Identification of Gene Polymorphisms Associated with Infectious Diseases

目的是查明导致传染病的遗传因素，以确定药物开发的目标和改善诊断/预后。感染是癌症的主要原因：HIV、EBV或丙型肝炎病毒（HCV）和乙型肝炎病毒（HBV）分别导致与艾滋病相关的恶性肿瘤、鼻咽癌（NPC）和肝细胞癌（HCC）。对于感染和导致这些病毒感染者患癌症的遗传变异之间的相互作用，人们知之甚少。丙型肝炎病毒和艾滋病毒都没有预防性疫苗或治疗方法，在全球人口中高度流行。我们关注与HIV-1、HCV和HBV感染易感性/耐药性和疾病结局相关的遗传因素。在中国和非洲开展病例对照和队列研究的国际合作，以及在美国开展的5个HIV-1纵向队列研究，分别研究HIV-1、HBV、HCV以及NPC和HCC。利用靶向和全基因组关联研究（GWAS），最先进的技术已被用于发现与这些感染及其结果相关的变异。这些研究可以部分解释个体之间在病毒感染、进展和疾病结局方面观察到的差异。此外，我们将深入了解不同人群中遗传变异对不同传染病患病率及其结果（例如hiv相关肾病或NPC）的贡献。这些研究将提供对生物学途径的见解，可能导致新的治疗方法或基因检测，以改善临床结果。鉴定APOL1的肾脏易感性突变：2008年，我们鉴定了Chr 22上一个与hiv相关肾病以及其他严重肾脏疾病风险增加相关的区域。肾脏风险等位基因在非裔美国人中很常见，但在欧洲人中很少见，因此为主要的健康差异提供了遗传基础。我们报道了最近在西非携带MYH9病毒的区域发生了选择，但在其他非洲人群中没有发生选择，这表明肾脏风险等位基因可能会追踪提供抵抗病原体保护的突变。在一项合作研究中，我们报告了APOL1的两种变异赋予对引起昏睡病的布氏罗得西亚锥虫（T.b.r）的保护作用。携带这两种突变任意组合的个体的血浆都能溶解结核杆菌，从而预防结核杆菌昏睡病。类似于镰状细胞特性，APOL1突变在携带者中提供对致命病原体的保护，但风险变异的纯合子和复杂杂合子更容易发生hiv相关肾病。为全球免疫系统建立非洲队列：在与哈佛大学和博茨瓦纳-哈佛伙伴关系的合作下，从艾滋病毒1型c型患者身上收集了6000多个DNA样本。博茨瓦纳是世界上艾滋病毒流行率最高的国家之一。该研究旨在探讨遗传因素对HIV获取、抗病毒治疗疗效和不良事件以及病毒载量/CD4轨迹的影响。这些样本将用于GWAS和下一代测序，以确定与南部非洲HIV-1发病机制相关的常见和罕见变异。APOBEC3基因及其在HIV/AIDS中的作用：APOBEC3基因家族通过脱胺细胞素导致HIV普遍高突变，从而赋予对逆转录病毒的抗性。我们测试了所有APOBEC3基因的遗传变异与HIV/AIDS的关系。APOBEC3F抑制HIV-1，并且与APOBEC3G不同，它部分抵抗hiv介导的降解。APOBEC3F的两个密码子改变变体与延迟到艾滋病的时间有关。29.5 kb的缺失去除了整个APOBEC3B基因。纯合子缺失与HIV-1获得、艾滋病进展和病毒设定点的不利结果显著相关。这些发现表明APOBEC3B的缺失可能会增加宿主对HIV-1获取的易感性和向艾滋病的进展。我们测试了APOBEC3G mRNA水平和HIV-1易感性的遗传变异的关联，并使用病毒载量和CD4 t细胞计数作为HIV-1亚型C感染高危南非妇女的结果。与hiv阳性妇女相比，hiv阴性妇女的APOBEC3G表达水平更高，包括来自同一个体的匹配感染前和感染后样本。两种变体分别与高病毒载量和低CD4 t细胞水平相关。这些数据表明，APOBEC3G转录在HIV-1感染后迅速下调，APOBEC3G变异可能影响HIV-1的早期发病机制。Chr 3趋化因子受体基因家族：Chr 3p21-22包含两个趋化因子受体基因簇，其中几个作为HIV-1的主要或次要辅助受体。我们对144个个体中的7种趋化因子受体进行了重测序，这些个体代表了HIV进展和感染的极端表型；发现了6个改变密码子的snp。在HIV-1/AIDS自然病史队列中，对CCR5、CCR2、CCR3、CCRL2、CXCR6、CCR8和CX3CR1的snp进行基因分型。发现CCR3和CCR8与艾滋病进展有显著的独立关联。值得注意的是，我们发现CCRL2 （Y167F）与肺囊虫性肺炎（PCP）相关的非保守性氨基酸变化。CCRL2参与肺树突状细胞运输，并可能通过诱导炎症影响PCP。HLA与鼻咽癌的相关性：一项来自世界上鼻咽癌发病率最高的地区之一广西的鼻咽癌队列病例对照研究显示，HLA与鼻咽癌地区有很强的相关性。这项研究首次表明，A*0206是南亚和东南亚独有的A2亚型，与鼻咽癌的高风险相关。与风险相关的因素在这一人群中更为常见。这些结果表明，广西人群中鼻咽癌的高发病率部分是由于NPC- hla风险等位基因的频率较高。艾滋病毒/艾滋病全球基因库：我们为三个国际全球基因库做出了贡献，以发现与艾滋病进展异常快或异常慢相关的遗传因素。总部位于美国的GWAS在PROX1基因附近发现了一个SNP，该SNP与艾滋病的延迟进展密切相关。我们在一个更大的自然历史HIV队列研究中重复了这种关联。PROX1是T细胞中干扰素γ表达的负调节因子，也可以减缓血管肿瘤的进展，如卡波西肉瘤（一种常见的艾滋病恶性肿瘤）。第二个GWAS也比较了一个法国队列中艾滋病快速进展者和缓慢进展者。本研究确定了CXCR6基因中的一个SNP，该SNP与精英对照组中极低的病毒载量相关，并在三个队列中进行了复制。第三次GWAS在5个美国队列中进行。本研究发现PARD3B是一种新的保护基因。这些研究增加了有效调节临床艾滋病进展的累积多基因宿主成分，为潜在的治疗新途径和改善艾滋病预后提供了前景。GWAS治疗HBV：我们在中国HBV队列（n=1700）中测试了HLA-DP snp对HBV主要结局的影响，包括HBV耐药性、清除率、慢性感染、肝硬化和HCC。发现SNP rs3077是HBV清除率的主要预测因子（P = 4.7x10-10），但对慢性感染患者肝硬化或肝细胞癌发生率无影响。这重复并证实了在亚洲人身上进行的已发表的GWAS。

The objectives are to identify genetic factors contributing to infectious diseases with the goals of identifying targets for drug development and improving diagnosis/prognosis. Infections are major causes of cancers: HIV, EBV, or the hepatitis C virus (HCV) and hepatitis B virus (HBV) contribute to AIDS-associated malignancies, nasopharyngeal carcinoma (NPC) and hepatocelluar carcinoma (HCC), respectively. Little is understood about the interplay between infection and genetic variation leading to cancer in persons infected with these viruses. Both HCV and HIV have no preventive vaccines or no curative treatment and are highly prevalent in the global population. We focused on genetic factors associated with susceptibility/resistance to HIV-1, HCV, and HBV infections and disease outcomes. International collaborations for case-control and cohort studies in China and Africa, in addition to five U.S.-based HIV-1 longitudinal cohorts, have been developed to investigate HIV-1, HBV, and HCV as well as NPC and HCC, respectively. Using both targeted and genome wide association studies (GWAS), state-of-the art technologies have been used to discover variation associated with these infections and their outcomes. These studies should explain in part the variance observed among individuals in viral infection, progression, and disease outcomes. In addition, we will gain insights of the contribution of genetic variation among diverse human populations to disparate prevalence rates for infectious diseases and their outcomes (e.g. HIV-associated nephropathy or NPC). These studies will provide insights into biological pathways that may lead to new therapeutics or genetic testing to improve clinical outcomes. Accomplishments Identification of renal susceptibility mutations in APOL1: In 2008 we identified a region on Chr 22 associated with increased risk of HIV-associated nephropathy as well as other severe forms of kidney disease. The renal risk alleles were frequent in African Americans but rare in Europeans thereby providing a genetic basis for a major health disparity. We reported that the region harboring MYH9 was under recent selection in west Africans but not in other African populations suggesting that the renal risk alleles may be tracking mutations that provide protection against a pathogen. In a collaborative study we reported that two variants in APOL1 confer protection against sleeping sickness-causing Trypanosoma brucei rhodesiense (T.b.r). Plasma from individuals carrying any combination of the two mutations lyse T.b. r., conferring protection against T.b.r. sleeping sickness. Analogous to the sickle cell trait, APOL1 mutations provide protection against a lethal pathogen in carriers but homozygotes and complex heterozygotes for the risk variants are more vulnerable to HIV-associated nephropathy. Development of an African cohort for a GWAS: In a collaboration with Harvard and the Botswana-Harvard Partnership, over 6,000 DNA samples have been collected from individuals with HIV-1 type C. Botswana has one of the highest HIV prevalence rates in the world. The study is powered to investigate the influence of genetic factors on HIV acquisition, antiviral treatment efficacy and adverse events, and viral load/CD4 trajectories. These samples will be used for a GWAS and next generation sequencing to identify common and rare variants that associated with HIV-1 pathogenesis in southern Africans. APOBEC3 Genes and their role in HIV/AIDS: The APOBEC3 gene family confers resistance to retroviruses by deaminating cytodine leading to pervasive hypermutation of HIV. We tested the association of genetic variants in all APOBEC3 genes with HIV/AIDS. APOBEC3F inhibits HIV-1 and unlike APOBEC3G is partially resistant to HIV-mediated degradation. Two codon-changing variants in APOBEC3F were associated with delayed time to AIDS. A 29.5-kb deletion removes the entire APOBEC3B gene. The homozygous deletion was significantly associated with unfavorable outcomes for HIV-1 acquisition, progression to AIDS, and viral set point. These findings suggest that the loss of APOBEC3B may increase host susceptibility to HIV-1 acquisition and progression to AIDS. We tested for association of APOBEC3G mRNA levels and genetic variants on HIV-1 susceptibility, and early disease pathogenesis using viral load and CD4 T-cell counts as outcomes in South African women at high risk for HIV-1 subtype C infection. APOBEC3G expression levels were higher in HIV-negative compared to HIV-positive women, including matched pre- and post-infection samples from the same individuals. Two variants were associated with high viral loads and low CD4 T-cell levels, respectively. These data suggest that APOBEC3G transcription is rapidly downregulated upon HIV-1 infection and APOBEC3G variation may affect early HIV-1 pathogenesis. Chr 3 chemokine receptor gene family: Chr 3p21-22 harbors two clusters of chemokine receptor genes, several of which serve as major or minor coreceptors of HIV-1. We resequenced 7 chemokine receptors in 144 individuals representing extreme phenotypes for HIV progression and infection; six codon-changing SNPs were discovered. SNPs were genotyped in CCR5, CCR2, CCR3, CCRL2, CXCR6, CCR8 and CX3CR1 in HIV-1/AIDS natural history cohorts. Significant independent associations with AIDS progression were identified for CCR3 and CCR8 . Notably, we identified a non-conservative amino acid change in CCRL2 (Y167F) association with pneumocystis pneumonia (PCP). CCRL2 is involved in lung dendritic cell trafficking and may affect PCP by inducing inflammation. HLA association with NPC: A case-control study of NPC cohort from Guangxi, a region with one of the highest NPC incidences in the world revealed strong associations with the HLA region. This study showed for the first time that A*0206, a unique A2 subtype to South and Southeast Asia, is associated with a high risk for NPC. Factors associated with risk were more frequent in this population. These results suggest that the high rate of NPC in the Guangxi population is due in part to the higher frequencies of NPC-HLA risk alleles. GWAS for HIV/AIDS: We have contributed to three international GWASs to discover genetic factors associated with unusually fast or slow progression to AIDS. The USA-based GWAS identified a SNP near the PROX1 gene strongly associated with delayed progression to AIDS. We replicated this association in a larger natural history HIV cohort study. PROX1 is a negative regulator of interferon-gamma expression in T cells and also mitigates the advancement of vascular neoplasms, such as Kaposi sarcoma, a common AIDS-defining malignancy. The second GWAS also compared rapid to slow progressors to AIDS in a French cohort. This study identified a SNP in the CXCR6 gene that was associated with extremely low viral load in elite controllers and was replicated in three cohorts. The third GWAS was performed on 5 USA cohorts. This study identified PARD3B as a novel protective gene. These studies adds to the cumulative polygenic host component that effectively regulates the progression to clinical AIDS, raising prospects for potential new avenues for therapy and improvements in AIDS prognosis. GWAS for HBV: We tested the effects of HLA-DP SNPs on major HBV outcomes in a Chinese HBV cohort (n=1700) comprising HBV resistance, clearance, chronic infection, cirrhosis and HCC. SNP rs3077 is found to be a major predictor for HBV clearance (P = 4.7x10-10), but has no influence on more cirrohsis or heptocellular carcinoma in persons with chronic infection. This replicates and confirms a published GWAS performed in Asians.