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Drieux F, Lemonnier F, Gaulard P. How molecular advances may improve the diagnosis and management of PTCL patients. Front Oncol 2023; 13:1202964. [PMID: 37427095 PMCID: PMC10328093 DOI: 10.3389/fonc.2023.1202964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 05/22/2023] [Indexed: 07/11/2023] Open
Abstract
Peripheral T-cell lymphomas (PTCL) comprised more than 30 rare heterogeneous entities, representing 10 to 15% of adult non-Hodgkin lymphomas. Although their diagnosis is still mainly based on clinical, pathological, and phenotypic features, molecular studies have allowed for a better understanding of the oncogenic mechanisms involved and the refinement of many PTCL entities in the recently updated classifications. The prognosis remains poor for most entities (5-year overall survival < 30%), with current conventional therapies based on anthracyclin-based polychemotherapy regimen, despite many years of clinical trials. The recent use of new targeted therapies appears to be promising for relapsed/refractory patients, such as demethylating agents in T-follicular helper (TFH) PTCL. However further studies are needed to evaluate the proper combination of these drugs in the setting of front-line therapy. In this review, we will summarize the oncogenic events for the main PTCL entities and report the molecular targets that have led to the development of new therapies. We will also discuss the development of innovative high throughput technologies that aid the routine workflow for the histopathological diagnosis and management of PTCL patients.
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Affiliation(s)
- Fanny Drieux
- Service d’Anatomie et de Cytologie Pathologiques, INSERM U1245, Centre Henri Becquerel, Rouen, France
| | - François Lemonnier
- Unité hémopathies Lymphoïdes, Hôpitaux Universitaires Henri Mondor, Assistance Publique des Hôpitaux de Paris, Créteil, France
- Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris Est Créteil, Créteil, France
| | - Philippe Gaulard
- Institut Mondor de Recherche Biomédicale, INSERM U955, Université Paris Est Créteil, Créteil, France
- Département de Pathologie, Hôpitaux Universitaires Henri Mondor, Assistance Publique des Hôpitaux de Paris, Créteil, France
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2
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Nozuma S, Matsuura E, Tanaka M, Kodama D, Matsuzaki T, Yoshimura A, Sakiyama Y, Nakahata S, Morishita K, Enose-Akahata Y, Jacoboson S, Kubota R, Takashima H. Identification and tracking of HTLV-1-infected T cell clones in virus-associated neurologic disease. JCI Insight 2023; 8:167422. [PMID: 37036006 PMCID: PMC10132145 DOI: 10.1172/jci.insight.167422] [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: 11/22/2022] [Accepted: 02/21/2023] [Indexed: 04/11/2023] Open
Abstract
Human T lymphotropic virus type 1-assoicated (HTLV-1-associated) myelopathy/tropical spastic paraparesis (HAM/TSP) is a neuroinflammatory disease caused by the persistent proliferation of HTLV-1-infected T cells. Here, we performed a T cell receptor (TCR) repertoire analysis focused on HTLV-1-infected cells to identify and track the infected T cell clones that are preserved in patients with HAM/TSP and migrate to the CNS. TCRβ repertoire analysis revealed higher clonal expansion in HTLV-1-infected cells compared with noninfected cells from patients with HAM/TSP and asymptomatic carriers (ACs). TCR clonality in HTLV-1-infected cells was similar in patients with HAM/TSP and ACs. Longitudinal analysis showed that the TCR repertoire signature in HTLV-1-infected cells remained stable, and highly expanded infected clones were preserved within each patient with HAM/TSP over years. Expanded HTLV-1-infected clones revealed different distributions between cerebrospinal fluid (CSF) and peripheral blood and were enriched in the CSF of patients with HAM/TSP. Cluster analysis showed similarity in TCRβ sequences in HTLV-1-infected cells, suggesting that they proliferate after common antigen stimulation. Our results indicate that exploring TCR repertoires of HTLV-1-infected cells can elucidate individual clonal dynamics and identify potential pathogenic clones expanded in the CNS.
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Affiliation(s)
- Satoshi Nozuma
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Eiji Matsuura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Masakazu Tanaka
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Daisuke Kodama
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Toshio Matsuzaki
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Akiko Yoshimura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yusuke Sakiyama
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shingo Nakahata
- Division of HTLV-1/ATL Carcinogenesis and Therapeutics, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Kazuhiro Morishita
- Project for Advanced Medical Research and Development, Project Research Division, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Yoshimi Enose-Akahata
- Viral Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorder and Stroke, NIH, Bethesda, Maryland, USA
| | - Steven Jacoboson
- Viral Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorder and Stroke, NIH, Bethesda, Maryland, USA
| | - Ryuji Kubota
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Hiroshi Takashima
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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3
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Itabashi K, Miyazawa T, Uchimaru K. How Can We Prevent Mother-to-Child Transmission of HTLV-1? Int J Mol Sci 2023; 24:ijms24086961. [PMID: 37108125 PMCID: PMC10138424 DOI: 10.3390/ijms24086961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
The perception of human T-cell leukemia virus type 1 (HTlV-1) infection as a "silent disease" has recently given way to concern that its presence may be having a variety of effects. HTLV-1 is known to cause adult T-cell leukemia (ATL), an aggressive cancer of peripheral CD4 T cells; however, it is also responsible for HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Most patients develop ATL as a result of HTLV-1 mother-to-child transmission. The primary route of mother-to-child transmission is through the mother's milk. In the absence of effective drug therapy, total artificial nutrition such as exclusive formula feeding is a reliable means of preventing mother-to-child transmission after birth, except for a small percentage of prenatal infections. A recent study found that the rate of mother-to-child transmission with short-term breastfeeding (within 90 days) did not exceed that of total artificial nutrition. Because these preventive measures are in exchange for the benefits of breastfeeding, clinical applications of antiretroviral drugs and immunotherapy with vaccines and neutralizing antibodies are urgently needed.
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Affiliation(s)
- Kazuo Itabashi
- Aiseikai-Memorial Ibaraki Welfare and Medical Center, Ibaraki 3100836, Japan
| | - Tokuo Miyazawa
- Department of Pediatrics, Showa University School of Medicine, Tokyo 1428666, Japan
| | - Kaoru Uchimaru
- Department of Hematology/Oncology, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Laboratory of Tumor Cell Biology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 1088639, Japan
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4
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Zuo X, Zhou R, Yang S, Ma G. HTLV-1 persistent infection and ATLL oncogenesis. J Med Virol 2023; 95:e28424. [PMID: 36546414 DOI: 10.1002/jmv.28424] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is an oncogenic retrovirus; whereas HTLV-1 mainly persists in the infected host cell as a provirus, it also causes a malignancy called adult T-cell leukemia/lymphoma (ATLL) in about 5% of infection. HTLV-1 replication is in most cases silent in vivo and viral de novo infection rarely occurs; HTLV-1 rather relies on clonal proliferation of infected T cells for viral propagation as it multiplies the number of the provirus copies. It is mechanistically elusive how leukemic clones emerge during the course of HTLV-1 infection in vivo and eventually cause the onset of ATLL. This review summarizes our current understanding of HTLV-1 persistence and oncogenesis, with the incorporation of recent cutting-edge discoveries obtained by high-throughput sequencing.
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Affiliation(s)
- Xiaorui Zuo
- Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ruoning Zhou
- Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Sikai Yang
- Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Guangyong Ma
- Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
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5
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Pellaers E, Bhat A, Christ F, Debyser Z. Determinants of Retroviral Integration and Implications for Gene Therapeutic MLV-Based Vectors and for a Cure for HIV-1 Infection. Viruses 2022; 15:32. [PMID: 36680071 PMCID: PMC9861059 DOI: 10.3390/v15010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
To complete their replication cycle, retroviruses need to integrate a DNA copy of their RNA genome into a host chromosome. Integration site selection is not random and is driven by multiple viral and cellular host factors specific to different classes of retroviruses. Today, overwhelming evidence from cell culture, animal experiments and clinical data suggests that integration sites are important for retroviral replication, oncogenesis and/or latency. In this review, we will summarize the increasing knowledge of the mechanisms underlying the integration site selection of the gammaretrovirus MLV and the lentivirus HIV-1. We will discuss how host factors of the integration site selection of retroviruses may steer the development of safer viral vectors for gene therapy. Next, we will discuss how altering the integration site preference of HIV-1 using small molecules could lead to a cure for HIV-1 infection.
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Affiliation(s)
| | | | | | - Zeger Debyser
- Molecular Virology and Gene Therapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
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6
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Tan BJY, Sugata K, Ono M, Satou Y. HTLV-1 persistence and leukemogenesis: A game of hide-and-seek with the host immune system. Front Immunol 2022; 13:991928. [PMID: 36300109 PMCID: PMC9591123 DOI: 10.3389/fimmu.2022.991928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1), a retrovirus which mainly infects CD4+ T cells and causes adult T-cell leukemia/lymphoma (ATL), is primarily transmitted via direct cell-to-cell transmission. This feature generates a wide variety of infected clones in hosts, which are maintained via clonal proliferation, resulting in the persistence and survival of the virus. The maintenance of the pool of infected cells is achieved by sculpting the immunophenotype of infected cells and modulating host immune responses to avoid immune surveillance. Here, we review the processes undertaken by HTLV-1 to modulate and subvert host immune responses which contributes to viral persistence and development of ATL.
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Affiliation(s)
- Benjy J. Y. Tan
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- *Correspondence: Benjy J. Y. Tan, ; Yorifumi Satou,
| | - Kenji Sugata
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Masahiro Ono
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- *Correspondence: Benjy J. Y. Tan, ; Yorifumi Satou,
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7
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Carcone A, Journo C, Dutartre H. Is the HTLV-1 Retrovirus Targeted by Host Restriction Factors? Viruses 2022; 14:v14081611. [PMID: 35893677 PMCID: PMC9332716 DOI: 10.3390/v14081611] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
Human T cell leukemia virus type 1 (HTLV-1), the etiological agent of adult T cell leukemia/lymphoma (ATLL) and of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), was identified a few years before Human Immunodeficiency Virus (HIV). However, forty years later, our comprehension of HTLV-1 immune detection and the host immune responses to HTLV-1 is far more limited than for HIV. In addition to innate and adaptive immune responses that rely on specialized cells of the immune system, host cells may also express a range of antiviral factors that inhibit viral replication at different stages of the cycle, in a cell-autonomous manner. Multiple antiviral factors allowing such an intrinsic immunity have been primarily and extensively described in the context HIV infection. Here, we provide an overview of whether known HIV restriction factors might act on HTLV-1 replication. Interestingly, many of them do not exert any antiviral activity against HTLV-1, and we discuss viral replication cycle specificities that could account for these differences. Finally, we highlight future research directions that could help to identify antiviral factors specific to HTLV-1.
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8
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Machado CB, da Cunha LS, Maués JHDS, Pessoa FMCDP, de Oliveira MB, Ribeiro RM, Lopes GS, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira-Nunes CA. Role of miRNAs in Human T Cell Leukemia Virus Type 1 Induced T Cell Leukemia: A Literature Review and Bioinformatics Approach. Int J Mol Sci 2022; 23:ijms23105486. [PMID: 35628297 PMCID: PMC9141946 DOI: 10.3390/ijms23105486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
Human T cell leukemia virus type 1 (HTLV-1) was identified as the first pathogenic human retrovirus and is estimated to infect 5 to 10 million individuals worldwide. Unlike other retroviruses, there is no effective therapy to prevent the onset of the most alarming diseases caused by HTLV-1, and the more severe cases manifest as the malignant phenotype of adult T cell leukemia (ATL). MicroRNA (miRNA) dysfunction is a common feature of leukemogenesis, and it is no different in ATL cases. Therefore, we sought to analyze studies that reported deregulated miRNA expression in HTLV-1 infected cells and patients’ samples to understand how this deregulation could induce malignancy. Through in silico analysis, we identified 12 miRNAs that stood out in the prediction of targets, and we performed functional annotation of the genes linked to these 12 miRNAs that appeared to have a major biological interaction. A total of 90 genes were enriched in 14 KEGG pathways with significant values, including TP53, WNT, MAPK, TGF-β, and Ras signaling pathways. These miRNAs and gene interactions are discussed in further detail for elucidation of how they may act as probable drivers for ATL onset, and while our data provide solid starting points for comprehension of miRNAs’ roles in HTLV-1 infection, continuous effort in oncologic research is still needed to improve our understanding of HTLV-1 induced leukemia.
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Affiliation(s)
- Caio Bezerra Machado
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | | | | | - Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.B.d.O.); (A.S.K.)
| | | | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.B.d.O.); (A.S.K.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil;
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.B.d.O.); (A.S.K.)
- Department of Health Sciences, Northeast Biotechnology Network (RENORBIO), Itaperi Campus, Ceará State University, Fortaleza 60740-903, CE, Brazil
- Correspondence:
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9
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Kiik H, Ramanayake S, Miura M, Tanaka Y, Melamed A, Bangham CRM. Time-course of host cell transcription during the HTLV-1 transcriptional burst. PLoS Pathog 2022; 18:e1010387. [PMID: 35576236 PMCID: PMC9135347 DOI: 10.1371/journal.ppat.1010387] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/26/2022] [Accepted: 04/22/2022] [Indexed: 12/30/2022] Open
Abstract
The human T-cell leukemia virus type 1 (HTLV-1) transactivator protein Tax has pleiotropic functions in the host cell affecting cell-cycle regulation, DNA damage response pathways and apoptosis. These actions of Tax have been implicated in the persistence and pathogenesis of HTLV-1-infected cells. It is now known that tax expression occurs in transcriptional bursts of the proviral plus-strand, but the effects of the burst on host transcription are not fully understood. We carried out RNA sequencing of two naturally-infected T-cell clones transduced with a Tax-responsive Timer protein, which undergoes a time-dependent shift in fluorescence emission, to study transcriptional changes during successive phases of the HTLV-1 plus-strand burst. We found that the transcriptional regulation of genes involved in the NF-κB pathway, cell-cycle regulation, DNA damage response and apoptosis inhibition were immediate effects accompanying the plus-strand burst, and are limited to the duration of the burst. The results distinguish between the immediate and delayed effects of HTLV-1 reactivation on host transcription, and between clone-specific effects and those observed in both clones. The major transcriptional changes in the infected host T-cells observed here, including NF-κB, are transient, suggesting that these pathways are not persistently activated at high levels in HTLV-1-infected cells. The two clones diverged strongly in their expression of genes regulating the cell cycle. Up-regulation of senescence markers was a delayed effect of the proviral plus-strand burst and the up-regulation of some pro-apoptotic genes outlasted the burst. We found that activation of the aryl hydrocarbon receptor (AhR) pathway enhanced and prolonged the proviral burst, but did not increase the rate of reactivation. Our results also suggest that sustained plus-strand expression is detrimental to the survival of infected cells.
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Affiliation(s)
- Helen Kiik
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Saumya Ramanayake
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Michi Miura
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Yuetsu Tanaka
- Department of Infectious Disease and Immunology, Okinawa-Asia Research Center of Medical Science, Faculty of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Anat Melamed
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Charles R. M. Bangham
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
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10
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Melamed A, Fitzgerald TW, Wang Y, Ma J, Birney E, Bangham CRM. Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription. SCIENCE ADVANCES 2022; 8:eabm6210. [PMID: 35486737 PMCID: PMC9054021 DOI: 10.1126/sciadv.abm6210] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
The human retroviruses HTLV-1 (human T cell leukemia virus type 1) and HIV-1 persist in vivo as a reservoir of latently infected T cell clones. It is poorly understood what determines which clones survive in the reservoir. We compared >160,000 HTLV-1 integration sites (>40,000 HIV-1 sites) from T cells isolated ex vivo from naturally infected individuals with >230,000 HTLV-1 integration sites (>65,000 HIV-1 sites) from in vitro infection to identify genomic features that determine selective clonal survival. Three statistically independent factors together explained >40% of the observed variance in HTLV-1 clonal survival in vivo: the radial intranuclear position of the provirus, its genomic distance from the centromere, and the intensity of local host genome transcription. The radial intranuclear position of the provirus and its distance from the centromere also explained ~7% of clonal persistence of HIV-1 in vivo. Selection for the intranuclear and intrachromosomal location of the provirus and host transcription intensity favors clonal persistence of human retroviruses in vivo.
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Affiliation(s)
- Anat Melamed
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | | | - Yuchuan Wang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ewan Birney
- European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Charles R. M. Bangham
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
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11
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Miura M, Naito T, Saito M. Current Perspectives in Human T-Cell Leukemia Virus Type 1 Infection and Its Associated Diseases. Front Med (Lausanne) 2022; 9:867478. [PMID: 35463007 PMCID: PMC9024061 DOI: 10.3389/fmed.2022.867478] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/15/2022] [Indexed: 11/25/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is a replication-competent human retrovirus associated with two distinct types of diseases: a malignancy of mature CD4+ T cells called adult T-cell leukemia-lymphoma (ATL) and a chronic inflammatory central nervous system disease HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). It was the first human retrovirus ever associated with a human cancer. Although most HTLV-1-infected individuals remain asymptomatic for life, a subpopulation develops ATL or HAM/TSP. Although the factors that cause these different manifestations of HTLV-1 infection are not fully understood, accumulating evidence suggests that the complex virus-host interactions, as well as the host immune response against HTLV-1 infection, appear to regulate the development of HTLV-1-associated diseases. This review outlines and discusses the current understanding, ongoing developments, and future perspectives of HTLV-1 research.
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12
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Moles R, Sarkis S, Galli V, Omsland M, Artesi M, Bissa M, McKinnon K, Brown S, Hahaut V, Washington-Parks R, Welsh J, Venzon DJ, Gutowska A, Doster MN, Breed MW, Killoran KE, Kramer J, Jones J, Moniuszko M, Van den Broeke A, Pise-Masison CA, Franchini G. NK cells and monocytes modulate primary HTLV-1 infection. PLoS Pathog 2022; 18:e1010416. [PMID: 35377924 PMCID: PMC9022856 DOI: 10.1371/journal.ppat.1010416] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 04/21/2022] [Accepted: 03/04/2022] [Indexed: 12/21/2022] Open
Abstract
We investigated the impact of monocytes, NK cells, and CD8+ T-cells in primary HTLV-1 infection by depleting cell subsets and exposing macaques to either HTLV-1 wild type (HTLV-1WT) or to the HTLV-1p12KO mutant unable to infect replete animals due to a single point mutation in orf-I that inhibits its expression. The orf-I encoded p8/p12 proteins counteract cytotoxic NK and CD8+ T-cells and favor viral DNA persistence in monocytes. Double NK and CD8+ T-cells or CD8 depletion alone accelerated seroconversion in all animals exposed to HTLV-1WT. In contrast, HTLV-1p12KO infectivity was fully restored only when NK cells were also depleted, demonstrating a critical role of NK cells in primary infection. Monocyte/macrophage depletion resulted in accelerated seroconversion in all animals exposed to HTLV-1WT, but antibody titers to the virus were low and not sustained. Seroconversion did not occur in most animals exposed to HTLV-1p12KO.In vitro experiments in human primary monocytes or THP-1 cells comparing HTLV-1WT and HTLV-1p12KO demonstrated that orf-I expression is associated with inhibition of inflammasome activation in primary cells, with increased CD47 “don’t-eat-me” signal surface expression in virus infected cells and decreased monocyte engulfment of infected cells. Collectively, our data demonstrate a critical role for innate NK cells in primary infection and suggest a dual role of monocytes in primary infection. On one hand, orf-I expression increases the chances of viral transmission by sparing infected cells from efferocytosis, and on the other may protect the engulfed infected cells by modulating inflammasome activation. These data also suggest that, once infection is established, the stoichiometry of orf-I expression may contribute to the chronic inflammation observed in HTLV-1 infection by modulating monocyte efferocytosis. The immune cells that inhibit or favor HTLV-1 infection are still unknown and their identification is critical for understanding viral pathogenesis and for the development of an effective HTLV-1 vaccine. Neutralizing antibodies are produced in natural HTLV-1 infection, but their impact is likely hampered by the virus’s ability to be transmitted from cell to cell via the virological synapse, cellular conduits, and biofilms. By depleting specific immune cell subsets in blood, we found that NK cells play a critical role in the containment of early HTLV-1 infection. Moreover, transient depletion of monocytes/macrophages results in early, but not sustained seroconversion, suggesting that early engagement of monocytes may be necessary for long-term productive infection. The engulfment of apoptotic T-cells infected by HTLV-1 may represent a viral strategy to persist in the host since the viral proteins encoded by orf-I and orf-II affect the function of receptors and proteins involved in efferocytosis. These results suggest that effective HTLV-1 vaccines must also elicit durable innate responses able to promptly clear virus invasion of monocytes through engulfment of infected T-cells to avoid the establishment of a vicious cycle that leads to chronic inflammation.
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Affiliation(s)
- Ramona Moles
- Animal Models and Retroviral Vaccines Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Sarkis Sarkis
- Animal Models and Retroviral Vaccines Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Veronica Galli
- Animal Models and Retroviral Vaccines Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Maria Omsland
- Animal Models and Retroviral Vaccines Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Maria Artesi
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
- Unit of Animal Genomics, GIGA, Université de Liège, Liège, Belgium
| | - Massimiliano Bissa
- Animal Models and Retroviral Vaccines Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Katherine McKinnon
- Vaccine Branch Flow Cytometry Core, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sophia Brown
- Vaccine Branch Flow Cytometry Core, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Vincent Hahaut
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
- Unit of Animal Genomics, GIGA, Université de Liège, Liège, Belgium
| | - Robyn Washington-Parks
- Animal Models and Retroviral Vaccines Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Joshua Welsh
- Translational Nanobiology Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - David J. Venzon
- Biostatistics and Data Management Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Anna Gutowska
- Animal Models and Retroviral Vaccines Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Melvin N. Doster
- Animal Models and Retroviral Vaccines Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Matthew W. Breed
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Kristin E. Killoran
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Joshua Kramer
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Jennifer Jones
- Translational Nanobiology Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Marcin Moniuszko
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Anne Van den Broeke
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
- Unit of Animal Genomics, GIGA, Université de Liège, Liège, Belgium
| | - Cynthia A. Pise-Masison
- Animal Models and Retroviral Vaccines Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail:
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13
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Katsuya H, Cook LBM, Rowan AG, Melamed A, Turpin J, Ito J, Islam S, Miyazato P, Jek Yang Tan B, Matsuo M, Miyakawa T, Nakata H, Matsushita S, Taylor GP, Bangham CRM, Kimura S, Satou Y. Clonality of HIV-1- and HTLV-1-Infected Cells in Naturally Coinfected Individuals. J Infect Dis 2022; 225:317-326. [PMID: 33844021 DOI: 10.1093/infdis/jiab202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/11/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Coinfection with human immunodeficiency virus type 1 (HIV-1) and human T-cell leukemia virus type 1 (HTLV-1) diminishes the value of the CD4+ T-cell count in diagnosing AIDS, and increases the rate of HTLV-1-associated myelopathy. It remains elusive how HIV-1/HTLV-1 coinfection is related to such characteristics. We investigated the mutual effect of HIV-1/HTLV-1 coinfection on their integration sites (ISs) and clonal expansion. METHODS We extracted DNA from longitudinal peripheral blood samples from 7 HIV-1/HTLV-1 coinfected, and 12 HIV-1 and 13 HTLV-1 monoinfected individuals. Proviral loads (PVL) were quantified using real-time polymerase chain reaction (PCR). Viral ISs and clonality were quantified by ligation-mediated PCR followed by high-throughput sequencing. RESULTS PVL of both HIV-1 and HTLV-1 in coinfected individuals was significantly higher than that of the respective virus in monoinfected individuals. The degree of oligoclonality of both HIV-1- and HTLV-1-infected cells in coinfected individuals was also greater than in monoinfected subjects. ISs of HIV-1 in cases of coinfection were more frequently located in intergenic regions and transcriptionally silent regions, compared with HIV-1 monoinfected individuals. CONCLUSIONS HIV-1/HTLV-1 coinfection makes an impact on the distribution of viral ISs and clonality of virus-infected cells and thus may alter the risks of both HTLV-1- and HIV-1-associated disease.
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Affiliation(s)
- Hiroo Katsuya
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan.,Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Lucy B M Cook
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Aileen G Rowan
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Anat Melamed
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Jocelyn Turpin
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Saiful Islam
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Paola Miyazato
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Benjy Jek Yang Tan
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Misaki Matsuo
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Toshikazu Miyakawa
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto, Japan
| | - Hirotomo Nakata
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto, Japan
| | - Shuzo Matsushita
- Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Graham P Taylor
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Charles R M Bangham
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Shinya Kimura
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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14
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New Approaches to Multi-Parametric HIV-1 Genetics Using Multiple Displacement Amplification: Determining the What, How, and Where of the HIV-1 Reservoir. Viruses 2021; 13:v13122475. [PMID: 34960744 PMCID: PMC8709494 DOI: 10.3390/v13122475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022] Open
Abstract
Development of potential HIV-1 curative interventions requires accurate characterization of the proviral reservoir, defined as host-integrated viral DNA genomes that drive rebound of viremia upon halting ART (antiretroviral therapy). Evaluation of such interventions necessitates methods capable of pinpointing the rare, genetically intact, replication-competent proviruses within a background of defective proviruses. This evaluation can be achieved by identifying the distinct integration sites of intact proviruses within host genomes and monitoring the dynamics of these proviruses and host cell lineages over longitudinal sampling. Until recently, molecular genetic approaches at the single proviral level have been generally limited to one of a few metrics, such as proviral genome sequence/intactness, host-proviral integration site, or replication competency. New approaches, taking advantage of MDA (multiple displacement amplification) for WGA (whole genome amplification), have enabled multiparametric proviral characterization at the single-genome level, including proviral genome sequence, host-proviral integration site, and phenotypic characterization of the host cell lineage, such as CD4 memory subset and antigen specificity. In this review, we will examine the workflow of MDA-augmented molecular genetic approaches to study the HIV-1 reservoir, highlighting technical advantages and flexibility. We focus on a collection of recent studies in which investigators have used these approaches to comprehensively characterize intact and defective proviruses from donors on ART, investigate mechanisms of elite control, and define cell lineage identity and antigen specificity of infected CD4+ T cell clones. The highlighted studies exemplify how these approaches and their future iterations will be key in defining the targets and evaluating the impacts of HIV curative interventions.
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15
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Enose-Akahata Y, Billioux BJ, Azodi S, Dwyer J, Vellucci A, Ngouth N, Nozuma S, Massoud R, Cortese I, Ohayon J, Jacobson S. Clinical trial of raltegravir, an integrase inhibitor, in HAM/TSP. Ann Clin Transl Neurol 2021; 8:1970-1985. [PMID: 34562313 PMCID: PMC8528465 DOI: 10.1002/acn3.51437] [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: 06/19/2021] [Accepted: 07/09/2021] [Indexed: 11/24/2022] Open
Abstract
Objective Human T‐cell lymphotropic virus 1 (HTLV‐1)‐associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a chronic, progressive myelopathy. A high proviral load (PVL) is one of the main risk factors for HAM/TSP. Recently, it was shown that raltegravir could inhibit cell‐free and cell‐to‐cell transmission of HTLV‐1 in vitro. Given the substantial clinical experience in human immunodeficiency virus infection and its excellent safety profile, this agent may be an attractive therapeutic option for HAM/TSP patients. Methods Sixteen subjects with HAM/TSP received raltegravir 400 mg orally twice daily in an initial 6‐month treatment phase, followed by a 9‐month post‐treatment phase. HTLV‐1 PVLs were assessed using droplet digital PCR from the PBMCs every 3 months, and from the CSF at baseline, month 6, and month 15. We also evaluated the ability of raltegravir to regulate abnormal immune responses in HAM/TSP patients. Results While a downward trend was observed in PBMC and/or CSF PVLs of some patients, raltegravir overall did not have any impact on the PVL in this HAM/TSP patient cohort. Clinically, all patients’ neurological scores and objective measurements remained relatively stable, with some expected variability. Immunologic studies showed alterations in the immune profiles of a subset of patients including decreased CD4+CD25+ T cells and spontaneous lymphoproliferation. Interpretation Raltegravir was generally well tolerated in this HAM/TSP patient cohort. A subset of patients exhibited a mild decrease in PVL as well as variations in their immune profiles after taking raltegravir. These findings suggest that raltegravir may be a therapeutic option in select HAM/TSP patients. Clinical Trial Registration Number NCT01867320.
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Affiliation(s)
- Yoshimi Enose-Akahata
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Bridgette Jeanne Billioux
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Shila Azodi
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Jennifer Dwyer
- Neuroimmunology Clinic, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Ashley Vellucci
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Nyater Ngouth
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Satoshi Nozuma
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Raya Massoud
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Irene Cortese
- Neuroimmunology Clinic, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Joan Ohayon
- Neuroimmunology Clinic, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Steven Jacobson
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
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16
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Barski MS, Minnell JJ, Maertens GN. PP2A Phosphatase as an Emerging Viral Host Factor. Front Cell Infect Microbiol 2021; 11:725615. [PMID: 34422684 PMCID: PMC8371333 DOI: 10.3389/fcimb.2021.725615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Protein phosphatase 2A (PP2A) is one of the most ubiquitous cellular proteins and is responsible for the vast majority of Ser/Thr phosphatase activity in eukaryotes. PP2A is a heterotrimer, and its assembly, intracellular localization, enzymatic activity, and substrate specificity are subject to dynamic regulation. Each of its subunits can be targeted by viral proteins to hijack and modulate its activity and downstream signaling to the advantage of the virus. Binding to PP2A is known to be essential to the life cycle of many viruses and seems to play a particularly crucial role for oncogenic viruses, which utilize PP2A to transform infected cells through controlling the cell cycle and apoptosis. Here we summarise the latest developments in the field of PP2A viral targeting; in particular recent discoveries of PP2A hijacking through molecular mimicry of a B56-specific motif by several different viruses. We also discuss the potential as well as shortcomings for therapeutic intervention in the face of our current understanding of viral PP2A targeting.
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Affiliation(s)
| | | | - Goedele Noella Maertens
- Department of Infectious Disease, Section of Molecular Virology, St Mary’s Hospital, Imperial College London, London, United Kingdom
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17
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Rosewick N, Hahaut V, Durkin K, Artesi M, Karpe S, Wayet J, Griebel P, Arsic N, Marçais A, Hermine O, Burny A, Georges M, Van den Broeke A. An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites. Front Microbiol 2020; 11:587306. [PMID: 33193242 PMCID: PMC7606357 DOI: 10.3389/fmicb.2020.587306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
The combined application of linear amplification-mediated PCR (LAM-PCR) protocols with next-generation sequencing (NGS) has had a large impact on our understanding of retroviral pathogenesis. Previously, considerable effort has been expended to optimize NGS methods to explore the genome-wide distribution of proviral integration sites and the clonal architecture of clinically important retroviruses like human T-cell leukemia virus type-1 (HTLV-1). Once sequencing data are generated, the application of rigorous bioinformatics analysis is central to the biological interpretation of the data. To better exploit the potential information available through these methods, we developed an optimized bioinformatics pipeline to analyze NGS clonality datasets. We found that short-read aligners, specifically designed to manage NGS datasets, provide increased speed, significantly reducing processing time and decreasing the computational burden. This is achieved while also accounting for sequencing base quality. We demonstrate the utility of an additional trimming step in the workflow, which adjusts for the number of reads supporting each insertion site. In addition, we developed a recall procedure to reduce bias associated with proviral integration within low complexity regions of the genome, providing a more accurate estimation of clone abundance. Finally, we recommend the application of a “clean-and-recover” step to clonality datasets generated from large cohorts and longitudinal studies. In summary, we report an optimized bioinformatics workflow for NGS clonality analysis and describe a new set of steps to guide the computational process. We demonstrate that the application of this protocol to the analysis of HTLV-1 and bovine leukemia virus (BLV) clonality datasets improves the quality of data processing and provides a more accurate definition of the clonal landscape in infected individuals. The optimized workflow and analysis recommendations can be implemented in the majority of bioinformatics pipelines developed to analyze LAM-PCR-based NGS clonality datasets.
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Affiliation(s)
- Nicolas Rosewick
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Vincent Hahaut
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Keith Durkin
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Maria Artesi
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Snehal Karpe
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Jérôme Wayet
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Philip Griebel
- VIDO-Intervac, University of Saskatchewan, Saskatoon, SK, Canada
| | - Natasa Arsic
- VIDO-Intervac, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ambroise Marçais
- Service d'hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance publique hôpitaux de Paris, Paris, France
| | - Olivier Hermine
- Service d'hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance publique hôpitaux de Paris, Paris, France.,Institut Imagine, INSERM U1163, CNRS ERL8654, Paris, France
| | - Arsène Burny
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
| | - Anne Van den Broeke
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Unit of Animal Genomics, GIGA, Université de Liège (ULiège), Liège, Belgium
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18
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Hirons A, Khoury G, Purcell DFJ. Human T-cell lymphotropic virus type-1: a lifelong persistent infection, yet never truly silent. THE LANCET. INFECTIOUS DISEASES 2020; 21:e2-e10. [PMID: 32986997 DOI: 10.1016/s1473-3099(20)30328-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/06/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
Abstract
Human T-cell lymphotropic virus type-1 (HTLV-1) has a large global burden and in some key communities, such as Indigenous Australians living in remote areas, greater than 45% of people are infected. Despite HTLV-1 causing serious malignancy and myelopathic paraparesis, and a significant association with a range of inflammatory comorbidities and secondary infections that shorten lifespan, few biomedical interventions are available. HTLV-1 starkly contrasts with other blood-borne sexually transmitted viral infections, such as, HIV, hepatitis B virus, and hepatitis C virus, with no antiviral treatments that reduce virus-infected cells, no rapid diagnostics or biomarker assays suitable for use in remote settings, and no effective vaccine. We review how the replication strategies and molecular properties of HTLV-1 establish a long-term stealthy viral pathogenesis through a fine-tuned balance of persistence, immune cell dysfunction, and proliferation of proviral infected cells that collectively present robust barriers to treatment and prevention. An understanding of the nature of the HTLV-1 provirus and opposing actions of viral-coded negative-sense HBZ and positive-sense regulatory proteins Tax, p12 and its cleaved product p8, and p30, is needed to improve the biomedical tools for preventing transmission and improving the long-term health of people with this lifelong infection.
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Affiliation(s)
- Ashley Hirons
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Georges Khoury
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Damian F J Purcell
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.
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19
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Jiang C, Lian X, Gao C, Sun X, Einkauf KB, Chevalier JM, Chen SMY, Hua S, Rhee B, Chang K, Blackmer JE, Osborn M, Peluso MJ, Hoh R, Somsouk M, Milush J, Bertagnolli LN, Sweet SE, Varriale JA, Burbelo PD, Chun TW, Laird GM, Serrao E, Engelman AN, Carrington M, Siliciano RF, Siliciano JM, Deeks SG, Walker BD, Lichterfeld M, Yu XG. Distinct viral reservoirs in individuals with spontaneous control of HIV-1. Nature 2020; 585:261-267. [PMID: 32848246 PMCID: PMC7837306 DOI: 10.1038/s41586-020-2651-8] [Citation(s) in RCA: 222] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 07/15/2020] [Indexed: 02/01/2023]
Abstract
Sustained, drug-free control of HIV-1 replication is naturally achieved in less than 0.5% of infected individuals (here termed 'elite controllers'), despite the presence of a replication-competent viral reservoir1. Inducing such an ability to spontaneously maintain undetectable plasma viraemia is a major objective of HIV-1 cure research, but the characteristics of proviral reservoirs in elite controllers remain to be determined. Here, using next-generation sequencing of near-full-length single HIV-1 genomes and corresponding chromosomal integration sites, we show that the proviral reservoirs of elite controllers frequently consist of oligoclonal to near-monoclonal clusters of intact proviral sequences. In contrast to individuals treated with long-term antiretroviral therapy, intact proviral sequences from elite controllers were integrated at highly distinct sites in the human genome and were preferentially located in centromeric satellite DNA or in Krüppel-associated box domain-containing zinc finger genes on chromosome 19, both of which are associated with heterochromatin features. Moreover, the integration sites of intact proviral sequences from elite controllers showed an increased distance to transcriptional start sites and accessible chromatin of the host genome and were enriched in repressive chromatin marks. These data suggest that a distinct configuration of the proviral reservoir represents a structural correlate of natural viral control, and that the quality, rather than the quantity, of viral reservoirs can be an important distinguishing feature for a functional cure of HIV-1 infection. Moreover, in one elite controller, we were unable to detect intact proviral sequences despite analysing more than 1.5 billion peripheral blood mononuclear cells, which raises the possibility that a sterilizing cure of HIV-1 infection, which has previously been observed only following allogeneic haematopoietic stem cell transplantation2,3, may be feasible in rare instances.
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Affiliation(s)
- Chenyang Jiang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Kevin B Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Joshua M Chevalier
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Stephane Hua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Ben Rhee
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Kaylee Chang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew Osborn
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael J Peluso
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Ma Somsouk
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Jeffrey Milush
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Lynn N Bertagnolli
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah E Sweet
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joseph A Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter D Burbelo
- Dental Clinical Research Core, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Tae-Wook Chun
- National Institute of Allergies and Infectious Diseases, Bethesda, MD, USA
| | | | - Erik Serrao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Janet M Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Steven G Deeks
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
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20
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Mohanty S, Harhaj EW. Mechanisms of Oncogenesis by HTLV-1 Tax. Pathogens 2020; 9:E543. [PMID: 32645846 PMCID: PMC7399876 DOI: 10.3390/pathogens9070543] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 01/23/2023] Open
Abstract
The human T-cell lymphotropic virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia/lymphoma (ATLL), a neoplasm of CD4+CD25+ T cells that occurs in 2-5% of infected individuals after decades of asymptomatic latent infection. Multiple HTLV-1-encoded regulatory proteins, including Tax and HTLV-1 basic leucine zipper factor (HBZ), play key roles in viral persistence and latency. The HTLV-1 Tax oncoprotein interacts with a plethora of host cellular proteins to regulate viral gene expression and also promote the aberrant activation of signaling pathways such as NF-κB to drive clonal proliferation and survival of T cells bearing the HTLV-1 provirus. Tax undergoes various post-translational modifications such as phosphorylation and ubiquitination that regulate its function and subcellular localization. Tax shuttles in different subcellular compartments for the activation of anti-apoptotic genes and deregulates the cell cycle with the induction of DNA damage for the accumulation of genomic instability that can result in cellular immortalization and malignant transformation. However, Tax is highly immunogenic and therefore HTLV-1 has evolved numerous strategies to tightly regulate Tax expression while maintaining the pool of anti-apoptotic genes through HBZ. In this review, we summarize the key findings on the oncogenic mechanisms used by Tax that set the stage for the development of ATLL, and the strategies used by HTLV-1 to tightly regulate Tax expression for immune evasion and viral persistence.
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Affiliation(s)
| | - Edward W. Harhaj
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA;
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21
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Bhatt V, Shi K, Salamango DJ, Moeller NH, Pandey KK, Bera S, Bohl HO, Kurniawan F, Orellana K, Zhang W, Grandgenett DP, Harris RS, Sundborger-Lunna AC, Aihara H. Structural basis of host protein hijacking in human T-cell leukemia virus integration. Nat Commun 2020; 11:3121. [PMID: 32561747 PMCID: PMC7305164 DOI: 10.1038/s41467-020-16963-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022] Open
Abstract
Integration of the reverse-transcribed viral DNA into host chromosomes is a critical step in the life-cycle of retroviruses, including an oncogenic delta(δ)-retrovirus human T-cell leukemia virus type-1 (HTLV-1). Retroviral integrase forms a higher order nucleoprotein assembly (intasome) to catalyze the integration reaction, in which the roles of host factors remain poorly understood. Here, we use cryo-electron microscopy to visualize the HTLV-1 intasome at 3.7-Å resolution. The structure together with functional analyses reveal that the B56γ (B'γ) subunit of an essential host enzyme, protein phosphatase 2 A (PP2A), is repurposed as an integral component of the intasome to mediate HTLV-1 integration. Our studies reveal a key host-virus interaction underlying the replication of an important human pathogen and highlight divergent integration strategies of retroviruses.
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Affiliation(s)
- Veer Bhatt
- The Hormel Institute, University of Minnesota, 801 16th Avenue N.E., Austin, MN, 55912, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
| | - Ke Shi
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Daniel J Salamango
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Nicholas H Moeller
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Krishan K Pandey
- Department of Molecular Microbiology and Immunology, Saint Louis University, 1100 S. Grand Boulevard, St. Louis, MO, 63104, USA
| | - Sibes Bera
- Department of Molecular Microbiology and Immunology, Saint Louis University, 1100 S. Grand Boulevard, St. Louis, MO, 63104, USA
| | - Heather O Bohl
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Fredy Kurniawan
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Kayo Orellana
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
| | - Wei Zhang
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
- Characterization Facility, College of Science and Engineering, University of Minnesota, 100 Union Street S.E., Minneapolis, MN, 55455, USA
| | - Duane P Grandgenett
- Department of Molecular Microbiology and Immunology, Saint Louis University, 1100 S. Grand Boulevard, St. Louis, MO, 63104, USA
| | - Reuben S Harris
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA
- Howard Hughes Medical Institute, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA
| | - Anna C Sundborger-Lunna
- The Hormel Institute, University of Minnesota, 801 16th Avenue N.E., Austin, MN, 55912, USA.
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA.
| | - Hideki Aihara
- Masonic Cancer Center, University of Minnesota, 2231 6th Street S.E., Minneapolis, MN, 55455, USA.
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA.
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street S.E., Minneapolis, MN, 55455, USA.
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22
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Enose-Akahata Y, Jacobson S. Immunovirological markers in HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Retrovirology 2019; 16:35. [PMID: 31783764 PMCID: PMC6884770 DOI: 10.1186/s12977-019-0499-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/23/2019] [Indexed: 02/06/2023] Open
Abstract
Human T cell lymphotropic virus 1 (HTLV-1) is a human retrovirus and infects approximately 10–20 million people worldwide. While the majority of infected people are asymptomatic carriers of HTLV-1, only 4% of infected people develop HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HAM/TSP is a chronic, progressive, neurological disease which usually progresses slowly without remission, and is characterized by perivascular inflammatory infiltrates in chronic inflammatory lesions of the central nervous system (CNS), primarily affecting the spinal cord. A high HTLV-1 proviral load, high levels of antibodies against HTLV-1 antigens, and elevated concentration of proteins are detected in cerebrospinal fluid (CSF) of HAM/TSP patients. These chronically activated immune responses against HTLV-1 and infiltration of inflammatory cells including HTLV-1 infected cells into the CNS contribute to clinical disability and underlie the pathogenesis of HAM/TSP. Since the disease development of HAM/TSP mainly occurs in adults, with a mean age at onset of 40–50 years, it is important for HTLV-1-infected carriers and HAM/TSP patients to be monitored throughout the disease process. Recent advances in technologies and findings provide new insights to virological and immunological aspects in both the CNS as well as in peripheral blood. In this review, we focus on understanding the inflammatory milieu in the CNS and discuss the immunopathogenic process in HTLV-1-associated neurologic diseases.
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Affiliation(s)
- Yoshimi Enose-Akahata
- Viral Immunology Section, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, 9000 Rockville Pike, Building 10 Room 5C-103, Bethesda, MD, USA
| | - Steven Jacobson
- Viral Immunology Section, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, 9000 Rockville Pike, Building 10 Room 5C-103, Bethesda, MD, USA.
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23
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Bangham CRM, Miura M, Kulkarni A, Matsuoka M. Regulation of Latency in the Human T Cell Leukemia Virus, HTLV-1. Annu Rev Virol 2019; 6:365-385. [PMID: 31283437 DOI: 10.1146/annurev-virology-092818-015501] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human T cell leukemia virus persists in vivo in 103 to 106 clones of T lymphocytes that appear to survive for the lifetime of the host. The plus strand of the provirus is typically transcriptionally silent in freshly isolated lymphocytes, but the strong, persistently activated cytotoxic T lymphocyte (CTL) response to the viral antigens indicates that the virus is not constantly latent in vivo. There is now evidence that the plus strand is transcribed in intense intermittent bursts that are triggered by cellular stress, modulated by hypoxia and glycolysis, and inhibited by polycomb repressive complex 1 (PRC1). The minus-strand gene hbz is transcribed at a lower, more constant level but is silent in a proportion of infected cells at a given time. Viral genes in the sense and antisense strands of the provirus play different respective roles in latency and de novo infection: Expression of the plus-strand gene tax is essential for de novo infection, whereas hbz appears to facilitate survival of the infected T cell clone in vivo.
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Affiliation(s)
- Charles R M Bangham
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, United Kingdom;
| | - Michi Miura
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, United Kingdom;
| | - Anurag Kulkarni
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1PG, United Kingdom;
| | - Masao Matsuoka
- Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.,Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan;
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24
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Mota TM, Jones RB. HTLV-1 as a Model for Virus and Host Coordinated Immunoediting. Front Immunol 2019; 10:2259. [PMID: 31616431 PMCID: PMC6768981 DOI: 10.3389/fimmu.2019.02259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/06/2019] [Indexed: 12/17/2022] Open
Abstract
Immunoediting is a process that occurs in cancer, whereby the immune system acts to initially repress, and subsequently promote the outgrowth of tumor cells through the stages of elimination, equilibrium, and escape. Here we present a model for a virus that causes cancer where immunoediting is coordinated through synergistic viral- and host-mediated events. We argue that the initial viral replication process of the Human T cell leukemia virus type I (HTLV-1), which causes adult T cell leukemia/lymphoma (ATL) in ~5% of individuals after decades of latency, harmonizes with the host immune system to create a population of cells destined for malignancy. Furthermore, we explore the possibility for HIV to fit into this model of immunoediting, and propose a non-malignant escape phase for HIV-infected cells that persist beyond equilibrium.
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Affiliation(s)
- Talia M Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, United States.,Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, United States
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25
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Novel Interactions between the Human T-Cell Leukemia Virus Type 1 Antisense Protein HBZ and the SWI/SNF Chromatin Remodeling Family: Implications for Viral Life Cycle. J Virol 2019; 93:JVI.00412-19. [PMID: 31142665 DOI: 10.1128/jvi.00412-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/19/2019] [Indexed: 12/15/2022] Open
Abstract
The human T-cell leukemia virus type 1 (HTLV-1) regulatory proteins Tax and HBZ play indispensable roles in regulating viral and cellular gene expression. BRG1, the ATPase subunit of the SWI/SNF chromatin remodeling complex, has been demonstrated to be essential not only for Tax transactivation but also for viral replication. We sought to investigate the physical interaction between HBZ and BRG1 and to determine the effect of these interactions on Tax-mediated long terminal repeat (LTR) activation. We reveal that HTLV-1 cell lines and adult T-cell leukemia (ATL) cells harbor high levels of BRG1. Using glutathione S-transferase (GST) pulldown and coimmunoprecipitation assays, we have demonstrated physical interactions between BRG1 and HBZ and characterized the protein domains involved. Moreover, we have identified the PBAF signature subunits BAF200 and BAF180 as novel interaction partners of HBZ, suggesting that the PBAF complex may be required for HTLV-1 transcriptional repression by HBZ. Additionally, we found that BRG1 expression translocates HBZ into distinct nuclear foci. We show that HBZ substantially represses HTLV-1 LTR activation by Tax/BRG1. Interestingly, we found that Tax stabilizes the expression of exogenous and endogenous BRG1 and that HBZ reverses this effect. Finally, using a chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) assay, we illustrate that HBZ facilitates the downregulation of HTLV-1 transcription by deregulating the recruitment of SWI/SNF complexes to the promoter. Overall, we conclude that SWI/SNF complexes, in addition to other cellular transcription factors, are involved in HBZ-mediated suppression of HTLV-1 viral gene expression.IMPORTANCE The pathogenic potential of HTLV-1 is linked to the indispensable multifaceted functions of the viral regulatory proteins Tax and HBZ, encoded by the sense and antisense viral transcripts, respectively. The interaction between Tax and the SWI/SNF family of chromatin remodeling complexes has been associated with HTLV-1 transcriptional activation. To date, the relationship between the SWI/SNF chromatin remodeling family and HBZ, the only viral protein that is consistently expressed in infected cells and ATL cells, has not been elucidated. Here, we have characterized the biological significance of the SWI/SNF family in regard to viral transcriptional repression by HBZ. This is important because it provides a better understanding of the function and role of HBZ in downregulating viral transcription and, hence, its contribution to viral latency and persistence in vivo, a process that may ultimately lead to the development of ATL.
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26
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Nozuma S, Jacobson S. Neuroimmunology of Human T-Lymphotropic Virus Type 1-Associated Myelopathy/Tropical Spastic Paraparesis. Front Microbiol 2019; 10:885. [PMID: 31105674 PMCID: PMC6492533 DOI: 10.3389/fmicb.2019.00885] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/05/2019] [Indexed: 12/14/2022] Open
Abstract
Human T-lymphotropic virus type 1 (HTLV-1) is the etiologic agent of both adult T-cell leukemia/lymphoma and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HAM/TSP is clinically characterized by chronic progressive spastic paraparesis, urinary incontinence, and mild sensory disturbance. Given its well-characterized clinical presentation and pathophysiology, which is similar to the progressive forms of multiple sclerosis (MS), HAM/TSP is an ideal system to better understand other neuroimmunological disorders such as MS. Since the discovery of HAM/TSP, large numbers of clinical, virological, molecular, and immunological studies have been published. The host-virus interaction and host immune response play an important role for the development with HAM/TSP. HTLV-1-infected circulating T-cells invade the central nervous system (CNS) and cause an immunopathogenic response against virus and possibly components of the CNS. Neural damage and subsequent degeneration can cause severe disability in patients with HAM/TSP. Little progress has been made in the discovery of objective biomarkers for grading stages and predicting progression of disease and the development of molecular targeted therapy based on the underlying pathological mechanisms. We review the recent understanding of immunopathological mechanism of HAM/TSP and discuss the unmet need for research on this disease.
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Affiliation(s)
- Satoshi Nozuma
- Viral Immunology Section, Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Steven Jacobson
- Viral Immunology Section, Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
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27
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Einkauf KB, Lee GQ, Gao C, Sharaf R, Sun X, Hua S, Chen SM, Jiang C, Lian X, Chowdhury FZ, Rosenberg ES, Chun TW, Li JZ, Yu XG, Lichterfeld M. Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy. J Clin Invest 2019; 129:988-998. [PMID: 30688658 DOI: 10.1172/jci124291] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/04/2018] [Indexed: 12/16/2022] Open
Abstract
Chromosomal integration of genome-intact HIV-1 sequences into the host genome creates a reservoir of virally infected cells that persists throughout life, necessitating indefinite antiretroviral suppression therapy. During effective antiviral treatment, the majority of these proviruses remain transcriptionally silent, but mechanisms responsible for viral latency are insufficiently clear. Here, we used matched integration site and proviral sequencing (MIP-Seq), an experimental approach involving multiple displacement amplification of individual proviral species, followed by near-full-length HIV-1 next-generation sequencing and corresponding chromosomal integration site analysis to selectively map the chromosomal positions of intact and defective proviruses in 3 HIV-1-infected individuals undergoing long-term antiretroviral therapy. Simultaneously, chromatin accessibility and gene expression in autologous CD4+ T cells were analyzed by assays for transposase-accessible chromatin using sequencing (ATAC-Seq) and RNA-Seq. We observed that in comparison to proviruses with defective sequences, intact HIV-1 proviruses were enriched for non-genic chromosomal positions and more frequently showed an opposite orientation relative to host genes. In addition, intact HIV-1 proviruses were preferentially integrated in either relative proximity to or increased distance from active transcriptional start sites and to accessible chromatin regions. These studies strongly suggest selection of intact proviruses with features of deeper viral latency during prolonged antiretroviral therapy, and may be informative for targeting the genome-intact viral reservoir.
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Affiliation(s)
- Kevin B Einkauf
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Guinevere Q Lee
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Radwa Sharaf
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Stephane Hua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samantha My Chen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Chenyang Jiang
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Xiaodong Lian
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Eric S Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Tae-Wook Chun
- National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, Maryland, USA
| | - Jonathan Z Li
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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28
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Miura M, Miyazato P, Satou Y, Tanaka Y, Bangham CRM. Epigenetic changes around the pX region and spontaneous HTLV-1 transcription are CTCF-independent. Wellcome Open Res 2018; 3:105. [PMID: 30607369 PMCID: PMC6305241 DOI: 10.12688/wellcomeopenres.14741.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2018] [Indexed: 12/13/2022] Open
Abstract
Background: The human retrovirus HTLV-1 inserts the viral complementary DNA of 9 kb into the host genome. Both plus- and minus-strands of the provirus are transcribed, respectively from the 5′ and 3′ long terminal repeats (LTR). Plus-strand expression is rapid and intense once activated, whereas the minus-strand is transcribed at a lower, more constant level. To identify how HTLV-1 transcription is regulated, we investigated the epigenetic modifications associated with the onset of spontaneous plus-strand expression and the potential impact of the host factor CTCF. Methods: Patient-derived peripheral blood mononuclear cells (PBMCs) and in vitro HTLV-1-infected T cell clones were examined. Cells were stained for the plus-strand-encoded viral protein Tax, and sorted into Tax
+ and Tax
– populations. Chromatin immunoprecipitation and methylated DNA immunoprecipitation were performed to identify epigenetic modifications in the provirus. Bisulfite-treated DNA fragments from the HTLV-1 LTRs were sequenced. Single-molecule RNA-FISH was performed, targeting HTLV-1 transcripts, for the estimation of transcription kinetics. The CRISPR/Cas9 technique was applied to alter the CTCF-binding site in the provirus, to test the impact of CTCF on the epigenetic modifications. Results: Changes in the histone modifications H3K4me3, H3K9Ac and H3K27Ac were strongly correlated with plus-strand expression. DNA in the body of the provirus was largely methylated except for the pX and 3′ LTR regions, regardless of Tax expression. The plus-strand promoter was hypomethylated when Tax was expressed. Removal of CTCF had no discernible impact on the viral transcription or epigenetic modifications. Conclusions: The histone modifications H3K4me3, H3K9Ac and H3K27Ac are highly dynamic in the HTLV-1 provirus: they show rapid change with the onset of Tax expression, and are reversible. The HTLV-1 provirus has an intrinsic pattern of epigenetic modifications that is independent of both the provirus insertion site and the chromatin architectural protein CTCF which binds to the HTLV-1 provirus.
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Affiliation(s)
- Michi Miura
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London, W2 1PG, UK
| | - Paola Miyazato
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Yorifumi Satou
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Yuetsu Tanaka
- Department of Immunology, University of the Ryukyus, Okinawa, 903-0215, Japan
| | - Charles R M Bangham
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London, W2 1PG, UK
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29
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Shifting Retroviral Vector Integrations Away from Transcriptional Start Sites via DNA-Binding Protein Domain Insertion into Integrase. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 12:58-70. [PMID: 30534579 PMCID: PMC6278723 DOI: 10.1016/j.omtm.2018.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 11/06/2018] [Indexed: 12/13/2022]
Abstract
The unique ability of retroviruses to integrate genes into host genomes is of great value for long-term expression in gene therapy, but only when integrations occur at safe genomic sites. To reap the benefit of using retroviruses without severe detrimental effects, we developed several murine leukemia virus (MLV)-based gammaretroviral vectors with safer integration patterns by perturbing the structure of the integrase via insertion of DNA-binding zinc-finger domains (ZFDs) into an internal position of the enzyme. ZFD insertion significantly reduced the inherent, strong MLV integration preference for genomic regions near transcriptional start sites (TSSs), which are the most dangerous spots. The altered retroviral integration pattern was related to increased formation of residual primer-binding site sequences at the 3' end of proviruses. Several ZFD insertion mutants showed lower frequencies of integrations into the TSS genome regions when having the residual primer-binding site sequences in the proviruses. Our findings not only can extend the use of retroviruses in biomedical applications, but also provide a glimpse into the mechanisms underlying retroviral integration.
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Miura M, Miyazato P, Satou Y, Tanaka Y, Bangham CR. Spontaneous HTLV-1 transcription is accompanied by distinct epigenetic changes in the 5′ and 3′ long terminal repeats. Wellcome Open Res 2018; 3:105. [DOI: 10.12688/wellcomeopenres.14741.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2018] [Indexed: 11/20/2022] Open
Abstract
Background:The human retrovirus HTLV-1 inserts the viral complementary DNA of 9 kb into the host genome. Both plus- and minus-strands of the provirus are transcribed, respectively from the 5′ and 3′ long terminal repeats (LTR). Plus-strand expression is rapid and intense once activated, whereas the minus-strand is transcribed at a lower, more constant level. To identify how HTLV-1 transcription is regulated, we investigated the epigenetic modifications associated with the onset of spontaneous plus-strand expression and the potential impact of the host factor CTCF.Methods:Patient-derived peripheral blood mononuclear cells (PBMCs) and in vitro HTLV-1-infected T cell clones were examined. Cells were stained for the plus-strand-encoded viral protein Tax, and sorted into Tax+and Tax–populations. Chromatin immunoprecipitation and methylated DNA immunoprecipitation were performed to identify epigenetic modifications in the provirus. Bisulfite-treated DNA fragments from the HTLV-1 LTRs were sequenced. Single-molecule RNA-FISH was performed, targeting HTLV-1 transcripts, for the estimation of transcription kinetics. The CRISPR/Cas9 technique was applied to alter the CTCF-binding site in the provirus, to test the impact of CTCF on the epigenetic modifications.Results:Changes in the histone modifications H3K4me3, H3K9Ac and H3K27Ac were strongly correlated with plus-strand expression. DNA in the body of the provirus was largely methylated except for the pX and 3′ LTR regions, regardless of Tax expression. The plus-strand promoter was hypomethylated when Tax was expressed. Removal of CTCF had no discernible impact on the viral transcription or epigenetic modifications.Conclusions:The histone modifications H3K4me3, H3K9Ac and H3K27Ac are highly dynamic in the HTLV-1 provirus: they show rapid change with the onset of Tax expression, and are reversible. The HTLV-1 provirus has an intrinsic pattern of epigenetic modifications that is independent of both the provirus insertion site and the chromatin architectural protein CTCF which binds to the HTLV-1 provirus.
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Phillips AA, Harewood JCK. Adult T Cell Leukemia-Lymphoma (ATL): State of the Art. Curr Hematol Malig Rep 2018; 13:300-307. [DOI: 10.1007/s11899-018-0458-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Bangham CRM, Matsuoka M. Human T-cell leukaemia virus type 1: parasitism and pathogenesis. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0272. [PMID: 28893939 PMCID: PMC5597739 DOI: 10.1098/rstb.2016.0272] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2017] [Indexed: 12/15/2022] Open
Abstract
Human T-cell leukaemia virus type 1 (HTLV-1) causes not only adult T-cell leukaemia-lymphoma (ATL), but also inflammatory diseases including HTLV-1-associated myelopathy/tropical spastic paraparesis. HTLV-1 transmits primarily through cell-to-cell contact, and generates abundant infected cells in the host in order to survive and transmit to a new host. The resulting high proviral load is closely associated with the development of ATL and inflammatory diseases. To increase the number of infected cells, HTLV-1 changes the immunophenotype of infected cells, induces proliferation and inhibits apoptosis through the cooperative actions of two viral genes, tax and HTLV-1 bZIP factor (HBZ). As a result, infected cells survive, proliferate and infiltrate into the tissues, which is critical for transmission of the virus. Thus, the strategy of this virus is indivisibly linked with its pathogenesis, providing a clue for prevention and treatment of HTLV-1-induced diseases. This article is part of the themed issue ‘Human oncogenic viruses’.
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Affiliation(s)
- Charles R M Bangham
- Division of Infectious Diseases, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| | - Masao Matsuoka
- Department of Hematology, Rheumatology, and Infectious Diseases, Kumamoto University Faculty of Life Sciences, 1-1-1 Honjo, Kumamoto 860-8556, Japan .,Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
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Kulkarni A, Bangham CRM. HTLV-1: Regulating the Balance Between Proviral Latency and Reactivation. Front Microbiol 2018; 9:449. [PMID: 29615991 PMCID: PMC5867303 DOI: 10.3389/fmicb.2018.00449] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/27/2018] [Indexed: 12/26/2022] Open
Abstract
HTLV-1 plus-strand transcription begins with the production of doubly-spliced tax/rex transcripts, the levels of which are usually undetectable in freshly isolated peripheral blood mononuclear cells (PBMCs) from HTLV-1-infected individuals. However, the presence of a sustained chronically active cytotoxic T-cell response to HTLV-1 antigens in virtually all HTLV-1-infected individuals, regardless of their proviral load, argues against complete latency of the virus in vivo. There is an immediate burst of plus-strand transcription when blood from infected individuals is cultured ex vivo. How is the HTLV-1 plus strand silenced in PBMCs? Is it silenced in other anatomical compartments within the host? What reactivates the latent provirus in fresh PBMCs? While plus-strand transcription of the provirus appears to be intermittent, the minus-strand hbz transcripts are present in a majority of cells, albeit at low levels. What regulates the difference between the 5'- and 3'-LTR promoter activities and thereby the tax-hbz interplay? Finally, T lymphocytes are a migratory population of cells that encounter variable environments in different compartments of the body. Could these micro-environment changes influence the reactivation kinetics of the provirus? In this review we discuss the questions raised above, focusing on the early events leading to HTLV-1 reactivation from latency, and suggest future research directions.
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Affiliation(s)
- Anurag Kulkarni
- Section of Virology, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Charles R M Bangham
- Section of Virology, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
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Mahgoub M, Yasunaga JI, Iwami S, Nakaoka S, Koizumi Y, Shimura K, Matsuoka M. Sporadic on/off switching of HTLV-1 Tax expression is crucial to maintain the whole population of virus-induced leukemic cells. Proc Natl Acad Sci U S A 2018; 115:E1269-E1278. [PMID: 29358408 PMCID: PMC5819419 DOI: 10.1073/pnas.1715724115] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Viruses causing chronic infection artfully manipulate infected cells to enable viral persistence in vivo under the pressure of immunity. Human T-cell leukemia virus type 1 (HTLV-1) establishes persistent infection mainly in CD4+ T cells in vivo and induces leukemia in this subset. HTLV-1-encoded Tax is a critical transactivator of viral replication and a potent oncoprotein, but its significance in pathogenesis remains obscure due to its very low level of expression in vivo. Here, we show that Tax is expressed in a minor fraction of leukemic cells at any given time, and importantly, its expression spontaneously switches between on and off states. Live cell imaging revealed that the average duration of one episode of Tax expression is ∼19 hours. Knockdown of Tax rapidly induced apoptosis in most cells, indicating that Tax is critical for maintaining the population, even if its short-term expression is limited to a small subpopulation. Single-cell analysis and computational simulation suggest that transient Tax expression triggers antiapoptotic machinery, and this effect continues even after Tax expression is diminished; this activation of the antiapoptotic machinery is the critical event for maintaining the population. In addition, Tax is induced by various cytotoxic stresses and also promotes HTLV-1 replication. Thus, it seems that Tax protects infected cells from apoptosis and increases the chance of viral transmission at a critical moment. Keeping the expression of Tax minimal but inducible on demand is, therefore, a fundamental strategy of HTLV-1 to promote persistent infection and leukemogenesis.
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Affiliation(s)
- Mohamed Mahgoub
- Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Jun-Ichirou Yasunaga
- Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan;
| | - Shingo Iwami
- Mathematical Biology Laboratory, Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 819-0395, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Saitama 332-0012, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Shinji Nakaoka
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Saitama 332-0012, Japan
- Institute of Industrial Sciences, The University of Tokyo, Tokyo 153-8505, Japan
| | - Yoshiki Koizumi
- School of Medicine, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Ishikawa 920-8640, Japan
| | - Kazuya Shimura
- Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Masao Matsuoka
- Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan;
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan
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Enose-Akahata Y, Vellucci A, Jacobson S. Role of HTLV-1 Tax and HBZ in the Pathogenesis of HAM/TSP. Front Microbiol 2017; 8:2563. [PMID: 29312243 PMCID: PMC5742587 DOI: 10.3389/fmicb.2017.02563] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/11/2017] [Indexed: 01/25/2023] Open
Abstract
Human T cell lymphotropic virus type 1 (HTLV-1) infection can lead to development of adult T cell leukemia/lymphoma (ATL) or HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) in a subset of infected subjects. Understanding the interaction between host and HTLV-1 and the molecular mechanisms associated with disease pathogenesis is critical for development efficient therapies. Two HTLV-1 genes, tax and HTLV-1 basic leucine zipper factor (HBZ), have been demonstrated to play important roles in HTLV-1 infectivity and the growth and survival of leukemic cells. Increased HTLV-1 Tax expression induces the expression of various cellular genes such as IL-2 and IL-15, which directly contributes to lymphocyte activation and immunopathogenesis in HAM/TSP patients. However, little is known about the molecular and cellular mechanism of HBZ in development of HAM/TSP. It has been reported that HBZ mRNA expression was detected in HAM/TSP patients higher than in asymptomatic carriers and correlated with proviral load and disease severity. Unlike HTLV-1 tax, HBZ escapes efficient anti-viral immune responses and therefore these reactivities are difficult to detect. Thus, it is important to focus on understanding the function and the role of HTLV-1 tax and HBZ in disease development of HAM/TSP and discuss the potential use of these HTLV-1 viral gene products as biomarkers and therapeutic targets for HAM/TSP.
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Affiliation(s)
- Yoshimi Enose-Akahata
- Viral Immunology Section, Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Ashley Vellucci
- Viral Immunology Section, Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Steven Jacobson
- Viral Immunology Section, Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
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Abstract
Human T cell leukemia virus type 1 (HTLV-1), also known as human T lymphotropic virus type 1, was the first exogenous human retrovirus discovered. Unlike the distantly related lentivirus HIV-1, HTLV-1 causes disease in only 5-10% of infected people, depending on their ethnic origin. But whereas HIV-1 infection and the consequent diseases can be efficiently contained in most cases by antiretroviral drug treatment, there is no satisfactory treatment for the malignant or inflammatory diseases caused by HTLV-1. The purpose of the present article is to review recent advances in the understanding of the mechanisms by which the virus persists in vivo and causes disabling or fatal diseases.
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Affiliation(s)
- Charles R M Bangham
- Division of Infectious Diseases, Faculty of Medicine, Imperial College, London W2 1PG, United Kingdom;
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Kulkarni A, Mateus M, Thinnes CC, McCullagh JS, Schofield CJ, Taylor GP, Bangham CRM. Glucose Metabolism and Oxygen Availability Govern Reactivation of the Latent Human Retrovirus HTLV-1. Cell Chem Biol 2017; 24:1377-1387.e3. [PMID: 28965728 PMCID: PMC5696563 DOI: 10.1016/j.chembiol.2017.08.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/24/2017] [Accepted: 08/17/2017] [Indexed: 12/30/2022]
Abstract
The human retrovirus HTLV-1 causes a hematological malignancy or neuroinflammatory disease in ∼10% of infected individuals. HTLV-1 primarily infects CD4+ T lymphocytes and persists as a provirus integrated in their genome. HTLV-1 appears transcriptionally latent in freshly isolated cells; however, the chronically active anti-HTLV-1 cytotoxic T cell response observed in infected individuals indicates frequent proviral expression in vivo. The kinetics and regulation of HTLV-1 proviral expression in vivo are poorly understood. By using hypoxia, small-molecule hypoxia mimics, and inhibitors of specific metabolic pathways, we show that physiologically relevant levels of hypoxia, as routinely encountered by circulating T cells in the lymphoid organs and bone marrow, significantly enhance HTLV-1 reactivation from latency. Furthermore, culturing naturally infected CD4+ T cells in glucose-free medium or chemical inhibition of glycolysis or the mitochondrial electron transport chain strongly suppresses HTLV-1 plus-strand transcription. We conclude that glucose metabolism and oxygen tension regulate HTLV-1 proviral latency and reactivation in vivo. Physiological (1%) hypoxia enhances HTLV-1 plus-strand transcription HTLV-1 transcription is hypoxia regulated but HIF independent Inhibition of glycolysis or the mitochondrial ETC suppresses HTLV-1 transcription Extracellular glucose concentration regulates HTLV-1 reactivation from latency
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Affiliation(s)
- Anurag Kulkarni
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK
| | - Manuel Mateus
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK
| | - Cyrille C Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - James S McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - Graham P Taylor
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK
| | - Charles R M Bangham
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK.
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Cook L, Melamed A, Yaguchi H, Bangham CR. The impact of HTLV-1 on the cellular genome. Curr Opin Virol 2017; 26:125-131. [PMID: 28822906 DOI: 10.1016/j.coviro.2017.07.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/12/2017] [Accepted: 07/18/2017] [Indexed: 10/19/2022]
Abstract
Human T-lymphotropic virus type-1 (HTLV-1) is the causative agent of adult T-cell leukaemia/lymphoma (ATL), an aggressive CD4+ T-cell malignancy. The mechanisms of leukaemogenesis in ATL are incompletely understood. Insertional mutagenesis has not previously been thought to contribute to the pathogenesis of ATL. However, the recent discovery that HTLV-1 binds the key chromatin architectural protein CTCF raises the hypothesis that HTLV-1 deregulates host gene expression by causing abnormal chromatin looping, bringing the strong HTLV-1 promoter-enhancer near to host genes that lie up to 2Mb from the integrated provirus. Here we review current opinion on the mechanisms of oncogenesis in ATL, with particular emphasis on the local and distant impact of HTLV-1 on the structure and expression of the host genome.
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Affiliation(s)
- Lucy Cook
- Section of Virology, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom; National Centre for Human Retrovirology, Imperial College Healthcare NHS Trust, London, United Kingdom; Department of Haematology, Imperial College Healthcare NHS Trust, United Kingdom
| | - Anat Melamed
- Section of Virology, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom
| | - Hiroko Yaguchi
- Section of Virology, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom
| | - Charles Rm Bangham
- Section of Virology, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom.
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Zhyvoloup A, Melamed A, Anderson I, Planas D, Lee CH, Kriston-Vizi J, Ketteler R, Merritt A, Routy JP, Ancuta P, Bangham CRM, Fassati A. Digoxin reveals a functional connection between HIV-1 integration preference and T-cell activation. PLoS Pathog 2017; 13:e1006460. [PMID: 28727807 PMCID: PMC5519191 DOI: 10.1371/journal.ppat.1006460] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/08/2017] [Indexed: 12/23/2022] Open
Abstract
HIV-1 integrates more frequently into transcribed genes, however the biological significance of HIV-1 integration targeting has remained elusive. Using a selective high-throughput chemical screen, we discovered that the cardiac glycoside digoxin inhibits wild-type HIV-1 infection more potently than HIV-1 bearing a single point mutation (N74D) in the capsid protein. We confirmed that digoxin repressed viral gene expression by targeting the cellular Na+/K+ ATPase, but this did not explain its selectivity. Parallel RNAseq and integration mapping in infected cells demonstrated that digoxin inhibited expression of genes involved in T-cell activation and cell metabolism. Analysis of >400,000 unique integration sites showed that WT virus integrated more frequently than N74D mutant within or near genes susceptible to repression by digoxin and involved in T-cell activation and cell metabolism. Two main gene networks down-regulated by the drug were CD40L and CD38. Blocking CD40L by neutralizing antibodies selectively inhibited WT virus infection, phenocopying digoxin. Thus the selectivity of digoxin depends on a combination of integration targeting and repression of specific gene networks. The drug unmasked a functional connection between HIV-1 integration and T-cell activation. Our results suggest that HIV-1 evolved integration site selection to couple its early gene expression with the status of target CD4+ T-cells, which may affect latency and viral reactivation. HIV-1 integrates more frequently within transcribed host genes, however we do not understand the biological significance of this. We found that a drug called digoxin inhibits wild type HIV-1 more potently than an HIV-1 bearing a single point mutation in the capsid protein. Here we show that digoxin represses HIV-1 gene expression and in parallel inhibits CD4+ T-cell activation and metabolism. When we analysed the integration sites of wild type and mutant HIV-1, we discovered that wild type virus integrates within or near genes involved in CD4+ T-cell activation and metabolism more often than the mutant virus. Because these are the very same genes repressed by digoxin, the integration bias of wild type virus makes it more susceptible than mutant virus to silencing by the drug. Digoxin unmasked a functional link between HIV-1 integration and T-cell activation, which may affect HIV-1 latency and reactivation.
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Affiliation(s)
- Alexander Zhyvoloup
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Anat Melamed
- Department of Medicine, Imperial College, St. Mary's Campus, London, United Kingdom
| | - Ian Anderson
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Delphine Planas
- Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, University of Montreal and the Research Centre of the CHUM, Montreal, Québec, Canada
| | - Chen-Hsuin Lee
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Janos Kriston-Vizi
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Robin Ketteler
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Andy Merritt
- Centre for Therapeutics Discovery, MRC Technology, Mill Hill, London, United Kingdom
| | - Jean-Pierre Routy
- McGill University Health Centre, Glen site, Montreal, Québec, Canada
| | - Petronela Ancuta
- Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, University of Montreal and the Research Centre of the CHUM, Montreal, Québec, Canada
| | | | - Ariberto Fassati
- Division of Infection & Immunity, University College London, London, United Kingdom
- * E-mail:
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Farmanbar A, Firouzi S, Makałowski W, Iwanaga M, Uchimaru K, Utsunomiya A, Watanabe T, Nakai K. Inferring clonal structure in HTLV-1-infected individuals: towards bridging the gap between analysis and visualization. Hum Genomics 2017; 11:15. [PMID: 28697807 PMCID: PMC5505134 DOI: 10.1186/s40246-017-0112-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 07/05/2017] [Indexed: 12/12/2022] Open
Abstract
Background Human T cell leukemia virus type 1 (HTLV-1) causes adult T cell leukemia (ATL) in a proportion of infected individuals after a long latency period. Development of ATL is a multistep clonal process that can be investigated by monitoring the clonal expansion of HTLV-1-infected cells by isolation of provirus integration sites. The clonal composition (size, number, and combinations of clones) during the latency period in a given infected individual has not been clearly elucidated. Methods We used high-throughput sequencing technology coupled with a tag system for isolating integration sites and measuring clone sizes from 60 clinical samples. We assessed the role of clonality and clone size dynamics in ATL onset by modeling data from high-throughput monitoring of HTLV-1 integration sites using single- and multiple-time-point samples. Results From four size categories analyzed, we found that big clones (B; 513–2048 infected cells) and very big clones (VB; >2048 infected cells) had prognostic value. No sample harbored two or more VB clones or three or more B clones. We examined the role of clone size, clone combination, and the number of integration sites in the prognosis of infected individuals. We found a moderate reverse correlation between the total number of clones and the size of the largest clone. We devised a data-driven model that allows intuitive representation of clonal composition. Conclusions This integration site-based clonality tree model represents the complexity of clonality and provides a global view of clonality data that facilitates the analysis, interpretation, understanding, and visualization of the behavior of clones on inter- and intra-individual scales. It is fully data-driven, intuitively depicts the clonality patterns of HTLV-1-infected individuals and can assist in early risk assessment of ATL onset by reflecting the prognosis of infected individuals. This model should assist in assimilating information on clonal composition and understanding clonal expansion in HTLV-1-infected individuals. Electronic supplementary material The online version of this article (doi:10.1186/s40246-017-0112-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amir Farmanbar
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan.,Laboratory of Functional Analysis in silico, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Sanaz Firouzi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan.
| | - Wojciech Makałowski
- Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Muenster, Germany
| | - Masako Iwanaga
- Department of Frontier Life Science, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kaoru Uchimaru
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan
| | - Atae Utsunomiya
- Department of Hematology, Imamura General Hospital, Kagoshima, Japan
| | - Toshiki Watanabe
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan.,Department of Advanced Medical Innovation, St. Marianna University Graduate School of Medicine, Kanagawa, Japan
| | - Kenta Nakai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan. .,Laboratory of Functional Analysis in silico, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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Clonality of HTLV-1-infected T cells as a risk indicator for development and progression of adult T-cell leukemia. Blood Adv 2017; 1:1195-1205. [PMID: 29296760 DOI: 10.1182/bloodadvances.2017005900] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022] Open
Abstract
Adult T-cell leukemia (ATL) is an aggressive T-cell malignancy caused by human T-cell leukemia virus type 1 (HTLV-1) that develops along a carcinogenic process involving 5 or more genetic events in infected cells. The lifetime incidence of ATL among HTLV-1-infected individuals is approximately 5%. Although epidemiologic studies have revealed risk factors for ATL, the molecular mechanisms that determine the fates of carriers remain unclear. A better understanding of clonal composition and related longitudinal dynamics would clarify the process of ATL leukemogenesis and provide insights into the mechanisms underlying the proliferation of a malignant clone. Genomic DNA samples and clinical information were obtained from individuals enrolled in the Joint Study for Predisposing Factors for ATL Development, a Japanese prospective cohort study. Forty-seven longitudinal samples from 20 individuals (9 asymptomatic carriers and 11 patients with ATL at enrollment) were subjected to a clonality analysis. A method based on next-generation sequencing was used to characterize clones on the basis of integration sites. Relationships were analyzed among clonal patterns, clone sizes, and clinical status, including ATL onset and progression. Among carriers, those exhibiting an oligoclonal or monoclonal pattern with largely expanded clones subsequently progressed to ATL. All indolent patients who progressed to acute-type ATL exhibited monoclonal expansion. In both situations, the major expanded clone after progression was derived from the largest pre-existing clone. This study has provided the first detailed information regarding the dynamics of HTLV-1-infected T-cell clones and collectively suggests that the clonality of HTLV-1-infected cells could be a useful predictive marker of ATL onset and progression.
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Rosewick N, Durkin K, Artesi M, Marçais A, Hahaut V, Griebel P, Arsic N, Avettand-Fenoel V, Burny A, Charlier C, Hermine O, Georges M, Van den Broeke A. Cis-perturbation of cancer drivers by the HTLV-1/BLV proviruses is an early determinant of leukemogenesis. Nat Commun 2017; 8:15264. [PMID: 28534499 PMCID: PMC5457497 DOI: 10.1038/ncomms15264] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 03/14/2017] [Indexed: 12/12/2022] Open
Abstract
Human T-cell leukaemia virus type-1 (HTLV-1) and bovine leukaemia virus (BLV) infect T- and B-lymphocytes, respectively, provoking a polyclonal expansion that will evolve into an aggressive monoclonal leukaemia in ∼5% of individuals following a protracted latency period. It is generally assumed that early oncogenic changes are largely dependent on virus-encoded products, especially TAX and HBZ, while progression to acute leukaemia/lymphoma involves somatic mutations, yet that both are independent of proviral integration site that has been found to be very variable between tumours. Here, we show that HTLV-1/BLV proviruses are integrated near cancer drivers which they affect either by provirus-dependent transcription termination or as a result of viral antisense RNA-dependent cis-perturbation. The same pattern is observed at polyclonal non-malignant stages, indicating that provirus-dependent host gene perturbation contributes to the initial selection of the multiple clones characterizing the asymptomatic stage, requiring additional alterations in the clone that will evolve into full-blown leukaemia/lymphoma. Human T-cell leukaemia virus type-1 and bovine leukaemia virus infect T and B lymphocytes and lead to aggressive leukaemia. Here, the authors show these proviruses integrate near cancer drivers perturbing transcription termination or antisense RNA-dependent interaction, suggesting post-transcriptional mechanisms in some cases.
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Affiliation(s)
- Nicolas Rosewick
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Keith Durkin
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Maria Artesi
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Ambroise Marçais
- Service d'hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance publique hôpitaux de Paris, 149-161 rue de Sèvres, Paris 75010, France
| | - Vincent Hahaut
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Philip Griebel
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Canada S7N 5E3
| | - Natasa Arsic
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Canada S7N 5E3
| | - Véronique Avettand-Fenoel
- Laboratoire de Virologie, AP-HP, Hôpital Necker-Enfants Malades, Université Paris Descartes, Sorbonne Paris Cité, EA7327, 149 rue de Sèvres, Paris 75010, France
| | - Arsène Burny
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, Brussels 1000, Belgium
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Olivier Hermine
- Service d'hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance publique hôpitaux de Paris, 149-161 rue de Sèvres, Paris 75010, France.,INSERM U1163-ERL8254, Institut Imagine, 24 B Boulevard du Montparnasse, Paris 75010, France
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Anne Van den Broeke
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium.,Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, Brussels 1000, Belgium
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43
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RNA stability regulates human T cell leukemia virus type 1 gene expression in chronically-infected CD4 T cells. Virology 2017; 508:7-17. [PMID: 28478312 DOI: 10.1016/j.virol.2017.04.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 11/22/2022]
Abstract
Regulation of expression of HTLV-1 gene products from integrated proviruses plays an important role in HTLV-1-associated disease pathogenesis. Previous studies have shown that T cell receptor (TCR)- and phorbol ester (PMA) stimulation of chronically infected CD4 T cells increases the expression of integrated HTLV-1 proviruses in latently infected cells, however the mechanism remains unknown. Analysis of HTLV-1 RNA and protein species following PMA treatment of the latently HTLV-1-infected, FS and SP T cell lines demonstrated rapid induction of tax/rex mRNA. This rapid increase in tax/rex mRNA was associated with markedly enhanced tax/rex mRNA stability while the stability of unspliced or singly spliced HTLV-1 RNAs did not increase. Tax/rex mRNA in the HTLV-1 constitutively expressing cell lines exhibited high basal stability even without PMA treatment. Our data support a model whereby T cell activation leads to increased HTLV-1 gene expression at least in part through increased tax/rex mRNA stability.
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Araya N, Sato T, Coler-Reilly A, Yagishita N, Yamano Y. Developing novel treatments for HTLV-1-associated myelopathy (HAM) by investigating molecular pathomechanisms. ACTA ACUST UNITED AC 2017; 39:207-12. [PMID: 27320936 DOI: 10.2177/jsci.39.207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A small percentage of those infected with human T-lymphotropic virus type 1 (HTLV-1) develop HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), a debilitating neurodegenerative disease. This disease impacts essential bodily functions, and since currently available treatments are considered to be poorly effective, there is a dire need to develop a truly effective treatment to suppress disease progression. Recently, the authors and others have determined that HTLV-1 in HAM/TSP patients primarily infects T cells expressing the chemokine receptor CCR4. The authors postulated that HTLV-1 causes these T cells to develop Th1-like functions that are critical for the pathogenesis of HAM/TSP. They described an inflammatory positive feedback loop in which cross-talk between these abnormal Th1-like cells and astrocytes produce and maintain spinal cord lesions in HAM/TSP patients. When an anti-CCR4 antibody was tested against cells from HAM/TSP patients, the antibody instigated the destruction of the CCR4-positive cells, reducing the number of infected cells and the amount of inflammatory activity. Thus, the anti-CCR4 antibody is expected to become a fundamentally new treatment for HAM/TSP that directly targets infected cells. The treatment is currently being tested in clinical trials.
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Affiliation(s)
- Natsumi Araya
- Department of Advanced Medical Innovation, Institute of Medical Science, St. Marianna University School of Medicine
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Watanabe T. Adult T-cell leukemia: molecular basis for clonal expansion and transformation of HTLV-1-infected T cells. Blood 2017; 129:1071-1081. [PMID: 28115366 PMCID: PMC5374731 DOI: 10.1182/blood-2016-09-692574] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/21/2016] [Indexed: 02/07/2023] Open
Abstract
Adult T-cell leukemia (ATL) is an aggressive T-cell malignancy caused by human T-cell leukemia virus type 1 (HTLV-1) that develops through a multistep carcinogenesis process involving 5 or more genetic events. We provide a comprehensive overview of recently uncovered information on the molecular basis of leukemogenesis in ATL. Broadly, the landscape of genetic abnormalities in ATL that include alterations highly enriched in genes for T-cell receptor-NF-κB signaling such as PLCG1, PRKCB, and CARD11 and gain-of function mutations in CCR4 and CCR7 Conversely, the epigenetic landscape of ATL can be summarized as polycomb repressive complex 2 hyperactivation with genome-wide H3K27 me3 accumulation as the basis of the unique transcriptome of ATL cells. Expression of H3K27 methyltransferase enhancer of zeste 2 was shown to be induced by HTLV-1 Tax and NF-κB. Furthermore, provirus integration site analysis with high-throughput sequencing enabled the analysis of clonal composition and cell number of each clone in vivo, whereas multicolor flow cytometric analysis with CD7 and cell adhesion molecule 1 enabled the identification of HTLV-1-infected CD4+ T cells in vivo. Sorted immortalized but untransformed cells displayed epigenetic changes closely overlapping those observed in terminally transformed ATL cells, suggesting that epigenetic abnormalities are likely earlier events in leukemogenesis. These new findings broaden the scope of conceptualization of the molecular mechanisms of leukemogenesis, dissecting them into immortalization and clonal progression. These recent findings also open a new direction of drug development for ATL prevention and treatment because epigenetic marks can be reprogrammed. Mechanisms underlying initial immortalization and progressive accumulation of these abnormalities remain to be elucidated.
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Affiliation(s)
- Toshiki Watanabe
- Department of Advanced Medical Innovation, St. Marianna University Graduate School of Medicine, Kanagawa, Japan; and Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
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Chan CP, Kok KH, Jin DY. Human T-Cell Leukemia Virus Type 1 Infection and Adult T-Cell Leukemia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1018:147-166. [PMID: 29052136 DOI: 10.1007/978-981-10-5765-6_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is the first retrovirus discovered to cause adult T-cell leukemia (ATL), a highly aggressive blood cancer. HTLV-1 research in the past 35 years has been most revealing in the mechanisms of viral oncogenesis. HTLV-1 establishes a lifelong persistent infection in CD4+ T lymphocytes. The infection outcome is governed by host immunity. ATL develops in 2-5% of infected individuals 30-50 years after initial exposure. HTLV-1 encodes two oncoproteins Tax and HBZ, which are required for initiation of cellular transformation and maintenance of cell proliferation, respectively. HTLV-1 oncogenesis is driven by a clonal selection and expansion process during which both host and viral factors cooperate to impair genome stability, immune surveillance, and other mechanisms of tumor suppression. A better understanding of HTLV-1 biology and leukemogenesis will reveal new strategies and modalities for ATL prevention and treatment.
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Affiliation(s)
- Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong
| | - Kin-Hang Kok
- Department of Microbiology, The University of Hong Kong, 145 Pokfulam Road, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong.
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Gillet NA, Melamed A, Bangham CRM. High-Throughput Mapping and Clonal Quantification of Retroviral Integration Sites. Methods Mol Biol 2017; 1582:127-141. [PMID: 28357667 DOI: 10.1007/978-1-4939-6872-5_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We describe here a method to identify the position of retroviral insertion sites and simultaneously to quantify the absolute abundance of each clone, i.e., the number of cells having the provirus inserted at a given place in the host genome. The method is based on random shearing of the host cell DNA, followed by a linker-mediated PCR to amplify the genomic regions flanking the proviruses, and high-throughput sequencing of the amplicons. The quantification of the abundance of each infected clone allowed us to develop two new metrics: i. the oligoclonality index, which quantifies the nonuniformity of the distribution of clone abundance, and ii. an estimator of the total number of clones in the body of the host. These new tools are valuable for the study of retroviral infections and can also be adapted for the tracking of gene-edited cells.
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Affiliation(s)
- Nicolas A Gillet
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA) of University of Liège (ULg), B34, 1 avenue de l'Hôpital, 4000, Liège, Belgium
- Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège (ULg), 13 Avenue Maréchal Juin, 5030, Gembloux, Belgium
| | - Anat Melamed
- Section of Virology, Wright-Fleming Institute, Imperial College School of Medicine, London, UK
| | - Charles R M Bangham
- Section of Virology, Wright-Fleming Institute, Imperial College School of Medicine, London, UK.
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48
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Rowan AG, Witkover A, Melamed A, Tanaka Y, Cook LBM, Fields P, Taylor GP, Bangham CRM. T Cell Receptor Vβ Staining Identifies the Malignant Clone in Adult T cell Leukemia and Reveals Killing of Leukemia Cells by Autologous CD8+ T cells. PLoS Pathog 2016; 12:e1006030. [PMID: 27893842 PMCID: PMC5125714 DOI: 10.1371/journal.ppat.1006030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/28/2016] [Indexed: 11/19/2022] Open
Abstract
There is growing evidence that CD8+ cytotoxic T lymphocyte (CTL) responses can contribute to long-term remission of many malignancies. The etiological agent of adult T-cell leukemia/lymphoma (ATL), human T lymphotropic virus type-1 (HTLV-1), contains highly immunogenic CTL epitopes, but ATL patients typically have low frequencies of cytokine-producing HTLV-1-specific CD8+ cells in the circulation. It remains unclear whether patients with ATL possess CTLs that can kill the malignant HTLV-1 infected clone. Here we used flow cytometric staining of TCRVβ and cell adhesion molecule-1 (CADM1) to identify monoclonal populations of HTLV-1-infected T cells in the peripheral blood of patients with ATL. Thus, we quantified the rate of CD8+-mediated killing of the putative malignant clone in ex vivo blood samples. We observed that CD8+ cells from ATL patients were unable to lyse autologous ATL clones when tested directly ex vivo. However, short in vitro culture restored the ability of CD8+ cells to kill ex vivo ATL clones in some donors. The capacity of CD8+ cells to lyse HTLV-1 infected cells which expressed the viral sense strand gene products was significantly enhanced after in vitro culture, and donors with an ATL clone that expressed the HTLV-1 Tax gene were most likely to make a detectable lytic CD8+ response to the ATL cells. We conclude that some patients with ATL possess functional tumour-specific CTLs which could be exploited to contribute to control of the disease.
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Affiliation(s)
- Aileen G. Rowan
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Aviva Witkover
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Anat Melamed
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Yuetsu Tanaka
- Department of Immunology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Lucy B. M. Cook
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Paul Fields
- Guy’s and St Thomas’ Hospital, London, United Kingdom
| | - Graham P. Taylor
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Charles R. M. Bangham
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
- * E-mail:
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49
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Retroviruses integrate into a shared, non-palindromic DNA motif. Nat Microbiol 2016; 2:16212. [PMID: 27841853 DOI: 10.1038/nmicrobiol.2016.212] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/21/2016] [Indexed: 12/12/2022]
Abstract
Many DNA-binding factors, such as transcription factors, form oligomeric complexes with structural symmetry that bind to palindromic DNA sequences1. Palindromic consensus nucleotide sequences are also found at the genomic integration sites of retroviruses2-6 and other transposable elements7-9, and it has been suggested that this palindromic consensus arises as a consequence of the structural symmetry in the integrase complex2,3. However, we show here that the palindromic consensus sequence is not present in individual integration sites of human T-cell lymphotropic virus type 1 (HTLV-1) and human immunodeficiency virus type 1 (HIV-1), but arises in the population average as a consequence of the existence of a non-palindromic nucleotide motif that occurs in approximately equal proportions on the plus strand and the minus strand of the host genome. We develop a generally applicable algorithm to sort the individual integration site sequences into plus-strand and minus-strand subpopulations, and use this to identify the integration site nucleotide motifs of five retroviruses of different genera: HTLV-1, HIV-1, murine leukaemia virus (MLV), avian sarcoma leucosis virus (ASLV) and prototype foamy virus (PFV). The results reveal a non-palindromic motif that is shared between these retroviruses.
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Abstract
PURPOSE OF REVIEW To discuss current understanding of the mechanisms of human T-lymphotropic virus type-1 (HTLV-1) tumorigenesis and current and potential treatment strategies for adult T-cell leukaemia/lymphoma (ATL), an aggressive malignant disease of CD4 cells caused by HTLV-1. RECENT FINDINGS Treatment of the aggressive subtypes of ATL remains inadequate, with little improvement in overall survival in the 30 years since HTLV-1 was discovered. Detailed analysis of the clonal expansion of HTLV-1 has provided new insight into pathogenesis. Most HTLV-1-infected cells, including ATL, express CCR4 which can be targeted. Reports of antitumour effects with allogeneic bone marrow transplantation provide a rationale for novel immunotherapy approaches. Progress has been made in the indolent subtypes of ATL with the use of 'antiviral' therapies. SUMMARY ATL has poor prognosis. There is a major, urgent, unmet clinical need to identify HTLV carriers who will develop ATL to develop biomarkers of transforming disease and disease progression and to provide novel treatment approaches within the context of clinical trials. Several strategies now include putative or actual antiviral therapy. Potentially, the risk of ATL would be reduced by eliminating some or all infected clones. HTLV-1 infection, and hence ATL, can be prevented by antenatal HTLV-1 screening.
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