Integration and Validation of Single-Cell Neuronal and Immune Molecular Responses in SUD and HIV - Abstract HIV-associated neurocognitive disorders (HAND), substance use disorders (SUD), Alzheimer's Disease (AD), and neuropsychiatric conditions share converging mechanisms of neuroinflammation, immune dysregulation, synaptic dysfunction, and neuronal injury that accelerate cognitive decline. Moreover, SUD and neuropsychiatric disorders co-occur at higher frequencies in persons living with HIV (PLWH) than in the non-HIV population, making it difficult to untangle the influence of these shared genetic mechanisms on progression of the diseases. The Single Cell Opioid Responses in the Context of HIV (SCORCH) consortium aims to address this complex interplay between HIV, substance use disorders (SUDs), and neuropsychiatric conditions. Leveraging the extensive data from SCORCH, PsychENCODE, and Alzheimer’s Disease (AD) datasets, our proposal aims to uncover the genetic and molecular mechanisms driving the interactions between HIV, neuropsychiatric, and neurodegenerative conditions. We employ advanced computational techniques to identify differences in gene expression across disorders, with a focus on identifying shared and distinct drivers of HIV and SUD impact on psychiatric genes and pathways (HAND), and their interplay with Psychiatric disorders (Psych) and dementia/cognitive impairment (DCI). In Aim 1, we leverage single-cell transcriptomics and spatial datasets with advanced machine learning algorithms including contextualized learning, module analysis, and cell-projected phenotypes to discover shared and distinct differentially-expressed genes (DEGs), pathways, modules, and cell types underlying HAND-Psych-DCI. In Aim 2 we also leverage single-cell epigenomics and genetics datasets to infer cell-cell-communication between microglia and neuronal cells, gene-regulatory networks, upstream regulators/TFs, cell-cell communication, and causal drivers, and create a public resource and interactive website for broad data dissemination of all primary, secondary, and tertiary analyses and results for the broader scientific community. In Aim 3 we perform experimental characterization and mechanistic testing in vivo. We develop viral tools for targeting and tracing cholinergic neurons in the mouse basal nucleus of Meynert (BNM), investigate the effects of bidirectional modulation using DREADDs in these neurons, and assess the functional implications of HIV-associated inflammatory signaling. The successful execution of our study will elucidate clinically relevant connections between HIV, neuropsychiatric, and neurodegenerative disorders by examining single-cell transcriptional changes in an integrated experimental and computational framework. This approach enables us to dissect distinct molecular pathways across brain regions and cell types, providing a deeper understanding of the unique and shared mechanisms underlying these conditions. The insights gained will be crucial in guiding the development of new therapeutic strategies.
