Using Omics to Understand the Effects of Drug Abuse on HIV Latent Reservoir

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PROJECT SUMMARY/ABSTRACT Goals of this study are to advance understanding of the biology linking cocaine abuse (CA) to HIV latent reservoir (HLR). We hypothesize that gene regulation is a primary link. We propose a novel genome-wide RNA expression (RNAexp) study to discover gene regulatory pathways from CA to increased HLR, followed by DNA methylation (DNAm) and mediation analyses to assess linkages for nominated pathways. With the success of combination antiretroviral therapy (cART) and public health strategies to reduce HIV incidence, much of the HIV burden in developed countries is now as a chronic disease, including among drug users. As a chronic disease, the search for an HIV cure is dependent on understanding and eliminating HLR (i.e., the replication competent but silenced HIV provirus integrated into host cells' DNA, which reactivates with cessation of cART). Cocaine is one of the most frequently abused illicit drugs among HIV+ individuals. CA is associated with accelerated HIV progression, which persists even with cART. Corroboratively, we also observe slower decline in HIV viral load (VL) among cART adherent CAs than adherent nonusers. With VL being associated with HLR quantity, understanding the biological effects of CA on HLR are critical. We focus on gene regulation because it is a biological connecting point for the interplay between CA and HLR. It is clear that both CA and cART affect gene regulation, that disruption of normal gene regulation is important for HIV viral replication and infectivity, and that gene regulation plays an important role in establishing and reactivating HLR. To our knowledge, there are no studies quantifying the likely differences in HLR by drug use overall or by CA specifically, nor studies of biological pathways linking CA to HLR. Thus, we propose the following aims: • Aim 1: Quantify the HLR and determine differences associated with CA. • Aim 2: Determine the effects of CA on gene regulation among HIV+ individuals. • Aim 3: Test CA differentially regulated genes as biological mediators between CA and HLR. This study is significant and innovative (e.g., first estimation of HLR among CAs, first genome-wide study of CA effects on gene regulation in CD4 T cells, first test of gene regulation as a mediator between CA and HLR). Our sequentially designed, high-risk / high-reward proposal, fits well with this R61/R33 mechanism: determining significant differences in HLR by CA and related differential gene expression during the R61 phase, and assessing gene regulation as mediators in the R33 phase. This study is likely to produce important new insights into key elements of HIV as a chronic disease among CAs, providing a basis for targeting unique features of CA that increase HLR and make an HIV cure more challenging in this population.