Identification of Genetic Factors Associated with Infectious Diseases

与传染病相关的遗传因素的鉴定

• 批准号: 8937699
• 负责人: Cheryl Winkler
• 金额: $ 45.52万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8937699
• 关键词: Accounting; Acquired Immunodeficiency Syndrome; Affect; African American; Age; Age related macular degeneration; Aging; Agreement; Alleles; American; Anti-Retroviral Agents; Antiviral Agents; Binding; Bioinformatics; Biological Assay; CCR; CD4 Lymphocyte Count; CUL5 gene; Cancer Etiology; Candidate Disease Gene; Carcinogenesis Mechanism; Cardiovascular system; China; Chinese People; Chromosomes, Human, Pair 22; Chronic; Chronic Disease; Chronic Hepatitis; Cirrhosis; Clinical Data; Clinical Management; Codon Nucleotides; Collaborations; Communicable Diseases; Confounding Factors (Epidemiology); DNA-Protein Interaction; Data; Development; Disease; Environmental Risk Factor; Epigenetic Process; European; Far East; Gene Expression; Gene Targeting; Genes; Genetic; Genomics; Genotype; Goals; HIV; HIV-1; HLA-DPB1 gene; HLA-DQ Antigens; Haplotypes; Hela Cells; Hepatitis B Surface Antigens; Hepatitis B Virus; Hispanics; Hospitals; Host resistance; Human; In Vitro; Incidence; Individual; Infection; Inflammatory; Injury; Institutes; Integration Host Factors; International; Journals; Kidney; Kidney Diseases; Lead; Longitudinal Studies; Malignant Neoplasms; Malignant neoplasm of liver; Measures; Metabolic; Methylation; Modification; Monitor; Natural Immunity; Nuclear Proteins; Organ; Outcome; Pathogenesis; Pathway interactions; Patients; Pharmacotherapy; Phenotype; Population; Predisposition; Premature aging syndrome; Primary carcinoma of the liver cells; Protein Isoforms; Proteins; Publishing; Quality Control; Quantitative Trait Loci; Reading; Reporter Genes; Research Personnel; Resistance; Retinal; Risk; Role; Running; Sampling; Signal Transduction; Site; Staging; Technology; Universities; Vaccines; Variant; Viral; Viral Pathogenesis; Virus Diseases; Work; acquired immunity; antiretroviral therapy; arteriole; base; carcinogenesis; cohort; follow-up; gene discovery; genetic variant; genome wide association study; genome-wide; global health; immune function; insight; interest; lipid disorder; novel; pandemic disease; pathogen; promoter; resistance factors; viral RNA; viral resistance

This project's focus is on two infectious diseases that continue to have tremendous impact on global health. Human Immunodeficiency Virus (HIV) is pandemic and Hepatitis B Virus (HBV) infection and HBV-associated hepatocellular carcinoma (HCC) is prevalent in East Asia, globally affecting millions of people and having no cure. The objective of this project is to identify host factors that contribute to the occurrence and development of these, and potentially other, infectious diseases. We aim to identify host genetic factors that affect host innate restriction or susceptibility in acquisition, replication, and pathogenesis of viral pathogens, and carcinogenesis, the mechanisms of which are not fully understood. The identification of host proteins involved in viral replication, in innate or acquired immunity, or in carcinogenesis pathways will provide critical insights for the rational development of antiviral drugs and effective vaccines. Our strategy is to search for genetic variants that differentially affect rates of infection, or the course of pathogenesis, and which thereby identify the variant-containing gene as conferring restriction or susceptibility to infection or progression. We are using both targeted gene and genome wide association study (GWAS) approaches, including Illumina and Affymetrix chip technologies, to discover genes associated with HIV-1, HBV infection and HBV-associated liver cancer. Accomplishments 1) HIV-1 resistant APOBEC3 (A3) genes. Six of the seven A3 genes (including A3B, A3G and A3F) are human innate resistance factors that confer resistance to HIV-1 by causing hypermutation of viral RNA. Previously we discovered genetic factors in the APOBEC3G and CUL5 pathway that affect AIDS progression. The seven APOBEC3 genes (A-H) are clustered in a 100 kb region in chromosome 22. We assessed the influence of the genetic variants and haplotype in all APOBEC3 genes (A-H) on HIV-1 infection and disease courses. Besides the associations we previous found in A3G and A3B, we have identified A3F genetic variants that retard AIDS progression. In vitro, APOBEC3F strongly inhibits HIV-1 and is partially resistant to HIV-1 vif, unlike APOBEC3G. We found that codon-changing variants rs5750728 (intronic or codon-changing 78 V/A in different isoforms) and 231 I/V were associated with protection from progression to AIDS in European Americans. We found that rs5750728 alters binding to nuclear proteins in HeLa cells, suggesting a regulator role. In collaboration with researchers at Johns Hopkins University, the interaction of the APOBEC3F with HIV-1 vif was evaluated; the carrying codon-changing SNP 231 I/V was shown to confer stronger resistance to vif that degrades A3F, possibly leading to more abundant A3F to inhibit HIV-1. It is of interest that in the alignment of A3F and vif sequences, the A3F region carrying 231 I/V appears to either be mimicked by or has co-evolved with HIV-1 vif. This may reveal a mechanism allowing HIV-1 to evade A3F by adapting to host A3F sequences. 2) ZNRD1 and HIV-1 infection. We investigated the effect of the SNPs in the ZNRD1 region on HIV-1 infection and progression in five U.S-based HIV-1 longitudinal cohorts. A haplotype in the ZNRD1 gene showed significant association with host restriction to HIV-1 acquisition. The functional relevance of the associated variant was demonstrated in a gene reporter assay that showed one promoter variant (rs3132130) increased the ZNRD1 gene expression. Further, in a DNA-protein interaction assay, the variant also confers differential allele-specific binding to nuclear proteins. Our findings provide novel evidence of significant roles of ZRND1 in modulating HIV/AIDS. This work has been published in Journal of Infectious Diseases, June 2014. 3) GWAS of HBV and HCC. HBV infection is extremely prevalent in China (HBsAg carrier rate was 7% in 2006). Many HBV infected patients develop cirrhosis and hepatocellular carcinoma (HCC). MGE has an ongoing collaboration with Dr. Zeng Zheng, Beijing University First Hospital, for genetic studies in a Chinese Hepatitis B virus infection cohort. This HBV cohort, initiated by MGE, is collaboration between 13 major institutes in China and MGE. The HBV cohort comprises the full spectrum of the HBV outcomes: HBV resistance, HBV clearance, chronic hepatitis, cirrhosis and HCC, making this the most comprehensive sample set covering natural HBV outcomes available. Our GWAS was performed on 1200 samples using the affymetrix SNP6.0 chip. We have completed quality control of genotyping calls and performed GWAS association analyses. The genotypes from 6 top associated SNPs were verified using a second TaqMan assay, and the association signals were validated in expanded sample sets in the same cohort. The GWAS identified HLA-DPA1 and HLA-DPB1 region as major genetic factors for HBV clearance and infection that passed the genome wide significance threshold. These results are in agreement of GWAS results from other groups as well as our previous published finding, in which HLA-DPA1 rs3077 was associated with not only reduced risk to HBV infection but also HBV clearance. We detected an association with host resistance to HBV infection in the HLA-DQ1 region that passed the genome wide significance (p5e-8). The top HLA-DQ1 SNP is an eQTL associated with HLA-DQ expression level in two published genome wide QTL studies. 5) We contributed genotype-phenotype data from the HIV/AIDS GWAS to the International for the Genomics of HIV to identify common variants associated with HIV acquisition. The conclusion of the study, published in PLoS Pathogens, was that genetic influences on HIV acquisition are either rare or have small effects. 6) We have initiated a longitudinal study of differential methylation in PBMCs from HIV-infected subjects at different stages of disease, comparing pre-infection samples from each subject with samples from the same subject at later stages of disease. We ran 82 samples from the DCG cohort on the Illumina Infinium 450 methylation chip. We are collaborating with the CCR bioinformatics group (CCR-IFX) to analyze the chip data. Quality of the reads was confirmed by the ability of the methylation data to predict the CD4 count of individuals, as confirmed by measured CD4 counts. Initial results show approximately 150 sites differentially methylated between pre- and post-infection samples, after correcting for age, CD4 count, and other confounding variables. 7) The Longitudinal Studies of Ocular Complications of AIDS (LSOCA) comprises 2393 patients with AIDS and with detailed follow-up clinical data to monitor incidence of ocular complications of AIDS and to determine the effect of antiretroviral treatment on immune function on the risk of ocular disease. We have genotyped this cohort for 15 candidate genes associated with age-related macular degeneration and for APOL1 variants for association with retinal arteriole injury and renal disease; analysis is ongoing.

该项目的重点是两种继续对全球健康产生巨大影响的传染病。人类免疫缺陷病毒 (HIV) 正在流行，乙型肝炎病毒 (HBV) 感染和 HBV 相关肝细胞癌 (HCC) 在东亚流行，影响全球数百万人，且无法治愈。该项目的目标是确定导致这些以及潜在的其他传染病发生和发展的宿主因素。我们的目标是确定影响宿主先天限制或易感性的宿主遗传因素，这些因素包括病毒病原体的获得、复制和发病机制以及致癌作用，其机制尚不完全清楚。鉴定参与病毒复制、先天或获得性免疫或致癌途径的宿主蛋白将为合理开发抗病毒药物和有效疫苗提供重要见解。我们的策略是寻找对感染率或发病机制进程产生不同影响的遗传变异，从而识别出含有变异的基因，从而赋予对感染或进展的限制或易感性。我们正在使用靶向基因和全基因组关联研究 (GWAS) 方法，包括 Illumina 和 Affymetrix 芯片技术，来发现与 HIV-1、HBV 感染和 HBV 相关肝癌相关的基因。成就 1) HIV-1 抗性 APOBEC3 (A3) 基因。 7 个 A3 基因中的 6 个（包括 A3B、A3G 和 A3F）是人类先天抵抗因子，它们通过引起病毒 RNA 的超突变而赋予对 HIV-1 的抵抗力。此前我们发现 APOBEC3G 和 CUL5 通路中的遗传因素会影响艾滋病的进展。七个 APOBEC3 基因 (A-H) 聚集在 22 号染色体的 100 kb 区域。我们评估了所有 APOBEC3 基因 (A-H) 中的遗传变异和单倍型对 HIV-1 感染和疾病进程的影响。除了我们之前在 A3G 和 A3B 中发现的关联之外，我们还发现了 A3F 基因变异，可以延缓艾滋病的进展。在体外，与 APOBEC3G 不同，APOBEC3F 强烈抑制 HIV-1，并且对 HIV-1 vif 具有部分耐药性。我们发现，密码子改变变体 rs5750728（不同异构体中的内含子或密码子改变 78 V/A）和 231 I/V 与欧洲裔美国人免于进展为艾滋病的保护相关。我们发现 rs5750728 改变了 HeLa 细胞中与核蛋白的结合，表明其具有调节作用。与约翰霍普金斯大学的研究人员合作，评估了 APOBEC3F 与 HIV-1 vif 的相互作用；携带密码子改变的 SNP 231 I/V 被证明对降解 A3F 的 vif 具有更强的抵抗力，可能导致更丰富的 A3F 来抑制 HIV-1。有趣的是，在 A3F 和 vif 序列的比对中，携带 231 I/V 的 A3F 区域似乎是被 HIV-1 vif 模仿或共同进化的。这可能揭示了 HIV-1 通过适应宿主 A3F 序列来逃避 A3F 的机制。 2）ZNRD1和HIV-1感染。我们在美国的五个 HIV-1 纵向队列中研究了 ZNRD1 区域的 SNP 对 HIV-1 感染和进展的影响。 ZNRD1 基因中的单倍型显示与宿主对 HIV-1 获得的限制显着相关。基因报告基因检测证明了相关变体的功能相关性，该检测显示一种启动子变体 (rs3132130) 增加了 ZNRD1 基因表达。此外，在 DNA-蛋白质相互作用测定中，该变体还赋予与核蛋白质的差异等位基因特异性结合。我们的研究结果提供了 ZRND1 在调节 HIV/AIDS 中的重要作用的新证据。该工作已发表于《传染病杂志》，2014 年 6 月。 3) HBV 和 HCC 的 GWAS。乙型肝炎病毒感染在中国极为普遍（2006年HBsAg携带率为7%）。许多感染 HBV 的患者会发展为肝硬化和肝细胞癌 (HCC)。 MGE 正在与北京大学第一医院的曾政博士合作，对中国乙型肝炎病毒感染队列进行基因研究。该乙型肝炎队列由 MGE 发起，是中国 13 个主要机构与 MGE 合作的结果。 HBV 队列包含全部 HBV 结果：HBV 耐药、HBV 清除、慢性肝炎、肝硬化和 HCC，使其成为涵盖现有 HBV 自然结果的最全面的样本集。我们使用 affymetrix SNP6.0 芯片对 1200 个样本进行了 GWAS。我们已经完成了基因分型调用的质量控制并进行了 GWAS 关联分析。使用第二次 TaqMan 测定验证了 6 个最相关 SNP 的基因型，并在同一队列的扩展样本集中验证了关联信号。 GWAS 将 HLA-DPA1 和 HLA-DPB1 区域确定为 HBV 清除和感染的主要遗传因素，并通过了全基因组显着性阈值。这些结果与其他小组的 GWAS 结果以及我们之前发表的发现一致，其中 HLA-DPA1 rs3077 不仅与 HBV 感染风险降低相关，而且与 HBV 清除相关。我们在 HLA-DQ1 区域检测到与宿主对 HBV 感染的抵抗力之间的关联，该区域通过了全基因组显着性 (p5e-8)。在两项已发表的全基因组 QTL 研究中，顶级 HLA-DQ1 SNP 是与 HLA-DQ 表达水平相关的 eQTL。 5) 我们向国际艾滋病毒基因组学组织贡献了来自艾滋病毒/艾滋病 GWAS 的基因型-表型数据，以识别与艾滋病毒感染相关的常见变异。这项发表在《公共科学图书馆病原体》上的研究结论是，遗传对艾滋病毒感染的影响要么很少，要么影响很小。 6) 我们启动了一项针对不同疾病阶段的 HIV 感染者的 PBMC 差异甲基化的纵向研究，将每个受试者的感染前样本与同一受试者在疾病后期的样本进行比较。我们在 Illumina Infinium 450 甲基化芯片上运行了来自 DCG 队列的 82 个样本。我们正在与 CCR 生物信息学小组 (CCR-IFX) 合​​作分析芯片数据。读取的质量通过甲基化数据预测个体 CD4 计数的能力得到证实，正如测量的 CD4 计数所证实的那样。初步结果显示，在校正年龄、CD4 计数和其他混杂变量后，感染前和感染后样本之间大约有 150 个位点存在差异甲基化。 7) 艾滋病眼部并发症的纵向研究 (LSOCA) 包括 2393 名艾滋病患者，并提供详细的随访临床数据，以监测艾滋病眼部并发症的发生率，并确定抗逆转录病毒治疗对免疫功能的影响对眼部疾病风险的影响。疾病。我们对这个队列中与年龄相关性黄斑变性相关的 15 个候选基因以及与视网膜小动脉损伤和肾脏疾病相关的 APOL1 变异体进行了基因分型；分析正在进行中。