Genome wide methylation profiling of HCV pathogenesis to develop diabetes and diabetic complications.

HCV is key pathological factor for inducting insulin resistance. Such HCV induced insulin resistance is linked with metabolic syndrome, type2 diabetes mellitus, extrahepatic manifestations, hepatic fibrosis progression and development of hepatocellular carcinoma. DNA methylation alterations can cause developmental abnormalities, tumors and other diseases. In our study, PBMCs were isolated and genomic DNA was extracted. DNA fragmentation was achieved by sonication to 200-400 bp, subsequently end repair and adenylation was perfomed. Manufacturer's guidelines were followed to ligate Cytosine-methylated barcodes to sonicated DNA. EZ DNA Methylation-GoldTM Kit was then employed to treat these DNA segments twice with bisulfite. A Library was maintained, sequenced on an Illumina platform and 150 /125 bp paired-end reads generated. GO seq R package was used to perform Gene Ontology (GO) enrichment analysis for genes linked to DMRs and DMPs; gene length bias was corrected. We identified 12945 significant hypermethylated DMRs among all samples that were screened as those with at least 0.1 methylation level differences and p value less than 0.05. Fisher's exact test with FDR multiple test correction is used for identification of DMPs and DMRs. High throughput bisulfite sequencing (Illumina) was carried out and bioinformatics analysis was performed to analyze methylation status. Gene ontology (GO) and KEGG pathway enrichment analysis showed differentially methylated regions enriched in various pathways that include PI3K-AKT/IRS1 signaling pathway, metabolic pathway, oxidative phosphorylation, Renin-angiotensin system that are all involved in developing type-2 diabetes (T2D). Our study provides supporting evidence for significant involvement of HCV infection in development of epigenetic modifications in regulation of metabolic disorders like T2D and its complications.