Relationship between HLA‐DPA1 mRNA expression and susceptibility to hepatitis B

Abstract

Chronic hepatitis B virus (HBV) infection is influenced by both viral and host factors. In genome‐wide association studies, the human leucocyte antigen HLA‐DPA1 and related polymorphism rs3077 were found to be associated with susceptibility to and spontaneous clearance of HBV infection. Here, we evaluated the association between HLA‐DPA1 mRNA expression and the risk of HBV infection. HLA‐DPA1 and rs3077 polymorphisms were investigated in 169 patients with chronic HBV and 217 healthy controls (HCs) from Sichuan Han blood donors using sequence‐based typing and meta‐analysis for HLA‐DPA1 alleles. HLA‐DPA1 mRNA levels were measured by real‐time polymerase chain reaction. The results showed that HLA‐DPA1 and rs3077 were associated with HBV infection in the Sichuan population. Rs3077T and DPA1*01:03 played protective roles in HBV infection, and rs3077C and DPA1*02:02 increased susceptibility to HBV infection. We found that the HLA‐DPA1 mRNA expression was decreased in the CHB group; in particular, the 3077CT, 3077TT, DPA1*01:03 and DPA1*02:01 alleles showed a significant decrease. Our results demonstrated, for the first time, that expression of HLA‐DPA1 alleles and rs3077 affected the risk of HBV infection. Genotypes with lower HLA‐DPA1 expression had a greater susceptibility to HBV infection. Thus, further independent studies are needed to strengthen the associations of these polymorphisms with susceptibility to and clearance of HBV infection in Chinese populations.

Expression estimation and eQTL mapping for HLA genes with a personalized pipeline

“…A similar pattern holds for the rank 1 eQTL which we mapped for HLA-DQB1 , which is in high LD ( D ′ = 1) with a variant reported by Raj et al [45] within a super-enhancer which regulates HLA-DQA1 , HLA-DQB1 and HLA-DRB1 . For HLA-DP we also found strong association ( D ′ = 1) between our eQTLs and previous SNPs with regulatory role for HLA-DPB1 [13] and HLA-DPA1 [51] (S3 Table).…”

“…Next we investigated whether the eQTLs which we mapped share the same causal signal as those reported by previous studies. We first queried selected publications which focused on expression of genes with immune function, and that described SNPs with a functional role on HLA expression (in some cases with experimental validation) [12, 13, 42, 45, 49–51].…”

Variation of HLA-DPB1 Gene in Hepatitis B Infection

“…The peripheral blood of all samples and DNA extraction were performed as consistent with previous reported [19,20] . Genotyping was performed using sequence based typing (PCR-SBT).…”

“…The PCR products were analyzed by an ABI 3730 DNA Sequencer (Applied Biosystem, Foster City, CA). Group-speci c sequencing primers used to resolve alternative genotypes, the primers based on ambiguous genotypes obtained HLA-DPB1 mRNA level measurement RNA were prepared from cell suspensions of each sample freshly isolated peripheral blood mononuclear cell (PBMC) using a TRIzol method (Invitrogen), the RNA extraction and cDNA preparation were also consistent with previous reported [19,20] .…”

“…ELB algorithm was used to estimate the gametic phase of the genotype data generated at all the polymorphic positions within the gene region when the recessive alleles are present. The statistical signi cance of the linkage disequilibrium between each of the allele pairs was evaluated by the approximate X 2 reported by previously [19] . All statistical signi cance was de ned as P<0.05.…”