Identification of Gene Polymorphisms Associated with Infectious Diseases

我实验室的主要目标是确定导致传染病和其他复杂疾病的宿主因素。传染病对全球健康的巨大影响，以及许多人类病原体与常见癌症的关联，需要多种研究策略来阐明感染机制和发病机制。我们的策略是寻找对感染率或发病过程有不同影响的遗传变异，从而确定含有该变异的基因参与了感染或发病过程，增加对发病机制的了解，并指出治疗干预的目标。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。利用靶向基因和全基因组关联方法，我们采用了高通量基因分型技术，包括Illumina和Affymetrix，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。研究成果：APOBEC3G是一种人类对HIV-1的先天抗性因子，被整合到出芽病毒粒子中。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。然而，在泛素化途径中，人类APOBEC3G抗HIV-1活性通过与Cullin5 （CUL5）复合物的相互作用被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，我们之前已经表明，编码APOBEC3G基因的多态性与HIV-1感染者的艾滋病进展率和CD4+ T细胞下降的轨迹有关。我们还发现CUL5中的变异等位基因和单倍型簇影响CD4+ t细胞耗竭率。这些发现强调了APOBEC3G-CUL5通路的重要性。由于在22号染色体上有7个APOBEC3基因（a - h）聚集在一个100kb的区域，其中大多数也具有抗HIV-1活性，我们试图测试所有APOBEC3基因（a - h）的遗传变异和单倍型对HIV-1感染和病程的影响。APOBEC3B基因缺失是HIV的危险因素：APOBEC3B是APOBEC3家族的7个成员之一，在体外已被证明可以抑制HIV-1的复制，并且是唯一不受HIV-1 vif抑制的APOBEC3蛋白。一个29.5 kb的缺失，全球总频率为22%，删除了整个APOBEC3B基因，并被假设影响HIV-1的发病机制。我们在4000多名受试者中研究了APOBEC3B基因缺失对HIV-1感染和疾病进展的影响。半合子基因型对EA和AA的感染和进展均无影响。然而，在EA中，纯合子缺失与感染易感性增加显著相关（OR = 7.37， P=0.024），在724例HIV-1未感染者和1950例HIV-1感染者中14例未观察到纯合子缺失。缺失等位基因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（log10斜率= +0.43，P= 0.048）相关。这些发现表明APOBEC3B基因的缺失增加了宿主对HIV-1感染和进展的易感性。如果这些结果得到证实，则表明APOBEC3B缺失可能对APOBEC3B缺失等位基因更为常见的亚洲血统人群中的HIV-1流行有相当大的影响。APOBEC3F基因变异保护艾滋病进展：APOBEC3F强烈抑制HIV-1，与APOBEC3G不同，APOBEC3F对vif有部分抗性。我们发现，在欧洲裔美国人中，两种氨基酸改变变体与预防艾滋病进展相关（RH=0.70， P= 0.007）。正在对变异的功能机制进行评估。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。DARC对HIV-1感染易感性或艾滋病进展没有影响：最近有报道称，趋化因子Duffy抗原受体（DARC）无效表型与非洲裔美国人HIV-1感染风险增加40%显着相关，并将其结果外推到非洲，表明非洲11%的HIV-1负担是由于DARC无效表型的存在。DARC零等位基因存在于90%以上的撒哈拉以南非洲人中，并传递对间日疟原虫疟疾的抗性，该突变在非非洲人群中不存在，除非通过混合。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。HLA-C等位基因强烈保护艾滋病进展：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（Euro-CHAVI）中，靠近或位于HLA-C、ZNRD1和ZNF39基因的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纵向队列中调查了该地区snp对艾滋病进展的影响。在调整包括HLA等位基因在内的其他已知协变量后，HLA- c rs9264942与保护欧美人进展为艾滋病（相对危险度[RH] = 0.72, 95% CI, 0.60-0.86， P= 0.0003）和死亡（RH=0.64, 95% CI, 0.53-0.78， P=6.3 × 10-6）密切相关。由于该SNP在该人群中非常常见（等位基因频率为39%），因此其对HIV-1流行的影响是巨大的。ZNRD1和RNF39的snp也有轻微影响。白细胞介素-18启动子的调控多态性与HCV清除相关：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。已知两种IL-18启动子多态性（-607 C/A和-137 G/C）及其单倍型影响IL-18的表达。我们研究了这些多态性在决定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。在idu中，IL18 -607A（优势比[OR]， 3.68； 95%可信区间[CI]，1.85-7.34）和IL[摘要截短于7800个字符]

The major objective of my laboratory is to identify host factors that contribute to infectious and other complex diseases. The tremendous impact of infectious diseases on global health, and the association of many human pathogens with common cancers, call for multiple research strategies to elucidate the mechanisms of infection and pathogenesis. Our strategy is to search for genetic variants that differentially affect rates of infection, or the course of pathogenesis, and which thereby identify the gene containing the variant as participating in the process of infection or pathogenesis, increasing knowledge of the mechanisms of pathogenesis and pointing to targets for therapeutic intervention. 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, including Illumina and Affymetrix, 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. Accomplishments: 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, however, disarmed by HIV-1 vif by interaction with Cullin5 (CUL5) complex, in the ubiquitination pathway 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 in the gene encoding APOBEC3G is associated with rate of progression to AIDS and trajectory of CD4+ T cell decline in HIV-1-infected persons. We also discovered that variant alleles and haplotype clusters in CUL5 influences the rate of CD4+ T-cell depletion. These findings highlight the importance of APOBEC3G-CUL5 pathway. Since there are seven APOBEC3 genes (A-H) clustered in a 100 kb region in chromosome 22 and most of which also confer anti-HIV-1 activity, We sought to test the influence of the genetic variants and haplotype in all APOBEC3 genes (A-H) on HIV-1 infection and disease courses. APOBEC3B gene deletion is an HIV risk factor: APOBEC3B, one of seven members of APOBEC3 family, has been shown to inhibit HIV-1 replication in vitro and is the only APOBEC3 protein not inhibited by HIV-1 vif. A 29.5-kb deletion, with an overall global frequency of 22%, removes the entire APOBEC3B gene and has been hypothesized to effect HIV-1 pathogenesis. We examined the impact of the APOBEC3B gene deletion on HIV-1 infection and disease progression in more than 4000 subjects. The hemizygous genotype had no effect on either infection or progression in either EA or AA. However, in EA, the homozygous deletion was significantly associated with increased susceptibility to infection (OR = 7.37, P=0.024), with none observed in 724 HIV-1 uninfected persons and 14 observed in 1950 HIV-1 infected persons. Homozygosity for the deletion allele was also associated with more rapid progression to AIDS (RH = 3.82, P=0.03) and higher viral load (slope on a log10 scale= +0.43, p=0.048). These findings indicate that deletion of APOBEC3B gene increases host susceptibility to HIV-1 infection and progression. These results, if confirmed, suggest that the APOBEC3B deletion may have considerable impact on the HIV-1 epidemic in populations with Asian ancestry where the APOBEC3B deletion allele is much more common. APOBEC3F genetic variants protect AIDS progression: APOBEC3F strongly inhibits HIV-1 and unlike APOBEC3G is partially resistant to vif. We found that two amino acid changing variants were associated with protection to progression to AIDS (RH=0.70, P= 0.007) in European Americans. Assessing of variants functional mechanism is ongoing. The relative contribution of each APOBEC3 gene and their interaction on viral infection are under investigation. DARC has no effect on HIV-1 infection susceptibility or progression to AIDS: Recently, it was reported that the Duffy antigen receptor for chemokine (DARC) null phenotype was significantly associated with a 40% increase in HIV-1 infection risk in African Americans and extrapolated their results to Africa, suggesting that 11% of the HIV-1 burden in Africa was due to the presence of the DARC null phenotype. The DARC null allele occurs in more than 90% of subSaharan Africans, and conveys resistance to Plasmodium vivax malariathe mutation is absent in non-African populations except by admixture. 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. A HLA-C allele strongly protects AIDS progression: A recent genome-wide association study (GWAS) of host determinants for HIV-1 disease revealed that SNPs near or in genes HLA-C, ZNRD1 and ZNF39 were associated viral load setpoint or disease progression among European HIV-1 cohorts (Euro-CHAVI). We investigated the effect of the SNPs in this region on AIDS progression in five U.S-based HIV-1 longitudinal cohorts. After adjusting other known covariates including HLA alleles, HLA-C rs9264942 was strongly associated with protection of progression to AIDS (Relative hazard [RH] = 0.72, 95% CI, 0.60-0.86, P = 0.0003) and death (RH=0.64, 95% CI, 0.53-0.78, P=6.3 x 10-6) in European Americans. As this SNP is very common (allele frequency, 39%) in this population, its impact on HIV-1 epidemic is substantial. Minor effects of SNPs of ZNRD1 and RNF39 were also observed. Regulatory polymorphisms in the interleukin-18 promoter are associated with 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 IL-18 promoter polymorphisms (-607 C/A and -137 G/C) and their haplotypes were known to affect the IL-18 expression. We examined the role of these polymorphisms in determining 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. Among IDUs, IL18 -607A (Odds ratio [OR], 3.68; 95% confidence interval [CI],1.85-7.34) and IL [summary truncated at 7800 characters]