Specific HLA-DQB1 alleles associated with risk for development of hepatocellular carcinoma: A meta-analysis

Molecular Analysis of HLA Genes in Romanian Patients with Chronic Hepatitis B Virus Infection

Hepatitis B, a persistent inflammatory liver condition, stands as a significant global health issue. In Romania, the prevalence of chronic hepatitis B virus (CHB) infection ranks among the highest in the European Union. The HLA genotype significantly impacts hepatitis B virus infection progression, indicating that certain HLA variants can affect the infection's outcome. The primary goal of the present work is to identify HLA alleles and specific amino acid residues linked to hepatitis B within the Romanian population. The study enrolled 247 patients with chronic hepatitis B; HLA typing was performed using next-generation sequencing. This study's main findings include the identification of certain HLA alleles, such as DQB1*06:03:01, DRB1*13:01:01, DQB1*06:02:01, DQA1*01:03:01, DRB5*01:01:01, and DRB1*15:01:01, which exhibit a significant protective effect against HBV. Additionally, the amino acid residue alanine at DQB1_38 is associated with a protective role, while valine presence may signal an increased risk of hepatitis B. The present findings are important in addressing the urgent need for improved methods of diagnosing and managing CHB, particularly when considering the disease's presence in diverse population groups and geographical regions.

Gene variations related to the hepatocellular carcinoma: Results from a field synopsis and Bayesian revaluation

Hepatocellular carcinoma (HCC) is considered as the second cause of cancer-related deaths worldwide. Genetic variations are associated with HCC risk, an issue that has been the subject of several meta-analyses. However, meta-analyses have an important limitation on the likelihood of false positive data. Henceforth, this study aimed to assess the level of noteworthiness in the meta-analyses by means of a Bayesian approach. A systematic search was performed for meta-analyses with associations between gene polymorphisms and HCC. The calculations for the False-Positive Rate Probability (FPRP) and the Bayesian False Discovery Probability (BFDP) were performed to assess the noteworthiness with a statistical power of 1.2 and 1.5 of Odds Ratio at a prior probability of 10^-3 and 10^-5. The quality of studies was evaluated by the Venice criteria. As additional analyses, the gene-gene and protein-protein networks were designed for these genes and products. As results, we found 33 meta-analytic studies on 45 polymorphisms occurring in 35 genes. A total of 1,280 values for FPRP and BFDP were obtained. Seventy-five for FPRP (5.86%) and 95 for BFDP (14.79%) were noteworthy. In conclusion, the polymorphisms in CCND1, CTLA4, EGF, IL6, IL12A, KIF1B, MDM2, MICA, miR-499, MTHFR, PNPLA3, STAT4, TM6SF2, and XPD genes were considered as noteworthy biomarkers for HCC risk.

Association between the HLA-DQB1 Gene Polymorphism and Chronic Progression of Hepatitis B in Indonesia

BACKGROUND: The progression of hepatitis B is affected by the activity of T lymphocytes. Activation of T lymphocytes requires a primary signal originating from the presentation of antigen by HLA molecules to T cell receptors. HLA-DQB1 gene polymorphisms can affect the ability of HLA to bind and present viral antigens to T cells, thus affecting T cell activation and potentially associated with the progression of chronic hepatitis B. AIM: We aimed to investigate the polymorphisms of the HLA-DQB1 gene and its influence on chronic hepatitis B progression of chronic hepatitis B patients in Indonesia. METHODS: This cross-sectional research studied chronic hepatitis B patients at the Internal Medicine Department, Arifin Ahmad Hospital, Pekanbaru, from January 2018 to December 2018. Subjects were grouped into three categories: (1) Inactive chronic hepatitis B, (2) active chronic hepatitis B, and (3) end stage liver disease (ESLD) which consisted of patients with liver cirrhosis and hepatocellular carcinoma. Examination of the HLA-DQB1 gene polymorphism was performed with the SSP-PCR method and sequenced to verify the PCR results. Analysis results of p < 0.05 were considered statistically significant. RESULTS: The most common allele in patients with chronic hepatitis B was the HLA-DQB1 0301. The HLA-DQB1 0301 allele found primarily in the inactive chronic hepatitis B group. The DQB1 0501 allele found to be more abundant in patients with active chronic hepatitis B. The HLA DQB1 0502 allele only found in patients with chronic hepatitis B with ESLD. CONCLUSIONS: The HLA-DQB1 gene polymorphism is associated with the progression of chronic hepatitis B in chronic hepatitis B patients in Indonesia.

HLA-DQB1-AS1 Promotes Cell Proliferation, Inhibits Apoptosis, and Binds with ZRANB2 Protein in Hepatocellular Carcinoma

Major histocompatibility complex, class II, DQ beta 1 antisense RNA 1 (HLA-DQB1-AS1) conferred the susceptibility to hepatocellular carcinoma. Sustaining cell growth and resisting apoptosis are two hallmarks of hepatocellular carcinoma. The present study explored the role of HLA-DQB1-AS1 in the proliferation and apoptosis of hepatocellular carcinoma cells and investigated its downstream pathway. Colony formation assay was performed to assess cell proliferation. Cell apoptosis was assessed with the TdT-mediated dUTP nick end labeling method. HLA-DQB1-AS1 deficiency exerts antiproliferative and proapoptotic effects on hepatocellular carcinoma cells. Moreover, based on bioinformatic analysis combined with the results of RNA immunoprecipitation assay, HLA-DQB1-AS1 was revealed to bind with zinc finger RANBP2-type containing 2 (ZRANB2) protein. ZRANB2 was upregulated in hepatocellular carcinoma at a clinical and cellular level. HLA-DQB1-AS1 caused no significant effects on ZRANB2 mRNA and protein expression. ZRANB2 knockdown suppressed cell proliferation and enhanced cell apoptosis of hepatocellular carcinoma. Moreover, ZRANB2 overexpression rescued the anticancer effect of silenced HLA-DQB1-AS1 in hepatocellular carcinoma cells. In conclusion, HLA-DQB1-AS1 promotes cell proliferation and inhibits apoptosis in hepatocellular carcinoma by the interaction with ZRANB2 protein.

Genetic variants in HLA-DP/DQ contribute to risk of acute myeloid leukemia: A case-control study in Chinese

Human leukocyte antigens (HLA) are heterodimeric cell surface molecules that bind short peptides derived from non-self and self proteins. Accumulative evidence showed that specific alleles of HLA class II were associated with the susceptibility to malignant tumors including acute leukemia. In this study, we investigated the association between four single nucleotide polymorphisms (SNPs) at HLA-DP/DQ and acute myeloid leukemia (AML) risk. We genotyped four SNPs in HLA-DP (rs3077 G > A and rs9277535 G > A) and HLA-DQ (rs2856718 A > G and rs7453920 G > A) in a case-control study of 545 AML cases and 1034 cancer-free controls using Taqman allelic discrimination assay. The associations between these SNPs and AML risk were estimated by computing the odds ratios (ORs) and their 95% confidence intervals (CIs) from multivariate logistic regression analysis. We found significant associations of the variant alleles in HLA-DP (rs3077 and rs9277535) and HLA-DQ rs7453920 with increased AML risk (adjusted OR = 1.29, 95%CI = 1.10-1.51for rs3077 in additive model; adjusted OR = 1.29, 95%CI = 1.11-1.51 for rs9277535 in additive model; adjusted OR = 3.18, 95%CI = 1.86-5.46 for rs7453920 in recessive model). When combining the effects of rs3077, rs9277535 and rs7453920, we found that AML risk was significantly increased with the increasing number of variant alleles of the three SNPs in a dose-dependent manner (P for trend < 0.001). Besides, we found multiplicative interaction between rs3077 and age (≤45 years old and > 45 years old; P = 0.046). In conclusion, HLA-DP and HLA-DQ loci are candidate susceptibility regions for AML in Han Chinese.

Association between HLA-DQB1 polymorphisms and pemphigus vulgaris: A meta-analysis

OBJECTIVE

This study was performed to systematically summarize the results on the association of HLA-DQB1 polymorphisms with pemphigus vulgaris (PV) and other related factors.

METHODS

A comprehensive literature search of PubMed, The Cochrane Library, Embase, and Google Scholar database was conducted to identify relevant articles in English, with the last report up to November 1, 2016. Heterogeneity test was performed, and publication bias was evaluated. Stata software 12.0 was used to perform the meta-analysis. Odds ratios (ORs) and 95% confidence intervals (CI) were used to describe the correlation by random-effects model.

RESULTS

18 studies were obtained after searching databases: 10 studies were about Caucasian, and 8 articles were about non-Caucasian. Meta-analysis revealed that the allele and phenotype frequencies of DQB1*05 were markedly higher in PV patients than in controls [P < 0.001, OR: 2.640, 95%CI: 1.570-4.441; P = 0.030, OR 3.688, 95%CI: 1.138-11.946]. In addition, DQB1*03 was significantly increased at the allele level [P < 0.001, OR: 2.080, 95%CI: 1.507-2.869], and DQB1*02 was significantly decreased in PV at the allele and phenotype levels [P = 0.002, OR: 0.450, 95%CI: 0.289-0.702; P = 0.001, OR: 0.293, 95%CI: 0.146-0.587]. When based on each subtype of HLA-DQB1, DQB1*05:03 and DQB1*03:02 may play susceptibility roles in PV, and DQB1*03:03, DQB1*05:01 and DQB1*06:01 are negatively associated with PV.

CONCLUSION

In summary, our study suggests that alleles from the groups DQB1*05 and DQB1*03, concretely DQB1*05:03 and DQB1*03:02, respectively, may be the susceptibility factors for PV at allele and phenotype levels, whereas DQB1*05:01, DQB1*02, DQB1*06:01, and DQB1*03:03 are negatively associated with PV.

Polymorphisms of HLA-DQB1 predict survival of hepatitis B virus-related hepatocellular carcinoma patients receiving hepatic resection

OBJECTIVE

Human leukocyte antigen (HLA)-DQB1 genetic polymorphisms are associated with an increased risk of hepatitis B virus-related hepatocellular carcinoma (HBV-related HCC). We aimed to evaluate the influence of genetic polymorphisms in HLA-DQB1 exon region and neighboring single nucleotide polymorphisms (SNPs rs9275572 and rs2244546) on survival of HBV-related HCC patients undergoing hepatic resection.

METHODOLOGY

All SNPs were genotyped by sequencing DNA isolated from tumor samples of 483 patients with HBV-related HCC.

RESULTS

We identified rs9275572 and HLA-DQB1 haplotype CCCCC (constituted by rs1130375C, rs12722107C, rs12722106C, rs36222416C and rs3189152C) were significantly associated with overall survival (OS) of HBV-related HCC patients (P=0.015 and 0.049, respectively), after adjusting for serum AFP level, the Barcelona Clinic Liver Cancer (BCLC) stages, Child-Pugh score, regional invasion, radical hepatic resection and adjuvant antiviral treatment. In stratified analyses, the AG/GG genotype of rs9275572 significantly decreased risk of death among patients with younger age, serum AFP levels ≥400ng/mL, tumor size ≥10cm, BCLC stage A and radical hepatic resection. HLA-DQB1 haplotype CCCCC was significantly protective for male patients, patients with serum AFP levels <400ng/mL, tumor size ≥10cm, BCLC stage B/C, postoperative adjuvant TACE/TAC/TAE, radical hepatic resection and patients with adjuvant antiviral treatment. Moreover, gene-dosage effects were also observed, patients with SNP rs9275572 AG/GG genotypes and Block2 CCCCC haplotype had a decreased risk of death compared to others after adjusting for serum AFP level, BCLC stages, Child-Pugh score, regional invasion, radical hepatic resection and adjuvant antiviral treatment (adjusted HR=0.38, 95% CI=0.20-0.73, P=0.004).

CONCLUSIONS

The AG/GG genotype of rs9275572 and HLA-DQB1 Block2 CCCCC haplotype may have protective effects in HBV-related HCC patients receiving hepatic resection.

Relationship between HLA-DRB1 allele polymorphisms and familial aggregations of hepatocellular carcinoma

OBJECTIVE

We explored the relationship between HLA-DRB1 allele polymorphisms and familial aggregation of hepatocellular carcinoma (fhcc).

METHODS

Polymerase chain reaction sequence-specific primers were used to determine HLA-DRB1 genotypes for 130 members of families with 2 or more liver cancer patients and for 130 members of families without any diagnosed cancers. The genotype profiles were then compared to explore the relationship between HLA-DRB1 gene polymorphism and fhcc.

RESULT

Of 11 selected alleles, the frequencies of DRB1*11 and DRB1*12 were significantly lower in the fhcc group than in no-cancer group (p < 0.05; odds ratio: 0.286; 95% confidence interval: 0.091 to 0.901; and odds ratio: 0.493; 95% confidence interval: 0.292 to 0.893). Differences in the frequencies of the other 9 alleles were not statistically significant in the two groups (p > 0.05).

CONCLUSIONS

Our research suggests that if genetic factors play a role in fhcc, the deficiency in the DRB1*11 and DRB1*12 alleles might be the risk factor at work in Guangxi Zhuang Autonomous Region, P.R.C.

Serological tumor markers of hepatocellular carcinoma: a meta-analysis

BACKGROUND

The clinical value of serum α-fetoprotein (AFP) to detect hepatocellular carcinoma (HCC) has been questioned due to its low sensitivity and specificity. Other than AFP, several new serum biomarkers including glypican-3 (GPC3), des-γ-carboxy prothrombin (DCP), α-L-fucosidase enzyme (AFU) and vascular endothelial growth factor (VEGF) have been identified as useful HCC markers.

MATERIAL AND METHODS

A systematic search on PubMed, Web of Science and others was performed. Twenty-six case-control studies on HCC-related biomarkers published from 2000 to 2014 were included in this analysis. Data on sensitivity and specificity of tests were extracted and analyzed using the Meta-DiSc 1.4 statistical program. Fixed or random-effects models were used depending on the absence or presence of significant heterogeneity. Summary receiver operating characteristic (sROC) curves were obtained to evaluate the accuracy of the studied markers.

RESULTS

The areas under the sROC curve of AFP, GPC3, DCP, AFU, VEGF and the combination of each of the last 4 markers with AFP were 0.869, 0.928, 0.832, 0.851, 0.834, 0.964, 0.972, 0.873 and 0.948, respectively. A combination of AFP+GPC3, AFP+DCP or AFP+VEGF was superior to AFP alone in detecting HCC. The area under the sROC curve of GPC3 alone was significantly higher than that of AFP, whereas the areas of DCP, AFU and VEGF were comparable to that of AFP.

CONCLUSIONS

GPC3, DCP, AFU and VEGF are suitable markers for HCC, and their determination with AFP may prove to be useful in the diagnosis and screening of HCC.

Relationship between HLA-DRB1*03/04 alleles and familial clustering of hepatocellular carcinoma in Guangxi

AIM: To investigate the relationship between HLA-DRB1*03/04 alleles and familial clustering of hepatocellular carcinoma (HCC) to identify genes related to susceptibility to HCC in Guangxi, China.

METHODS: One hundred and fifty members whose families have had two or more HCC patients were selected as the case group, and 150 members whose families have had only one HCC case and 150 members from families without any cancer were selected as controls. Peripheral blood samples were collected to extract DNA for testing HLA-DRB1*03/04 alleles by PCR-SSP.

RESULTS: The frequency of the HLA-DRB1*03 /04 alleles were all slightly higher in the case group than those in the two control groups. The difference in HLA-DRB1*03 allele distribution among the three groups was not statistically significant (χ² = 1.074, P= 0.584), but the difference in HLA-DRB1*04 allele distribution was significant (χ² = 8.748, P = 0.013).

CONCLUSION: HLA-DRB1*04 allele, not HLA-DRB1*03 allele, might be associated with familial clustering of hepatocellular carcinoma in Guangxi, China.

Genetic variants in STAT4 and HLA-DQ genes confer risk of hepatitis B virus-related hepatocellular carcinoma

To identify genetic susceptibility loci for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) in the Chinese population, we carried out a genome-wide association study (GWAS) in 2,514 chronic HBV carriers (1,161 HCC cases and 1,353 controls) followed by a 2-stage validation among 6 independent populations of chronic HBV carriers (4,319 cases and 4,966 controls). The joint analyses showed that HCC risk was significantly associated with two independent loci: rs7574865 at STAT4, P(meta) = 2.48 × 10(-10), odds ratio (OR) = 1.21; and rs9275319 at HLA-DQ, P(meta) = 2.72 × 10(-17), OR = 1.49. The risk allele G at rs7574865 was significantly associated with lower mRNA levels of STAT4 in both the HCC tissues and nontumor tissues of 155 individuals with HBV-related HCC (P(trend) = 0.0008 and 0.0002, respectively). We also found significantly lower mRNA expression of STAT4 in HCC tumor tissues compared with paired adjacent nontumor tissues (P = 2.33 × 10(-14)).

Association between HLA-DRB1 polymorphisms and pemphigus vulgaris: a meta-analysis

Summary

Background Several studies have reported that HLA-DRB1 may be correlated with pemphigus vulgaris (PV), but most have been based on small samples and the results remain inconsistent and unclear.

Objectives To investigate the correlation between DRB1 and PV by a meta-analysis of case–control/nonfamily studies.

Methods PubMed, Wiley Online Library, ScienceDirect, Google Scholar, Cochrane Library, Chinese National Knowledge Infrastructure and Wanfang databases were searched for studies including: (i) ‘pemphigus’; and (ii) ‘human leukocyte antigen’, ‘HLA’, ‘major histocompatibility complex’, ‘MHC’ or ‘DRB1’. Eighteen selected studies were used in meta-analyses to evaluate DRB1 alleles and phenotypes by calculating the respective odds ratios (ORs) and 95% confidence intervals (CIs). Stratified meta-analyses and meta-regression analysis were also conducted.

Results The frequencies of three genotypes (allele and phenotype, respectively) were significantly increased in PV: DRB1*04 [P-value for comparability (Pc) < 0·00001, OR 3·61, 95% CI 2·28–5·71; Pc = 0·0002, OR 4·14, 95% CI 1·98–8·65], DRB1*08 (Pc = 0·03, OR 2·25, 95% CI 1·07–4·70; Pc = 0·0003, OR 2·46, 95% CI 1·51–4·01) and DRB1*14 (Pc < 0·00001, OR 6·47, 95% CI 4·52–9·26; Pc < 0·00001, OR 9·68, 95% CI 4·47–20·98). Three others (allele and phenotype, respectively) were significantly decreased in PV: DRB1*03 (Pc < 0·00001, OR 0·28, 95% CI 0·19–0·41; Pc = 0·0001, OR 0·25, 95% CI 0·12–0·51), DRB1*07 (Pc = 0·004, OR 0·45, 95% CI 0·26–0·78; Pc = 0·0002, OR 0·27, 95% CI 0·14–0·54) and DRB1*15 (Pc = 0·001, OR 0·35, 95% CI 0·18–0·66; Pc = 0·002, OR 0·32, 95% CI 0·16–0·65). Ethnicity partially explained the heterogeneity of DRB1*07, DRB1*08 and DRB1*14 phenotypes.

Conclusions Our findings suggest that DRB1*04, DRB1*08 and DRB1*14 are statistically significant susceptibility factors for PV. Conversely, DRB1*03, DRB1*07 and DRB1*15 may be negatively associated with PV. Specific HLA-DRB1 types may influence the susceptibility or resistance to PV, which needs further investigations.

GWAS identifies novel susceptibility loci on 6p21.32 and 21q21.3 for hepatocellular carcinoma in chronic hepatitis B virus carriers

Genome-wide association studies (GWAS) have recently identified KIF1B as susceptibility locus for hepatitis B virus (HBV)–related hepatocellular carcinoma (HCC). To further identify novel susceptibility loci associated with HBV–related HCC and replicate the previously reported association, we performed a large three-stage GWAS in the Han Chinese population. 523,663 autosomal SNPs in 1,538 HBV–positive HCC patients and 1,465 chronic HBV carriers were genotyped for the discovery stage. Top candidate SNPs were genotyped in the initial validation samples of 2,112 HBV–positive HCC cases and 2,208 HBV carriers and then in the second validation samples of 1,021 cases and 1,491 HBV carriers. We discovered two novel associations at rs9272105 (HLA-DQA1/DRB1) on 6p21.32 (OR = 1.30, P = 1.13×10⁻¹⁹) and rs455804 (GRIK1) on 21q21.3 (OR = 0.84, P = 1.86×10⁻⁸), which were further replicated in the fourth independent sample of 1,298 cases and 1,026 controls (rs9272105: OR = 1.25, P = 1.71×10⁻⁴; rs455804: OR = 0.84, P = 6.92×10⁻³). We also revealed the associations of HLA-DRB1*0405 and 0901*0602, which could partially account for the association at rs9272105. The association at rs455804 implicates GRIK1 as a novel susceptibility gene for HBV–related HCC, suggesting the involvement of glutamate signaling in the development of HBV–related HCC.

Previous studies strongly suggest the importance of genetic susceptibility for hepatocellular carcinoma (HCC). However, the studies about genetic etiology on HBV–related HCC were limited. Our genome-wide association study included 523,663 autosomal SNPs in 1,538 HBV–positive HCC patients and 1,465 chronic HBV carriers for the discovery analysis. 2,112 HBV–positive HCC cases and 2,208 HBV carriers (the initial validation), and 1,021 cases and 1,491 HBV carriers (the second validation), were then analyzed for validation. The fourth independent samples of 1,298 cases and 1,026 controls were analyzed as replication. We discovered two novel associations at rs9272105 (HLA-DQA1/DRB1) on 6p21.32 and rs455804 (GRIK1) on 21q21.3. HLA-DRB1 molecules play an important role in chronic HBV infection and progression to HCC. The association at rs455804 implicates GRIK1 as a novel susceptibility gene for HBV–related HCC, suggesting the involvement of glutamate signaling in the development of HBV–related HCC.

Association between HLA-DQB1 gene and patients with acute lymphoblastic leukemia (ALL)

Acute lymphoblastic leukemia (ALL) affects both children and adults. Survival in ALL has improved in recent decades due to recognition of its biological heterogeneity. Although children have higher remission and cure rates than adults, both populations have benefited from these improvements. Our aim in this study is to determine the association between HLA-DQB1 genes with childhood and adult ALL patients. To define this association, we compared HLA-DQB1 allele frequencies and allele carrier frequencies in a cohort of 135 adults and children with ALL with 150 controls, using polymerase chain reaction with sequence-specific primers. Allele carrier frequencies in childhood ALL show a deficiency in DQ2 (*0201) (P 0.049 and RR 0.75), but an increase in DQ5 (*0501-*0504) and DQ7 (*0301, *0304) compared to the control group (P 0.001 RR 1.89, P 0.003 RR 1.48, respectively). Allele carrier frequencies in adult ALL indicated an increase in DQ5 (*0501-*0504) (P0.045 RR 2.28). Allelic frequencies in childhood ALL revealed the same increase in DQ5 and DQ7, and a decrease in DQ2. In adult ALL it shows a decrease in DQ7. Therefore, our results in adult ALL were similar to childhood ALL addressing DQ5 allele carriers, which showed an increase in both age groups. We suggest that DQ5 could be more strongly considered as an ALL susceptibility allele, and that this allele may underlie a pathogenic phenotype with a major role in the immunologic process involved in both adults and children with ALL.