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Solis-Leal A, Boby N, Mallick S, Cheng Y, Wu F, De La Torre G, Dufour J, Alvarez X, Shivanna V, Liu Y, Fennessey CM, Lifson JD, Li Q, Keele BF, Ling B. Lymphoid tissues contribute to plasma viral clonotypes early after antiretroviral therapy interruption in SIV-infected rhesus macaques. Sci Transl Med 2023; 15:eadi9867. [PMID: 38091409 DOI: 10.1126/scitranslmed.adi9867] [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: 06/01/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023]
Abstract
The rebound-competent viral reservoir, composed of a virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after ART interruption (ATI), remains the biggest obstacle to treating HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop therapeutic strategies for reducing the rebound-competent viral reservoir. In this study, barcoded simian immunodeficiency virus (SIV), SIVmac239M, was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood and tissues from secondary lymphoid organs (spleen, mesenteric lymph nodes, and inguinal lymph nodes) and from the colon, ileum, lung, liver, and brain were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX and RNAscope in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy, although plasma viral RNA remained below 22 copies per milliliter. Among the tissues studied, mesenteric lymph nodes, inguinal lymph nodes, and spleen contained viral barcodes detected in plasma. CD4+ T cells were the main cell type harboring viral RNA after ATI. Furthermore, T cell zones in lymphoid tissues showed higher viral RNA abundance than B cell zones for most animals. These findings are consistent with lymphoid tissues contributing to the virus present in plasma early after ATI.
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Affiliation(s)
- Antonio Solis-Leal
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Nongthombam Boby
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Suvadip Mallick
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Yilun Cheng
- Nebraska Center for Virology and School of Biological Sciences, University of Nebraska-Lincoln, 1400 R St, Lincoln, NE 68588, USA
| | - Fei Wu
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Grey De La Torre
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Jason Dufour
- Tulane National Primate Research Center, 18703 Three Rivers Rd, Covington, LA 70433, USA
| | - Xavier Alvarez
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Vinay Shivanna
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
| | - Yaozhong Liu
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal St, New Orleans, LA 70112, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Qingsheng Li
- Nebraska Center for Virology and School of Biological Sciences, University of Nebraska-Lincoln, 1400 R St, Lincoln, NE 68588, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory, 8560 Progress Drive, Frederick, MD 21701, USA
| | - Binhua Ling
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, 8715 W Military Dr, San Antonio, TX 78227, USA
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Podgorski RM, Robinson JA, Smith MD, Mallick S, Zhao H, Veazey RS, Kolson DL, Bar KJ, Burdo TH. Transmitted/founder SHIV.D replicates in the brain, causes neuropathogenesis, and persists on combination antiretroviral therapy in rhesus macaques. Retrovirology 2023; 20:13. [PMID: 37563642 PMCID: PMC10413509 DOI: 10.1186/s12977-023-00628-5] [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] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
A biologically relevant non-human primate (NHP) model of HIV persistence in the central nervous system (CNS) is necessary. Most current NHP/SIV models of HIV infection fail to recapitulate viral persistence in the CNS without encephalitis or fail to employ viruses that authentically represent the ongoing HIV-1 pandemic. Here, we demonstrate viral replication in the brain and neuropathogenesis after combination antiretroviral therapy (ART) in rhesus macaques (RMs) using novel macrophage-tropic transmitted/founder (TF) simian-human immunodeficiency virus SHIV.D.191,859 (SHIV.D). Quantitative immunohistochemistry (IHC) and DNA/RNAscope in situ hybridization (ISH) were performed on three brain regions from six SHIV.D-infected RMs; two necropsied while viremic, two during analytical treatment interruptions, and two on suppressive ART. We demonstrated myeloid-mediated neuroinflammation, viral replication, and proviral DNA in the brain in all animals. These results demonstrate that TF SHIV.D models native HIV-1 CNS replication, pathogenesis, and persistence on ART in rhesus macaques.
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Affiliation(s)
- Rachel M Podgorski
- Center for NeuroVirology and Gene Editing, Department of Microbiology, Immunology, and Inflammation, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Jake A Robinson
- Center for NeuroVirology and Gene Editing, Department of Microbiology, Immunology, and Inflammation, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Mandy D Smith
- Center for NeuroVirology and Gene Editing, Department of Microbiology, Immunology, and Inflammation, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Suvadip Mallick
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Huaqing Zhao
- Center for Biostatistics and Epidemiology, Department of Biomedical Education and Data Science, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Ronald S Veazey
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Dennis L Kolson
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharine J Bar
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Tricia H Burdo
- Center for NeuroVirology and Gene Editing, Department of Microbiology, Immunology, and Inflammation, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
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Solis-Leal A, Boby N, Mallick S, Cheng Y, Wu F, De La Torre G, Dufour J, Alvarez X, Shivanna V, Liu Y, Fennessey CM, Lifson JD, Li Q, Keele BF, Ling B. Lymphoid tissues contribute to viral clonotypes present in plasma at early post-ATI in SIV-infected rhesus macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542512. [PMID: 37398418 PMCID: PMC10312542 DOI: 10.1101/2023.05.30.542512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The rebound-competent viral reservoir (RCVR), comprised of virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after antiretroviral therapy interruption (ATI), remains the biggest obstacle to the eradication of HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop targeted therapeutic strategies for reducing the RCVR. In this study, barcoded SIVmac239M was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood, lymphoid tissues (LTs, spleen, mesenteric and inguinal lymph nodes), and non-lymphoid tissues (NLTs, colon, ileum, lung, liver, and brain) were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX/RNAscope/ in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy although plasma viral RNA remained < 22 copies/mL. Among the tissues studied, mesenteric and inguinal lymph nodes, and spleen contained viral barcodes detected in plasma, and trended to have higher cell-associated viral loads, higher intact provirus levels, and greater diversity of viral barcodes. CD4+ T cells were the main cell type harboring viral RNA (vRNA) after ATI. Further, T cell zones in LTs showed higher vRNA levels than B cell zones for most animals. These findings are consistent with LTs contributing to virus present in plasma early after ATI. One Sentence Summary The reemerging of SIV clonotypes at early post-ATI are likely from the secondary lymphoid tissues.
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Li S, Moog C, Zhang T, Su B. HIV reservoir: antiviral immune responses and immune interventions for curing HIV infection. Chin Med J (Engl) 2022; 135:2667-2676. [PMID: 36719355 PMCID: PMC9943973 DOI: 10.1097/cm9.0000000000002479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Indexed: 02/01/2023] Open
Abstract
ABSTRACT Antiretroviral therapy against human immunodeficiency virus (HIV) is effective in controlling viral replication but cannot completely eliminate HIV due to the persistence of the HIV reservoir. Innate and adaptive immune responses have been proposed to contribute to preventing HIV acquisition, controlling HIV replication and eliminating HIV-infected cells. However, the immune responses naturally induced in HIV-infected individuals rarely eradicate HIV infection, which may be caused by immune escape, an inadequate magnitude and breadth of immune responses, and immune exhaustion. Optimizing these immune responses may solve the problems of epitope escape and insufficient sustained memory responses. Moreover, immune interventions aimed at improving host immune response can reduce HIV reservoirs, which have become one focus in the development of innovative strategies to eliminate HIV reservoirs. In this review, we focus on the immune response against HIV and how antiviral immune responses affect HIV reservoirs. We also discuss the development of innovative strategies aiming to eliminate HIV reservoirs and promoting functional cure of HIV infection.
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Affiliation(s)
- Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Christiane Moog
- Laboratoire d’ImmunoRhumatologie Moléculaire, Institut national de la santé et de la recherche médicale (INSERM) UMR_S 1109, Institut thématique interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg 67000, France
| | - Tong Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Sino-French Joint Laboratory for Research on Humoral Immune Response to HIV Infection, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
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Chen J, Zhou T, Zhang Y, Luo S, Chen H, Chen D, Li C, Li W. The reservoir of latent HIV. Front Cell Infect Microbiol 2022; 12:945956. [PMID: 35967854 PMCID: PMC9368196 DOI: 10.3389/fcimb.2022.945956] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
The persistence of latent reservoir of the human immunodeficiency virus (HIV) is currently the major challenge in curing HIV infection. After HIV infects the human body, the latent HIV is unable to be recognized by the body’s immune system. Currently, the widely adopted antiretroviral therapy (ART) is also unble to eliminate it, thus hindering the progress of HIV treatment. This review discusses the existence of latent HIV vault for HIV treatment, its formation and factors affecting its formation, cell, and tissue localization, methods for detection and removing latent reservoir, to provide a comprehensive understanding of latent HIV vault, in order to assist in the future research and play a potential role in achieving HIV treatment.
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Affiliation(s)
- Jing Chen
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Tong Zhou
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuan Zhang
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Shumin Luo
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Huan Chen
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Dexi Chen
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Chuanyun Li
- Beijing Youan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Chuanyun Li, ; Weihua Li,
| | - Weihua Li
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Chuanyun Li, ; Weihua Li,
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Abstract
Combination antiretroviral therapy (cART) dramatically changed the face of the HIV/AIDS pandemic, making it one of the most prominent medical breakthroughs of the past 3 decades. However, as the life span of persons living with HIV (PLWH) continues to approach that of the general population, the same cannot be said regarding their quality of life. PLWH are affected by comorbid conditions such as high blood pressure, diabetes, and neurocognitive impairment at a higher rate and increased severity than their age-matched counterparts. PLWH also have higher levels of inflammation, the drivers of which are not entirely clear. As cART treatment is lifelong, we assessed here the effects of cART, independent of HIV, on primary human monocyte-derived macrophages (MDMs). MDMs were unskewed or skewed to an alternative phenotype and treated with Atripla or Triumeq, two first-line cART treatments. We report that Triumeq skewed alternative MDMs toward an inflammatory nonsenescent phenotype. Both Atripla and Triumeq caused mitochondrial dysfunction, specifically efavirenz and abacavir. Additionally, transcriptome sequencing (RNA-seq) demonstrated that both Atripla and Triumeq caused differential regulation of genes involved in immune regulation and cell cycle and DNA repair. Collectively, our data demonstrate that cART, independent of HIV, alters the MDM phenotype. This suggests that cART may contribute to cell dysregulation in PLWH that subsequently results in increased susceptibility to comorbidities.
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Rojas M, Luz-Crawford P, Soto-Rifo R, Reyes-Cerpa S, Toro-Ascuy D. The Landscape of IFN/ISG Signaling in HIV-1-Infected Macrophages and Its Possible Role in the HIV-1 Latency. Cells 2021; 10:2378. [PMID: 34572027 PMCID: PMC8467246 DOI: 10.3390/cells10092378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 12/15/2022] Open
Abstract
A key characteristic of Human immunodeficiency virus type 1 (HIV-1) infection is the generation of latent viral reservoirs, which have been associated with chronic immune activation and sustained inflammation. Macrophages play a protagonist role in this context since they are persistently infected while being a major effector of the innate immune response through the generation of type-I interferons (type I IFN) and IFN-stimulated genes (ISGs). The balance in the IFN signaling and the ISG induction is critical to promote a successful HIV-1 infection. Classically, the IFNs response is fine-tuned by opposing promotive and suppressive signals. In this context, it was described that HIV-1-infected macrophages can also synthesize some antiviral effector ISGs and, positive and negative regulators of the IFN/ISG signaling. Recently, epitranscriptomic regulatory mechanisms were described, being the N6-methylation (m6A) modification on mRNAs one of the most relevant. The epitranscriptomic regulation can affect not only IFN/ISG signaling, but also type I IFN expression, and viral fitness through modifications to HIV-1 RNA. Thus, the establishment of replication-competent latent HIV-1 infected macrophages may be due to non-classical mechanisms of type I IFN that modulate the activation of the IFN/ISG signaling network.
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Affiliation(s)
- Masyelly Rojas
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile;
- Centro de Investigación e Innovación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile;
| | - Patricia Luz-Crawford
- Centro de Investigación e Innovación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago 7620001, Chile;
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program, Faculty of Medicine, Institute of Biomedical Sciences, Universidad of Chile, Santiago 8389100, Chile;
| | - Sebastián Reyes-Cerpa
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Daniela Toro-Ascuy
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8910060, Chile;
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