Genome-Wide Association Study Reveals Host Genetic Factors for Liver Diseases

Human Leukocyte Antigen Polymorphism HLA-A*24:02 is Associated with Acute Liver Disease in HBV-Infected Han Chinese Adults

BACKGROUND

Whether polymorphic Human Leukocyte Antigen (HLA)-A, HLA-B and HLA-DRB1 alleles were associated with acute liver disease after hepatitis B virus (HBV) infections was investigated.

METHODS

In this study, from initially 100 participants in each group, HLA-A, HLA-B and HLA-DRB1 sequences were available from 86 acute hepatitis B (AHB) patients and from 84 HBV-resistant individuals (controls), using sequencing-based typing allele groups and alleles that exhibited differences in distribution between the case and control groups were subjected to chi-squared and logistic regression analyses to identify those associated with AHB. A dose response analysis was also performed on the effect of HLA-A*24:02 allele number on acute liver disease following HBV infection.

RESULTS

The frequency distribution of HLA-B and HLA-DRB1 alleles in the control group were in Hardy-Weinberg Equilibrium (P > .05). HLA-A*24:02 (χ2 = 6.949, P = .008) occurred most frequently in the AHB and HLA-DRB1*12:02 (χ2 = 7.768, P = .005) in the control group. With adjustment for sex, the logistic regression model showed that the HLA-A*24:02 allele was significantly associated with AHB liver injury (P = .0326, OR = 2.270, 95% CI: 1.070-4.816), whereas the other HLA-A, HLA-B, and HLA-DRB1 alleles were not (P > .05). A linear response was observed for the association between HLA-A*24:02 allele number and acute liver disease after HBV infections (χ2 = 4.428, P = .025).

CONCLUSION

The HLA-A*24:02 allele may influence the severity of the cellular response to HBV infection, increasing the elimination of HBV-infected hepatocytes. The HLA-A*24:02 allele may be a potential screening marker for identifying people or regional populations in China at higher risk of acute liver disease following HBV infection.

Possible association of HLA-DP polymorphism and antiretroviral therapy with hepatitis B virus clearance in an HIV-infected Vietnamese population

There is little evidence regarding the association between hepatitis B virus (HBV) chronicity and HLA-DP among the HIV-infected Vietnamese population. To study this, we conducted a cross-sectional analysis and a prospective study involving an HIV-infected Vietnamese cohort. The association between HBV chronicity and HLA-DP single nucleotide polymorphisms (SNPs) of rs3077 and rs9277535 among Vietnamese patients with previous HBV exposure was first evaluated. In addition, treatment-naive patients with chronic HBV infection were followed between 2012 and 2017 for HBV clearance after the initiation of antiretroviral therapy (ART). A total of 820 subjects with previous HBV exposure were included in the cross-sectional study. Among them, 147 (17.9 %) had chronic HBV infection, and 673 (82.1 %) achieved HBV clearance. The proportions of minor allele homozygotes of rs3077 and rs9277535 were 10.9 % and 15.2 % (p = 0.481) and 4.1 % and 11.7 % (p = 0.003), respectively. Multivariate analysis showed that rs9277535 minor homozygote was a significant protective factor against chronic HBV infection (odds ratio [OR], 0.271; 95 % confidence interval [CI]; 0.114-0.642, p = 0.001). Further, none of the 43 patients in the prospective study, who received ART possessed the rs9277535 minor homozygote. The average follow-up period was 4.8 years, and 10 subjects (23.3 %, 4.9 %/person-years) achieved HBV clearance. Univariate analysis revealed that the SNPs were not significantly associated with HBV clearance. In conclusion, our study confirmed that the rs9277535 minor allele homozygote was significantly associated with HBV clearance among HIV-infected Vietnamese patients.

Analysis of hepatitis B virus genotype and gene mutation in patients with advanced liver disease in East Kalimantan, Indonesia

Liver cirrhosis (LC) and hepatocellular carcinoma (HCC) are life-threatening conditions frequently associated with chronic hepatitis B virus (HBV) infection in Asian countries, including Indonesia. HBV genotypes and several specific mutations are associated with disease progression. To clarify the geographical variation in viral characteristics, HBV genotypes and gene mutations were investigated in patients with advanced liver disease (ALD) in Samarinda, East Kalimantan, Indonesia. Sera were collected from 41 patients with ALD at Abdul Wahab Sjahranie Hospital and HBV carriers from Red Cross Center blood bank in Samarinda, and screened for hepatitis B surface antigen and hepatitis B e-antigen. Liver function data were obtained from the medical records from each patient. HBV genotype and gene mutations were determined by polymerase chain reaction sequencing. Analysis of HBV isolates indicated that genotype B was the most frequent genotype, at 85.4 and 97.8%, followed by C, at 14.6 and 2.2%, in patients with ALD and in HBV carriers, respectively. The C1505A mutation in X region, T1753V and A1762T/G1764A mutations in the basal core promoter region and C1858T in precore (PC) region were frequent and only detected in patients with ALD (28.9, 40, 73.5 and 17.6%, respectively), whereas the G1896A mutation in the PC region was frequently detected in HBV carriers. The presence of HBV genotype B and certain HBV gene mutations were characteristic of patients with ALD in East Kalimantan.

Current hepatitis B virus infection situation in Indonesia and its genetic diversity

Indonesia has a moderate to high endemicity of hepatitis B virus (HBV) infection. The risk for chronic HBV infection is highest among those infected during infancy. Since 1997, hepatitis B (HepB) vaccination of newborns has been fully integrated into the National Immunization Program. Although HBV infection has been reduced by the universal newborn HepB immunization program, it continues to occur in Indonesia. The low birth dose coverage and the presence of vaccine escape mutants might contribute to this endemicity among children. Although limited information is available for an analysis of occult HBV infection (OBI), several variations and substitutions in the pre-S/S region have been detected in Indonesian HBV strains. Additionally, persistent infection and disease progression of chronic hepatitis B are related to not only viral factors but also the host genome. Indonesia is one of the most ethnically heterogeneous nations, with Javanese and Sundanese as the two highest ethnic groups. This multi-ethnicity makes genomic research in Indonesia difficult. In this article, we focused on and reviewed the following aspects: the current hepatitis B immunization program and its efficacy, OBI, HBV infection among high-risk patients, such as hemodialysis patients, and research regarding the host genome in Indonesia.

Understanding of HLA-conferred susceptibility to chronic hepatitis B infection requires HLA genotyping-based association analysis

Associations of variants located in the HLA class II region with chronic hepatitis B (CHB) infection have been identified in Asian populations. Here, HLA imputation method was applied to determine HLA alleles using genome-wide SNP typing data of 1,975 Japanese individuals (1,033 HBV patients and 942 healthy controls). Together with data of an additional 1,481 Japanese healthy controls, association tests of six HLA loci including HLA-A, C, B, DRB1, DQB1, and DPB1, were performed. Although the strongest association was detected at a SNP located in the HLA-DP locus in a SNP-based GWAS using data from the 1,975 Japanese individuals, HLA genotyping-based analysis identified DQB1*06:01 as having the strongest association, showing a greater association with CHB susceptibility (OR = 1.76, P = 6.57 × 10(-18)) than any one of five HLA-DPB1 alleles that were previously reported as CHB susceptibility alleles. Moreover, HLA haplotype analysis showed that, among the five previously reported HLA-DPB1 susceptibility and protective alleles, the association of two DPB1 alleles (DPB1*09:01, and *04:01) had come from linkage disequilibrium with HLA-DR-DQ haplotypes, DRB1*15:02-DQB1*06:01 and DRB1*13:02-DQB1*06:04, respectively. The present study showed an example that SNP-based GWAS does not necessarily detect the primary susceptibility locus in the HLA region.

Effects of HLA-DPB1 genotypes on chronic hepatitis B infection in Japanese individuals

Significant associations of HLA-DP alleles with chronic hepatitis B (CHB) infection are evident in Asian and Arabian populations, including Japanese, Han Chinese, Korean, and Saudi Arabian populations. Here, significant associations between CHB infection and five DPB1 alleles (two susceptibility alleles, DPB1(*) 05:01 and (*) 09:01, and three protective alleles, DPB1(*) 02:01, (*) 04:01, and (*) 04:02) were confirmed in a population comprising of 2582 Japanese individuals. Furthermore, odds ratios for CHB were higher for those with both DPB1 susceptibility alleles than for those with only one susceptibility allele; therefore, effects of susceptibility alleles were additive for risk of CHB infection. Similarly, protective alleles showed an additive effect on protection from CHB infection. Moreover, heterozygotes of any protective allele showed stronger association with CHB than did homozygotes, suggesting that heterozygotes may bind a greater variety of hepatitis B-derived peptides, and thus present these peptides more efficiently to T-cell receptors than homozygotes. Notably, compound heterozygote of the protective allele (any one of DPB1*02:01, *04:01, and *04:02) and the susceptible allele DPB1*05:01 was significantly associated with protection against CHB infection, which indicates that one protective HLA-DPB1 molecule can provide dominant protection. Identification of the HLA-DPB1 genotypes associated with susceptibility to and protection from CHB infection is essential for future analysis of the mechanisms responsible for immune recognition of hepatitis B virus antigens by HLA-DPB1 molecules.