Identification of Key Genes and Pathways in Genotoxic Stress Induced Endothelial Dysfunction: Results of Whole Transcriptome Sequencing

Abstract

Atherosclerosis is a leading cause of cardiovascular morbidity and mortality worldwide. Endothelial disfunction underlying the atherogenesis can be triggered by genotoxic stress in endothelial cells. In the presented research whole transcriptome sequencing (RNA-seq) of human coronary artery (HCAEC) and internal thoracic artery (HITAEC) endothelial cells in vitro exposed to 500 ng/mL mitomycin C (treatment group) or 0.9% NaCl (control group) was performed. Resulting to bioinformatic analysis, 56 upregulated differentially expressed genes (DEGs) and 6 downregulated DEGs with absolute fold change ≥ 2 and FDR p-value < 0.05 were selected in HCAEC exposed to mitomycin C compared to the control group; in HITAEC only one upregulated DEG was found. According to Gene Ontology enrichment analysis, DEGs in HCAEC were classified into 25 functional groups of biological processes, while in HITAEC we found no statistically significant (FDR p-value < 0.05) groups. The four largest groups containing more than 50% DEGs (“signal transduction”, “response to stimulus”, “biological regulation”, and “regulation of biological process”) were identified. Finally, candidate DEGs and pathways underlying the genotoxic stress induced endothelial disfunction have been discovered that could improve our understanding of fundamental basis of atherogenesis and help to justification of genotoxic stress as a novel risk factor for atherosclerosis.

Keywords: DNA damage; RNA-seq; atherogenesis; bioinformatic analysis; differentially expressed genes; endothelial disfunction; gene ontology enrichment; genotoxic stress; mutagenesis; transcriptomic signature.

Figure 1

Heatmaps of differentially expressed genes (DEGs) identified in (A) Human Coronary Artery Endothelial Cells (HCAEC) and (B) Human Internal Thoracic Endothelial Cells (HITAEC) exposed to mitomycin C (MMC) in comparison with the non-exposed control (only those having FDR p-value < 0.05 are presented in the heatmaps). Top panel—the results of hierarchical sample clustering (C1, C2, C3, and C4—the control group, T1, T2, T3, and T4—the treatment group). Left panel—the results of hierarchical DEGs clustering (DEGs labeling based on Ensembl annotation). Bottom panel—the absolute fold change.

Figure 2

Quantity of differentially expressed genes (DEGs) identified in Human Coronary Artery Endothelial Cells (HCAEC) exposed to mitomycin C (MMC) in comparison with the non-exposed control in functional groups of biological processes according to Gene Ontology enrichment analysis.