Goals of this study are to advance understanding of the biology linking cocaine abuse (CA) to the 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. We will use available data and biospecimens from 600 participants in the Women's Interagency HIV Study (WIHS) divided into discovery (N1=400) and replication (N2=200) samples. We focus on gene regulation because it is a biological connecting point for the interplay between CA and the HLR. It is clear that both CA and combination antiretroviral therapy (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 the HLR. To our knowledge, there are no studies quantifying the likely differences in the HLR by drug use overall or by CA specifically, nor studies of biological pathways linking CA to the HLR. Thus, we propose the following aims: ? Aim 1: Quantify the HIV Latent Reservoir 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 administrative supplement would provide funds for multiple-PI Dr. Aouizerat at New York University to purchase laboratory equipment (QX200? Droplet Digital? PCR System) that will allow investigators to use the recently developed intact proviral DNA assay (IPDA: Bruner et al. Nature 2019) to quantify the HLR. IPDA uses a two-step ddPCR approach that can distinguish replication competent and incompetent provirus, which is a substantial advance over viral outgrowth assays that under count the HLR and standard ddPCR HIV DNA detection that over counts the HLR. This equipment is needed to apply this newly developed HLR assay within the timeline of the parent grant. The QX200? Droplet Digital? PCR System from BioRad costs $137K after negotiation of a price reduction from $173K from the vendor, of which Dr. Aouizerat can cover $37K from internal NYU funding.
This administrative supplement would provide funds to purchase laboratory equipment that will allow investigators to use the recently developed intact proviral DNA assay (IPDA: Bruner et al. Nature 2019) to quantify the HIV latent reservoir. IPDA uses a new approach that is a substantial advance over prior methods in that it accurately identifies latent HIV virus that can replicate. This equipment is needed to apply this newly developed HIV latent reservoir assay within the timeline of the parent grant.
