Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation

Despite the success of antiretroviral therapy,human immunodeficiency virus(HIV)cannot be cured because of a reservoir of latently infected cells that evades therapy.To understand the mechanisms of HIV latency,we employed an integrated single-cell RNA sequencing(scRNA-seq)and single-cell assay for transposase-accessible chromatin with sequencing(scATAC-seq)approach to simultaneously profile the transcriptomic and epigenomic characteristics of~125,000 latently infected primary CD4^(+)T cells after reactivation using three different latency reversing agents.Differentially expressed genes and differentially accessible motifs were used to examine transcriptional pathways and transcription factor(TF)activities across the cell population.We identified cellular transcripts and TFs whose expression/activity was correlated with viral reactivation and demonstrated that a machine learning model trained on these data was 75%-79%accurate at predicting viral reactivation.Finally,we validated the role of two candidate HIV-regulating factors,FOXP1 and GATA3,in viral transcription.These data demonstrate the power of integrated multimodal single-cell analysis to uncover novel relationships between host cell factors and HIV latency.

Recombinant HIV to kill latent reservoir cells: a hypothetical therapeutic strategy

Latency is the pivotal factor that governs the long-term pathogenecity and persistence of HIV-1 infection.It is also the primary impediment to cure and successful treatment,resulting in patient death.Latency of HIV-1 infection promotes failure of the conventional antiretroviral therapy(ART).Cessation of ART immediately leads to viral reactivation and attainment of viral load in peripheral circulation.ART comes with severe side effects and is ineffective at treating latent infection.To eliminate latent infection,alternate therapeutic strategies such as Shock and Kill,Block and Lock,gene editing and vaccination have been proposed.Although these strategies have experimentally been proven successful,they possess major limitations.Hence,in this hypothesis,an alternate therapeutic strategy has been proposed to solve the threat of HIV-latency.The proposed model encompasses the generation and administration of recombinant HIV-1 particles whose genomes having pro-apoptotic gene,tBid,will activate apoptotic cell death pathways after infecting only the latent cells,thereby removing latent HIV host cells from patients’bodies.

Moving Toward a Functional Cure for HIV-1

Despite the recent success of suppressing human immunodeficiency virus 1(HIV-1)replication in the peripheral blood with antiretroviral therapy,elimination of the provirus from infected cells remains challenging because the virus can integrate into the host genome and become a latent proviral reservoir.The removal of these latent viral reservoirs from tissue containing infected resting memory CD4+T cells remains a major barrier to developing a cure for HIV-1.Several novel strategies have recently been developed for curing HIV infection.These include stem cell transplantation with CCR5-D32 mutated cells,initial antiretroviral treatment in the very early stage of HIV infection,gene editing to excise the HIV genome or generate CCR5-mutated HIV-1-resistant cells,“shock-and-kill”to reactivate latent HIV using latency reversal agents combined with enhanced immune clearance methods,and an emerging“block-and-lock”strategy to reactivate latent HIV using latency reversal agents combined with enhanced immune clearance methods.However,the high risks and limitations to scale-up in clinics,as well as poor performance in clinical trials,have hampered these efforts.This review aims to describe the present efforts that are being made to combat HIV latency,and critically discuss the limitations and future of the cure for HIV-1.