Golebiewski, A. K. | Search bioRxiv

bioRxiv2025

Inflammation-Induced Alternative Splicing in Human Endothelial Cells Reveals Genetic Mechanisms of Cardiovascular Disease Risk

Alternative splicing modulates mRNA protein-coding sequence, stability, and translation rates, although it has not been comprehensively annotated in human endothelial cells (ECs). EC dysfunction is a hallmark of complex inflammatory diseases, including cancer and atherosclerosis. Therefore, this study modeled acute inflammation in vitro using 53 genetically distinct human aortic EC lines exposed to interleukin-1{beta} (IL-1{beta}) or control media. This approach identified 1,224 differentially spliced transcripts (DSTs) between IL-1{beta} and control conditions. DSTs were enriched for alternative first (AF) exons, including several novel mRNA isoforms of disease-associated and metabolic genes. It was hypothesized and confirmed that AF splicing was driven by alternative promoters using ATAC-seq and ChIP-seq data. To identify alternative promoters driving IL-1{beta}-dependent AF isoforms, a quantitative measure of promoter activity ratios was defined, and analysis found that histone 3 lysine 27 acetylation and binding of the transcription factors ERG and RELA often correlated with alternative promoter usage. Finally, the effect of common genetic variants on alternative first exon usage was interrogated through splicing quantitative trait locus (sQTL) analysis. Significant sQTLs were next submitted to genetic colocalization analysis with cardiovascular-related associations identified by genome-wide association studies (GWAS), finding colocalized signals at 66 human disease loci corresponding to 30 genes and 39 variants. These genetically regulated splicing differences provide plausible mechanisms explaining some of the genetic risk for cardiovascular-related diseases. Among the top signals are novel isoforms of Endothelial Protein C Receptor (PROCR) and Distal Membrane Arm Assembly Component 2 (DMAC2), whose splicing patterns colocalize with risk for coronary artery disease (CAD). This study demonstrates the prevalence of inducible alternative promoters and supports that ECs express numerous novel transcripts regulated by genetics and inflammation that are consistent with driving individual risk for cardiovascular disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/667484v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1a702c6org.highwire.dtl.DTLVardef@1a71602org.highwire.dtl.DTLVardef@961cbaorg.highwire.dtl.DTLVardef@13802eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2023

Multiomics of human aortic endothelial cells reveals cell subtypes with heterogeneous responses to canonical endothelial-to-mesenchymal perturbations

ObjectiveEndothelial cells (ECs), macrophages, and vascular smooth muscle cells (VSMCs) are major cell types in atherosclerosis progression, and heterogeneity in EC sub-phenotypes are becoming increasingly appreciated. Still, studies quantifying EC heterogeneity across whole transcriptomes and epigenomes in both in vitro and in vivo models are lacking. Approach and ResultsTo create an in vitro dataset to study human EC heterogeneity, multiomic profiling concurrently measuring transcriptomes and accessible chromatin in the same single cells was performed on six distinct primary cultures of human aortic ECs (HAECs). To model pro-inflammatory and activating environments characteristic of the atherosclerotic microenvironment in vitro, HAECs from at least three donors were exposed to three distinct perturbations with their respective controls: transforming growth factor beta-2 (TGFB2), interleukin-1 beta (IL1B), and siRNA-mediated knock-down of the endothelial transcription factor ERG (siERG). To form a comprehensive in vivo/ex vivo dataset of human atherosclerotic cell types, meta-analysis of single cell transcriptomes across 17 human arterial specimens was performed. Two computational approaches quantitatively evaluated the similarity in molecular profiles between heterogeneous in vitro and in vivo cell profiles. HAEC cultures were reproducibly populated by 4 major clusters with distinct pathway enrichment profiles: EC1-angiogenic, EC2-proliferative, EC3-activated/mesenchymal-like, and EC4-mesenchymal. Exposure to siERG, IL1B or TGFB2 elicited mostly distinct transcriptional and accessible chromatin responses. EC1 and EC2, the most canonically healthy EC populations, were affected predominantly by siERG; the activated cluster EC3 was most responsive to IL1B; and the mesenchymal population EC4 was most affected by TGFB2. Quantitative comparisons between in vitro and in vivo transcriptomes confirmed EC1 and EC2 as most canonically EC-like, and EC4 as most mesenchymal with minimal effects elicited by siERG and IL1B. Lastly, accessible chromatin regions unique to EC2 and EC4 were most enriched for coronary artery disease (CAD)-associated SNPs from GWAS, suggesting these cell phenotypes harbor CAD-modulating mechanisms. ConclusionPrimary EC cultures contain markedly heterogeneous cell subtypes defined by their molecular profiles. Surprisingly, the perturbations used here, which have been reported by others to be involved in the pathogenesis of atherosclerosis as well as induce endothelial-to-mesenchymal transition (EndMT), only modestly shifted cells between subpopulations, suggesting relatively stable molecular phenotypes in culture. Identifying consistently heterogeneous EC subpopulations between in vitro and in vivo models should pave the way for improving in vitro systems while enabling the mechanisms governing heterogeneous cell state decisions.

genomics↗