Jul 2026· International Journal of Molecular Sciences· Vol 27, pp. 6025· 0 citations· 40 references
Medicine
TL;DR
Investigating HERV-K transcription in particular of Human MMTV-like (HML) group-2 and 6 in peripheral blood of people with HIV found that HERV-K transcripts may be detected during both acute and chronic phases of the infection, with HML-6 showing higher expression compared to HML-2, predominantly within myeloid cells.
Abstract
Human endogenous retroviruses (HERVs) originate from ancient retroviral integration into the primate germline. Although most are defective proviruses, the most recently endogenized groups, like the HERV-K family, retain intact ORFs encoding retroviral proteins. HERVs usually remain transcriptionally silent, yet this status is reversible. Multiple HIV-HERV interactions, mainly mediated by the HIV Tat protein, lead to HERV transcription and protein production. The present study investigates HERV-K transcription in particular of Human MMTV-like (HML) group-2 and 6 in peripheral blood of people with HIV (PWH). Using different experimental approaches—such as single-cell and plasma transcriptomics-, we found that HERV-K transcripts may be detected during both acute and chronic phases of the infection, with HML-6 showing higher expression compared to HML-2, predominantly within myeloid cells. Effective combined antiretroviral therapy (cART) was able to significantly reduce HML-6 transcription, regardless of whether the treatment was initiated in the acute or late chronic phases of HIV infection. Notably, chronic infections showed higher HML-6 transcript levels compared to acute infections in both naïve and successfully cART-treated subjects, potentially associated with persistent immune dysregulation observed in chronic HIV infection, although a direct causal role of HML-6 expression remains to be established.
It is proposed that defective HIV proviruses contribute to chronic inflammation in PWH through an MDA5-dependent induction of type I interferon pathways.
Jonathan Kilroy, Aparna Deokar, Samantha D. Patalano et al.· Journal of Virology· 0 citations
PURPOSE OF REVIEW
People with HIV (PWH) require lifelong antiretroviral therapy (ART) to maintain viral suppression, yet integrated HIV DNA persists in long-lived cellular reservoirs in blood and tissues. Most integrated proviruses are defective, meaning they contain deletions, hypermutation, packaging-signal defects, splice defects, or other defects that prevent production of replication-competent viruses. However, these genomes are not necessarily biologically inert as many remain capable of transcription and, in some cases, translation of viral proteins.
RECENT FINDINGS
Recent evidence has demonstrated that the brain is a stable reservoir of both intact and defective HIV despite viral suppression with ART. Whilst intact replication capable proviruses are known to induce cell activation and pathology, recent studies suggest that defective proviruses with large internal deletions and hypermutation can remain transcriptionally, and in some cases, translationally active and have now been linked with persistent immune activation during ART. Therefore, transcriptionally active defective proviral DNA may be a contributor to underlying neuropathogenesis in ART-suppressed PWH.
SUMMARY
Defective HIV proviruses make up the majority of the proviral reservoir across blood and tissue compartments. Although they are replication-incompetent, many remain transcriptionally and translationally competent and may contribute to chronic inflammation, antigen persistence, and neuropathology in ART-suppressed PWH.
Emily K Chalmers, Janna Jamal Eddine, Liam Yucel et al.· Current Opinion in HIV and A...· 0 citations
The persistent HIV reservoir includes latently infected cells, which upon antiretroviral treatment (ART) interruption, reactivate HIV-1 expression and fuel rebound of disease progression. People living with HIV, even on ART, experience chronic inflammation associated with accelerated aging and comorbidities of the central nervous system, gut, and heart. The persistent reservoir is mostly composed of defective proviral genomes, unable to produce infectious virus due to deleterious mutations. However, the contribution of these defective viruses to chronic disease has not been well characterized. We have demonstrated that an intragenic element in the Env region of the HIV genome drives transcription of non-canonical RNA in defective proviruses. We hypothesize that these transcripts from defective proviruses contribute to chronic inflammation.
To model defective proviruses, we used CRISPR-Cas9 to engineer cells harboring HIV genomes with a nonfunctional 5’ LTR.
We observed a correlation between levels of internally driven transcripts and in vitro pro-inflammatory cytokine production in Jurkats, macrophage-like ThP1 cells, and cells differentiated into macrophages. Additionally, we confirmed nuclear export of these transcripts and that shRNA-mediated MAVS knockdown in ThP1s decreases the inflammatory response.
We propose a model that innate immune sensing of these transcripts activates a MAVS-dependent pathway to contribute to chronic inflammation and HIV-associated comorbidities.
NIH RO1 AI187175, NIH RO1 AI138960, NIH RO1 DA055488, CFAR P30AI042853, Boston University Undergraduate Research Opportunities Program Faculty Matching Grant
Viral Immunology (VIR)
Aparna Deokar, Jonathan Kilroy, H. Akiyama et al.· Journal of Immunology· 0 citations
HIV-1 enters the central nervous system early after infection and establishes a long-lived reservoir that persists despite antiretroviral therapy. Single-cell and single-nucleus RNA sequencing provide powerful approaches to study HIV infection in the human brain, yet standardized and sensitive methods for identifying rare HIV-infected cells in these datasets remain limited. Here, we present a scalable multi-reference framework for detecting HIV RNA–positive cells in human CNS single-nucleus RNA-seq data. The pipeline integrates a modified HIV reference genome, subject-specific variant-updated HIV references, and a comprehensive HIV strain collection to improve viral read recovery and specificity.
We applied this framework to 250 post-mortem brain samples from the SCORCH (Single Cell Opioid Responses in the Context of HIV) consortium spanning 12 brain regions and 102 donors, including people with and without HIV (PWH and PWoH). After screening, 48 samples from 35 donors comprising 559,207 high-quality nuclei were analyzed in depth. We identified 1,939 HIV RNA–positive cells exclusively in samples from PWH. Using conservative thresholds, 908 high-confidence infected cells were retained for downstream analyses. HIV RNA-positive cells were rare overall and strongly enriched in cases with HIV encephalitis. Microglia constituted the predominant infected population (79% of HIV RNA-positive cells), with substantially smaller contributions from oligodendrocytes, astrocytes, and neurons. In non-encephalitic brains, detectable infection was largely restricted to microglia, whereas in encephalitic tissue HIV RNA–positive cells were distributed across multiple CNS (Central Nervous System) lineages. Viral RNA burden followed a long-tailed distribution, with microglia retaining higher HIV transcript counts than other cell types. Recovered HIV reads were concentrated in the U3 region of the 5′ LTR and in the env gene, implicating regulatory and entry-associated regions as focal points of viral diversity in the brain.
Together, these data establish a harmonized framework for identifying rare HIV-infected cells in CNS single-cell datasets and provide large-scale quantitative evidence that microglia represent the dominant and most persistent HIV-infected population in the human brain. This work offers a reference strategy and resource for future NeuroHIV studies aimed at defining, monitoring, and ultimately targeting CNS viral reservoirs.
Yuan-Yuan Cai, Nicholas C. Jacobs, Dana Gabuzda et al.· Virology Journal· 0 citations
Background Immunological non-responders (INRs) and immunological responders (IRs) exhibit distinct patterns of immune reconstitution despite suppressive antiretroviral therapy (ART); however, the genetic characteristics of the HIV-1 reservoir in these groups remain poorly understood. This study investigates the landscape of HIV-1 proviruses in INRs and IRs, and its potential association with immune reconstitution. Methods Peripheral blood mononuclear cells (PBMCs) from 10 ART-treated INRs and 10 IRs were analyzed using near-full-length HIV-1 DNA amplification and PacBio third-generation sequencing to characterize genetically intact and defective proviral genomes. Intact open reading frames (ORFs) were further inferred using the CFEIntact tool. Results Compared with IRs, INRs had a higher total proviral genome per 106 PBMCs, although the difference did not reach statistically significance. INRs also displayed a significantly higher level of intact proviral genomes per 106 PBMCs and a trend toward a higher proportion of intact sequences. Defective proviruses remained the predominant component of the reservoir in both groups and were broadly comparable in number and composition. In both cohorts, proviral defects were more frequently observed in the 3′ half of the genome. Discussion Our study reveals a distinct proviral landscape in ART-treated INRs, characterized by elevated levels of intact proviral genomes. These observations suggest that the intact component of the reservoir may represent a clinically relevant feature of incomplete immune reconstitution, and provide a rationale for further studies of reservoir-directed interventions in this population.
Shengquan Tang, Yue Wang, Yanqiu Lu et al.· Frontiers in Immunology· 0 citations
ABSTRACT Human immunodeficiency virus type 1 (HIV-1) persists in latent reservoirs, mainly within CD4+ T cells, which are refractory to antiretroviral therapy, and can lead to rapid viral rebound upon treatment interruption. The “shock and kill” strategy aims to eliminate latent reservoirs by inducing viral transcription through latency-reversing agents (LRAs), thereby exposing infected cells to immune-mediated clearance. We developed and validated a simple, low-cost, and highly reproducible in vitro screening protocol to evaluate the efficacy and safety of LRAs, using a two-color flow cytometry assay on ACH2 cells, a well-characterized model of HIV-1 latency. Using this method, we identified PEP005 and CUDC-907 as the most potent LRAs across multiple experimental settings. Their reactivation capacity was further confirmed through transcriptomic analysis, which revealed a significant upregulation of viral RNA copies following stimulation. In addition, we collaborated with Dompé for using the Exscalate platform, an innovative computer-aided drug discovery approach, together with the experimental validation, which led to the identification of Tandutinib, a tyrosine kinase and mTOR inhibitor, as a novel LRA candidate with appreciable latency-reversing activity in the ACH2 model. While the ACH2 cell line does not fully recapitulate the complexity of HIV latency in vivo, it offers a robust and scalable system for early-stage screening and prioritization of candidate LRAs. Importantly, the future application of these LRAs in ex vivo samples derived from people living with HIV, with a particular focus on pediatric samples, will be crucial to deepen our understanding of latency reactivation in clinically relevant settings and age-specific immune environments. IMPORTANCE This study addresses a major obstacle to curing human immunodeficiency virus type 1 (HIV-1) infection: the persistence of latent viral reservoirs that are not eliminated by current therapies. We developed a simple and reproducible assay to identify compounds capable of reactivating latent virus, a key step in cure strategies. Using this approach, we identified effective latency-reversing compounds and, through collaboration with Dompé using the EXSCALATE platform, we also identified Tandutinib as a promising new candidate for further investigation. This study addresses a major obstacle to curing human immunodeficiency virus type 1 (HIV-1) infection: the persistence of latent viral reservoirs that are not eliminated by current therapies. We developed a simple and reproducible assay to identify compounds capable of reactivating latent virus, a key step in cure strategies. Using this approach, we identified effective latency-reversing compounds and, through collaboration with Dompé using the EXSCALATE platform, we also identified Tandutinib as a promising new candidate for further investigation.
A. Neri, Arianna Rotili, Elena Morrocchi et al.· Microbiology spectrum· 0 citations
