Regulation of HIV Latency by Host Cell Transcriptional and Epigenetic Networks

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Principal Investigator: Edward P Browne
Organization: UNIV OF NORTH CAROLINA CHAPEL HILL
Fiscal Year: 2024
Award: $415,427
Funding agency: National Institute of Allergy and Infectious Diseases

Project summary:
Antiretroviral therapy (ART) has been successful at treating HIV infection and allowing people with HIV (PWH)
to lead relatively normal lives. Nevertheless, a cure for HIV has remained elusive, and interruption of ART
results in rapid viral rebound. HIV persists during therapy by its ability to enter a state of latent infection in CD4
T cells. A key challenge in the field is defining the molecular mechanisms that regulate HIV expression and
contribute to maintaining the latent state. HIV expression in latently infected cells is repressed by the
formation of heterochromatin at the integrated provirus that restricts access by key activating transcription
factors (TFs) and RNAPol2. Latency reversing agents (LRAs) have been developed that target HIV regulating
transcriptional pathways. However, most LRAs reactivate only a fraction of the reservoir, suggesting that
latency reversal is inefficient with single agents. We have carried out a set of single cell analyses to
characterize the transcriptomic and epigenomic states of latently infected cells, leading to the discovery of a
latency associated `signature' in primary CD4 T cells. Since then, we have performed a targeted CRISPR
screen of latency-associated genes as well as a chemical screen to identify a set of validated novel host cell
factors that individually regulate HIV latency. In this proposal we will capitalize on these findings to identify
novel combinations of gene knockouts and small molecule inhibitors that can synergize with our validated HIV
regulating factors to achieve broad reactivation of the clinical reservoir. To achieve this, we will take a novel
experimental approach involving both combination CRISPR/LRA screening and using cutting edge
interpretable machine learning tools to define the key drivers of HIV reactivation. Additionally, we will develop
a novel lipid nanoparticle platform for RNA-mediated reprogramming of latently infected cells to promote viral
reactivation.

Terms: <2019-nCoV vaccine><AIDS Virus><Acquired Immune Deficiency Syndrome Virus><Acquired Immunodeficiency Syndrome Virus><Animal Model><Animal Models and Related Studies><Basal Transcription Factor><Basal transcription factor genes><Benchmarking><Best Practice Analysis><CD4 Cells><CD4 Positive T Lymphocytes><CD4 T cells><CD4 helper T cell><CD4 lymphocyte><CD4+ T-Lymphocyte><CD4-Positive Lymphocytes><COVID-19 vaccine><CRISPR><CRISPR editing screen><CRISPR screen><CRISPR-based screen><CRISPR/Cas system><CRISPR/Cas9 screen><Cell Body><Cell Line><Cell model><CellLine><Cells><Cellular model><Chemicals><Chromatin><Clinical><Clinical Research><Clinical Study><Clustered Regularly Interspaced Short Palindromic Repeats><Collaborations><Complex><Data><Data Set><Drug Combinations><Engineering><Environment><Epigenetic><Epigenetic Change><Epigenetic Mechanism><Epigenetic Process><Gene Combinations><Gene Transcription><General Transcription Factor Gene><General Transcription Factors><Genes><Genetic Transcription><HIV><HIV Infections><HTLV-III Infections><HTLV-III-LAV Infections><Heterochromatin><Host Factor><Host Factor Protein><Human Immunodeficiency Viruses><Human T-Lymphotropic Virus Type III Infections><Immune system><Individual><Integration Host Factors><Interpretable ML><Interpretable machine learning><Interruption><Intervention><Intervention Strategies><Knock-out><Knockout><LAV-HTLV-III><Lead><Libraries><Logic><Lymphadenopathy-Associated Virus><Mediating><Messenger RNA><Modeling><Molecular><Nature><Non-Polyadenylated RNA><Pathway interactions><Pb element><Persons><Population><Provirus Integration><Proviruses><RNA><RNA Expression><RNA Gene Products><RNA delivery><Regulation><Repression><Research><Rest><Ribonucleic Acid><SARS-CoV-2 vaccine><SARS-coronavirus-2 vaccine><Severe Acute Respiratory Syndrome CoV 2 vaccine><Severe acute respiratory syndrome coronavirus 2 vaccine><Short interfering RNA><Small Interfering RNA><Strains Cell Lines><T4 Cells><T4 Lymphocytes><Testing><Training><Transcript><Transcription><Transcription Factor Proto-Oncogene><Transcription factor genes><Universities><Viral><Virus-HIV><access restrictions><analytical tool><antiretroviral therapy><antiretroviral treatment><benchmark><clustered regularly interspaced short palindromic repeats screen><combinatorial><computer based prediction><coronavirus disease 2019 vaccine><coronavirus disease-19 vaccine><cultured cell line><epigenetically><epigenome><epigenomics><explainable ML><explainable machine learning><global gene expression><global transcription profile><heavy metal Pb><heavy metal lead><improved><integration site><interventional strategy><knockout gene><latency/reactivation><latent infection><lipid based nanoparticle><lipid nanoparticle><mRNA><machine learning based model><machine learning model><model of animal><nCoV vaccine><nCoV-19 vaccine><nCoV19 vaccine><novel><pathway><predictive modeling><programs><reactivation from latency><screening><screenings><siRNA><single cell analysis><small molecular inhibitor><small molecule><small molecule inhibitor><success><synergism><tool><transcription factor><transcriptome><transcriptomics><vaccine against 2019-nCov><vaccine against COVID-19><vaccine against SARS-CoV-2><vaccine against SARS-coronavirus-2><vaccine against Severe Acute Respiratory Syndrome CoV 2><vaccine against Severe acute respiratory syndrome coronavirus 2><vaccine candidates against SARS-CoV-2><vaccine for novel coronavirus><vaccines preventing COVID><vaccines to prevent COVID><viral rebound><virus rebound>