HERV proteogenomics of narcotic-driven HIV latency

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Abstract HIV eradication requires the elimination of latent reservoirs composed by cells harboring persistent proviruses. The brain is an anatomical site that is poorly accessible to the immune system as well as therapeutic agents. It also harbors a specific type of cells, microglia, where HIV can silently persist for long periods of time. Human endogenous retroviruses (HERVs) are a group of transposable elements, which are mostly held in an inactive state by different epigenetic mechanisms. Narcotic use induces changes the epigenetic landscape that can influence latency establishment and HERV expression. This project’s goal is to test the hypothesis that the distinct HERV expression signatures detected in HIV LTR-silent infection affect latency establishment and that this can be influenced by narcotic treatment. Furthermore, latent HIV-specific HERV expression can be exploited for the discovery of HIV latency specific markers. In order to investigate these hypotheses, it is crucial to determine the precise identity of the HERV elements expressed during latency. The experimental strategy is based on our newly developed reporter virus, which distinguishes latently infected from productively infected microglia cells in combination with our established proteogenomic approach which integrates HERV-specific RNA expression analysis with mass spec analysis. Such highly specialized processing is required because of the repetitive nature of HERVs that so far has undermined their detailed investigation. The RNA and protein expression blueprint obtained will inform on the ranking of the latent HIV- specific HERVs whose relevance will be investigated utilizing state of the art CRISPR-based expression induction in primary microglia as well as for the detection their expression in brain tissue form HIV patients with and without documented history on narcotic use. We expect that the innovative experimental approach proposed will provide insight into HERV RNA/protein expression landscapes in latently infected primary microglia and offer potential causal links between latency establishment, HERV expression and substance abuse. Even though there are high-risk aspects in this proposal, the experimental strategy proposed will deliver predictable, high gain benefits in our understanding of the complex biology underlying HIV latency in the brain compartment.