1
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Valyaeva AA, Tikhomirova MA, Potashnikova DM, Bogomazova AN, Snigiryova GP, Penin AA, Logacheva MD, Arifulin EA, Shmakova AA, Germini D, Kachalova AI, Saidova AA, Zharikova AA, Musinova YR, Mironov AA, Vassetzky YS, Sheval EV. Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients. PeerJ 2022; 10:e13986. [PMID: 36275462 PMCID: PMC9586123 DOI: 10.7717/peerj.13986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/11/2022] [Indexed: 01/19/2023] Open
Abstract
An increased frequency of B-cell lymphomas is observed in human immunodeficiency virus-1 (HIV-1)-infected patients, although HIV-1 does not infect B cells. Development of B-cell lymphomas may be potentially due to the action of the HIV-1 Tat protein, which is actively released from HIV-1-infected cells, on uninfected B cells. The exact mechanism of Tat-induced B-cell lymphomagenesis has not yet been precisely identified. Here, we ectopically expressed either Tat or its TatC22G mutant devoid of transactivation activity in the RPMI 8866 lymphoblastoid B cell line and performed a genome-wide analysis of host gene expression. Stable expression of both Tat and TatC22G led to substantial modifications of the host transcriptome, including pronounced changes in antiviral response and cell cycle pathways. We did not find any strong action of Tat on cell proliferation, but during prolonged culturing, Tat-expressing cells were displaced by non-expressing cells, indicating that Tat expression slightly inhibited cell growth. We also found an increased frequency of chromosome aberrations in cells expressing Tat. Thus, Tat can modify gene expression in cultured B cells, leading to subtle modifications in cellular growth and chromosome instability, which could promote lymphomagenesis over time.
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Affiliation(s)
- Anna A. Valyaeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria A. Tikhomirova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Koltzov Institute of Developmental Biology, Moscow, Russia
| | - Daria M. Potashnikova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra N. Bogomazova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | | | | | - Maria D. Logacheva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Eugene A. Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna A. Shmakova
- Koltzov Institute of Developmental Biology, Moscow, Russia,UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Diego Germini
- UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Anastasia I. Kachalova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aleena A. Saidova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - Anastasia A. Zharikova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yana R. Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Koltzov Institute of Developmental Biology, Moscow, Russia
| | - Andrey A. Mironov
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Institute for Information Transmission Problems, Moscow, Russia
| | - Yegor S. Vassetzky
- Koltzov Institute of Developmental Biology, Moscow, Russia,UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Eugene V. Sheval
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
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2
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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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3
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HIV UTR, LTR, and Epigenetic Immunity. Viruses 2022; 14:v14051084. [PMID: 35632825 PMCID: PMC9146425 DOI: 10.3390/v14051084] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/05/2022] [Accepted: 05/13/2022] [Indexed: 02/06/2023] Open
Abstract
The duel between humans and viruses is unending. In this review, we examine the HIV RNA in the form of un-translated terminal region (UTR), the viral DNA in the form of long terminal repeat (LTR), and the immunity of human DNA in a format of epigenetic regulation. We explore the ways in which the human immune responses to invading pathogenic viral nucleic acids can inhibit HIV infection, exemplified by a chromatin vaccine (cVaccine) to elicit the immunity of our genome—epigenetic immunity towards a cure.
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4
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Chen X, Jia L, Zhang X, Zhang T, Zhang Y. One arrow for two targets: potential co-treatment regimens for lymphoma and HIV. Blood Rev 2022; 55:100965. [DOI: 10.1016/j.blre.2022.100965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/08/2022] [Accepted: 04/18/2022] [Indexed: 12/27/2022]
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5
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Boulad F, Maggio A, Wang X, Moi P, Acuto S, Kogel F, Takpradit C, Prockop S, Mansilla-Soto J, Cabriolu A, Odak A, Qu J, Thummar K, Du F, Shen L, Raso S, Barone R, Di Maggio R, Pitrolo L, Giambona A, Mingoia M, Everett JK, Hokama P, Roche AM, Cantu VA, Adhikari H, Reddy S, Bouhassira E, Mohandas N, Bushman FD, Rivière I, Sadelain M. Lentiviral globin gene therapy with reduced-intensity conditioning in adults with β-thalassemia: a phase 1 trial. Nat Med 2022; 28:63-70. [PMID: 34980909 PMCID: PMC9380046 DOI: 10.1038/s41591-021-01554-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/23/2021] [Indexed: 01/05/2023]
Abstract
β-Thalassemias are inherited anemias that are caused by the absent or insufficient production of the β chain of hemoglobin. Here we report 6-8-year follow-up of four adult patients with transfusion-dependent β-thalassemia who were infused with autologous CD34+ cells transduced with the TNS9.3.55 lentiviral globin vector after reduced-intensity conditioning (RIC) in a phase 1 clinical trial ( NCT01639690) . Patients were monitored for insertional mutagenesis and the generation of a replication-competent lentivirus (safety and tolerability of the infusion product after RIC-primary endpoint) and engraftment of genetically modified autologous CD34+ cells, expression of the transduced β-globin gene and post-transplant transfusion requirements (efficacy-secondary endpoint). No unexpected safety issues occurred during conditioning and cell product infusion. Hematopoietic gene marking was very stable but low, reducing transfusion requirements in two patients, albeit not achieving transfusion independence. Our findings suggest that non-myeloablative conditioning can achieve durable stem cell engraftment but underscore a minimum CD34+ cell transduction requirement for effective therapy. Moderate clonal expansions were associated with integrations near cancer-related genes, suggestive of non-erythroid activity of globin vectors in stem/progenitor cells. These correlative findings highlight the necessity of cautiously monitoring patients harboring globin vectors.
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Affiliation(s)
- Farid Boulad
- Stem Cell Transplant and Cellular Therapy Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aurelio Maggio
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Xiuyan Wang
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paolo Moi
- Ospedale Pediatrico Microcitemie 'A.Cao', A.O. 'G.Brotzu', Cagliari, Italy
| | - Santina Acuto
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Friederike Kogel
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chayamon Takpradit
- Stem Cell Transplant and Cellular Therapy Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pediatrics, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Susan Prockop
- Stem Cell Transplant and Cellular Therapy Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge Mansilla-Soto
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Annalisa Cabriolu
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ashlesha Odak
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinrong Qu
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Keyur Thummar
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fang Du
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lingbo Shen
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simona Raso
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Rita Barone
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Rosario Di Maggio
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Lorella Pitrolo
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Antonino Giambona
- Department of Hematology and Rare Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Maura Mingoia
- Ospedale Pediatrico Microcitemie 'A.Cao', A.O. 'G.Brotzu', Cagliari, Italy
| | - John K Everett
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Pascha Hokama
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aoife M Roche
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Vito Adrian Cantu
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hriju Adhikari
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shantan Reddy
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eric Bouhassira
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - Narla Mohandas
- Laboratory of Red Cell Physiology, New York Blood Center, New York, NY, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Isabelle Rivière
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell Therapy and Cell Engineering Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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6
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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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7
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Mellors JW, Guo S, Naqvi A, Brandt LD, Su L, Sun Z, Joseph KW, Demirov D, Halvas EK, Butcher D, Scott B, Hamilton A, Heil M, Karim B, Wu X, Hughes SH. Insertional activation of STAT3 and LCK by HIV-1 proviruses in T cell lymphomas. SCIENCE ADVANCES 2021; 7:eabi8795. [PMID: 34644108 PMCID: PMC8514100 DOI: 10.1126/sciadv.abi8795] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Retroviruses cause cancers in animals by integrating in or near oncogenes. Although HIV-1 infection increases the risk of cancer, most of the risk is associated with immunodeficiency and coinfection by oncogenic virus (Epstein-Barr virus, Kaposi sarcoma herpesvirus, and human papillomavirus). HIV-1 proviruses integrated in some oncogenes cause clonal expansion of infected T cells in vivo; however, the infected cells are not transformed, and it is generally believed that HIV-1 does not cause cancer directly. We show that HIV-1 proviruses integrated in the first introns of signal transducer and activator of transcription 3 (STAT3) and lymphocyte-specific protein tyrosine kinase (LCK) can play an important role in the development of T cell lymphomas. The development of these cancers appears to be a multistep process involving additional nonviral mutations, which could help explain why T cell lymphomas are rare in persons with HIV-1 infection.
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Affiliation(s)
- John W. Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shuang Guo
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Asma Naqvi
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leah D. Brandt
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ling Su
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Zhonghe Sun
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kevin W. Joseph
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dimiter Demirov
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elias K. Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Donna Butcher
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Beth Scott
- Roche Molecular Diagnostics, Pleasanton, CA, USA
| | | | | | - Baktiar Karim
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, MD, USA
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8
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Yeh YHJ, Yang K, Razmi A, Ho YC. The Clonal Expansion Dynamics of the HIV-1 Reservoir: Mechanisms of Integration Site-Dependent Proliferation and HIV-1 Persistence. Viruses 2021; 13:1858. [PMID: 34578439 PMCID: PMC8473165 DOI: 10.3390/v13091858] [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: 08/25/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
More than 50% of the HIV-1 latent reservoir is maintained by clonal expansion. The clonally expanded HIV-1-infected cells can contribute to persistent nonsuppressible low-level viremia and viral rebound. HIV-1 integration site and proviral genome landscape profiling reveals the clonal expansion dynamics of HIV-1-infected cells. In individuals under long-term suppressive antiretroviral therapy (ART), HIV-1 integration sites are enriched in specific locations in certain cancer-related genes in the same orientation as the host transcription unit. Single-cell transcriptome analysis revealed that HIV-1 drives aberrant cancer-related gene expression through HIV-1-to-host RNA splicing. Furthermore, the HIV-1 promoter dominates over the host gene promoter and drives high levels of cancer-related gene expression. When HIV-1 integrates into cancer-related genes and causes gain of function of oncogenes or loss of function of tumor suppressor genes, HIV-1 insertional mutagenesis drives the proliferation of HIV-1-infected cells and may cause cancer in rare cases. HIV-1-driven aberrant cancer-related gene expression at the integration site can be suppressed by CRISPR-mediated inhibition of the HIV-1 promoter or by HIV-1 suppressing agents. Given that ART does not suppress HIV-1 promoter activity, therapeutic agents that suppress HIV-1 transcription and halt the clonal expansion of HIV-1-infected cells should be explored to block the clonal expansion of the HIV-1 latent reservoir.
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Affiliation(s)
| | | | | | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA; (Y.-H.J.Y.); (K.Y.); (A.R.)
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9
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Wright IA, Bale MJ, Shao W, Hu WS, Coffin JM, Van Zyl GU, Kearney MF. HIVIntact: a python-based tool for HIV-1 genome intactness inference. Retrovirology 2021; 18:16. [PMID: 34176496 PMCID: PMC8237426 DOI: 10.1186/s12977-021-00561-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
The characterisation of the HIV-1 reservoir, which consists of replication-competent integrated proviruses that persist on antiretroviral therapy (ART), is made difficult by the rarity of intact proviruses relative to those that are defective. While the only conclusive test for the replication-competence of HIV-1 proviruses is carried out in cell culture, genetic characterization of genomes by near full-length (NFL) PCR and sequencing can be used to determine whether particular proviruses have insertions, deletions, or substitutions that render them defective. Proviruses that are not excluded by having such defects can be classified as genetically intact and, possibly, replication competent. Identifying and quantifying proviruses that are potentially replication-competent is important for the development of strategies towards a functional cure. However, to date, there are no programs that can be incorporated into deep-sequencing pipelines for the automated characterization and annotation of HIV genomes. Existing programs that perform this work require manual intervention, cannot be widely installed, and do not have easily adjustable settings. Here, we present HIVIntact, a python-based software tool that characterises genomic defects in NFL HIV-1 sequences, allowing putative intact genomes to be identified in-silico. Unlike other applications that assess the genetic intactness of HIV genomes, this tool can be incorporated into existing sequence-analysis pipelines and applied to large next-generation sequencing datasets. ![]()
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Affiliation(s)
- Imogen A Wright
- Division of Medical Virology, University of Stellenbosch, Tygerberg Hospital, Cape Town, South Africa.
| | - Michael J Bale
- HIV Dynamics and Replication Program, CCR, NCI-Frederick, Frederick, MD, USA.,Weill Cornell Medical College, NY, New York, USA
| | - Wei Shao
- Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Wei-Shau Hu
- HIV Dynamics and Replication Program, CCR, NCI-Frederick, Frederick, MD, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA
| | - Gert U Van Zyl
- Division of Medical Virology, University of Stellenbosch, Tygerberg Hospital, Cape Town, South Africa
| | - Mary F Kearney
- HIV Dynamics and Replication Program, CCR, NCI-Frederick, Frederick, MD, USA
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10
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Abstract
In vivo clonal expansion of HIV-infected T cells is an important mechanism of viral persistence. In some cases, clonal expansion is driven by HIV proviral DNA integrated into one of a handful of genes. To investigate this phenomenon in vitro, we infected primary CD4+ T cells with an HIV construct expressing GFP and, after nearly 2 mo of culture and multiple rounds of activation, analyzed the resulting integration site distribution. In each of three replicates from each of two donors, we detected large clusters of integration sites with multiple breakpoints, implying clonal selection. These clusters all mapped to a narrow region within the STAT3 gene. The presence of hybrid transcripts splicing HIV to STAT3 sequences supports a model of LTR-driven STAT3 overexpression as a driver of preferential growth. Thus, HIV integration patterns linked to selective T cell outgrowth can be reproduced in cell culture. The single report of an HIV provirus in a case of AIDS-associated B-cell lymphoma with an HIV provirus in the same part of STAT3 also has implications for HIV-induced malignancy.
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11
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Cascione L, Aresu L, Baudis M, Bertoni F. DNA Copy Number Changes in Diffuse Large B Cell Lymphomas. Front Oncol 2020; 10:584095. [PMID: 33344238 PMCID: PMC7740002 DOI: 10.3389/fonc.2020.584095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022] Open
Abstract
Copy number aberrations (CNV/CNA) represent a major contribution to the somatic mutation landscapes in cancers, and their identification can lead to the discovery of oncogenetic targets as well as improved disease (sub-) classification. Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma in Western Countries and up to 40% of the affected individuals still succumb to the disease. DLBCL is an heterogenous group of disorders, and we call DLBCL today is not necessarily the same disease of a few years ago. This review focuses on types and frequencies of regional DNA CNVs in DLBCL, not otherwise specified, and in two particular conditions, the transformation from indolent lymphomas and the DLBCL in individuals with immunodeficiency.
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Affiliation(s)
- Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Luca Aresu
- Department of Veterinary Science, University of Turin, Grugliasco, Italy
| | - Michael Baudis
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Molecular Life Science, University of Zurich, Zurich, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland.,Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
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12
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Virgilio MC, Collins KL. The Impact of Cellular Proliferation on the HIV-1 Reservoir. Viruses 2020; 12:v12020127. [PMID: 31973022 PMCID: PMC7077244 DOI: 10.3390/v12020127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/25/2022] Open
Abstract
Human immunodeficiency virus (HIV) is a chronic infection that destroys the immune system in infected individuals. Although antiretroviral therapy is effective at preventing infection of new cells, it is not curative. The inability to clear infection is due to the presence of a rare, but long-lasting latent cellular reservoir. These cells harboring silent integrated proviral genomes have the potential to become activated at any moment, making therapy necessary for life. Latently-infected cells can also proliferate and expand the viral reservoir through several methods including homeostatic proliferation and differentiation. The chromosomal location of HIV proviruses within cells influences the survival and proliferative potential of host cells. Proliferating, latently-infected cells can harbor proviruses that are both replication-competent and defective. Replication-competent proviral genomes contribute to viral rebound in an infected individual. The majority of available techniques can only assess the integration site or the proviral genome, but not both, preventing reliable evaluation of HIV reservoirs.
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Affiliation(s)
- Maria C. Virgilio
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kathleen L. Collins
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence:
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Mullins JI, Frenkel LM. Clonal Expansion of Human Immunodeficiency Virus-Infected Cells and Human Immunodeficiency Virus Persistence During Antiretroviral Therapy. J Infect Dis 2017; 215:S119-S127. [PMID: 28520966 DOI: 10.1093/infdis/jiw636] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The latent HIV-1 reservoir in blood decays very slowly, even during prolonged suppression of viral replication by antiretroviral therapy (ART). Mechanisms for reservoir persistence include replenishment through low-level viral replication, longevity and homeostatic proliferation of memory T cells, and most recently appreciated, clonal expansion of HIV-infected cells. Clonally expanded cells make up a large and increasing fraction of the residual infected cell population on ART, and insertion of HIV proviruses into certain host cellular genes has been associated with this proliferation. That the vast majority of proviruses are defective clouds our assessment of the degree to which clonally expanded cells harbor infectious viruses, and thus the extent to which they contribute to reservoirs relevant to curing infection. This review summarizes past studies that have defined our current understanding and the gaps in our knowledge of the mechanisms by which proviral integration and clonal expansion sustain the HIV reservoir.
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Affiliation(s)
- James I Mullins
- Departments of Microbiology, Medicine, Global Health and Laboratory Medicine, University of Washington, Seattle, WA, US
| | - Lisa M Frenkel
- Departments of Pediatrics, Medicine, Global Health and Laboratory Medicine, University of Washington, Seattle, WA, US.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, US
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Hou H, Wang JZ, Liu BG, Zhang T. Pin1 liberates the human immunodeficiency virus type-1 (HIV-1): Must we stop it? Gene 2015; 565:9-14. [PMID: 25913034 DOI: 10.1016/j.gene.2015.04.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 03/07/2015] [Accepted: 04/20/2015] [Indexed: 11/16/2022]
Abstract
Acquired immune deficiency syndrome (AIDS) is mainly caused by the human immunodeficiency virus type-1 (HIV-1). To our knowledge, this is the first review focusing on the vital role of Pin1 in the infection of HIV-1 and the development of AIDS. We and others have demonstrated that Pin1, the only known cis-to-trans isomerase recognizing the pThr/pSer-Pro motifs in proteins, plays striking roles in several human diseases. Interestingly, recent evidence gradually indicates that Pin1 regulates several key steps of the life cycle of HIV-1, including the uncoating of the HIV-1 core, the reverse transcription of the RNA genome of HIV-1, and the integration of the HIV-1 cDNA into human chromosomes. Whereas inhibiting Pin1 suppresses all of these key steps and attenuates the replication of HIV-1, at the same time different PIN1 gene variants are correlated with the susceptibility to HIV-1 infection. Furthermore, Pin1 potentially promotes HIV-1 infection by activating multiple oncogenes and inactivating multiple tumor suppressors, extending the life span of HIV-infected cells. These descriptions suggest Pin1 as a promising therapeutic target for the prevention of HIV-1 and highlight the possibility of blocking the development of AIDS by Pin1 inhibitors.
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Affiliation(s)
- Hai Hou
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Jing-Zhang Wang
- Affiliated Hospital, College of Medicine, Hebei University of Engineering, Handan 056002, Hebei, PR China.
| | - Bao-Guo Liu
- Affiliated Hospital, College of Medicine, Hebei University of Engineering, Handan 056002, Hebei, PR China
| | - Ting Zhang
- Affiliated Hospital, College of Medicine, Hebei University of Engineering, Handan 056002, Hebei, PR China
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Maldarelli F, Wu X, Su L, Simonetti FR, Shao W, Hill S, Spindler J, Ferris AL, Mellors JW, Kearney MF, Coffin JM, Hughes SH. HIV latency. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science 2014; 345:179-83. [PMID: 24968937 DOI: 10.1126/science.1254194] [Citation(s) in RCA: 637] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The persistence of HIV-infected cells in individuals on suppressive combination antiretroviral therapy (cART) presents a major barrier for curing HIV infections. HIV integrates its DNA into many sites in the host genome; we identified 2410 integration sites in peripheral blood lymphocytes of five infected individuals on cART. About 40% of the integrations were in clonally expanded cells. Approximately 50% of the infected cells in one patient were from a single clone, and some clones persisted for many years. There were multiple independent integrations in several genes, including MKL2 and BACH2; many of these integrations were in clonally expanded cells. Our findings show that HIV integration sites can play a critical role in expansion and persistence of HIV-infected cells.
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Affiliation(s)
- F Maldarelli
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - X Wu
- Leidos Biomedical Research, Frederick, MD 21702, USA
| | - L Su
- Leidos Biomedical Research, Frederick, MD 21702, USA
| | - F R Simonetti
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA. Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, 20122 Milan, Italy
| | - W Shao
- Leidos Biomedical Research, Frederick, MD 21702, USA
| | - S Hill
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - J Spindler
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - A L Ferris
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - J W Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - M F Kearney
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - J M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
| | - S H Hughes
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA.
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Tedeschi R, Bortolin MT, Bidoli E, Zanussi S, Pratesi C, Vaccher E, Tirelli U, De Paoli P. Assessment of immunovirological features in HIV related non-Hodgkin lymphoma patients and their impact on outcome. J Clin Virol 2012; 53:297-301. [PMID: 22244256 DOI: 10.1016/j.jcv.2011.12.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 12/13/2011] [Accepted: 12/19/2011] [Indexed: 12/25/2022]
Abstract
BACKGROUND Despite the era of highly active antiretroviral therapy, non-Hodgkin lymphoma (NHL) remains one of the main causes of death in HIV-infected patients, with a wide variation on the outcome. OBJECTIVES We investigated immunological status and EBV, HHV8, HIV viral load in a group of HIV-infected patients at diagnosis of NHL to evaluate their prognostic significance. STUDY DESIGN Eighty-one consecutive HIV+ NHL patients were studied. CD4 and CD8 cell counts, HHV8 DNA, EBV DNA, HIV RNA and HIV DNA were assessed at diagnosis and at 3 months after chemotherapy initiation. Hazard ratios (HRs) and corresponding 95% confidence intervals (CIs) of disease free survival (DFS) and overall survival (OS) were computed according to CD4 and CD8 cell counts, EBV DNA, HIV RNA and HIV DNA. HRs were, thereafter, computed also for continuous variation of CD4, CD8 cell counts and EBV DNA. RESULTS In the multivariate analysis, CD4<160 and CD8<590 cell/μl and EBV DNA≥300 c/ml were independently associated to DFS (HR=2.98; 95%CI: 1.26-7.03; HR=2.65, 95%CI: 1.13-6.19; HR=4.01; 95%CI: 1.81-8.91) and OS (HR=3.32; 95%CI: 1.41-7.83; HR=4.62, 95%CI: 1.91-11.19; HR=3.11, 95%CI: 1.42-6.80). HRs for DFS and OS decreased continuously with increasing CD4 and CD8 cell counts, while they increased continuously with increasing EBV DNA levels. CONCLUSIONS The association with survival of low CD4 and CD8 cell counts and detectable EBV viremia, measured at lymphoma's diagnosis, identified three independent prognostic biomarkers that might help in the management of NHL HIV+ patients, offering complementary information in the ascertainment of their outcome.
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Affiliation(s)
- Rosamaria Tedeschi
- Microbiology-Immunology and Virology Unit, Centro di Riferimento Oncologico, IRCCS, via F. Gallini 2, 33081 Aviano, Italy.
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Bortolin MT, Zanussi S, Talamini R, Simonelli C, Pratesi C, Tedeschi R, Abbruzzese L, Manuele R, Rupolo M, Tirelli U, De Paoli P. Predictive value of HIV type 1 DNA levels on overall survival in HIV-related lymphoma Patients treated with high-dose chemotherapy (HDC) plus autologous stem cell transplantation (ASCT). AIDS Res Hum Retroviruses 2010; 26:245-51. [PMID: 20156109 DOI: 10.1089/aid.2009.0081] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The kinetics and predictive value of HIV-1 DNA (HIV DNA) levels in relapsed or refractory HIV lymphoma patients, treated with high-dose chemotherapy (HDC) followed by autologous stem cell transplantation (ASCT), were investigated. HIV DNA was measured by real-time PCR in the peripheral blood mononuclear cells (PBMCs) of 22 patients observed for a median follow-up of 31.0 months. At baseline, HIV DNA was found to be correlated with HIV-1 RNA (HIV RNA) (r = 0.56), but not with CD4(+) counts (r = -0.10). HIV RNA load was under control for the entire follow-up, while HIV DNA levels were almost always detectable (baseline levels vs. 1 year from ASCT levels, p > 0.05). Baseline HIV DNA levels were significantly different between alive and deceased patients (p = 0.03), and the overall survival (OS) analysis showed that for patients with higher HIV DNA levels at baseline there was a higher and nearly significant risk of death if compared to patients with lower levels (HR, 8.33, 95% CI, 0.99-70.06, p = 0.05). Our study demonstrated that high HIV DNA levels at baseline could predict overall survival after ASCT in one of the largest cohorts of HIV lymphoma patients treated with salvage therapy.
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Affiliation(s)
- Maria Teresa Bortolin
- Microbiology, Immunology and Virology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Stefania Zanussi
- Microbiology, Immunology and Virology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Renato Talamini
- Epidemiology and Biostatistics Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Cecilia Simonelli
- Division of Medical Oncology A, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Chiara Pratesi
- Microbiology, Immunology and Virology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Rosamaria Tedeschi
- Microbiology, Immunology and Virology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Luciano Abbruzzese
- Blood Bank and Department of Clinical Pathology and Immunohaematology, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Rosa Manuele
- Division of Medical Oncology A, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Maurizio Rupolo
- Division of Medical Oncology A, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Umberto Tirelli
- Division of Medical Oncology A, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Paolo De Paoli
- Microbiology, Immunology and Virology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
- Scientific Directorate, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
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