Multi-OMICS identification and validation of mechanisms triggered by Immune interventions aimed at reducing the size of the replication competent Reservoir

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In spite of antiretroviral (ART) drugs which effectively control plasma viremia, a pool of HIV latently infected cells form a persistent reservoir that prevents clearance of virally infected cells. Upon cessation of ART treatment, this reservoir leads to a rapid rebound in plasma viremia, even if ART is initiated early during acute infection. Eradicating or permanently silencing this reservoir is the focus of many HIV cure strategies. Immune dysfunction including impaired T cell responses are a hallmark of HIV disease. Immune directed cure strategies seek to overcome this dysregulation to restore normal immune function and promote killing of HIV infected cells. The limited clinical efficacy of immune-based cure strategies to date suggests that there may be more to restoring immune function than targeting T and B cells. We hypothesize that cure strategies which activate and restore normal innate and adaptive immune function will more effectively reduce the HIV reservoir and limit viral rebound after cessation of ART. To test this hypothesis, we will employ an expansive multi-Omic platform consisting of virological, immunological and molecular assays to define the role of simultaneous re- invigoration of the innate and adaptive immune systems by 3 distinct cure strategies on HIV reservoir dynamics and viral rebound after discontinuing ART. The first strategy (Project 1) will investigate how co-treatment with Lefitolimod (innate immune TLR9 agonist) and broadly neutralizing antibodies promotes clearance of the HIV reservoir by priming innate immune responses and providing the antibodies to target infected cells using Fc- mediated innate immune effector functions. The second strategy (Project 2) will test how blockade of the PD- 1/PD-L1 signaling axis by monoclonal antibody therapy leads to enhanced inflammatory monocyte/macrophage responses and restored CD4 and CD8 T cell function. The third strategy (Project 3) will study how engraftment with allogeneic hematopoietic stem cells expressing the CCR5D32 mutation or autologous infusion of CCR5 deleted CD4+ T cells repopulate the immune compartment with functional effector cells that are refractory to HIV infection leading to killing of the HIV reservoir and a lack of viral rebound. For all Projects, we will define how differences in the host environment resulting from host and microbial metabolites modulate the immunological mechanisms identified to mediate clearance of the HIV reservoir and/or limit viral rebound. Analysis of results will be performed by a dedicated Machine Learning and Modeling Core. This core will ultimately be responsible for generating integrated multi-Omic network models which predict the microbiome/metabolite features which directly regulate the immune mechanisms associated with reduction in either the HIV reservoir or viral rebound; both within each cohort/Project and across Projects to identify common features to multiple strategies. Our team of experts have collaborated extensively and are uniquely positioned to complete the goals of this program.