Oscillatory and elevated flow distinctly regulate gene expression in human coronary artery endothelial cells

  1. Giulio Vidotto
  2. Sara Luzzi
  3. Jon Humphries
  4. Robert Beal
  5. David G McVey
  6. Christopher P Nelson
  7. Thomas R Webb
  8. Martin J Humphries
  9. Graham Smith
  10. Stephen J White
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Abstract

Objective

Coronary artery disease (CAD) remains a leading cause of mortality globally. Atherosclerosis develops at arterial sites exposed to disturbed, low, or oscillatory shear stress, while acute coronary syndromes-triggered by plaque rupture or erosion predominantly occurs in regions subjected to elevated shear stress. The response of endothelial cells to disturbed flow has received significant attention, however, the response to elevated flow is less well studied. We addressed this shortfall by providing a comprehensive analysis of mRNA, microRNA and proteome expression in primary human coronary artery endothelial cells (HCAECs) cultured under different flow environments and identify novel changes in gene expression that may play a role in promoting both atherogenesis and plaque erosion.

Approach and Results

We conducted a comprehensive multi-omic analysis of HCAECs cultured for 72 hours under oscillatory shear stress (OSS), physiological laminar shear stress (LSS), and elevated shear stress (ESS). Our results identified 2,175 shear-regulated genes, with 1,218 uniquely responsive to OSS and 665 to ESS. Both OSS and ESS induced significant changes in RNA isoform selection, affecting 580 and 848 genes respectively. Signalling pathways regulating CAD pathogenesis including HIPPO, TGFβ/BMP, and IRF, showed altered RNA isoform selection which may influence plaque development and plaque erosion. 65% of LD-filtered CAD-associated genetic variants from two recent multi-population meta-analyses contained at least one OSS or ESS-regulated gene within 250Kb. Proteomic analysis identified 289 proteins differentially expressed under OSS and 171 under ESS, with notable discordance between mRNA and protein changes observed in 28.7% (OSS vs LSS) and 16.6% (ESS vs LSS) genes. Additionally, 40 shear-responsive microRNAs were identified, potentially contributing this discordance.

Conclusion

Both oscillatory and elevated flow trigger distinct HCAEC gene expression programmes, affecting mRNA, microRNA, splicing, and protein expression, modulating pathways central to CAD pathogenesis.

Highlights

What was known

  • The flow environment within arteries mediates a significant contribution to atherosclerotic plaque development, through alteration of endothelial gene expression and function

  • Disturbed or reversing flow promotes plaque formation and progression

  • Plaque disruption via rupture or erosion most frequently occurs where the endothelium is exposed to elevated flow

What is new

  • We present an integrated analysis comparing both oscillatory and elevated flow to physiological laminar flow and demonstrate that elevated flow evokes a significant and largely unique regulation of the transcriptome, miRome and proteome

  • Identify shear stress as a significant regulator of alternative splicing, with elevated flow causing the greatest shift in alternative transcript selection

  • Identify 135 oscillatory, and 101 elevated differentially expressed genes in proximity to CAD risk loci

  • Provide a novel model highlighting the putative impact of miRs in regulating the expression of genes where there is discordance between their mRNA expression and protein expression levels under different flow environments

Article activity feed

  1. Version published to 10.1101/2025.10.10.681055 on bioRxiv