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O'Brien TR, Yang HI, Groover S, Jeng WJ. Genetic Factors That Affect Spontaneous Clearance of Hepatitis C or B Virus, Response to Treatment, and Disease Progression. Gastroenterology 2019; 156:400-417. [PMID: 30287169 DOI: 10.1053/j.gastro.2018.09.052] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) and hepatitis B virus (HBV) infections can lead to cirrhosis, end-stage liver disease, and hepatocellular carcinoma. Over the past decade, studies of individuals infected with these viruses have established genetic associations with the probability of developing a chronic infection, risk of disease progression, and likelihood of treatment response. We review genetic and genomic methods that have been used to study risk of HBV and HCV infection and patient outcomes. For example, genome-wide association studies have linked a region containing the interferon lambda genes to spontaneous and treatment-induced clearance of HCV. We review the genetic variants associated with HCV and HBV infection, and how these variants affect specific expression or activities of their products. Further studies of these variants could provide insights into risk factors for and mechanisms of chronic infection and disease progression, as well as new strategies for treatment.
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Affiliation(s)
- Thomas R O'Brien
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland.
| | - Hwai-I Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Sarah Groover
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma
| | - Wen-Juei Jeng
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan; Liver Research Unit, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
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52
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Liu Y, Song C, Ni H, Jiao W, Gan W, Dong X, Liu J, Zhu L, Zhai X, Hu Z, Li J. UBE2L3, a susceptibility gene that plays oncogenic role in hepatitis B-related hepatocellular carcinoma. J Viral Hepat 2018; 25:1363-1371. [PMID: 29969176 DOI: 10.1111/jvh.12963] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/11/2018] [Indexed: 12/22/2022]
Abstract
Previously, we identified UBE2L3 as a susceptibility gene for chronic hepatitis B virus (HBV) infection through genome-wide association study. Here, we analysed the association between genetic variants of UBE2L3 and the susceptibility to HBV-related hepatocellular carcinoma (HCC) and further explored its role in HCC. This case-control study included 1344 subjects who cleared HBV, 1560 HBV carriers and 1057 HBV-related HCC patients. Two single nucleotide polymorphisms (SNPs) were genotyped, including rs2266959 and rs4821116. Logistic regression analysis was performed to compute the odds ratio (OR) and 95% confidence interval (CI). We further analysed the expression of UBE2L3 and its association with pathological features based on The Cancer Genome Atlas (TCGA) data and our tissue microarray. Proliferation and migration assays were performed in hepatoma cell lines with or without UBE2L3 knockdown. Further RNA-seq analysis was performed to explore the underlying oncogenic mechanism. The variant genotypes of rs4821116 in UBE2L3 were associated with decreased risk for HCC and chronic HBV infection. Moreover, based on both TCGA and our tissue microarray data, higher levels of UBE2L3 expression were correlated with higher tumour grade, advanced tumour stage and poor survival. In vitro analysis revealed that UBE2L3 may promote hepatocyte proliferation and migration. RNA-seq analysis showed that UBE2L3 was inversely correlated with CDKN2B, a negative regulator of cell cycle, and CLDN1, loss of which may promote cancer metastasis. In conclusion, UBE2L3 may also be a susceptibility gene in HBV-related HCC, and it may promote HCC proliferation and migration by negatively regulating CDKN2B and CLDN1.
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Affiliation(s)
- Yao Liu
- Department of Pathology, Medical College of Soochow University, Suzhou, China
| | - Ci Song
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hengli Ni
- Department of Pathology, Medical College of Soochow University, Suzhou, China
| | - Weijuan Jiao
- Department of Pathology, Medical College of Soochow University, Suzhou, China
| | - Wenjuan Gan
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaoqiang Dong
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jibin Liu
- Department of Hepatobiliary Surgery, Nantong Tumor Hospital, Nantong, China
| | - Liguo Zhu
- Department of Infection Diseases, Jiangsu Province Center for Disease Prevention and Control, Nanjing, China
| | - Xiangjun Zhai
- Department of Infection Diseases, Jiangsu Province Center for Disease Prevention and Control, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jianming Li
- Department of Pathology, Medical College of Soochow University, Suzhou, China
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Riazalhosseini B, Mohamed Z, Apalasamy YD, Shafie NS, Mohamed R. Interleukin-6 gene variants are associated with reduced risk of chronicity in hepatitis B virus infection in a Malaysian population. Biomed Rep 2018; 9:213-220. [PMID: 30271596 DOI: 10.3892/br.2018.1126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/29/2018] [Indexed: 02/06/2023] Open
Abstract
Interleukin-6 (IL-6) is a cytokine with a critical role in regulating the immune response to infectious disease. Studies have indicated that polymorphisms in the IL-6 gene may be linked to hepatitis B virus (HBV) infection. The purpose of the present study was to examine the association among IL-6 SNPs and haplotypes with HBV infection risk in a Malaysian population. A total of 1,246 Malaysian subjects with and without chronic hepatitis B were recruited for this study. Three IL-6 polymorphisms (rs2069837, rs1800796 and rs2066992) were genotyped using a Sequenom MassARRAY® platform. The results suggested that GC and CC genotypes of rs1800796 as well as GT and TT genotypes of rs2066992 were associated with protection against HBV infection (P<0.001). Furthermore, haplotypes GG and CT exhibited a significant association with protection against HBV (P=0.003 and =0.005, respectively); and haplotypes GG and CT exhibited a significant association with clearance of HBV infection (P=0.035 and =0.037, respectively). The present study indicates that two IL-6 SNPs (rs1800796 and rs2066992) are associated with clearance of chronic HBV or protection against HBV infection at allelic, genotypic and haplotypic levels.
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Affiliation(s)
- Behnaz Riazalhosseini
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Zahurin Mohamed
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yamunah Devi Apalasamy
- Social Wellbeing Research Centre, Faculty of Economics and Administration, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Noor Shafila Shafie
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Rosmawati Mohamed
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
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54
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Nishida N, Sugiyama M, Sawai H, Nishina S, Sakai A, Ohashi J, Khor S, Kakisaka K, Tsuchiura T, Hino K, Sumazaki R, Takikawa Y, Murata K, Kanda T, Yokosuka O, Tokunaga K, Mizokami M. Key HLA-DRB1-DQB1 haplotypes and role of the BTNL2 gene for response to a hepatitis B vaccine. Hepatology 2018; 68. [PMID: 29534301 PMCID: PMC6175380 DOI: 10.1002/hep.29876] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Approximately 5-10% of individuals who are vaccinated with a hepatitis B (HB) vaccine designed based on the hepatitis B virus (HBV) genotype C fail to acquire protective levels of antibodies. Here, host genetic factors behind low immune response to this HB vaccine were investigated by a genome-wide association study (GWAS) and Human Leukocyte Antigen (HLA) association tests. The GWAS and HLA association tests were carried out using a total of 1,193 Japanese individuals including 107 low responders, 351 intermediate responders, and 735 high responders. Classical HLA class II alleles were statistically imputed using the genome-wide SNP typing data. The GWAS identified independent associations of HLA-DRB1-DQB1, HLA-DPB1 and BTNL2 genes with immune response to a HB vaccine designed based on the HBV genotype C. Five HLA-DRB1-DQB1 haplotypes and two DPB1 alleles showed significant associations with response to the HB vaccine in a comparison of three groups of 1,193 HB vaccinated individuals. When frequencies of DRB1-DQB1 haplotypes and DPB1 alleles were compared between low immune responders and HBV patients, significant associations were identified for three DRB1-DQB1 haplotypes, and no association was identified for any of the DPB1 alleles. In contrast, no association was identified for DRB1-DQB1 haplotypes and DPB1 alleles in a comparison between high immune responders and healthy individuals. Conclusion: The findings in this study clearly show the importance of HLA-DR-DQ (i.e., recognition of a vaccine related HB surface antigen (HBsAg) by specific DR-DQ haplotypes) and BTNL2 molecules (i.e., high immune response to HB vaccine) for response to a HB vaccine designed based on the HBV genotype C. (Hepatology 2018).
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Affiliation(s)
- Nao Nishida
- Genome Medical Science ProjectNational Center for Global Health and MedicineIchikawaJapan,Department of Human Genetics, Graduate School of MedicineThe University of TokyoBunkyo‐kuJapan
| | - Masaya Sugiyama
- Genome Medical Science ProjectNational Center for Global Health and MedicineIchikawaJapan
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of MedicineThe University of TokyoBunkyo‐kuJapan
| | - Sohji Nishina
- Department of Hepatology and PancreatologyKawasaki Medical SchoolOkayamaJapan
| | - Aiko Sakai
- Department of Child Health, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoBunkyo‐kuJapan
| | - Seik‐Soon Khor
- Department of Human Genetics, Graduate School of MedicineThe University of TokyoBunkyo‐kuJapan
| | - Keisuke Kakisaka
- Division of Hepatology, Department of Internal MedicineIwate Medical UniversityMoriokaJapan
| | - Takayo Tsuchiura
- Genome Medical Science ProjectNational Center for Global Health and MedicineIchikawaJapan
| | - Keisuke Hino
- Department of Hepatology and PancreatologyKawasaki Medical SchoolOkayamaJapan
| | - Ryo Sumazaki
- Department of Child Health, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Yasuhiro Takikawa
- Division of Hepatology, Department of Internal MedicineIwate Medical UniversityMoriokaJapan
| | - Kazumoto Murata
- Genome Medical Science ProjectNational Center for Global Health and MedicineIchikawaJapan,Department of GastroenterologyInternational University of Health and Welfare, Graduate School of Medical SciencesChibaJapan
| | - Tatsuo Kanda
- Department of Gastroenterology and Nephrology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Osamu Yokosuka
- Department of Gastroenterology and Nephrology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of MedicineThe University of TokyoBunkyo‐kuJapan
| | - Masashi Mizokami
- Genome Medical Science ProjectNational Center for Global Health and MedicineIchikawaJapan
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Akcay IM, Katrinli S, Ozdil K, Doganay GD, Doganay L. Host genetic factors affecting hepatitis B infection outcomes: Insights from genome-wide association studies. World J Gastroenterol 2018; 24:3347-3360. [PMID: 30122875 PMCID: PMC6092584 DOI: 10.3748/wjg.v24.i30.3347] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/29/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023] Open
Abstract
The clinical outcome of Hepatitis B Virus (HBV) infection depends on the success or failure of the immune responses to HBV, and varies widely among individuals, ranging from asymptomatic self-limited infection, inactive carrier state, chronic hepatitis, cirrhosis, hepatocellular carcinoma, to liver failure. Genome-wide association studies (GWAS) identified key genetic factors influencing the pathogenesis of HBV-related traits. In this review, we discuss GWAS for persistence of HBV infection, antibody response to hepatitis B vaccine, and HBV-related advanced liver diseases. HBV persistence is associated with multiple genes with diverse roles in immune mechanisms. The strongest associations are found within the classical human leukocyte antigen (HLA) genes, highlighting the central role of antigen presentation in the immune response to HBV. Associated variants affect both epitope binding specificities and expression levels of HLA molecules. Several other susceptibility genes regulate the magnitude of adaptive immune responses, determining immunity vs tolerance. HBV persistence and nonresponse to vaccine share the same risk variants, implying overlapping genetic bases. On the other hand, the risk variants for HBV-related advanced liver diseases are largely different, suggesting different host-virus dynamics in acute vs chronic HBV infections. The findings of these GWAS are likely to pave the way for developing more effective preventive and therapeutic interventions by personalizing the management of HBV infection.
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Affiliation(s)
- Izzet Mehmet Akcay
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul 34469, Turkey
| | - Seyma Katrinli
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul 34469, Turkey
| | - Kamil Ozdil
- Department of Gastroenterology and Hepatology, Umraniye Teaching and Research Hospital, Istanbul 34764, Turkey
| | - Gizem Dinler Doganay
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul 34469, Turkey
| | - Levent Doganay
- Department of Gastroenterology and Hepatology, Umraniye Teaching and Research Hospital, Istanbul 34764, Turkey
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56
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Yamazaki T, Umemura T, Joshita S, Yoshizawa K, Tanaka E, Ota M. A cis-eQTL of HLA-DPB1 Affects Susceptibility to Type 1 Autoimmune Hepatitis. Sci Rep 2018; 8:11924. [PMID: 30093645 PMCID: PMC6085285 DOI: 10.1038/s41598-018-30406-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
Autoimmune hepatitis (AIH) is a chronic inflammatory liver disease characterized by an autoimmune reaction to hepatocytes. A single nucleotide polymorphism in the 3′ untranslated region of HLA-DPB1, rs9277534, is associated with HLA-DPB1 expression. rs9277534 has been linked to hepatitis B virus recovery/persistence and the risk of graft-versus-host disease with HLA-DPB1 mismatching transplantation of hematopoietic cells, but its role along with that of HLA-DP expression in AIH have not been fully clarified. We genotyped rs9277534 in 146 Japanese patients with AIH and 326 healthy subjects. HLA-DPB1 expression was determined by quantitative PCR. HLA-DPB1 expression was significantly higher for rs9277534G than for rs9277534A (P < 0.05). rs9277534 genotype was in strong linkage disequilibrium with the HLA-DPB1 allele (pairwise D′ = 0.82–1.00). Although HLA-DP alleles were not significantly associated with AIH, the frequency of the rs9277534G allele was significantly higher in AIH patients compared with healthy subjects (P = 0.002, odds ratio [OR] = 1.56). Logistic regression analysis revealed that the HLA-DRB1*04:05 allele (P < 0.001, OR = 4.61) and rs9277534 (P = 0.004, OR = 1.67) were independently associated with AIH susceptibility. rs9277534G in the HLA-DP gene is an eQTL that affects gene expression and may contribute to AIH susceptibility.
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Affiliation(s)
- Tomoo Yamazaki
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Takeji Umemura
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan. .,Research Center for Next Generation Medicine, Shinshu University, Matsumoto, Japan.
| | - Satoru Joshita
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan.,Research Center for Next Generation Medicine, Shinshu University, Matsumoto, Japan
| | - Kaname Yoshizawa
- Department of Gastroenterology, NHO Ueda Medical Center, Ueda, Japan
| | - Eiji Tanaka
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Masao Ota
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
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57
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Brandt DYC, César J, Goudet J, Meyer D. The Effect of Balancing Selection on Population Differentiation: A Study with HLA Genes. G3 (BETHESDA, MD.) 2018; 8:2805-2815. [PMID: 29950428 PMCID: PMC6071603 DOI: 10.1534/g3.118.200367] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/21/2018] [Indexed: 01/10/2023]
Abstract
Balancing selection is defined as a class of selective regimes that maintain polymorphism above what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation, as measured by FST. However, balancing selection regimes in which different sets of alleles are maintained in different populations could increase population differentiation. To tackle the connection between balancing selection and population differentiation, we investigated population differentiation at the HLA genes, which constitute the most striking example of balancing selection in humans. We found that population differentiation of single nucleotide polymorphisms (SNPs) at the HLA genes is on average lower than that of SNPs in other genomic regions. We show that these results require using a computation that accounts for the dependence of FST on allele frequencies. However, in pairs of closely related populations, where genome-wide differentiation is low, differentiation at HLA is higher than in other genomic regions. Such increased population differentiation at HLA genes for recently diverged population pairs was reproduced in simulations of overdominant selection, as long as the fitness of the homozygotes differs between the diverging populations. The results give insight into a possible "divergent overdominance" mechanism for the nature of balancing selection on HLA genes across human populations.
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Affiliation(s)
- Débora Y C Brandt
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jônatas César
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Diogo Meyer
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, SP, Brazil
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58
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Wu XL, Li ZY, Bi XY, Zhao H, Zhao JJ, Zhou JG, Han Y, Huang Z, Zhang YF, Cai JQ. Human leukocyte antigen gene polymorphisms are associated with systemic inflammation in hepatitis B virus-related hepatocellular carcinoma. Cancer Manag Res 2018; 10:2315-2324. [PMID: 30104900 PMCID: PMC6074760 DOI: 10.2147/cmar.s167574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Systemic inflammation (SI) is associated with tumor progression and overall survival (OS) in patients with hepatocellular carcinoma (HCC). The presence of some single nucleotide polymorphisms (SNPs) in the human leukocyte antigen (HLA) region can influence the prognosis of patients with hepatitis B virus (HBV)-related HCC, although the mechanism remains unknown. This study aimed to analyze the correlations between HLA gene polymorphisms and SI. Patients and methods This study included 330 patients with HCC. The clinical parameters were reviewed, and five SNPs, namely rs2647073, rs3997872, rs3077, rs7453920, and rs7768538, were genotyped using the MassARRAY system. Results The rs3997872, rs7453920, and rs7768538 genotypes were found to be significantly associated with OS (P<0.05). The rs7453920 genotype was significantly associated with the neutrophil/lymphocyte ratio (NLR; P=0.001), which was used as an SI index with a threshold determined by receiver operating characteristic analysis. An elevated NLR was also an independent predictor of OS according to univariate and multivariate analyses (P<0.001). Conclusion Our data show that HLA gene polymorphisms are associated with SI in patients with HBV-related HCC, and the absence of minor allele A (rs7453920) promotes SI and shortens OS.
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Affiliation(s)
| | - Zhi-Yu Li
- Department of Hepatobiliary Surgery,
| | - Xin-Yu Bi
- Department of Hepatobiliary Surgery,
| | - Hong Zhao
- Department of Hepatobiliary Surgery,
| | | | | | - Yue Han
- Department of Interventional Therapies, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
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Lumley SF, McNaughton AL, Klenerman P, Lythgoe KA, Matthews PC. Hepatitis B Virus Adaptation to the CD8+ T Cell Response: Consequences for Host and Pathogen. Front Immunol 2018; 9:1561. [PMID: 30061882 PMCID: PMC6054973 DOI: 10.3389/fimmu.2018.01561] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022] Open
Abstract
Chronic viral hepatitis infections are a major public health concern, with an estimated 290 million individuals infected with hepatitis B virus (HBV) globally. This virus has been a passenger in human populations for >30,000 years, and remains highly prevalent in some settings. In order for this endemic pathogen to persist, viral adaptation to host immune responses is pre-requisite. Here, we focus on the interplay between HBV infection and the CD8+ T cell response. We present the evidence that CD8+ T cells play an important role in control of chronic HBV infection and that the selective pressure imposed on HBV through evasion of these immune responses can potentially influence viral diversity, chronicity, and the outcome of infection, and highlight where there are gaps in current knowledge. Understanding the nature and mechanisms of HBV evolution and persistence could shed light on differential disease outcomes, including cirrhosis and hepatocellular carcinoma, and help reach the goal of global HBV elimination by guiding the design of new strategies, including vaccines and therapeutics.
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Affiliation(s)
- Sheila F. Lumley
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Anna L. McNaughton
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford BRC, John Radcliffe Hospital, Oxford, United Kingdom
| | - Katrina A. Lythgoe
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Philippa C. Matthews
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford BRC, John Radcliffe Hospital, Oxford, United Kingdom
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60
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Kim TH, Lee EJ, Choi JH, Yim SY, Lee S, Kang J, Lee YR, Lee HA, Choi HS, Kim ES, Keum B, Seo YS, Yim HJ, Jeen YT, Chun HJ, Lee HS, Kim CD, Woo HG, Um SH. Identification of novel susceptibility loci associated with hepatitis B surface antigen seroclearance in chronic hepatitis B. PLoS One 2018; 13:e0199094. [PMID: 29975729 PMCID: PMC6033413 DOI: 10.1371/journal.pone.0199094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 05/31/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND/AIMS The seroclearance of hepatitis B virus (HBV) surface antigen (HBsAg) is regarded as a functional cure of chronic hepatitis B (CHB) although it occurs rarely. Recently, several genome-wide association studies (GWASs) revealed various genetic alterations related to the clinical course of HBV infection. However, all of these studies focused on the progression of HBV infection to chronicity and had limited application because of the heterogeneity of HBV genotypes. In the present study, we aimed to determine susceptibility genetic markers for seroclearance of HBsAg in CHB patients with a homogenous viral genotype. METHODS One hundred patients with CHB who had experienced HBsAg seroclearance before 60 years of age and another 100 with CHB showing high serum levels of HBsAg even after 60 years of age were enrolled. Extreme-phenotype GWAS was conducted using blood samples of participants. RESULTS We identified three single nucleotide polymorphisms, rs7944135 (P = 4.17 × 10-6, odds ratio [OR] = 4.16, 95% confidence interval [CI] = 2.27-7.63) at 11q12.1, rs171941 (P = 3.52×10-6, OR = 3.69, 95% CI = 2.13-6.42) at 5q14.1, and rs6462008 (P = 3.40×10-6, OR = 0.34, 95% CI = 0.22-0.54) at 7p15.2 as novel susceptibility loci associated with HBsAg seroclearance in patients with CHB. The flanking genes at these loci including MPEG1, DTX4, MTX3, and HOXA13 were suggested to have functional significance. In addition, through functional analysis, CXCL13 was also presumed to be related. CONCLUSIONS To the best of our knowledge, this study is the first GWAS regarding the seroclearance of HBsAg in CHB patients. We identify new susceptibility loci for cure of CHB, providing new insights into its pathophysiology.
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Affiliation(s)
- Tae Hyung Kim
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Eun-Ju Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea
| | - Ji-Hye Choi
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea
- Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
| | - Sun Young Yim
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Sunwon Lee
- Department of Computer Science and Engineering, Korea University College of Informatics, Seoul, Korea
| | - Jaewoo Kang
- Department of Computer Science and Engineering, Korea University College of Informatics, Seoul, Korea
| | - Yoo Ra Lee
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Han Ah Lee
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Hyuk Soon Choi
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Eun Sun Kim
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Bora Keum
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Yeon Seok Seo
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Hyung Joon Yim
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Yoon Tae Jeen
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Hoon Jai Chun
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Hong Sik Lee
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chang Duck Kim
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Hyun Goo Woo
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea
- Department of Biomedical Science, Graduate School, Ajou University, Suwon, Korea
- * E-mail: (HGW); (SHU)
| | - Soon Ho Um
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
- * E-mail: (HGW); (SHU)
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Tan W, Xia J, Dan Y, Li M, Lin S, Pan X, Wang H, Tang Y, Liu N, Tan S, Liu M, He W, Zhang W, Mao Q, Wang Y, Deng G. Genome-wide association study identifies HLA-DR variants conferring risk of HBV-related acute-on-chronic liver failure. Gut 2018; 67:757-766. [PMID: 28130311 DOI: 10.1136/gutjnl-2016-313035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Acute-on-chronic liver failure (ACLF) is an extreme condition after severe acute exacerbation of chronic hepatitis B; however, the underlying genetic factors involved in its onset and progression are currently unclear. DESIGN We carried out a genome-wide association study among 399 HBV-related ACLFs (cases) and 401 asymptomatic HBV carriers (AsCs, as controls) without antiviral treatment. The initial findings were replicated in four independent case-control sets (a total of 901 ACLFs and 1686 AsCs). The roles of risk variants on clinical traits of ACLF were also analysed. RESULTS Among 1300 ACLFs and 2087 AsCs, we identified rs3129859 at human leucocyte antigen (HLA) class II region (chromosome 6p21.32) associated with HBV-related ACLF (combined P dominant =2.64×10-20, OR=1.83). Analysis identified HLA-DRB1*12:02 as the top susceptible HLA allele associated with ACLF (p=3.94×10-6, OR=2.05). The association of rs3129859 was robust in ACLF subgroups (ACLFs with liver cirrhosis, p=1.36×10-16; ACLFs without liver cirrhosis, p=1.52×10-7), and patients at low-replicative phase (p=6.36×10-11, OR=2.29) or HBV e antigen-negative chronic hepatitis B phase (p=1.51×10-14, OR=1.86). Clinical traits analysis in patients with ACLF showed that the risky rs3129859*C allele was also associated with prolonged prothrombin time, faster progression to ascites development and higher 28-day mortality. CONCLUSIONS Our genome-wide association study identified HLA-DR as the major locus for susceptibility to HBV-related ACLF. Our findings highlight the importance of HLA class II restricted CD4+ T-cell pathway on the immunopathogenesis of HBV-related ACLF.
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Affiliation(s)
- Wenting Tan
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Jie Xia
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China.,Clinical and Research Center of Liver Failure, The 302nd Hospital, Beijing, China
| | - Yunjie Dan
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Mengying Li
- Department of Infectious Diseases, The 303rd Hospital, Nanning, Guangxi, China
| | - Shide Lin
- Department of Infectious Diseases, The Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China
| | - Xingnan Pan
- Clinical Liver Center, The 180th Hospital, Quanzhou, Fujian, China
| | - Huifen Wang
- Clinical and Research Center of Liver Failure, The 302nd Hospital, Beijing, China
| | - Yingzi Tang
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Nana Liu
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Shun Tan
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Ming Liu
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Weiwei He
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Qing Mao
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Yuming Wang
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China
| | - Guohong Deng
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, China.,Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing, China.,Institute of Immunology, Third Military Medical University, Chongqing, China
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Li X, Zhou TC, Wu CH, Tao LL, Bi R, Chen LJ, Deng DY, Liu C, Otecko NO, Tang Y, Lai X, Zhang L, Wei J. Correlations between mitochondrial DNA haplogroup D5 and chronic hepatitis B virus infection in Yunnan, China. Sci Rep 2018; 8:869. [PMID: 29343698 PMCID: PMC5772044 DOI: 10.1038/s41598-018-19184-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial abnormality is frequently reported in individuals with hepatitis B virus (HBV) infection, but the associated hosts’ mitochondrial genetic factors remain obscure. We hypothesized that mitochondria may affect host susceptibility to HBV infection. In this study, we aimed to detect the association between chronic HBV infection and mitochondrial DNA in Chinese from Yunnan, Southwest China. A total of 272 individuals with chronic HBV infection (CHB), 310 who had never been infected by HBV (healthy controls, HC) and 278 with a trace of HBV infection (spontaneously recovered, SR) were analysed for mtDNA sequence variations and classified into respective haplogroups. Haplogroup frequencies were compared between HBV infected patients, HCs and SRs. Haplogroup D5 presented a higher frequency in CHBs than in HCs (P = 0.017, OR = 2.87, 95% confidence interval [CI] = (1.21–6.81)) and SRs (P = 0.049, OR = 2.90, 95% CI = 1.01–8.35). The network of haplogroup D5 revealed a distinct distribution pattern between CHBs and non-CHBs. A trend of higher viral load among CHBs with haplogroup D5 was observed. Our results indicate the risk potential of mtDNA haplogroup D5 in chronic HBV infection in Yunnan, China.
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Affiliation(s)
- Xiao Li
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Tai-Cheng Zhou
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Chang-Hui Wu
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Li-Lin Tao
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, Yunnan, China
| | - Li-Jun Chen
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - De-Yao Deng
- Clinical Laboratory of the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Chang Liu
- Clinical Laboratory of the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Yang Tang
- The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, 650000, China
| | - Xin Lai
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China
| | - Liang Zhang
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China.
| | - Jia Wei
- Central Lab, Liver Disease Research Center, the Second People's Hospital of Yunnan Province, Kunming, 650203, Yunnan, China.
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63
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Sy BT, Hoan NX, Tong HV, Meyer CG, Toan NL, Song LH, Bock CT, Velavan TP. Genetic variants of interferon regulatory factor 5 associated with chronic hepatitis B infection. World J Gastroenterol 2018; 24:248-256. [PMID: 29375210 PMCID: PMC5768943 DOI: 10.3748/wjg.v24.i2.248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/15/2017] [Accepted: 11/27/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate possible effects of IRF5 polymorphisms in the 3’ UTR region of the IFR5 locus on susceptibility to hepatitis B virus (HBV) infection and progression of liver diseases among clinically classified Vietnamese patients.
METHODS Four IFR5 SNPs (rs13242262A/T, rs77416878C/T, rs10488630A/G, and rs2280714T/C) were genotyped in clinically classified HBV patients [chronic hepatitis B (CHB). n = 99; liver cirrhosis (LC), n = 131; hepatocellular carcinoma (HCC), n = 149] and in 242 healthy controls by direct sequencing and TaqMan real-time PCR assays.
RESULTS Comparing patients and controls, no significant association was observed for the four IFR5 variants. However, the alleles rs13242262T and rs10488630G contributed to an increased risk of liver cirrhosis (LC vs CHB: OR = 1.5, 95%CI: 1.1-2.3, adjusted P = 0.04; LC vs CHB: OR = 1.7, 95%CI: 1.1-2.6, adjusted P = 0.019). Haplotype IRF5*TCGT constructed from 4 SNPs was observed frequently in LC compared to CHB patients (OR = 2.1, 95%CI: 1.2-3.3, adjusted P = 0.008). Haplotype IRF5*TCAT occurred rather among CHB patients than in the other HBV patient groups (LC vs CHB: OR = 0.4, 95%CI: 0.2-0.8, adjusted P = 0.03; HCC vs CHB: OR = 0.3, 95%CI: 0.15-0.7, adjusted P = 0.003). The IRF5*TCAT haplotype was also associated with increased levels of ALT, AST and bilirubin.
CONCLUSION Our study shows that IFR5 variants may contribute as a host factor in determining the pathogenesis in chronic HBV infections.
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Affiliation(s)
- Bui Tien Sy
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam
- Institute of Clinical Infectious Diseases, 108 Military Central Hospital, Hanoi, Vietnam
| | - Nghiem Xuan Hoan
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam
- Institute of Clinical Infectious Diseases, 108 Military Central Hospital, Hanoi, Vietnam
- Institute of Tropical Medicine, University of Tübingen, Tübingen 72074, Germany
| | - Hoang Van Tong
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam
- Department of Pathophysiology, Vietnam Military Medical University, Hanoi, Vietnam
| | - Christian G Meyer
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam
- Institute of Tropical Medicine, University of Tübingen, Tübingen 72074, Germany
| | - Nguyen Linh Toan
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam
- Department of Pathophysiology, Vietnam Military Medical University, Hanoi, Vietnam
| | - Le Huu Song
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam
- Institute of Clinical Infectious Diseases, 108 Military Central Hospital, Hanoi, Vietnam
| | - Claus-Thomas Bock
- Institute of Tropical Medicine, University of Tübingen, Tübingen 72074, Germany
- Department of Infectious Diseases, Robert Koch Institute, Berlin 13302, Germany
| | - Thirumalaisamy P Velavan
- Vietnamese-German Center of Excellence in Medical Research, Hanoi, Vietnam
- Institute of Tropical Medicine, University of Tübingen, Tübingen 72074, Germany
- Department of Pathophysiology, Vietnam Military Medical University, Hanoi, Vietnam
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64
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Liu Z, Song C, Wen J, Xu L, Liu Y, Zhu J, Zhu L, Hu Z, Ma H, Liu L. Hepatitis B virus genotypes, expression quantitative trait loci for ZNRD1-AS1 and their interactions in hepatocellular carcinoma. Oncotarget 2018; 7:44076-44083. [PMID: 27286450 PMCID: PMC5190080 DOI: 10.18632/oncotarget.9854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/01/2016] [Indexed: 12/13/2022] Open
Abstract
Genetic variants in zinc ribbon domain-containing 1 antisense RNA 1 (ZNRD1-AS1) have been reported to be associated with development of hepatocellular carcinoma (HCC). We sought to determine the influences of ZNRD1-AS1 polymorphisms and their interactions with Hepatitis B virus (HBV) genotypes on the risk of HCC. In this study, we conducted a large population case-control study with 1,507 HBV-related HCC cases and 1,560 HBV persistent carriers. Three single-nucleotide polymorphisms (SNPs) in ZNRD1-AS1 (rs3757328, rs6940552 and rs9261204) were genotyped using a TaqMan allelic discrimination assay, and the HBV genotypes were identified by multiplex PCR. We found consistently significant associations between the ZNRD1-AS1 rs6940552 and rs9261204 SNPs with an increased risk of HCC (additive genetic model: adjusted OR = 1.16, 95% CI = 1.03-1.32 for rs6940552; adjusted OR =1.20, 95% CI = 1.06-1.35 for rs9261204) and found a borderline association between rs3757328 and HCC risk. Besides, we observed a dose-dependent relationship between increasing numbers of variant alleles of the SNPs and HCC risk (P for trend <0.001). Moreover, we observed a stronger combined effect of the three SNPs on HCC risk among the subjects infected with non-B genotype HBV (adjusted OR = 1.26, 95% CI = 1.05-1.50) compared with HBV B-related genotypes (adjusted OR = 0.89, 95% CI = 0.69-1.15; P= 0.029 for heterogeneity test). We also found that a multiplicative interaction between the variant alleles and the HBV genotype significantly affected HCC susceptibility (P = 0.030). Together, these results indicate that ZNRD1-AS1 may influence HCC risk accompanied by HBV genotypes.
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Affiliation(s)
- Zhenzhen Liu
- Digestive Endoscopy Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ci Song
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Juan Wen
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Nanjing, China
| | - Lu Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yao Liu
- Pathology Center and Department of Pathology, Soochow University, Suzhou, China
| | - Jian Zhu
- Qidong Liver Cancer Institute, The First People's Hospital of Qidong, Qidong, China
| | - Liguo Zhu
- Department of Infection Diseases, Jiangsu Province Center for Disease Prevention and Control, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Li Liu
- Digestive Endoscopy Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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65
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Virological and Clinical Characteristics of Hepatitis B Virus Genotype A. J Gastroenterol 2018; 53:18-26. [PMID: 28687901 DOI: 10.1007/s00535-017-1367-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/30/2017] [Indexed: 02/04/2023]
Abstract
Hepatitis B virus (HBV) infection is one of the most prevalent chronic viral infections in humans. The overall prevalence of hepatitis B surface antigen (HBsAg) is reported to be 3.6%; however, it varies depending upon the geographic area. HBV is classified into ten genotypes (A through J) on the basis of an intergroup genomic divergence of > 8%. Specifically, HBV genotype A exhibits several unique virological and clinical characteristics and can be further classified into seven subtypes. Among them, subtype A2 or Ae (A2/[e]) is occasionally responsible for nosocomial infection and among homosexual males. Regarding virological factors, the G1896A precore mutation is rarely observed in genotype A as it would disrupt an essential stem-loop structure in the ε signal essential for pregenomic RNA packaging. HBV genotype A also harbors a 6-nucleotide C-terminal insertion in the hepatitis B-e antigen (HBeAg) precursor, resulting in a variable-length HBeAg protein product observed in serum of positive patients. These molecular traits likely contribute to the specific clinical presentation of genotype A-infected patients, such as mild acute hepatitis B (AHB), longer persistence of HBsAg positivity in AHB, and increased chronicity after AHB in adults. However, genotype A shows a better response to interferon than other genotypes in chronic hepatitis B patients. Here, we review the virological and clinical characteristics of HBV genotype A that will be useful in elucidating the association among persistent viral infection, host genetic factors, and treatment in future studies.
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66
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Li T, Liu F, Zhang L, Ye Q, Fan X, Xue Y, Wang L. Host genetic factors in predicting response status in chronic hepatitis B patients discontinuing nucleos(t)ide analogs. Saudi J Gastroenterol 2018; 24:30-36. [PMID: 29451182 PMCID: PMC5848322 DOI: 10.4103/sjg.sjg_228_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND/AIMS The optimal duration of nucleos(t)ide analogs (NAs) therapy in chronic hepatitis B (CHB) patients remains unsatisfactory. Previous studies have confirmed the important role of host genetic factors in determining the outcome of HBV infection. This study tries to determine the role of host genetic factors in predicting response status in CHB patients discontinuing NAs according to stringent cessation criteria. PATIENTS AND METHODS Participating patients came from a prospective NAs- discontinuation cohort since June 1999. Six single-nucleotide polymorphisms (SNPs) were selected according to previous report. SNaPshot assay was used for DNA SNPs analyses. RESULTS Seventy-six CHB patients were enrolled in our study, of which 61 patients were HBeAg-positive and 15 patients were HBeAg-negative. rs1883832 in the Kozak sequence of CD40 displayed an AUROC of 0.778 in predicting response status in CHB patients with HBeAg seroconversion and a genotype of CT was associated with sustained response in this subpopulation. The diagnostic performance of combinative index (rs1883832, age, and HBsAg at discontinuation) seemed to be better than that of rs1883832, but no statistical difference was observed. rs1883832 was also evaluated as an independent factor for response status by multivariate logistic regression. For HBeAg-negative CHB patients, rs9277535 at HLA-DP presents a Spearman correlation coefficient of 0.582 (P = 0.023) with virological relapse after discontinuation of NAs. CONCLUSIONS rs1883832 serves as a valuable predictive factor for CHB patients with HBeAg seroconversion. rs9277535 at HLA-DP might also be a valuable predictive factor for CHB patients with HBeAg-negative, however, further verifications are recommended due to study limitations.
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Affiliation(s)
- Tao Li
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Shandong, China
| | - Feng Liu
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Shandong, China
| | - Lixin Zhang
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Shandong, China
| | - Qian Ye
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Shandong, China
| | - Xiaoping Fan
- Department of Hepatopathy, Qingdao Infectious Disease Hospital, Shandong, China
| | - Yan Xue
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Shandong, China
| | - Lei Wang
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Shandong, China,Address for correspondence: Prof. Lei Wang, Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Shandong, China. E-mail:
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Qiu B, Jiang W, Olyaee M, Shimura K, Miyakawa A, Hu H, Zhu Y, Tang L. Advances in the genome-wide association study of chronic hepatitis B susceptibility in Asian population. Eur J Med Res 2017; 22:55. [PMID: 29282121 PMCID: PMC5745855 DOI: 10.1186/s40001-017-0288-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 11/01/2017] [Indexed: 12/16/2022] Open
Abstract
Chronic hepatitis B (CHB) is the most common chronic liver disease resulting from viral infection and has become a serious threat to human health. Each year, about 1.2 million people in the world die from diseases caused by chronic infection of hepatitis B virus. The genetic polymorphism is significantly associated with the susceptibility to chronic hepatitis B. Genome-wide association study was recently developed and has become an important tool to detect susceptibility genes of CHB. To date, a number of CHB-associated susceptibility loci and regions have been identified by scientists over the world. To clearly understand the role of susceptibility loci in the occurrence of CHB is important for the early diagnosis and prevention of CHB.
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Affiliation(s)
- Bing Qiu
- Department of Gastroenterology, Heilongjiang Province Hospital, 82 Zhongshan Road, Harbin, 150036, Heilongjiang, People's Republic of China.
| | - Wei Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Jiamusi University, Jiamusi, 154002, People's Republic of China
| | - Mojtaba Olyaee
- Division of Gastroenterology, Department of Internal Medicine, University of Kansas, Medical Center, Kansas City, 66160, USA
| | - Kenji Shimura
- Department of Gastroenterology, Asahi General Hospital, Chiba, 289-2511, Japan
| | - Akihiro Miyakawa
- Department of Gastroenterology, Asahi General Hospital, Chiba, 289-2511, Japan
| | - Huijing Hu
- Department of Laboratory Diagnosis, Heilongjiang Province Hospital, Harbin, 150036, People's Republic of China
| | - Yongcui Zhu
- Department of Gastroenterology, Heilongjiang Province Hospital, 82 Zhongshan Road, Harbin, 150036, Heilongjiang, People's Republic of China
| | - Lixin Tang
- Department of Gastroenterology, Heilongjiang Province Hospital, 82 Zhongshan Road, Harbin, 150036, Heilongjiang, People's Republic of China
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Yu F, Ma N, Zhang X, Tian S, Geng L, Xu W, Wang M, Jia Y, Liu X, Ma J, Quan Y, Zhang C, Guo L, An W, Liu D. Comprehensive investigating of cytokine and receptor related genes variants in patients with chronic hepatitis B virus infection. Cytokine 2017; 103:10-14. [PMID: 29287219 DOI: 10.1016/j.cyto.2017.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/12/2017] [Accepted: 12/15/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Chronic hepatitis B virus (HBV) infection is a global health problem and the outcome are associated with both viral factors and host genetic factors. High Throughput Sequencing (HTS) technology were used to identify variants associated with liver disease. METHODS Fifty-five Chronic hepatitis B (CHB) patients, fifty-three self-healing HBV (SH) patients and 53 healthy controls (HC) were recruited, 404 cytokine and cytokine receptor related genes were captured and sequenced at high depth (>900X), both variant (Fischer's exact test, P value < 0.05) and gene (SKAT-O gene level test, adjust P value < 0.05) level association were used to identify variants and genes associated with CHB. RESULTS Total 5083 variants have been detected, fifty-four variants were found associated with CHB, most (29/32) variants were located in HLA region, including HLA-B, HLA-C, HLA-DQA1, HLA-DQB1, HLA-DQB2, HLA-DRB1 and HLA-DRB5. Several missense variants were found associated with CHB, including p.E226K in PVR (poliovirus receptor), p.E400A and p.C431R in IL4R (interleukin 4 receptor). Four variants located in 3'UTR (untranslated region) have also been found associated with CHB. CONCLUSION Our study revealed that high through target region sequencing, combined with association analysis at variant and gene level, would be a good way to found variants and genes associated with CHB even at small sample size. Our data implied that chronic hepatitis B patients who carry these variants need intensive monitoring.
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Affiliation(s)
- Fengxue Yu
- Department of Science and Technology, The Hebei Key Laboratory of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
| | - Ning Ma
- Department of Social Medicine and Health Care Management, Hebei Medical University, Shijiazhuang, China
| | - Xiaolin Zhang
- Division of Epidemiology, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Suzhai Tian
- Department of Science and Technology, The Hebei Key Laboratory of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lianxia Geng
- Department of Science and Technology, The Hebei Key Laboratory of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Weili Xu
- Department of Pediatric Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Mingbang Wang
- Shenzhen Following Precision Medical Research institute, Shenzhen, Guangdong, China
| | - Yuan Jia
- Department of Infectious Disease Control, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xuechen Liu
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Junji Ma
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yuan Quan
- Department of Infectious Disease, Hebei Chest Hospital, Shijiazhuang, China
| | - Chaojun Zhang
- Department of Central Laboratory, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lina Guo
- Department of Central Laboratory, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wenting An
- Department of Central Laboratory, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Dianwu Liu
- Division of Epidemiology, School of Public Health, Hebei Medical University, Shijiazhuang, China
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Peeridogaheh H, Meshkat Z, Habibzadeh S, Arzanlou M, Shahi JM, Rostami S, Gerayli S, Teimourpour R. Current concepts on immunopathogenesis of hepatitis B virus infection. Virus Res 2017; 245:29-43. [PMID: 29273341 DOI: 10.1016/j.virusres.2017.12.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 10/04/2017] [Accepted: 12/18/2017] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) infection is a leading cause of liver damage and hepatic inflammation. Upon infection, effective antiviral responses by CD8+ T cells, CD4+ T cells, Natural killer (NK) cells, and monocytes can lead to partial or complete eradication of the viral infection. To date, many studies have shown that the production of inhibitory cytokines such as Interleukin 10 (IL-10), Transforming growth factor beta (TGF-β), along with dysfunction of the dendritic cells (DCs), and the absence of efficient innate immune responses could lead to T cell exhaustion, development of persistent infection, and inability to eradicate the viral infection from liver. Understanding the immunopathogenesis of the virus could be useful in providing further insights toward novel strategies in the eradication of HBV infection.
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Affiliation(s)
- Hadi Peeridogaheh
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Zahra Meshkat
- Antimicrobial Resistance Research Center, Bu Ali Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, IR Iran
| | - Shahram Habibzadeh
- Department of Infectious Diseases, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mohsen Arzanlou
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Jafar Mohammad Shahi
- Department of Infectious Diseases, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Sina Rostami
- Department of Clinical and Molecular Medicine Faculty of Medicine and Health Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sina Gerayli
- Departments of Biology, Western University, London, Ontario, N6A 5B7, Canada
| | - Roghayeh Teimourpour
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran.
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70
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Song Y, Shen Y, Xia X, Zhang AM. Association between genetic polymorphisms of the IL28B gene and leukomonocyte in Chinese hepatitis B virus-infected individuals. PeerJ 2017; 5:e4149. [PMID: 29302390 PMCID: PMC5740955 DOI: 10.7717/peerj.4149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/13/2017] [Indexed: 02/06/2023] Open
Abstract
Background Hepatitis B infection is one of the most severe hepatic diseases in China. Thus, understanding the genetic pathogenesis of hepatitis B virus (HBV)-infected individuals is important. Although no consistent result is obtained in different populations, HBV treatment effect is reportedly associated with the IL28B gene. Methods To investigate the role of the IL28B gene in HBV-infected individuals in Yunnan, China, we screened genotypes of three single nucleotide polymorphisms (SNPs, rs12979860, rs8099917, and rs12980275) in HBV-infected individuals and general controls by using SnapShot and sequencing. Results Results showed no significant difference was found in genotypes, alleles, and haplotypes frequency between the HBV-infected individuals and controls. After dividing the HBV-infected individuals into patients in acute infection, chronic HBV patients, and patients undergoing convalescence, the genotype GT (P = 0.033) and allele G (P = 0.038) of rs8099917 showed statistically higher frequency in the acutely infectious individuals than in the HBV patients undergoing convalescence. HBV viral load was higher in the acutely infectious patients than in the chronic infection group. Strikingly, we found that leukomonocyte (LYM) level was associated with SNPs in the IL28B gene. In addition, the LYM levels were lower in the HBV-infected individuals with genotype CC of rs12979860 and AA of rs12980275 than in the patients with other genotypes of these two SNPs. Conclusion Our results suggested genetic polymorphisms of the IL28B gene were associated with LYM level of HBV-infected individuals.
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Affiliation(s)
- Yuzhu Song
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yunsong Shen
- First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
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71
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Liu F, Zeng J, Zhu D, Zhang R, Xu X, Wang M, Zhang Y, Xia H, Feng Z. Association of polymorphism in the VEGFA gene 3'-UTR +936T/C with susceptibility to biliary atresia in a Southern Chinese Han population. J Clin Lab Anal 2017; 32:e22342. [PMID: 29251369 DOI: 10.1002/jcla.22342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 09/20/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Biliary atresia (BA) is a neonatal disease characterized by chronic inflammation of the bile ducts and progressive aggravation of jaundice, but with a poor prognosis and high mortality. The etiology of BA is still uncertain which may be related to gene defect, virus infection, immune disorder, gene polymorphism. As a proinflammatory cytokine, VEGFA gene polymorphism (rs3025039) has been shown to be related to the pathogenesis of BA in Taiwanese population. METHODS We investigated the association between VEGFA gene polymorphism (rs3025039) and BA susceptibility using the largest case-control cohort, totaling with 506 BA patients and 1473 healthy controls in a Southern Chinese Han population. VEGFA gene polymorphism (rs3025039) was genotyped using the MassARRAY iPLEX Gold system (Sequenom). Odds ratios (OR) and 95% confidence intervals (CIs) were used to access the association between the VEGFA gene polymorphism (rs3025039) and BA risk. RESULTS No significant association was found between the VEGFA gene polymorphism (rs3025039) and BA risk in the overall analysis. CONCLUSION These results suggest that VEGFA gene polymorphism (rs3025039) may not be associated with the risk of BA in the Southern Chinese Han population.
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Affiliation(s)
- Fei Liu
- Southern Medical University, Guangzhou, Guangdong.,Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong
| | - Jixiao Zeng
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong
| | - Deli Zhu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong
| | - Ruizhong Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong
| | - Xiaogang Xu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong
| | - Mengmeng Wang
- Department of Anesthesiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong
| | - Yan Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong
| | - Huimin Xia
- Southern Medical University, Guangzhou, Guangdong.,Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong
| | - Zhichun Feng
- Southern Medical University, Guangzhou, Guangdong.,Division of Neonatology, Affiliated BaYi Children's Hospital, Clinical Medical College in PLAArmy General Hospital, Southern Medical University, Beijing, China.,National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China.,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
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72
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Comprehensive investigation of cytokine- and immune-related gene variants in HBV-associated hepatocellular carcinoma patients. Biosci Rep 2017; 37:BSR20171263. [PMID: 29138264 PMCID: PMC5725607 DOI: 10.1042/bsr20171263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/08/2017] [Accepted: 11/13/2017] [Indexed: 02/06/2023] Open
Abstract
Host genotype may be closely related to the different outcomes of Hepatitis B virus (HBV) infection. To identify the association of variants and HBV infection, we comprehensively investigated the cytokine- and immune-related gene mutations in patients with HBV associated hepatocellular carcinoma (HBV-HCC). Fifty-three HBV-HCC patients, 53 self-healing cases (SH) with HBV infection history and 53 healthy controls (HCs) were recruited, the whole exon region of 404 genes were sequenced at >900× depth. Comprehensive variants and gene levels were compared between HCC and HC, and HCC and SH. Thirty-nine variants (adjusted P<0.0001, Fisher's exact test) and 11 genes (adjusted P<0.0001, optimal unified approach for rare variant association test (SKAT-O) gene level test) were strongly associated with HBV-HCC. Thirty-four variants were from eight human leukocyte antigen (HLA) genes that were previously reported to be associated with HBV-HCC. The novelties of our study are: five variants (rs579876, rs579877, rs368692979, NM_145007:c.*131_*130delTG, NM_139165:exon5:c.623-2->TT) from three genes (REAT1E, NOD-like receptor (NLR) protein 11 (NLRP11), hydroxy-carboxylic acid receptor 2 (HCAR2)) were found strongly associated with HBV-HCC. We found 39 different variants in 11 genes that were significantly related to HBV-HCC. Five of them were new findings. Our data implied that chronic hepatitis B patients who carry these variants are at a high risk of developing HCC.
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73
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Quantitative assessment of HLA-DQ gene polymorphisms with the development of hepatitis B virus infection, clearance, liver cirrhosis, and hepatocellular carcinoma. Oncotarget 2017; 9:96-109. [PMID: 29416599 PMCID: PMC5787527 DOI: 10.18632/oncotarget.22941] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/03/2017] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B is one of the most common infectious diseases, which leads to public health problems in the world, especially in Asian counties. In recent years, extensive human genetic association studies have been carried out to identify susceptible genes and genetic polymorphisms to understand the genetic contributions to the disease progression of HBV infection. HLA-DQ gene variations have been reported to be associated with HBV infection/clearance, disease progression and the development of hepatitis B-related complications, including liver cirrhosis (LC) and hepatocellular carcinoma (HCC). However, the results are either inconclusive or controversial. Therefore, to derive a more precise estimation of the association, a meta-analysis was performed. Our data revealed that the HLA-DQ alleles rs2856718-G, rs7453920-A and rs9275319-G were significantly associated with decreased risk of HBV infection and HBV natural clearance. Logistic regression analyses showed that HLA-DQ alleles rs9275572-A significantly increased HBV infection clearance, and decreased HBV natural clearance. However, rs2856718-G and rs9275572-A were not associated with development of cirrhosis. The HLA-DQ polymorphisms (rs2856718 and rs9275572) were associated with a decreased HBV-related HCC risk in all genetic models, but rs9272105-A increased the risk of HBV-related HCC. In addition, no significant association was observed between HLA-DQ rs9275319-G polymorphism and HBV-related HCC. These stratified analyses were limited due to relatively modest size of correlational studies. In future, further investigation on a large population and different ethnicities are warranted. Our findings contribute to the personalized care and prognosis in hepatitis B.
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74
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Tai D, Jeng W, Lin C. A global perspective on hepatitis B-related single nucleotide polymorphisms and evolution during human migration. Hepatol Commun 2017; 1:1005-1013. [PMID: 29404438 PMCID: PMC5721408 DOI: 10.1002/hep4.1113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 07/25/2017] [Accepted: 09/27/2017] [Indexed: 02/05/2023] Open
Abstract
Genome-wide association studies have indicated that human leukocyte antigen (HLA)-DP and HLA-DQ play roles in persistent hepatitis B virus (HBV) infection in Asia. To understand the evolution of HBV-related single nucleotide polymorphisms (SNPs) and to correlate these SNPs with chronic HBV infection among different populations, we conducted a global perspective study on hepatitis-related SNPs. We selected 12 HBV-related SNPs on the HLA locus and two HBV and three hepatitis C virus immune-related SNPs for analysis. Five nasopharyngeal carcinoma-related SNPs served as controls. All SNP data worldwide from 26 populations were downloaded from 1,000 genomes. We found a dramatic difference in the allele frequency in most of the HBV- and HLA-related SNPs in East Asia compared to the other continents. A sharp change in allele frequency in 8 of 12 SNPs was found between Bengali populations in Bangladesh and Chinese Dai populations in Xishuangbanna, China (P < 0.001); these areas represent the junction of South and East Asia. For the immune-related SNPs, significant changes were found after leaving Africa. Most of these genes shifted from higher expression genotypes in Africa to lower expression genotypes in either Europe or South Asia (P < 0.001). During this two-stage adaptation, immunity adjusted toward a weak immune response, which could have been a survival strategy during human migration to East Asia. The prevalence of chronic HBV infection in Africa is as high as in Asia; however, the HBV-related SNP genotypes are not present in Africa, and so the genetic mechanism of chronic HBV infection in Africa needs further exploration. Conclusion: Two stages of genetic changes toward a weak immune response occurred when humans migrated out of Africa. These changes could be a survival strategy for avoiding cytokine storms and surviving in new environments. (Hepatology Communications 2017;1:1005-1013).
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Affiliation(s)
- Dar‐In Tai
- Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Memorial HospitalLinkou Medical CenterTaoyuan CityTaiwan
| | - Wen‐Juei Jeng
- Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Memorial HospitalLinkou Medical CenterTaoyuan CityTaiwan
| | - Chun‐Yen Lin
- Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Memorial HospitalLinkou Medical CenterTaoyuan CityTaiwan
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75
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Mozzi A, Pontremoli C, Sironi M. Genetic susceptibility to infectious diseases: Current status and future perspectives from genome-wide approaches. INFECTION GENETICS AND EVOLUTION 2017; 66:286-307. [PMID: 28951201 PMCID: PMC7106304 DOI: 10.1016/j.meegid.2017.09.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies (GWASs) have been widely applied to identify genetic factors that affect complex diseases or traits. Presently, the GWAS Catalog includes > 2800 human studies. Of these, only a minority have investigated the susceptibility to infectious diseases or the response to therapies for the treatment or prevention of infections. Despite their limited application in the field, GWASs have provided valuable insights by pinpointing associations to both innate and adaptive immune response loci, as well as novel unexpected risk factors for infection susceptibility. Herein, we discuss some issues and caveats of GWASs for infectious diseases, we review the most recent findings ensuing from these studies, and we provide a brief summary of selected GWASs for infections in non-human mammals. We conclude that, although the general trend in the field of complex traits is to shift from GWAS to next-generation sequencing, important knowledge on infectious disease-related traits can be still gained by GWASs, especially for those conditions that have never been investigated using this approach. We suggest that future studies will benefit from the leveraging of information from the host's and pathogen's genomes, as well as from the exploration of models that incorporate heterogeneity across populations and phenotypes. Interactions within HLA genes or among HLA variants and polymorphisms located outside the major histocompatibility complex may also play an important role in shaping the susceptibility and response to invading pathogens. Relatively few GWASs for infectious diseases were performed. Phenotype heterogeneity and case/control misclassification can affect GWAS power. Adaptive and innate immunity loci were identified in several infectious disease GWASs. Unexpected loci (e.g., lncRNAs) were also associated with infection susceptibility. GWASs should integrate host and pathogen diversity and use complex association models.
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Affiliation(s)
- Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E.MEDEA, 23842 Bosisio Parini, Italy
| | - Chiara Pontremoli
- Bioinformatics, Scientific Institute IRCCS E.MEDEA, 23842 Bosisio Parini, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E.MEDEA, 23842 Bosisio Parini, Italy.
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76
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Okada Y, Uno N, Sato S, Mori S, Sasaki D, Kaku N, Kosai K, Morinaga Y, Hasegawa H, Yanagihara K. Strong influence of human leukocyte antigen-DP variants on response to hepatitis B vaccine in a Japanese population. Vaccine 2017; 35:5662-5665. [PMID: 28882445 DOI: 10.1016/j.vaccine.2017.08.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/14/2017] [Accepted: 08/19/2017] [Indexed: 12/17/2022]
Abstract
Genome-wide association studies (GWASs) have reported that human leukocyte antigen (HLA) variants are associated with chronic hepatitis B, spontaneous hepatitis B virus (HBV) clearance, and response to hepatitis B vaccine. Single nucleotide polymorphisms (SNPs) in HLA-DP (rs9277535 and rs3077) and HLA-DQ (rs2856718 and rs7453920) have been repeatedly associated with chronic hepatitis B and spontaneous HBV clearance. However, the data on the SNPs associated with response to hepatitis B vaccine are inconclusive. The objective of this study was to determine whether these four HLA SNPs that have been identified as risk loci for chronic HBV infection are associated with response to hepatitis B vaccine in a Japanese population. We enrolled 278 medical students who received hepatitis B vaccination and measured anti-hepatitis B surface (HBs) antibody titers 1month after a three-dose vaccination series. We found that rs9277535 and rs3077 in HLA-DP were strongly associated with response to hepatitis B vaccine (odds ratio [OR]=0.31 and 0.32, P=0.004 and 0.010, respectively). These two SNPs were significantly associated with anti-HBs titers in an allele-dependent manner. On the other hand, rs2856718 and rs7453920 in HLA-DQ were not associated with response to hepatitis B vaccine. These results indicate that rs9277535 and rs3077 in HLA-DP are the major determinants of response to hepatitis B vaccine, whereas rs2856718 and rs7453920 in HLA-DQ have little effect on the immune response to hepatitis B vaccine.
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Affiliation(s)
- Yuya Okada
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Naoki Uno
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan.
| | - Shuntaro Sato
- Clinical Research Center, Nagasaki University Hospital, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Sayaka Mori
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Daisuke Sasaki
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Norihito Kaku
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Kosuke Kosai
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Yoshitomo Morinaga
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
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77
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Long-term hepatitis B infection in a scalable hepatic co-culture system. Nat Commun 2017; 8:125. [PMID: 28743900 PMCID: PMC5527081 DOI: 10.1038/s41467-017-00200-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/08/2017] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus causes chronic infections in 250 million people worldwide. Chronic hepatitis B virus carriers are at risk of developing fibrosis, cirrhosis, and hepatocellular carcinoma. A prophylactic vaccine exists and currently available antivirals can suppress but rarely cure chronic infections. The study of hepatitis B virus and development of curative antivirals are hampered by a scarcity of models that mimic infection in a physiologically relevant, cellular context. Here, we show that cell-culture and patient-derived hepatitis B virus can establish persistent infection for over 30 days in a self-assembling, primary hepatocyte co-culture system. Importantly, infection can be established without antiviral immune suppression, and susceptibility is not donor dependent. The platform is scalable to microwell formats, and we provide proof-of-concept for its use in testing entry inhibitors and antiviral compounds. The lack of models that mimic hepatitis B virus (HBV) infection in a physiologically relevant context has hampered drug development. Here, Winer et al. establish a self-assembling, primary hepatocyte co-culture system that can be infected with patient-derived HBV without further modifications.
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78
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Matzaraki V, Kumar V, Wijmenga C, Zhernakova A. The MHC locus and genetic susceptibility to autoimmune and infectious diseases. Genome Biol 2017. [PMID: 28449694 DOI: 10.1186/s13059-017-1207-1.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.
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Affiliation(s)
- Vasiliki Matzaraki
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands. .,Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, PO Box 4950 Nydalen, 0424, Oslo, Norway.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
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79
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Matzaraki V, Kumar V, Wijmenga C, Zhernakova A. The MHC locus and genetic susceptibility to autoimmune and infectious diseases. Genome Biol 2017; 18:76. [PMID: 28449694 PMCID: PMC5406920 DOI: 10.1186/s13059-017-1207-1] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.
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Affiliation(s)
- Vasiliki Matzaraki
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands. .,Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, PO Box 4950 Nydalen, 0424, Oslo, Norway.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
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80
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Langlais D, Fodil N, Gros P. Genetics of Infectious and Inflammatory Diseases: Overlapping Discoveries from Association and Exome-Sequencing Studies. Annu Rev Immunol 2017; 35:1-30. [DOI: 10.1146/annurev-immunol-051116-052442] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David Langlais
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Nassima Fodil
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Philippe Gros
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
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81
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Relationship between HLA-DQ Gene Polymorphism and Hepatitis B Virus Infection. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9679843. [PMID: 28512640 PMCID: PMC5420426 DOI: 10.1155/2017/9679843] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/21/2017] [Accepted: 04/02/2017] [Indexed: 12/24/2022]
Abstract
Hepatitis B virus (HBV) infection is the predominant risk factor for chronic hepatitis B (CHB). The association between HBV infection and human leukocyte antigen- (HLA-) DQ polymorphism (rs2856718 and rs7453920) has been demonstrated in other studies; however, the results were controversial or inconclusive. Therefore, to derive a more precise estimation of the association, a meta-analysis was performed. Crude odds ratios (ORs) and their 95% confidence intervals (CIs) were used to assess the strength of association between HLA-DQ polymorphism (rs2856718 and rs7453920) and HBV infection risk. A total of 11 articles were used to evaluate the effect of the two polymorphisms on risk of HBV infection. The pooled data showed that HLA-DQ rs2856718-G polymorphism showed protection against HBV infection, and rs2856718-A was a risk factor for chronic HBV infection. The pooled risk estimates indicated that HLA-DQ rs7453920-A polymorphism was associated with decreased risk of HBV infection, and rs7453920-G serves as a risk factor in HBV infection. However, these stratified analyses were lacking credibility due to the limitation of correlational study numbers; further investigation on a large population and different ethnicities is warranted.
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82
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Zhang Y, Li Y, Wu M, Cao P, Liu X, Ren Q, Zhai Y, Xie B, Hu Y, Hu Z, Bei J, Ping J, Liu X, Yu Y, Guo B, Lu H, Liu G, Zhang H, Cui Y, Mo Z, Shen H, Zeng YX, He F, Zhang H, Zhou G. Comprehensive assessment showed no associations of variants at the SLC10A1 locus with susceptibility to persistent HBV infection among Southern Chinese. Sci Rep 2017; 7:46490. [PMID: 28429786 PMCID: PMC5399367 DOI: 10.1038/srep46490] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/17/2017] [Indexed: 02/07/2023] Open
Abstract
The sodium taurocholate cotransporting polypeptide (NTCP) encoded by SLC10A1 was recently demonstrated to be a functional receptor for hepatitis B virus (HBV). The role of SLC10A1 polymorphisms, particularly the Ser267Phe variant (rs2296651) in exon 4, has been frequently investigated in regard to risk of persistent HBV infection. However, these investigations have generated conflicting results. To examine whether common genetic variation at the SLC10A1 locus is associated with risk of persistent HBV infection, haplotype-tagging and imputed single nucleotide polymorphisms (SNPs) were assessed in two case-control sample sets, totally including 2,550 cases (persistently HBV infected subjects, PIs) and 2,124 controls (spontaneously recovered subjects, SRs) of Southern Chinese ancestry. To test whether rare or subpolymorphic SLC10A1 variants are associated with disease risk, the gene's exons in 244 cases were sequenced. Overall, we found neither SNPs nor haplotypes of SLC10A1 showed significant association in the two sample sets. Furthermore, no significant associations of rare variants or copy number variation covering SLC10A1 were observed. Finally, expression quantitative trait locus analyses revealed that SNPs potentially affecting SLC10A1 expression also showed no significant associations. We conclude that genetic variation at the SLC10A1 locus is not likely a major risk factor of persistent HBV infection among Southern Chinese.
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Affiliation(s)
- Ying Zhang
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Yuanfeng Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Miantao Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Pengbo Cao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Xiaomin Liu
- Department of Laboratory Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qian Ren
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Yun Zhai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Bobo Xie
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Yanling Hu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, MOE Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jinxin Bei
- State Key Laboratory of Oncology in Southern China, Guangzhou, China
| | - Jie Ping
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Xinyi Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Yinghua Yu
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Bingqian Guo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Hui Lu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Guanjun Liu
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Haitao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Ying Cui
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, MOE Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in Southern China, Guangzhou, China
| | - Fuchu He
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Hongxing Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
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83
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Su M, Chen H, Zeng Y, Chen T, Chen J, Jiang L, Liu C, Yang B, Ou Q. Association of Genetic Variation of CIITA and NTCP with Chronic Hepatitis B Virus Infection in Han Chinese Populations. HEPATITIS MONTHLY 2017; 17. [DOI: 10.5812/hepatmon.33646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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84
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Liu Y, Zhou Q, He XS, Song LM, Chen L, Jiao WJ, Shen T, Yao S, Wu H, Hu ZB, Gao TM, Li JM. Genetic variants in ERBB4 is associated with chronic hepatitis B virus infection. Oncotarget 2016; 7:4981-92. [PMID: 26701850 PMCID: PMC4826259 DOI: 10.18632/oncotarget.6650] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/05/2015] [Indexed: 12/22/2022] Open
Abstract
Background The role of ERBB4 in liver disease has seldom been reported. This study aims to find genetic markers at ERBB4 for chronic hepatitis B virus (HBV) infection and determine the role of ERBB4 in liver injury. Methods We selected and genotyped three single nucleotide polymorphisms and one insertion/deletion (Ins/Del) at the 5′ and 3′ untranslated region (UTR) of ERBB4 in a case-control study including 1344 pairs of HBV carriers and HBV natural clearance subjects. The luciferase reporter system was applied to study the regulative role of Ins/Del on ERBB4. Further, ERBB4 knockout mice were used to study the role of ERBB4 in liver injury. Proteomic quantification was performed by HPLC-MS/MS analysis to identify liver protein profile change between liver-specific ERBB4 knockout and control mice. Results rs6147150 Ins/Del and rs1836724 T>C at the 3′ UTR of ERBB4 were associated with reduced risk of chronic HBV infection (P = 0.002 and 0.004, respectively). Besides, the 12bp deletion at the 3′ UTR increased ERBB4 expression due to lacking let-7c binding site. In addition, loss of ERBB4 led to more severe acute or chronic inflammation in mouse liver injury models. Further, quantitative proteomic analysis and data from the cancer genome atlas revealed that ACLY, an enzyme key for de novo lipogenesis, was negatively correlated with ERBB4. Conclusions ERBB4 plays protective role from liver injury and its 3′UTR genetic variants could be genetic markers for chronic HBV infection.
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Affiliation(s)
- Yao Liu
- Department of Pathology, Medical College of Soochow University, Suzhou 215123, People's Republic of China.,Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Qun Zhou
- Department of Pathology, Medical College of Soochow University, Suzhou 215123, People's Republic of China
| | - Xiao-Shun He
- Department of Pathology, Medical College of Soochow University, Suzhou 215123, People's Republic of China
| | - Li-Ming Song
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Lin Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Wei-Juan Jiao
- Department of Pathology, Medical College of Soochow University, Suzhou 215123, People's Republic of China
| | - Tong Shen
- Department of Pathology, Medical College of Soochow University, Suzhou 215123, People's Republic of China
| | - Su Yao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Hua Wu
- Department of Pathology, Medical College of Soochow University, Suzhou 215123, People's Republic of China
| | - Zhi-Bin Hu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing 211166, People's Republic of China
| | - Tian-Ming Gao
- Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Jian-Ming Li
- Department of Pathology, Medical College of Soochow University, Suzhou 215123, People's Republic of China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, People's Republic of China
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85
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Moudi B, Heidari Z, Mahmoudzadeh-Sagheb H. Impact of host gene polymorphisms on susceptibility to chronic hepatitis B virus infection. INFECTION GENETICS AND EVOLUTION 2016; 44:94-105. [DOI: 10.1016/j.meegid.2016.06.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/21/2016] [Accepted: 06/22/2016] [Indexed: 12/15/2022]
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86
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Rehman SU, Rauf M, Abbas Z, Hamed MH, Qadri I. Role of Some Predominant Host Immunomodulators' Single Nucleotide Polymorphisms in Severity of Hepatitis B Virus and Hepatitis C Virus Infection. Viral Immunol 2016; 29:536-545. [PMID: 27676210 DOI: 10.1089/vim.2016.0062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatitis B and C infections can be either acute or chronic. The chronic infection can culminate in liver cirrhosis and hepatocellular carcinoma. Influence of the host genetic makeup on conversion of acute to chronic infection, development of cirrhosis, and hepatocellular carcinoma is an interesting area of research. Variability in different immune system genes may account for such differences in the outcome of infection. This article discusses single nucleotide polymorphisms in different host immunomodulator genes that have been frequently reported to influence the outcome of infection and severity of disease. The genetic variability could be utilized for the prediction of disease outcome and treatment responses.
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Affiliation(s)
- Shafiq Ur Rehman
- 1 Department of Microbiology and Molecular Genetics, University of the Punjab , Lahore, Pakistan
| | - Mahd Rauf
- 1 Department of Microbiology and Molecular Genetics, University of the Punjab , Lahore, Pakistan
| | - Zaigham Abbas
- 1 Department of Microbiology and Molecular Genetics, University of the Punjab , Lahore, Pakistan
| | - Muhammed Haroon Hamed
- 2 Department of Biological Sciences, King Abdul Aziz University , Jeddah, Kingdom of Saudi Arabia
| | - Ishtiaq Qadri
- 2 Department of Biological Sciences, King Abdul Aziz University , Jeddah, Kingdom of Saudi Arabia
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87
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Sun L, Zhang X, He L. GWAS promotes precision medicine in China. J Genet Genomics 2016; 43:477-9. [DOI: 10.1016/j.jgg.2016.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 05/30/2016] [Accepted: 05/30/2016] [Indexed: 11/28/2022]
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88
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Stelma F, Jansen L, Sinnige MJ, van Dort KA, Takkenberg RB, Janssen HLA, Reesink HW, Kootstra NA. HLA-C and KIR combined genotype as new response marker for HBeAg-positive chronic hepatitis B patients treated with interferon-based combination therapy. J Viral Hepat 2016; 23:652-9. [PMID: 26945896 DOI: 10.1111/jvh.12525] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/20/2016] [Indexed: 12/24/2022]
Abstract
Current treatment for chronic hepatitis B infection (CHB) consists of interferon-based therapy. However, for unknown reasons, a large proportion of patients with CHB do not respond to this treatment. Hence, there is a pressing need to establish response markers to select patients who will benefit from therapy and to spare potential nonresponders from unnecessary side effects of antiviral therapy. Here, we assessed whether HLA-C and KIR genotypes were associated with treatment outcome for CHB. Twelve SNPs in or near the HLA-C gene were genotyped in 86 CHB patients (41 HBeAg positive; 45 HBeAg negative) treated with peginterferon alfa-2a + adefovir. Genotyping of killer immunoglobin-like receptors (KIRs) was performed by SSP-PCR. One SNP in HLA-C (rs2308557) was significantly associated with combined response in HBeAg-positive CHB patients (P = 0.003). This SNP is linked to the HLA-C group C1 or C2 classification, which controls KIR binding. The combination of KIR2DL1 with its ligand HLA-C2 was observed significantly more often in HBeAg-positive patients with a combined response (13/14) than in nonresponders (11/27, P = 0.001). Patients with the KIR2DL1/C2 genotype had significantly higher baseline ALT levels (136 vs 50 U/L, P = 0.002) than patients without this combination. Furthermore, KIR2DL1-C2 predicted response independent of HBV genotype and ALT at baseline. HLA-C and KIR genotype is strongly associated with response in HBeAg-positive CHB patients treated with interferon-based therapy. In combination with other known response markers, HLA-C/KIR genotype could enable the selection of patients more likely to respond to interferon-based therapy.
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Affiliation(s)
- F Stelma
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, the Netherlands.,Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands
| | - L Jansen
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, the Netherlands.,Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands
| | - M J Sinnige
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands
| | - K A van Dort
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands
| | - R B Takkenberg
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, the Netherlands
| | - H L A Janssen
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, the Netherlands.,Toronto Centre for Liver Disease, Toronto Western & General Hospital, University Health Network, Toronto, Canada
| | - H W Reesink
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, the Netherlands.,Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands
| | - N A Kootstra
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands
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89
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Fan J, Huang X, Chen J, Cai Y, Xiong L, Mu L, Zhou L. Host Genetic Variants in HLA Loci Influence Risk for Hepatitis B Virus Infection in Children. HEPATITIS MONTHLY 2016; 16:e37786. [PMID: 27795724 PMCID: PMC5070562 DOI: 10.5812/hepatmon.37786] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatitis B virus (HBV) infection is a serious public health problem in China and worldwide. Mother-to-child transmission is one of HBV's main transmission routes in highly endemic regions. Genome-wide association studies (GWAS) identify single nucleotide polymorphisms (SNPs) at HLA loci as associated with HBV infection. However, the mechanisms of HBV perinatal transmission and breakthrough in children have not yet been clearly defined. OBJECTIVES We aimed to explore the association between SNPs at HLA loci and HBV infection and breakthrough in children. METHODS A total of 274 HBV-infected children and 353 controls were selected among children aged between 6 months and 12 years in China. Seven SNPs at HLA-DP and HLA-DQ loci were genotyped to analyze their association with HBV infection in children. RESULTS Alleles G in both HLA-DPA1 rs3077 and HLA-DPB1 rs9277535 were found to be significantly associated with HBV infection in children with odds ratios (OR) of 1.309 (95% CI 1.046 to 1.639) and 1.411 (95% CI 1.125 to 1.771), respectively. In addition, overdominant analysis found that the rs2281388 (HLA-DPB1) GA genotype and the rs9366816 (HLA-DPB2) TC genotype were related to HBV infection (rs2281388, OR = 1.422, 95% CI: 1.032-1.961; rs9366816, OR = 1.444, 95% CI: 1.045-1.994). Furthermore, this study highlighted that rs9277535 was also significantly associated with HBV breakthrough infection in children whose mothers were positive for hepatitis B surface antigen (HBsAg). CONCLUSIONS Our study confirmed that genetic variants in HLA-DPA1 and HLA-DPB1 loci have significant associations with HBV infection, especially with HBV breakthrough in children. This study provides insight into HBV infection in children and is valuable for the targeted management of, and control strategies for, this disease.
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Affiliation(s)
- Jie Fan
- Department of Epidemiology, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Xin Huang
- Department of Epidemiology, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
| | - Juan Chen
- Key Laboratory of Molecular Biology for Infectious Diseases, Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yiling Cai
- Obstetrics and Gynecology Department, Chengdu Women and Children’s Central Hospital, Sichuan Province, China
| | - Lin Xiong
- Maternal and Child Health Hospital of Chongqing Yuzhong District, Chongqing, China
| | - Lihong Mu
- Department of Epidemiology, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
- Corresponding Authors: Lihong Mu, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, School of Public Health and Management, Chongqing Medical University, Chongqing, China. Tel/Fax: +86-2368485008, E-mail: ; Li Zhou, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, School of Public Health and Management, Chongqing Medical University, Chongqing, China. Tel/Fax: +86-2368486780, E-mail:
| | - Li Zhou
- Department of Epidemiology, School of Public Health and Management, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, Chongqing Medical University, Chongqing, China
- Key Laboratory of Molecular Biology for Infectious Diseases, Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- Corresponding Authors: Lihong Mu, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, School of Public Health and Management, Chongqing Medical University, Chongqing, China. Tel/Fax: +86-2368485008, E-mail: ; Li Zhou, Research Center for Medicine and Social Development, Innovation Center for Social Risk Governance in Health, School of Public Health and Management, Chongqing Medical University, Chongqing, China. Tel/Fax: +86-2368486780, E-mail:
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90
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Jiang X, Su K, Tao J, Fan R, Xu Y, Han H, Li L, Li MD. Association of STAT4 polymorphisms with hepatitis B virus infection and clearance in Chinese Han population. Amino Acids 2016; 48:2589-2598. [PMID: 27444301 DOI: 10.1007/s00726-016-2283-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 06/18/2016] [Indexed: 12/22/2022]
Abstract
Genome-wide association study indicates that STAT4 is a plausible candidate for an association study with HBV-related liver diseases. We aimed to examine the roles of STAT4 polymorphisms on HBV-related liver diseases in a Chinese Han population. We selected 13 SNPs in STAT4 based on the HapMap database to investigate their associations in 3,033 participants. SNP rs7574865 was significantly associated with HBV infection [odds ratio (OR) 1.15; 95 % confidence interval (CI) 1.00, 1.31; P = 0.046] and clearance (OR 1.17; 95 % CI 1.02, 1.33; P = 0.028). Further, haplotype-based association analysis indicated that the haplotype CTCTT, formed by SNPs rs8179673, rs7574865, rs4274624, rs11889341, and rs10168266, was significantly associated with HBV infection (OR 0.87; 95 % CI 0.76, 0.99; P = 0.022) and clearance (OR 0.86; 95 % CI 0.75, 0.99; P = 0.018). Bioinformatics analysis of these SNPs predicted that they participate in transcriptional regulation. Taken together, our findings demonstrate that variants in STAT4 play a critical role in HBV infection and clearance in the Chinese Han population.
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Affiliation(s)
- Xianzhong Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kunkai Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingjing Tao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Rongli Fan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haijun Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Ming D Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Research Center for Air Pollution and Health, Zhejiang University, Zhejiang, China. .,Institute of NeuroImmune Pharmacology, Seton Hall University, South Orange, NJ, USA.
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91
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Genome-wide association study identifies 8p21.3 associated with persistent hepatitis B virus infection among Chinese. Nat Commun 2016; 7:11664. [PMID: 27244555 PMCID: PMC4895015 DOI: 10.1038/ncomms11664] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 04/18/2016] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a common infectious disease. Here we perform a genome-wide association study (GWAS) among Chinese populations to identify novel genetic loci involved in persistent HBV infection. GWAS scan is performed in 1,251 persistently HBV infected subjects (PIs, cases) and 1,057 spontaneously recovered subjects (SRs, controls), followed by replications in four independent populations totally consisting of 3,905 PIs and 3,356 SRs. We identify a novel locus at 8p21.3 (index rs7000921, odds ratio=0.78, P=3.2 × 10−12). Furthermore, we identify significant expression quantitative trait locus associations for INTS10 gene at 8p21.3. We demonstrate that INST10 suppresses HBV replication via IRF3 in liver cells. In clinical plasma samples, we confirm that INST10 levels are significantly decreased in PIs compared with SRs, and negatively correlated with the HBV load. These findings highlight a novel antiviral gene INTS10 at 8p21.3 in the clearance of HBV infection. This genome-wide association study on persistent hepatitis B virus (HBV) infection among Chinese confirms previously associated genetic loci while discovering a novel protective locus at 8p21.3. The study also demonstrates the nearby gene INST10 suppresses HBV replication in vitro.
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92
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Genetic variant in CXCL13 gene is associated with susceptibility to intrauterine infection of hepatitis B virus. Sci Rep 2016; 6:26465. [PMID: 27212637 PMCID: PMC4876436 DOI: 10.1038/srep26465] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/04/2016] [Indexed: 02/07/2023] Open
Abstract
Intrauterine infection of hepatitis B virus (HBV), which accounts for the majority of mother-to-child transmission, is one of the main reasons for the failure of combined immunoprophylaxis against the transmission. Recent studies have identified that genetic background might influence the susceptibility to intrauterine infection of HBV. We conducted this study to investigate the associations between 10 genetic variants in 9 genes (SLC10A1, HLA-DP, HLA-C, CXCR5, CXCL13, TLR3, TLR4, TLR9 and UBE2L3) of mothers and their neonates and HBV intrauterine infection. A significantly decreased risk of HBV intrauterine transmission were found among mothers who carried the rs355687 CT genotypes in CXCL13 gene compared to those with CC genotypes (OR = 0.25, 95% CI, 0.08–0.82, P = 0.022); and a marginally significantly decreased risk was also observed under the dominant model (OR = 0.34, 95% CI, 0.11–1.01, P = 0.052). Besides, neonatal rs3130542 in HLA-C gene was found to be marginally significantly associated with decreased risk of HBV intrauterine infection under the additive model (OR = 0.55, 95% CI, 0.29–1.04, P = 0.064). However, we found no evidence of associations between the remaining 8 SNPs and risk of HBV intrauterine infection among mothers and their neonates. In conclusion, this study suggested that genetic variant in CXCL13 gene was associated with susceptibility to intrauterine infection of HBV.
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93
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Zhou F, Cao H, Zuo X, Zhang T, Zhang X, Liu X, Xu R, Chen G, Zhang Y, Zheng X, Jin X, Gao J, Mei J, Sheng Y, Li Q, Liang B, Shen J, Shen C, Jiang H, Zhu C, Fan X, Xu F, Yue M, Yin X, Ye C, Zhang C, Liu X, Yu L, Wu J, Chen M, Zhuang X, Tang L, Shao H, Wu L, Li J, Xu Y, Zhang Y, Zhao S, Wang Y, Li G, Xu H, Zeng L, Wang J, Bai M, Chen Y, Chen W, Kang T, Wu Y, Xu X, Zhu Z, Cui Y, Wang Z, Yang C, Wang P, Xiang L, Chen X, Zhang A, Gao X, Zhang F, Xu J, Zheng M, Zheng J, Zhang J, Yu X, Li Y, Yang S, Yang H, Wang J, Liu J, Hammarström L, Sun L, Wang J, Zhang X. Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease. Nat Genet 2016; 48:740-6. [PMID: 27213287 DOI: 10.1038/ng.3576] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/29/2016] [Indexed: 12/13/2022]
Abstract
The human major histocompatibility complex (MHC) region has been shown to be associated with numerous diseases. However, it remains a challenge to pinpoint the causal variants for these associations because of the extreme complexity of the region. We thus sequenced the entire 5-Mb MHC region in 20,635 individuals of Han Chinese ancestry (10,689 controls and 9,946 patients with psoriasis) and constructed a Han-MHC database that includes both variants and HLA gene typing results of high accuracy. We further identified multiple independent new susceptibility loci in HLA-C, HLA-B, HLA-DPB1 and BTNL2 and an intergenic variant, rs118179173, associated with psoriasis and confirmed the well-established risk allele HLA-C*06:02. We anticipate that our Han-MHC reference panel built by deep sequencing of a large number of samples will serve as a useful tool for investigating the role of the MHC region in a variety of diseases and thus advance understanding of the pathogenesis of these disorders.
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Affiliation(s)
- Fusheng Zhou
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Hongzhi Cao
- BGI-Shenzhen, Shenzhen, China.,iCarbonX, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xianbo Zuo
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Xiaoguang Zhang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Ricong Xu
- Department of Nephrology, First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, China
| | - Gang Chen
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yuanwei Zhang
- BGI-Shenzhen, Shenzhen, China.,School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xiaodong Zheng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
| | - Jinping Gao
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Yujun Sheng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Bo Liang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Changbing Shen
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Caihong Zhu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xing Fan
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Fengping Xu
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Min Yue
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xianyong Yin
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Chen Ye
- BGI-Shenzhen, Shenzhen, China
| | - Cuicui Zhang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liang Yu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Mengyun Chen
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Lili Tang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Longmao Wu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Jian Li
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yu Xu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Suli Zhao
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yu Wang
- BGI-Shenzhen, Shenzhen, China
| | - Ge Li
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Lei Zeng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | | | | | | | | | - Yanyan Wu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | - Zhengwei Zhu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Zaixing Wang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Chunjun Yang
- Department of Dermatology, No. 2 Hospital, Anhui Medical University, Hefei, China
| | - Peiguang Wang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Leihong Xiang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Anping Zhang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xinghua Gao
- Department of Dermatology, No. 1 Hospital of China Medical University, Shenyang, China
| | - Furen Zhang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, China
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital and Collaborative Innovation Center of Complex and Severe Skin Disease, Fudan University, Shanghai, China
| | - Min Zheng
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Zheng
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jianzhong Zhang
- Department of Dermatology, Peking University People's Hospital, Beijing, China
| | - Xueqing Yu
- Department of Nephrology, First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, China
| | - Yingrui Li
- BGI-Shenzhen, Shenzhen, China.,iCarbonX, Shenzhen, China.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Sen Yang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jianjun Liu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Lennart Hammarström
- BGI-Shenzhen, Shenzhen, China.,Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Liangdan Sun
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.,iCarbonX, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Princess Al-Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China.,Department of Medicine, University of Hong Kong, Hong Kong, China.,State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China
| | - Xuejun Zhang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China.,Department of Dermatology, China-Japan Friendship Hospital, Beijing, China.,Department of Dermatology, No. 2 Hospital, Anhui Medical University, Hefei, China.,Department of Dermatology, Huashan Hospital and Collaborative Innovation Center of Complex and Severe Skin Disease, Fudan University, Shanghai, China
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94
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Understanding of HLA-conferred susceptibility to chronic hepatitis B infection requires HLA genotyping-based association analysis. Sci Rep 2016; 6:24767. [PMID: 27091392 PMCID: PMC4835786 DOI: 10.1038/srep24767] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/04/2016] [Indexed: 12/12/2022] Open
Abstract
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.
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95
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Matthews PC, Carlson JM, Beloukas A, Malik A, Jooste P, Ogwu A, Shapiro R, Riddell L, Chen F, Luzzi G, Jesuthasan G, Jeffery K, Jojic N, Ndung'u T, Carrington M, Goulder PJR, Geretti AM, Klenerman P. HLA-A is a Predictor of Hepatitis B e Antigen Status in HIV-Positive African Adults. J Infect Dis 2016; 213:1248-52. [PMID: 26655301 PMCID: PMC4799671 DOI: 10.1093/infdis/jiv592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/01/2015] [Indexed: 01/06/2023] Open
Abstract
Outcomes of chronic infection with hepatitis B virus (HBV) are varied, with increased morbidity reported in the context of human immunodeficiency virus (HIV) coinfection. The factors driving different outcomes are not well understood, but there is increasing interest in an HLA class I effect. We therefore studied the influence of HLA class I on HBV in an African HIV-positive cohort. We demonstrated that virologic markers of HBV disease activity (hepatitis B e antigen status or HBV DNA level) are associated with HLA-A genotype. This finding supports the role of the CD8(+) T-cell response in HBV control, and potentially informs future therapeutic T-cell vaccine strategies.
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Affiliation(s)
- Philippa C Matthews
- Nuffield Department of Medicine Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust
| | | | - Apostolos Beloukas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool
| | - Amna Malik
- Department of Paediatrics, University of Oxford
| | - Pieter Jooste
- Paediatric Department, Kimberley Hospital, Northern Cape
| | - Anthony Ogwu
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston
| | - Lynn Riddell
- Integrated Sexual Health Services, Northampton General Hospital, Cliftonville
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading
| | - Graz Luzzi
- Department of Sexual Health, High Wycombe Hospital, Buckinghamshire, United Kingdom
| | - Gerald Jesuthasan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust
| | - Katie Jeffery
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust
| | - Nebojsa Jojic
- Microsoft Research, eScience Group, Redmond, Washington
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine KwaZulu-Natal Research Institute for Tuberculosis and HIV, University of KwaZulu-Natal, South Africa Max Planck Institute for Infection Biology, Berlin, Germany The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | - Mary Carrington
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland
| | - Philip J R Goulder
- Department of Paediatrics, University of Oxford HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine
| | - Anna Maria Geretti
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool
| | - Paul Klenerman
- Nuffield Department of Medicine Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford
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96
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Mathew S, Abdel-Hafiz H, Raza A, Fatima K, Qadri I. Host nucleotide polymorphism in hepatitis B virus-associated hepatocellular carcinoma. World J Hepatol 2016; 8:485-498. [PMID: 27057306 PMCID: PMC4820640 DOI: 10.4254/wjh.v8.i10.485] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 12/04/2015] [Accepted: 03/09/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is etiologically linked with hepatitis B virus (HBV) and is the leading cause of death amongst 80% of HBV patients. Among HBV affected patients, genetic factors are also involved in modifying the risk factors of HCC. However, the genetic factors that regulate progression to HCC still remain to be determined. In this review, we discuss several single nucleotide polymorphisms (SNPs) which were reportedly associated with increased or reduced risk of HCC occurrence in patients with chronic HBV infection such as cyclooxygenase (COX)-2 expression specifically at COX-2 -1195G/A in Chinese, Turkish and Egyptian populations, tumor necrosis factor α and the three most commonly studied SNPs: PAT-/+, Lys939Gln (A33512C, rs2228001) and Ala499Val (C21151T, rs2228000). In genome-wide association studies, strong associations have also been found at loci 1p36.22, 11q22.3, 6p21 (rs1419881, rs3997872, rs7453920 and rs7768538), 8p12 (rs2275959 and rs37821974) and 22q11.21. The genes implicated in these studies include HLA-DQB2, HLA-DQA1, TCF19, HLA-C, UBE2L3, LTL, FDX1, MICA, UBE4B and PG. The SNPs found to be associated with the above-mentioned genes still require validation in association studies in order to be considered good prognostic candidates for HCC. Screening of these polymorphisms is very beneficial in clinical experiments to stratify the higher or lower risk for HCC and may help in designing effective and efficient HCC surveillance programs for chronic HBV-infected patients if further genetic vulnerabilities are detected.
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97
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Wasityastuti W, Yano Y, Ratnasari N, Triyono T, Triwikatmani C, Indrarti F, Heriyanto DS, Yamani LN, Liang Y, Utsumi T, Hayashi Y. Protective effects of HLA-DPA1/DPB1 variants against Hepatitis B virus infection in an Indonesian population. INFECTION GENETICS AND EVOLUTION 2016; 41:177-184. [PMID: 27051043 DOI: 10.1016/j.meegid.2016.03.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 03/07/2016] [Accepted: 03/30/2016] [Indexed: 01/01/2023]
Abstract
Human leukocyte antigen (HLA) DPA1/DPB1 variants have been reported to influence Hepatitis B virus (HBV) infection. HLA-DPA1/DPB1 plays a pivotal role in antigen presentation to CD4(+) helper T cells and influences the outcome of HBV infection. To investigate the influence of HLA-DP variants on the outcome of HBV infection in an Indonesian population where it has the third-highest prevalence of HBV infection worldwide, we performed a case-control study of 686 participants, including patients with HBV-related advanced or nonadvanced liver disease, patients with spontaneously resolved HBV, and healthy controls. Single-nucleotide polymorphisms in HLA-DPA1 (rs3077) and HLA-DPB1 (rs3135021, rs9277535, and rs228388) were genotyped using real-time TaqMan® genotyping assays. Because rs2281388 deviated from Hardy-Weinberg equilibrium, it was excluded from subsequent analyses. The results of logistic regression analyses showed that the HLA-DPB1 rs9277535 variants were associated with a reduced risk of persistent HBV infection (odds ratio [OR] 0.70, 95% confidence interval [95% CI] 0.52-0.96, P=0.026, additive genetic model; OR 0.60, 95% CI 0.38-0.96, P=0.033, dominant genetic model). The HLA-DPA1 rs3077 variant was associated with a protective effect increasing the spontaneously resolved HBV infection (OR 0.64, 95% CI 0.41-0.98, P=0.039, dominant genetic model). By contrast, the HLA-DPB1 rs3135021 variant was not associated with the outcome of HBV infection, including susceptibility, spontaneously resolved, or disease progression. Combinations of haplotype markers were also associated with HBV susceptibility (CA for rs3077-rs9277535, OR 0.57, 95% CI 0.36-0.92, P=0.021; GA for rs3135021-rs9277535, OR 0.56, 95% CI 0.36-0.86, P=0.0087). In conclusion, these findings confirm that HLA-DPA1/DPB1 variants were associated with the outcomes of HBV infection in an Indonesian population.
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Affiliation(s)
- Widya Wasityastuti
- Division of Molecular Medicine & Medical Genetics, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; Division of Infectious Disease Pathology, Department of Microbiology and Infectious Diseases, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; Department of Physiology, Faculty of Medicine, Gadjah Mada University, Yogyakarta 55281, Indonesia
| | - Yoshihiko Yano
- Department of Gastroenterology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan.
| | - Neneng Ratnasari
- Subdivision of Gastroenterohepatology, Department of Internal Medicine, Dr. Sardjito Hospital, Faculty of Medicine, Gadjah Mada University, Yogyakarta 55281, Indonesia
| | - Teguh Triyono
- Department of Clinical Pathology, Dr. Sardjito Hospital, Faculty of Medicine, Gadjah Mada University, Yogyakarta 55281, Indonesia
| | - Catharina Triwikatmani
- Subdivision of Gastroenterohepatology, Department of Internal Medicine, Dr. Sardjito Hospital, Faculty of Medicine, Gadjah Mada University, Yogyakarta 55281, Indonesia
| | - Fahmi Indrarti
- Subdivision of Gastroenterohepatology, Department of Internal Medicine, Dr. Sardjito Hospital, Faculty of Medicine, Gadjah Mada University, Yogyakarta 55281, Indonesia
| | - Didik Setyo Heriyanto
- Department of Anatomical Pathology, Dr. Sardjito Hospital, Faculty of Medicine, Gadjah Mada University, Yogyakarta 55281, Indonesia
| | - Laura Navika Yamani
- Division of Molecular Medicine & Medical Genetics, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; Division of Infectious Disease Pathology, Department of Microbiology and Infectious Diseases, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Yujiao Liang
- Division of Molecular Medicine & Medical Genetics, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; Division of Infectious Disease Pathology, Department of Microbiology and Infectious Diseases, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Takako Utsumi
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; Indonesia-Japan Collaborative Research Centre for Emerging and Re-emerging Infectious Disease, Institute of Tropical Disease, Airlangga University, Surabaya 60115, Indonesia
| | - Yoshitake Hayashi
- Division of Molecular Medicine & Medical Genetics, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; Division of Infectious Disease Pathology, Department of Microbiology and Infectious Diseases, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
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98
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Zhu M, Dai J, Wang C, Wang Y, Qin N, Ma H, Song C, Zhai X, Yang Y, Liu J, Liu L, Li S, Liu J, Yang H, Zhu F, Shi Y, Shen H, Jin G, Zhou W, Hu Z. Fine mapping the MHC region identified four independent variants modifying susceptibility to chronic hepatitis B in Han Chinese. Hum Mol Genet 2016; 25:1225-32. [DOI: 10.1093/hmg/ddw003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/05/2016] [Indexed: 02/06/2023] Open
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99
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Hepatitis B virus genotype, mutations, human leukocyte antigen polymorphisms and their interactions in hepatocellular carcinoma: a multi-centre case-control study. Sci Rep 2015; 5:16489. [PMID: 26568165 PMCID: PMC4644975 DOI: 10.1038/srep16489] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 10/14/2015] [Indexed: 12/25/2022] Open
Abstract
Three genome-wide association studies (GWAS) have been conducted on the genetic susceptibility of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC), two of which consistently identified tagging single nucleotide polymorphisms (SNPs) around HLA-DQ/DR. In contrast, large multi-centre association studies between HBV genotype, mutations and the risk of HCC are relatively rare, and their interactions with host variants are even less. We performed a multi-centre study of 1,507 HBV-related HCC cases and 1,560 HBV persistent carriers as controls to evaluate the effects of HBV genotype, mutations, GWAS-identified HLA-DQ/DR SNPs (rs9272105 and rs9275319) and their interactions on HCC risk. We found HBV genotype C was more frequent in HBV-related HCC. And 11 HBV hotspot mutations were independently and significantly associated with HCC risk. We also detected significant interactions of rs9272105 with both the HBV genotype and mutations. Through stepwise regression analysis, HBV genotype, the 11 mutations, HLA-DQ/DR SNPs, and the interaction of rs9272105 with mutation A1752G were all entered into the HCC prediction model, and the area under the curve for the panel including the HLA-DQ/DR SNPs, HBV genotype and mutations was 0.840. The HBV genotype, the mutations and the HLA-DQ/DR SNPs may serve as biomarkers for the surveillance of HBV persistent carriers.
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100
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Quantitative assessment of common genetic variations in HLA-DP with hepatitis B virus infection, clearance and hepatocellular carcinoma development. Sci Rep 2015; 5:14933. [PMID: 26462556 PMCID: PMC4604517 DOI: 10.1038/srep14933] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 09/11/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) infection is the predominant risk factor for chronic hepatitis B (CHB), liver cirrhosis (LC) and hepatocellular carcinoma (HCC). Recently, genome-wide association studies have identified human leukocyte antigen (HLA)-DP polymorphisms (rs3077 and rs9277535) as a new chronic HBV infection susceptibility locus. Since then, the relationship between HLA-DP polymorphisms and various outcomes of HBV infection has been reported. However, the results have been inconclusive. To derive a more precise estimation of the relationship between HLA-DP polymorphisms and various outcomes of HBV infection, a meta-analysis of 62,050 subjects from 29 case-control studies was performed. We found that rs3077 and rs9277535 in HLA-DP significantly decreased HBV infection risks and increased HBV clearance possibility in a dose-dependent manner. In the subgroup analysis by ethnicity, study design and sample size, significant associations were found for these polymorphisms in almost all comparisons. Meanwhile, haplotype analyses of the two polymorphisms revealed a significant association between the combination of these alleles and HBV infection outcomes. However, no significant results were observed in HCC development. Our results further confirm that genetic variants in the HLA-DP locus are strongly associated with reduced HBV infection and increased the likelihood of spontaneous viral clearance.
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