Time series analysis reveals the effect of shear stress profile on endothelial gene expression

Endothelial cells (ECs) are central to vascular homeostasis, and their dysfunction is a key driver of atherosclerosis (AS). Hemodynamic forces, particularly laminar and disturbed flow (LF, laminar flow; DF, disturbed flow) patterns, differentially regulate ECs phenotypes via mechanosensing and epigenetic mechanisms. However, prior studies, largely reliant on single time-point analysis at isolated time points, fail to capture the dynamic gene expression responses of ECs to shear stress (SS). To address this, our study employs a time-series approach to dynamically delineate how distinct flow patterns shape ECs transcriptomes over time, aiming to identify pivotal regulatory genes and provide novel insights into AS pathogenesis.

In this study, samples were collected at multiple time points (0, 0.5, 2, 4, 6, 12, and 24 h) under LF or DF stimulation and subjected to RNA-seq. Time-series analysis was then performed to correlate data across these time points, thereby dynamically reflecting the effects of SS induced by different blood flow patterns on gene expression in endothelial cells. We identified two specific modules through weighted gene co-expression network analysis (WGCNA) to elucidate the effects of different blood flow patterns on ECs. Subsequently, a multi-database integration analysis was performed to screen for candidate genes.

RNA-seq analysis of the multi-time-point transcriptomes of endothelial cells under different blood flow patterns revealed, through time-series analysis, that LF exerts a protective effect on homeostasis, whereas DF drives energy metabolism dysregulation, protein damage, and immunosuppression. WGCNA further identified that DF-specific modules were enriched in the endoplasmic reticulum stress pathway, while LF-specific modules were enriched in the oxidative phosphorylation pathway. Based on a multi-dataset cross-screening, the core genes HMOX1 and PTGIS were identified; HMOX1 was upregulated upon LF stimulation but downregulated in inflammatory and plaque tissues.

Through transcriptomic sequencing and RT-qPCR validation, this study's further analysis of the HMOX1 gene reinforces the role of blood flow patterns in the progression of atherosclerosis and provides a basis for exploring hemodynamic-related diagnostic markers and therapeutic strategies. Further research on mechanosensitive genes and their signaling pathways may offer insights into the prevention and treatment of cardiovascular diseases.