Genome wide DNA methylation and transcriptome integration analysis reveals potential markers in type A aortic dissection pathogenesis

Type A aortic dissection (TAAD) is a vascular disease with high mortality; however, the role of gene methylation in its pathogenesis has received little attention. This study aimed to identify candidate markers of TAAD by integrating methylation and transcriptome sequencing analyses. Aortic tissue samples from five TAAD cases and five controls were sequenced on Illumina Hiseq sequencing platform and Infinium Methylation EPIC BeadChip microarray. A series of bioinformatics analyses and machine learning algorithms were used to identify key methylated genes from the differentially expressed genes and differentially methylated sites between TAAD and controls. An overexpression vector of ZC3H12A was constructed, and human vascular smooth muscle cells (HVSMCs) were transfected with the vector to explore the effects of key methylated genes on cell proliferation, migration, and phenotypic switch. Differential analysis and integration of gene expression and methylation levels between TAAD and control samples suggested 239 differentially methylated genes, mainly involved in nicotinamide nucleotide biosynthetic and metabolic processes. By applying protein-to-protein network and machine learning algorithms, we finally identified three methylated genes, including ZC3H12A, IRAK2, and CCL5, which could be used as potential markers of TAAD. Both correlation analysis and experimental validation results indicated that expression levels of these genes were significantly negatively regulated by their methylation levels. Among them, ZC3H12A was confirmed to significantly promote the proliferation and migration in HVSMCs in vitro, while inhibiting their phenotypic transformation. Three methylated genes were identified as potential diagnostic markers for TAAD. Among them, ZC3H12A might contribute to disease progression.