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Terrazzan A, Vanini R, Ancona P, Bianchi N, Taccioli C, Aguiari G. State-of-the-art in transposable element modulation affected by drugs in malignant prostatic cancer cells. J Cell Biochem 2024; 125:e30557. [PMID: 38501160 DOI: 10.1002/jcb.30557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024]
Abstract
Over recent years, the investigation of transposable elements (TEs) has granted researchers a deeper comprehension of their characteristics and functions, particularly regarding their significance in the mechanisms contributing to cancer development. This manuscript focuses on prostate carcinoma cell lines and offers a comprehensive review intended to scrutinize the associations and interactions between TEs and genes, as well as their response to treatment using various chemical drugs, emphasizing their involvement in cancer progression. We assembled a compendium of articles retrieved from the PubMed database to construct networks demonstrating correlations with genes and pharmaceuticals. In doing so, we linked the transposition of certain TE types to the expression of specific transcripts directly implicated in carcinogenesis. Additionally, we underline that treatment employing different drugs revealed unique patterns of TE reactivation. Our hypothesis gathers the current understanding and guides research toward evidence-based investigations, emphasizing the association between antiviral drugs, chemotherapy, and the reduced expression of TEs in patients affected by prostate cancer.
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Affiliation(s)
- Anna Terrazzan
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Laboratory for Advanced Therapy Technologies (LTTA), University of Ferrara, Ferrara, Italy
| | - Riccardo Vanini
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Pietro Ancona
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Nicoletta Bianchi
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Cristian Taccioli
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Padua, Italy
| | - Gianluca Aguiari
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
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2
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Ramirez P, Sun W, Kazempour Dehkordi S, Zare H, Fongang B, Bieniek KF, Frost B. Nanopore-based DNA long-read sequencing analysis of the aged human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578450. [PMID: 38370753 PMCID: PMC10871260 DOI: 10.1101/2024.02.01.578450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Aging disrupts cellular processes such as DNA repair and epigenetic control, leading to a gradual buildup of genomic alterations that can have detrimental effects in post-mitotic cells. Genomic alterations in regions of the genome that are rich in repetitive sequences, often termed "dark loci," are difficult to resolve using traditional sequencing approaches. New long-read technologies offer promising avenues for exploration of previously inaccessible regions of the genome. Using nanopore-based long-read whole-genome sequencing of DNA extracted from aged 18 human brains, we identify previously unreported structural variants and methylation patterns within repetitive DNA, focusing on transposable elements ("jumping genes") as crucial sources of variation, particularly in dark loci. Our analyses reveal potential somatic insertion variants and provides DNA methylation frequencies for many retrotransposon families. We further demonstrate the utility of this technology for the study of these challenging genomic regions in brains affected by Alzheimer's disease and identify significant differences in DNA methylation in pathologically normal brains versus those affected by Alzheimer's disease. Highlighting the power of this approach, we discover specific polymorphic retrotransposons with altered DNA methylation patterns. These retrotransposon loci have the potential to contribute to pathology, warranting further investigation in Alzheimer's disease research. Taken together, our study provides the first long-read DNA sequencing-based analysis of retrotransposon sequences, structural variants, and DNA methylation in the aging brain affected with Alzheimer's disease neuropathology.
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Affiliation(s)
- Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Wenyan Sun
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
- School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri
| | - Shiva Kazempour Dehkordi
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Kevin F. Bieniek
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Pathology, University of Texas Health San Antonio, San Antonio, Texas
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
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Hekim N, Gunes S, Ergun S, Asci R. Insertional Variations of Human Endogenous Virus K6 and K11 in Normozoospermic Men. Reprod Sci 2024; 31:267-274. [PMID: 37710087 DOI: 10.1007/s43032-023-01346-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023]
Abstract
Male infertility is a multifactorial heterogeneous reproductive disorder in which genetic, epigenetic, and environmental factors play a role in the development of disease. Recent studies have shown that retrotransposon expression alterations may be related to impairment of spermatogenesis. Therefore, in this pilot study, we aimed to investigate whether HERV-K6 and HERV-K11 insertional variations have a role in idiopathic infertility among normozoospermic men. Genomic DNA isolated from the blood samples of 41 infertile normozoospermic and 45 fertile normozoospermic men were analyzed by inter-retrotransposon polymorphism polymerase chain reaction. HERV-K6 variation rates in the infertile and the fertile group were 0-58.3% and 0-53.4%, respectively. The variation rates of HERV-K11 were 0-75.0% in infertile and 0-77.8% in fertile men. The HERV-K6 and HERV-K11 insertion rates of the fertile group were higher than the infertile group (P < 0.0001 and P = 0.007, respectively). The findings of the study suggest that HERV-K6 and HERV-K11 retrotransposon insertion show variation among individuals, and their insertions might be associated with male infertility.
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Affiliation(s)
- Neslihan Hekim
- Faculty of Medicine, Department of Medical Biology, Ondokuz Mayis University, Samsun, 55139, Turkey.
| | - Sezgin Gunes
- Faculty of Medicine, Department of Medical Biology, Ondokuz Mayis University, Samsun, 55139, Turkey
- Graduate Institute, Department of Molecular Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Sercan Ergun
- Faculty of Medicine, Department of Medical Biology, Ondokuz Mayis University, Samsun, 55139, Turkey
- Graduate Institute, Department of Molecular Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Ramazan Asci
- Graduate Institute, Department of Molecular Medicine, Ondokuz Mayis University, Samsun, Turkey
- Faculty of Medicine, Department of Urology, Ondokuz Mayis University, Samsun, Turkey
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4
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Human Endogenous Retroviruses: Friends and Foes in Urology Clinics. Int Neurourol J 2022; 26:275-287. [PMID: 36599336 PMCID: PMC9816444 DOI: 10.5213/inj.2244284.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are originated from ancient exogenous retroviruses, which infected human germ line cells millions of years ago. HERVs have generally lost their replication and retrotransposition abilities, but adopted physiological roles in human biology. Though mostly inactive, HERVs can be reactivated by internal and external factors such as inflammations and environmental conditions. Their aberrant expression can participate in various human malignancies with complex etiology. This review describes the features and functions of HERVs in urological subjects, such as urological cancers and human reproduction. It provides the current knowledge of the HERVs and useful insights helping practice in urology clinics.
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Agoni L. Alternative and aberrant splicing of human endogenous retroviruses in cancer. What about head and neck? —A mini review. Front Oncol 2022; 12:1019085. [PMID: 36338752 PMCID: PMC9631305 DOI: 10.3389/fonc.2022.1019085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are transcribed in many cancer types, including head and neck cancer. Because of accumulating mutations at proviral loci over evolutionary time, HERVs are functionally defective and cannot complete their viral life cycle. Despite that, HERV transcripts, including full-length viral RNAs and viral RNAs spliced as expected at the conventional viral splice sites, can be detected in particular conditions, such as cancer. Interestingly, non-viral–related transcription, including aberrant, non-conventionally spliced RNAs, has been reported as well. The role of HERV transcription in cancer and its contribution to oncogenesis or progression are still debated. Nonetheless, HERVs may constitute a suitable cancer biomarker or a target for therapy. Thus, ongoing research aims both to clarify the basic mechanisms underlying HERV transcription in cancer and to exploit its potential toward clinical application. In this mini-review, we summarize the current knowledge, the most recent findings, and the future perspectives of research on HERV transcription and splicing, with particular focus on head and neck cancer.
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Dittmar T, Weiler J, Luo T, Hass R. Cell-Cell Fusion Mediated by Viruses and HERV-Derived Fusogens in Cancer Initiation and Progression. Cancers (Basel) 2021; 13:5363. [PMID: 34771528 PMCID: PMC8582398 DOI: 10.3390/cancers13215363] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 12/13/2022] Open
Abstract
Cell fusion is a well-known, but still scarcely understood biological phenomenon, which might play a role in cancer initiation, progression and formation of metastases. Although the merging of two (cancer) cells appears simple, the entire process is highly complex, energy-dependent and tightly regulated. Among cell fusion-inducing and -regulating factors, so-called fusogens have been identified as a specific type of proteins that are indispensable for overcoming fusion-associated energetic barriers and final merging of plasma membranes. About 8% of the human genome is of retroviral origin and some well-known fusogens, such as syncytin-1, are expressed by human (cancer) cells. Likewise, enveloped viruses can enable and facilitate cell fusion due to evolutionarily optimized fusogens, and are also capable to induce bi- and multinucleation underlining their fusion capacity. Moreover, multinucleated giant cancer cells have been found in tumors derived from oncogenic viruses. Accordingly, a potential correlation between viruses and fusogens of human endogenous retroviral origin in cancer cell fusion will be summarized in this review.
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Affiliation(s)
- Thomas Dittmar
- Institute of Immunology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58448 Witten, Germany;
| | - Julian Weiler
- Institute of Immunology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58448 Witten, Germany;
| | - Tianjiao Luo
- Biochemistry and Tumor Biology Laboratory, Department of Obstetrics and Gynecology, Hannover Medical School, 30625 Hannover, Germany;
| | - Ralf Hass
- Biochemistry and Tumor Biology Laboratory, Department of Obstetrics and Gynecology, Hannover Medical School, 30625 Hannover, Germany;
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7
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Karlik E, Gurbuz O, Yildiz Y, Gozukirmizi N. Endogenous retrovirus HERV-K6 and HERV-K11 polymorphisms’ analyses in head and neck squamous cell carcinoma patients. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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8
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Dervan E, Bhattacharyya DD, McAuliffe JD, Khan FH, Glynn SA. Ancient Adversary - HERV-K (HML-2) in Cancer. Front Oncol 2021; 11:658489. [PMID: 34055625 PMCID: PMC8155577 DOI: 10.3389/fonc.2021.658489] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
Human endogenous retroviruses (HERV), ancient integrations of exogenous viruses, make up 8% of our genome. Long thought of as mere vestigial genetic elements, evidence is now accumulating to suggest a potential functional role in numerous pathologies including neurodegenerative diseases, autoimmune disorders, and multiple cancers. The youngest member of this group of transposable elements is HERV-K (HML-2). Like the majority of HERV sequences, significant post-insertional mutations have disarmed HERV-K (HML-2), preventing it from producing infectious viral particles. However, some insertions have retained limited coding capacity, and complete open reading frames for all its constituent proteins can be found throughout the genome. For this reason HERV-K (HML-2) has garnered more attention than its peers. The tight epigenetic control thought to suppress expression in healthy tissue is lost during carcinogenesis. Upregulation of HERV-K (HML-2) derived mRNA and protein has been reported in a variety of solid and liquid tumour types, and while causality has yet to be established, progressively more data are emerging to suggest this phenomenon may contribute to tumour growth and metastatic capacity. Herein we discuss its potential utility as a diagnostic tool and therapeutic target in light of the current in vitro, in vivo and clinical evidence linking HERV-K (HML-2) to tumour progression.
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Affiliation(s)
- Eoin Dervan
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), Galway, Ireland
| | - Dibyangana D Bhattacharyya
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), Galway, Ireland.,Laboratory of Cancer ImmunoMetabolism, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Jake D McAuliffe
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), Galway, Ireland
| | - Faizan H Khan
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), Galway, Ireland
| | - Sharon A Glynn
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), Galway, Ireland
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9
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The Regulation and Functions of Endogenous Retrovirus in Embryo Development and Stem Cell Differentiation. Stem Cells Int 2021; 2021:6660936. [PMID: 33727936 PMCID: PMC7937486 DOI: 10.1155/2021/6660936] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/19/2021] [Indexed: 11/17/2022] Open
Abstract
Endogenous retroviruses (ERVs) are repetitive sequences in the genome, belonging to the retrotransposon family. During the course of life, ERVs are associated with multiple aspects of chromatin and transcriptional regulation in development and pathological conditions. In mammalian embryos, ERVs are extensively activated in early embryo development, but with a highly restricted spatial-temporal pattern; and they are drastically silenced during differentiation with exceptions in extraembryonic tissue and germlines. The dynamic activation pattern of ERVs raises questions about how ERVs are regulated in the life cycle and whether they are functionally important to cell fate decision during early embryo and somatic cell development. Therefore, in this review, we focus on the pieces of evidence demonstrating regulations and functions of ERVs during stem cell differentiation, which suggests that ERV activation is not a passive result of cell fate transition but the active epigenetic and transcriptional regulation during mammalian development and stem cell differentiation.
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Tatkiewicz W, Dickie J, Bedford F, Jones A, Atkin M, Kiernan M, Maze EA, Agit B, Farnham G, Kanapin A, Belshaw R. Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines. Mob DNA 2020; 11:9. [PMID: 32055257 PMCID: PMC7007669 DOI: 10.1186/s13100-020-0204-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/14/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The cell-surface attachment protein (Env) of the HERV-K(HML-2) lineage of endogenous retroviruses is a potentially attractive tumour-associated antigen for anti-cancer immunotherapy. The human genome contains around 100 integrated copies (called proviruses or loci) of the HERV-K(HML-2) virus and we argue that it is important for therapy development to know which and how many of these contribute to protein expression, and how this varies across tissues. We measured relative provirus expression in HERV-K(HML-2), using enriched RNA-Seq analysis with both short- and long-read sequencing, in three Mantle Cell Lymphoma cell lines (JVM2, Granta519 and REC1). We also confirmed expression of the Env protein in two of our cell lines using Western blotting, and analysed provirus expression data from all other relevant published studies. RESULTS Firstly, in both our and other reanalysed studies, approximately 10% of the transcripts mapping to HERV-K(HML-2) came from Env-encoding proviruses. Secondly, in one cell line the majority of the protein expression appears to come from one provirus (12q14.1). Thirdly, we find a strong tissue-specific pattern of provirus expression. CONCLUSIONS A possible dependency of Env expression on a single provirus, combined with the earlier observation that this provirus is not present in all individuals and a general pattern of tissue-specific expression among proviruses, has serious implications for future HERV-K(HML-2)-targeted immunotherapy. Further research into HERV-K(HML-2) as a possible tumour-associated antigen in blood cancers requires a more targeted, proteome-based, screening protocol that will consider these polymorphisms within HERV-K(HML-2). We include a plan (and necessary alignments) for such work.
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Affiliation(s)
- Witold Tatkiewicz
- Peninsula Medical School, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - James Dickie
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Franchesca Bedford
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Alexander Jones
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Mark Atkin
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Michele Kiernan
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Emmanuel Atangana Maze
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Bora Agit
- Peninsula Medical School, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Garry Farnham
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Alexander Kanapin
- Department of Oncology, University of Oxford, Oxford, UK
- Current address: Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Robert Belshaw
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
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Kesäniemi J, Lavrinienko A, Tukalenko E, Mappes T, Watts PC, Jurvansuu J. Infection Load and Prevalence of Novel Viruses Identified from the Bank Vole Do Not Associate with Exposure to Environmental Radioactivity. Viruses 2019; 12:E44. [PMID: 31905955 PMCID: PMC7019477 DOI: 10.3390/v12010044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/27/2019] [Accepted: 12/27/2019] [Indexed: 12/13/2022] Open
Abstract
Bank voles (Myodes glareolus) are host to many zoonotic viruses. As bank voles inhabiting areas contaminated by radionuclides show signs of immunosuppression, resistance to apoptosis, and elevated DNA repair activity, we predicted an association between virome composition and exposure to radionuclides. To test this hypothesis, we studied the bank vole virome in samples of plasma derived from animals inhabiting areas of Ukraine (contaminated areas surrounding the former nuclear power plant at Chernobyl, and uncontaminated areas close to Kyiv) that differed in level of environmental radiation contamination. We discovered four strains of hepacivirus and four new virus sequences: two adeno-associated viruses, an arterivirus, and a mosavirus. However, viral prevalence and viral load, and the ability to cause a systemic infection, was not dependent on the level of environmental radiation.
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Affiliation(s)
- Jenni Kesäniemi
- Finland Ecology and Genetics Research Unit, University of Oulu, 90014 Oulu, Finland;
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland; (A.L.); (T.M.); (P.C.W.)
| | - Eugene Tukalenko
- National Research Center for Radiation Medicine of the National Academy of Medical Science, 02000 Kyiv, Ukraine;
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland; (A.L.); (T.M.); (P.C.W.)
| | - Phillip C. Watts
- Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland; (A.L.); (T.M.); (P.C.W.)
| | - Jaana Jurvansuu
- Finland Ecology and Genetics Research Unit, University of Oulu, 90014 Oulu, Finland;
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12
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Kanzaki LIB. HTLV-1: A real pathogen or a runaway guest of a diseased cell? J Biosci 2018; 43:785-795. [PMID: 30207322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The human T-cell lymphotropic virus type 1 (HTLV-1) is a deltaretrovirus claimed to be aetiologically linked to the adult T-cell leukaemia/lymphoma (ATLL) and associated myelopathy/tropical spastic paraparesis (HAM/TSP) besides other minor pathologies. HTLV-1 infection is worldwide distributed, despite its heterogeneous prevalence. Environmental factors and host-genetic background are very likely to determine the epidemiological profile of HTLV-1 prevalence and related disease confinement in distinct human ethnic populations and geographical coordinates, which raises the question if the virus is a real pathogen or a runaway well-organized packed genome of a burden host cell near death process. New methodological approaches need to be proposed and applied in order to prove or discard the hypotheses emerged in the present review.
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Affiliation(s)
- L I B Kanzaki
- Laboratory of Bioprospection, Department of Pharmacy, University of Brasilia, Brası´lia, DF CEP 70.910-900, Brazil,
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14
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Li M, Radvanyi L, Yin B, Rycaj K, Li J, Chivukula R, Lin K, Lu Y, Shen J, Chang DZ, Li D, Johanning GL, Wang-Johanning F. Downregulation of Human Endogenous Retrovirus Type K (HERV-K) Viral env RNA in Pancreatic Cancer Cells Decreases Cell Proliferation and Tumor Growth. Clin Cancer Res 2017; 23:5892-5911. [PMID: 28679769 DOI: 10.1158/1078-0432.ccr-17-0001] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 05/09/2017] [Accepted: 06/29/2017] [Indexed: 12/23/2022]
Abstract
Purpose: We investigated the role of the human endogenous retrovirus type K (HERV-K) envelope (env) gene in pancreatic cancer.Experimental Design: shRNA was employed to knockdown (KD) the expression of HERV-K in pancreatic cancer cells.Results: HERV-K env expression was detected in seven pancreatic cancer cell lines and in 80% of pancreatic cancer patient biopsies, but not in two normal pancreatic cell lines or uninvolved normal tissues. A new HERV-K splice variant was discovered in several pancreatic cancer cell lines. Reverse transcriptase activity and virus-like particles were observed in culture media supernatant obtained from Panc-1 and Panc-2 cells. HERV-K viral RNA levels and anti-HERV-K antibody titers were significantly higher in pancreatic cancer patient sera (N = 106) than in normal donor sera (N = 40). Importantly, the in vitro and in vivo growth rates of three pancreatic cancer cell lines were significantly reduced after HERV-K KD by shRNA targeting HERV-K env, and there was reduced metastasis to lung after treatment. RNA-Seq results revealed changes in gene expression after HERV-K env KD, including RAS and TP53. Furthermore, downregulation of HERV-K Env protein expression by shRNA also resulted in decreased expression of RAS, p-ERK, p-RSK, and p-AKT in several pancreatic cancer cells or tumors.Conclusions: These results demonstrate that HERV-K influences signal transduction via the RAS-ERK-RSK pathway in pancreatic cancer. Our data highlight the potentially important role of HERV-K in tumorigenesis and progression of pancreatic cancer, and indicate that HERV-K viral proteins may be attractive biomarkers and/or tumor-associated antigens, as well as potentially useful targets for detection, diagnosis, and immunotherapy of pancreatic cancer. Clin Cancer Res; 23(19); 5892-911. ©2017 AACR.
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Affiliation(s)
- Ming Li
- Viral Oncology Program, Center for Cancer and Metabolism, SRI International, Menlo Park, California
| | - Laszlo Radvanyi
- EMD Serono Research and Development Institute, Billerica, Massachusetts
| | - Bingnan Yin
- Department of Inflammation and Epigenetics, Methodist Research Institute, Houston, Texas
| | | | - Jia Li
- Viral Oncology Program, Center for Cancer and Metabolism, SRI International, Menlo Park, California
| | - Raghavender Chivukula
- Viral Oncology Program, Center for Cancer and Metabolism, SRI International, Menlo Park, California
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, the University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, the University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - JianJun Shen
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, the University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - David Z Chang
- Virginia Oncology Associates, Newport News, Virginia
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gary L Johanning
- Viral Oncology Program, Center for Cancer and Metabolism, SRI International, Menlo Park, California
| | - Feng Wang-Johanning
- Viral Oncology Program, Center for Cancer and Metabolism, SRI International, Menlo Park, California.
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15
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Bae JH, Eo J, Kim TO, Yi JM. Biological changes of transposable elements by radiation: recent progress. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0256-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Abstract
One lineage of human endogenous retroviruses (HERVs), HERV-K(HML2), is upregulated in many cancers, some autoimmune/inflammatory diseases, and HIV-infected cells. Despite 3 decades of research, it is not known if these viruses play a causal role in disease, and there has been recent interest in whether they can be used as immunotherapy targets. Resolution of both these questions will be helped by an ability to distinguish between the effects of different integrated copies of the virus (loci). Research so far has concentrated on the 20 or so recently integrated loci that, with one exception, are in the human reference genome sequence. However, this viral lineage has been copying in the human population within the last million years, so some loci will inevitably be present in the human population but absent from the reference sequence. We therefore performed the first detailed search for such loci by mining whole-genome sequences generated by next-generation sequencing. We found a total of 17 loci, and the frequency of their presence ranged from only 2 of the 358 individuals examined to over 95% of them. On average, each individual had six loci that are not in the human reference genome sequence. Comparing the number of loci that we found to an expectation derived from a neutral population genetic model suggests that the lineage was copying until at least ∼250,000 years ago. IMPORTANCE About 5% of the human genome sequence is composed of the remains of retroviruses that over millions of years have integrated into the chromosomes of egg and/or sperm precursor cells. There are indications that protein expression of these viruses is higher in some diseases, and we need to know (i) whether these viruses have a role in causing disease and (ii) whether they can be used as immunotherapy targets in some of them. Answering both questions requires a better understanding of how individuals differ in the viruses that they carry. We carried out the first careful search for new viruses in some of the many human genome sequences that are now available thanks to advances in sequencing technology. We also compared the number that we found to a theoretical expectation to see if it is likely that these viruses are still replicating in the human population today.
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HIV-1 interacts with human endogenous retrovirus K (HML-2) envelopes derived from human primary lymphocytes. J Virol 2014; 88:6213-23. [PMID: 24648457 DOI: 10.1128/jvi.00669-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Human endogenous retroviruses (HERVs) are viruses that have colonized the germ line and spread through vertical passage. Only the more recently acquired HERVs, such as the HERV-K (HML-2) group, maintain coding open reading frames. Expression of HERV-Ks has been linked to different pathological conditions, including HIV infection, but our knowledge on which specific HERV-Ks are expressed in primary lymphocytes currently is very limited. To identify the most expressed HERV-Ks in an unbiased manner, we analyzed their expression patterns in peripheral blood lymphocytes using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing. We observe that three HERV-Ks (KII, K102, and K18) constitute over 90% of the total HERV-K expression in primary human lymphocytes of five different donors. We also show experimentally that two of these HERV-K env sequences (K18 and K102) retain their ability to produce full-length and posttranslationally processed envelope proteins in cell culture. We show that HERV-K18 Env can be incorporated into HIV-1 but not simian immunodeficiency virus (SIV) particles. Moreover, HERV-K18 Env incorporation into HIV-1 virions is dependent on HIV-1 matrix. Taken together, we generated high-resolution HERV-K expression profiles specific for activated human lymphocytes. We found that one of the most abundantly expressed HERV-K envelopes not only makes a full-length protein but also specifically interacts with HIV-1. Our findings raise the possibility that these endogenous retroviral Env proteins could directly influence HIV-1 replication. IMPORTANCE Here, we report the HERV-K expression profile of primary lymphocytes from 5 different healthy donors. We used a novel deep-sequencing technology (PacBio SMRT) that produces the long reads necessary to discriminate the complexity of HERV-K expression. We find that primary lymphocytes express up to 32 different HERV-K envelopes, and that at least two of the most expressed Env proteins retain their ability to make a protein. Importantly, one of them, the envelope glycoprotein of HERV-K18, is incorporated into HIV-1 in an HIV matrix-specific fashion. The ramifications of such interactions are discussed, as the possibility of HIV-1 target tissue broadening and immune evasion are considered.
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