Network Preservation Analysis Reveals Dysregulated Metabolic Pathways in Human Vascular Smooth Muscle Cell Phenotypic Switching

Abstract

Background: Vascular smooth muscle cells are key players involved in atherosclerosis, the underlying cause of coronary artery disease. They can play either beneficial or detrimental roles in lesion pathogenesis, depending on the nature of their phenotypic changes. An in-depth characterization of their gene regulatory networks can help better understand how their dysfunction may impact disease progression. Methods: We conducted a gene expression network preservation analysis in aortic smooth muscle cells isolated from 151 multiethnic heart transplant donors cultured under quiescent or proliferative conditions. Results: We identified 86 groups of coexpressed genes (modules) across the 2 conditions and focused on the 18 modules that are least preserved between the phenotypic conditions. Three of these modules were significantly enriched for genes belonging to proliferation, migration, cell adhesion, and cell differentiation pathways, characteristic of phenotypically modulated proliferative vascular smooth muscle cells. The majority of the modules, however, were enriched for metabolic pathways consisting of both nitrogen-related and glycolysis-related processes. Therefore, we explored correlations between nitrogen metabolism-related genes and coronary artery disease–associated genes and found significant correlations, suggesting the involvement of the nitrogen metabolism pathway in coronary artery disease pathogenesis. We also created gene regulatory networks enriched for genes in glycolysis and predicted key regulatory genes driving glycolysis dysregulation. Conclusions: Our work suggests that dysregulation of vascular smooth muscle cell metabolism participates in phenotypic transitioning, which may contribute to disease progression, and suggests that AMT and mannose phosphate isomerase may play an important role in regulating nitrogen and glycolysis-related metabolism in smooth muscle cells.

Single-Cell Gene-Regulatory Networks of Advanced Symptomatic Atherosclerosis

“…We also note that since Smart-seq2 is a fluorescent-activated cell sorting-based technique relying on extracting atherosclerosis-relevant cell types using antibodies some cells may not be recognized and therefore lost in the subsequent analysis. Additionally, although the cultured primary vascular SMCs exposed to serum-free medium for 24 hours have previously been used to model contractile SMCs, 44,45 establishing the exact phenotypic nature of SMCs in vitro is difficult. Last, like published scRNAseq studies, 3,6,7,10,11 we relied on a relatively small but compared with earlier studies larger number of carotid plaques and mouse aortic arches.…”