Single-cell multi-omic analysis of opioid-mediated HIV disease pathogenesis

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Abstract Routine HIV treatment with combination antiretroviral therapy (cART) eliminates nearly all actively infected cells. Nevertheless, the small reservoir of residual cells, some of which can remain dormant for long periods of time before becoming active and producing new virus particles, represents a crucial barrier to completely curing the disease. Substance use disorders introduce further challenges—for example, many immune cells express opioid receptors and undergo significant molecular changes after opioid exposure, which can increase their vulnerability to HIV infection. Our recent work suggests that the global transcriptomic and epigenomic changes during hematopoietic differentiation affect viral latency and activation. Additionally, we recently found that global inhibition of histone deacetylase activity in HSPCs increases viral activation, further implicating epigenomic changes in activation. Deciphering the contributions of addictive substances, inflammatory stimuli, and cell state to HIV infection and latency is crucial for ongoing efforts to cure HIV. In particular, the following fundamental questions remain unanswered: How does substance use change the transcriptomic and epigenomic states of immune cells? How do these changes in turn affect HIV infection and latency? How do the effects of substance use on HIV infection and latency vary across different immune cell types and states? Here, we will combine our experimental platform for identifying latently and actively infected cells, single-cell transcriptome, and epigenome sequencing, and our recently developed computational integration methods to investigate these questions. Our interdisciplinary team combines expertise in HIV basic science, HIV clinical treatment, and bioinformatics to develop an experimental and computational framework for integrated gene expression, chromatin accessibility, histone modification, and insertion site profiling into a single picture of how opioids affect viral infection and latency. Specifically, this project will (1) use single-cell RNA-seq, single-cell ATAC-seq, and single-cell Cut&Tag to map diversity of infected cell response to opioid exposure, (2) investigate the relationship between immune cell type and differentiation state and viral activation, and (3) determine viral integration sites through single-cell RNA-seq. Together, these aims will produce a comprehensive, integrated transcriptomic and epigenomic atlas of how HIV-infected immune cells respond to opioid exposure as well as how opioids impact HIV infection. Our work also develops a broadly applicable experimental and computational framework, laying a foundation for the discovery of novel insights into HIV infection and latency in the context of substance use disorders.