Network preservation analysis reveals dysregulated metabolic pathways in human vascular smooth muscle cell phenotypic switching

Abstract

Vascular smooth muscle cells (VSMCs) are key players involved in atherosclerosis, the underlying cause of coronary artery disease (CAD). 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. We conducted a gene expression network preservation analysis in aortic SMCs isolated from 151 multi-ethnic heart transplant donors cultured under quiescent or proliferative conditions. We identified 86 groups of co-expressed genes (modules) across the two 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 VSMCs. 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 CAD-associated genes and found significant correlations, suggesting the involvement of the nitrogen metabolism pathway in CAD pathogenesis. for six genes in the nitrogen metabolism pathway. We also created gene regulatory networks enriched for genes in glycolysis and predicted key regulatory genes driving glycolysis dysregulation. Our work suggests that dysregulation of VSMC metabolism participates in phenotypic transitioning, which may contribute to disease progression and suggests that AMT and MPI may play an important role in regulating nitrogen and glycolysis related metabolism in SMCs.