Macrophages and Microglia, Gene Expression and Chromatin: Illuminating the Myeloid Viral Reservoir in the Brain through Single Cell Analyses

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Project Summary An innovative approach is proposed to determine the Role of Myeloid Cells in Persistence and Eradication of HIV-1 Reservoirs from the Brain, in response to RFA-MH-20-702. We will perform using the gold-standard nonhuman primate system, in SIV-infected animals with chronic viral suppression using combination antiretroviral therapy. The infected cells in the brain will be uncovered by intra-CNS anti-CD8 treatment, following subsequently by myeloid cell isolation and purification, single-cell RNA sequencing (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq), followed by bioinformatic analysis and validation. This will give result into unparalleled insight into the nature of the myeloid cells in which SIV, as a model for HIV, persists in the brain, combining individual cellular transcriptomes with epigenetic information on the whole genome. These will be done in a new paired format, obtaining linked information on the two modalities from the same cell. combined with sensitive assays for virus in the brain. This will take place in the context of a two-year R21 under two Specific Aims. In Aim 1, we will uncover the SIV-infected cells in the brain in the presence of suppressive cART, allowing their identification and, in comparison with the information on the companion uninfected cells, as well as known data on brain myeloid cells from single cell and other studies, the phenotype of brain myeloid cells in which SIV/HIV can persist. In Aim 2, in-depth molecular characterization of these cells will be performed, yielding additional information on their phenotype, as well as upstream control mechanisms, transcriptional potential, as well as relationships to genes and their control regions that affect HIV, CNS disease, and other conditions. We will ensure our data adhere to the Findable, Accessible, Interoperable, and Reusable (FAIR) standards in order that we and others can utilize this information in future strategies to silence or clear virus from the brain. These studies are designed with rigor and reproducibility factored in, thus the results from these studies will provide new insights into the role of myeloid cells in persistence and eradication of HIV-1 reservoirs from the brain.