1
|
Chisca M, Larouche JD, Xing Q, Kassiotis G. Antibodies against endogenous retroviruses. Immunol Rev 2024. [PMID: 39152687 DOI: 10.1111/imr.13378] [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] [Indexed: 08/19/2024]
Abstract
The human genome harbors hundreds of thousands of integrations of ancient retroviruses, amassed over millions of years of evolution. To reduce further amplification in the genome, the host prevents transcription of these now endogenous retroviruses (ERVs) through epigenetic repression and, with evolutionary time, ERVs are incapacitated by accumulating mutations and deletions. However, several members of recently endogenized ERV groups still retain the capacity to produce viral RNA, retroviral proteins, and higher order structures, including virions. The retention of viral characteristics, combined with the reversible nature of epigenetic repression, particularly as seen in cancer, allow for immunologically unanticipated ERV expression, perceived by the adaptive immune system as a genuine retroviral infection, to which it has to respond. Accordingly, antibodies reactive with ERV antigens have been detected in diverse disorders and, occasionally, in healthy individuals. Although they are part of self, the retroviral legacy of ERV antigens, and association with and, possibly, causation of disease states may set them apart from typical self-antigens. Consequently, the pathogenic or, indeed, host-protective capacity of antibodies targeting ERV antigens is likely to be context-dependent. Here, we review the immunogenicity of typical ERV proteins, with emphasis on the antibody response and its potential disease implications.
Collapse
Affiliation(s)
- Mihaela Chisca
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | | | - Qi Xing
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| |
Collapse
|
2
|
Halcrow PW, Quansah DN, Kumar N, Steiner JP, Nath A, Geiger JD. HERV-K (HML-2) Envelope Protein Induces Mitochondrial Depolarization and Neurotoxicity via Endolysosome Iron Dyshomeostasis. J Neurosci 2024; 44:e0826232024. [PMID: 38383499 PMCID: PMC10993035 DOI: 10.1523/jneurosci.0826-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 01/08/2024] [Accepted: 02/10/2024] [Indexed: 02/23/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are associated with the pathogenesis of amyotrophic lateral sclerosis (ALS); a disease characterized by motor neuron degeneration and cell death. The HERV-K subtype HML-2 envelope protein (HERV-K Env) is expressed in the brain, spinal cord, and cerebrospinal fluid of people living with ALS and through CD98 receptor-linked interactions causes neurodegeneration. HERV-K Env-induced increases in oxidative stress are implicated in the pathogenesis of ALS, and ferrous iron (Fe2+) generates reactive oxygen species (ROS). Endolysosome stores of Fe2+ are central to iron trafficking and endolysosome deacidification releases Fe2+ into the cytoplasm. Because HERV-K Env is an arginine-rich protein that is likely endocytosed and arginine is a pH-elevating amino acid, it is important to determine HERV-K Env effects on endolysosome pH and whether HERV-K Env-induced neurotoxicity is downstream of Fe2+ released from endolysosomes. Here, we showed using SH-SY5Y human neuroblastoma cells and primary cultures of human cortical neurons (HCNs, information on age and sex was not available) that HERV-K Env (1) is endocytosed via CD98 receptors, (2) concentration dependently deacidified endolysosomes, (3) decreased endolysosome Fe2+ concentrations, (4) increased cytosolic and mitochondrial Fe2+ and ROS levels, (5) depolarized mitochondrial membrane potential, and (6) induced cell death, effects blocked by an antibody against the CD98 receptor and by the endolysosome iron chelator deferoxamine. Thus, HERV-K Env-induced increases in cytosolic and mitochondrial Fe2+ and ROS as well as cell death appear to be mechanistically caused by HERV-K Env endocytosis, endolysosome deacidification, and endolysosome Fe2+ efflux into the cytoplasm.
Collapse
Affiliation(s)
- Peter W. Halcrow
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202
| | - Darius N.K. Quansah
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202
| | - Nirmal Kumar
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202
| | - Joseph P. Steiner
- Section for Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892
| | - Avindra Nath
- Section for Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892
| | - Jonathan D. Geiger
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202
| |
Collapse
|
3
|
Ebrahim T, Ebrahim AS, Kandouz M. Diversity of Intercellular Communication Modes: A Cancer Biology Perspective. Cells 2024; 13:495. [PMID: 38534339 DOI: 10.3390/cells13060495] [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: 01/05/2024] [Revised: 02/27/2024] [Accepted: 03/10/2024] [Indexed: 03/28/2024] Open
Abstract
From the moment a cell is on the path to malignant transformation, its interaction with other cells from the microenvironment becomes altered. The flow of molecular information is at the heart of the cellular and systemic fate in tumors, and various processes participate in conveying key molecular information from or to certain cancer cells. For instance, the loss of tight junction molecules is part of the signal sent to cancer cells so that they are no longer bound to the primary tumors and are thus free to travel and metastasize. Upon the targeting of a single cell by a therapeutic drug, gap junctions are able to communicate death information to by-standing cells. The discovery of the importance of novel modes of cell-cell communication such as different types of extracellular vesicles or tunneling nanotubes is changing the way scientists look at these processes. However, are they all actively involved in different contexts at the same time or are they recruited to fulfill specific tasks? What does the multiplicity of modes mean for the overall progression of the disease? Here, we extend an open invitation to think about the overall significance of these questions, rather than engage in an elusive attempt at a systematic repertory of the mechanisms at play.
Collapse
Affiliation(s)
- Thanzeela Ebrahim
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Abdul Shukkur Ebrahim
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Mustapha Kandouz
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48202, USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48202, USA
| |
Collapse
|
4
|
Dopkins N, Singh B, Michael S, Zhang P, Marston JL, Fei T, Singh M, Feschotte C, Collins N, Bendall ML, Nixon DF. Ribosomal profiling of human endogenous retroviruses in healthy tissues. BMC Genomics 2024; 25:5. [PMID: 38166631 PMCID: PMC10759522 DOI: 10.1186/s12864-023-09909-x] [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: 06/05/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are the germline embedded proviral fragments of ancient retroviral infections that make up roughly 8% of the human genome. Our understanding of HERVs in physiology primarily surrounds their non-coding functions, while their protein coding capacity remains virtually uncharacterized. Therefore, we applied the bioinformatic pipeline "hervQuant" to high-resolution ribosomal profiling of healthy tissues to provide a comprehensive overview of translationally active HERVs. We find that HERVs account for 0.1-0.4% of all translation in distinct tissue-specific profiles. Collectively, our study further supports claims that HERVs are actively translated throughout healthy tissues to provide sequences of retroviral origin to the human proteome.
Collapse
Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
| | - Bhavya Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Panpan Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Jez L Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Manvendra Singh
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Nicholas Collins
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| |
Collapse
|
5
|
Dubowsky M, Theunissen F, Carr JM, Rogers ML. The Molecular Link Between TDP-43, Endogenous Retroviruses and Inflammatory Neurodegeneration in Amyotrophic Lateral Sclerosis: a Potential Target for Triumeq, an Antiretroviral Therapy. Mol Neurobiol 2023; 60:6330-6345. [PMID: 37450244 PMCID: PMC10533598 DOI: 10.1007/s12035-023-03472-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease (MND), is a progressive neurological disorder, characterised by the death of upper and lower motor neurons. The aetiology of ALS remains unknown, and treatment options are limited. Endogenous retroviruses (ERVs), specifically human endogenous retrovirus type K (HERV-K), have been proposed to be involved in the propagation of neurodegeneration in ALS. ERVs are genomic remnants of ancient viral infection events, with most being inactive and not retaining the capacity to encode a fully infectious virus. However, some ERVs retain the ability to be activated and transcribed, and ERV transcripts have been found to be elevated within the brain tissue of MND patients. A hallmark of ALS pathology is altered localisation of the transactive response (TAR) DNA binding protein 43 kDa (TDP-43), which is normally found within the nucleus of neuronal and glial cells and is involved in RNA regulation. In ALS, TDP-43 aggregates within the cytoplasm and facilitates neurodegeneration. The involvement of ERVs in ALS pathology is thought to occur through TDP-43 and neuroinflammatory mediators. In this review, the proposed involvement of TDP-43, HERV-K and immune regulators on the onset and progression of ALS will be discussed. Furthermore, the evidence supporting a therapy based on targeting ERVs in ALS will be reviewed.
Collapse
Affiliation(s)
- Megan Dubowsky
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia.
| | - Frances Theunissen
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - Jillian M Carr
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - Mary-Louise Rogers
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| |
Collapse
|
6
|
Costa B, Vale N. Exploring HERV-K (HML-2) Influence in Cancer and Prospects for Therapeutic Interventions. Int J Mol Sci 2023; 24:14631. [PMID: 37834078 PMCID: PMC10572383 DOI: 10.3390/ijms241914631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
This review investigates the intricate role of human endogenous retroviruses (HERVs) in cancer development and progression, explicitly focusing on HERV-K (HML-2). This paper sheds light on the latest research advancements and potential treatment strategies by examining the historical context of HERVs and their involvement in critical biological processes such as embryonic development, immune response, and disease progression. This review covers computational modeling for drug-target binding assessment, systems biology modeling for simulating HERV-K viral cargo dynamics, and using antiviral drugs to combat HERV-induced diseases. The findings presented in this review contribute to our understanding of HERV-mediated disease mechanisms and provide insights into future therapeutic approaches. They emphasize why HERV-K holds significant promise as a biomarker and a target.
Collapse
Affiliation(s)
- Bárbara Costa
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal
| | - Nuno Vale
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal
| |
Collapse
|
7
|
Singh B, Dopkins N, Fei T, Marston JL, Michael S, Reyes-Gopar H, Curty G, Heymann JJ, Chadburn A, Martin P, Leal FE, Cesarman E, Nixon DF, Bendall ML. Locus specific human endogenous retroviruses reveal new lymphoma subtypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544208. [PMID: 37333202 PMCID: PMC10274920 DOI: 10.1101/2023.06.08.544208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The heterogeneity of cancers are driven by diverse mechanisms underlying oncogenesis such as differential 'cell-of-origin' (COO) progenitors, mutagenesis, and viral infections. Classification of B-cell lymphomas have been defined by considering these characteristics. However, the expression and contribution of transposable elements (TEs) to B cell lymphoma oncogenesis or classification have been overlooked. We hypothesized that incorporating TE signatures would increase the resolution of B-cell identity during healthy and malignant conditions. Here, we present the first comprehensive, locus-specific characterization of TE expression in benign germinal center (GC) B-cells, diffuse large B-cell lymphoma (DLBCL), Epstein-Barr virus (EBV)-positive and EBV-negative Burkitt lymphoma (BL), and follicular lymphoma (FL). Our findings demonstrate unique human endogenous retrovirus (HERV) signatures in the GC and lymphoma subtypes whose activity can be used in combination with gene expression to define B-cell lineage in lymphoid malignancies, highlighting the potential of retrotranscriptomic analyses as a tool in lymphoma classification, diagnosis, and the identification of novel treatment groups.
Collapse
Affiliation(s)
- Bhavya Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jez L. Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Helena Reyes-Gopar
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Genómica Computacional, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Gislaine Curty
- Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Jonas J. Heymann
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Peter Martin
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Fabio E. Leal
- Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew L. Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
8
|
Tavakolian S, Iranshahi M, Faghihloo E. The Evaluation of HERV-K np9, rec, gag Expression in Isolated Human Peripheral Blood Mononuclear Cell (PBMC) of Gastric and Colon Cancer. Adv Biomed Res 2023; 12:131. [PMID: 37434925 PMCID: PMC10331531 DOI: 10.4103/abr.abr_288_22] [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: 08/24/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 07/13/2023] Open
Abstract
Background In the current age of diagnostic approaches in cancer, countless efforts have been allocated to identify novel and efficient biomarkers to detect cancer in its early stages. We focused on evaluating the correlation between the progression of gastrointestinal cancer, a leading cause of cancer death worldwide, and human endogenous retrovirus (HERV). Materials and Methods In this study, we conducted a study on the peripheral blood mononuclear cells (PBMC) gathered from gastric and colon cancer patients. We focused on HERV-K rec, np9, gag expression analysis by quantitative real-time PCR, after extraction of RNA and synthesizing cDNA. Results Unlike np9 whose expression increased significantly in the colon and gastric cancers, the mRNA level of the rec gene declined in both cancers. Moreover, our data illustrated that the over-expression of the gag gene was only observed in colon cancerous cells rather than gastric malignancy. Conclusions Overall, given the correlation between the expression level of HERV-associated genes and gastrointestinal cancer, our study suggests that these genes could be considered beneficial markers for cancer diagnosis. However, researchers should conduct studies in future articles on whether these genes can be employed as biomarkers in gastrointestinal cancer.
Collapse
Affiliation(s)
- Shaian Tavakolian
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Iranshahi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
9
|
Daradoumis J, Ragonnaud E, Skandorff I, Nielsen KN, Bermejo AV, Andersson AM, Schroedel S, Thirion C, Neukirch L, Holst PJ. An Endogenous Retrovirus Vaccine Encoding an Envelope with a Mutated Immunosuppressive Domain in Combination with Anti-PD1 Treatment Eradicates Established Tumours in Mice. Viruses 2023; 15:v15040926. [PMID: 37112906 PMCID: PMC10141008 DOI: 10.3390/v15040926] [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: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Endogenous retroviruses (ERVs) account for 8% of our genome, and, although they are usually silent in healthy tissues, they become reactivated and expressed in pathological conditions such as cancer. Several studies support a functional role of ERVs in tumour development and progression, specifically through their envelope (Env) protein, which contains a region described as an immunosuppressive domain (ISD). We have previously shown that targeting of the murine ERV (MelARV) Env using virus-like vaccine (VLV) technology, consisting of an adenoviral vector encoding virus-like particles (VLPs), induces protection against small tumours in mice. Here, we investigate the potency and efficacy of a novel MelARV VLV with a mutated ISD (ISDmut) that can modify the properties of the adenoviral vaccine-encoded Env protein. We show that the modification of the vaccine's ISD significantly enhanced T-cell immunogenicity in both prime and prime-boost vaccination regimens. The modified VLV in combination with an α-PD1 checkpoint inhibitor (CPI) exhibited excellent curative efficacy against large established colorectal CT26 tumours in mice. Furthermore, only ISDmut-vaccinated mice that survived CT26 challenge were additionally protected against rechallenge with a triple-negative breast cancer cell line (4T1), showing that our modified VLV provides cross-protection against different tumour types expressing ERV-derived antigens. We envision that translating these findings and technology into human ERVs (HERVs) could provide new treatment opportunities for cancer patients with unmet medical needs.
Collapse
Affiliation(s)
- Joana Daradoumis
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Emeline Ragonnaud
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Isabella Skandorff
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | | | - Amaia Vergara Bermejo
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Anne-Marie Andersson
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | | | | | - Lasse Neukirch
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Peter Johannes Holst
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| |
Collapse
|
10
|
Liu X, Liu Z, Wu Z, Ren J, Fan Y, Sun L, Cao G, Niu Y, Zhang B, Ji Q, Jiang X, Wang C, Wang Q, Ji Z, Li L, Esteban CR, Yan K, Li W, Cai Y, Wang S, Zheng A, Zhang YE, Tan S, Cai Y, Song M, Lu F, Tang F, Ji W, Zhou Q, Belmonte JCI, Zhang W, Qu J, Liu GH. Resurrection of endogenous retroviruses during aging reinforces senescence. Cell 2023; 186:287-304.e26. [PMID: 36610399 DOI: 10.1016/j.cell.2022.12.017] [Citation(s) in RCA: 108] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 10/13/2022] [Accepted: 12/08/2022] [Indexed: 01/09/2023]
Abstract
Whether and how certain transposable elements with viral origins, such as endogenous retroviruses (ERVs) dormant in our genomes, can become awakened and contribute to the aging process is largely unknown. In human senescent cells, we found that HERVK (HML-2), the most recently integrated human ERVs, are unlocked to transcribe viral genes and produce retrovirus-like particles (RVLPs). These HERVK RVLPs constitute a transmissible message to elicit senescence phenotypes in young cells, which can be blocked by neutralizing antibodies. The activation of ERVs was also observed in organs of aged primates and mice as well as in human tissues and serum from the elderly. Their repression alleviates cellular senescence and tissue degeneration and, to some extent, organismal aging. These findings indicate that the resurrection of ERVs is a hallmark and driving force of cellular senescence and tissue aging.
Collapse
Affiliation(s)
- Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Sun
- NHC Beijing Institute of Geriatrics, NHC Key Laboratory of Geriatrics, Institute of Geriatric Medicine of Chinese Academy of Medical Sciences, National Center of Gerontology/Beijing Hospital, Beijing 100730, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Baohu Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cui Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhejun Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanzhu Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing Municipal Geriatric Medical Research Center, Beijing 100053, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China
| | - Aihua Zheng
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong E Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingao Cai
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Moshi Song
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Falong Lu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuchou Tang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
11
|
Guo C, Lv H, Bai Y, Guo M, Li P, Tong S, He K. Circular RNAs in extracellular vesicles: Promising candidate biomarkers for schizophrenia. Front Genet 2023; 13:997322. [PMID: 36685830 PMCID: PMC9852742 DOI: 10.3389/fgene.2022.997322] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023] Open
Abstract
As one of common and severe mental illnesses, schizophrenia is difficult to be diagnosed exactly. Both its pathogenesis and the causes of its development are still uncertain because of its etiology complexity. At present, the diagnosis of schizophrenia is mainly based on the patient's symptoms and signs, lacking reliable biomarkers that can be used for diagnosis. Circular RNAs in extracellular vesicles (EV circRNAs) can be used as promising candidate biomarkers for schizophrenia and other diseases, for they are not only high stability and disease specificity, but also are rich in contents and easy to be detected. The review is to focus on the research progress of the correlation between circRNAs and schizophrenia, and then to explores the possibility of EV circRNAs as new biomarkers for the schizophrenia diagnosis.
Collapse
Affiliation(s)
- Chuang Guo
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Haibing Lv
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Yulong Bai
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Meng Guo
- Network Center, Inner Mongolia Minzu University, Tongliao, China
| | - Pengfei Li
- Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, China
| | - Shuping Tong
- Affiliated Hospital of Inner Mongolia Minzu University, Tongliao, China
| | - Kuanjun He
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China,*Correspondence: Kuanjun He,
| |
Collapse
|
12
|
Calero-Layana M, López-Cruz C, Ocaña A, Tejera E, Armijos-Jaramillo V. Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes. PeerJ 2022; 10:e14431. [PMID: 36575684 PMCID: PMC9790151 DOI: 10.7717/peerj.14431] [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: 08/22/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022] Open
Abstract
Background Endogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes: gag, pol, and env, each of which encodes viral proteins that can be conserved or not. ERVs have been observed in a wide range of vertebrate genomes and their functions are associated with viral silencing and gene regulation. Results In this work, we studied the evolutionary history of endogenous retroviruses associated with five human genes (INPP5B, DET1, PSMA1, USH2A, and MACROD2), which are located within intron sections. To verify the retroviral origin of the candidates, several approaches were used to detect and locate ERV elements. Both orthologous and paralogous genes were identified by Ensembl and then analyzed for ERV presence using RetroTector. A phylogenetic tree was reconstructed to identify the minimum time point of ERV acquisition. From that search, we detected ERVs throughout the primate lineage and in some other groups. Also, we identified the minimum origin of the ERVs from the parvorder Catarrhini to the Homininae subfamily. Conclusions With the data collected, and by observing the transcription factors annotated inside ERVs, we propose that these elements play a relevant role in gene expression regulation and they probably possess important features for tumorigenesis control.
Collapse
Affiliation(s)
- Melissa Calero-Layana
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador
| | - Carmen López-Cruz
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador
| | - Agustín Ocaña
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador
| | - Eduardo Tejera
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador,Grupo de Bio-Quimioinformática, Universidad de las Americas, Quito, Ecuador
| | - Vinicio Armijos-Jaramillo
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador,Grupo de Bio-Quimioinformática, Universidad de las Americas, Quito, Ecuador
| |
Collapse
|
13
|
Burn A, Roy F, Freeman M, Coffin JM. Widespread expression of the ancient HERV-K (HML-2) provirus group in normal human tissues. PLoS Biol 2022; 20:e3001826. [PMID: 36256614 PMCID: PMC9578601 DOI: 10.1371/journal.pbio.3001826] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/13/2022] [Indexed: 11/11/2022] Open
Abstract
Human endogenous retrovirus (HERV) transcripts are known to be highly expressed in cancers, yet their activity in nondiseased tissue is largely unknown. Using the GTEx RNA-seq dataset from normal tissue sampled at autopsy, we characterized individual expression of the recent HERV-K (HML-2) provirus group across 13,000 different samples of 54 different tissues from 948 individuals. HML-2 transcripts could be identified in every tissue sampled and were elevated in the cerebellum, pituitary, testis, and thyroid. A total of 37 different individual proviruses were expressed in 1 or more tissues, representing all 3 LTR5 subgroups. Nine proviruses were identified as having long terminal repeat (LTR)-driven transcription, 7 of which belonged to the most recent LTR5HS subgroup. Proviruses of different subgroups displayed a bias in tissue expression, which may be associated with differences in transcription factor binding sites in their LTRs. Provirus expression was greater in evolutionarily older proviruses with an earliest shared ancestor of gorilla or older. HML-2 expression was significantly affected by biological sex in 1 tissue, while age and timing of death (Hardy score) had little effect. Proviruses containing intact gag, pro, and env open reading frames (ORFs) were expressed in the dataset, with almost every tissue measured potentially expressing at least 1 intact ORF (gag). Human endogenous retrovirus (HERV) transcripts are known to be highly expressed in cancers, but what is their activity in normal tissue? This study uses unique patterns of HERV-K RNA expression in the large GEx dataset from non-diseased tissue sites to provide new insights into both the coevolution of HERV-K with our primate ancestors and their current role in human biology.
Collapse
Affiliation(s)
- Aidan Burn
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Farrah Roy
- Immuneering Corporation, Cambridge, Massachusetts, United States of America
| | - Michael Freeman
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - John M. Coffin
- Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
14
|
Srinivasachar Badarinarayan S, Sauter D. Not all viruses cause disease: HERV-K(HML-2) in healthy human tissues. PLoS Biol 2022; 20:e3001884. [PMID: 36315578 PMCID: PMC9648852 DOI: 10.1371/journal.pbio.3001884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/10/2022] [Indexed: 11/12/2022] Open
Abstract
Human endogenous retroviruses (HERVs) make up a significant part of our genome. While their expression is frequently associated with disease, a new study in PLOS Biology found that HERV-K(HML-2) is expressed in more than 50 healthy tissues.
Collapse
Affiliation(s)
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| |
Collapse
|
15
|
Maze EA, Agit B, Reeves S, Hilton DA, Parkinson DB, Laraba L, Ercolano E, Kurian KM, Hanemann CO, Belshaw RD, Ammoun S. Human endogenous retrovirus type K promotes proliferation and confers sensitivity to anti-retroviral drugs in Merlin-negative schwannoma and meningioma. Cancer Res 2021; 82:235-247. [PMID: 34853069 DOI: 10.1158/0008-5472.can-20-3857] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/04/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022]
Abstract
Deficiency of the tumour suppressor Merlin causes development of schwannoma, meningioma, and ependymoma tumours, which can occur spontaneously or in the hereditary disease neurofibromatosis type 2 (NF2). Merlin mutations are also relevant in a variety of other tumours. Surgery and radiotherapy are current first-line treatments; however, tumours frequently recur with limited treatment options. Here, we use human Merlin-negative schwannoma and meningioma primary cells to investigate the involvement of the endogenous retrovirus HERV-K in tumour development. HERV-K proteins previously implicated in tumorigenesis were overexpressed in schwannoma and all meningioma grades, and disease-associated CRL4DCAF1 and YAP/TEAD pathways were implicated in this overexpression. In normal Schwann cells, ectopic overexpression of HERV-K Env increased proliferation and upregulated expression of c-Jun and pERK1/2, which are key components of known tumorigenic pathways in schwannoma, JNK/c-Jun and RAS/RAF/MEK/ERK. Furthermore, FDA-approved retroviral protease inhibitors ritonavir, atazanavir, and lopinavir reduced proliferation of schwannoma and grade I meningioma cells. These results identify HERV-K as a critical regulator of progression in Merlin-deficient tumours and offer potential strategies for therapeutic intervention.
Collapse
Affiliation(s)
- Emmanuel A Maze
- School of Biomedical Sciences, Faculty of Health Medicine, Dentistry and Human Sciences, Plymouth University
| | - Bora Agit
- Faculty of Health Medicine, Dentistry and Human Sciences, Plymouth University
| | - Shona Reeves
- Faculty of Health Medicine, Dentistry and Human Sciences, Plymouth University
| | - David A Hilton
- Faculty of Health Medicine, Dentistry and Human Sciences, Plymouth University
| | - David B Parkinson
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry
| | - Liyam Laraba
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry
| | | | - Kathreena M Kurian
- Department of Neuropathology, Brain Tumour Research Group, Frenchay Hospital, University of Bristol
| | - C Oliver Hanemann
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry
| | | | - Sylwia Ammoun
- Faculty of Health Medicine, Dentistry and Human Sciences, Plymouth University
| |
Collapse
|
16
|
A Comprehensive Analysis of Human Endogenous Retroviruses HERV-K (HML.2) from Teratocarcinoma Cell Lines and Detection of Viral Cargo in Microvesicles. Int J Mol Sci 2021; 22:ijms222212398. [PMID: 34830279 PMCID: PMC8619701 DOI: 10.3390/ijms222212398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
About 8% of our genome is composed of sequences from Human Endogenous Retroviruses (HERVs). The HERV-K (HML.2) family, here abbreviated HML.2, is able to produce virus particles that were detected in cell lines, malignant tumors and in autoimmune diseases. Parameters and properties of HML.2 released from teratocarcinoma cell lines GH and Tera-1 were investigated in detail. In most experiments, analyzed viruses were purified by density gradient centrifugation. HML.2 structural proteins, reverse transcriptase (RT) activity, viral RNA (vRNA) and particle morphology were analyzed. The HML.2 markers were predominantly detected in fractions with a buoyant density of 1.16 g/cm3. Deglycosylation of TM revealed truncated forms of transmembrane (TM) protein. Free virions and extracellular vesicles (presumably microvesicles—MVs) with HML.2 elements, including budding intermediates, were detected by electron microscopy. Viral elements and assembled virions captured and exported by MVs can boost specific immune responses and trigger immunomodulation in recipient cells. Sequencing of cDNA clones demonstrated exclusive presence of HERV-K108 env in HML.2 from Tera-1 cells. Not counting two recombinant variants, four known env sequences were found in HML.2 from GH cells. Obtained results shed light on parameters and morphology of HML.2. A possible mechanism of HML.2-induced diseases is discussed.
Collapse
|
17
|
Tavakolian S, Goudarzi H, Moridi A, Faghihloo E. Analysing the HERV-K env, np9, rec and gag expression in cervical tissues. New Microbes New Infect 2021; 44:100936. [PMID: 34621524 PMCID: PMC8484807 DOI: 10.1016/j.nmni.2021.100936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Cervical cancer is considered to be the fourth common cancer. It is assumed that numerous risk factors, especially infectious ones, can have a detrimental effect on cervical cancer. In this study, we evaluated the expression of Herv-K env, np9, rec and gag in cervical tissues. After RNA extraction and cDNA sensitizing of 12 cervical cancer tissues and CIN3, 51 CIN1,2 and 18 normal ones, Herv-K env, np9, rec and gag were assessed using quantitative real-time PCR analysis. There was a decrease in the level of HERV-K env expression in cervical cancer and CIN 1-3 in compression with normal tissues. Cervical cancer and CIN3 indicated the most increase in expression. Meanwhile, we observed an increase in gag and rec expression in CIN 1,2; although cervical cancer and CIN 3 had a decrease in rec and gag expression, we did not report any changes in np expression. In conclusion, given the relationship between HERV-associated genes and cervical cancer, our study suggests that these genes can be useful for cancer diagnosis. However, further investigations are needed to provide a better perspective about the effectiveness of these genes in the diagnostic strategies of gastrointestinal cancer. These results are just an observation that could open a wider investigation to test the correlation between the expression of these genes and cervical cancer.
Collapse
Affiliation(s)
- S Tavakolian
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - H Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - A Moridi
- Clinical Research Development Center, Mahdiyeh Educational Hospital, Shahid Beheshti University Of Medical Sciences, Tehran, Iran
| | - E Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
18
|
Human Endogenous Retrovirus as Therapeutic Targets in Neurologic Disease. Pharmaceuticals (Basel) 2021; 14:ph14060495. [PMID: 34073730 PMCID: PMC8225122 DOI: 10.3390/ph14060495] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/15/2021] [Accepted: 05/17/2021] [Indexed: 01/16/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are ancient retroviral DNA sequences established into germline. They contain regulatory elements and encoded proteins few of which may provide benefits to hosts when co-opted as cellular genes. Their tight regulation is mainly achieved by epigenetic mechanisms, which can be altered by environmental factors, e.g., viral infections, leading to HERV activation. The aberrant expression of HERVs associates with neurological diseases, such as multiple sclerosis (MS) or amyotrophic lateral sclerosis (ALS), inflammatory processes and neurodegeneration. This review summarizes the recent advances on the epigenetic mechanisms controlling HERV expression and the pathogenic effects triggered by HERV de-repression. This article ends by describing new, promising therapies, targeting HERV elements, one of which, temelimab, has completed phase II trials with encouraging results in treating MS. The information gathered here may turn helpful in the design of new strategies to unveil epigenetic failures behind HERV-triggered diseases, opening new possibilities for druggable targets and/or for extending the use of temelimab to treat other associated diseases.
Collapse
|
19
|
Srinivasachar Badarinarayan S, Sauter D. Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections. J Virol 2021; 95:e02299-20. [PMID: 33883223 PMCID: PMC8315955 DOI: 10.1128/jvi.02299-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/30/2021] [Indexed: 01/15/2023] Open
Abstract
Long disregarded as junk DNA or genomic dark matter, endogenous retroviruses (ERVs) have turned out to represent important components of the antiviral immune response. These remnants of once-infectious retroviruses not only regulate cellular immune activation, but may even directly target invading viral pathogens. In this Gem, we summarize mechanisms by which retroviral fossils protect us from viral infections. One focus will be on recent advances in the role of ERVs as regulators of antiviral gene expression.
Collapse
MESH Headings
- Animals
- Endogenous Retroviruses/genetics
- Endogenous Retroviruses/physiology
- Enhancer Elements, Genetic
- Gene Expression Regulation
- Humans
- Immunity, Cellular
- Promoter Regions, Genetic
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Pattern Recognition/metabolism
- Receptors, Virus/antagonists & inhibitors
- Receptors, Virus/metabolism
- Retroelements
- Viral Proteins/metabolism
- Virion/metabolism
- Virus Diseases/genetics
- Virus Diseases/immunology
- Virus Diseases/virology
Collapse
Affiliation(s)
- Smitha Srinivasachar Badarinarayan
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Germany
| |
Collapse
|
20
|
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: 24] [Impact Index Per Article: 8.0] [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.
Collapse
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
| |
Collapse
|
21
|
Jansz N, Faulkner GJ. Endogenous retroviruses in the origins and treatment of cancer. Genome Biol 2021; 22:147. [PMID: 33971937 PMCID: PMC8108463 DOI: 10.1186/s13059-021-02357-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/21/2021] [Indexed: 02/07/2023] Open
Abstract
Endogenous retroviruses (ERVs) are emerging as promising therapeutic targets in cancer. As remnants of ancient retroviral infections, ERV-derived regulatory elements coordinate expression from gene networks, including those underpinning embryogenesis and immune cell function. ERV activation can promote an interferon response, a phenomenon termed viral mimicry. Although ERV expression is associated with cancer, and provisionally with autoimmune and neurodegenerative diseases, ERV-mediated inflammation is being explored as a way to sensitize tumors to immunotherapy. Here we review ERV co-option in development and innate immunity, the aberrant contribution of ERVs to tumorigenesis, and the wider biomedical potential of therapies directed at ERVs.
Collapse
Affiliation(s)
- Natasha Jansz
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia.
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia. .,Queensland Brain Institute, University of Queensland, Brisbane, QLD, 4072, Australia.
| |
Collapse
|
22
|
Human Endogenous Retrovirus K Rec forms a Regulatory Loop with MITF that Opposes the Progression of Melanoma to an Invasive Stage. Viruses 2020; 12:v12111303. [PMID: 33202765 PMCID: PMC7696977 DOI: 10.3390/v12111303] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/19/2022] Open
Abstract
The HML2 subfamily of HERV-K (henceforth HERV-K) represents the most recently endogenized retrovirus in the human genome. While the products of certain HERV-K genomic copies are expressed in normal tissues, they are upregulated in several pathological conditions, including various tumors. It remains unclear whether HERV-K(HML2)-encoded products overexpressed in cancer contribute to disease progression or are merely by-products of tumorigenesis. Here, we focus on the regulatory activities of the Long Terminal Repeats (LTR5_Hs) of HERV-K and the potential role of the HERV-K-encoded Rec in melanoma. Our regulatory genomics analysis of LTR5_Hs loci indicates that Melanocyte Inducing Transcription Factor (MITF) (also known as binds to a canonical E-box motif (CA(C/T)GTG) within these elements in proliferative type of melanoma, and that depletion of MITF results in reduced HERV-K expression. In turn, experimentally depleting Rec in a proliferative melanoma cell line leads to lower mRNA levels of MITF and its predicted target genes. Furthermore, Rec knockdown leads to an upregulation of epithelial-to-mesenchymal associated genes and an enhanced invasion phenotype of proliferative melanoma cells. Together these results suggest the existence of a regulatory loop between MITF and Rec that may modulate the transition from proliferative to invasive stages of melanoma. Because HERV-K(HML2) elements are restricted to hominoid primates, these findings might explain certain species-specific features of melanoma progression and point to some limitations of animal models in melanoma studies.
Collapse
|
23
|
Gröger V, Wieland L, Naumann M, Meinecke AC, Meinhardt B, Rossner S, Ihling C, Emmer A, Staege MS, Cynis H. Formation of HERV-K and HERV-Fc1 Envelope Family Members is Suppressed on Transcriptional and Translational Level. Int J Mol Sci 2020; 21:ijms21217855. [PMID: 33113941 PMCID: PMC7660216 DOI: 10.3390/ijms21217855] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022] Open
Abstract
The human genome comprises 8% sequences of retroviral origin, so-called human endogenous retroviruses (HERVs). Most of these proviral sequences are defective, but some possess open reading frames. They can lead to the formation of viral transcripts, when activated by intrinsic and extrinsic factors. HERVs are thought to play a pathological role in inflammatory diseases and cancer. Since the consequences of activated proviral sequences in the human body are largely unexplored, selected envelope proteins of human endogenous retroviruses associated with inflammatory diseases, namely HERV-K18, HERV-K113, and HERV-Fc1, were investigated in the present study. A formation of glycosylated envelope proteins was demonstrated in different mammalian cell lines. Nevertheless, protein maturation seemed to be incomplete as no transport to the plasma membrane was observed. Instead, the proteins remained in the ER where they induced the expression of genes involved in unfolded protein response, such as HSPA5 and sXBP1. Furthermore, low expression levels of native envelope proteins were increased by codon optimization. Cell-free expression systems showed that both the transcriptional and translational level is affected. By generating different codon-optimized variants of HERV-K113 envelope, the influence of single rare t-RNA pools in certain cell lines was demonstrated. The mRNA secondary structure also appears to play an important role in the translation of the tested viral envelope proteins. In summary, the formation of certain HERV proteins is basically possible. However, their complete maturation and thus full biologic activity seems to depend on additional factors that might be disease-specific and await elucidation in the future.
Collapse
Affiliation(s)
- Victoria Gröger
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.G.); (M.N.); (A.-C.M.)
| | - Lisa Wieland
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06097 Halle, Germany; (L.W.); (B.M.); (A.E.)
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06097 Halle, Germany
| | - Marcel Naumann
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.G.); (M.N.); (A.-C.M.)
| | - Ann-Christin Meinecke
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.G.); (M.N.); (A.-C.M.)
| | - Beate Meinhardt
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06097 Halle, Germany; (L.W.); (B.M.); (A.E.)
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06097 Halle, Germany
| | - Steffen Rossner
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstraße 19, 04103 Leipzig, Germany;
| | - Christian Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120 Halle, Germany;
| | - Alexander Emmer
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06097 Halle, Germany; (L.W.); (B.M.); (A.E.)
| | - Martin S. Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06097 Halle, Germany
- Correspondence: (M.S.S.); (H.C.); Tel.: +49-345-5577280 (M.S.S.); +49-345-13142835 (H.C.); Fax: +49-345-5577275 (M.S.S.); +49-345-13142801 (H.C.)
| | - Holger Cynis
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.G.); (M.N.); (A.-C.M.)
- Correspondence: (M.S.S.); (H.C.); Tel.: +49-345-5577280 (M.S.S.); +49-345-13142835 (H.C.); Fax: +49-345-5577275 (M.S.S.); +49-345-13142801 (H.C.)
| |
Collapse
|
24
|
Pro-Inflammatory Signaling Upregulates a Neurotoxic Conotoxin-Like Protein Encrypted Within Human Endogenous Retrovirus-K. Cells 2020; 9:cells9071584. [PMID: 32629888 PMCID: PMC7407490 DOI: 10.3390/cells9071584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/20/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
Motor neuron degeneration and spinal cord demyelination are hallmark pathological events in Amyotrophic Lateral Sclerosis (ALS). Endogenous retrovirus-K (ERVK) expression has an established association with ALS neuropathology, with murine modeling pointing to a role for the ERVK envelope (env) gene in disease processes. Here, we describe a novel viral protein cryptically encoded within the ERVK env transcript, which resembles two distinct cysteine-rich neurotoxic proteins: conotoxin proteins found in marine snails and the Human Immunodeficiency Virus (HIV) Tat protein. Consistent with Nuclear factor-kappa B (NF-κB)-induced retrotransposon expression, the ERVK conotoxin-like protein (CTXLP) is induced by inflammatory signaling. CTXLP is found in the nucleus, impacting innate immune gene expression and NF-κB p65 activity. Using human autopsy specimens from patients with ALS, we further showcase CTXLP expression in degenerating motor cortex and spinal cord tissues, concomitant with inflammation linked pathways, including enhancement of necroptosis marker mixed lineage kinase domain-like (MLKL) protein and oligodendrocyte maturation/myelination inhibitor Nogo-A. These findings identify CTXLP as a novel ERVK protein product, which may act as an effector in ALS neuropathology.
Collapse
|
25
|
Kaplan MH, Contreras-Galindo R, Jiagge E, Merajver SD, Newman L, Bigman G, Dosik MH, Palapattu GS, Siddiqui J, Chinnaiyan AM, Adebamowo S, Adebamowo C. Is the HERV-K HML-2 Xq21.33, an endogenous retrovirus mutated by gene conversion of chromosome X in a subset of African populations, associated with human breast cancer? Infect Agent Cancer 2020; 15:19. [PMID: 32165916 PMCID: PMC7060579 DOI: 10.1186/s13027-020-00284-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023] Open
Abstract
The human endogenous retroviruses HERV-K HML-2 have been considered a possible cause of human breast cancer (BrC). A HERV-K HML-2 fully intact provirus Xq21.33 was recently identified in some West African people. We used PCR technology to search for the Xq21.33 provirus in DNA from Nigerian women with BrC and controls. to see if Xq21.33 plays any role in predisposing to BrC. This provirus was detected in 27 of 216 (12.5%) women with BrC and in 22 of 219 (10.0%) controls. These results were not statistically significant. The prevalence of provirus in premenopausal control women 44 years or younger [18/157 (11.46%)} vs women with BrC [12/117 (10.26%)] showed no statistical difference. The prevalence of virus in postmenopausal control women > 45 yrs. was 7.4% (4/54) vs 15.31% (15/98) in postmenopausal women with BrC. These changes were not statistically significant at <.05, but the actual p value of <.0.079, suggests that Xq21.33 might play some role in predisposing to BrC in postmenopausal women. Provirus was present in Ghanaian women (6/87), in 1/6 Pygmy populations and in African American men (4/45) and women (6/68), but not in any Caucasian women (0/109). Two BrC cell lines (HCC 70 and DT22) from African American women had Xq21.33. Env regions of the virus which differed by 2-3 SNPs did not alter the protein sequence of the virus. SNP at 5730 and 8529 were seen in all persons with provirus, while 54% had an additional SNP at 7596.Two Nigerian women and 2 Ghanaian women had additional unusual SNPs. Homozygosity was seen in (5/27) BrC and (2/22) control women. The genetic variation and homozygosity patterns suggested that there was gene conversion of this X chromosome associated virus. The suggestive finding in this preliminary data of possible increased prevalence of Xq21.33 provirus in post-menopausal Nigerian women with BrC should be clarified by a more statistically powered study sample to see if postmenopausal African and/or African American women carriers of Xq21.33 might show increased risk of BrC. The implication of finding such a link would be the development of antiretroviral drugs that might aid in preventing BrC in Xq21.33+ women.
Collapse
Affiliation(s)
- Mark H. Kaplan
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - Evelyn Jiagge
- Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Mi USA
| | - Sofia D. Merajver
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109 USA
| | - Lisa Newman
- Weill Cornell Medicine, New York, NY 10021 USA
| | - Galya Bigman
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Michael H. Dosik
- Department of Internal Medicine, Renaissance School of Medicine at Stony Brook Medical, Stony Brook, NY 11794 USA
| | | | - Javed Siddiqui
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109 USA
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Arul M. Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109 USA
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Sally Adebamowo
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Clement Adebamowo
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109 USA
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| |
Collapse
|
26
|
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: 13] [Impact Index Per Article: 3.3] [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.
Collapse
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
| |
Collapse
|
27
|
Tavakolian S, Goudarzi H, Lak E, Faghihloo E. The evaluation of HERV-K env, np9, rec, gag expression in normal, polyp and cancerous tissues of gastric and colon. Future Virol 2019. [DOI: 10.2217/fvl-2019-0114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aim: Gastrointestinal cancer is one of the most alarming cancers worldwide. Infections exert an impact on tumor progression in gastrointestinal tissues. The alteration in the expression of human endogenous retrovirus-K ( HERV-K) genes could remarkably induce oncogenic activity. Materials & methods: In 22 gastric and 23 colon cancer patients, the expression level of HERV-K env, rec, gag and np9 were evaluated. Results: While there was a slight increase in the expression of HERV-K env in colon cancer tissues, the expression level of this gene decreased in gastric tissues. Moreover, the expression of both np9 and gag HERV-K were upregulated only in colon cancer. Nevertheless, rec HERV-K was downregulated in gastric cancer tissues. Conclusion: HERV-K-associated genes can be used as a possible biomarker for cancers diagnosis.
Collapse
Affiliation(s)
- Shaian Tavakolian
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elena Lak
- Department of gastric & liver, Emam Hossein hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
28
|
Tavakolian S, Goudarzi H, Faghihloo E. Evaluating the expression level of HERV-K env, np9, rec and gag in breast tissue. Infect Agent Cancer 2019; 14:42. [PMID: 31798679 PMCID: PMC6884765 DOI: 10.1186/s13027-019-0260-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Breast cancer is one of the most common health problems. It has been suggested that several risk factors, either considered as external or internal, play a critical role in the pathogenesis of breast cancer, which among them, HERV-k, has the most fundamental role. In the present study, we aimed to evaluate the role of HERV-k env, gag, rec, np9 expressions in breast cancer progression. MATERIALS AND METHODS We collected 40 breast cancer tissues and their normal adjacent ones. After extracting the RNA of breast samples, we evaluated the expression of HERV-k env, gag, rec, np9 by using Quantitative real-time PCR (qRT-PCR). RESULTS The resulting data revealed that while there was a meaningful increase in the expression level of HERV-k env, gag and np9 in breast cancer tissues (P ≤ 0.01, 0.05, 0.05, respectively), we failed to find any significant elevation in the expression level of rec mRNA level. CONCLUSION The results of our study suggested that there is a plausible correlation between the mRNA expression level of HERV-K env, gag and np9 and the progression of breast cancer, proposing these markers as promising biomarkers to diagnose breast cancer.
Collapse
Affiliation(s)
- Shaian Tavakolian
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
29
|
Tracking the Fate of Endogenous Retrovirus Segregation in Wild and Domestic Cats. J Virol 2019; 93:JVI.01324-19. [PMID: 31534037 DOI: 10.1128/jvi.01324-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/09/2019] [Indexed: 12/26/2022] Open
Abstract
Endogenous retroviruses (ERVs) of domestic cats (ERV-DCs) are one of the youngest feline ERV groups in domestic cats (Felis silvestris catus); some members are replication competent (ERV-DC10, ERV-DC18, and ERV-DC14), produce the antiretroviral soluble factor Refrex-1 (ERV-DC7 and ERV-DC16), or can generate recombinant feline leukemia virus (FeLV). Here, we investigated ERV-DC in European wildcats (Felis silvestris silvestris) and detected four loci: ERV-DC6, ERV-DC7, ERV-DC14, and ERV-DC16. ERV-DC14 was detected at a high frequency in European wildcats; however, it was replication defective due to a single G → A nucleotide substitution, resulting in an E148K substitution in the ERV-DC14 envelope (Env). This mutation results in a cleavage-defective Env that is not incorporated into viral particles. Introduction of the same mutation into feline and murine infectious gammaretroviruses resulted in a similar Env dysfunction. Interestingly, the same mutation was found in an FeLV isolate from naturally occurring thymic lymphoma and a mouse ERV, suggesting a common mechanism of virus inactivation. Refrex-1 was present in European wildcats; however, ERV-DC16, but not ERV-DC7, was unfixed in European wildcats. Thus, Refrex-1 has had an antiviral role throughout the evolution of the genus Felis, predating cat exposure to feline retroviruses. ERV-DC sequence diversity was present across wild and domestic cats but was locus dependent. In conclusion, ERVs have evolved species-specific phenotypes through the interplay between ERVs and their hosts. The mechanism of viral inactivation may be similar irrespective of the evolutionary history of retroviruses. The tracking of ancestral retroviruses can shed light on their roles in pathogenesis and host-virus evolution.IMPORTANCE Domestic cats (Felis silvestris catus) were domesticated from wildcats approximately 9,000 years ago via close interaction between humans and cats. During cat evolution, various exogenous retroviruses infected different cat lineages and generated numerous ERVs in the host genome, some of which remain replication competent. Here, we detected several ERV-DC loci in Felis silvestris silvestris Notably, a species-specific single nucleotide polymorphism in the ERV-DC14 env gene, which results in a replication-defective product, is highly prevalent in European wildcats, unlike the replication-competent ERV-DC14 that is commonly present in domestic cats. The presence of the same lethal mutation in the env genes of both FeLV and murine ERV provides a common mechanism shared by endogenous and exogenous retroviruses by which ERVs can be inactivated after endogenization. The antiviral role of Refrex-1 predates cat exposure to feline retroviruses. The existence of two ERV-DC14 phenotypes provides a unique model for understanding both ERV fate and cat domestication.
Collapse
|
30
|
Garcia-Montojo M, Doucet-O'Hare T, Henderson L, Nath A. Human endogenous retrovirus-K (HML-2): a comprehensive review. Crit Rev Microbiol 2018; 44:715-738. [PMID: 30318978 DOI: 10.1080/1040841x.2018.1501345] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The human genome contains a large number of retroviral elements acquired over the process of evolution, some of which are specific to primates. However, as many of these are defective or silenced through epigenetic changes, they were historically considered "junk DNA" and their potential role in human physiology or pathological circumstances have been poorly studied. The most recently acquired, human endogenous retrovirus-K (HERV-K), has multiple copies in the human genome and some of them have complete open reading frames that are transcribed and translated, especially in early embryogenesis. Phylogenetically, HERV-K is considered a supergroup of viruses. One of the subtypes, termed HML-2, seems to be the most active and hence, it is the best studied. Aberrant expression of HML-2 in adult tissues has been associated with certain types of cancer and with neurodegenerative diseases. This review discusses the discovery of these viruses, their classification, structure, regulation and potential for replication, physiological roles, and their involvement in disease pathogenesis. Finally, it presents different therapeutic approaches being considered to target these viruses.
Collapse
Affiliation(s)
- Marta Garcia-Montojo
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Tara Doucet-O'Hare
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Lisa Henderson
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Avindra Nath
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| |
Collapse
|
31
|
Disruption by SaCas9 Endonuclease of HERV-K env, a Retroviral Gene with Oncogenic and Neuropathogenic Potential, Inhibits Molecules Involved in Cancer and Amyotrophic Lateral Sclerosis. Viruses 2018; 10:v10080412. [PMID: 30087231 PMCID: PMC6115762 DOI: 10.3390/v10080412] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/14/2022] Open
Abstract
The human endogenous retrovirus (HERV)-K, human mouse mammary tumor virus like-2 (HML-2) subgroup of HERVs is activated in several tumors and has been related to prostate cancer progression and motor neuron diseases. The cellular splicing factor 2/alternative splicing factor (SF2/ASF) is a positive regulator of gene expression, coded by a potent proto-oncogene, amplified, and abnormally expressed in tumors. TAR DNA-binding protein-43 (TDP-43) is a DNA/RNA-binding protein, negative regulator of alternative splicing, known for causing neurodegeneration, and with complex roles in oncogenesis. We used the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, with the Cas9 system from Staphylococcus aureus (SaCas9), to disrupt the HERV-K(HML-2)env gene, and evaluated the effects on cultured cells. The tool was tested on human prostate cancer LNCaP cells, whose HERV-Kenv transcription profile is known. It caused HERV-K(HML-2)env disruption (the first reported of a HERV gene), as evaluated by DNA sequencing, and inhibition of env transcripts and proteins. The HERV-K(HML-2)env disruption was found to interfere with important regulators of cell expression and proliferation, involved in manaling, RNA-binding, and alternative splicing, such as epidermal growth factor receptor (EGF-R), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), SF2/ASF, and TDP-43. These novel findings suggest that HERV-K is not an innocent bystander, they reinforce its links to oncogenesis and motor neuron diseases, and they open potential innovative therapeutic options.
Collapse
|
32
|
Robinson-McCarthy LR, McCarthy KR, Raaben M, Piccinotti S, Nieuwenhuis J, Stubbs SH, Bakkers MJG, Whelan SPJ. Reconstruction of the cell entry pathway of an extinct virus. PLoS Pathog 2018; 14:e1007123. [PMID: 30080900 PMCID: PMC6095630 DOI: 10.1371/journal.ppat.1007123] [Citation(s) in RCA: 15] [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: 05/23/2018] [Revised: 08/16/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Endogenous retroviruses (ERVs), remnants of ancient germline infections, comprise 8% of the human genome. The most recently integrated includes human ERV-K (HERV-K) where several envelope (env) sequences remain intact. Viral pseudotypes decorated with one of those Envs are infectious. Using a recombinant vesicular stomatitis virus encoding HERV-K Env as its sole attachment and fusion protein (VSV-HERVK) we conducted a genome-wide haploid genetic screen to interrogate the host requirements for infection. This screen identified 11 genes involved in heparan sulfate biosynthesis. Genetic inhibition or chemical removal of heparan sulfate and addition of excess soluble heparan sulfate inhibit infection. Direct binding of heparin to soluble HERV-K Env and purified VSV-HERVK defines it as critical for viral attachment. Cell surface bound VSV-HERVK particles are triggered to infect on exposure to acidic pH, whereas acid pH pretreatment of virions blocks infection. Testing of additional endogenous HERV-K env sequences reveals they bind heparin and mediate acid pH triggered fusion. This work reconstructs and defines key steps in the infectious entry pathway of an extinct virus.
Collapse
Affiliation(s)
- Lindsey R. Robinson-McCarthy
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kevin R. McCarthy
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Matthijs Raaben
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Silvia Piccinotti
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joppe Nieuwenhuis
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sarah H. Stubbs
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mark J. G. Bakkers
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sean P. J. Whelan
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|
33
|
Klein SJ, O'Neill RJ. Transposable elements: genome innovation, chromosome diversity, and centromere conflict. Chromosome Res 2018; 26:5-23. [PMID: 29332159 PMCID: PMC5857280 DOI: 10.1007/s10577-017-9569-5] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 12/21/2022]
Abstract
Although it was nearly 70 years ago when transposable elements (TEs) were first discovered “jumping” from one genomic location to another, TEs are now recognized as contributors to genomic innovations as well as genome instability across a wide variety of species. In this review, we illustrate the ways in which active TEs, specifically retroelements, can create novel chromosome rearrangements and impact gene expression, leading to disease in some cases and species-specific diversity in others. We explore the ways in which eukaryotic genomes have evolved defense mechanisms to temper TE activity and the ways in which TEs continue to influence genome structure despite being rendered transpositionally inactive. Finally, we focus on the role of TEs in the establishment, maintenance, and stabilization of critical, yet rapidly evolving, chromosome features: eukaryotic centromeres. Across centromeres, specific types of TEs participate in genomic conflict, a balancing act wherein they are actively inserting into centromeric domains yet are harnessed for the recruitment of centromeric histones and potentially new centromere formation.
Collapse
Affiliation(s)
- Savannah J Klein
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA.
| |
Collapse
|
34
|
Rascovan N, Duraisamy R, Desnues C. Metagenomics and the Human Virome in Asymptomatic Individuals. Annu Rev Microbiol 2017; 70:125-41. [PMID: 27607550 DOI: 10.1146/annurev-micro-102215-095431] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High-throughput sequencing technologies have revolutionized how we think about viruses. Investigators can now go beyond pathogenic viruses and have access to the thousands of viruses that inhabit our bodies without causing clinical symptoms. By studying their interactions with each other, with other microbes, and with host genetics and immune systems, we can learn how they affect health and disease. This article reviews current knowledge of the composition and diversity of the human virome in physiologically healthy individuals. It focuses on recent results from metagenomics studies and discusses the contribution of bacteriophages and eukaryotic viruses to human health.
Collapse
Affiliation(s)
- Nicolás Rascovan
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
| | - Raja Duraisamy
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
| | - Christelle Desnues
- Faculté de Médecine, Aix Marseille Université, 13385 Marseille, France.,URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13385 Marseille, France;
| |
Collapse
|
35
|
Lemaître C, Tsang J, Bireau C, Heidmann T, Dewannieux M. A human endogenous retrovirus-derived gene that can contribute to oncogenesis by activating the ERK pathway and inducing migration and invasion. PLoS Pathog 2017. [PMID: 28651004 PMCID: PMC5501692 DOI: 10.1371/journal.ppat.1006451] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Endogenous retroviruses are cellular genes of retroviral origin captured by their host during the course of evolution and represent around 8% of the human genome. Although most are defective and transcriptionally silenced, some are still able to generate retroviral-like particles and proteins. Among these, the HERV-K(HML2) family is remarkable since its members have amplified relatively recently and many of them still have full length coding genes. Furthermore, they are induced in cancers, especially in melanoma, breast cancer and germ cell tumours, where viral particles, as well as the envelope protein (Env), can be detected. Here we show that HERV-K(HML2) Env per se has oncogenic properties. Its expression in a non-tumourigenic human breast epithelial cell line induces epithelial to mesenchymal transition (EMT), often associated with tumour aggressiveness and metastasis. In our model, this is typified by key modifications in a set of molecular markers, changes in cell morphology and enhanced cell motility. Remarkably, microarrays performed in 293T cells reveal that HERV-K(HML2) Env is a strong inducer of several transcription factors, namely ETV4, ETV5 and EGR1, which are downstream effectors of the MAPK ERK1/2 and are associated with cellular transformation. We demonstrate that HERV-K(HML2) Env effectively activates the ERK1/2 pathway in our experimental setting and that this activation depends on the Env cytoplasmic tail. In addition, this phenomenon is very specific, being absent with every other retroviral Env tested, except for Jaagsiekte Sheep Retrovirus (JSRV) Env, which is already known to have transforming properties in vivo. Though HERV-K Env is not directly transforming by itself, the newly discovered properties of this protein may contribute to oncogenesis. Nearly half the DNA of mammals consists of reitarated, selfish elements that can move and amplify within the genome. With time, some of these elements are recruited by the host and the proteins they encode are used to fulfill physiological functions, whereas other elements have conserved some of their pathological properties and contribute to the development of diseases. The human HERV-K(HML2) elements originated from an ancestral infection of the primate germline by an infectious retrovirus that has been maintained and amplified in the human lineage. It is associated with several pathologies in modern humans, in particular cancer of the breast, germline and skin. We show that the HERV-K(HML2) envelope protein is able to activate a major cellular signalling pathway often involved in human cancers, and that its expression promotes a series of cellular changes that are characteristic of cancer development. Altogether, this study indicates that the expression of HERV-K(HML2) elements is not only a marker of cancer, but can also directly participate to tumourigenesis via the newly discovered oncogenic properties carried by the envelope protein.
Collapse
Affiliation(s)
- Cécile Lemaître
- CNRS, UMR 9196, Institut Gustave Roussy, Villejuif, France
- Université Paris-Sud, Orsay, France
- Université Paris Denis Diderot, Sorbonne Paris-Cité, Paris, France
| | - Jhen Tsang
- CNRS, UMR 9196, Institut Gustave Roussy, Villejuif, France
- Université Paris-Sud, Orsay, France
| | - Caroline Bireau
- CNRS, UMR 9196, Institut Gustave Roussy, Villejuif, France
- Université Paris-Sud, Orsay, France
| | - Thierry Heidmann
- CNRS, UMR 9196, Institut Gustave Roussy, Villejuif, France
- Université Paris-Sud, Orsay, France
- * E-mail: (MD); (TH)
| | - Marie Dewannieux
- CNRS, UMR 9196, Institut Gustave Roussy, Villejuif, France
- Université Paris-Sud, Orsay, France
- * E-mail: (MD); (TH)
| |
Collapse
|
36
|
Terry SN, Manganaro L, Cuesta-Dominguez A, Brinzevich D, Simon V, Mulder LCF. Expression of HERV-K108 envelope interferes with HIV-1 production. Virology 2017; 509:52-59. [PMID: 28605635 DOI: 10.1016/j.virol.2017.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/30/2017] [Accepted: 06/02/2017] [Indexed: 11/16/2022]
Abstract
The human endogenous retroviruses (HERV)-K of the HML-2 group include full-length or near full-length elements encoding functional proteins, and are classified as type-1 or type-2 (type-1 has a deletion in the 5' end of the env gene). Because proteins of different retroviruses can interact, we hypothesized that HERV-K envelope (Env) could influence HIV-1 replication. Here we describe the negative effect of envelope expression of certain type-2 HERV-Ks on HIV-1 production. All HIV-1 and SIV strains tested were susceptible to various degrees to inhibition by the HERV-K108 envelope. We identified four residues within HERV-K108 Env as being critical to inhibit HIV-1 production. No inhibition was observed on EGFP expression, indicating that HERV-K Env does not affect general protein production. These findings demonstrate that envelope proteins from some endogenous retroviruses can limit production of exogenous lentiviruses such as HIV-1. Future studies will elucidate the mechanism mediating HIV-1 inhibition by HERV Envs.
Collapse
Affiliation(s)
- Sandra N Terry
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lara Manganaro
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alvaro Cuesta-Dominguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daria Brinzevich
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lubbertus C F Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
37
|
Johanning GL, Malouf GG, Zheng X, Esteva FJ, Weinstein JN, Wang-Johanning F, Su X. Expression of human endogenous retrovirus-K is strongly associated with the basal-like breast cancer phenotype. Sci Rep 2017; 7:41960. [PMID: 28165048 PMCID: PMC5292751 DOI: 10.1038/srep41960] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/03/2017] [Indexed: 12/18/2022] Open
Abstract
Human endogenous retroviruses (HERVs), which make up approximately 8% of the human genome, are overexpressed in some breast cancer cells and tissues but without regard to cancer subtype. We, therefore, analyzed TCGA RNA-Seq data to evaluate differences in expression of the HERV-K family in breast cancers of the various subtypes. Four HERV-K loci on different chromosomes were analyzed in basal, Her2E, LumA, and LumB breast cancer subtypes of 512 breast cancer patients with invasive ductal carcinoma (IDC). The results for all four loci showed higher HERV-K expression in the basal subtype, suggesting similar mechanisms of regulation regardless of locus. Expression of the HERV-K envelope gene (env) was highly significantly increased in basal tumors in comparison with the also-upregulated expression of other HERV-K genes. Analysis of reverse-phase protein array data indicated that increased expression of HERV-K is associated with decreased mutation of H-Ras (wild-type). Our results show elevation of HERV-K expression exclusively in the basal subtype of IDC breast cancer (as opposed to the other subtypes) and suggest HERV-K as a possible target for cancer vaccines or immunotherapy against this highly aggressive form of breast cancer.
Collapse
Affiliation(s)
- Gary L Johanning
- SRI International, Biosciences Division, 333 Ravenswood Ave, Menlo Park, CA, USA
| | - Gabriel G Malouf
- Department of Medical Oncology, Groupe Hospitalier Pitié-Salpêtrière, Université Pierre and Marie Curie (Paris VI), GRC5, ONCOTYPE-Uro, Institut Universitaire de Cancérologie, Assistance-Publique Hôpitaux de Paris, Paris, France
| | - Xiaofeng Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francisco J Esteva
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Feng Wang-Johanning
- SRI International, Biosciences Division, 333 Ravenswood Ave, Menlo Park, CA, USA
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
38
|
Contribution of Syncytins and Other Endogenous Retroviral Envelopes to Human Placenta Pathologies. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 145:111-162. [DOI: 10.1016/bs.pmbts.2016.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
39
|
Li F, Karlsson H. Expression and regulation of human endogenous retrovirus W elements. APMIS 2016; 124:52-66. [PMID: 26818262 DOI: 10.1111/apm.12478] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 10/12/2015] [Indexed: 01/06/2023]
Abstract
Human endogenous retroviruses (HERV) comprise 8% of the human genome and can be classified into at least 31 families. A typical HERV provirus consists of internal gag, pol and env genes, flanked by two long terminal repeats (LTRs). No single provirus is capable of engendering infectious particles. HERV are by nature repetitive and have with few notable exceptions lost their protein-coding capacity. Therefore, HERV have consistently been excluded from array-based expression studies and hence little is known of their expression, regulation, and potential functional significance. An increasing number of studies have, however, observed expression of the W family of HERV in various human tissues and cells, predominantly in placenta. HERV-W LTRs act as promoters in directing transcription of HERV-W members, contribute to their tissue-specific and highly diversified expression pattern. Furthermore, leaky transcription originating from adjacent genes plays a role in the transcription initiation of HERV-W psudoelements. It has been reported that HERV-W elements, including ERVWE1 (the so far only known HERV-W locus harboring a gene (env) functionally adopted by the human host to critically participate in placenta biogenesis), can become transactivated in a range of human non-placental cell-lines during exogenous virus infections. Aberrant expression of HERV-W has been associated with human diseases, such as cancer, multiple sclerosis, and schizophrenia. Based on published reports, transcriptional activities of HERV-W appear to be influenced by several mechanisms; binding of transcription factors to LTR promoters and enhancers outside of LTRs, genetic variation and alteration in DNA methylation and histone modification. Emerging mechanistic studies support the notion that HERV-W represents a potential marker or mediator of environmental exposures (e.g., virus infection) in the development of chronic complex diseases.
Collapse
Affiliation(s)
- Fang Li
- Department of Basic Medical Science, Changsha Medical University, Changsha, China.,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Håkan Karlsson
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
40
|
Sokol M, Jessen KM, Pedersen FS. Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses. APMIS 2016; 124:127-39. [PMID: 26818267 DOI: 10.1111/apm.12477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/12/2015] [Indexed: 12/13/2022]
Abstract
Several studies have shown that human endogenous retroviruses and endogenous retrovirus-like repeats (here collectively HERVs) impose direct regulation on human genes through enhancer and promoter motifs present in their long terminal repeats (LTRs). Although chimeric transcription in which novel gene isoforms containing retroviral and human sequence are transcribed from viral promoters are commonly associated with disease, regulation by HERVs is beneficial in other settings; for example, in human testis chimeric isoforms of TP63 induced by an ERV9 LTR protect the male germ line upon DNA damage by inducing apoptosis, whereas in the human globin locus the γ- and β-globin switch during normal hematopoiesis is mediated by complex interactions of an ERV9 LTR and surrounding human sequence. The advent of deep sequencing or next-generation sequencing (NGS) has revolutionized the way researchers solve important scientific questions and develop novel hypotheses in relation to human genome regulation. We recently applied next-generation paired-end RNA-sequencing (RNA-seq) together with chromatin immunoprecipitation with sequencing (ChIP-seq) to examine ERV9 chimeric transcription in human reference cell lines from Encyclopedia of DNA Elements (ENCODE). This led to the discovery of advanced regulation mechanisms by ERV9s and other HERVs across numerous human loci including transcription of large gene-unannotated genomic regions, as well as cooperative regulation by multiple HERVs and non-LTR repeats such as Alu elements. In this article, well-established examples of human gene regulation by HERVs are reviewed followed by a description of paired-end RNA-seq, and its application in identifying chimeric transcription genome-widely. Based on integrative analyses of RNA-seq and ChIP-seq, data we then present novel examples of regulation by ERV9s of tumor suppressor genes CADM2 and SEMA3A, as well as transcription of an unannotated region. Taken together, this article highlights the high suitability of contemporary sequencing methods in future analyses of human biology in relation to evolutionary acquired retroviruses in the human genome.
Collapse
Affiliation(s)
- Martin Sokol
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Finn Skou Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| |
Collapse
|
41
|
Abstract
Mammalian life begins with a cell-cell fusion event, i.e. the fusion of the spermatozoid with the oocyte and needs further cell-cell fusion processes for the development, growth, and maintenance of tissues and organs over the whole life span. Furthermore, cellular fusion plays a role in infection, cancer, and stem cell-dependent regeneration as well as including an expanded meaning of partial cellular fusion, nanotube formation, and microparticle-cell fusion. The cellular fusion process is highly regulated by proteins which carry the information to organize and regulate membranes allowing the merge of two separate lipid bilayers into one. The regulation of this genetically and epigenetically controlled process is achieved by different kinds of signals leading to communication of fusing cells. The local cellular and extracellular environment additionally initiates specific cell signaling necessary for the induction of the cell-cell fusion process. Common motifs exist in distinct cell-cell fusion processes and their regulation. However, there is specific regulation of different cell-cell fusion processes, e.g. myoblast, placental, osteoclast, and stem cell fusion. Hence, specialized fusion events vary between cell types and species. Molecular mechanisms remain largely unknown, especially limited knowledge is present for cancer and stem cell fusion mechanisms and regulation. More research is necessary for the understanding of cellular fusion processes which can lead to development of new therapeutic strategies grounding on cellular fusion regulation.
Collapse
Affiliation(s)
- Lena Willkomm
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiovascular Research and Sport Medicine, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany
| | | |
Collapse
|
42
|
Infectious Entry Pathway Mediated by the Human Endogenous Retrovirus K Envelope Protein. J Virol 2016; 90:3640-9. [PMID: 26792739 DOI: 10.1128/jvi.03136-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/12/2016] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Endogenous retroviruses (ERVs), the majority of which exist as degraded remnants of ancient viruses, comprise approximately 8% of the human genome. The youngest human ERVs (HERVs) belong to the HERV-K(HML-2) subgroup and were endogenized within the past 1 million years. The viral envelope protein (ENV) facilitates the earliest events of endogenization (cellular attachment and entry), and here, we characterize the requirements for HERV-K ENV to mediate infectious cell entry. Cell-cell fusion assays indicate that a minimum of two events are required for fusion, proteolytic processing by furin-like proteases and exposure to acidic pH. We generated an infectious autonomously replicating recombinant vesicular stomatitis virus (VSV) in which the glycoprotein was replaced by HERV-K ENV. HERV-K ENV imparts an endocytic entry pathway that requires dynamin-mediated membrane scission and endosomal acidification but is distinct from clathrin-dependent or macropinocytic uptake pathways. The lack of impediments to the replication of the VSV core in eukaryotic cells allowed us to broadly survey the HERV-K ENV-dictated tropism. Unlike extant betaretroviral envelopes, which impart a narrow species tropism, we found that HERV-K ENV mediates broad tropism encompassing cells from multiple mammalian and nonmammalian species. We conclude that HERV-K ENV dictates an evolutionarily conserved entry pathway and that the restriction of HERV-K to primate genomes reflects downstream stages of the viral replication cycle. IMPORTANCE Approximately 8% of the human genome is of retroviral origin. While many of those viral genomes have become inactivated, some copies of the most recently endogenized human retrovirus, HERV-K, can encode individual functional proteins. Here, we characterize the envelope protein (ENV) of the virus to define how it mediates infection of cells. We demonstrate that HERV-K ENV undergoes a proteolytic processing step and triggers membrane fusion in response to acidic pH--a strategy common to many viral fusogens. Our data suggest that the infectious entry pathway mediated by this ENV requires endosomal acidification and the GTPase dynamin but does not require clathrin-dependent uptake. In marked contrast to other betaretroviruses, HERV-K ENV imparts broad species tropism in cultured cells. This work provides new insights into the entry pathway of an extinct human virus and provides a powerful tool to further probe the endocytic route by which HERV-K infects cells.
Collapse
|
43
|
Buslei R, Strissel PL, Henke C, Schey R, Lang N, Ruebner M, Stolt CC, Fabry B, Buchfelder M, Strick R. Activation and regulation of endogenous retroviral genes in the human pituitary gland and related endocrine tumours. Neuropathol Appl Neurobiol 2015; 41:180-200. [PMID: 24635849 DOI: 10.1111/nan.12136] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022]
Abstract
AIMS Adenohypophysis (AH) hormone-producing cells represent the origin of diverse groups of pituitary adenomas (PA). Deregulation of hypothalamic hormone receptors, growth factors and cAMP signalling have been implicated in the aetiology of PA. Endogenous retroviruses (ERVs) are derived from past exogenous retroviral infections and represent more than 8% of the human genome. Some ERV genes encode open reading frames and produce functional proteins, for example, the ERVW-1 envelope gene Syncytin-1, essential for placentogenesis, but also deregulated in human tumours. Data concerning ERV expression in the AH and related endocrine tumours are missing. METHODS Syncytin-1 protein was analysed in normal AH (n = 15) and compared with five PA subtypes (n = 117) by immunohistochemistry. Absolute gene expression of 20 ERV functional envelope genes and ERVW-5 gag was measured. PA tissues were examined for Syncytin-1 and the cAMP signalling marker phospho-CREB-Ser133 using immunohistochemistry. Isolated primary human PA cells were treated with different hormones. Murine embryonic and adult pituitary gland ERV expressions were compared with human AH. RESULTS Syncytin-1 protein colocalized with corticotropic cells of AH. In contrast, all PA demonstrated significant Syncytin-1 protein overexpression, supporting deregulation. All other ERV genes showed significant up-regulations in different PA subtypes. Phospho-CREB-Ser133 and Syncytin-1 colocalized in PA cells. Cultivated primary PA cells with ACTH or CRH induced their respective receptors and ERV genes. Syncytin-A/-B, murine orthologues to human Syncytin-1/-2, localized to embryonic and adult pituitary glands demonstrating functional mammalian conservation. CONCLUSIONS Deregulated ERV genes may contribute to PA development via cAMP signalling.
Collapse
Affiliation(s)
- Rolf Buslei
- Institute of Neuropathology, University-Clinic Erlangen, Lab for Molecular Medicine, Erlangen, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Ancestral Mutations Acquired in Refrex-1, a Restriction Factor against Feline Retroviruses, during its Cooption and Domestication. J Virol 2015; 90:1470-85. [PMID: 26581999 DOI: 10.1128/jvi.01904-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/13/2015] [Indexed: 01/03/2023] Open
Abstract
UNLABELLED Endogenous retroviruses (ERVs) are remnants of ancestral retroviral infections of germ cells. Retroviral endogenization is an adaptation process for the host genome, and ERVs are gradually attenuated or inactivated by mutation. However, some ERVs that have been "domesticated" by their hosts eventually gain physiological functions, such as placentation or viral resistance. We previously reported the discovery of Refrex-1, a soluble antiretroviral factor in domestic cats that specifically inhibits infection by feline leukemia virus subgroup D (FeLV-D), a chimeric virus of FeLV, and a feline ERV, ERV-DC. Refrex-1 is a truncated envelope protein (Env) encoded by both ERV-DC7 and ERV-DC16 proviral loci. Here, we reconstituted ancestral and functional Env from ERV-DC7 and ERV-DC16 envelope genes (env) by inducing reverse mutations. Unexpectedly, ERV-DC7 and ERV-DC16 full-length Env (ERV-DC7 fl and ERV-DC16 fl), reconstructed by removing stop codons, did not produce infectious viral particles. ERV-DC7 fl and ERV-DC16 fl were highly expressed in cells but were not cleaved into surface subunits (SU) and transmembrane subunits, nor were they incorporated into virions. G407R/N427I-A429T and Y431D substitutions within the SU C-terminal domain of ERV-DC7 fl and ERV-DC16 fl, respectively, caused these dysfunctions. The residues glycine 407 and tyrosine 431 are relatively conserved among infectious gammaretroviruses, and their substitution causes the same dysfunctions as the tested retroviruses. Our results reveal that specific mutations within the SU C-terminal domain suppressed Env cleavage and incorporation into virions and indicate that these mutations contributed to the domestication of Refrex-1 through multistep events that occurred in the postintegration period. IMPORTANCE Domestic cats are colonized with various exogenous retroviruses (exRVs), such as feline leukemia virus (FeLV), and their genomes contain numerous ERVs, some of which are replication-competent proviruses. The feline hosts, exRVs, and ERVs have complicated genetic interactions and provide an interesting field model for triangular relationships: recombination between FeLV and ERV-DC, which is a feline ERV, generated FeLV-D, a chimeric virus, and FeLV-D is restricted by Refrex-1, an antiretroviral factor corresponding to truncated Env of ERV-DC7 and ERV-DC16. Here, we reconstructed ancestral, functional Env from ERV-DC7 and ERV-DC16 env by inducing reverse mutations to elucidate how Refrex-1 was generated from its ancestor. Our results reveal that they were repeatedly inactivated by mutations preventing Env maturation. Our results provide insights into how ERVs were "domesticated" by their hosts and identify the mutations that mediated these evolutions. Notably, experiments that restore inactivated ERVs might uncover previously unrecognized features or properties of retroviruses.
Collapse
|
45
|
Kramer P, Lausch V, Volkwein A, Hanke K, Hohn O, Bannert N. The human endogenous retrovirus K(HML-2) has a broad envelope-mediated cellular tropism and is prone to inhibition at a post-entry, pre-integration step. Virology 2015; 487:121-8. [PMID: 26517399 DOI: 10.1016/j.virol.2015.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 11/28/2022]
Abstract
The HERV-K(HML-2) family is the most recent addition to the collection of human endogenous retroviruses. It comprises proviruses that encode functional proteins that can assemble into replication defective particles carrying the envelope protein. Using a reconstituted HERV-K113 envelope sequence, we have analyzed its ability to mediate entry into a set of 33 cell lines from 10 species. Of these, 30 were permissive, demonstrating an amphotropism consistent with a broad expression of receptor protein(s). In an initial effort to identify a receptor for HERV-K(HML-2) we investigated whether transferrin receptor 1 and hyaluronidase 2, known cellular receptors of the closely related betaretroviruses mouse mammary tumor virus (MMTV) and Jaagsiekte sheep retrovirus (JSRV), could facilitate HERV-K(HML-2) entry. However, neither of these proteins could serve as a receptor for HERV-K(HML-2). Moreover, during attempts to further characterize the tropism of HERV-K(HML-2), we identified a cellular activity that inhibits infection at a post-entry, pre-integration step.
Collapse
Affiliation(s)
- Philipp Kramer
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany
| | - Veronika Lausch
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany
| | - Alexander Volkwein
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany
| | - Kirsten Hanke
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany
| | - Oliver Hohn
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany
| | - Norbert Bannert
- Robert Koch Institute, Division for HIV and Other Retroviruses, Nordufer 20, 13353 Berlin, Germany.
| |
Collapse
|
46
|
Suntsova M, Garazha A, Ivanova A, Kaminsky D, Zhavoronkov A, Buzdin A. Molecular functions of human endogenous retroviruses in health and disease. Cell Mol Life Sci 2015; 72:3653-75. [PMID: 26082181 PMCID: PMC11113533 DOI: 10.1007/s00018-015-1947-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 05/29/2015] [Accepted: 06/03/2015] [Indexed: 12/13/2022]
Abstract
Human endogenous retroviruses (HERVs) and related genetic elements form 504 distinct families and occupy ~8% of human genome. Recent success of high-throughput experimental technologies facilitated understanding functional impact of HERVs for molecular machinery of human cells. HERVs encode active retroviral proteins, which may exert important physiological functions in the body, but also may be involved in the progression of cancer and numerous human autoimmune, neurological and infectious diseases. The spectrum of related malignancies includes, but not limits to, multiple sclerosis, psoriasis, lupus, schizophrenia, multiple cancer types and HIV. In addition, HERVs regulate expression of the neighboring host genes and modify genomic regulatory landscape, e.g., by providing regulatory modules like transcription factor binding sites (TFBS). Indeed, recent bioinformatic profiling identified ~110,000 regulatory active HERV elements, which formed at least ~320,000 human TFBS. These and other peculiarities of HERVs might have played an important role in human evolution and speciation. In this paper, we focus on the current progress in understanding of normal and pathological molecular niches of HERVs, on their implications in human evolution, normal physiology and disease. We also review the available databases dealing with various aspects of HERV genetics.
Collapse
Affiliation(s)
- Maria Suntsova
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia.
| | - Andrew Garazha
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia.
| | - Alena Ivanova
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
| | - Dmitry Kaminsky
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
| | - Alex Zhavoronkov
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
- Department of Translational and Regenerative Medicine, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow, 141700, Russia.
| | - Anton Buzdin
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR.
- National Research Centre "Kurchatov Institute", Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, 1, Akademika Kurchatova sq., Moscow, 123182, Russia.
| |
Collapse
|
47
|
Abstract
Endogenous retroviruses comprise millions of discrete genetic loci distributed within the genomes of extant vertebrates. These sequences, which are clearly related to exogenous retroviruses, represent retroviral infections of the deep past, and their abundance suggests that retroviruses were a near-constant presence throughout the evolutionary history of modern vertebrates. Endogenous retroviruses contribute in myriad ways to the evolution of host genomes, as mutagens and as sources of genetic novelty (both coding and regulatory) to be acted upon by the twin engines of random genetic drift and natural selection. Importantly, the richness and complexity of endogenous retrovirus data can be used to understand how viruses spread and adapt on evolutionary timescales by combining population genetics and evolutionary theory with a detailed understanding of retrovirus biology (gleaned from the study of extant retroviruses). In addition to revealing the impact of viruses on organismal evolution, such studies can help us better understand, by looking back in time, how life-history traits, as well as ecological and geological events, influence the movement of viruses within and between populations.
Collapse
Affiliation(s)
- Welkin E Johnson
- Biology Department, Boston College, Chestnut Hill, Massachusetts 02467;
| |
Collapse
|
48
|
Contreras-Galindo R, Kaplan MH, Dube D, Gonzalez-Hernandez MJ, Chan S, Meng F, Dai M, Omenn GS, Gitlin SD, Markovitz DM. Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K-Related Sequences. J Virol 2015; 89:7187-201. [PMID: 25926654 PMCID: PMC4473553 DOI: 10.1128/jvi.00544-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/25/2015] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Human endogenous retroviruses (HERV) make up 8% of the human genome. While the youngest of these retroviruses, HERV-K(HML-2), termed HK2, is able to code for all viral proteins and produce virus-like particles, it is not known if these virus particles package and transmit HK2-related sequences. Here, we analyzed the capacity of HK2 for packaging and transmitting HK2 sequences. We created an HK2 probe, termed Bogota, which can be packaged into HK2 viruses, and transfected it into cells that make HK2 particles. Supernatants of the transfected cells, which contained HK2 viral particles, then were added to target cells, and the transmissibility of the HK2 Bogota reporter was tracked by G418 resistance. Our studies revealed that contemporary HK2 virions produced by some teratocarcinoma and breast cancer cell lines, as well as by peripheral blood lymphocytes from lymphoma patients, can package HK2 Bogota probes, and these viruses transmitted these probes to other cells. After transmission, HK2 Bogota transcripts undergo reverse transcription, a step impaired by antiretroviral agents or by introduction of mutations into the probe sequences required for reverse transcription. HK2 viruses were more efficiently transmitted in the presence of HK2 Rec or HIV-1 Tat and Vif. Transmitted Bogota probes formed episomes but did not integrate into the cellular genome. Resistance to integration might explain the relatively low number of HK2 insertions that were acquired during the last 25 million years of evolution. Whether transient transmission of modern HK2 sequences, which encode two putative oncoproteins, can lead to disease remains to be studied. IMPORTANCE Retroviruses invaded the genome of human ancestors over the course of millions of years, yet these viruses generally have been inactivated during evolution, with only remnants of these infectious sequences remaining in the human genome. One of these viruses, termed HK2, still is capable of producing virus particles, although these particles have been regarded as being noninfectious. Using a genetic probe derived from HK2, we have discovered that HK2 viruses produced in modern humans can package HK2 sequences and transmit them to various other cells. Furthermore, the genetic sequences packaged in HK2 undergo reverse transcription. The transmitted probe circularized in the cell and failed to integrate into the cellular genome. These findings suggest that modern HK2 viruses can package viral RNA and transmit it to other cells. Contrary to previous views, we provide evidence of an extracellular viral phase of modern HK2 viruses. We have no evidence of sustained, spreading infection.
Collapse
Affiliation(s)
| | - Mark H Kaplan
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Derek Dube
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Marta J Gonzalez-Hernandez
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA Programs in Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Susana Chan
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Fan Meng
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, USA Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA
| | - Manhong Dai
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Gilbert S Omenn
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Scott D Gitlin
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA Veteran Affairs Health System, Ann Arbor, Michigan, USA
| | - David M Markovitz
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA Programs in Immunology, University of Michigan, Ann Arbor, Michigan, USA Programs in Cancer Biology, University of Michigan, Ann Arbor, Michigan, USA Programs in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
49
|
Macfarlane CM, Badge RM. Genome-wide amplification of proviral sequences reveals new polymorphic HERV-K(HML-2) proviruses in humans and chimpanzees that are absent from genome assemblies. Retrovirology 2015; 12:35. [PMID: 25927962 PMCID: PMC4422153 DOI: 10.1186/s12977-015-0162-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To date, the human population census of proviruses of the Betaretrovirus-like human endogenous retroviral (HERV-K) (HML-2) family has been compiled from a limited number of complete genomes, making it certain that rare polymorphic loci are under-represented and are yet to be described. RESULTS Here we describe a suppression PCR-based method called genome-wide amplification of proviral sequences (GAPS) that selectively amplifies DNA fragments containing the termini of HERV-K(HML-2) proviral sequences and their flanking genomic sequences. We analysed the HERV-K(HML-2) proviral content of 101 unrelated humans, 4 common chimpanzees and three centre d'etude du polymorphisme humain (CEPH) pedigrees (44 individuals). The technique isolated HERV-K(HML-2) proviruses that had integrated in the genomes of the great apes throughout their divergence and included evolutionarily young elements still unfixed for presence/absence. CONCLUSIONS By examining the HERV-K(HML-2) proviral content of 145 humans we detected a new insertionally polymorphic Type I HERV-K(HML-2) provirus. We also observed provirus versus solo long terminal repeat (LTR) polymorphism within humans at a previously unreported, but ancient, locus. Finally, we report two novel chimpanzee specific proviruses, one of which is dimorphic for a provirus versus solo LTR. Thus GAPS enables the isolation of uncharacterised HERV-K(HML-2) proviral sequences and provides a direct means to assess inter-individual genetic variation associated with HERV-K(HML-2) proviruses.
Collapse
Affiliation(s)
- Catriona M Macfarlane
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Richard M Badge
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| |
Collapse
|
50
|
Smith JA, Leonardi T, Huang B, Iraci N, Vega B, Pluchino S. Extracellular vesicles and their synthetic analogues in aging and age-associated brain diseases. Biogerontology 2015; 16:147-85. [PMID: 24973266 PMCID: PMC4578234 DOI: 10.1007/s10522-014-9510-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/16/2014] [Indexed: 02/06/2023]
Abstract
Multicellular organisms rely upon diverse and complex intercellular communications networks for a myriad of physiological processes. Disruption of these processes is implicated in the onset and propagation of disease and disorder, including the mechanisms of senescence at both cellular and organismal levels. In recent years, secreted extracellular vesicles (EVs) have been identified as a particularly novel vector by which cell-to-cell communications are enacted. EVs actively and specifically traffic bioactive proteins, nucleic acids, and metabolites between cells at local and systemic levels, modulating cellular responses in a bidirectional manner under both homeostatic and pathological conditions. EVs are being implicated not only in the generic aging process, but also as vehicles of pathology in a number of age-related diseases, including cancer and neurodegenerative and disease. Thus, circulating EVs-or specific EV cargoes-are being utilised as putative biomarkers of disease. On the other hand, EVs, as targeted intercellular shuttles of multipotent bioactive payloads, have demonstrated promising therapeutic properties, which can potentially be modulated and enhanced through cellular engineering. Furthermore, there is considerable interest in employing nanomedicinal approaches to mimic the putative therapeutic properties of EVs by employing synthetic analogues for targeted drug delivery. Herein we describe what is known about the origin and nature of EVs and subsequently review their putative roles in biology and medicine (including the use of synthetic EV analogues), with a particular focus on their role in aging and age-related brain diseases.
Collapse
Affiliation(s)
- J A Smith
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, CB2 0PY, UK
| | | | | | | | | | | |
Collapse
|