Identification of Gene Polymorphisms Associated with Infectious Diseases

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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]