Integrated epigenomic and network analysis identifies novel DNA methylation signature in atrial fibrillation

Abstract

Abstract Background CD4+ T cells are associated with atrial fibrillation (AF) pathogenesis but mechanistic insights as well as epigenetic phenomena underlying the onset and progression of AF are not fully understood. Purpose To identify differential methylation signature in circulating CD4+ T lymphocytes isolated from AF patients and HS enrolled in the DIANA clinical trial through epigenome and network medicine approaches. Methods DNA was extracted from CD4+ T lymphocytes obtained from patients diagnosed with AF (n = 10) vs patients with no known arrhythmias (n = 11). DNA was then used for paired-end reduced representation bisulfite sequencing to quantify differentially methylated regions (DMRs). NetworkAnalyst tool was interrogated in order to build a specific protein-protein interaction network and identify hub differentially methylated genes (DMGs) in AF. We considered the centrality degree as main network topological measure and defined hubs those DMGs with a centrality degree > 10. Results The analysis provided 7,846 DMRs (P<0.05), associated with 5,373 annotated genes, among which 7,075 hyper-methylated and 771 hypo-methylated regions were uncovered (Figure 1A). Among the identified DMRs, 3,601 were located within gene promoters of which 3,513 were hypermethylated while 88 hypomethylated. Network analysis including the 50 top hyper- and hypomethylated DMGs, according to the differential methylation values, provided a heart specific subnetwork with 56 nodes and 611 edges and 51 seeds (Figure 1B). Although the DNA methylation trend showed a predominant hypermethylation pattern in CD4+ T cells from AF patients (Figure 1A), network analysis demonstrated that hypomethylation was prevalent in the top 15 hub DMGs. In particular, GSTK1, WWP1, PSMD6, TFRC, CDK5R1, HSPG2, WDFY3, WT1, USP49, ACOT7, LAMB2, ITGB7, SHARPIN, and PLXNB2 emerged as hypomethylated hub DMGs, while AIFM1, PFDN1, LMO3, CDK5RAP2, COL4A1, SEPT8, and CYTH4 resulted hypermethylated hub DMGs. Interestingly, several genes are involved in pathological mechanisms of AF in cardiac tissues such as inflammation, fibrosis and cardiac remodeling. Conclusions Our preliminary data represent the first global methylation analysis in circulating CD4+ T cells in AF. The validation of specific genomic regions and the detection of molecular pathways characterized by aberrant DNA methylation changes may help to clarify pathological mechanisms underlying AF, thus providing an important translational impact for novel diagnostic biomarker discovery and therapeutic target identification.Figure 1