CNS Viral Persistence and Neuropsychiatric Perturbations in HIV: Single cell and Molecular Interrogation

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Project Abstract Despite prolonged suppression of HIV on antiretroviral therapy (ART), eradication or sustained remission of the infection has not been achieved. Low levels of HIV DNA are still detectable in peripheral blood mononuclear cells (PBMC) from people living with HIV (PWH) taking ART, and cells containing rebound-competent virus can reside in sanctuary tissue sites, including lymph nodes, gut, genital tract and the central nervous system (CNS). In a study conducted within the AIDS Clinical Trials Group, we have recently used highly sensitive virologic assays in living donors to detect HIV DNA in cerebrospinal fluid (CSF) cells in up to 50% on long-term ART. Importantly, those with detectable CSF HIV DNA had poorer global cognitive function that those in whom CSF HIV DNA was not detected. We have subsequently shown higher concentrations of HIV DNA in CD4+ T cells from CSF compared to contemporaneous PBMC, and that atypical cell lineages including myeloid cells may be infected in CSF. Finally, we have successfully used single cell transcriptomics to identify unique and rare cell types in the CSF in PWH associated with HIV disease status and have further demonstrated the ability to identify cellular transcripts enriched in PWH versus healthy controls. Critical gaps in understanding CNS HIV persistence include what the characteristics and function of infected immune cells are in CSF, whether HIV proviruses in CSF are intact and genetically compartmentalized compared to proviruses in blood, and how these features relate to neuropsychiatric function of long-term HIV. Since the number of cells present in CSF is low in PWH suppressed on ART, thorough, simultaneous characterization of the immunologic and virologic landscape of the CNS has not been achieved. Using optimized lumbar puncture procedures and novel molecular techniques, we have overcome these obstacles to both rigorously examine the phenotype of CSF cells and thoroughly characterize the size, stability, intactness, and sequence diversity of persistent HIV in CSF compared to blood. We will use single cell technology to measure the transcriptional and cytokine profile of CNS cells combined with novel quantification of intact HIV DNA and single genome sequencing to discover new correlations within the CNS reservoir. Most importantly, we propose to rigorously examine the cognitive function and mental health of people living with HIV using sophisticated implementation of the new NIMH Research Domain Criteria (RDoC) framework, and how differences in neuropsychiatric outcomes relate to specific immunological and virological characteristics of the CNS in a diverse cohort of participants with a range of neuropsychiatric comorbidity.