Identification of Gene Polymorphisms Associated with Infectious Diseases

我的实验室小组的主要目标是确定导致感染性疾病和其他复杂疾病的宿主因素，以确定治疗干预的目标，提高诊断，并为临床和疫苗试验的解释提供信息。病毒感染现在被认为是常见癌症的主要原因，但对感染和宿主遗传因素之间的相互作用知之甚少，导致感染艾滋病毒或丙型肝炎病毒和乙型肝炎病毒的人发生癌症。丙型肝炎病毒和艾滋病毒都没有预防性疫苗，也没有治愈性治疗，在全球人口中高度流行。我们的重点是发现调节HIV-1、HCV和HBV感染及相关疾病的遗传因素。为此，我们开展了国际合作，在中国和南部非洲建立病例对照和队列研究，以及在美国建立的五个HIV-1纵向队列，分别调查HIV-1、HBV和HCV以及与EBV和HB病毒相关的常见癌症，NPC和HCC。我们与博茨瓦纳哈佛伙伴关系建立了合作关系，在受HIV-1亚型C感染严重影响的地区调查HIV-1感染、进展和对抗逆转录病毒治疗的反应的遗传相关性，全球大多数HIV-1感染都是由这种亚型引起的。使用靶向基因和全基因组关联方法，我们采用高通量基因分型技术来发现与hiv -1相关肾病和艾滋病进展相关的基因。每当观察到显著关联时，实验室使用精细制图来确定假定的因果等位基因，并使用功能分析来评估对基因转录和蛋白质水平的影响。APOBEC3G是一种人类对HIV-1的先天抗性因子，被纳入出芽病毒粒子中。APOBEC3G在缺乏HIV-1编码的病毒感染因子（vif）的情况下，引起新生cDNA的高突变，有效地预防病毒感染。人类APOBEC3G抗HIV-1活性通过与Cullin5 （CUL5）复合物相互作用而被HIV-1 vif解除，从而导致APOBEC3G的降解。通过对具有不同临床结果的HIV-1自然史队列的研究，我们之前已经证明APOBEC3G基因多态性与HIV-1感染者的艾滋病进展速度和CD4+ T细胞下降轨迹相关。我们还发现CUL5的多态性影响CD4+ t细胞耗损率。7个apobec3 / apobec3基因（a - h）聚集在一条染色体上，大多数具有抗hiv -1活性。我们研究了所有&lt；i>APOBEC3</i&gt；基因变异对HIV-1感染和疾病进展的影响。APOBEC3B已被证明能在体外抑制HIV-1复制，并且是唯一不被HIV-1 vif抑制的APOBEC3B蛋白。全球超过22%的人口携带APOBEC3B基因缺失，导致APOBEC3B蛋白消失。我们在4000多名受试者中研究了APOBEC3B&lt；/i&gt；基因缺失对HIV-1感染和疾病进展的影响。我们发现，由于携带两个基因缺失拷贝而不表达APOBEC3B蛋白的个体更容易感染HIV-1 （OR = 7.37， P=0.024）。缺失的纯合性也与艾滋病的快速进展（RH = 3.82， P=0.03）和更高的病毒载量（P= 0.048）相关。APOBEC3B</i&gt；缺失可能对具有亚洲血统的人群中的HIV-1流行有相当大的影响，因为APOBEC3B&lt；/i&gt；缺失等位基因在亚洲人群中更为常见。我们还发现，APOBEC3F</i&gt；密码子改变突变导致抗逆转录病毒活性功能的增强。APOBEC3F强烈抑制HIV-1，并部分抵抗vif。我们发现两种氨基酸改变变异与延迟发展为艾滋病相关（RH=0.70， P= 0.007）。每个APOBEC3基因的相对贡献及其在病毒感染中的相互作用正在研究中。最近，据报道，趋化因子Duffy抗原受体（DARC）零表型使非洲裔美国人感染HIV-1的风险增加了40%。研究表明，非洲艾滋病毒感染负担增加的11%是由于红细胞表面缺乏DARC蛋白。超过90%的撒哈拉以南非洲人存在DARC零表型，并传递了对间日疟原虫疟疾的抗性。我们在一组非裔美国人中检查了相同的多态性，其中90%以上的人通过注射吸毒感染，并发现DARC无效组和DARC阳性组在感染易感性方面没有关联。与其他研究一起，我们有效地排除了DARC作为撒哈拉以南非洲艾滋病毒感染负担增加的遗传原因。最近一项HIV-1疾病宿主决定因素的全基因组关联研究（GWAS）显示，在欧洲HIV-1队列中，靠近或位于基因&lt；i>HLA-C</i&gt；、<i>ZNRD1</i&gt；和&lt；i>ZNF39</i&gt；的snp与病毒载量设定点或疾病进展相关。我们在美国的5个HIV-1纵向队列中研究了&lt；I >ZNRD1<I/I&gt；区域的snp对HIV-1感染和进展的影响。在调整其他已知协变量（包括&lt；i>HLA</i&gt；等位基因）后，在欧洲裔美国人中，<i>HLA-C</i&gt；与艾滋病和死亡的有利结局密切相关（相对危险度[RH] = 0.72， P= 0.0003）和（RH=0.64， P=6.3 × 10-6）。发现&lt；i>ZNRD1</i&gt；基因单倍型与HIV-1感染保护显著相关，且不依赖于HLA-C，从而为&lt；i>ZNRD1</i&gt；的独立作用提供了新的证据。先前&lt；i>ZNDR1</i&gt；在使用沉默RNA敲除宿主基因的体外实验中被证明是HIV依赖性基因。这些发现表明HLA-C&lt；/i&gt；和ZRND1&lt；/i&gt；在调节HIV/AIDS中具有独立且重要的作用。白细胞介素-18启动子的调控多态性与丙型肝炎病毒（HCV）清除有关：免疫反应是决定HCV感染结果的关键。白细胞介素(IL)-18是Th1/Th2驱动的免疫反应的关键介质。研究了已知影响IL-18表达水平的两种IL-18 / IL-18启动子多态性在HCV清除或持久性中的作用。对HCV清除和持续存在的非裔美国注射吸毒者（IDUs）和主要通过血浆输血感染的欧美血友病患者进行基因分型。IL-18</i&gt；多态性与静脉吸毒者的HCV清除率显著相关。在注射药物中，il -607A（优势比[OR]， 3.68； 95%可信区间[CI]，1.85-7.34）和il -137C（优势比[OR]， 2.33; 95% CI, 1.24-4.36）与HCV清除率显著相关。这些结果提示，在某些高危人群中，IL18</i&gt；启动子多态性可能影响HCV感染的预后。这项工作表明，使用免疫修饰的疗法可能促进慢性感染患者的HCV清除。

The major objectives of my laboratory group are to identify host factors that contribute to infectious and other complex diseases with the goals of identifying targets for therapeutic intervention, improving diagnosis, and informing interpretation of clinical and vaccine trials. Viral infections are now recognized as major causes of common cancers, but little is understood about the interplay between infection and host genetic factors leading to cancer development in persons infected with HIV or the hepatitis C and B viruses. Both HCV and HIV have no preventive vaccines and no curative treatment and are highly prevalent in the global population. Our focus has been to discover genetic factors modulating HIV-1, HCV, and HBV infections and associated diseases. To this end, we have developed international collaborations to establish case-control and cohort studies in China and southern Africa, in addition to five established U.S.-based HIV-1 longitudinal cohorts, to investigate HIV-1, HBV, and HCV as well as the common carcinomas, NPC and HCC, associated with the EBV and HB viruses, respectively. We have established a collaboration with the Botswana Harvard Partnership to investigate the genetic correlates of HIV-1 infection, progression, and response to antiretroviral therapy in a region severely impacted by HIV-1 subtype C infection, the subtype responsible for the majority of HIV-1 infections globally. Using both targeted gene and genome wide association approaches, we have employed high throughput genotyping technologies to discover genes associated with HIV-1-associated nephropathy and with progression to AIDS. Whenever a significant association is observed, the laboratory uses fine mapping to identify putative causal alleles and functional assays to assess effects on gene transcription and protein levels. <B>Accomplishments</B> APOBEC3G is a human innate resistance factor to HIV-1 that is incorporated into budding virions. APOBEC3G, in the absence of HIV-1 encoded viral infectivity factor (vif), causes hypermutation of the nascent cDNA, effectively preventing viral infection. Human APOBEC3Gs anti-HIV-1 activity is disarmed by HIV-1 vif by interaction with Cullin5 (CUL5) complex leading to the degradation of APOBEC3G. Through a study of HIV-1 natural history cohorts with different clinical outcomes, we have previously shown that polymorphism APOBEC3G gene is associated with rate of progression to AIDS and trajectory of CD4+ T cell decline in HIV-1-infected persons. We also discovered that polymorphism in CUL5 influences the rate of CD4+ T-cell depletion. Seven <i>APOBEC3</i> genes (A-H) cluster together on a single chromosome and most confer anti-HIV-1 activity. We investigated the influence of genetic variation in all <i>APOBEC3</i> genes on HIV-1 infection and disease progression. APOBEC3B has been shown to inhibit HIV-1 replication in vitro and is the only APOBEC3B protein not inhibited by HIV-1 vif. More than 22% of the global population carry a deletion of the APOBEC3B gene resulting in abrogation of APOBEC protein. We examined the impact of the <i>APOBEC3B</i> gene deletion on HIV-1 infection and disease progression in more than 4000 subjects. We found that individuals who do not express APOBEC3B protein because they carry two copies of the gene deletion were much more likely to be infected with HIV-1 (OR = 7.37, P=0.024). Homozygosity for the deletion was also associated with more rapid progression to AIDS (RH = 3.82, P=0.03) and higher viral load (p=0.048). The <i>APOBEC3B</i> deletion may have considerable impact on the HIV-1 epidemic in populations with Asian ancestry where the <i>APOBEC3B</i> deletion allele is much more common. We also found that codon changing mutations in <i>APOBEC3F</i> resulted in a gain of function of antiretroviral activity. APOBEC3F strongly inhibits HIV-1 and is partially resistant to vif. We found that two amino acid changing variants were associated with delayed progression to AIDS (RH=0.70, P= 0.007). The relative contribution of each APOBEC3 gene and their interaction on viral infection are under investigation. Recently, it was reported that the Duffy antigen receptor for chemokine (DARC) null phenotype increased risk of HIV-1 infection in African Americans by 40%. It was suggested that 11% of the increased burden for HIV infection in Africa was due to the absence of the DARC protein on the surfaces of red blood cells. The DARC null phenotype occurs in more than 90% of subSaharan Africans, and conveys resistance to <i>Plasmodium vivax</i> malaria. We examined the same polymorphism in a group of African Americans, more than 90% of whom were infected by injecting drug use and found no association between DARC null group and the DARC positive group for infection susceptibility. Together with other studies, we effectively ruled out DARC as a genetic cause for the increased burden of HIV infection in sub-Saharan Africa. A recent genome-wide association study (GWAS) of host determinants for HIV-1 disease revealed that SNPs near or in genes <i>HLA-C</i>, <i>ZNRD1</i> and <i>ZNF39</i> were associated viral load setpoint or disease progression among European HIV-1 cohorts. We investigated the effect of the SNPs in the <i>ZNRD1<I/I> region on HIV-1 infection and progression in five U.S-based HIV-1 longitudinal cohorts. After adjusting other known covariates including <i>HLA</i> alleles, <i>HLA-C</i> was strongly associated with favorable outcomes for AIDS and death (Relative hazard [RH] = 0.72, P = 0.0003) and (RH=0.64, P=6.3 x 10-6) in European Americans. A haplotype in the <i>ZNRD1</i> gene showed significant association with protection of HIV-1 infection, which was independent of HLA-C, thus providing a novel evidence for an independent role of <i>ZNRD1</i>. Previously <i>ZNDR1</i> was shown to be an HIV dependency gene in an in vitro experiment using silencing RNA to knock-down host genes. The findings suggest independent and significant roles of <i>HLA-C</i> and <i>ZRND1</i> in modulating HIV/AIDS. Regulatory polymorphisms in the interleukin-18 promoter are associated with hepatitis C virus (HCV) clearance: The immune response is critical in determining the outcome of HCV infection. Interleukin (IL)-18 is a pivotal mediator of Th1/Th2 driven immune response. Two <i>IL-18</i> promoter polymorphisms known to affect IL-18 expression levels were examined for their role in HCV clearance or persistence. Genotyping was performed among African American injecting drug users (IDUs) with HCV clearance and HCV persistence, and among European American hemophiliacs mainly infected through plasma transfusion. <i>IL-18</i> polymorphisms were significantly associated with HCV clearance in intravenous drug users. Among IDUs, IL18 -607A (Odds ratio [OR], 3.68; 95% confidence interval [CI],1.85-7.34) and IL18 -137C (OR, 2.33; 95% CI, 1.24-4.36) were significantly associated with HCV clearance. These results suggest that <i>IL18</i> promoter polymorphism may affect the outcome of HCV infection in certain risk groups. This work suggests that therapies using immune modification may promote HCV clearance in persons with chronic infections.