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Wang L, Yukselten Y, Nuwagaba J, Sutton RE. JAK/STAT signaling pathway affects CCR5 expression in human CD4 + T cells. SCIENCE ADVANCES 2024; 10:eadl0368. [PMID: 38507500 PMCID: PMC10954213 DOI: 10.1126/sciadv.adl0368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
CCR5 serves as R5-tropic HIV co-receptor. Knocking out CCR5 in HIV patients, which has occurred <10 times, is believed important for cure. JAK/STAT inhibitors tofacitinib and ruxolitinib inhibit CCR5 expression in HIV+ viremic patients. We investigated the association of JAK/STAT signaling pathway with CCR5/CCR2 expression in human primary CD4+ T cells and confirmed its importance. Six of nine JAK/STAT inhibitors that reduced CCR5/CCR2 expression were identified. Inhibitor-treated CD4+ T cells were relatively resistant, specifically to R5-tropic HIV infection. Furthermore, single JAK2, STAT3, STAT5A, and STAT5B knockout and different combinations of JAK/STAT knockout significantly reduced CCR2/CCR5 expression of both RNA and protein levels, indicating that CCR5/CCR2 expression was positively regulated by JAK-STAT pathway in CD4+ T cells. Serum and glucocorticoid-regulated kinase 1 (SGK1) knockout affected CCR2/CCR5 gene expression, suggesting that SGK1 is involved in CCR2/CCR5 regulation. If cell surface CCR5 levels can be specifically and markedly down-regulated without adverse effects, that may have a major impact on the HIV cure agenda.
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Affiliation(s)
- Lingyun Wang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Yunus Yukselten
- Section of Infectious Diseases, Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Julius Nuwagaba
- Section of Infectious Diseases, Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Richard E. Sutton
- Section of Infectious Diseases, Department of Internal Medicine, Yale University, New Haven, CT, USA
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2
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Park JE, Kim TS, Zeng Y, Mikolaj M, Il Ahn J, Alam MS, Monnie CM, Shi V, Zhou M, Chun TW, Maldarelli F, Narayan K, Ahn J, Ashwell JD, Strebel K, Lee KS. Centrosome amplification and aneuploidy driven by the HIV-1-induced Vpr•VprBP•Plk4 complex in CD4 + T cells. Nat Commun 2024; 15:2017. [PMID: 38443376 PMCID: PMC10914751 DOI: 10.1038/s41467-024-46306-8] [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: 05/09/2023] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
HIV-1 infection elevates the risk of developing various cancers, including T-cell lymphoma. Whether HIV-1-encoded proteins directly contribute to oncogenesis remains unknown. We observe that approximately 1-5% of CD4+ T cells from the blood of people living with HIV-1 exhibit over-duplicated centrioles, suggesting that centrosome amplification underlies the development of HIV-1-associated cancers by driving aneuploidy. Through affinity purification, biochemical, and cellular analyses, we discover that Vpr, an accessory protein of HIV-1, hijacks the centriole duplication machinery and induces centrosome amplification and aneuploidy. Mechanistically, Vpr forms a cooperative ternary complex with an E3 ligase subunit, VprBP, and polo-like kinase 4 (Plk4). Unexpectedly, however, the complex enhances Plk4's functionality by promoting its relocalization to the procentriole assembly and induces centrosome amplification. Loss of either Vpr's C-terminal 17 residues or VprBP acidic region, the two elements required for binding to Plk4 cryptic polo-box, abrogates Vpr's capacity to induce these events. Furthermore, HIV-1 WT, but not its Vpr mutant, induces multiple centrosomes and aneuploidy in human primary CD4+ T cells. We propose that the Vpr•VprBP•Plk4 complex serves as a molecular link that connects HIV-1 infection to oncogenesis and that inhibiting the Vpr C-terminal motif may reduce the occurrence of HIV-1-associated cancers.
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Affiliation(s)
- Jung-Eun Park
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tae-Sung Kim
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yan Zeng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Melissa Mikolaj
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jong Il Ahn
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Muhammad S Alam
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christina M Monnie
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Victoria Shi
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ming Zhou
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Jonathan D Ashwell
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Klaus Strebel
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kyung S Lee
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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3
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Rausch JW, Parvez S, Pathak S, Capoferri AA, Kearney MF. HIV Expression in Infected T Cell Clones. Viruses 2024; 16:108. [PMID: 38257808 PMCID: PMC10820123 DOI: 10.3390/v16010108] [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: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
The principal barrier to an HIV-1 cure is the persistence of infected cells harboring replication-competent proviruses despite antiretroviral therapy (ART). HIV-1 transcriptional suppression, referred to as viral latency, is foremost among persistence determinants, as it allows infected cells to evade the cytopathic effects of virion production and killing by cytotoxic T lymphocytes (CTL) and other immune factors. HIV-1 persistence is also governed by cellular proliferation, an innate and essential capacity of CD4+ T cells that both sustains cell populations over time and enables a robust directed response to immunological threats. However, when HIV-1 infects CD4+ T cells, this capacity for proliferation can enable surreptitious HIV-1 propagation without the deleterious effects of viral gene expression in latently infected cells. Over time on ART, the HIV-1 reservoir is shaped by both persistence determinants, with selective forces most often favoring clonally expanded infected cell populations harboring transcriptionally quiescent proviruses. Moreover, if HIV latency is incomplete or sporadically reversed in clonal infected cell populations that are replenished faster than they are depleted, such populations could both persist indefinitely and contribute to low-level persistent viremia during ART and viremic rebound if treatment is withdrawn. In this review, select genetic, epigenetic, cellular, and immunological determinants of viral transcriptional suppression and clonal expansion of HIV-1 reservoir T cells, interdependencies among these determinants, and implications for HIV-1 persistence will be presented and discussed.
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Affiliation(s)
- Jason W. Rausch
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; (S.P.); (S.P.); (A.A.C.); (M.F.K.)
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4
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Ameya G, Birri DJ. The molecular mechanisms of virus-induced human cancers. Microb Pathog 2023; 183:106292. [PMID: 37557930 DOI: 10.1016/j.micpath.2023.106292] [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: 04/15/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 08/11/2023]
Abstract
Cancer is a serious public health problem globally. Many human cancers are induced by viruses. Understanding of the mechanisms by which oncogenic (tumorigenic) viruses induce cancer is essential in the prevention and control of cancer. This review covers comprehensive characteristics and molecular mechanisms of the main virus-attributed cancers caused by human papillomavirus, hepatitis B virus, hepatitis C virus, Epstein-Barr virus, human herpesvirus type 8, human T-cell lymphotropic virus, human polyomaviruses, Merkel cell polyomavirus, and HIV. Oncogenic viruses employ biological processes to replicate and avoid detection by host cell immune systems. Tumorigenic infectious agents activate oncogenes in a variety of ways, allowing the pathogen to block host tumour suppressor proteins, inhibit apoptosis, enhance cell proliferation, and promote invasion of host cells. Furthermore, this review assesses many pathways of viruses linked to cancer, including host cellular communication perturbation, DNA damage mechanisms, immunity, and microRNA targets that promote the beginning and progression of cancer. The current cancer prevention is primarily focused on non-communicable diseases, but infection-attributable cancer also needs attention to significantly reduce the rising cancer burden and related deaths.
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Affiliation(s)
- Gemechu Ameya
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Kotebe Metropolitan University, Addis Ababa, Ethiopia; Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dagim Jirata Birri
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia.
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5
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Botha JC, Demirov D, Gordijn C, Katusiime MG, Bale MJ, Wu X, Wells D, Hughes SH, Cotton MF, Mellors JW, Kearney MF, van Zyl GU. The largest HIV-1-infected T cell clones in children on long-term combination antiretroviral therapy contain solo LTRs. mBio 2023; 14:e0111623. [PMID: 37530525 PMCID: PMC10470503 DOI: 10.1128/mbio.01116-23] [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: 05/04/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023] Open
Abstract
Combination antiretroviral therapy (cART) suppresses viral replication but does not cure HIV infection because a reservoir of infectious (intact) HIV proviruses persists in long-lived CD4+T cells. However, a large majority (>95%) of HIV-infected cells that persist on effective cART carry defective (non-infectious) proviruses. Defective proviruses consisting of only a single LTR (solo long terminal repeat) are commonly found as endogenous retroviruses in many animal species, but the frequency of solo-LTR HIV proviruses has not been well defined. Here we show that, in five pediatric donors whose viremia was suppressed on cART for at least 5 years, the proviruses in the nine largest clones of HIV-infected cells were solo LTRs. The sizes of five of these clones were assayed longitudinally by integration site-specific quantitative PCR. Minor waxing and waning of the clones was observed, suggesting that these clones are generally stable over time. Our findings show that solo LTRs comprise a large fraction of the proviruses in infected cell clones that persist in children on long-term cART. IMPORTANCE This work highlights that severely deleted HIV-1 proviruses comprise a significant proportion of the proviral landscape and are often overlooked.
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Affiliation(s)
| | - Dimiter Demirov
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | - Mary Grace Katusiime
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Michael J. Bale
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Xiaolin Wu
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Daria Wells
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | | | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
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6
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Silver S, Schmelz M. The AIDS and Cancer Specimen Resource (ACSR): HIV malignancy specimens and data available at no cost. AIDS Res Ther 2023; 20:61. [PMID: 37641153 PMCID: PMC10464020 DOI: 10.1186/s12981-023-00558-4] [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: 07/11/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
The goal of the AIDS and Cancer Specimen Resource (ACSR) is to play a major role in the advancement of HIV/AIDS cancer-related research/treatment by providing richly annotated biospecimens and data to researchers at no cost. The ACSR acquires, stores, and equitably distributes these samples and associated clinical data to investigators conducting HIV/AIDS-related research, at no costs. Currently, it is the only biorepository of human biospecimens from people with HIV and cancer available to eligible researchers globally who are studying HIV associated malignancies.This review describes the history and organizational structure of the ACSR, its types of specimens in its inventory, and the process of requesting specimens. In addition, the review provides an overview of research that was performed over the last 5 years with its support and gives a summary of important new findings acquired by this research into the development of cancers in people with HIV, including both Aids-related and non-Aids-related malignancies.
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Affiliation(s)
- Sylvia Silver
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington, DC, USA
| | - Monika Schmelz
- Department of Pathology, University of Arizona, 1501 N. Campbell Ave, Tucson, AZ, 85724, USA.
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7
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Park JE, Kim TS, Zeng Y, Monnie CM, Alam MS, Zhou M, Mikolaj M, Maldarelli F, Narayan K, Ahn J, Ashwell JD, Strebel K, Lee KS. Centrosome amplification and aneuploidy driven by the HIV-1-induced Vpr•VprBP•Plk4 complex in CD4 + T cells. RESEARCH SQUARE 2023:rs.3.rs-2924123. [PMID: 37645926 PMCID: PMC10462243 DOI: 10.21203/rs.3.rs-2924123/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
HIV-1 infection elevates the risk of developing various cancers, including T-cell lymphoma. Whether HIV-1-encoded proteins directly contribute to oncogenesis remains unknown. We observed that approximately 1-5% of CD4+ T cells from the blood of people living with HIV-1 exhibit over-duplicated centrioles, suggesting that centrosome amplification underlies the development of HIV-1-associated cancers by driving aneuploidy. Through affinity purification, biochemical, and cell biology analyses, we discovered that Vpr, an accessory protein of HIV-1, hijacks the centriole duplication machinery and induces centrosome amplification and aneuploidy. Mechanistically, Vpr formed a cooperative ternary complex with an E3 ligase subunit, VprBP, and polo-like kinase 4 (Plk4). Unexpectedly, however, the complex enhanced Plk4's functionality by promoting its relocalization to the procentriole assembly and induced centrosome amplification. Loss of either Vpr's C-terminal 17 residues or VprBP acidic region, the two elements required for binding to Plk4 cryptic polo-box, abrogated Vpr's capacity to induce all these events. Furthermore, HIV-1 WT, but not its Vpr mutant, induced multiple centrosomes and aneuploidy in primary CD4+ T cells. We propose that the Vpr•VprBP•Plk4 complex serves as a molecular link that connects HIV-1 infection to oncogenesis and that inhibiting the Vpr C-terminal motif may reduce the occurrence of HIV-1-associated cancers.
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Affiliation(s)
- Jung-Eun Park
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- These authors contributed equally to this work
| | - Tae-Sung Kim
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- These authors contributed equally to this work
| | - Yan Zeng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christina M. Monnie
- Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, RM 1055, 3501 Fifth Ave., Pittsburgh, PA, 15260, USA
| | - Muhammad S. Alam
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ming Zhou
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702, USA
| | - Melissa Mikolaj
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jinwoo Ahn
- Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, RM 1055, 3501 Fifth Ave., Pittsburgh, PA, 15260, USA
| | - Jonathan D. Ashwell
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Klaus Strebel
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Kyung S. Lee
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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8
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Collora JA, Ho YC. Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation. Genome Res 2023; 33:891-906. [PMID: 37295842 PMCID: PMC10519397 DOI: 10.1101/gr.277698.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
Abstract
HIV-1 integration introduces ectopic transcription factor binding sites into host chromatin. We postulate that the integrated provirus serves as an ectopic enhancer that recruits additional transcription factors to the integration locus, increases chromatin accessibility, changes 3D chromatin interactions, and enhances both retroviral and host gene expression. We used four well-characterized HIV-1-infected cell line clones having unique integration sites and low to high levels of HIV-1 expression. Using single-cell DOGMA-seq, which captured the heterogeneity of HIV-1 expression and host chromatin accessibility, we found that HIV-1 transcription correlated with HIV-1 accessibility and host chromatin accessibility. HIV-1 integration increased local host chromatin accessibility within an ∼5- to 30-kb distance. CRISPRa- and CRISPRi-mediated HIV-1 promoter activation and inhibition confirmed integration site-dependent HIV-1-driven changes of host chromatin accessibility. HIV-1 did not drive chromatin confirmation changes at the genomic level (by Hi-C) or the enhancer connectome (by H3K27ac HiChIP). Using 4C-seq to interrogate HIV-1-chromatin interactions, we found that HIV-1 interacted with host chromatin ∼100-300 kb from the integration site. By identifying chromatin regions having both increased transcription factor activity (by ATAC-seq) and HIV-1-chromatin interaction (by 4C-seq), we identified enrichment of ETS, RUNT, and ZNF-family transcription factor binding that may mediate HIV-1-host chromatin interactions. Our study has found that HIV-1 promoter activity increases host chromatin accessibility, and HIV-1 interacted with host chromatin within the existing chromatin boundaries in an integration site-dependent manner.
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Affiliation(s)
- Jack A Collora
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06519, USA
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9
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Shah R, Gallardo CM, Jung YH, Clock B, Dixon JR, McFadden WM, Majumder K, Pintel DJ, Corces VG, Torbett BE, Tedbury PR, Sarafianos SG. Activation of HIV-1 proviruses increases downstream chromatin accessibility. iScience 2022; 25:105490. [PMID: 36505924 PMCID: PMC9732416 DOI: 10.1016/j.isci.2022.105490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
It is unclear how the activation of HIV-1 transcription affects chromatin structure. We interrogated chromatin organization both genome-wide and nearby HIV-1 integration sites using Hi-C and ATAC-seq. In conjunction, we analyzed the transcription of the HIV-1 genome and neighboring genes. We found that long-range chromatin contacts did not differ significantly between uninfected cells and those harboring an integrated HIV-1 genome, whether the HIV-1 genome was actively transcribed or inactive. Instead, the activation of HIV-1 transcription changes chromatin accessibility immediately downstream of the provirus, demonstrating that HIV-1 can alter local cellular chromatin structure. Finally, we examined HIV-1 and neighboring host gene transcripts with long-read sequencing and found populations of chimeric RNAs both virus-to-host and host-to-virus. Thus, multiomics profiling revealed that the activation of HIV-1 transcription led to local changes in chromatin organization and altered the expression of neighboring host genes.
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Affiliation(s)
- Raven Shah
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Christian M. Gallardo
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Yoonhee H. Jung
- Department of Biology, Emory University, Atlanta, GA 30329, USA
| | - Ben Clock
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jesse R. Dixon
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - William M. McFadden
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Kinjal Majumder
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David J. Pintel
- Department of Molecular Microbiology and Immunology, Christopher S. Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | | | - Bruce E. Torbett
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Philip R. Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
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10
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Cornetta K, Lin TY, Pellin D, Kohn DB. Meeting FDA Guidance recommendations for replication-competent virus and insertional oncogenesis testing. Mol Ther Methods Clin Dev 2022; 28:28-39. [PMID: 36588821 PMCID: PMC9791246 DOI: 10.1016/j.omtm.2022.11.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Integrating vectors are associated with alterations in cellular function related to disruption of normal gene function. This has been associated with clonal expansion of cells and, in some instances, cancer. These events have been associated with replication-defective vectors and suggest that the inadvertent exposure to a replication-competent virus arising during vector manufacture would significantly increase the risk of treatment-related adverse events. These risks have led regulatory agencies to require specific monitoring for replication-competent viruses, both prior to and after treatment of patients with gene therapy products. Monitoring the risk of cell expansion and malignancy is also required. In this review, we discuss the rational potential approaches and challenges to meeting the US FDA expectations listed in current guidance documents.
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Affiliation(s)
- Kenneth Cornetta
- Gene Therapy Testing Laboratory, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA,National Gene Vector Biorepository, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA,Corresponding author Kenneth Cornetta, MD, Department of Medical and Molecular Genetics, Indiana University School of Medicine, R3 C602, 980 West Walnut Street, Indianapolis, IN 46202, USA.
| | - Tsai-Yu Lin
- Gene Therapy Testing Laboratory, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA,National Gene Vector Biorepository, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Danilo Pellin
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Donald B. Kohn
- Departments of Microbiology, Immunology and Molecular Genetics, and Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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11
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Lurain K, Ramaswami R, Yarchoan R. The role of viruses in HIV-associated lymphomas. Semin Hematol 2022; 59:183-191. [PMID: 36805886 PMCID: PMC9971650 DOI: 10.1053/j.seminhematol.2022.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/15/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022]
Abstract
Lymphomas are among the most common cancers in people with HIV (PWH). The lymphoma subtypes and pathogenesis of lymphoma in PWH are different from the immunocompetent population. It is well-known that HIV causes severe CD4+ T cell lymphopenia in the absence of antiretroviral therapy (ART); however, the risk of developing certain subtypes of lymphoma remains elevated even in people receiving ART with preserved CD4+ T cells. HIV contributes to lymphomagenesis and causes decreased immune surveillance via T cell depletion and dysregulation, B cell dysregulation, and the potential contribution of HIV-encoded proteins. The oncogenic gammaherpesviruses, Epstein-Barr virus (EBV) and Kaposi sarcoma herpesvirus (KSHV, also known as human herpesvirus 8), are the causative agents in the majority of HIV-associated lymphomas. HIV-associated T cell depletion and dysregulation allows EBV and KSHV to proliferate in infected B cells. Specific EBV- and KSHV-encoded proteins participate in B cell activation, and proliferation leading to B cell transformation. Understanding the distinct pathogenesis of HIV-associated lymphomas affords opportunities to develop therapies that specifically target these unique aspects and improve lymphoma outcomes in PWH. Agents being studied that target the specific roles of HIV, EBV, and KSHV in lymphomagenesis include immunotherapies, targeted agents, and cellular therapies.
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Affiliation(s)
- Kathryn Lurain
- HIV & AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD.
| | - Ramya Ramaswami
- HIV & AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Robert Yarchoan
- HIV & AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
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12
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Linden N, Jones RB. Potential multi-modal effects of provirus integration on HIV-1 persistence: lessons from other viruses. Trends Immunol 2022; 43:617-629. [PMID: 35817699 PMCID: PMC9429957 DOI: 10.1016/j.it.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/29/2022]
Abstract
Despite antiretroviral therapy (ART), HIV-1 persists as proviruses integrated into the genomic DNA of CD4+ T cells. The mechanisms underlying the persistence and clonal expansion of these cells remain incompletely understood. Cases have been described in which proviral integration can alter host gene expression to drive cellular proliferation. Here, we review observations from other genome-integrating human viruses to propose additional putative modalities by which HIV-1 integration may alter cellular function to favor persistence, such as by altering susceptibility to cytotoxicity in virus-expressing cells. We propose that signals implicating such mechanisms may have been masked thus far by the preponderance of defective and/or nonreactivatable HIV-1 proviruses, but could be revealed by focusing on the integration sites of intact proviruses with expression potential.
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Affiliation(s)
- Noemi Linden
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA.
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13
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Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones. Immunity 2022; 55:1013-1031.e7. [PMID: 35320704 PMCID: PMC9203927 DOI: 10.1016/j.immuni.2022.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/19/2022] [Accepted: 03/08/2022] [Indexed: 02/02/2023]
Abstract
Understanding the drivers and markers of clonally expanding HIV-1-infected CD4+ T cells is essential for HIV-1 eradication. We used single-cell ECCITE-seq, which captures surface protein expression, cellular transcriptome, HIV-1 RNA, and TCR sequences within the same single cell to track clonal expansion dynamics in longitudinally archived samples from six HIV-1-infected individuals (during viremia and after suppressive antiretroviral therapy) and two uninfected individuals, in unstimulated conditions and after CMV and HIV-1 antigen stimulation. Despite antiretroviral therapy, persistent antigen and TNF responses shaped T cell clonal expansion. HIV-1 resided in Th1-polarized, antigen-responding T cells expressing BCL2 and SERPINB9 that may resist cell death. HIV-1 RNA+ T cell clones were larger in clone size, established during viremia, persistent after viral suppression, and enriched in GZMB+ cytotoxic effector memory Th1 cells. Targeting HIV-1-infected cytotoxic CD4+ T cells and drivers of clonal expansion provides another direction for HIV-1 eradication.
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14
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Fert A, Raymond Marchand L, Wiche Salinas TR, Ancuta P. Targeting Th17 cells in HIV-1 remission/cure interventions. Trends Immunol 2022; 43:580-594. [PMID: 35659433 DOI: 10.1016/j.it.2022.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 12/14/2022]
Abstract
Since the discovery of HIV-1, progress has been made in deciphering the viral replication cycle and mechanisms of host-pathogen interactions that has facilitated the implementation of effective antiretroviral therapies (ARTs). Major barriers to HIV-1 remission/cure include the persistence of viral reservoirs (VRs) in long-lived CD4+ T cells, residual viral transcription, and lack of mucosal immunity restoration during ART, which together fuel systemic inflammation. Recently, T helper (Th)17-polarized cells were identified as major contributors to the pool of transcriptionally/translationally competent VRs. In this review, we discuss the functional features of Th17 cells that were elucidated by fundamental immunology studies in the context of autoimmunity. We also highlight recent discoveries supporting the possibility of extrapolating this knowledge toward the identification of new putative Th17-targeted HIV-1 remission/cure strategies.
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Affiliation(s)
- Augustine Fert
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Laurence Raymond Marchand
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Tomas Raul Wiche Salinas
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Petronela Ancuta
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada; Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania; The Research Institute of the University of Bucharest, Bucharest, Romania.
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15
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Eshetu A, Ho YC. A multidimensional HIV-1 persistence model for clonal expansion and viral rebound in vitro. CELL REPORTS METHODS 2021; 1:100134. [PMID: 35475216 PMCID: PMC9017154 DOI: 10.1016/j.crmeth.2021.100134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using a replication-competent virus for prolonged in vitro culture, Matsuda et al. captured the heterogenous HIV-1 genome and integration site landscape, examined viral cytopathic effects and clonal expansion capacity, and tested drugs that can eliminate HIV-1-infected cells.
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Affiliation(s)
- Amare Eshetu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
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16
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Liu G, Sohn S, Liu N, Raj A, Schwarz UD, Schroers J. Single-Crystal Nanostructure Arrays Forming Epitaxially through Thermomechanical Nanomolding. NANO LETTERS 2021; 21:10054-10061. [PMID: 34809433 DOI: 10.1021/acs.nanolett.1c03744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
For nanostructures in advanced electronic and plasmonic systems, a single-crystal structure with controlled orientation is essential. However, the fabrication of such devices has remained challenging, as current nanofabrication methods often suffer from either polycrystalline growth or the difficulty of integrating single crystals with substrates in desired orientations and locations to create functional devices. Here we report a thermomechanical method for the controlled growth of single-crystal nanowire arrays, which enables the simultaneous synthesis, alignment, and patterning of nanowires. Within such diffusion-based thermomechanical nanomolding (TMNM), the substrate material diffuses into nanosized cavities under an applied pressure gradient at a molding temperature of ∼0.4 times the material's melting temperature. Vertically grown face-centered cubic (fcc) nanowires with the [110] direction in an epitaxial relationship with the (110) substrate are demonstrated. The ability to control the crystal structure through the substrate takes TMNM a major step further, potentially allowing all fcc and body-centered cubic (bcc) materials to be integrated as single crystals into devices.
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Affiliation(s)
- Guannan Liu
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06511, United States
| | - Sungwoo Sohn
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06511, United States
| | - Naijia Liu
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06511, United States
| | - Arindam Raj
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06511, United States
| | - Udo D Schwarz
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06511, United States
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Jan Schroers
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06511, United States
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17
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Coffin JM, Hughes SH. Clonal Expansion of Infected CD4+ T Cells in People Living with HIV. Viruses 2021; 13:v13102078. [PMID: 34696507 PMCID: PMC8537114 DOI: 10.3390/v13102078] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 01/16/2023] Open
Abstract
HIV infection is not curable with current antiretroviral therapy (ART) because a small fraction of CD4+ T cells infected prior to ART initiation persists. Understanding the nature of this latent reservoir and how it is created is essential to development of potentially curative strategies. The discovery that a large fraction of the persistently infected cells in individuals on suppressive ART are members of large clones greatly changed our view of the reservoir and how it arises. Rather than being the products of infection of resting cells, as was once thought, HIV persistence is largely or entirely a consequence of infection of cells that are either expanding or are destined to expand, primarily due to antigen-driven activation. Although most of the clones carry defective proviruses, some carry intact infectious proviruses; these clones comprise the majority of the reservoir. A large majority of both the defective and the intact infectious proviruses in clones of infected cells are transcriptionally silent; however, a small fraction expresses a few copies of unspliced HIV RNA. A much smaller fraction is responsible for production of low levels of infectious virus, which can rekindle infection when ART is stopped. Further understanding of the reservoir will be needed to clarify the mechanism(s) by which provirus expression is controlled in the clones of cells that constitute the reservoir.
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Affiliation(s)
- John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA;
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute in Frederick, Frederick, MD 21702, USA
- Correspondence:
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