Identification of atheroprone shear stress responsive regulatory elements in endothelial cells

Abstract

Aims Oscillatory shear stress (OSS) is an atheroprone haemodynamic force that occurs in areas of vessel irregularities and is implicated in the pathogenesis of atherosclerosis. Changes in signalling and transcriptional programme in response to OSS have been vigorously studied; however, the underlying changes in the chromatin landscape controlling transcription remain to be elucidated. Here, we investigated the changes in the regulatory element (RE) landscape of endothelial cells under atheroprone OSS conditions in an in vitro model. Methods and results Analyses of H3K27ac chromatin immunoprecipitation-Seq enrichment and RNA-Seq in primary human umbilical vein endothelial cells 6 h after onset of OSS identified 2806 differential responsive REs and 33 differentially expressed genes compared with control cells kept under static conditions. Furthermore, gene ontology analyses of putative RE-associated genes uncovered enrichment of WNT/HIPPO pathway and cytoskeleton reorganization signatures. Transcription factor (TF) binding motif analysis within RE sequences identified over-representation of ETS, Zinc finger, and activator protein 1 TF families that regulate cell cycle, proliferation, and apoptosis, implicating them in the development of atherosclerosis. Importantly, we confirmed the activation of EGR1 as well as the YAP/TAZ complex early (6 h) after onset of OSS in both cultured human vein and artery endothelial cells and, by undertaking luciferase assays, functionally verified their role in RE activation in response to OSS. Conclusions Based on the identification and verification of specific responsive REs early upon OSS exposure, we propose an expanded mechanism of how OSS might contribute to the development of atherosclerosis.

Endothelial reprogramming by disturbed flow revealed by single-cell RNA and chromatin accessibility study

“…In contrast, TF motifs for TEF, ETV3, RELA, FOS::JUN, TEAD1, and STAT1 were enriched in E5-E8 exposed to d-flow conditions ( Figure 6C). Identification of the motifs for KLF4 (identical to the KLF2 motif), FOS:JUN (AP1), RELA, and TEAD1 as the most flow-sensitive TF motifs were expected, confirming the validity of our analysis (Bondareva et al, 2019;Fraineau et al, 2015;Kempe et al, 2005;Sangwung et al, 2017). We attempted to look for the shear stress response element (SSRE) (Resnick et al, 1993), but failed due to the lack of a defined list of TFs for the SSRE in our database.…”

A molecular map of lymph node blood vascular endothelium at single cell resolution

“…Compared to CapEC1, CapEC2 also show reduced Gja4 and Id1 and enrichment for genes in the MAPK cascade (GO:0000165) and WNT signaling (GO:0060070; Supplementary Fig. 3 ), characteristics that parallel findings from a ChIP-seq-based analysis of a disturbed oscillatory shear stress response 31 . These CapEC2 features suggest exposure to gradient or disturbed shear stress.…”

“…CapEC2 express Egr1, Cxcl1 and genes reflecting NFkB activation ( Nfkbia, Nfkbid, Nfkbiz ) and JNK activation ( Jun, Junb, Jund, Fos, Fosb, Atf3 ). These genes and pathways are induced by spatial gradients in fluid shear stress 28–31 . 32,33 .…”

Computational Characterization of the Dish-In-A-Dish, A High Yield Culture Platform for Endothelial Shear Stress Studies on the Orbital Shaker

“…Oscillatory and low laminar (<0.2 Pa) shear stress patterns are atheroprone. Cells subjected to this type of shear stress align poorly and show an increased expression of proinflammatory markers such as monocyte chemoattractant protein 1 (MCP1), a chemokine involved in monocyte attraction, and cadherin-2 (CDH2), a mesenchymal marker [5][6][7][8][9]. High laminar flow profiles (shear stresses > 1 Pa) are considered atheroprotective [7,10].…”