforts from FinnGen and UKBB. Credible set variants are shaded grey and have the highest magnitude of association to CAD. (D-E) Using a MAGMA gene prioritization approach, we identified CAD-specific genes by calculating genome-wide ZSTAT scores for genes in comparison to a GWAS. Genes with ZSTAT scores exceeding the 0.95 percentile were considered significantly related to the GWAS trait. (D) First, we prioritized 9p21.3 genes against a CAD GWAS. The results indicated that MTAP, CDKN2A, and CDKN2B surpassed the significance cutoff. (E) To assess disease specificity, we then compared these results against a T2D GWAS. This analysis highlighted that MTAP’s association with CAD is disease-specific, as it did not meet the significance cutoff for T2D. (F) Converging evidence for CAD effector gene prioritization. The matrix denotes evidence to provide support (colored blue) for CAD driver genes across different modalities. Top scoring genes have the highest count across all evidence.

Article Snippet: We utilized human vascular fibroblasts (Cell Systems, ACBRI 5118) and primary human coronary artery smooth muscle cells (ATCC; PCS-100-021).

Techniques: Genome Wide, Comparison

Journal: bioRxiv

Article Title: The 9p21.3 Coronary Artery Disease Risk Locus Modulates Vascular Cell-State Transitions via Enhancer-Driven Regulation of MTAP

doi: 10.1101/2025.11.18.689066

Figure Lengend Snippet: (A) Uniform manifold approximation and projection (UMAP) of scMultiome (scATAC-seq + scRNA-seq) data from Human left anterior descending (LAD) coronary artery, with cells colored by cell types (B) Density plot showing cell type specific markers for vascular smooth muscle cell ( ACTA2 , MYH11 , MYL9 , and TAGLN ) and vascular fibroblasts ( LUM , DCN , COL3A1 , and LAMA2 ). (C) Bar plot showing significant 9p21.3 tile-to-gene pair counts of 9p21.3 cis-expressing genes ( MTAP , DMRTA1 , and CDKN2B-AS1 ) stratified by genotype at rs1537371 in vascular fibroblasts and smooth muscle cells (D) Genomic track shows accessibility of 9p21.3 locus at rs1537371 SNP in vascular fibroblast. (E) Allelic dependent pseudobulk mRNA expression of MTAP in vascular fibroblast (F) Genomic track shows accessibility of 9p21.3 locus at rs1537371 SNP in vascular smooth muscle. (G) Allelic dependent pseudobulk expression of MTAP in vascular smooth muscle

Article Snippet: We utilized human vascular fibroblasts (Cell Systems, ACBRI 5118) and primary human coronary artery smooth muscle cells (ATCC; PCS-100-021).

Techniques: Expressing