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Ranga U, Panchapakesan A, Saini C. HIV-1 subtypes and latent reservoirs. Curr Opin HIV AIDS 2024; 19:87-92. [PMID: 38169308 DOI: 10.1097/coh.0000000000000835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
PURPOSE OF REVIEW We explore the current status of research on HIV-1 subtype-specific variations and their impact on HIV-1 latency. We also briefly address the controversy surrounding the decision-making process governing the ON/OFF states of HIV-1 transcription, specifically focusing on the regulatory elements, the long terminal repeat (LTR), and Tat. Understanding the decision-making process is crucial for developing effective intervention strategies, such as the 'shock-and-kill' approach, to reactivate latent HIV-1. RECENT FINDINGS Attention has been drawn to subtype-specific transcription factor binding site (TFBS) variations and the possible impact of these variations on viral latency. Further, diverse subtype-specific assays have been developed to quantify the latent viral reservoirs. One interesting observation is the relatively larger latent reservoirs in HIV-1B infection than those of other viral subtypes, which needs rigorous validation. The emergence of LTR-variant viral strains in HIV-1C demonstrating significantly higher levels of latency reversal has been reported. SUMMARY Despite persistent and substantial efforts, latent HIV-1 remains a formidable challenge to a functional cure. Determined and continued commitment is needed to understand the ON/OFF decision-making process of HIV-1 latency, develop rigorous assays for accurately quantifying the latent reservoirs, and identify potent latency-reversing agents and cocktails targeting multiple latency stages. The review emphasizes the importance of including diverse viral subtypes in future latency research.
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Affiliation(s)
- Udaykumar Ranga
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, Karnataka
| | - Arun Panchapakesan
- Molecular Biology Laboratory, Y R Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, Tamil Nadu, India
| | - Chhavi Saini
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, Karnataka
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Moar P, Premeaux TA, Atkins A, Ndhlovu LC. The latent HIV reservoir: current advances in genetic sequencing approaches. mBio 2023; 14:e0134423. [PMID: 37811964 PMCID: PMC10653892 DOI: 10.1128/mbio.01344-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
Multiple cellular HIV reservoirs in diverse anatomical sites can undergo clonal expansion and persist for years despite suppressive antiretroviral therapy, posing a major barrier toward an HIV cure. Commonly adopted assays to assess HIV reservoir size mainly consist of PCR-based measures of cell-associated total proviral DNA, intact proviruses and transcriptionally competent provirus (viral RNA), flow cytometry and microscopy-based methods to measure translationally competent provirus (viral protein), and quantitative viral outgrowth assay, the gold standard to measure replication-competent provirus; yet no assay alone can provide a comprehensive view of the total HIV reservoir or its dynamics. Furthermore, the detection of extant provirus by these measures does not preclude defects affecting replication competence. An accurate measure of the latent reservoir is essential for evaluating the efficacy of HIV cure strategies. Recent approaches have been developed, which generate proviral sequence data to create a more detailed profile of the latent reservoir. These sequencing approaches are valuable tools to understand the complex multicellular processes in a diverse range of tissues and cell types and have provided insights into the mechanisms of HIV establishment and persistence. These advancements over previous sequencing methods have allowed multiplexing and new assays have emerged, which can document transcriptional activity, chromosome accessibility, and in-depth cellular phenotypes harboring latent HIV, enabling the characterization of rare infected cells across restrictive sites such as the brain. In this manuscript, we provide a review of HIV sequencing-based assays adopted to address challenges in quantifying and characterizing the latent HIV reservoir.
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Affiliation(s)
- Preeti Moar
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Thomas A. Premeaux
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Andrew Atkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York City, New York, USA
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Pascucci GR, Morrocchi E, Pighi C, Rotili A, Neri A, Medri C, Olivieri G, Sanna M, Rasi G, Persaud D, Chahroudi A, Lichterfeld M, Nastouli E, Cancrini C, Amodio D, Rossi P, Cotugno N, Palma P. How CD4 + T Cells Transcriptional Profile Is Affected by Culture Conditions: Towards the Design of Optimal In Vitro HIV Reactivation Assays. Biomedicines 2023; 11:888. [PMID: 36979867 PMCID: PMC10045592 DOI: 10.3390/biomedicines11030888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/15/2023] [Accepted: 02/25/2023] [Indexed: 03/16/2023] Open
Abstract
Most of the current assays directed at the investigation of HIV reactivation are based on cultures of infected cells such as Peripheral Blood Mononuclear Cells (PBMCs) or isolated CD4+ T cells, stimulated in vitro with different activator molecules. The culture media in these in vitro tests lack many age- and donor-specific immunomodulatory components normally found within the autologous plasma. This triggered our interest in understanding the impact that different matrices and cell types have on T cell transcriptional profiles following in vitro culture and stimulation. METHODS Unstimulated or stimulated CD4+ T cells of three young adults with perinatal HIV-infection were isolated from PBMCs before or after culture in RPMI medium or autologous plasma. Transcriptomes were sequenced using Oxford Nanopore technologies. RESULTS Transcriptional profiles revealed the activation of similar pathways upon stimulation in both media with a higher magnitude of TCR cascade activation in CD4+ lymphocytes cultured in RPMI. CONCLUSIONS These results suggest that for studies aiming at quantifying the magnitude of biological mechanisms under T cell activation, the autologous plasma could better approximate the in vivo environment. Conversely, if the study aims at defining qualitative aspects, then RPMI culture could provide more evident results.
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Affiliation(s)
- Giuseppe Rubens Pascucci
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Elena Morrocchi
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Chiara Pighi
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Arianna Rotili
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Alessia Neri
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Chiara Medri
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Giulio Olivieri
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Marco Sanna
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Gianmarco Rasi
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Deborah Persaud
- Department of Pediatric Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ann Chahroudi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines, Children’s Healthcare of Atlanta and Emory University, Atlanta, GA 30322, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Eleni Nastouli
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Caterina Cancrini
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Donato Amodio
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
| | - Paolo Rossi
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Nicola Cotugno
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Paolo Palma
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, 00165 Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
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