UC Davis

Despite the advent and implementation of Anti-retroviral therapy (ART) in 1987, people living with HIV (PLWH) continue to experience a high incidence of age-associated comorbidities, particularly HIV associated neurocognitive disorders (HAND) which affect 40-70% of PLWH. Research over the past four decades has predominantly focused on the role of myeloid cells in the development of HAND due, in part, to the initial discovery of HIV-infected myeloid cells in the post-mortem brain tissue of AIDS patients. My dissertation examines the understudied role of T lymphocytes in HAND, in light of three significant advancements in the fields of HIV and neuroimmunology. Firstly, ART treatment has not only stabilized disease progression but has also led to the reconstitution and stabilization of CD4 T cells, highlighting a newfound potential role for CD4 T cells in the neurological disease process. Secondly, we now recognize that T cells are an important immune population within the central nervous system (CNS) both during homeostasis and disease. Thirdly, data from neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Multiple Sclerosis highlight a critical role for T cells in contributing to neuroinflammation and disease progression. Together, these advancements collectively provide a strong rationale for developing a more comprehensive understanding of the role of T cells in HAND. Given the early establishment of transmitted/founder (T/F) HIV in the CNS, the surveillance of the CNS by CCR5 (R5) + T helper 1 cells, which serve as primary HIV targets, and the influence of T-cell derived cytokines on microglial activation, we hypothesized that T cells are pivotal in acute CNS viral seeding and neuroinflammation. We tested this hypothesis in rhesus macaques (Macaca mulatta) - among the most robust models for studying the CNS and HIV pathogenesis. We employed models of both acute and chronic simian HIV (SHIV) infection using distinct strains: the R5/CD4 tropic T/F SHIV C.CH505, the virulent R5-T cell-tropic SIVmac251, and the macrophage-tropic SIVCL757, used in studies of neuro-HIV. Together, our studies with these distinct viruses offer the following insights into the role of CD4 T cells in the brain during HIV infection. In Chapter II, we presented RNA sequencing and viral load data across four synapse-dense regions of the brain susceptible to HIV infection (Prefrontal Cortex (PFC), Superior Temporal Sulcus, Caudate Nucleus, Hippocampus). First, our data demonstrated that these synapse-dense cognitive regions are rich in immune gene signatures at homeostasis. Following infection with T/F SHIV.C.CH505, our analysis showed activation of biological pathways consistent with T cell recruitment and microglial activation. Despite relatively low plasma and cerebrospinal fluid (CSF) viral loads, we observed viral (v)RNA and vDNA within these regions - an observation aligning with infiltration of SIV infected Th1 CD4 T cells into the PFC. In Chapter III, we delved deeply into the phenotype of CD4 T cells within the CNS, including the brain and its associated border tissues. Our rationale for this comprehensive analysis was to delineate target cells in these regions to better understand susceptibility to viral establishment. We conducted single-cell analysis of CD45+ immune cells in brain parenchyma, comparing them to counterparts in the spleen of both uninfected macaques and those acutely infected with SIVmac251. The data demonstrated colocalization of viral transcripts within CD4 clusters and furthermore showed induction of antiviral responses during acute SIV infection. This supports the observations made in Chapter II that target cells for HIV populate the CNS, including the dura, choroid plexus stroma, and the skull bone marrow. Correspondingly, during the acute phase of SIVmac251 infection, we observed significant levels of viral RNA and DNA in these regions. In animals chronically infected with SIVmac251 (40 weeks) and treated with suboptimal ART, our data demonstrated that despite CSF viral suppression, there is incomplete reconstitution of CD4 T cells in the brain and surrounding CNS tissues underscoring their active engagement during acute and chronic phases of SIVmac251 infection. In Chapter IV, we comprehensively assessed phenotypic and functional features of CCR7+ cells identified in Chapter III. Leveraging single-transcriptomic analysis, ATAC-seq, spatial transcriptomics and flow cytometry we show that CCR7+ CD4 T cells in the brain have T lymphocyte central memory-like features. Moreover, the skull bone marrow emerged as a potential niche for CCR7+ CD4 T cells. In a cohort of macaques chronically infected (112 weeks) with SIVCL757 and treated with suboptimal ART, we noted a decrease in CCR7+ CD4 T cells within the brain in parallel with evidence for microglial activation and induction of neurodegenerative pathways. These findings suggested that changes in CD4 T cell subsets within the CNS may drive neuroinflammation during chronic HIV infection. In summary, the findings across my three chapters lead to three major conclusions. First, the presence of both CCR5 and CCR7 CD4 T cells in the parenchymal and border regions of the CNS, renders this organ susceptible to initial HIV infection and establishment of latent reservoirs. Second, our studies of acute infection with two viruses - SHIVC.CH505 and SIVmac251- suggests that CD4 T cells within the brain parenchyma are actively engaged during acute HIV infection serving as both viral targets and mediators of neuroinflammation. Third, our models of chronic infection under suboptimal ART with two viruses - SIVmac251 and SIVCL757 - demonstrate that inadequate CD4 T cell reconstitution together with reduction of CCR7+ CD4 T cells may underlie neuroimmune dysregulation in HIV-infected patients on ART.