High-Definition Characterization of the Persistence and Perturbation of the HIV Reservoir: Project 2

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Abstract A considerable number of clinical, neuropathological, immunohistochemical and immunological studies suggest that human brain cells, in particular those of myeloid origin, are susceptible to HIV-1; infection of these cells may contribute to neurocognitive dysfunction and viral long-term persistence despite ART. However, among all anatomical tissue locations in the human body, the central nervous system (CNS) arguably represents the most difficult one to access and to evaluate for viral infection and persistence. Recently, significant progress has been made in defining viral reservoirs using novel next-generation sequencing approaches, frequently allowing viral sequence profiling at single-genome or single-cell resolution. Using such technologies, it is possible to profile the evolutionary dynamics of viral species in the CNS in great detail, and to obtain rare insight into the underlying mechanisms and pathways that influence HIV-1 reservoir establishment and persistence in the CNS. Here, we propose a collaborative, interdisciplinary research project involving investigators with complementary experience in neurology, neuropathology, virology, computational modeling and clinical care of HIV-1 patients to advance the current understanding of the CNS as an anatomical site for long-term persistence of replication-competent HIV-1. In specific aim 1, we will leverage a unique collection of paired CSF and plasma samples from longitudinally-followed, untreated HIV-1 patients to evaluate phylogenetic associations and interrelated viral population genomics between viral sequences from the CNS and alternative anatomical compartments; these studies will be instrumental for tracking the seeding and establishment of long-lasting viral reservoirs pre-ART. In specific aim 2, we will use autopsy material from ART-treated HIV-1 patients with suppressed viremia at death to profile the frequency, clonality, chromosomal location and replication competence of proviruses isolated from sorted CNS cells, in particular from myeloid parenchymal microglia, from myeloid perivascular macrophages and astrocytes. Together, these studies will allow for a deep characterization of HIV-1 reservoir cell dynamics in the CNS, and may be informative for future clinical strategies aiming at HIV-1 eradication and cure.