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Capoferri AA, Wiegand A, Hong F, Jacobs JL, Spindler J, Musick A, Bale MJ, Shao W, Sobolewski MD, Cillo AR, Luke BT, Fennessey CM, Gorelick RJ, Hoh R, Halvas EK, Deeks SG, Coffin JM, Mellors JW, Kearney MF. HIV-1 control in vivo is related to the number but not the fraction of infected cells with viral unspliced RNA. Proc Natl Acad Sci U S A 2024; 121:e2405210121. [PMID: 39190360 DOI: 10.1073/pnas.2405210121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/22/2024] [Indexed: 08/28/2024] Open
Abstract
In the absence of antiretroviral therapy (ART), a subset of individuals, termed HIV controllers, have levels of plasma viremia that are orders of magnitude lower than non-controllers (NC) who are at higher risk for HIV disease progression. In addition to having fewer infected cells resulting in fewer cells with HIV RNA, it is possible that lower levels of plasma viremia in controllers are due to a lower fraction of the infected cells having HIV-1 unspliced RNA (HIV usRNA) compared with NC. To directly test this possibility, we used sensitive and quantitative single-cell sequencing methods to compare the fraction of infected cells that contain one or more copies of HIV usRNA in peripheral blood mononuclear cells (PBMC) obtained from controllers and NC. The fraction of infected cells containing HIV usRNA did not differ between the two groups. Rather, the levels of viremia were strongly associated with the total number of infected cells that had HIV usRNA, as reported by others, with controllers having 34-fold fewer infected cells per million PBMC. These results reveal that viremic control is not associated with a lower fraction of proviruses expressing HIV usRNA, unlike what is reported for elite controllers, but is only related to having fewer infected cells overall, maybe reflecting greater immune clearance of infected cells. Our findings show that proviral silencing is not a key mechanism for viremic control and will help to refine strategies toward achieving HIV remission without ART.
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Affiliation(s)
- Adam A Capoferri
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
- Department of Microbiology and Immunology, Georgetown University, Washington, DC 20007
| | - Ann Wiegand
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
| | - Feiyu Hong
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Jana L Jacobs
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Jonathan Spindler
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
| | - Andrew Musick
- Leidos Biomedical Research, Inc., Frederick National Laboratories for Cancer Research, Frederick, MD 21702
| | - Michael J Bale
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Wei Shao
- Leidos Biomedical Research, Inc., Frederick National Laboratories for Cancer Research, Frederick, MD 21702
| | - Michele D Sobolewski
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Anthony R Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Brian T Luke
- Leidos Biomedical Research, Inc., Frederick National Laboratories for Cancer Research, Frederick, MD 21702
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, CA 94143
| | - Elias K Halvas
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA 94143
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Mary F Kearney
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
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2
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Teixeira AR, Bittar C, Silva Santos GS, Oliveira TY, Huang AS, Linden N, Ferreira IATM, Murdza T, Muecksch F, Jones RB, Caskey M, Jankovic M, Nussenzweig MC. Transcription of HIV-1 at sites of intact latent provirus integration. J Exp Med 2024; 221:e20240391. [PMID: 39141127 DOI: 10.1084/jem.20240391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/21/2024] [Accepted: 07/30/2024] [Indexed: 08/15/2024] Open
Abstract
HIV-1 antiretroviral therapy is highly effective but fails to eliminate a reservoir of latent proviruses, leading to a requirement for life-long treatment. How the site of integration of authentic intact latent proviruses might impact their own or neighboring gene expression or reservoir dynamics is poorly understood. Here, we report on proviral and neighboring gene transcription at sites of intact latent HIV-1 integration in cultured T cells obtained directly from people living with HIV, as well as engineered primary T cells and cell lines. Proviral gene expression was correlated to the level of endogenous gene expression under resting but not activated conditions. Notably, latent proviral promoters were 100-10,000× less active than in productively infected cells and had little or no measurable impact on neighboring gene expression under resting or activated conditions. Thus, the site of integration has a dominant effect on the transcriptional activity of intact HIV-1 proviruses in the latent reservoir, thereby influencing cytopathic effects and proviral immune evasion.
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Affiliation(s)
- Ana Rafaela Teixeira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Cintia Bittar
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | | | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | | | - Noemi Linden
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Isabella A T M Ferreira
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tetyana Murdza
- Department of Infectious Diseases, Medical Faculty Heidelberg, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany
| | - Frauke Muecksch
- Department of Infectious Diseases, Medical Faculty Heidelberg, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany
- Department of Infectious Diseases, Virology, Chica and Heinz Schaller (CHS) Research Group, University Hospital Heidelberg, Heidelberg, Germany
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute , Chevy Chase, MD, USA
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3
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Cai JF, Zhou JS, Meng ZY, Wu ZQ, Zhao JC, Peng HX, Liang XY, Chen JJ, Wang PP, Deng K. Ripretinib inhibits HIV-1 transcription through modulation of PI3K-AKT-mTOR. Acta Pharmacol Sin 2024; 45:1632-1643. [PMID: 38627462 PMCID: PMC11272926 DOI: 10.1038/s41401-024-01282-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 07/27/2024] Open
Abstract
Despite the effectiveness of antiretroviral therapy (ART) in prolonging the lifespan of individuals infected with HIV-1, it does not offer a cure for acquired immunodeficiency syndrome (AIDS). The "block and lock" approach aims to maintain the provirus in a state of extended transcriptional arrest. By employing the "block and lock" strategy, researchers endeavor to impede disease progression by preventing viral rebound for an extended duration following patient stops receiving ART. The crux of this strategy lies in the utilization of latency-promoting agents (LPAs) that are suitable for impeding HIV-1 provirus transcription. However, previously documented LPAs exhibited limited efficacy in primary cells or samples obtained from patients, underscoring the significance of identifying novel LPAs that yield substantial outcomes. In this study, we performed high-throughput screening of FDA-approved compound library in the J-Lat A2 cell line to discover more efficacious LPAs. We discovered ripretinib being an LPA candidate, which was validated and observed to hinder proviral activation in cell models harboring latent infections, as well as CD4+ T cells derived from infected patients. We demonstrated that ripretinib effectively impeded proviral activation through inhibition of the PI3K-AKT-mTOR signaling pathway in the HIV-1 latent cells, thereby suppressing the opening states of cellular chromatin. The results of this research offer a promising drug candidate for the implementation of the "block and lock" strategy in the pursuit of an HIV-1 cure.
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Affiliation(s)
- Jin-Feng Cai
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jia-Sheng Zhou
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zhuo-Yue Meng
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zi-Qi Wu
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jia-Cong Zhao
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Hai-Xiang Peng
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xin-Yu Liang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jun-Jian Chen
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Pei-Pei Wang
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
| | - Kai Deng
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
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4
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Lee GQ, Khadka P, Gowanlock SN, Copertino DC, Duncan MC, Omondi FH, Kinloch NN, Kasule J, Kityamuweesi T, Buule P, Jamiru S, Tomusange S, Anok A, Chen Z, Jones RB, Galiwango RM, Reynolds SJ, Quinn TC, Brumme ZL, Redd AD, Prodger JL. HIV-1 subtype A1, D, and recombinant proviral genome landscapes during long-term suppressive therapy. Nat Commun 2024; 15:5480. [PMID: 38956017 PMCID: PMC11219899 DOI: 10.1038/s41467-024-48985-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/13/2024] [Indexed: 07/04/2024] Open
Abstract
The primary obstacle to curing HIV-1 is a reservoir of CD4+ cells that contain stably integrated provirus. Previous studies characterizing the proviral landscape, which have been predominantly conducted in males in the United States and Europe living with HIV-1 subtype B, have revealed that most proviruses that persist during antiretroviral therapy (ART) are defective. In contrast, less is known about proviral landscapes in females with non-B subtypes, which represents the largest group of individuals living with HIV-1. Here, we analyze genomic DNA from resting CD4+ T-cells from 16 female and seven male Ugandans with HIV-1 receiving suppressive ART (n = 23). We perform near-full-length proviral sequencing at limiting dilution to examine the proviral genetic landscape, yielding 607 HIV-1 subtype A1, D, and recombinant proviral sequences (mean 26/person). We observe that intact genomes are relatively rare and clonal expansion occurs in both intact and defective genomes. Our modification of the primers and probes of the Intact Proviral DNA Assay (IPDA), developed for subtype B, rescues intact provirus detection in Ugandan samples for which the original IPDA fails. This work will facilitate research on HIV-1 persistence and cure strategies in Africa, where the burden of HIV-1 is heaviest.
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Affiliation(s)
- Guinevere Q Lee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA.
| | - Pragya Khadka
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Sarah N Gowanlock
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Dennis C Copertino
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | | | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Zhengming Chen
- Department of Population Health Sciences, Division of Biostatistics, Weill Cornell Medicine, New York, NY, USA
| | - R Brad Jones
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | | | - Steven J Reynolds
- Rakai Health Sciences Program, Kalisizo, Uganda
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, London, ON, Canada
- Department of Epidemiology and Biostatistics, Western University, London, ON, Canada
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5
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Klotman ME, Haynes BF. The other pandemic: lessons from 40 years of HIV research. J Clin Invest 2024; 134:e183039. [PMID: 38949029 PMCID: PMC11213503 DOI: 10.1172/jci183039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024] Open
Affiliation(s)
- Mary E. Klotman
- Department of Medicine
- Department of Molecular Genetics and Microbiology
- Department of Pathology
| | - Barton F. Haynes
- Department of Medicine
- Integrative Immunobiology, and
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
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6
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Shahid A, Jones BR, Duncan MC, MacLennan S, Dapp MJ, Kuniholm MH, Aouizerat B, Archin NM, Gange S, Ofotokun I, Fischl MA, Kassaye S, Goldstein H, Anastos K, Joy JB, Brumme ZL. A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapy. RESEARCH SQUARE 2024:rs.3.rs-4549934. [PMID: 38947061 PMCID: PMC11213167 DOI: 10.21203/rs.3.rs-4549934/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Hypermutated proviruses, which arise in a single HIV replication cycle when host antiviral APOBEC3 proteins introduce extensive G-to-A mutations throughout the viral genome, persist in all people living with HIV receiving antiretroviral therapy (ART). But, the within-host evolutionary origins of hypermutated sequences are incompletely understood because phylogenetic inference algorithms, which assume that mutations gradually accumulate over generations, incorrectly reconstruct their ancestor-descendant relationships. Using > 1400 longitudinal single-genome-amplified HIV env-gp120 sequences isolated from six women over a median 18 years of follow-up - including plasma HIV RNA sequences collected over a median 9 years between seroconversion and ART initiation, and > 500 proviruses isolated over a median 9 years on ART - we evaluated three approaches for removing hypermutation from nucleotide alignments. Our goals were to 1) reconstruct accurate phylogenies that can be used for molecular dating and 2) phylogenetically infer the integration dates of hypermutated proviruses persisting during ART. Two of the tested approaches (stripping all positions containing putative APOBEC3 mutations from the alignment, or replacing individual putative APOBEC3 mutations in hypermutated sequences with the ambiguous base R) consistently normalized tree topologies, eliminated erroneous clustering of hypermutated proviruses, and brought env-intact and hypermutated proviruses into comparable ranges with respect to multiple tree-based metrics. Importantly, these corrected trees produced integration date estimates for env-intact proviruses that were highly concordant with those from benchmark trees that excluded hypermutated sequences, indicating that the corrected trees can be used for molecular dating. Use of these trees to infer the integration dates of hypermutated proviruses persisting during ART revealed that these spanned a wide age range, with the oldest ones dating to shortly after infection. This indicates that hypermutated proviruses, like other provirus types, begin to be seeded into the proviral pool immediately following infection, and can persist for decades. In two of the six participants, hypermutated proviruses differed from env-intact ones in terms of their age distributions, suggesting that different provirus types decay at heterogeneous rates in some hosts. These simple approaches to reconstruct hypermutated provirus' evolutionary histories, allow insights into their in vivo origins and longevity, towards a more comprehensive understanding of HIV persistence during ART.
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Affiliation(s)
- Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Bradley R Jones
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Signe MacLennan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael J Dapp
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Mark H Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, USA
| | | | - Nancie M Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Stephen Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Igho Ofotokun
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Margaret A Fischl
- Division of Infectious Diseases, Department of Medicine, University of Miami School of Medicine, Miami, Florida, USA
| | - Seble Kassaye
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
| | - Harris Goldstein
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jeffrey B Joy
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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7
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Reddy K, Lee GQ, Reddy N, Chikowore TJ, Baisley K, Dong KL, Walker BD, Yu XG, Lichterfeld M, Ndung’u T. Differences in HIV-1 reservoir size, landscape characteristics and decay dynamics in acute and chronic treated HIV-1 Clade C infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.16.24302713. [PMID: 38947072 PMCID: PMC11213047 DOI: 10.1101/2024.02.16.24302713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background Persisting HIV reservoir viruses in resting CD4 T cells and other cellular subsets are the main barrier to cure efforts. Antiretroviral therapy (ART) intensification by early initiation has been shown to enable post-treatment viral control in some cases but the underlying mechanisms are not fully understood. We hypothesized that ART initiated during the hyperacute phase of infection before peak will affect the size, decay dynamics and landscape characteristics of HIV-1 subtype C viral reservoirs. Methods We studied 35 women at high risk of infection from Durban, South Africa identified with hyperacute HIV infection by twice weekly testing for plasma HIV-1 RNA. Study participants included 11 who started ART at a median of 456 (297-1203) days post onset of viremia (DPOV), and 24 who started ART at a median of 1 (1-3) DPOV. We used peripheral blood mononuclear cells (PBMC) to measure total HIV-1 DNA by ddPCR and to sequence reservoir viral genomes by full length individual proviral sequencing (FLIP-seq) from onset of detection of HIV up to 1 year post treatment initiation. Results Whereas ART in hyperacute infection blunted peak viremia compared to untreated individuals (p<0.0001), there was no difference in total HIV-1 DNA measured contemporaneously (p=0.104). There was a steady decline of total HIV DNA in early treated persons over 1 year of ART (p=0.0004), with no significant change observed in the late treated group. Total HIV-1 DNA after one year of treatment was lower in the early treated compared to the late treated group (p=0.02). Generation of 697 single viral genome sequences revealed a difference in the longitudinal proviral genetic landscape over one year between untreated, late treated, and early treated infection: the relative contribution of intact genomes to the total pool of HIV-1 DNA after 1 year was higher in untreated infection (31%) compared to late treated (14%) and early treated infection (0%). Treatment initiated in both late and early infection resulted in a more rapid decay of intact (13% and 51% per month) versus defective (2% and 35% per month) viral genomes. However, intact genomes were still observed one year post chronic treatment initiation in contrast to early treatment where intact genomes were no longer detectable. Moreover, early ART reduced phylogenetic diversity of intact genomes and limited the seeding and persistence of cytotoxic T lymphocyte immune escape variants in the reservoir. Conclusions Overall, our results show that whereas ART initiated in hyperacute HIV-1 subtype C infection did not impact reservoir seeding, it was nevertheless associated with more rapid decay of intact viral genomes, decreased genetic complexity and immune escape in reservoirs, which could accelerate reservoir clearance when combined with other interventional strategies.
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Affiliation(s)
- Kavidha Reddy
- Africa Health Research Institute, Durban, South Africa
| | | | - Nicole Reddy
- Africa Health Research Institute, Durban, South Africa
- University of KwaZulu-Natal, Durban, South Africa
| | - Tatenda J.B. Chikowore
- Africa Health Research Institute, Durban, South Africa
- University College of London, London, UK
| | - Kathy Baisley
- Africa Health Research Institute, Durban, South Africa
- London School of Hygiene and Tropical Medicine, London, UK
| | - Krista L. Dong
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- HIV Pathogenesis Programme (HPP), The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Harvard Medical School, Boston, Massachusetts, USA
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- HIV Pathogenesis Programme (HPP), The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Harvard Medical School, Boston, Massachusetts, USA
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Thumbi Ndung’u
- Africa Health Research Institute, Durban, South Africa
- University of KwaZulu-Natal, Durban, South Africa
- University College of London, London, UK
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- HIV Pathogenesis Programme (HPP), The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
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8
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Armani-Tourret M, Bone B, Tan TS, Sun W, Bellefroid M, Struyve T, Louella M, Yu XG, Lichterfeld M. Immune targeting of HIV-1 reservoir cells: a path to elimination strategies and cure. Nat Rev Microbiol 2024; 22:328-344. [PMID: 38337034 PMCID: PMC11131351 DOI: 10.1038/s41579-024-01010-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Successful approaches for eradication or cure of HIV-1 infection are likely to include immunological mechanisms, but remarkably little is known about how human immune responses can recognize and interact with the few HIV-1-infected cells that harbour genome-intact viral DNA, persist long term despite antiretroviral therapy and represent the main barrier to a cure. For a long time regarded as being completely shielded from host immune responses due to viral latency, these cells do, on closer examination with single-cell analytic techniques, display discrete footprints of immune selection, implying that human immune responses may be able to effectively engage and target at least some of these cells. The failure to eliminate rebound-competent virally infected cells in the majority of persons likely reflects the evolution of a highly selected pool of reservoir cells that are effectively camouflaged from immune recognition or rely on sophisticated approaches for resisting immune-mediated killing. Understanding the fine-tuned interplay between host immune responses and viral reservoir cells will help to design improved interventions that exploit the immunological vulnerabilities of HIV-1 reservoir cells.
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Affiliation(s)
- Marie Armani-Tourret
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Benjamin Bone
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Toong Seng Tan
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Weiwei Sun
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Maxime Bellefroid
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Tine Struyve
- HIV Cure Research Center, Ghent University, Ghent, Belgium
| | - Michael Louella
- Community Advisory Board, Delaney AIDS Research Enterprise (DARE), San Francisco, CA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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9
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Banga R, Perreau M. The multifaceted nature of HIV tissue reservoirs. Curr Opin HIV AIDS 2024; 19:116-123. [PMID: 38547340 PMCID: PMC10990014 DOI: 10.1097/coh.0000000000000851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
PURPOSE OF REVIEW To underline the complexity and the heterogeneity of the HIV reservoir. RECENT FINDINGS While lymphoid tissues (spleen, lymph nodes, gut-associated lymphoid tissue) harbor specific subsets of specialized CD4 + T cells enriched in HIV-infected cells, non-CD4 + T cell reservoirs such as tissue-resident macrophages and dendritic cells have also been implicated to contribute to viral persistence. Moreover, studies have applied highly sensitive tools to detect transcriptional activity within HIV-infected cells during prolonged ART and revealed a broader spectrum of transcriptional activity for proviruses than previously thought. Finally, while a combination of factors might be involved in the regulation of HIV persistence within different tissues and remains to be fully elucidated, recent results from autopsy samples of HIV-infected ART suppressed individuals indicate extensive clonality of HIV reservoirs in multiple tissues and suggest that the recirculation of HIV-infected cells and their local expansions in tissues may also contribute to the complexity of the HIV reservoirs in humans. SUMMARY HIV persistence in blood and multiple tissues despite long-standing and potent therapy is one of the major barriers to a cure. Given that the HIV reservoir is established early and is highly complex based on its composition, viral diversity, tissue distribution, transcriptional activity, replication competence, migration dynamics and proliferative potential across the human body and possible compartmentalization in specific tissues, combinatorial therapeutic approaches are needed that may synergize to target multiple viral reservoirs to achieve a cure for HIV infection.
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Affiliation(s)
- Riddhima Banga
- Divisions of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
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10
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Bone B, Lichterfeld M. "Block and lock" viral integration sites in persons with drug-free control of HIV-1 infection. Curr Opin HIV AIDS 2024; 19:110-115. [PMID: 38457193 DOI: 10.1097/coh.0000000000000845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
PURPOSE OF REVIEW Elite controllers (ECs) and Posttreatment controllers (PTCs) represent a small subset of individuals who are capable of maintaining drug-free control of HIV plasma viral loads despite the persistence of a replication-competent viral reservoir. This review aims to curate recent experimental studies evaluating viral reservoirs that distinguish EC/PTC and may contribute to their ability to maintain undetectable viral loads in the absence of antiretroviral therapy. RECENT FINDINGS Recent studies on ECs have demonstrated that integration sites of intact proviruses in EC/PTC are markedly biased towards heterochromatin regions; in contrast, intact proviruses in accessible and permissive chromatin were profoundly underrepresented. Of note, no such biases were noted when CD4 + T cells from EC were infected directly ex vivo, suggesting that the viral reservoir profile in EC is not related to altered integration site preferences during acute infection, but instead represents the result of immune-mediated selection mechanisms that can eliminate proviruses in transcriptionally-active euchromatin regions while promoting preferential persistence of intact proviruses in nonpermissive genome regions. Proviral transcription in such "blocked and locked" regions may be restricted through epigenetic mechanisms, protecting them from immune-recognition but presumably limiting their ability to drive viral rebound. While the exact immune mechanisms driving this selection process remain undefined, recent single-cell analytic approaches support the hypothesis that HIV reservoir cells are subject to immune selection pressure by host factors. SUMMARY A "blocked and locked" viral reservoir profile may constitute a structural virological correlate of a functional cure of HIV-1 infection. Further research into the immunological mechanism promoting HIV-1 reservoir selection and evolution in EC/PTC is warranted and could inform foreseeable cure strategies.
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Affiliation(s)
- Benjamin Bone
- Infectious Disease Division, Brigham Women's Hospital, Boston
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham Women's Hospital, Boston
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
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11
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Teixeira AR, Bittar C, Silva Santos GS, Oliveira TY, Huang AS, Linden N, Ferreira IA, Murdza T, Muecksch F, Jones RB, Caskey M, Jankovic M, Nussenzweig MC. Transcription of HIV-1 at sites of intact latent provirus integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591331. [PMID: 38746186 PMCID: PMC11092494 DOI: 10.1101/2024.04.26.591331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
HIV-1 anti-retroviral therapy is highly effective but fails to eliminate a reservoir of latent proviruses leading to a requirement for life-long treatment. How the site of integration of authentic intact latent proviruses might impact their own or neighboring gene expression or reservoir dynamics is poorly understood. Here we report on proviral and neighboring gene transcription at sites of intact latent HIV-1 integration in cultured T cells obtained directly from people living with HIV, as well as engineered primary T cells and cell lines. Proviral gene expression was correlated to the level of endogenous gene expression under resting but not activated conditions. Notably, latent proviral promoters were 10010,000X less active than in productively infected cells and had little or no measurable impact on neighboring gene expression under resting or activated conditions. Thus, the site of integration has a dominant effect on the transcriptional activity of intact HIV-1 proviruses in the latent reservoir thereby influencing cytopathic effects and proviral immune evasion.
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Affiliation(s)
- Ana Rafaela Teixeira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Cintia Bittar
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | | | - Thiago Y. Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | | | - Noemi Linden
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Isabella A.T.M. Ferreira
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Tetyana Murdza
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany
| | - Frauke Muecksch
- Department of Infectious Diseases, Heidelberg University, Medical Faculty Heidelberg, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg, Germany
- Chica and Heinz Schaller (CHS) Research Group, Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - R. Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute
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12
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Roux H, Chomont N. Measuring Human Immunodeficiency Virus Reservoirs: Do We Need to Choose Between Quantity and Quality? J Infect Dis 2024; 229:635-643. [PMID: 37665978 PMCID: PMC10938203 DOI: 10.1093/infdis/jiad381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/17/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023] Open
Abstract
The persistence of latent viral genomes in people receiving antiretroviral therapy (ART) is the main obstacle to a cure for human immunodeficiency virus (HIV) infection. Viral reservoirs can be defined as cells harboring HIV genomes that have the ability to produce infectious virions. Precise quantification of the cellular reservoirs of HIV is challenging because these cells are rare, heterogeneous, and outnumbered by a larger number of cells carrying defective genomes. In addition, measuring the inducibility of these proviruses requires functional assays and remains technically difficult. The recent development of single-cell and single-viral genome approaches revealed additional layers of complexity: the cell subsets that harbor proviruses are heterogeneous and their ability to be induced is variable. A substantial fraction of intact HIV genomes may be permanently silenced after years of ART, revealing the underappreciated importance of induction assays. As such, a simple approach that would assess simultaneously the genetic intactness and the inducibility of the reservoir is still lacking. In this study, we review recent advances in the development of methods to quantify and characterize persistently infected cells, and we discuss how these findings can inform the design of future assays aimed at measuring the size of the intact and inducible HIV reservoir.
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Affiliation(s)
- Hélène Roux
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
| | - Nicolas Chomont
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
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13
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Koofhethile CK, Gao C, Chang C, Lian X, Shapiro R, Yu XG, Lichterfeld M, Kanki PJ. The HIV-2 proviral landscape is dominated by defective proviruses. AIDS 2024; 38:309-316. [PMID: 37916471 PMCID: PMC10842655 DOI: 10.1097/qad.0000000000003776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Compared with HIV-1 infection, HIV-2 infection is associated with a slower progression to AIDS. Understanding the persistence of HIV-2 infection might inform the mechanisms responsible for differences in the pathogenicity of HIV-2 versus HIV-1. METHODS In this study, we analyzed the genetic composition of the proviral reservoir in archived blood samples collected from 13 untreated HIV-2-infected adults from Senegal. We used single-genome, near-full-length individual proviral sequencing (FLIP-Seq) to assess the relative frequency of intact and defective proviruses. RESULTS Ten out of 13 (77%) study participants demonstrated virologic suppression (<90 HIV RNA copies/ml) while the remaining 3 (23%) had detectable HIV RNA. We obtained 363 proviral sequences from peripheral blood mononuclear cells (PBMCs) from the 13 study participants. Within these sequences, 342 (94%) defective proviruses were detected. Twenty-one (6%) intact proviruses were detected from three study participants, with one study participant displaying a large clone consisting of 16 genome-intact sequences. CONCLUSION This data suggests that similar to HIV-1 infection, the proviral landscape of HIV-2 is dominated by defective proviruses.
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Affiliation(s)
- Catherine K. Koofhethile
- Harvard T.H. Chan School of Public Health, Boston
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | | | | | | | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
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14
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Armani-Tourret M, Gao C, Hartana CA, Sun W, Carrere L, Vela L, Hochroth A, Bellefroid M, Sbrolla A, Shea K, Flynn T, Roseto I, Rassadkina Y, Lee C, Giguel F, Malhotra R, Bushman FD, Gandhi RT, Yu XG, Kuritzkes DR, Lichterfeld M. Selection of epigenetically privileged HIV-1 proviruses during treatment with panobinostat and interferon-α2a. Cell 2024; 187:1238-1254.e14. [PMID: 38367616 PMCID: PMC10903630 DOI: 10.1016/j.cell.2024.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/26/2023] [Accepted: 01/24/2024] [Indexed: 02/19/2024]
Abstract
CD4+ T cells with latent HIV-1 infection persist despite treatment with antiretroviral agents and represent the main barrier to a cure of HIV-1 infection. Pharmacological disruption of viral latency may expose HIV-1-infected cells to host immune activity, but the clinical efficacy of latency-reversing agents for reducing HIV-1 persistence remains to be proven. Here, we show in a randomized-controlled human clinical trial that the histone deacetylase inhibitor panobinostat, when administered in combination with pegylated interferon-α2a, induces a structural transformation of the HIV-1 reservoir cell pool, characterized by a disproportionate overrepresentation of HIV-1 proviruses integrated in ZNF genes and in chromatin regions with reduced H3K27ac marks, the molecular target sites for panobinostat. By contrast, proviruses near H3K27ac marks were actively selected against, likely due to increased susceptibility to panobinostat. These data suggest that latency-reversing treatment can increase the immunological vulnerability of HIV-1 reservoir cells and accelerate the selection of epigenetically privileged HIV-1 proviruses.
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Affiliation(s)
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ciputra Adijaya Hartana
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - WeiWei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Leah Carrere
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Liliana Vela
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | | | - Amy Sbrolla
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Katrina Shea
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Theresa Flynn
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Isabelle Roseto
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Carole Lee
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Francoise Giguel
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rajeev Malhotra
- Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rajesh T Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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15
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Faua C, Ursenbach A, Fuchs A, Caspar S, Jegou F, Ruch Y, Hoellinger B, Laugel E, Velay A, Rey D, Fafi-Kremer S, Gantner P. HIV Productively Infects Highly Differentiated and Exhausted CD4+ T Cells During AIDS. Pathog Immun 2024; 8:92-114. [PMID: 38420260 PMCID: PMC10901154 DOI: 10.20411/pai.v8i2.638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Background Throughout HIV infection, productively infected cells generate billions of viral particles and are thus responsible for body-wide HIV dissemination, but their phenotype during AIDS is unknown. As AIDS is associated with immunological changes, analyzing the phenotype of productively infected cells can help understand HIV production during this terminal stage. Methods Blood samples from 15 untreated viremic participants (recent infection, n=5; long-term infection, n=5; active opportunistic AIDS-defining disease, n=5) and 5 participants virologically controlled on antiretroviral therapy (ART) enrolled in the Analysis of the Persistence, Reservoir and HIV Latency (APRIL) study (NCT05752318) were analyzed. Cells expressing the capsid protein p24 (p24+ cells) after 18 hours of resting or 24 hours of stimulation (HIV-Flow) revealed productively infected cells from viremic participants or translation-competent reservoir cells from treated participants, respectively. Results The frequency of productively infected cells tended to be higher during AIDS in comparison with recent and long-term infections (median, 340, 72, and 32/million CD4+ T cells, respectively) and correlated with the plasma viral load at all stages of infection. Altogether, these cells were more frequently CD4low, HLA-ABClow, CD45RA-, Ki67+, PD-1+, with a non-negligible contribution from pTfh (CXCR5+PD-1+) cells, and were not significantly enriched in HIV coreceptors CCR5 nor CXCR4 expression. The comparison markers expression between stages showed that productively infected cells during AIDS were enriched in memory and exhausted cells. In contrast, the frequencies of infected pTfh were lower during AIDS compared to non-AIDS stages. A UMAP analysis revealed that total CD4+ T cells were grouped in 7 clusters and that productive p24+ cells were skewed to given clusters throughout the course of infection. Overall, the preferential targets of HIV during the latest stages seemed to be more frequently highly differentiated (memory, TTD-like) and exhausted cells and less frequently pTfh-like cells. In contrast, translation-competent reservoir cells were less frequent (5/million CD4+ T cells) and expressed more frequently HLA-ABC and less frequently PD-1. Conclusions In long-term infection and AIDS, productively infected cells were differentiated and exhausted. This could indicate that cells with these given features are responsible for HIV production and dissemination in an immune dysfunction environment occurring during the last stages of infection.
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Affiliation(s)
- Clayton Faua
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
| | - Axel Ursenbach
- Le Trait d'Union, HIV-Infection Care Center, Strasbourg University Hospital, Strasbourg, France
| | - Anne Fuchs
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Stéphanie Caspar
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Frédérick Jegou
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Yvon Ruch
- Infectious Diseases Department, Strasbourg University Hospital, Strasbourg, France
| | - Baptiste Hoellinger
- Infectious Diseases Department, Strasbourg University Hospital, Strasbourg, France
| | - Elodie Laugel
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Aurélie Velay
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - David Rey
- Le Trait d'Union, HIV-Infection Care Center, Strasbourg University Hospital, Strasbourg, France
| | - Samira Fafi-Kremer
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Pierre Gantner
- INSERM UMR_S1109, Strasbourg University, Strasbourg, France
- Clinical Virology Laboratory, Strasbourg University Hospital, Strasbourg, France
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16
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Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobarrubias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time. J Virol 2024; 98:e0165523. [PMID: 38214547 PMCID: PMC10878278 DOI: 10.1128/jvi.01655-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Within-host HIV populations continually diversify during untreated infection, and this diversity persists within infected cell reservoirs during antiretroviral therapy (ART). Achieving a better understanding of on-ART proviral evolutionary dynamics, and a better appreciation of how the overall persisting pool of (largely genetically defective) proviruses differs from the much smaller replication-competent HIV reservoir, is critical to HIV cure efforts. We reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study who experienced HIV seroconversion, and used these data to characterize the diversity, lineage origins, and ages of proviral env-gp120 sequences sampled longitudinally up to 12 years on ART. We also studied HIV sequences emerging from the reservoir in two participants. We observed that proviral clonality generally increased over time on ART, with clones frequently persisting long term. While on-ART proviral integration dates generally spanned the duration of untreated infection, HIV emerging in plasma was exclusively younger (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained stable during ART in all but one participant, in whom there was evidence that younger proviruses had been preferentially eliminated after 12 years on ART. Analysis of the gag region in three participants corroborated our env-gp120-based observations, indicating that our observations are not influenced by the HIV region studied. Our results underscore the remarkable genetic stability of the distinct proviral sequences that persist in blood during ART. Our results also suggest that the replication-competent HIV reservoir is a genetically restricted, younger subset of this overall proviral pool.IMPORTANCECharacterizing the genetically diverse HIV sequences that persist in the reservoir despite antiretroviral therapy (ART) is critical to cure efforts. Our observations confirm that proviruses persisting in blood on ART, which are largely genetically defective, broadly reflect the extent of within-host HIV evolution pre-ART. Moreover, on-ART clonal expansion is not appreciably accompanied by the loss of distinct proviral lineages. In fact, on-ART proviral genetic composition remained stable in all but one participant, in whom, after 12 years on ART, proviruses dating to around near ART initiation had been preferentially eliminated. We also identified recombinant proviruses between parental sequence fragments of different ages. Though rare, such sequences suggest that reservoir cells can be superinfected with HIV from another infection era. Overall, our finding that the replication-competent reservoir in blood is a genetically restricted, younger subset of all persisting proviruses suggests that HIV cure strategies will need to eliminate a reservoir that differs in key respects from the overall proviral pool.
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Affiliation(s)
- Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Signe MacLennan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Zhong Dang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Kyle Cobarrubias
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Maggie C. Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Michael J. Dapp
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Nancie M. Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Margaret A. Fischl
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, USA
| | - Igho Ofotokun
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Adaora Adimora
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephen Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Mark H. Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, New York, USA
| | - Seble Kassaye
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
| | - James I. Mullins
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Global Health, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Harris Goldstein
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, New York, USA
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - the MACS/WIHS combined cohort study (MWCSS)OfotokunIghovwerha1ShethAnandi1WingoodGina1BrownTodd2MargolickJoseph2AnastosKathryn3HannaDavid3SharmaAnjali3GustafsonDeborah4WilsonTracey4D’SouzaGypsyamber5GangeStephen5TopperElizabeth5CohenMardge6FrenchAudrey6WolinskySteven7PalellaFrank7StosorValentina7AouizeratBradley8PriceJennifer8TienPhyllis8DetelsRoger9MimiagaMatthew9KassayeSeble10MerensteinDaniel10AlcaideMaria11FischlMargaret11JonesDeborah11MartinsonJeremy12RinaldoCharles12KempfMirjam-Colette13Dionne-OdomJodie13Konkle-ParkerDeborah13BrockJames B.13AdimoraAdaora14Floris-MooreMichelle14Emory University, Atlanta, Georgia, USAJohns Hopkins University, Baltimore, Maryland, USAAlbert Einstein College of Medicine, Bronx, New York, USASuny Downstate Medical Center, Brooklyn, New York, USAJohns Hopkins University, Baltimore, Maryland, USAHektoen Institute for Medical Research, Chicago, Illinois, USANorthwestern University at Chicago, Chicago, Illinois, USAUniversity of California San Francisco, San Francisco, California, USAUniversity of California Los Angeles, Los Angeles, California, USAGeorgetown University, Washington, DC, USAUniversity of Miami School of Medicine, Coral Gables, Florida, USAUniversity of Pittsburgh, Pittsburgh, Pennsylvania, USAUniversity of Alabama Birmingham, Birmingham, Alabama, USAUniversity of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- College of Dentistry, New York University, New York, New York, USA
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, New York, USA
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
- Department of Global Health, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, School of Medicine, Seattle, Washington, USA
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, New York, USA
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
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17
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Reeves DB, Rigau DN, Romero A, Zhang H, Simonetti FR, Varriale J, Hoh R, Zhang L, Smith KN, Montaner LJ, Rubin LH, Gange SJ, Roan NR, Tien PC, Margolick JB, Peluso MJ, Deeks SG, Schiffer JT, Siliciano JD, Siliciano RF, Antar AAR. Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.13.24302704. [PMID: 38405967 PMCID: PMC10888981 DOI: 10.1101/2024.02.13.24302704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The latent reservoir of HIV persists for decades in people living with HIV (PWH) on antiretroviral therapy (ART). To determine if persistence arises from the natural dynamics of memory CD4+ T cells harboring HIV, we compared the clonal dynamics of HIV proviruses to that of memory CD4+ T cell receptors (TCRβ) from the same PWH and from HIV-seronegative people. We show that clonal dominance of HIV proviruses and antigen-specific CD4+ T cells are similar but that the field's understanding of the persistence of the less clonally dominant reservoir is significantly limited by undersampling. We demonstrate that increasing reservoir clonality over time and differential decay of intact and defective proviruses cannot be explained by mCD4+ T cell kinetics alone. Finally, we develop a stochastic model of TCRβ and proviruses that recapitulates experimental observations and suggests that HIV-specific negative selection mediates approximately 6% of intact and 2% of defective proviral clearance. Thus, HIV persistence is mostly, but not entirely, driven by natural mCD4+ T cell kinetics.
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18
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Vellas C, Nayrac M, Collercandy N, Requena M, Jeanne N, Latour J, Dimeglio C, Cazabat M, Barange K, Alric L, Carrere N, Martin-Blondel G, Izopet J, Delobel P. Intact proviruses are enriched in the colon and associated with PD-1 +TIGIT - mucosal CD4 + T cells of people with HIV-1 on antiretroviral therapy. EBioMedicine 2024; 100:104954. [PMID: 38160480 PMCID: PMC10792747 DOI: 10.1016/j.ebiom.2023.104954] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND The persistence of intact replication-competent HIV-1 proviruses is responsible for the virological rebound off treatment. The gut could be a major reservoir of HIV-1 due to the high number of infected target cells. METHODS We collected blood samples and intestinal biopsies (duodenum, ileum, colon) from 42 people with HIV-1 receiving effective antiretroviral therapy. We used the Intact Proviral DNA Assay to estimate the frequency of intact HIV-1 proviruses in the blood and in the intestinal mucosa of these individuals. We analyzed the genetic complexity of the HIV-1 reservoir by performing single-molecule next-generation sequencing of HIV-1 env DNA. The activation/exhaustion profile of mucosal T lymphocytes was assessed by flow cytometry. FINDINGS Intact proviruses are particularly enriched in the colon. Residual HIV-1 transcription in the gut is associated with persistent mucosal and systemic immune activation. The HIV-1 intestinal reservoir appears to be shaped by the proliferation of provirus-hosting cells. The genetic complexity of the viral reservoir in the colon is positively associated with TIGIT expression but negatively with PD-1, and inversely related to its intact content. The size of the intact reservoir in the colon is associated with PD-1+TIGIT- mucosal CD4+ T cells, particularly in CD27+ memory cells, whose proliferation and survival could contribute to the enrichment of the viral reservoir by intact proviruses. INTERPRETATION Enrichment in intact proviruses makes the gut a key compartment for HIV-1 persistence on antiretroviral therapy. FUNDING This project was supported by grants from the ANRS-MIE (ANRS EP61 GALT), Sidaction, and the Institut Universitaire de France.
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Affiliation(s)
- Camille Vellas
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse F-31300, France
| | - Manon Nayrac
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse F-31300, France
| | - Nived Collercandy
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse F-31300, France; CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse F-31300, France
| | - Mary Requena
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse F-31300, France; CHU de Toulouse, Laboratoire de Virologie, Toulouse F-31300, France
| | - Nicolas Jeanne
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse F-31300, France; CHU de Toulouse, Laboratoire de Virologie, Toulouse F-31300, France
| | - Justine Latour
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse F-31300, France; CHU de Toulouse, Laboratoire de Virologie, Toulouse F-31300, France
| | - Chloé Dimeglio
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse F-31300, France
| | - Michelle Cazabat
- CHU de Toulouse, Laboratoire de Virologie, Toulouse F-31300, France
| | - Karl Barange
- CHU de Toulouse, Service d'Hépato-Gastro-Entérologie, Toulouse F-31400, France
| | - Laurent Alric
- Université Toulouse III Paul Sabatier, Toulouse F-31400, France; CHU de Toulouse, Service de Médecine Interne et Immunologie clinique, Toulouse F-31400, France
| | - Nicolas Carrere
- Université Toulouse III Paul Sabatier, Toulouse F-31400, France; CHU de Toulouse, Service de Chirurgie Générale et Digestive, Toulouse F-31400, France
| | - Guillaume Martin-Blondel
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse F-31300, France; CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse F-31300, France; Université Toulouse III Paul Sabatier, Toulouse F-31400, France
| | - Jacques Izopet
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse F-31300, France; CHU de Toulouse, Laboratoire de Virologie, Toulouse F-31300, France; Université Toulouse III Paul Sabatier, Toulouse F-31400, France
| | - Pierre Delobel
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases, Toulouse F-31300, France; CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse F-31300, France; Université Toulouse III Paul Sabatier, Toulouse F-31400, France.
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19
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. mBio 2023; 14:e0241723. [PMID: 37971267 PMCID: PMC10746175 DOI: 10.1128/mbio.02417-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Characterizing the human immunodeficiency virus (HIV) reservoir that endures despite antiretroviral therapy (ART) is critical to cure efforts. We observed that the oldest proviruses persisting during ART were exclusively defective, while intact proviruses (and rebound HIV) dated to nearer ART initiation. This helps explain why studies that sampled sub-genomic proviruses on-ART (which are largely defective) routinely found sequences dating to early infection, whereas those that sampled replication-competent HIV found almost none. Together with our findings that intact proviruses were more likely to be clonal, and that on-ART low-level/isolated viremia originated from proviruses of varying ages (including possibly defective ones), our observations indicate that (i) on-ART and rebound viremia can have distinct within-host origins, (ii) intact proviruses have shorter lifespans than grossly defective ones and thus depend more heavily on clonal expansion for persistence, and (iii) an HIV reservoir predominantly "dating" to near ART initiation will be substantially adapted to within-host pressures, complicating immune-based cure strategies.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Experimental Medicine Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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20
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Cossarini F, Aberg JA, Chen BK, Mehandru S. Viral Persistence in the Gut-Associated Lymphoid Tissue and Barriers to HIV Cure. AIDS Res Hum Retroviruses 2023; 40:54-65. [PMID: 37450338 PMCID: PMC10790554 DOI: 10.1089/aid.2022.0180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
More than 40 years after the first reported cases of what then became known as acquired immunodeficiency syndrome (AIDS), tremendous progress has been achieved in transforming the disease from almost universally fatal to a chronic manageable condition. Nonetheless, the efforts to find a preventative vaccine or a cure for the underlying infection with Human Immunodeficiency Virus (HIV) remain largely unsuccessful. Many challenges intrinsic to the virus characteristics and host response need to be overcome for either goal to be achieved. This article will review the obstacles to an effective HIV cure, specifically the steps involved in the generation of HIV latency, focusing on the role of the gut-associated lymphoid tissue, which has received less attention compared with the peripheral blood, despite being the largest repository of lymphoid tissue in the human body, and a large site for HIV persistence.
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Affiliation(s)
- Francesca Cossarini
- Division of Infectious Diseases, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School at Mount Sinai, New York, New York, USA
| | - Judith A. Aberg
- Division of Infectious Diseases, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
| | - Benjamin K. Chen
- Division of Infectious Diseases, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School at Mount Sinai, New York, New York, USA
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School at Mount Sinai, New York, New York, USA
- Division of Gastroenterology, Department of Medicine, Icahn School at Mount Sinai, New York, New York, USA
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21
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Więcek K, Chen HC. Understanding latent HIV-1 reservoirs through host genomics approaches. iScience 2023; 26:108342. [PMID: 38026212 PMCID: PMC10665824 DOI: 10.1016/j.isci.2023.108342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Genetically intact HIV-1 proviruses are a major concern with regard to curing infection because they cause viral rebound after the cessation of antiretroviral therapy. However, intact proviruses are not prevalent in HIV-1 reservoirs. As such, it is essential to precisely determine the position of these proviruses before putting forward a better antiretroviral cure. Recently, a revised HIV-1 deeply latent reservoir concept has been proposed, stating that the progress of the establishment of HIV-1 reservoirs is influenced by immune-mediated selection during the course of infection. This selection force leads to the persistence of genetically intact proviruses as those with the best fit to avoid clearance. This hypothesis refreshes our understanding of HIV-1 latent reservoirs. For this reason, we reviewed current studies relevant to this theme and provide our perspectives to reinforce the overall understanding of HIV-1 latency in the context of the host genome.
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Affiliation(s)
- Kamil Więcek
- Epigenetics of Infectious Diseases Research Group, Population Diagnostics Center, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Stablowicka 147, 54-066 Wroclaw, Poland
| | - Heng-Chang Chen
- Epigenetics of Infectious Diseases Research Group, Population Diagnostics Center, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Stablowicka 147, 54-066 Wroclaw, Poland
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22
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Wei Y, Davenport TC, Collora JA, Ma HK, Pinto-Santini D, Lama J, Alfaro R, Duerr A, Ho YC. Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence. Immunity 2023; 56:2584-2601.e7. [PMID: 37922905 PMCID: PMC10843106 DOI: 10.1016/j.immuni.2023.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/26/2023] [Accepted: 10/04/2023] [Indexed: 11/07/2023]
Abstract
Understanding how HIV-1-infected cells proliferate and persist is key to HIV-1 eradication, but the heterogeneity and rarity of HIV-1-infected cells hamper mechanistic interrogations. Here, we used single-cell DOGMA-seq to simultaneously capture transcription factor accessibility, transcriptome, surface proteins, HIV-1 DNA, and HIV-1 RNA in memory CD4+ T cells from six people living with HIV-1 during viremia and after suppressive antiretroviral therapy. We identified increased transcription factor accessibility in latent HIV-1-infected cells (RORC) and transcriptionally active HIV-1-infected cells (interferon regulatory transcription factor [IRF] and activator protein 1 [AP-1]). A proliferation program (IKZF3, IL21, BIRC5, and MKI67 co-expression) promoted the survival of transcriptionally active HIV-1-infected cells. Both latent and transcriptionally active HIV-1-infected cells had increased IKZF3 (Aiolos) expression. Distinct epigenetic programs drove the heterogeneous cellular states of HIV-1-infected cells: IRF:activation, Eomes:cytotoxic effector differentiation, AP-1:migration, and cell death. Our study revealed the single-cell epigenetic, transcriptional, and protein states of latent and transcriptionally active HIV-1-infected cells and cellular programs promoting HIV-1 persistence.
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Affiliation(s)
- Yulong Wei
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Timothy C Davenport
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Jack A Collora
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Haocong Katherine Ma
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Delia Pinto-Santini
- Vaccine and Infectious Disease, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Javier Lama
- Asociación Civil Impacta Salud y Educación, Lima 15063, Perú
| | - Ricardo Alfaro
- Centro de Investigaciones Tecnológicas Biomédicas y Medioambientales (CITBM), Lima 07006, Perú
| | - Ann Duerr
- Vaccine and Infectious Disease, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA.
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23
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Lambrechts L, Bonine N, Verstraeten R, Pardons M, Noppe Y, Rutsaert S, Van Nieuwerburgh F, Van Criekinge W, Cole B, Vandekerckhove L. HIV-PULSE: a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization. Nucleic Acids Res 2023; 51:e102. [PMID: 37819007 PMCID: PMC10639044 DOI: 10.1093/nar/gkad790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 07/25/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
A deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIV Proviral UMI-mediated Long-read Sequencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11 vs 18%) and overall good concordance, although at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.
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Affiliation(s)
- Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Noah Bonine
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Rita Verstraeten
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Marion Pardons
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Ytse Noppe
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Wim Van Criekinge
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Basiel Cole
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
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24
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Sun W, Rassadkina Y, Gao C, Collens SI, Lian X, Solomon IH, Mukerji SS, Yu XG, Lichterfeld M. Persistence of intact HIV-1 proviruses in the brain during antiretroviral therapy. eLife 2023; 12:RP89837. [PMID: 37938115 PMCID: PMC10631759 DOI: 10.7554/elife.89837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
HIV-1 reservoir cells that circulate in peripheral blood during suppressive antiretroviral therapy (ART) have been well characterized, but little is known about the dissemination of HIV-1-infected cells across multiple anatomical tissues, especially the CNS. Here, we performed single-genome, near full-length HIV-1 next-generation sequencing to evaluate the proviral landscape in distinct anatomical compartments, including multiple CNS tissues, from 3 ART-treated participants at autopsy. While lymph nodes and, to a lesser extent, gastrointestinal and genitourinary tissues represented tissue hotspots for the persistence of intact proviruses, we also observed intact proviruses in CNS tissue sections, particularly in the basal ganglia. Multi-compartment dissemination of clonal intact and defective proviral sequences occurred across multiple anatomical tissues, including the CNS, and evidence for the clonal proliferation of HIV-1-infected cells was found in the basal ganglia, in the frontal lobe, in the thalamus and in periventricular white matter. Deep analysis of HIV-1 reservoirs in distinct tissues will be informative for advancing HIV-1 cure strategies.
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Affiliation(s)
- Weiwei Sun
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | | | - Ce Gao
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | | | - Xiaodong Lian
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Isaac H Solomon
- Department of Pathology, Brigham and Women’s HospitalBostonUnited States
| | - Shibani S Mukerji
- Department of Neurology, Massachusetts General HospitalBostonUnited States
| | - Xu G Yu
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Infectious Disease Division, Brigham and Women’s HospitalBostonUnited States
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Infectious Disease Division, Brigham and Women’s HospitalBostonUnited States
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25
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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: 0] [Impact Index Per Article: 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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26
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Kumar MR, Fray EJ, Bender AM, Zitzmann C, Ribeiro RM, Perelson AS, Barouch DH, Siliciano JD, Siliciano RF. Biphasic decay of intact SHIV genomes following initiation of antiretroviral therapy complicates analysis of interventions targeting the reservoir. Proc Natl Acad Sci U S A 2023; 120:e2313209120. [PMID: 37844236 PMCID: PMC10614214 DOI: 10.1073/pnas.2313209120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/05/2023] [Indexed: 10/18/2023] Open
Abstract
The latent reservoir for HIV-1 in resting CD4+ T cells persists despite antiretroviral therapy (ART) and precludes cure. Reservoir-targeting interventions are evaluated in ART-treated macaques infected with simian immunodeficiency virus (SIV) or simian-human immunodeficiency virus (SHIV). Efficacy is determined by reservoir measurements before and after the intervention. However, most proviruses persisting in the setting of ART are defective. In addition, intact HIV-1 and SIV genomes undergo complex, multiphasic decay observable when new infection events are blocked by ART. Intervention-induced elimination of latently infected cells must be distinguished from natural decay. Here, we address these issues for SHIV. We describe an intact proviral DNA assay that allows digital counting of SHIV genomes lacking common fatal defects. We show that intact SHIV genomes in circulating CD4+ T cells undergo biphasic decay during the first year of ART, with a rapid first phase (t1/2 = 30.1 d) and a slower second phase (t1/2 = 8.1 mo) that is still more rapid that the slow decay observed in people with HIV-1 on long-term ART (t1/2 = 3.7 y). In SHIV models, most interventions are tested during 2nd phase decay. Natural 2nd phase decay must be considered in evaluating interventions as most infected cells present at this time do not become part of the stable reservoir. In addition, for interventions tested during 2nd phase decay, a caveat is that the intervention may not be equally effective in people with HIV on long-term ART whose reservoirs are dominated by latently infected cells with a slower decay rate.
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Affiliation(s)
- Mithra R. Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Emily J. Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Alexandra M. Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | | | | | | | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA02215
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
- HHMI, Baltimore, MD21205
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27
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Banga R, Procopio FA, Lana E, Gladkov GT, Roseto I, Parsons EM, Lian X, Armani-Tourret M, Bellefroid M, Gao C, Kauzlaric A, Foglierini M, Alfageme-Abello O, Sluka SHM, Munoz O, Mastrangelo A, Fenwick C, Muller Y, Mkindi CG, Daubenberger C, Cavassini M, Trunfio R, Déglise S, Corpataux JM, Delorenzi M, Lichterfeld M, Pantaleo G, Perreau M. Lymph node dendritic cells harbor inducible replication-competent HIV despite years of suppressive ART. Cell Host Microbe 2023; 31:1714-1731.e9. [PMID: 37751747 PMCID: PMC11068440 DOI: 10.1016/j.chom.2023.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/02/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Although gut and lymph node (LN) memory CD4 T cells represent major HIV and simian immunodeficiency virus (SIV) tissue reservoirs, the study of the role of dendritic cells (DCs) in HIV persistence has long been limited to the blood due to difficulties to access lymphoid tissue samples. In this study, we show that LN migratory and resident DC subpopulations harbor distinct phenotypic and transcriptomic profiles. Interestingly, both LN DC subpopulations contain HIV intact provirus and inducible replication-competent HIV despite the expression of the antiviral restriction factor SAMHD1. Notably, LN DC subpopulations isolated from HIV-infected individuals treated for up to 14 years are transcriptionally silent but harbor replication-competent virus that can be induced upon TLR7/8 stimulation. Taken together, these results uncover a potential important contribution of LN DCs to HIV infection in the presence of ART.
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Affiliation(s)
- Riddhima Banga
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Francesco Andrea Procopio
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Erica Lana
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | | | | | - Elizabeth M Parsons
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Annamaria Kauzlaric
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathilde Foglierini
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Oscar Alfageme-Abello
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Susanna H M Sluka
- Newborn Screening Switzerland, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Olivia Munoz
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Andrea Mastrangelo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Craig Fenwick
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Yannick Muller
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Catherine Gerald Mkindi
- Ifakara Health Institute, Bagamoyo, United Republic of Tanzania; Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Matthias Cavassini
- Services of Infectious Diseases, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Rafael Trunfio
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Sébastien Déglise
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Jean-Marc Corpataux
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Mauro Delorenzi
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Giuseppe Pantaleo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Matthieu Perreau
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.
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Dufour C, Ruiz MJ, Pagliuzza A, Richard C, Shahid A, Fromentin R, Ponte R, Cattin A, Wiche Salinas TR, Salahuddin S, Sandstrom T, Schinkel SB, Costiniuk CT, Jenabian MA, Ancuta P, Routy JP, Cohen ÉA, Brumme ZL, Power C, Angel JB, Chomont N. Near full-length HIV sequencing in multiple tissues collected postmortem reveals shared clonal expansions across distinct reservoirs during ART. Cell Rep 2023; 42:113053. [PMID: 37676762 DOI: 10.1016/j.celrep.2023.113053] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/05/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
HIV persists in tissues during antiretroviral therapy (ART), but the relative contribution of different anatomical compartments to the viral reservoir in humans remains unknown. We performed an extensive characterization of HIV reservoirs in two men who donated their bodies to HIV cure research and who had been on suppressive ART for years. HIV DNA is detected in all tissues, with large variations across anatomical compartments and between participants. Intact HIV genomes represent 2% and 25% of all proviruses in the two participants and are mainly detected in secondary lymphoid organs, with the spleen and mediastinal lymph nodes harboring intact viral genomes in both individuals. Multiple copies of identical HIV genomes are found in all tissues, indicating that clonal expansions are common in anatomical sites. The majority (>85%) of these expanded clones are shared across multiple tissues. These findings suggest that infected cells expand, migrate, and possibly circulate between anatomical sites.
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Affiliation(s)
- Caroline Dufour
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Maria Julia Ruiz
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | | | | | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Rémi Fromentin
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Rosalie Ponte
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada; Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Amélie Cattin
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Tomas Raul Wiche Salinas
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Syim Salahuddin
- Département de Sciences Biologiques, Université du Québec à Montréal, Montreal, QC, Canada
| | - Teslin Sandstrom
- Ottawa Hospital Research Institute, Ottawa, ON, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada
| | | | - Cecilia T Costiniuk
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC, Canada; Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Mohammad-Ali Jenabian
- Département de Sciences Biologiques, Université du Québec à Montréal, Montreal, QC, Canada
| | - Petronela Ancuta
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada
| | - Jean-Pierre Routy
- Research Institute of McGill University Health Centre, Montreal, QC, Canada; Division of Hematology, McGill University Health Centre, Montreal, QC, Canada
| | - Éric A Cohen
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Christopher Power
- Department of Medicine (Neurology), University of Alberta, 6-11 Heritage Medical Research Center, Edmonton, AB, Canada; Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
| | - Jonathan B Angel
- Ottawa Hospital Research Institute, Ottawa, ON, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada; Division of Infectious Diseases, Ottawa Hospital-General Campus, Ottawa, ON, Canada
| | - Nicolas Chomont
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Centre de Recherche du CHUM, Montreal, QC Canada.
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29
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Kulkarni S, Endsley JJ, Lai Z, Bradley T, Sharan R. Single-Cell Transcriptomics of Mtb/HIV Co-Infection. Cells 2023; 12:2295. [PMID: 37759517 PMCID: PMC10529032 DOI: 10.3390/cells12182295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) co-infection continues to pose a significant healthcare burden. HIV co-infection during TB predisposes the host to the reactivation of latent TB infection (LTBI), worsening disease conditions and mortality. There is a lack of biomarkers of LTBI reactivation and/or immune-related transcriptional signatures to distinguish active TB from LTBI and predict TB reactivation upon HIV co-infection. Characterizing individual cells using next-generation sequencing-based technologies has facilitated novel biological discoveries about infectious diseases, including TB and HIV pathogenesis. Compared to the more conventional sequencing techniques that provide a bulk assessment, single-cell RNA sequencing (scRNA-seq) can reveal complex and new cell types and identify more high-resolution cellular heterogeneity. This review will summarize the progress made in defining the immune atlas of TB and HIV infections using scRNA-seq, including host-pathogen interactions, heterogeneity in HIV pathogenesis, and the animal models employed to model disease. This review will also address the tools needed to bridge the gap between disease outcomes in single infection vs. co-infection. Finally, it will elaborate on the translational benefits of single-cell sequencing in TB/HIV diagnosis in humans.
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Affiliation(s)
- Smita Kulkarni
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Janice J. Endsley
- Departments of Microbiology & Immunology and Pathology, The University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Zhao Lai
- Greehey Children’s Cancer Research Institute, The University of Texas Health San Antonio, San Antonio, TX 78229, USA;
| | - Todd Bradley
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA;
- Departments of Pediatrics and Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO 66160, USA
- Department of Pediatrics, UMKC School of Medicine, Kansas City, MO 64108, USA
| | - Riti Sharan
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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30
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Dubé M, Tastet O, Dufour C, Sannier G, Brassard N, Delgado GG, Pagliuzza A, Richard C, Nayrac M, Routy JP, Prat A, Estes JD, Fromentin R, Chomont N, Kaufmann DE. Spontaneous HIV expression during suppressive ART is associated with the magnitude and function of HIV-specific CD4 + and CD8 + T cells. Cell Host Microbe 2023; 31:1507-1522.e5. [PMID: 37708853 PMCID: PMC10542967 DOI: 10.1016/j.chom.2023.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/01/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
Abstract
Spontaneous transcription and translation of HIV can persist during suppressive antiretroviral therapy (ART). The quantity, phenotype, and biological relevance of this spontaneously "active" reservoir remain unclear. Using multiplexed single-cell RNAflow-fluorescence in situ hybridization (FISH), we detect active HIV transcription in 14/18 people with HIV on suppressive ART, with a median of 28/million CD4+ T cells. While these cells predominantly exhibit abortive transcription, p24-expressing cells are evident in 39% of participants. Phenotypically diverse, active reservoirs are enriched in central memory T cells and CCR6- and activation-marker-expressing cells. The magnitude of the active reservoir positively correlates with total HIV-specific CD4+ and CD8+ T cell responses and with multiple HIV-specific T cell clusters identified by unsupervised analysis. These associations are particularly strong with p24-expressing active reservoir cells. Single-cell vDNA sequencing shows that active reservoirs are largely dominated by defective proviruses. Our data suggest that these reservoirs maintain HIV-specific CD4+ and CD8+ T responses during suppressive ART.
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Affiliation(s)
- Mathieu Dubé
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada.
| | - Olivier Tastet
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Caroline Dufour
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Gérémy Sannier
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Nathalie Brassard
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Gloria-Gabrielle Delgado
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Amélie Pagliuzza
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Corentin Richard
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Manon Nayrac
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illnesses Service and Division of Hematology, McGill University Health Centre (CUSM), Montreal, QC H4A 3J1, Canada; Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Alexandre Prat
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Rémi Fromentin
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Nicolas Chomont
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Daniel E Kaufmann
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; Division of Infectious Diseases, Department of Medicine, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland.
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31
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Wong M, Wei Y, Ho YC. Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels. Curr Opin HIV AIDS 2023; 18:246-256. [PMID: 37535039 PMCID: PMC10442869 DOI: 10.1097/coh.0000000000000809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
PURPOSE OF REVIEW The success of HIV-1 eradication strategies relies on in-depth understanding of HIV-1-infected cells. However, HIV-1-infected cells are extremely heterogeneous and rare. Single-cell multiomic approaches resolve the heterogeneity and rarity of HIV-1-infected cells. RECENT FINDINGS Advancement in single-cell multiomic approaches enabled HIV-1 reservoir profiling across the epigenetic (ATAC-seq), transcriptional (RNA-seq), and protein levels (CITE-seq). Using HIV-1 RNA as a surrogate, ECCITE-seq identified enrichment of HIV-1-infected cells in clonally expanded cytotoxic CD4+ T cells. Using HIV-1 DNA PCR-activated microfluidic sorting, FIND-seq captured the bulk transcriptome of HIV-1 DNA+ cells. Using targeted HIV-1 DNA amplification, PheP-seq identified surface protein expression of intact versus defective HIV-1-infected cells. Using ATAC-seq to identify HIV-1 DNA, ASAP-seq captured transcription factor activity and surface protein expression of HIV-1 DNA+ cells. Combining HIV-1 mapping by ATAC-seq and HIV-1 RNA mapping by RNA-seq, DOGMA-seq captured the epigenetic, transcriptional, and surface protein expression of latent and transcriptionally active HIV-1-infected cells. To identify reproducible biological insights and authentic HIV-1-infected cells and avoid false-positive discovery of artifacts, we reviewed current practices of single-cell multiomic experimental design and bioinformatic analysis. SUMMARY Single-cell multiomic approaches may identify innovative mechanisms of HIV-1 persistence, nominate therapeutic strategies, and accelerate discoveries.
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Affiliation(s)
- Michelle Wong
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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32
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Pitman MC, Meagher N, Price DJ, Rhodes A, Chang JJ, Scher B, Allan B, Street A, McMahon JH, Rasmussen TA, Cameron PU, Hoy JF, Kent SJ, Lewin SR. Effect of high dose vitamin D 3 on the HIV-1 reservoir: A pilot randomised controlled trial. J Virus Erad 2023; 9:100345. [PMID: 37753336 PMCID: PMC10518338 DOI: 10.1016/j.jve.2023.100345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/27/2023] [Indexed: 09/28/2023] Open
Abstract
Introduction Antiretroviral therapy for people living with HIV-1 must be taken lifelong due to the persistence of latent virus in long-lived and proliferating CD4+ T cells. Vitamin D3 is a steroidal gene transcription regulator which exerts diverse effects on immune and epithelial cells including reductions in CD4+ T cell proliferation and improvement in gut barrier integrity. We hypothesised that a high dose of vitamin D3 would reduce the size of the HIV-1 reservoir by reducing CD4+ T cell proliferation. Methods We performed a randomised placebo-controlled trial evaluating the effect of 24 weeks of vitamin D3 (10,000 international units per day) on the HIV-1 reservoir and immunologic parameters in 30 adults on antiretroviral therapy; participants were followed for 12 weeks post-treatment. The primary endpoint was the effect on total HIV-1 DNA at week 24. Parameters were assessed using mixed-effects models. Results We found no effect of vitamin D3 on the change in total HIV-1 DNA from week 0 to week 24 relative to placebo. There were also no changes in integrated HIV-1 DNA, 2-long-terminal repeat (2-LTR) circles or cell-associated HIV-1 RNA. Vitamin D3 induced a significant increase in the proportion of central memory CD4+ and CD8+ T cells, a reduction in the proportion of senescent CD8+ T cells and a reduction in the natural killer cell frequency at all time points including week 36, 12 weeks after the study drug cessation. At week 36, there was a significant reduction in total HIV-1 DNA relative to placebo and persistently elevated 25-hydroxyvitamin D levels. No significant safety issues were identified. Conclusions Vitamin D3 administration had a significant impact on the T cell differentiation but overall effects on the HIV-1 reservoir were limited and a reduction in HIV-1 DNA was only seen following cessation of the study drug. Additional studies are required to determine whether the dose and duration of vitamin D3 can be optimised to promote a continued depletion of the HIV-1 reservoir over time. Trial registration ClinicalTrials.gov NCT03426592.
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Affiliation(s)
- Matthew C. Pitman
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
| | - Niamh Meagher
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Level 3, 207 Bouverie St, Parkville, Victoria, 3010, Australia
| | - David J. Price
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Level 3, 207 Bouverie St, Parkville, Victoria, 3010, Australia
| | - Ajantha Rhodes
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
| | - J. Judy Chang
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
| | - Barbara Scher
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
| | - Brent Allan
- Living Positive Victoria, Ground Floor, 95 Coventry St, Southbank, Victoria, 3006, Australia
| | - Alan Street
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
| | - James H. McMahon
- Department of Infectious Diseases, The Alfred and Monash University, 55 Commercial Rd, Melbourne, Victoria, 3004, Australia
| | - Thomas A. Rasmussen
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
| | - Paul U. Cameron
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
| | - Jennifer F. Hoy
- Department of Infectious Diseases, The Alfred and Monash University, 55 Commercial Rd, Melbourne, Victoria, 3004, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
- Department of Infectious Diseases, The Alfred and Monash University, 55 Commercial Rd, Melbourne, Victoria, 3004, Australia
- Melbourne Sexual Health Centre, The Alfred, 580 Swanston St, Carlton, Victoria, 3053, Australia
| | - Sharon R. Lewin
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, Victoria, 3000, Australia
- Department of Infectious Diseases, The Alfred and Monash University, 55 Commercial Rd, Melbourne, Victoria, 3004, Australia
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33
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Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobamibias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time. RESEARCH SQUARE 2023:rs.3.rs-3259040. [PMID: 37645749 PMCID: PMC10462229 DOI: 10.21203/rs.3.rs-3259040/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Within-host HIV populations continually diversify during untreated infection, and members of these diverse forms persist within infected cell reservoirs, even during antiretroviral therapy (ART). Characterizing the diverse viral sequences that persist during ART is critical to HIV cure efforts, but our knowledge of on-ART proviral evolutionary dynamics remains incomplete, as does our understanding of the differences between the overall pool of persisting proviral DNA (which is largely genetically defective) and the subset of intact HIV sequences capable of reactivating. Here, we reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study (WIHS) who experienced HIV seroconversion. We measured diversity, lineage origins and ages of proviral sequences (env-gp120) sampled up to four times, up to 12 years on ART. We used the same techniques to study HIV sequences emerging from the reservoir in two participants. Proviral clonality generally increased over time on ART, with clones frequently persisting across multiple time points. The integration dates of proviruses persisting on ART generally spanned the duration of untreated infection (though were often skewed towards years immediately pre-ART), while in contrast, reservoir-origin viremia emerging in plasma was exclusively "younger" (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained highly stable during ART in all but one participant in whom, after 12 years, there was evidence that "younger" proviruses had been preferentially eliminated. Analysis of within-host recombinant proviral sequences also suggested that HIV reservoirs can be superinfected with virus reactivated from an older era, yielding infectious viral progeny with mosaic genomes of sequences with different ages. Overall, results underscore the remarkable genetic stability of distinct proviral sequences that persist on ART, yet suggest that replication-competent HIV reservoir represents a genetically-restricted and overall "younger" subset of the overall persisting proviral pool in blood.
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Affiliation(s)
- Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Signe MacLennan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Bradley R Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zhong Dang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Kyle Cobamibias
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Michael J Dapp
- Department of Microbiology, University of Washington, School of Medicine, Seattle, WA, USA
| | - Nande M Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, NC, USA
| | - Margaret A Fischl
- Department of Medicine, University of Miami School of Medicine, Miami, FL, USA
| | - Igho Ofotokun
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Adaora Adimora
- Departments of Medicine and Epidemiology, University of North Carolina School of Medicine, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Stephen Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Mark H Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, NY, USA
| | - Seble Kassaye
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
| | - James I Mullins
- Department of Microbiology, University of Washington, School of Medicine, Seattle, WA, USA
| | - Harris Goldstein
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
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34
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Sun W, Rassadkina Y, Gao C, Collens SI, Lian X, Solomon IH, Mukerji S, Yu XG, Lichterfeld M. Persistence of intact HIV-1 proviruses in the brain during antiretroviral therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546135. [PMID: 37425847 PMCID: PMC10327102 DOI: 10.1101/2023.06.26.546135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
HIV-1 reservoir cells that circulate in peripheral blood during suppressive antiretroviral therapy (ART) have been well characterized, but little is known about the dissemination of HIV-1-infected cells across multiple anatomical tissues, especially the central nervous system (CNS). Here, we performed single-genome, near full-length HIV-1 next-generation sequencing to evaluate the proviral landscape in distinct anatomical compartments, including multiple CNS tissues, from 3 ART-treated participants at autopsy. While lymph nodes and, to a lesser extent, gastrointestinal and genitourinary tissues represented tissue hotspots for the persistence of intact proviruses, we also observed intact proviruses in CNS tissue sections, particularly in the basal ganglia. Multi-compartment dissemination of clonal intact and defective proviral sequences occurred across multiple anatomical tissues, including the CNS, and evidence for the clonal proliferation of HIV-1-infected cells was found in the basal ganglia, in the frontal lobe, in the thalamus and in periventricular white matter. Deep analysis of HIV-1 reservoirs in distinct tissues will be informative for advancing HIV-1 cure strategies.
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Affiliation(s)
- Weiwei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
| | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
| | | | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Shibani Mukerji
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA
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35
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Hartana CA, Broncano PG, Maswabi K, Ajibola G, Moyo S, Mohammed T, Maphorisa C, Makhema J, Powis KM, Lockman S, Burbelo PD, Gao C, Yu XG, Kuritzkes DR, Shapiro R, Lichterfeld M. Immune Modulation of HIV-1 Reservoir Size in Early-Treated Neonates. J Infect Dis 2023; 228:281-286. [PMID: 37201510 PMCID: PMC10420392 DOI: 10.1093/infdis/jiad173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/20/2023] Open
Abstract
Immune mechanisms that modulate human immunodeficiency virus-1 (HIV-1) reservoir size in neonates are poorly understood. Using samples from neonates who initiated antiretroviral therapy shortly after birth, we demonstrate that interleukin-8-secreting CD4 T cells, which are selectively expanded in early infancy, are more resistant to HIV-1 infection and inversely correlated with the frequency of intact proviruses at birth. Moreover, newborns with HIV-1 infection displayed a distinct B-cell profile at birth, with reduction of memory B cells and expansion of plasmablasts and transitional B cells; however, B-cell immune perturbations were unrelated to HIV-1 reservoir size and normalized after initiation of antiretroviral therapy. Clinical Trials Registration. NCT02369406.
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Affiliation(s)
- Ciputra Adijaya Hartana
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Pilar Garcia Broncano
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Kenneth Maswabi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Kathleen M Powis
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine and Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Shahin Lockman
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard Medical School, Boston, Massachusetts, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Ce Gao
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Xu G Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Mathias Lichterfeld
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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36
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Tumpach C, Rhodes A, Kim Y, Ong J, Liu H, Chibo D, Druce J, Williamson D, Hoh R, Deeks SG, Yukl SA, Roche M, Lewin SR, Telwatte S. Adaptation of Droplet Digital PCR-Based HIV Transcription Profiling to Digital PCR and Association of HIV Transcription and Total or Intact HIV DNA. Viruses 2023; 15:1606. [PMID: 37515292 PMCID: PMC10384802 DOI: 10.3390/v15071606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
In most people living with HIV (PLWH) on effective antiretroviral therapy (ART), cell-associated viral transcripts are readily detectable in CD4+ T cells despite the absence of viremia. Quantification of HIV RNA species provides insights into the transcriptional activity of proviruses that persist in cells and tissues throughout the body during ART ('HIV reservoir'). One such technique for HIV RNA quantitation, 'HIV transcription profiling', developed in the Yukl laboratory, measures a series of HIV RNA species using droplet digital PCR. To take advantage of advances in digital (d)PCR, we adapted the 'HIV transcription profiling' technique to Qiagen's dPCR platform (QIAcuity) and compared its performance to droplet digital (dd)PCR (Bio-Rad QX200 system). Using RNA standards, the two technologies were tested in parallel and assessed for multiple parameters including sensitivity, specificity, linearity, and intra- and inter-assay variability. The newly validated dPCR assays were then applied to samples from PLWH to determine HIV transcriptional activity relative to HIV reservoir size. We report that HIV transcriptional profiling was readily adapted to dPCR and assays performed similarly to ddPCR, with no differences in assay characteristics. We applied these assays in a cohort of 23 PLWH and found that HIV reservoir size, based on genetically intact proviral DNA, does not predict HIV transcriptional activity. In contrast, levels of total DNA correlated with levels of most HIV transcripts (initiated, proximally and distally elongated, unspliced, and completed, but not multiply spliced), suggesting that a considerable proportion of HIV transcripts likely originate from defective proviruses. These findings may have implications for measuring and assessing curative strategies and clinical trial outcomes.
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Affiliation(s)
- Carolin Tumpach
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Ajantha Rhodes
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Youry Kim
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jesslyn Ong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Haoming Liu
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Doris Chibo
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Deborah Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Walter and Eliza Hall Institute, Melbourne 3052, Australia
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Steven G. Deeks
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Steven A. Yukl
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
- San Francisco Veteran Affairs Medical Center, San Francisco, CA 94121, USA
| | - Michael Roche
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Infectious and Inflammatory Diseases Theme, School of Health and Biomedical Sciences, RMIT University, Melbourne 3000, Australia
| | - Sharon R. Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne 3004, Australia
| | - Sushama Telwatte
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
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37
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Shapiro RL, Ajibola G, Maswabi K, Hughes M, Nelson BS, Niesar A, Holme MP, Powis KM, Sakoi M, Batlang O, Moyo S, Mohammed T, Maphorisa C, Bennett K, Hu Z, Giguel F, Reeves JD, Reeves MA, Gao C, Yu X, Ackerman ME, McDermott A, Cooper M, Caskey M, Gama L, Jean-Philippe P, Yin DE, Capparelli EV, Lockman S, Makhema J, Kuritzkes DR, Lichterfeld M. Broadly neutralizing antibody treatment maintained HIV suppression in children with favorable reservoir characteristics in Botswana. Sci Transl Med 2023; 15:eadh0004. [PMID: 37406137 PMCID: PMC10683791 DOI: 10.1126/scitranslmed.adh0004] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/26/2023] [Indexed: 07/07/2023]
Abstract
Broadly neutralizing antibodies (bNAbs) may provide an alternative to standard antiretroviral treatment (ART) for controlling HIV-1 replication and may have immunotherapeutic effects against HIV-1 reservoirs. We conducted a prospective clinical trial with two HIV-1 bNAbs (VRC01LS and 10-1074) in children (n = 25) who had previously initiated small-molecule ART treatment before 7 days of age and who continued treatment for at least 96 weeks. Both bNAbs were dosed intravenously every 4 weeks, overlapping with ART for at least 8 weeks and then continued for up to 24 weeks or until detectable viremia of HIV-1 RNA rose above 400 copies per milliliter in the absence of ART. Eleven (44%) children maintained HIV-1 RNA below 400 copies per milliliter through 24 weeks of bNAb-only treatment; 14 (56%) had detectable viremia above 400 copies per milliliter at a median of 4 weeks. Archived HIV-1 provirus susceptible to 10-1074, lower birth HIV-1 DNA reservoir in peripheral blood mononuclear cells, sustained viral suppression throughout early life, and combined negative qualitative HIV-1 DNA polymerase chain reaction and negative HIV-1 serology at entry were associated with maintaining suppression on bNAbs alone. This proof-of-concept study suggests that bNAbs may represent a promising treatment modality for infants and children living with HIV-1. Future studies using newer bNAb combinations with greater breadth and potency are warranted.
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Affiliation(s)
- Roger L. Shapiro
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Botswana Harvard Health Partnership; Gaborone, Botswana
| | | | | | - Michael Hughes
- Department of Biostatistics, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
| | - Bryan S. Nelson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
| | - Aischa Niesar
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
| | - Molly Pretorius Holme
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
| | - Kathleen M. Powis
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Botswana Harvard Health Partnership; Gaborone, Botswana
- Departments of Internal Medicine and Pediatrics, Massachusetts General Hospital; Boston, MA 02114, USA
| | - Maureen Sakoi
- Botswana Harvard Health Partnership; Gaborone, Botswana
| | | | - Sikhulile Moyo
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Botswana Harvard Health Partnership; Gaborone, Botswana
| | | | | | - Kara Bennett
- Bennett Statistical Consulting, Inc.; Ballston Lake, NY 12019, USA
| | - Zixin Hu
- Division of Infectious Diseases, Brigham and Women’s Hospital; Boston, MA 02115, USA
| | - Francoise Giguel
- Division of Infectious Diseases, Brigham and Women’s Hospital; Boston, MA 02115, USA
| | | | - Michael A. Reeves
- Labcorp-Monogram Biosciences, Inc.; South San Francisco, CA 94080, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
| | - Xu Yu
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
| | | | | | - Marlene Cooper
- Frontier Science and Technology Research Foundation, Inc.; Amherst, NY 14226, USA
| | | | - Lucio Gama
- Vaccine Research Center; Bethesda, MD 20892, USA
| | - Patrick Jean-Philippe
- National Institute of Allergy and Infectious Diseases, National Institutes of Health; Rockville, MD 20892, USA
| | - Dwight E. Yin
- National Institute of Allergy and Infectious Diseases, National Institutes of Health; Rockville, MD 20892, USA
| | - Edmund V. Capparelli
- Department of Pediatrics, University of California San Diego; La Jolla, CA 92037, USA
| | - Shahin Lockman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Botswana Harvard Health Partnership; Gaborone, Botswana
- Division of Infectious Diseases, Brigham and Women’s Hospital; Boston, MA 02115, USA
| | - Joseph Makhema
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Botswana Harvard Health Partnership; Gaborone, Botswana
| | - Daniel R. Kuritzkes
- Division of Infectious Diseases, Brigham and Women’s Hospital; Boston, MA 02115, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Division of Infectious Diseases, Brigham and Women’s Hospital; Boston, MA 02115, USA
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38
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Sanders-Beer BE, Archin NM, Brumme ZL, Busch MP, Deleage C, O'Doherty U, Hughes SH, Jerome KR, Jones RB, Karn J, Kearney MF, Keele BF, Kulpa DA, Laird GM, Li JZ, Lichterfeld MD, Nussenzweig MC, Persaud D, Yukl SA, Siliciano RF, Mellors JW. Current HIV/SIV Reservoir Assays for Preclinical and Clinical Applications: Recommendations from the Experts 2022 NIAID Workshop Summary. AIDS Res Hum Retroviruses 2023; 40:7-21. [PMID: 37126090 DOI: 10.1089/aid.2022.0188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Since the first HIV-cured person was reported in 2009, a strong interest in developing highly sensitive HIV and SIV reservoir assays has emerged. In particular, the question arose about the comparative value of state-of-the-art assays to measure and characterize the HIV reservoir, and how these assays can be applied to accurately detect changes in the reservoir during efforts to develop a cure for HIV infection. Second, it is important to consider the impact on the outcome of clinical trials if these relatively new HIV reservoir assays are incorporated into clinical trial endpoints and/or used for clinical decision-making. To understand the advantages and limitations and the regulatory implications of HIV reservoir assays, the National Institute of Allergy and Infectious Diseases (NIAID) sponsored and convened a meeting on September 16, 2022, to discuss the state of knowledge concerning these questions and best practices for selecting HIV reservoir assays for a particular research question or clinical trial protocol.
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Affiliation(s)
- Brigitte E Sanders-Beer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nancie M Archin
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael P Busch
- Vitalant Research Institute, University of California, San Francisco, California, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, and Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mathias D Lichterfeld
- Brigham and Women's Hospital and Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Deborah Persaud
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven A Yukl
- Department of Medicine, University of California San Francisco (UCSF) and San Francisco VA Medical Center, San Francisco, California, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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39
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Faua C, Fafi-Kremer S, Gantner P. Antigen specificities of HIV-infected cells: A role in infection and persistence? J Virus Erad 2023; 9:100329. [PMID: 37440870 PMCID: PMC10334354 DOI: 10.1016/j.jve.2023.100329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/12/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Antigen-experienced memory CD4+ T cells are the major target of HIV infection and support both productive and latent infections, thus playing a key role in HIV dissemination and persistence, respectively. Here, we reviewed studies that have shown direct association between HIV infection and antigen specificity. During untreated infection, some HIV-specific cells host productive infection, while other pathogen-specific cells such as cytomegalovirus (CMV) and Mycobacterium tuberculosis also contribute to viral persistence on antiretroviral therapy (ART). These patterns could be explained by phenotypic features differing between these pathogen-specific cells. Mechanisms involved in these preferential infection and selection processes include HIV entry and restriction, cell exhaustion, survival, self-renewal and immune escape. For instance, MIP-1β expressing cells such as CMV-specific memory cells were shown to resist infection by HIV CCR5 coreceptor downregulation/inhibition. Conversely, HIV-infected CMV-specific cells undergo clonal expansion during ART. We have identified several research areas that need further focus such as the role of other pathogens, viral genome intactness, inducibility and phenotypic features. However, given the sheer diversity of both the CD4+ T cell repertoire and antigenic history of each individual, studying HIV-infected, antigen-experienced cells still imposes numerous challenges.
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Affiliation(s)
- Clayton Faua
- INSERM UMR_S1109, University of Strasbourg, Strasbourg, France
| | - Samira Fafi-Kremer
- INSERM UMR_S1109, University of Strasbourg, Strasbourg, France
- Medical Virology Laboratory, University Hospital of Strasbourg, Strasbourg, France
| | - Pierre Gantner
- INSERM UMR_S1109, University of Strasbourg, Strasbourg, France
- Medical Virology Laboratory, University Hospital of Strasbourg, Strasbourg, France
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40
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Esmaeilzadeh E, Etemad B, Lavine CL, Garneau L, Li Y, Regan J, Wong C, Sharaf R, Connick E, Volberding P, Sagar M, Seaman MS, Li JZ. Autologous neutralizing antibodies increase with early antiretroviral therapy and shape HIV rebound after treatment interruption. Sci Transl Med 2023; 15:eabq4490. [PMID: 37163616 PMCID: PMC10576978 DOI: 10.1126/scitranslmed.abq4490] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/10/2023] [Indexed: 05/12/2023]
Abstract
Early initiation of antiretroviral therapy (ART) alters viral rebound kinetics after analytic treatment interruption (ATI) and may play a role in promoting HIV-1 remission. Autologous neutralizing antibodies (aNAbs) represent a key adaptive immune response in people living with HIV-1. We aimed to investigate the role of aNAbs in shaping post-ATI HIV-1 rebound variants. We performed single-genome amplification of HIV-1 env from pre-ART and post-ATI plasma samples of 12 individuals who initiated ART early after infection. aNAb activity was quantified using pseudoviruses derived from the most common plasma variant, and the serum dilution that inhibited 50% of viral infections was determined. aNAb responses matured while participants were on suppressive ART, because on-ART plasma and purified immunoglobulin G (IgG) demonstrated improved neutralizing activity against pre-ART HIV-1 strains when compared with pre-ART plasma or purified IgG. Post-ATI aNAb responses exerted selective pressure on the rebounding viruses, because the post-ATI HIV-1 strains were more resistant to post-ATI plasma neutralization compared with the pre-ART virus. Several pre-ATI features distinguished post-treatment controllers from noncontrollers, including an infecting HIV-1 sequence that was more similar to consensus HIV-1 subtype B, more restricted proviral diversity, and a stronger aNAb response. Post-treatment control was also associated with the evolution of distinct N-glycosylation profiles in the HIV-1 envelope. In summary, aNAb responses appeared to mature after early initiation of ART and applied selective pressure on rebounding viruses. The combination of aNAb activity with select HIV-1 sequence and reservoir features identified individuals with a greater chance of post-treatment control.
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Affiliation(s)
| | - Behzad Etemad
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Lauren Garneau
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Yijia Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - James Regan
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Colline Wong
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Radwa Sharaf
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Paul Volberding
- University of California, San Francisco, San Francisco, CA 94158, USA
| | - Manish Sagar
- Boston University Chobanian and Avedesian School of Medicine, Boston, MA 02118, USA
| | | | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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41
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536611. [PMID: 37090500 PMCID: PMC10120704 DOI: 10.1101/2023.04.12.536611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In order to cure HIV, we need to better understand the within-host evolutionary origins of the small reservoir of genome-intact proviruses that persists within infected cells during antiretroviral therapy (ART). Most prior studies on reservoir evolutionary dynamics however did not discriminate genome-intact proviruses from the vast background of defective ones. We reconstructed within-host pre-ART HIV evolutionary histories in six individuals and leveraged this information to infer the ages of intact and defective proviruses sampled after an average >9 years on ART, along with the ages of rebound and low-level/isolated viremia occurring during this time. We observed that the longest-lived proviruses persisting on ART were exclusively defective, usually due to large deletions. In contrast, intact proviruses and rebound HIV exclusively dated to the years immediately preceding ART. These observations are consistent with genome-intact proviruses having shorter lifespans, likely due to the cumulative risk of elimination following viral reactivation and protein production. Consistent with this, intact proviruses (and those with packaging signal defects) were three times more likely to be genetically identical compared to other proviral types, highlighting clonal expansion as particularly important in ensuring their survival. By contrast, low-level/isolated viremia sequences were genetically heterogeneous and sometimes ancestral, where viremia may have originated from defective proviruses. Results reveal that the HIV reservoir is dominated by clonally-enriched and genetically younger sequences that date to the untreated infection period when viral populations had been under within-host selection pressures for the longest duration. Knowledge of these qualities may help focus strategies for reservoir elimination.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
| | | | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Experimental Medicine Program, University of British Columbia, Vancouver, BC
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby BC
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
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42
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Pasternak AO, Berkhout B. HIV persistence: silence or resistance? Curr Opin Virol 2023; 59:101301. [PMID: 36805974 DOI: 10.1016/j.coviro.2023.101301] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 02/19/2023]
Abstract
Despite decades of suppressive antiretroviral therapy, human immunodeficiency virus (HIV) reservoirs in infected individuals persist and fuel viral rebound once therapy is interrupted. The persistence of viral reservoirs is the main obstacle to achieving HIV eradication or a long-term remission. The last decade has seen a profound change in our understanding of the mechanisms behind HIV persistence, which appears to be much more complex than originally assumed. In addition to the persistence of transcriptionally silent proviruses in a stable latent reservoir that is invisible to the immune system, HIV is increasingly recognized to persist by resistance to the immune clearance, which appears to play a surprisingly prominent role in shaping the reservoir. In this review, we discuss some emerging insights into the mechanisms of HIV persistence, as well as their implications for the development of strategies towards an HIV cure.
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Affiliation(s)
- Alexander O Pasternak
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
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43
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White JA, Wu F, Yasin S, Moskovljevic M, Varriale J, Dragoni F, Camilo-Contreras A, Duan J, Zheng MY, Tadzong NF, Patel HB, Quiambao JMC, Rhodehouse K, Zhang H, Lai J, Beg SA, Delannoy M, Kilcrease C, Hoffmann CJ, Poulin S, Chano F, Tremblay C, Cherian J, Barditch-Crovo P, Chida N, Moore RD, Summers MF, Siliciano RF, Siliciano JD, Simonetti FR. Clonally expanded HIV-1 proviruses with 5'-leader defects can give rise to nonsuppressible residual viremia. J Clin Invest 2023; 133:165245. [PMID: 36602866 PMCID: PMC10014112 DOI: 10.1172/jci165245] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
BackgroundAntiretroviral therapy (ART) halts HIV-1 replication, decreasing viremia to below the detection limit of clinical assays. However, some individuals experience persistent nonsuppressible viremia (NSV) originating from CD4+ T cell clones carrying infectious proviruses. Defective proviruses represent over 90% of all proviruses persisting during ART and can express viral genes, but whether they can cause NSV and complicate ART management is unknown.MethodsWe undertook an in-depth characterization of proviruses causing NSV in 4 study participants with optimal adherence and no drug resistance. We investigated the impact of the observed defects on 5'-leader RNA properties, virus infectivity, and gene expression. Integration-site specific assays were used to track these proviruses over time and among cell subsets.ResultsClones carrying proviruses with 5'-leader defects can cause persistent NSV up to approximately 103 copies/mL. These proviruses had small, often identical deletions or point mutations involving the major splicing donor (MSD) site and showed partially reduced RNA dimerization and nucleocapsid binding. Nevertheless, they were inducible and produced noninfectious virions containing viral RNA, but lacking envelope.ConclusionThese findings show that proviruses with 5'-leader defects in CD4+ T cell clones can give rise to NSV, affecting clinical care. Sequencing of the 5'-leader can help in understanding failure to completely suppress viremia.FundingOffice of the NIH Director and National Institute of Dental and Craniofacial Research, NIH; Howard Hughes Medical Institute; Johns Hopkins University Center for AIDS Research; National Institute for Allergy and Infectious Diseases (NIAID), NIH, to the PAVE, BEAT-HIV, and DARE Martin Delaney collaboratories.
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Affiliation(s)
- Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Saif Yasin
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Milica Moskovljevic
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Filippo Dragoni
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Jiayi Duan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mei Y Zheng
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Ndeh F Tadzong
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Heer B Patel
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Jeanelle Mae C Quiambao
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Kyle Rhodehouse
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Delannoy
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christin Kilcrease
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christopher J Hoffmann
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Cécile Tremblay
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Canada.,Département de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Canada
| | - Jerald Cherian
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patricia Barditch-Crovo
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Natasha Chida
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael F Summers
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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44
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Fray EJ, Wu F, Simonetti FR, Zitzmann C, Sambaturu N, Molina-Paris C, Bender AM, Liu PT, Ventura JD, Wiseman RW, O'Connor DH, Geleziunas R, Leitner T, Ribeiro RM, Perelson AS, Barouch DH, Siliciano JD, Siliciano RF. Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants. Cell Host Microbe 2023; 31:356-372.e5. [PMID: 36809762 PMCID: PMC10583177 DOI: 10.1016/j.chom.2023.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/02/2022] [Accepted: 01/24/2023] [Indexed: 02/22/2023]
Abstract
The decay kinetics of HIV-1-infected cells are critical to understand virus persistence. We evaluated the frequency of simian immunodeficiency virus (SIV)-infected cells for 4 years of antiretroviral therapy (ART). The intact proviral DNA assay (IPDA) and an assay for hypermutated proviruses revealed short- and long-term infected cell dynamics in macaques starting ART ∼1 year after infection. Intact SIV genomes in circulating CD4+T cells showed triphasic decay with an initial phase slower than the decay of the plasma virus, a second phase faster than the second phase decay of intact HIV-1, and a stable third phase reached after 1.6-2.9 years. Hypermutated proviruses showed bi- or mono-phasic decay, reflecting different selective pressures. Viruses replicating at ART initiation had mutations conferring antibody escape. With time on ART, viruses with fewer mutations became more prominent, reflecting decay of variants replicating at ART initiation. Collectively, these findings confirm ART efficacy and indicate that cells enter the reservoir throughout untreated infection.
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Affiliation(s)
- Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | | | - Alexandra M Bender
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Po-Ting Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - John D Ventura
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | | | - Thomas Leitner
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ruy M Ribeiro
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
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45
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Dufour C, Richard C, Pardons M, Massanella M, Ackaoui A, Murrell B, Routy B, Thomas R, Routy JP, Fromentin R, Chomont N. Phenotypic characterization of single CD4+ T cells harboring genetically intact and inducible HIV genomes. Nat Commun 2023; 14:1115. [PMID: 36849523 PMCID: PMC9971253 DOI: 10.1038/s41467-023-36772-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
The phenotype of the rare HIV-infected cells persisting during antiretroviral therapies (ART) remains elusive. We developed a single-cell approach that combines the phenotypic analysis of HIV-infected cells with near full-length sequencing of their associated proviruses to characterize the viral reservoir in 6 male individuals on suppressive ART. We show that individual cells carrying clonally expanded identical proviruses display very diverse phenotypes, indicating that cellular proliferation contributes to the phenotypic diversification of the HIV reservoir. Unlike most viral genomes persisting on ART, inducible and translation-competent proviruses rarely present large deletions but are enriched in defects in the Ψ locus. Interestingly, the few cells harboring genetically intact and inducible viral genomes express higher levels of the integrin VLA-4 compared to uninfected cells or cells with defective proviruses. Viral outgrowth assay confirmed that memory CD4+ T cells expressing high levels of VLA-4 are highly enriched in replication-competent HIV (27-fold enrichment). We conclude that although clonal expansions diversify the phenotype of HIV reservoir cells, CD4+ T cells harboring replication-competent HIV retain VLA-4 expression.
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Affiliation(s)
- Caroline Dufour
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Corentin Richard
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Marion Pardons
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Marta Massanella
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Antoine Ackaoui
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Bertrand Routy
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Réjean Thomas
- Clinique médicale l'Actuel, Montreal, H2L 4P9, Quebec, Canada
| | - Jean-Pierre Routy
- Division of Hematology & Chronic Viral Illness Service, McGill University Health Centre, Montreal, H4A 3J1, Quebec, Canada
| | - Rémi Fromentin
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, H2X 0A9, Quebec, Canada.
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46
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The Dynamic Linkage between Provirus Integration Sites and the Host Functional Genome Property Alongside HIV-1 Infections Associated with Antiretroviral Therapy. Vaccines (Basel) 2023; 11:vaccines11020402. [PMID: 36851277 PMCID: PMC9963931 DOI: 10.3390/vaccines11020402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
(1) Background: The HIV-1 latent reservoir harboring replication-competent proviruses is the major barrier in the quest for an HIV-1 infection cure. HIV-1 infection at all stages of disease progression is associated with immune activation and dysfunctional production of proinflammatory soluble factors (cytokines and chemokines), and it is expected that during HIV-1 infection, different immune components and immune cells, in turn, participate in immune responses, subsequently activating downstream biological pathways. However, the functional interaction between HIV-1 integration and the activation of host biological pathways is presently not fully understood. (2) Methods: In this work, I used genes targeted by proviruses from published datasets to seek enriched immunologic signatures and host biological pathways alongside HIV-1 infections based on MSigDb and KEGG over-representation analysis. (3) Results: I observed that different combinations of immunologic signatures of immune cell types and proinflammatory soluble factors appeared alongside HIV-1 infections associated with antiretroviral therapy. Moreover, enriched KEGG pathways were often related to "cancer specific types", "immune system", "infectious disease viral", and "signal transduction". (4) Conclusions: The observations in this work suggest that the gene sets harboring provirus integration sites may define specific immune cells and proinflammatory soluble factors during HIV-1 infections associated with antiretroviral therapy.
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47
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Clark IC, Mudvari P, Thaploo S, Smith S, Abu-Laban M, Hamouda M, Theberge M, Shah S, Ko SH, Pérez L, Bunis DG, Lee JS, Kilam D, Zakaria S, Choi S, Darko S, Henry AR, Wheeler MA, Hoh R, Butrus S, Deeks SG, Quintana FJ, Douek DC, Abate AR, Boritz EA. HIV silencing and cell survival signatures in infected T cell reservoirs. Nature 2023; 614:318-325. [PMID: 36599978 PMCID: PMC9908556 DOI: 10.1038/s41586-022-05556-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/11/2022] [Indexed: 01/06/2023]
Abstract
Rare CD4 T cells that contain HIV under antiretroviral therapy represent an important barrier to HIV cure1-3, but the infeasibility of isolating and characterizing these cells in their natural state has led to uncertainty about whether they possess distinctive attributes that HIV cure-directed therapies might exploit. Here we address this challenge using a microfluidic technology that isolates the transcriptomes of HIV-infected cells based solely on the detection of HIV DNA. HIV-DNA+ memory CD4 T cells in the blood from people receiving antiretroviral therapy showed inhibition of six transcriptomic pathways, including death receptor signalling, necroptosis signalling and antiproliferative Gα12/13 signalling. Moreover, two groups of genes identified by network co-expression analysis were significantly associated with HIV-DNA+ cells. These genes (n = 145) accounted for just 0.81% of the measured transcriptome and included negative regulators of HIV transcription that were higher in HIV-DNA+ cells, positive regulators of HIV transcription that were lower in HIV-DNA+ cells, and other genes involved in RNA processing, negative regulation of mRNA translation, and regulation of cell state and fate. These findings reveal that HIV-infected memory CD4 T cells under antiretroviral therapy are a distinctive population with host gene expression patterns that favour HIV silencing, cell survival and cell proliferation, with important implications for the development of HIV cure strategies.
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Affiliation(s)
- Iain C Clark
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California, San Francisco, San Francisco, CA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Bioengineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Prakriti Mudvari
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel Smith
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mohammad Abu-Laban
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mehdi Hamouda
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marc Theberge
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sakshi Shah
- Department of Bioengineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Sung Hee Ko
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Liliana Pérez
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel G Bunis
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James S Lee
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Divya Kilam
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Saami Zakaria
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sally Choi
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy R Henry
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Salwan Butrus
- Department of Chemical and Biomolecular Engineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California, San Francisco, San Francisco, CA, USA.
| | - Eli A Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Sun W, Gao C, Hartana CA, Osborn MR, Einkauf KB, Lian X, Bone B, Bonheur N, Chun TW, Rosenberg ES, Walker BD, Yu XG, Lichterfeld M. Phenotypic signatures of immune selection in HIV-1 reservoir cells. Nature 2023; 614:309-317. [PMID: 36599977 PMCID: PMC9908552 DOI: 10.1038/s41586-022-05538-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 11/08/2022] [Indexed: 01/06/2023]
Abstract
Human immunodeficiency virus 1 (HIV-1) reservoir cells persist lifelong despite antiretroviral treatment1,2 but may be vulnerable to host immune responses that could be exploited in strategies to cure HIV-1. Here we used a single-cell, next-generation sequencing approach for the direct ex vivo phenotypic profiling of individual HIV-1-infected memory CD4+ T cells from peripheral blood and lymph nodes of people living with HIV-1 and receiving antiretroviral treatment for approximately 10 years. We demonstrate that in peripheral blood, cells harbouring genome-intact proviruses and large clones of virally infected cells frequently express ensemble signatures of surface markers conferring increased resistance to immune-mediated killing by cytotoxic T and natural killer cells, paired with elevated levels of expression of immune checkpoint markers likely to limit proviral gene transcription; this phenotypic profile might reduce HIV-1 reservoir cell exposure to and killing by cellular host immune responses. Viral reservoir cells harbouring intact HIV-1 from lymph nodes exhibited a phenotypic signature primarily characterized by upregulation of surface markers promoting cell survival, including CD44, CD28, CD127 and the IL-21 receptor. Together, these results suggest compartmentalized phenotypic signatures of immune selection in HIV-1 reservoir cells, implying that only small subsets of infected cells with optimal adaptation to their anatomical immune microenvironment are able to survive during long-term antiretroviral treatment. The identification of phenotypic markers distinguishing viral reservoir cells may inform future approaches for strategies to cure and eradicate HIV-1.
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Affiliation(s)
- Weiwei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Kevin B Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin Bone
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Tae-Wook Chun
- National Institute of Allergies and Infectious Diseases, Bethesda, MD, USA
| | - Eric S Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Medical Engineering and Sciences and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
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Koofhethile CK, Rinaldi S, Rassadkina Y, Dinh VB, Gao C, Pallikkuth S, Garcia-Broncano P, de Armas LR, Pahwa R, Cotugno N, Vaz P, Lain MG, Palma P, Yu XG, Shapiro R, Pahwa S, Lichterfeld M. HIV-1 reservoir evolution in infants infected with clade C from Mozambique. Int J Infect Dis 2023; 127:129-136. [PMID: 36476348 PMCID: PMC9892347 DOI: 10.1016/j.ijid.2022.11.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The persistence of HIV-1-infected cells during antiretroviral therapy is well documented but may be modulated by early initiation of antiretroviral therapy in infants. METHODS Here, we longitudinally analyzed the proviral landscape in nine infants with vertical HIV-1 infection from Mozambique over a median period of 24 months, using single-genome, near full-length, next-generation proviral sequencing. RESULTS We observed a rapid decline in the frequency of intact proviruses, leading to a disproportional under-representation of intact HIV-1 sequences within the total number of HIV-1 DNA sequences after 12-24 months of therapy. In addition, proviral integration site profiling in one infant demonstrated clonal expansion of infected cells harboring intact proviruses and indicated that viral rebound was associated with an integration site profile dominated by intact proviruses integrated into genic and accessible chromatin locations. CONCLUSION Together, these results permit rare insight into the evolution of the HIV-1 reservoir in infants infected with HIV-1 and suggest that the rapid decline of intact proviruses, relative to defective proviruses, may be attributed to a higher vulnerability of genome-intact proviruses to antiviral immunity. Technologies to analyze combinations of intact proviral sequences and corresponding integration sites permit a high-resolution analysis of HIV-1 reservoir cells after early antiretroviral treatment initiation in infants.
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Affiliation(s)
- Catherine K Koofhethile
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA; Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | | | | | - Nicola Cotugno
- Academic Department of Pediatrics, Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Paula Vaz
- Fundação Ariel Glaser contra o SIDA Pediátrico, Maputo, Mozambique
| | | | - Paolo Palma
- Academic Department of Pediatrics, Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy; Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Roger Shapiro
- Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.
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50
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Abstract
OBJECTIVES Despite suppressive antiretroviral therapy (ART), HIV can persist in a diverse range of CD4+ T-cell subsets. Through longitudinal env sampling from people with HIV (PWH) on ART, we characterized the persistence and phenotypic properties of HIV envs over two time-points (T1 and T2). METHODS Longitudinal blood and lymphoid tissue samples were obtained from eight PWH on suppressive ART. Single genome amplification (SGA) was performed on env to understand the genetic diversity and degree of clonal expansions over time. A subset of envs were used to generate pseudovirus particles to assess sensitivity to autologous plasma IgG and broadly neutralizing antibodies (bNAbs). RESULTS Identical env sequences indicating clonal expansion persisted between T1 and T2 and within multiple T-cell subsets. At both time-points, CXCR4-tropic (X4) Envs were more prevalent in naive and central memory cells; the proportion of X4 Envs did not significantly change in each subset between T1 and T2. Autologous purified plasma IgG showed variable neutralization of Envs, with no significant difference in neutralization between R5 and X4 Envs. X4 Envs were more sensitive to neutralization with clinical bNAbs, with CD4-binding site bNAbs demonstrating high breadth and potency against Envs. CONCLUSION Our data suggest the viral reservoir in PWH on ART was predominantly maintained over time through proliferation and potentially differentiation of infected cells. We found the humoral immune response to Envs within the latent reservoir was variable between PWH. Finally, we identified coreceptor usage can influence bNAb sensitivity and may need to be considered for future bNAb immunotherapy approaches.
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