Integrative Analysis Of Expression And DNA Methylation Profile Of HBV Infection

Currently, it is widely accepted that HBV infection related liver diseases are caused byhost immune responses towards HBV. Immune responses have heterogeneity based on thefactors, such as host and the virus. However, the immune response heterogeneity is one ofthe key factors which are significantly related to the natural courses and different prognosis.To date, there are huge research data related to HBV infection immune responses, but thereare no exact answers aimed to the several key problems, such as the relationships acuteinfection and innate immunity, different natural courses after acquiring HBV infectionbetween neonates and adulthood, HBV immune escape strategies. During the past decade,epigenetic regulation on gene expression is one of the most important concerns, especially,gene promoter CpG island mehtylation status is closely related to gene expression. And HBVcan induce host and viral DNA mehtylation status change by regulation of host DNAmethylferase. we aimed to integrate the result of whole genome expression data and wholegenome promoter CpG island methylation data, to screen the epigenetic modulated, immunerelated genes.We used whole genome array techniques and computational bioinformatic method:(1)To study expression profiles of HBV infection (acute, chronic and healthy controls)with whole genome expression array.(2)To study promoter CpG island methylation status with whole genome promoter CpGisland methylation array.(3)Integrate the expression and DNA methylation profiles to find out the epigeneticmodulated differentially expressed genes.The major results are as follows.(1)Toll like receptor signaling pathway was significantly enriched to the acute HBVinfection, especially compared to the immune tolerant phase, with higher expression a clusterof ISGs, such as IFI27, IFI30and IFITM3. Acute phase had higher TLR6expression levelcompared to immune tolerant phase and immune clearance phase.(2)Leukocyte transendothelial migration signaling pathway was significantly enriched to the acute versus chronic infection. The genes enriched to this pathway are ITGB1,ITGA4,ACTB,VCL,MYL9,NCF1,NCF4,PIK3R5and CDC42, and their expressionlevels were significantly higher in acute phase.(3) FCGRs family activating receptors(FCGR1A,FCGR1B,FCGR2A,FCGR3A) weresignifcantly higher expression levels in acute phase compared to immune tolerant phase.(4)Compared to the healthy controls, acute phase showed global aberrant methylationstatus around whole genome. With intergrative analysis, a cluster of high expression,hypomethylated genes were enriched to the immune process, especially, genes related to theT cell receptor signaling, such as NFKB2, CTLA4, CD3E, MAPK3and LCK,were alsoincluded.(5) Differentially methylated genes between chronic infection and healthy controls,were enriched to the multiple cancer associated signaling pathway. With intergrative analysis,GSTP1, RASF1A, CDKN2A, which were repeatedly reported to shows aberrent methylationstatus in hepatocellular carcinoma in previous studies.(6)Differentially methylated genes between acute and chronic phase predominanlyenriched the inhibitory receptors of immune cells, such as CTLA4, LILRA1, LILRB1andNCF1.In this study, we present the first genome wide intergrative analysis of expression andDNA methylation profilling related to HBV infection. In conclusion, we proposed that innateimmune responses definitely function in the process of acute HBV infection phase, while,the main component of this innate immune response is the toll like receptor signalingpathway and subsequent type I IFN signaling pathway and IFN stimulated genes. Acute andchronic phases show global aberrant methylation status, after intergrative analysis, somegenes are indicated to be associated with cancer development and immune response process.