We propose to move the field of HIV pathogenesis forward by identifying novel host genetic factors for HIV acquisition through large-scale genome-wide association studies (GWAS) and gene expression. Keys to success of our initial GWAS and the proposed work are: (1) comparing highly exposed HIV- controls to HIV+ cases;(2) large sample sizes;and (3) integration of functional biology with statistical association results. 50% o the variability in HIV susceptibility is attributable to host genetics. Identifying such genetic factors is essential to understanding HIV pathogenesis and targeting drug development. Mechanisms underlying the only genetic variant conclusively associated with HIV acquisition, a deletion in CCR5, gave rise to maraviroc, an antiretroviral drug. Host genetics of acquisition has seen little progress in the ensuing 17 years, until now. Our initial GWAS (n=3,136) identified and independently replicated a novel association between a variant in the FERM and PDZ domain containing 1 gene (FRMPD1) and HIV acquisition. Using gene expression data and literature, we proposed a mechanism by which the single nucleotide polymorphism (SNP) rs4878712 exerts a protective effect on HIV acquisition. This combination of statistical evidence and biologically plausible links to HIV provide a strong foundation for deeper investigation of host genetics of HIV acquisition in the proposed study.
Aim 1 : Identify novel genetic associations with HIV acquisition in an extended GWAS of highly exposed HIV- controls and HIV+ cases (N=9,291). To extend discovery we will more than double our initial GWAS discovery sample size, use the joint 2 degree-of-freedom meta-analysis method, which accounts for gene-by-HIV exposure risk interactions and increases statistical power, and build in replication analyses.
Aim 2 : Identify genes that are differentially expressed between HIV+ cases and highly exposed HIV- controls to characterize biological pathways that contribute to HIV susceptibility. Using gene expression data we will identify genes that are up or down regulated among highly exposed HIV- controls compared to HIV+ cases, which will nominate biological pathways affecting susceptibility to HIV-1 infection.
Aim 3 : Identify variants driving differential gene expression between HIV+ cases and highly exposed HIV- controls, and test their association with HIV acquisition. We will map expression quantitative trait loci (eQTLs) for the genes differentially expressed by HIV status in Aim 2, evaluate the potential function of variants associated with HIV acquisition from Aim 1, and test the top 10,000 eQTLs not included in the Aim 1 results for association with HIV acquisition in a focused meta-analysis. Understanding HIV pathogenesis is essential to developing new, more effective treatment and prophylactic medications. Host genetics are central to HIV pathogenesis. Applying these tools to HIV acquisition in the proposed cohorts is likely to lead to new discoveries that will highly impact the field.
This study applies a strong study design and new discovery tools to identify genetic factors contributing to susceptibility to HIV-1 infection. The study is nvel in accounting for the interaction between HIV risk behaviors and genes in ethnically diverse cohorts coupled with gene expression studies to discover new genetic factors contributing to susceptibility to HIV-1 and examine biological function of identified genetic factors. The results of this study may identify important biological pathways and targets for developing medications or vaccines for HIV-1.