Multiomics Analysis of Skeletal Muscle Identifies Dysregulation of Hypoxia-Induced Genes in Peripheral Artery Disease

Epigenetic modifications such as DNA methylation play a critical role in hypoxic cell programs. However, no previous studies have investigated the epigenetic regulation of gene expression in peripheral artery disease (PAD), a condition characterized by intermittent ischemia. Our study aims to examine how PAD affects the DNA methylome in skeletal muscle of patients with PAD with intermittent claudication or critical limb ischemia compared with non-PAD controls.

This was a cross-sectional study evaluating differences in the DNA methylome and transcriptome using reduced representation bisulfite sequencing, and small and bulk RNA sequencing, in skeletal muscle from non-PAD controls, intermittent claudication, and critical limb ischemia. We also assessed changes in DNA methylation and gene expression by comparing patients with intermittent claudication at baseline and 6 months following revascularization operation.

The multiomics approach identified hypoxia-related genes in PAD skeletal muscle that are potentially regulated at the level of methylation. Specifically, binding and expression target analysis revealed that epigenetic modifications to the DNA methylome may contribute to modulation of the mRNA expression of family with sequence similarity 20, member C and endothelial PAS domain-containing protein 1, also known as hypoxia-inducible factor-2α. Furthermore, the AP-1 (activator protein-1) early response transcription factors FOS and FOSB emerged as the primary genes that may be influenced by revascularization operations.

Our findings identify novel hypoxia-related genes potentially regulated by DNA methylation in PAD skeletal muscle.