1
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Kim DY, Kim H, Ko EJ, Koh SB, Kim H, Lee JY, Lee CM, Eo WK, Kim KH, Cha HJ. Correlation analysis of cancer stem cell marker CD133 and human endogenous retrovirus (HERV)-K env in SKOV3 ovarian cancer cells. Genes Genomics 2024; 46:511-518. [PMID: 38457096 DOI: 10.1007/s13258-024-01499-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/24/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Human endogenous retrovirus (HERV)-K is a type of retrovirus that is present in the human genome, and its expression is usually silenced in healthy tissues. The precise mechanism by which HERV-K env influences cancer stemness is not fully understood, but it has been suggested that HERV-K env may activate various signaling pathways that promote stemness traits in cancer cells. OBJECTIVE To establish the connection between HERV-K env expression and cancer stemness in ovarian cancer cells, we carried out correlation analyses between HERV-K env and the cancer stem cell (CSC) marker known as the cluster of differentiation 133 (CD133) gene in SKOV3 ovarian cancer cells. METHOD To perform correlation analysis between HERV-K env and CSCs, ovarian cancer cells were cultured in a medium designed for cancer stem cell induction. The expression of HERV-K env and CD133 genes was verified using quantitative real-time polymerase chain reaction (RT-qPCR) and Western blot analyses. Additionally, the expression of stemness-related markers, such as OCT-4 and Nanog, was also confirmed using RT-qPCR. RESULTS In the stem cell induction medium, the number of tumorsphere-type SKOV3 cells increased, and the expression of CD133 and HERV-K env genes was up-regulated. Additionally, other stemness-related markers like OCT-4 and Nanog also exhibited increased expression when cultured in the cancer stem cell induction medium. However, when HERV-K env knockout (KO) SKOV3 cells were cultured in the same cancer stem cell induction medium, there was a significant decrease in the number of tumorsphere-type cells compared to mock SKOV3 cells subjected to the same conditions. Furthermore, the expression of CD133, Nanog, and OCT-4 did not show a significant increase in HERV-K env KO SKOV3 cells compared to mock SKOV3 cells cultured in the same cancer stem cell induction medium. CONCLUSION These findings indicate that the expression of HERV-K env increased in SKOV3 cells when cultured in cancer stem cell induction media, and cancer stem cell induction was inhibited by KO of HERV-K env in SKOV3 cells. These results suggest a strong association between HERV-K env and stemness in SKOV3 ovarian cancer cells.
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Affiliation(s)
- Do-Ye Kim
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan, Republic of Korea
| | - Heungyeol Kim
- Department of Obstetrics and Gynecology, Hannah Hospital, Busan, Republic of Korea
| | - Eun-Ji Ko
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan, Republic of Korea
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Suk Bong Koh
- Department of Obstetrics and Gynecology, Daegu Catholic University School of Medicine, Daegu, Republic of Korea
| | - Hongbae Kim
- Department of Obstetrics and Gynecology, Kangnam Sacred Heart Hospital, Hallym University Medical Center, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Ji Young Lee
- Department of Obstetrics and Gynecology, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Chul Min Lee
- Department of Obstetrics and Gynecology, Ilsan Medical Center School of Medicine, Cha University, Seoul, Republic of Korea
| | - Wan Kyu Eo
- Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Ki Hyung Kim
- Department of Obstetrics and Gynecology, Biomedical Research Institute and Pusan Cancer Center, Pusan National University Hospital, Pusan National University School of Medicine, Busan, Republic of Korea.
- Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea.
| | - Hee-Jae Cha
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan, Republic of Korea.
- Institute for Medical Science, Kosin University College of Medicine, Busan, Republic of Korea.
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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.
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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
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3
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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.
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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
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4
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DiRusso JA, Clark AT. Transposable elements in early human embryo development and embryo models. Curr Opin Genet Dev 2023; 81:102086. [PMID: 37441874 PMCID: PMC10917458 DOI: 10.1016/j.gde.2023.102086] [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: 01/27/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
Abstract
Transposable elements (TEs), long discounted as 'selfish genomic elements,' are increasingly appreciated as the drivers of genomic evolution, genome organization, and gene regulation. TEs are particularly important in early embryo development, where advances in stem cell technologies, in tandem with improved computational and next-generation sequencing approaches, have provided an unprecedented opportunity to study the contribution of TEs to early mammalian development. Here, we summarize advances in our understanding of TEs in early human development and expand on how new stem cell-based embryo models can be leveraged to augment this understanding.
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Affiliation(s)
- Jonathan A DiRusso
- Department of Molecular, Cell and Developmental Biology, University of California, 90095 Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, 90095 Los Angeles, CA, USA.; Molecular Biology Institute, University of California, 90095 Los Angeles, CA, USA; Center for Reproductive Science, Health and Education, University of California, 90095 Los Angeles, CA, USA
| | - Amander T Clark
- Department of Molecular, Cell and Developmental Biology, University of California, 90095 Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, 90095 Los Angeles, CA, USA.; Molecular Biology Institute, University of California, 90095 Los Angeles, CA, USA; Center for Reproductive Science, Health and Education, University of California, 90095 Los Angeles, CA, USA.
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5
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Rivas SR, Valdez MJM, Govindarajan V, Seetharam D, Doucet-O’Hare TT, Heiss JD, Shah AH. The Role of HERV-K in Cancer Stemness. Viruses 2022; 14:v14092019. [PMID: 36146825 PMCID: PMC9504571 DOI: 10.3390/v14092019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 12/15/2022] Open
Abstract
Human endogenous retrovirus-K (HERV-K) is the most recently integrated retrovirus in the human genome, with implications for multiple disorders, including cancer. Although typically transcriptionally silenced in normal adult cells, dysregulation of HERV-K (HML-2) elements has been observed in cancer, including breast, germ cell tumors, pancreatic, melanoma, and brain cancer. While multiple methods of carcinogenesis have been proposed, here we discuss the role of HERV-K (HML-2) in the promotion and maintenance of the stem-cell in cancer. Aberrant expression of HERV-K has been shown to promote expression of stem cell markers and promote dedifferentiation. In this review, we discuss HERV-K (HML-2) as a potential therapeutic target based on evidence that some tumors depend on the expression of its proteins for survival.
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Affiliation(s)
- Sarah R. Rivas
- Surgical Neurology Branch, National Institute of Neurological Diseases and Stroke, Bethesda, MD 20892, USA
- Correspondence: (S.R.R.); (A.H.S.)
| | - Mynor J. Mendez Valdez
- Section of Virology and Immunotherapy, Department of Neurosurgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Vaidya Govindarajan
- Section of Virology and Immunotherapy, Department of Neurosurgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Deepa Seetharam
- Section of Virology and Immunotherapy, Department of Neurosurgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Tara T. Doucet-O’Hare
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - John D. Heiss
- Surgical Neurology Branch, National Institute of Neurological Diseases and Stroke, Bethesda, MD 20892, USA
| | - Ashish H. Shah
- Section of Virology and Immunotherapy, Department of Neurosurgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Correspondence: (S.R.R.); (A.H.S.)
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6
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Zhang T, Zheng R, Li M, Yan C, Lan X, Tong B, Lu P, Jiang W. Active endogenous retroviral elements in human pluripotent stem cells play a role in regulating host gene expression. Nucleic Acids Res 2022; 50:4959-4973. [PMID: 35451484 PMCID: PMC9122532 DOI: 10.1093/nar/gkac265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/22/2022] [Accepted: 04/01/2022] [Indexed: 12/20/2022] Open
Abstract
Human endogenous retroviruses, also called LTR elements, can be bound by transcription factors and marked by different histone modifications in different biological contexts. Recently, individual LTR or certain subclasses of LTRs such as LTR7/HERVH and LTR5_Hs/HERVK families have been identified as cis-regulatory elements. However, there are still many LTR elements with unknown functions. Here, we dissected the landscape of histone modifications and regulatory map of LTRs by integrating 98 ChIP-seq data in human embryonic stem cells (ESCs), and annotated the active LTRs enriching enhancer/promoter-related histone marks. Notably, we found that MER57E3 functionally acted as proximal regulatory element to activate respective ZNF gene. Additionally, HERVK transcript could mainly function in nucleus to activate the adjacent genes. Since LTR5_Hs/LTR5 was bound by many early embryo-specific transcription factors, we further investigated the expression dynamics in different pluripotent states. LTR5_Hs/LTR5/HERVK exhibited higher expression level in naïve ESCs and extended pluripotent stem cells (EPSCs). Functionally, the LTR5_Hs/LTR5 with high activity could serve as a distal enhancer to regulate the host genes. Ultimately, our study not only provides a comprehensive regulatory map of LTRs in human ESCs, but also explores the regulatory models of MER57E3 and LTR5_Hs/LTR5 in host genome.
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Affiliation(s)
- Tianzhe Zhang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Ran Zheng
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Mao Li
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Chenchao Yan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Xianchun Lan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Bei Tong
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Pei Lu
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China.,Human Genetics Resource Preservation Center of Wuhan University, Wuhan 430071, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, China
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7
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A hypothesis: Retrotransposons as a relay of epigenetic marks in intergenerational epigenetic inheritance. Gene 2022; 817:146229. [PMID: 35063571 DOI: 10.1016/j.gene.2022.146229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/13/2021] [Accepted: 01/13/2022] [Indexed: 12/19/2022]
Abstract
Epigenetic marks in gametes, which both respond to the parental environmental factors and shape offspring phenotypes, are usually positioned to mediate intergenerational or transgenerational epigenetic inheritance. Nonetheless, the mechanisms through which gametic epigenetic signatures encode parental acquired phenotypes, and further initiate a cascade of molecular events to affect offspring phenotypes during early embryonic development, remain unclear. Retrotransposons are mobile DNA elements that could resist to genomic epigenetic reprogramming at specific loci and rewire the core regulatory networks of embryogenesis. Increasing evidences show that retrotransposons in the embryonic genome could interact with gametic epigenetic marks, which provides a tentative possibility that retrotransposons may serve as a relay of gametic epigenetic marks to transmit parental acquired traits. Here, we summarize the recent progress in exploring the crosstalk between gametic epigenetic marks and retrotransposons, and the regulation of gene expression and early embryonic development by retrotransposons. Accordingly, deciphering the mystery of interactions between gametic epigenetic marks and retrotransposons during early embryonic development will provide valuable insights into the intergenerational or transgenerational transmission of acquired traits.
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Müller MD, Holst PJ, Nielsen KN. A Systematic Review of Expression and Immunogenicity of Human Endogenous Retroviral Proteins in Cancer and Discussion of Therapeutic Approaches. Int J Mol Sci 2022; 23:ijms23031330. [PMID: 35163254 PMCID: PMC8836156 DOI: 10.3390/ijms23031330] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that have become fixed in the human genome. While HERV genes are typically silenced in healthy somatic cells, there are numerous reports of HERV transcription and translation across a wide spectrum of cancers, while T and B cell responses against HERV proteins have been detected in cancer patients. This review systematically categorizes the published evidence on the expression of and adaptive immune response against specific HERVs in distinct cancer types. A systematic literature search was performed using Medical Search Headings (MeSH) in the PubMed/Medline database. Papers were included if they described the translational activity of HERVs. We present multiple tables that pair the protein expression of specific HERVs and cancer types with information on the quality of the evidence. We find that HERV-K is the most investigated HERV. HERV-W (syncytin-1) is the second-most investigated, while other HERVs have received less attention. From a therapeutic perspective, HERV-K and HERV-E are the only HERVs with experimental demonstration of effective targeted therapies, but unspecific approaches using antiviral and demethylating agents in combination with chemo- and immunotherapies have also been investigated.
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Affiliation(s)
- Mikkel Dons Müller
- Institute of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark;
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9
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Xiang X, Tao Y, DiRusso J, Hsu FM, Zhang J, Xue Z, Pontis J, Trono D, Liu W, Clark AT. Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. Nat Commun 2022; 13:463. [PMID: 35075135 PMCID: PMC8786967 DOI: 10.1038/s41467-022-28105-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/16/2021] [Indexed: 12/26/2022] Open
Abstract
Germ cells are essential to pass DNA from one generation to the next. In human reproduction, germ cell development begins with the specification of primordial germ cells (PGCs) and a failure to specify PGCs leads to human infertility. Recent studies have revealed that the transcription factor network required for PGC specification has diverged in mammals, and this has a significant impact on our understanding of human reproduction. Here, we reveal that the Hominidae-specific Transposable Elements (TEs) LTR5Hs, may serve as TEENhancers (TE Embedded eNhancers) to facilitate PGC specification. LTR5Hs TEENhancers become transcriptionally active during PGC specification both in vivo and in vitro with epigenetic reprogramming leading to increased chromatin accessibility, localized DNA demethylation, enrichment of H3K27ac, and occupation of key hPGC transcription factors. Inactivation of LTR5Hs TEENhancers with KRAB mediated CRISPRi has a significant impact on germ cell specification. In summary, our data reveals the essential role of Hominidae-specific LTR5Hs TEENhancers in human germ cell development. The transcription factor network required for primordial germ cell (PGC) specification is known to diverge in mammals. Here the authors show that hominidae-specific transposable element (TE) LTR5Hs becomes transcriptionally active during PGC specification, and LTR5Hs inactivation abrogates human PGC specification
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Affiliation(s)
- Xinyu Xiang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Yu Tao
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jonathan DiRusso
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Fei-Man Hsu
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jinchun Zhang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Ziwei Xue
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fe ́de ́rale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fe ́de ́rale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China. .,Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310029, China. .,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China. .,Alibaba-Zhejiang University Joint Research Center of Future DigitalHealthcare, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Amander T Clark
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, 90095, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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10
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Endogenous Retroviral Elements in Human Development and Central Nervous System Embryonal Tumors. J Pers Med 2021; 11:jpm11121332. [PMID: 34945804 PMCID: PMC8708524 DOI: 10.3390/jpm11121332] [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: 10/28/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/21/2023] Open
Abstract
Human endogenous retroviruses (HERVs), which are critical to normal embryologic development and downregulated during normal maturation, have been implicated in a variety of cancers. Abnormal persistent production of HERVs has been suggested to play a role in oncogenesis and to confer stem cell properties to cells. We recently demonstrated that the most recently incorporated HERV element (HERV-K HML-2) has been associated with the pathogenesis of the embryonal atypical teratoid rhabdoid tumor (AT/RT), shifting our understanding of embryonal tumor development. HML-2 expression is vital for proper human development and its expression is suppressed via methylation or chromatin remodeling as cells differentiate. We previously found that dysfunctional chromatin remodeling due to loss of SMARCB1 expression induces HML-2 envelope (env) expression, impairing cellular differentiation and migration, and facilitating tumor growth in AT/RT. Epigenetic dysregulation in other embryonal tumors with concomitant expression of stem-cell markers may facilitate HML-2 expression. Future studies could utilize HML-2 as potential diagnostic criteria, use its expression as a treatment biomarker, and investigate the efficacy of therapies targeting cells with high HML-2 expression.
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Denner J. Porcine Endogenous Retroviruses and Xenotransplantation, 2021. Viruses 2021; 13:v13112156. [PMID: 34834962 PMCID: PMC8625113 DOI: 10.3390/v13112156] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/06/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Porcine endogenous retroviruses (PERVs) are integrated in the genome of all pigs, and some of them are able to infect human cells. Therefore, PERVs pose a risk for xenotransplantation, the transplantation of pig cells, tissues, or organ to humans in order to alleviate the shortage of human donor organs. Up to 2021, a huge body of knowledge about PERVs has been accumulated regarding their biology, including replication, recombination, origin, host range, and immunosuppressive properties. Until now, no PERV transmission has been observed in clinical trials transplanting pig islet cells into diabetic humans, in preclinical trials transplanting pig cells and organs into nonhuman primates with remarkable long survival times of the transplant, and in infection experiments with several animal species. Nevertheless, in order to prevent virus transmission to the recipient, numerous strategies have been developed, including selection of PERV-C-free animals, RNA interference, antiviral drugs, vaccination, and genome editing. Furthermore, at present there are no more experimental approaches to evaluate the full risk until we move to the clinic.
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Affiliation(s)
- Joachim Denner
- Department of Veterinary Medicine, Institute of Virology, Free University Berlin, 14163 Berlin, Germany
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12
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Dittmar T, Weiler J, Luo T, Hass R. Cell-Cell Fusion Mediated by Viruses and HERV-Derived Fusogens in Cancer Initiation and Progression. Cancers (Basel) 2021; 13:5363. [PMID: 34771528 PMCID: PMC8582398 DOI: 10.3390/cancers13215363] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 12/13/2022] Open
Abstract
Cell fusion is a well-known, but still scarcely understood biological phenomenon, which might play a role in cancer initiation, progression and formation of metastases. Although the merging of two (cancer) cells appears simple, the entire process is highly complex, energy-dependent and tightly regulated. Among cell fusion-inducing and -regulating factors, so-called fusogens have been identified as a specific type of proteins that are indispensable for overcoming fusion-associated energetic barriers and final merging of plasma membranes. About 8% of the human genome is of retroviral origin and some well-known fusogens, such as syncytin-1, are expressed by human (cancer) cells. Likewise, enveloped viruses can enable and facilitate cell fusion due to evolutionarily optimized fusogens, and are also capable to induce bi- and multinucleation underlining their fusion capacity. Moreover, multinucleated giant cancer cells have been found in tumors derived from oncogenic viruses. Accordingly, a potential correlation between viruses and fusogens of human endogenous retroviral origin in cancer cell fusion will be summarized in this review.
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Affiliation(s)
- Thomas Dittmar
- Institute of Immunology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58448 Witten, Germany;
| | - Julian Weiler
- Institute of Immunology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58448 Witten, Germany;
| | - Tianjiao Luo
- Biochemistry and Tumor Biology Laboratory, Department of Obstetrics and Gynecology, Hannover Medical School, 30625 Hannover, Germany;
| | - Ralf Hass
- Biochemistry and Tumor Biology Laboratory, Department of Obstetrics and Gynecology, Hannover Medical School, 30625 Hannover, Germany;
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13
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Babarinde IA, Ma G, Li Y, Deng B, Luo Z, Liu H, Abdul MM, Ward C, Chen M, Fu X, Shi L, Duttlinger M, He J, Sun L, Li W, Zhuang Q, Tong G, Frampton J, Cazier JB, Chen J, Jauch R, Esteban MA, Hutchins AP. Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells. Nucleic Acids Res 2021; 49:9132-9153. [PMID: 34390351 PMCID: PMC8450112 DOI: 10.1093/nar/gkab710] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) occupy nearly 40% of mammalian genomes and, whilst most are fragmentary and no longer capable of transposition, they can nevertheless contribute to cell function. TEs within genes transcribed by RNA polymerase II can be copied as parts of primary transcripts; however, their full contribution to mature transcript sequences remains unresolved. Here, using long and short read (LR and SR) RNA sequencing data, we show that 26% of coding and 65% of noncoding transcripts in human pluripotent stem cells (hPSCs) contain TE-derived sequences. Different TE families are incorporated into RNAs in unique patterns, with consequences to transcript structure and function. The presence of TE sequences within a transcript is correlated with TE-type specific changes in its subcellular distribution, alterations in steady-state levels and half-life, and differential association with RNA Binding Proteins (RBPs). We identify hPSC-specific incorporation of endogenous retroviruses (ERVs) and LINE:L1 into protein-coding mRNAs, which generate TE sequence-derived peptides. Finally, single cell RNA-seq reveals that hPSCs express ERV-containing transcripts, whilst differentiating subpopulations lack ERVs and express SINE and LINE-containing transcripts. Overall, our comprehensive analysis demonstrates that the incorporation of TE sequences into the RNAs of hPSCs is more widespread and has a greater impact than previously appreciated.
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Affiliation(s)
- Isaac A Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Gang Ma
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuhao Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Boping Deng
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Zhiwei Luo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Mazid Md Abdul
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Minchun Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiuling Fu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liyang Shi
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Martha Duttlinger
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Li Sun
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wenjuan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Qiang Zhuang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guoqing Tong
- Center for Reproductive Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200120, China
| | - Jon Frampton
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jean-Baptiste Cazier
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.,Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Jiekai Chen
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China.,Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Andrew P Hutchins
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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14
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The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency. PLoS Genet 2021; 17:e1009587. [PMID: 34033652 PMCID: PMC8184003 DOI: 10.1371/journal.pgen.1009587] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/07/2021] [Accepted: 05/06/2021] [Indexed: 12/29/2022] Open
Abstract
Human pluripotent stem cells (PSCs) express human endogenous retrovirus type-H (HERV-H), which exists as more than a thousand copies on the human genome and frequently produces chimeric transcripts as long-non-coding RNAs (lncRNAs) fused with downstream neighbor genes. Previous studies showed that HERV-H expression is required for the maintenance of PSC identity, and aberrant HERV-H expression attenuates neural differentiation potentials, however, little is known about the actual of function of HERV-H. In this study, we focused on ESRG, which is known as a PSC-related HERV-H-driven lncRNA. The global transcriptome data of various tissues and cell lines and quantitative expression analysis of PSCs showed that ESRG expression is much higher than other HERV-Hs and tightly silenced after differentiation. However, the loss of function by the complete excision of the entire ESRG gene body using a CRISPR/Cas9 platform revealed that ESRG is dispensable for the maintenance of the primed and naïve pluripotent states. The loss of ESRG hardly affected the global gene expression of PSCs or the differentiation potential toward trilineage. Differentiated cells derived from ESRG-deficient PSCs retained the potential to be reprogrammed into induced PSCs (iPSCs) by the forced expression of OCT3/4, SOX2, and KLF4. In conclusion, ESRG is dispensable for the maintenance and recapturing of human pluripotency. We have been interested in the role of human endogenous retrovirus (HERVs) in human pluripotent stem cells (PSCs). Although we and others have demonstrated that HERV expression is crucial for somatic cell reprogramming to a pluripotent state and the characteristics of PSCs. Little is known which one of more than 1,000 copies of HERVs is important. Thus, in this study, we focused on a HERV-related gene, ESRG which is expressed strongly and specifically in human PSCs but not in differentiated cells. Using a CRISPR/Cas9 platform, we generated complete knockout cell lines by deleting the entire gene body of ESRG. Our results demonstrate that ESRG is dispensable for the PSC characters such as gene expression, self-renewing capacity, and differentiation potential. In addition, ESRG does not contribute to the reprogramming of differentiated cells to a pluripotent state. Altogether, we concluded that ESRG is an excellent marker of pluripotency but dispensable for the PSC identity.
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15
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Dervan E, Bhattacharyya DD, McAuliffe JD, Khan FH, Glynn SA. Ancient Adversary - HERV-K (HML-2) in Cancer. Front Oncol 2021; 11:658489. [PMID: 34055625 PMCID: PMC8155577 DOI: 10.3389/fonc.2021.658489] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
Human endogenous retroviruses (HERV), ancient integrations of exogenous viruses, make up 8% of our genome. Long thought of as mere vestigial genetic elements, evidence is now accumulating to suggest a potential functional role in numerous pathologies including neurodegenerative diseases, autoimmune disorders, and multiple cancers. The youngest member of this group of transposable elements is HERV-K (HML-2). Like the majority of HERV sequences, significant post-insertional mutations have disarmed HERV-K (HML-2), preventing it from producing infectious viral particles. However, some insertions have retained limited coding capacity, and complete open reading frames for all its constituent proteins can be found throughout the genome. For this reason HERV-K (HML-2) has garnered more attention than its peers. The tight epigenetic control thought to suppress expression in healthy tissue is lost during carcinogenesis. Upregulation of HERV-K (HML-2) derived mRNA and protein has been reported in a variety of solid and liquid tumour types, and while causality has yet to be established, progressively more data are emerging to suggest this phenomenon may contribute to tumour growth and metastatic capacity. Herein we discuss its potential utility as a diagnostic tool and therapeutic target in light of the current in vitro, in vivo and clinical evidence linking HERV-K (HML-2) to tumour progression.
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Affiliation(s)
- Eoin Dervan
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), Galway, Ireland
| | - Dibyangana D Bhattacharyya
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), Galway, Ireland.,Laboratory of Cancer ImmunoMetabolism, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Jake D McAuliffe
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), Galway, Ireland
| | - Faizan H Khan
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), Galway, Ireland
| | - Sharon A Glynn
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway (NUIG), Galway, Ireland
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16
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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: 57] [Impact Index Per Article: 19.0] [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.
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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.
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17
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Wieland L, Engel K, Volkmer I, Krüger A, Posern G, Kornhuber ME, Staege MS, Emmer A. Overexpression of Endogenous Retroviruses and Malignancy Markers in Neuroblastoma Cell Lines by Medium-Induced Microenvironmental Changes. Front Oncol 2021; 11:637522. [PMID: 34026614 PMCID: PMC8138558 DOI: 10.3389/fonc.2021.637522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/09/2021] [Indexed: 12/21/2022] Open
Abstract
Neuroblastoma (NB) is the commonest solid tumor outside the central nervous system in infancy and childhood with a unique biological heterogeneity. In patients with advanced, metastasizing neuroblastoma, treatment failure and poor prognosis is often marked by resistance to chemo- or immunotherapy. Thus, identification of robust biomarkers seems essential for understanding tumor progression and developing effective therapy. Here, we have studied the expression of human endogenous retroviruses (HERV) as potential targets in NB cell lines during stem-cell medium-induced microenvironmental change. Quantitative PCR revealed that relative expression of the HERV-K family and HERV-W1 ENV were increased in all three NB cell lines after incubation in stem-cell medium. Virus transcriptome analyses revealed the transcriptional activation of three endogenous retrovirus elements: HERV-R ENV (ERV3-1), HERV-E1 and HERV-Fc2 ENV (ERVFC1-1). Known malignancy markers in NB, e.g. proto-oncogenic MYC or MYCN were expressed highly heterogeneously in the three investigated NB cell lines with up-regulation of MYC and MYCN upon medium-induced microenvironmental change. In addition, SiMa cells exclusively showed a phenotype switching from loosely-adherent monolayers to low proliferating grape-like cellular aggregates, which was accompanied by an enhanced CD133 expression. Interestingly, the overexpression of HERV was associated with a significant elevation of immune checkpoint molecule CD200 in both quantitative PCR and RNA-seq analysis suggesting tumor escape mechanism in NB cell lines after incubation in serum-free stem cell medium.
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Affiliation(s)
- Lisa Wieland
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany.,Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Kristina Engel
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ines Volkmer
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Anna Krüger
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Guido Posern
- Institute for Physiological Chemistry, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Malte E Kornhuber
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Martin S Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Alexander Emmer
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
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18
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Comment on: Endogenous retroviruses expressed in human tumours cannot be used as targets for anti-tumour vaccines. Transl Oncol 2021; 14:101041. [PMID: 33810829 PMCID: PMC8046944 DOI: 10.1016/j.tranon.2021.101041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/30/2022] Open
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19
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Engel K, Wieland L, Krüger A, Volkmer I, Cynis H, Emmer A, Staege MS. Identification of Differentially Expressed Human Endogenous Retrovirus Families in Human Leukemia and Lymphoma Cell Lines and Stem Cells. Front Oncol 2021; 11:637981. [PMID: 33996550 PMCID: PMC8117144 DOI: 10.3389/fonc.2021.637981] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/13/2021] [Indexed: 12/29/2022] Open
Abstract
Endogenous retroviruses (ERVs) are becoming more and more relevant in cancer research and might be potential targets. The oncogenic potential of human ERVs (HERVs) has been recognized and includes immunosuppression, cell fusion, antigenicity of viral proteins, and regulation of neighboring genes. To decipher the role of HERVs in human cancers, we used a bioinformatics approach and analyzed RNA sequencing data from the LL-100 panel, covering 22 entities of hematopoietic neoplasias including T cell, B cell and myeloid malignancies. We compared HERV expression in this panel with hematopoietic stem cells (HSCs), embryonic stem cells (ESCs) and normal blood cells. RNA sequencing data were mapped against a comprehensive synthetic viral metagenome with 116 HERV sequences from 14 different HERV families. Of these, 13 HERV families and elements were differently expressed in malignant hematopoietic cells and stem cells. We found transcriptional upregulation of HERVE family in acute megakaryocytic and erythroid leukemia and of HERVFc family in multiple myeloma/plasma cell leukemia (PCL). The HERVFc member HERVFc-1 was found transcriptionally active in the multiple myeloma cell line OPM-2 and also in the Hodgkin lymphoma cell line L-428. The expression of HERVFc-1 in L-428 cells was validated by qRT-PCR. We also confirm transcriptional downregulation of ERV3 in acute megakaryocytic and erythroid leukemia, and HERVK in acute monocytic and myelocytic leukemia and a depression of HERVF in all malignant entities. Most of the higher expressed HERV families could be detected in stem cells including HERVK (HML-2), HERV-like, HERVV, HERVT, ERV9, HERVW, HERVF, HERVMER, ERV3, HERVH and HERVPABLB.
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Affiliation(s)
- Kristina Engel
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Lisa Wieland
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany.,Department of Neurology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Anna Krüger
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ines Volkmer
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Holger Cynis
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Halle, Germany
| | - Alexander Emmer
- Department of Neurology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Martin S Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
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20
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Correa M, Lerat E, Birmelé E, Samson F, Bouillon B, Normand K, Rizzon C. The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality. Genome Biol Evol 2021; 13:6273345. [PMID: 33973013 PMCID: PMC8155550 DOI: 10.1093/gbe/evab062] [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] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) are major components of eukaryotic genomes and represent approximately 45% of the human genome. TEs can be important sources of novelty in genomes and there is increasing evidence that TEs contribute to the evolution of gene regulation in mammals. Gene duplication is an evolutionary mechanism that also provides new genetic material and opportunities to acquire new functions. To investigate how duplicated genes are maintained in genomes, here, we explored the TE environment of duplicated and singleton genes. We found that singleton genes have more short-interspersed nuclear elements and DNA transposons in their vicinity than duplicated genes, whereas long-interspersed nuclear elements and long-terminal repeat retrotransposons have accumulated more near duplicated genes. We also discovered that this result is highly associated with the degree of essentiality of the genes with an unexpected accumulation of short-interspersed nuclear elements and DNA transposons around the more-essential genes. Our results underline the importance of taking into account the TE environment of genes to better understand how duplicated genes are maintained in genomes.
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Affiliation(s)
- Margot Correa
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d'Evry Val d'Essonne, Evry, France
| | - Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Etienne Birmelé
- Laboratoire MAP5 UMR 8145, Université de Paris, Paris, France
| | - Franck Samson
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d'Evry Val d'Essonne, Evry, France
| | - Bérengère Bouillon
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d'Evry Val d'Essonne, Evry, France
| | - Kévin Normand
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d'Evry Val d'Essonne, Evry, France
| | - Carène Rizzon
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d'Evry Val d'Essonne, Evry, France
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21
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Krüger L, Nowak-Imialek M, Kristiansen Y, Herrmann D, Petersen B, Denner J. Unexpected low expression of porcine endogenous retroviruses (PERVs) in porcine expanded potential stem cells (EPSCs). Virus Res 2021; 294:198295. [PMID: 33422555 DOI: 10.1016/j.virusres.2021.198295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/29/2020] [Accepted: 01/03/2021] [Indexed: 10/22/2022]
Abstract
Expanded potential stem cells (EPSCs) have been recently derived from porcine preimplantation embryos (Gao et al., 2019). These cells were shown to express key pluripotency genes, to be genetically stable and differentiate to derivatives of the three germ layers and additionally to trophoblast. Their molecular features and expanded potency to contribute to all embryonic and extra-embryonic cell lineages are generally not seen in the embryo-derived or induced pluripotent stem cells (iPSCs). Therefore porcine EPSCs represent a unique state of cellular potency. In the past it had been shown that human and murine embryonic stem cells (ESCs) show an increased expression of murine and human endogenous retroviruses, respectively, and retroviral expression patterns were used as markers of ESC pluripotency. An increased expression of porcine endogenous retroviruses (PERVs) was also detected in porcine iPSCs. Here we investigated 24 passages of five different clones of porcine EPSCs derived from German landrace pigs and show that they harbour PERV-A, PERV-B and PERV-C, but their expression was very low and did not change during cultivation. No recombinant PERV-A/Cs were found in these cells. The low expression despite the presence of spliced mRNA, and negative infection assay and electron microscopy results indicate that no PERV particles were released. Therefore, the absence of PERV expression seems to be a unique feature of porcine EPSCs. Most importantly, the copy number of PERV proviruses was much lower in EPSCs than in young and older pigs (29.1 copies compared with 35.8), indicating an increase in copy number during life time.
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Affiliation(s)
- Luise Krüger
- Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany
| | - Monika Nowak-Imialek
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute (FLI), Mariensee, 31535, Neustadt, Germany; Klinik und Poliklinik Innere Medizin I, Klinikum rechts der Isar - Technical University of Munich, Munich, Germany
| | | | - Doris Herrmann
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute (FLI), Mariensee, 31535, Neustadt, Germany
| | - Björn Petersen
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute (FLI), Mariensee, 31535, Neustadt, Germany
| | - Joachim Denner
- Robert Koch Fellow, Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany; Institute of Virology, Free University Berlin, Robert von Ostertag-Straße 7-13, 14163, Berlin, Germany.
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22
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Wang T, Doucet-O’Hare TT, Henderson L, Abrams RPM, Nath A. Retroviral Elements in Human Evolution and Neural Development. JOURNAL OF EXPERIMENTAL NEUROLOGY 2021; 2:1-9. [PMID: 33693440 PMCID: PMC7943042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Tongguang Wang
- Translational Neuroscience Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Tara T. Doucet-O’Hare
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Lisa Henderson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Rachel P. M. Abrams
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Avindra Nath
- Translational Neuroscience Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA,Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA,Correspondence should be addressed to Avindra Nath;
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23
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Denner J. Endogenous retroviruses expressed in human tumours cannot be used as targets for anti-tumour vaccines. Transl Oncol 2020; 14:100941. [PMID: 33221683 PMCID: PMC7689320 DOI: 10.1016/j.tranon.2020.100941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 11/23/2022] Open
Abstract
Endogenous retroviruses are expressed in human tumours. In some animal tumour models passive and active immunization against retroviral antigens expressed in the tumour tissues helped to inhibit tumour development. Human tumour cells expressing human endogenous retroviruses (HERVs) transplanted into animals were also inhibited by antibodies against HERVs. Since HERVs are also expressed in the human placenta, on human stem cells and immune cells, immunisation against HERVs may be harmful if applied.
Many tumour cells express on their surface proteins of endogenous retroviruses (ERVs) and there are suggestions to use these retroviral antigens as target for anti-tumour vaccines. However, until now there is no convincing data showing that this strategy works, in contrast, there are considerations suggesting that this strategy may be harmful if applied.
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Affiliation(s)
- Joachim Denner
- Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.
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24
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Geis FK, Goff SP. Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview. Viruses 2020; 12:v12080884. [PMID: 32823517 PMCID: PMC7472088 DOI: 10.3390/v12080884] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Almost half of the human genome is made up of transposable elements (TEs), and about 8% consists of endogenous retroviruses (ERVs). ERVs are remnants of ancient exogenous retrovirus infections of the germ line. Most TEs are inactive and not detrimental to the host. They are tightly regulated to ensure genomic stability of the host and avoid deregulation of nearby gene loci. Histone-based posttranslational modifications such as H3K9 trimethylation are one of the main silencing mechanisms. Trim28 is one of the identified master regulators of silencing, which recruits most prominently the H3K9 methyltransferase Setdb1, among other factors. Sumoylation and ATP-dependent chromatin remodeling factors seem to contribute to proper localization of Trim28 to ERV sequences and promote Trim28 interaction with Setdb1. Additionally, DNA methylation as well as RNA-mediated targeting of TEs such as piRNA-based silencing play important roles in ERV regulation. Despite the involvement of ERV overexpression in several cancer types, autoimmune diseases, and viral pathologies, ERVs are now also appreciated for their potential positive role in evolution. ERVs can provide new regulatory gene elements or novel binding sites for transcription factors, and ERV gene products can even be repurposed for the benefit of the host.
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Affiliation(s)
- Franziska K. Geis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
| | - Stephen P. Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
- Correspondence: ; Tel.: +1-212-305-3794
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25
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Regulation of stem cell function and neuronal differentiation by HERV-K via mTOR pathway. Proc Natl Acad Sci U S A 2020; 117:17842-17853. [PMID: 32669437 DOI: 10.1073/pnas.2002427117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Stem cells are capable of unlimited proliferation but can be induced to form brain cells. Factors that specifically regulate human development are poorly understood. We found that human stem cells expressed high levels of the envelope protein of an endogenized human-specific retrovirus (HERV-K, HML-2) from loci in chromosomes 12 and 19. The envelope protein was expressed on the cell membrane of the stem cells and was critical in maintaining the stemness via interactions with CD98HC, leading to triggering of human-specific signaling pathways involving mammalian target of rapamycin (mTOR) and lysophosphatidylcholine acyltransferase (LPCAT1)-mediated epigenetic changes. Down-regulation or epigenetic silencing of HML-2 env resulted in dissociation of the stem cell colonies and enhanced differentiation along neuronal pathways. Thus HML-2 regulation is critical for human embryonic and neurodevelopment, while it's dysregulation may play a role in tumorigenesis and neurodegeneration.
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26
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Xue B, Zeng T, Jia L, Yang D, Lin SL, Sechi LA, Kelvin DJ. Identification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencing. Retrovirology 2020; 17:10. [PMID: 32375827 PMCID: PMC7201656 DOI: 10.1186/s12977-020-00519-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/23/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Human endogenous retroviruses (HERVs), suspected to be transposition-defective, may reshape the transcriptional network of the human genome by regulatory elements distributed in their long terminal repeats (LTRs). HERV-K (HML-2), the most preserved group with the least number of accumulated of mutations, has been associated with aberrant gene expression in tumorigenesis and autoimmune diseases. Because of the high sequence similarity between different HERV-Ks, current methods have limitations in providing genome-wide mapping specific for individual HERV-K (HML-2) members, a major barrier in delineating HERV-K (HML-2) function. RESULTS In an attempt to obtain detailed distribution information of HERV-K (HML-2), we utilized a PCR-based target enrichment sequencing protocol for HERV-K (HML-2) (PTESHK) loci, which not only maps the presence of reference loci, but also identifies non-reference loci, enabling determination of the genome-wide distribution of HERV-K (HML-2) loci. Here we report on the genomic data obtained from three individuals. We identified a total of 978 loci using this method, including 30 new reference loci and 5 non-reference loci. Among the 3 individuals in our study, 14 polymorphic HERV-K (HML-2) loci were identified, and solo-LTR330 and N6p21.32 were identified as polymorphic for the first time. CONCLUSIONS Interestingly, PTESHK provides an approach for the identification of the genome-wide distribution of HERV-K (HML-2) and can be used for the identification of polymorphic loci. Since polymorphic HERV-K (HML-2) integrations are suspected to be related to various diseases, PTESHK can supplement other emerging techniques in accessing polymorphic HERV-K (HML-2) elements in cancer and autoimmune diseases.
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Affiliation(s)
- Bei Xue
- Division of Immunology, Shantou University Medical College, Shantou, China
- The Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
- Canadian Center for Vaccinology, Dalhousie University, Halifax, Canada
| | - Tiansheng Zeng
- Division of Immunology, Shantou University Medical College, Shantou, China
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Lisha Jia
- Division of Immunology, Shantou University Medical College, Shantou, China
| | - Dongsheng Yang
- Division of Immunology, Shantou University Medical College, Shantou, China
| | - Stanley L Lin
- Division of Immunology, Shantou University Medical College, Shantou, China
| | - Leonardo A Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
| | - David J Kelvin
- Division of Immunology, Shantou University Medical College, Shantou, China.
- The Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada.
- Canadian Center for Vaccinology, Dalhousie University, Halifax, Canada.
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
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27
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Fuchs NV, Schieck M, Neuenkirch M, Tondera C, Schmitz H, Wendeburg L, Steinemann D, Elpers C, Rutsch F, König R. Generation of three induced pluripotent cell lines (iPSCs) from an Aicardi-Goutières syndrome (AGS) patient harboring a deletion in the genomic locus of the sterile alpha motif and HD domain containing protein 1 (SAMHD1). Stem Cell Res 2020; 43:101697. [PMID: 32062129 DOI: 10.1016/j.scr.2019.101697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/12/2019] [Accepted: 12/28/2019] [Indexed: 02/06/2023] Open
Abstract
Aicardi-Goutières syndrome (AGS) is a hereditary early onset encephalopathy. AGS patients display variable clinical manifestations including intracranial calcification, cerebral atrophy, white matter abnormalities and characteristic leukocytosis as well as a constitutive upregulation of type I IFN production indicative of a type I interferonopathy. Seven genes (SAMHD1, TREX1, RNASEH2B, RNASEH2C, RNASEH2A, ADAR1, IFIH1) have been associated with the AGS phenotype, up to now. Here, we describe the generation of three induced pluripotent stem cell lines from a patient with a deletion of coding exons 14 and 15 of the SAMHD1 gene.
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Affiliation(s)
- Nina V Fuchs
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Maximilian Schieck
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | - Christiane Tondera
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Heike Schmitz
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Lena Wendeburg
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Christiane Elpers
- Department of General Pediatrics, Muenster University Children's Hospital, Münster, Germany
| | - Frank Rutsch
- Department of General Pediatrics, Muenster University Children's Hospital, Münster, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany; Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, United States.
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28
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Acton O, Grant T, Nicastro G, Ball NJ, Goldstone DC, Robertson LE, Sader K, Nans A, Ramos A, Stoye JP, Taylor IA, Rosenthal PB. Structural basis for Fullerene geometry in a human endogenous retrovirus capsid. Nat Commun 2019; 10:5822. [PMID: 31862888 PMCID: PMC6925226 DOI: 10.1038/s41467-019-13786-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/28/2019] [Indexed: 01/09/2023] Open
Abstract
The HML2 (HERV-K) group constitutes the most recently acquired family of human endogenous retroviruses, with many proviruses less than one million years old. Many maintain intact open reading frames and provirus expression together with HML2 particle formation are observed in early stage human embryo development and are associated with pluripotency as well as inflammatory disease, cancers and HIV-1 infection. Here, we reconstruct the core structural protein (CA) of an HML2 retrovirus, assemble particles in vitro and employ single particle cryogenic electron microscopy (cryo-EM) to determine structures of four classes of CA Fullerene shell assemblies. These icosahedral and capsular assemblies reveal at high-resolution the molecular interactions that allow CA to form both pentamers and hexamers and show how invariant pentamers and structurally plastic hexamers associate to form the unique polyhedral structures found in retroviral cores.
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Affiliation(s)
- Oliver Acton
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Tim Grant
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Neil J Ball
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David C Goldstone
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Laura E Robertson
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Kasim Sader
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Thermo Fisher Scientific Materials and Structural Analysis, Eindhoven, Netherlands
| | - Andrea Nans
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andres Ramos
- Division of Molecular Structure, MRC National Institute for Medical Research, London, NW7 1AA, UK
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Jonathan P Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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29
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Fuchs NV, Schieck M, Neuenkirch M, Tondera C, Schmitz H, Steinemann D, Göhring G, König R. Induced pluripotent stem cell line (PEIi003-A) derived from an apparently healthy male individual. Stem Cell Res 2019; 42:101679. [PMID: 31837633 DOI: 10.1016/j.scr.2019.101679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 11/25/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are a useful tool to investigate pathomechanistic and cellular processes due to their differentiation potential into different somatic cell types in vitro. Here, we have generated iPSCs from an apparently healthy male individual using an integration-free reprogramming method. The resulting iPSCs are pluripotent and display a normal karyotype. Furthermore, we demonstrate that this iPSC line can be differentiated into all three germ layers.
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Affiliation(s)
- Nina V Fuchs
- Host‑Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Maximilian Schieck
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | - Christiane Tondera
- Host‑Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Heike Schmitz
- Host‑Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Renate König
- Host‑Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany; Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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30
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Fuchs NV, Schieck M, Neuenkirch M, Tondera C, Schmitz H, des Portes V, Germanaud D, Steinemann D, Göhring G, König R. Induced pluripotent stem cells (iPSCs) derived from a renpenning syndrome patient with c.459_462delAGAG mutation in PQBP1 (PEIi001-A). Stem Cell Res 2019; 41:101592. [PMID: 31698189 DOI: 10.1016/j.scr.2019.101592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 10/25/2022] Open
Abstract
The Renpenning syndrome spectrum is a rare X-linked mental retardation syndrome characterized by intellectual disability, microcephaly, low stature, lean body and hypogonadism. Mutations in the polyglutamine tract binding protein 1 (PQBP1) locus are causative for disease. Here, we describe the generation of an iPSC line from a patient mutated in the polar amino acid-rich domain of PQBP1 resulting in a C-terminal truncated protein (c.459_462 delAGAG, type p.R153fs193X).
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Affiliation(s)
- Nina V Fuchs
- Host‑Pathogen Interactions, Paul-Ehrlich-Institut, Langen 63225, Germany
| | - Maximilian Schieck
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | - Christiane Tondera
- Host‑Pathogen Interactions, Paul-Ehrlich-Institut, Langen 63225, Germany
| | - Heike Schmitz
- Host‑Pathogen Interactions, Paul-Ehrlich-Institut, Langen 63225, Germany
| | - Vincent des Portes
- National Reference Center for Fragile X and Other XLID, Biobank NeuroBioTec, Bron, France; Hospices Civils de Lyon, Université de Lyon and CNRS UMR 5304 (L2C2), Bron, France
| | - David Germanaud
- Université de Paris, UMR1141 NeuroDiderot, InDev team, Inserm, CEA, Paris, France; AP-HP, Hôpital Robert Debré, Service de Neurologie Pédiatrique et des Maladies Métaboliques, Paris, France
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Renate König
- Host‑Pathogen Interactions, Paul-Ehrlich-Institut, Langen 63225, Germany; Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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31
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The Concomitant Expression of Human Endogenous Retroviruses and Embryonic Genes in Cancer Cells under Microenvironmental Changes is a Potential Target for Antiretroviral Drugs. CANCER MICROENVIRONMENT 2019; 12:105-118. [PMID: 31691184 DOI: 10.1007/s12307-019-00231-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/20/2019] [Indexed: 01/26/2023]
Abstract
In our genomes there are thousands of copies of human endogenous retroviruses (HERVs) originated from the integration of exogenous retroviruses that infected germ line cells millions of years ago, and currently an altered expression of this elements has been associated to the onset, progression and acquisition of aggressiveness features of many cancers. The transcriptional reactivation of HERVs is mainly an effect of their responsiveness to some factors in cell microenvironment, such as nutrients, hormones and cytokines. We have already demonstrated that, under pressure of microenvironmental changes, HERV-K (HML-2) activation is required to maintain human melanoma cell plasticity and CD133+ cancer stem cells survival. In the present study, the transcriptional activity of HERV-K (HML-2), HERV-H, CD133 and the embryonic transcription factors OCT4, NANOG and SOX2 was evaluated during the in vitro treatment with antiretroviral drugs in cells from melanoma, liver and lung cancers exposed to microenvironmental changes. The exposure to stem cell medium induced a phenotype switching with the generation of sphere-like aggregates, characterized by the concomitant increase of HERV-K (HML-2) and HERV-H, CD133 and embryonic genes transcriptional activity. Although with heterogenic response among the different cell lines, the in vitro treatment with antiretroviral drugs affected HERVs transcriptional activity in parallel with the reduction of CD133 and embryonic genes expression, clonogenic activity and cell growth, accompanied by the induction of apoptosis. The responsiveness to antiretroviral drugs treatment of cancer cells with stemness features and expressing HERVs suggests the use of these drugs as innovative approach to treat aggressive tumours in combination with chemotherapeutic/radiotherapy regimens.
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32
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Garcia-Montojo M, Li W, Nath A. Technical considerations in detection of HERV-K in amyotrophic lateral sclerosis: selection of controls and the perils of qPCR. Acta Neuropathol Commun 2019; 7:101. [PMID: 31269986 PMCID: PMC6607509 DOI: 10.1186/s40478-019-0753-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/19/2019] [Indexed: 12/14/2022] Open
Affiliation(s)
- Marta Garcia-Montojo
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
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33
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Fu B, Ma H, Liu D. Endogenous Retroviruses Function as Gene Expression Regulatory Elements During Mammalian Pre-implantation Embryo Development. Int J Mol Sci 2019; 20:ijms20030790. [PMID: 30759824 PMCID: PMC6387303 DOI: 10.3390/ijms20030790] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 01/13/2023] Open
Abstract
Pre-implantation embryo development encompasses several key developmental events, especially the activation of zygotic genome activation (ZGA)-related genes. Endogenous retroviruses (ERVs), which are regarded as “deleterious genomic parasites”, were previously considered to be “junk DNA”. However, it is now known that ERVs, with limited conservatism across species, mediate conserved developmental processes (e.g., ZGA). Transcriptional activation of ERVs occurs during the transition from maternal control to zygotic genome control, signifying ZGA. ERVs are versatile participants in rewiring gene expression networks during epigenetic reprogramming. Particularly, a subtle balance exists between ERV activation and ERV repression in host–virus interplay, which leads to stage-specific ERV expression during pre-implantation embryo development. A large portion of somatic cell nuclear transfer (SCNT) embryos display developmental arrest and ZGA failure during pre-implantation embryo development. Furthermore, because of the close relationship between ERV activation and ZGA, exploring the regulatory mechanism underlying ERV activation may also shed more light on the enigma of SCNT embryo development in model animals.
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Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
| | - Hong Ma
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
| | - Di Liu
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
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34
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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: 110] [Impact Index Per Article: 18.3] [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.
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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
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35
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Matteucci C, Balestrieri E, Argaw-Denboba A, Sinibaldi-Vallebona P. Human endogenous retroviruses role in cancer cell stemness. Semin Cancer Biol 2018; 53:17-30. [PMID: 30317035 DOI: 10.1016/j.semcancer.2018.10.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/30/2018] [Accepted: 10/05/2018] [Indexed: 12/18/2022]
Abstract
Cancer incidence and mortality, metastasis, drug resistance and recurrence are still the critical issues of oncological diseases. In this scenario, increasing scientific evidences demonstrate that the activation of human endogenous retroviruses (HERVs) is involved in the aggressiveness of tumors such as melanoma, breast, germ cell, renal, ovarian, liver and haematological cancers. In their dynamic regulation, HERVs have also proved to be important determinants of pluripotency in human embryonic stem cells (ESC) and of the reprogramming process of induced pluripotent stem cells (iPSCs). In many types of tumors, essential characteristics of aggressiveness have been associated with the achievement of stemness features, often accompanied with the identification of defined subpopulations, termed cancer stem cells (CSCs), which possess stem cell-like properties and sustain tumorigenesis. Indeed, CSCs show high self-renewal capacity with a peculiar potential in tumor initiation, progression, metastasis, heterogeneity, recurrence, radiotherapy and drug resistance. However, HERVs role in CSCs biology is still not fully elucidated. In this regard, CD133 is a widely recognized marker of CSCs, and our group demonstrated, for the first time, the requirement of HERV-K activation to expand and maintain a CD133+ melanoma cell subpopulation with stemness features in response to microenvironmental modifications. The review will discuss HERVs expression as cancer hallmark, with particular focus on their role in the regulation of cancer stemness features and the potential involvement as targets for therapy.
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Affiliation(s)
- Claudia Matteucci
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy.
| | - Emanuela Balestrieri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy
| | - Ayele Argaw-Denboba
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy; European Molecular Biology Laboratory (EMBL), Adriano Buzzati-Traverso Campus, Monterotondo, Rome, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy; Institute of Translational Pharmacology, National Research Council, Via Fosso del Cavaliere, 100, 00133, Rome, Italy
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Wallace AD, Wendt GA, Barcellos LF, de Smith AJ, Walsh KM, Metayer C, Costello JF, Wiemels JL, Francis SS. To ERV Is Human: A Phenotype-Wide Scan Linking Polymorphic Human Endogenous Retrovirus-K Insertions to Complex Phenotypes. Front Genet 2018; 9:298. [PMID: 30154825 PMCID: PMC6102640 DOI: 10.3389/fgene.2018.00298] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
Approximately 8% of the human genome is comprised of endogenous retroviral insertions (ERVs) originating from historic retroviral integration into germ cells. The function of ERVs as regulators of gene expression is well established. Less well studied are insertional polymorphisms of ERVs and their contribution to the heritability of complex phenotypes. The most recent integration of ERV, HERV-K, is expressed in a range of complex human conditions from cancer to neurologic diseases. Using an in-house computational pipeline and whole-genome sequencing data from the diverse 1,000 Genomes Phase 3 population (n = 2,504), we identified 46 polymorphic HERV-K insertions that are tagged by adjacent single nucleotide polymorphisms (SNPs). To test the potential role of polymorphic HERV-K in the heritability of complex diseases, existing databases were queried for enrichment of established relationships between the HERV-K insertion-associated SNPs (hiSNPs), and tissue specific gene expression and disease phenotypes. Overall, hiSNPs for the 46 polymorphic HERV-K sites were statistically enriched (p < 1.0E-16) for eQTLs across 44 human tissues. Fifteen of the 46 HERV-K insertions had hiSNPs annotated in the EMBL-EBI GWAS Catalog and cumulatively associated with >100 phenotypes. Experimental factor ontology enrichment analysis suggests that polymorphic HERV-K specifically contribute to neurologic and immunologic disease phenotypes, including traits related to intra cranial volume (FDR 2.00E-09), Parkinson's disease (FDR 1.80E-09), and autoimmune diseases (FDR 1.80E-09). These results provide strong candidates for context-specific study of polymorphic HERV-K insertions in disease-related traits, serving as a roadmap for future studies of the heritability of complex disease.
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Affiliation(s)
- Amelia D Wallace
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - George A Wendt
- Division of Epidemiology, School of Community Health Sciences, University of Nevada, Reno, NV, United States
| | - Lisa F Barcellos
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Adam J de Smith
- Department of Epidemiology and Biostatistics, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Kyle M Walsh
- Department of Neurosurgery, Duke University, Durham, NC, United States
| | - Catherine Metayer
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Joseph F Costello
- Department of Neurosurgery, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurosurgery, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Stephen S Francis
- Division of Epidemiology, School of Community Health Sciences, University of Nevada, Reno, NV, United States.,Department of Epidemiology and Biostatistics, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
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Mayer J, Harz C, Sanchez L, Pereira GC, Maldener E, Heras SR, Ostrow LW, Ravits J, Batra R, Meese E, García-Pérez JL, Goodier JL. Transcriptional profiling of HERV-K(HML-2) in amyotrophic lateral sclerosis and potential implications for expression of HML-2 proteins. Mol Neurodegener 2018; 13:39. [PMID: 30068350 PMCID: PMC6091006 DOI: 10.1186/s13024-018-0275-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder. About 90% of ALS cases are without a known genetic cause. The human endogenous retrovirus multi-copy HERV-K(HML-2) group was recently reported to potentially contribute to neurodegeneration and disease pathogenesis in ALS because of transcriptional upregulation and toxic effects of HML-2 Envelope (Env) protein. Env and other proteins are encoded by some transcriptionally active HML-2 loci. However, more detailed information is required regarding which HML-2 loci are transcribed in ALS, which of their proteins are expressed, and differences between the disease and non-disease states. Methods For brain and spinal cord tissue samples from ALS patients and controls, we identified transcribed HML-2 loci by generating and mapping HML-2-specific cDNA sequences. We predicted expression of HML-2 env gene-derived proteins based on the observed cDNA sequences. Furthermore, we determined overall HML-2 transcript levels by RT-qPCR and investigated presence of HML-2 Env protein in ALS and control tissue samples by Western blotting. Results We identified 24 different transcribed HML-2 loci. Some of those loci are transcribed at relatively high levels. However, significant differences in HML-2 loci transcriptional activities were not seen when comparing ALS and controls. Likewise, overall HML-2 transcript levels, as determined by RT-qPCR, were not significantly different between ALS and controls. Indeed, we were unable to detect full-length HML-2 Env protein in ALS and control tissue samples despite reasonable sensitivity. Rather our analyses suggest that a number of HML-2 protein variants other than full-length Env may potentially be expressed in ALS patients. Conclusions Our results expand and refine recent publications on HERV-K(HML-2) and ALS. Some of our results are in conflict with recent findings and call for further specific analyses. Our profiling of HML-2 transcription in ALS opens up the possibility that HML-2 proteins other than canonical full-length Env may have to be considered when studying the role of HML-2 in ALS disease. Electronic supplementary material The online version of this article (10.1186/s13024-018-0275-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jens Mayer
- Department of Human Genetics, University of Saarland, Homburg, Germany.
| | - Christian Harz
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Gavin C Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Esther Maldener
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Sara R Heras
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain.,Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071, Granada, Spain
| | - Lyle W Ostrow
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 28217, USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, UCSD, San Diego, CA, USA
| | - Ranjan Batra
- Department of Neurosciences, School of Medicine, UCSD, San Diego, CA, USA
| | - Eckart Meese
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John L Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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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.
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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
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Trizzino M, Kapusta A, Brown CD. Transposable elements generate regulatory novelty in a tissue-specific fashion. BMC Genomics 2018; 19:468. [PMID: 29914366 PMCID: PMC6006921 DOI: 10.1186/s12864-018-4850-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/01/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Transposable elements (TE) are an important source of evolutionary novelty in gene regulation. However, the mechanisms by which TEs contribute to gene expression are largely uncharacterized. RESULTS Here, we leverage Roadmap and GTEx data to investigate the association of TEs with active and repressed chromatin in 24 tissues. We find 112 human TE families enriched in active regions of the genome across tissues. Short Interspersed Nuclear Elements (SINEs) and DNA transposons are the most frequently enriched classes, while Long Terminal Repeat Retrotransposons (LTRs) are often enriched in a tissue-specific manner. We report across-tissue variability in TE enrichment in active regions. Genes with consistent expression across tissues are less likely to be associated with TE insertions. TE presence in repressed regions similarly follows tissue-specific patterns. Moreover, different TE classes correlate with different repressive marks: LTRs and Long Interspersed Nuclear Elements (LINEs) are overrepresented in regions marked by H3K9me3, while the other TEs are more likely to overlap regions with H3K27me3. Young TEs are typically enriched in repressed regions and depleted in active regions. We detect multiple instances of TEs that are enriched in tissue-specific active regulatory regions. Such TEs contain binding sites for transcription factors that are master regulators for the given tissue. These TEs are enriched in intronic enhancers, and their tissue-specific enrichment correlates with tissue-specific variations in the expression of the nearest genes. CONCLUSIONS We provide an integrated overview of the contribution of TEs to human gene regulation. Expanding previous analyses, we demonstrate that TEs can potentially contribute to the turnover of regulatory sequences in a tissue-specific fashion.
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Affiliation(s)
- Marco Trizzino
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA. .,Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.,USTAR, Center for Genetic Discovery, Salt Lake City, UT, USA
| | - Christopher D Brown
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA. .,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA.
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40
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Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, Gilad Y. Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. eLife 2018; 7:33084. [PMID: 29648536 PMCID: PMC5943035 DOI: 10.7554/elife.33084] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 04/11/2018] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) comprise almost half of primate genomes and their aberrant regulation can result in deleterious effects. In pluripotent stem cells, rapidly evolving KRAB-ZNF genes target TEs for silencing by H3K9me3. To investigate the evolution of TE silencing, we performed H3K9me3 ChIP-seq experiments in induced pluripotent stem cells from 10 human and 7 chimpanzee individuals. We identified four million orthologous TEs and found the SVA and ERV families to be marked most frequently by H3K9me3. We found little evidence of inter-species differences in TE silencing, with as many as 82% of putatively silenced TEs marked at similar levels in humans and chimpanzees. TEs that are preferentially silenced in one species are a similar age to those silenced in both species and are not more likely to be associated with expression divergence of nearby orthologous genes. Our data suggest limited species-specificity of TE silencing across 6 million years of primate evolution.
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Affiliation(s)
- Michelle C Ward
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Medicine, University of Chicago, Chicago, United States
| | - Siming Zhao
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Bryan J Pavlovic
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Mohammad M Karimi
- MRC London Institute of Medical Sciences, Imperial College, London, United Kingdom
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Statistics, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Medicine, University of Chicago, Chicago, United States
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41
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HIV-1 Infection of Primary CD4 + T Cells Regulates the Expression of Specific Human Endogenous Retrovirus HERV-K (HML-2) Elements. J Virol 2017; 92:JVI.01507-17. [PMID: 29046457 DOI: 10.1128/jvi.01507-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/14/2017] [Indexed: 11/20/2022] Open
Abstract
Endogenous retroviruses (ERVs) occupy extensive regions of the human genome. Although many of these retroviral elements have lost their ability to replicate, those whose insertion took place more recently, such as the HML-2 group of HERV-K elements, still retain intact open reading frames and the capacity to produce certain viral RNA and/or proteins. Transcription of these ERVs is, however, tightly regulated by dedicated epigenetic control mechanisms. Nonetheless, it has been reported that some pathological states, such as viral infections and certain cancers, coincide with ERV expression, suggesting that transcriptional reawakening is possible. HML-2 elements are reportedly induced during HIV-1 infection, but the conserved nature of these elements has, until recently, rendered their expression profiling problematic. Here, we provide comprehensive HERV-K HML-2 expression profiles specific for productively HIV-1-infected primary human CD4+ T cells. We combined enrichment of HIV-1 infected cells using a reporter virus expressing a surface reporter for gentle and efficient purification with long-read single-molecule real-time sequencing. We show that three HML-2 proviruses-6q25.1, 8q24.3, and 19q13.42-are upregulated on average between 3- and 5-fold in HIV-1-infected CD4+ T cells. One provirus, HML-2 12q24.33, in contrast, was repressed in the presence of active HIV replication. In conclusion, this report identifies the HERV-K HML-2 loci whose expression profiles differ upon HIV-1 infection in primary human CD4+ T cells. These data will help pave the way for further studies on the influence of endogenous retroviruses on HIV-1 replication.IMPORTANCE Endogenous retroviruses inhabit big portions of our genome. Moreover, although they are mainly inert, some of the evolutionarily younger members maintain the ability to express both RNA and proteins. We have developed an approach using long-read single-molecule real-time (SMRT) sequencing that produces long reads that allow us to obtain detailed and accurate HERV-K HML-2 expression profiles. We applied this approach to study HERV-K expression in the presence or absence of productive HIV-1 infection of primary human CD4+ T cells. In addition to using SMRT sequencing, our strategy also includes the magnetic selection of the infected cells so that levels of background expression due to uninfected cells are kept at a minimum. The results presented here provide a blueprint for in-depth studies of the interactions of the authentic upregulated HERV-K HML-2 elements and HIV-1.
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Shan ZL, Zhu XY, Ma PP, Wang H, Chen J, Li J, Zhong L, Liu BZ. PML(NLS¯) protein: A novel marker for the early diagnosis of acute promyelocytic leukemia. Mol Med Rep 2017; 16:5418-5424. [PMID: 28849126 PMCID: PMC5647086 DOI: 10.3892/mmr.2017.7272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/15/2017] [Indexed: 12/31/2022] Open
Abstract
Promyelocyte leukemia-retinoic acid receptor α (PML-RARα) is known as a fusion gene of acute promyelocytic leukemia (APL). Previous studies have reported that neutrophil elastase (NE) cleaves PML-RARα in early myeloid cells, which leads to the removal of the nuclear localization signal (NLS) in PML and increases the incidence of APL. The resultant PML without the NLS is termed PML(NLS−). The aim of the present study was to verify the existence and location of the PML(NLS−) protein in NB4 cells. NB4 cells underwent electroporation with the pCMV-HA-NE plasmid to form NB4-HA-NE cells, which were then transplanted to produce tumors in nude mice and samples were collected from patients with APL. Western blot analysis, an immunofluorescence assay, confocal laser microscopy and immunohistochemistry were performed to detect the expression and localization of the PML(NLS−) protein. The findings demonstrated that PML(NLS−) was detectable in the cytoplasm of NB4-HA-NE cells, the tumors in nude mice and in neutrophils from patients with APL. This indicated that PML(NLS−) may be an effective and novel target for the diagnosis of APL.
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Affiliation(s)
- Zhi-Ling Shan
- Department of Laboratory Medicine and Central Laboratory of Yong‑chuan Hospital, Chongqing Medical University, Chongqing 402160, P.R. China
| | - Xin-Yu Zhu
- Department of Laboratory Medicine and Central Laboratory of Yong‑chuan Hospital, Chongqing Medical University, Chongqing 402160, P.R. China
| | - Peng-Peng Ma
- Department of Laboratory Medicine and Central Laboratory of Yong‑chuan Hospital, Chongqing Medical University, Chongqing 402160, P.R. China
| | - Hui Wang
- Department of Laboratory Medicine and Central Laboratory of Yong‑chuan Hospital, Chongqing Medical University, Chongqing 402160, P.R. China
| | - Jianbin Chen
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 630014, P.R. China
| | - Jun Li
- Department of Clinical Laboratory, The Third People's Hospital of Chongqing, Chongqing 400014, P.R. China
| | - Liang Zhong
- Key Laboratory of Laboratory Medical Diagnostics, Department of Laboratory Medicine, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Bei-Zhong Liu
- Department of Laboratory Medicine and Central Laboratory of Yong‑chuan Hospital, Chongqing Medical University, Chongqing 402160, P.R. China
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Meyer TJ, Rosenkrantz JL, Carbone L, Chavez SL. Endogenous Retroviruses: With Us and against Us. Front Chem 2017; 5:23. [PMID: 28439515 PMCID: PMC5384584 DOI: 10.3389/fchem.2017.00023] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/20/2017] [Indexed: 12/13/2022] Open
Abstract
Mammalian genomes are scattered with thousands of copies of endogenous retroviruses (ERVs), mobile genetic elements that are relics of ancient retroviral infections. After inserting copies into the germ line of a host, most ERVs accumulate mutations that prevent the normal assembly of infectious viral particles, becoming trapped in host genomes and unable to leave to infect other cells. While most copies of ERVs are inactive, some are transcribed and encode the proteins needed to generate new insertions at novel loci. In some cases, old copies are removed via recombination and other mechanisms. This creates a shifting landscape of ERV copies within host genomes. New insertions can disrupt normal expression of nearby genes via directly inserting into key regulatory elements or by containing regulatory motifs within their sequences. Further, the transcriptional silencing of ERVs via epigenetic modification may result in changes to the epigenetic regulation of adjacent genes. In these ways, ERVs can be potent sources of regulatory disruption as well as genetic innovation. Here, we provide a brief review of the association between ERVs and gene expression, especially as observed in pre-implantation development and placentation. Moreover, we will describe how disruption of the regulated mechanisms of ERVs may impact somatic tissues, mostly in the context of human disease, including cancer, neurodegenerative disorders, and schizophrenia. Lastly, we discuss the recent discovery that some ERVs may have been pressed into the service of their host genomes to aid in the innate immune response to exogenous viral infections.
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Affiliation(s)
- Thomas J Meyer
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science UniversityPortland, OR, USA
| | - Jimi L Rosenkrantz
- Department of Molecular and Medical Genetics, Oregon Health & Science UniversityPortland, OR, USA.,Division of Reproductive & Developmental Sciences, Oregon National Primate Research CenterPortland, OR, USA
| | - Lucia Carbone
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science UniversityPortland, OR, USA.,Department of Molecular and Medical Genetics, Oregon Health & Science UniversityPortland, OR, USA.,Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science UniversityPortland, OR, USA
| | - Shawn L Chavez
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research CenterPortland, OR, USA.,Departments of Obstetrics and Gynecology and Physiology and Pharmacology, Oregon Health & Science University School of MedicinePortland, OR, USA
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Benešová M, Trejbalová K, Kovářová D, Vernerová Z, Hron T, Kučerová D, Hejnar J. DNA hypomethylation and aberrant expression of the human endogenous retrovirus ERVWE1/syncytin-1 in seminomas. Retrovirology 2017; 14:20. [PMID: 28302141 PMCID: PMC5356313 DOI: 10.1186/s12977-017-0342-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Syncytin-1 and 2, human fusogenic glycoproteins encoded by the env genes of the endogenous retroviral loci ERVWE1 and ERVFRDE1, respectively, contribute to the differentiation of multinucleated syncytiotrophoblast in chorionic villi. In non-trophoblastic cells, however, the expression of syncytins has to be suppressed to avoid potential pathogenic effects. Previously, we have shown that the transcriptional suppression of ERVWE1 promoter is controlled epigenetically by DNA methylation and chromatin modifications. In this study, we describe the aberrant expression of syncytin-1 in biopsies of testicular germ cell tumors. RESULTS We found efficient expression and splicing of syncytin-1 in seminomas and mixed germ cell tumors with seminoma component. Although another fusogenic gene, syncytin-2 was also derepressed in seminomas, its expression was significantly lower than that of syncytin-1. Neither the transcription factor GCM1 nor the increased copy number of ERVWE1 were sufficient for this aberrant expression of syncytin-1 in seminomas. In accordance with our recent finding of the highly increased expression of TET1 dioxygenase in most seminomas, the ERVWE1 promoter was significantly hypomethylated in comparison with the matched controls. In contrast, 5-hydroxymethylcytosine levels were not detectable at the ERVWE1 promoter. We further describe that another endogenous retroviral element adjacent to ERVWE1 remains transcriptionally suppressed and two additional HERV-W family members are only slightly upregulated in seminomas. CONCLUSIONS We conclude that DNA demethylation of the ERVWE1 promoter in seminomas is a prerequisite for syncytin-1 derepression. We propose the spliced syncytin-1 expression as a marker of seminoma and suggest that aberrant expression of endogenous retroviruses might be a correlate of the hypomethylated genome of seminomas.
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Affiliation(s)
- Martina Benešová
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Kateřina Trejbalová
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic.
| | - Denisa Kovářová
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Zdenka Vernerová
- Department of Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Tomáš Hron
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Dana Kučerová
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Jiří Hejnar
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic.
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Argaw-Denboba A, Balestrieri E, Serafino A, Cipriani C, Bucci I, Sorrentino R, Sciamanna I, Gambacurta A, Sinibaldi-Vallebona P, Matteucci C. HERV-K activation is strictly required to sustain CD133+ melanoma cells with stemness features. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:20. [PMID: 28125999 PMCID: PMC5270369 DOI: 10.1186/s13046-016-0485-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/27/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND Melanoma is a heterogeneous tumor in which phenotype-switching and CD133 marker have been associated with metastasis promotion and chemotherapy resistance. CD133 positive (CD133+) subpopulation has also been suggested as putative cancer stem cell (CSC) of melanoma tumor. Human endogenous retrovirus type K (HERV-K) has been described to be aberrantly activated during melanoma progression and implicated in the etiopathogenesis of disease. Earlier, we reported that stress-induced HERV-K activation promotes cell malignant transformation and reduces the immunogenicity of melanoma cells. Herein, we investigated the correlation between HERV-K and the CD133+ melanoma cells during microenvironmental modifications. METHODS TVM-A12 cell line, isolated in our laboratory from a primary human melanoma lesion, and other commercial melanoma cell lines (G-361, WM-115, WM-266-4 and A375) were grown and maintained in the standard and stem cell media. RNA interference, Real-time PCR, flow cytometry analysis, self-renewal and migration/invasion assays were performed to characterize cell behavior and HERV-K expression. RESULTS Melanoma cells, exposed to stem cell media, undergo phenotype-switching and expansion of CD133+ melanoma cells, concomitantly promoted by HERV-K activation. Notably, the sorted CD133+ subpopulation showed stemness features, characterized by higher self-renewal ability, embryonic genes expression, migration and invasion capacities compared to the parental cell line. RNA interference-mediated downregulation experiments showed that HERV-K has a decisive role to expand and maintain the CD133+ melanoma subpopulation during microenvironmental modifications. Similarly, non nucleoside reverse transcriptase inhibitors (NNRTIs) efavirenz and nevirapine were effective to restrain the activation of HERV-K in melanoma cells, to antagonize CD133+ subpopulation expansion and to induce selective high level apoptosis in CD133+ cells. CONCLUSIONS HERV-K activation promotes melanoma cells phenotype-switching and is strictly required to expand and maintain the CD133+ melanoma cells with stemness features in response to microenvironmental modifications.
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Affiliation(s)
- Ayele Argaw-Denboba
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Emanuela Balestrieri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Annalucia Serafino
- Institute of Translational Pharmacology, National Research Council, Via Fosso del Cavaliere 100, 00133, Rome, Italy
| | - Chiara Cipriani
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Ilaria Bucci
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Roberta Sorrentino
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Ilaria Sciamanna
- S.B.G.S.A. Istituto Superiore di Sanità (Italian National Institute of Health), Viale Regina Elena 299, 00161, Rome, Italy
| | - Alessandra Gambacurta
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.,Institute of Translational Pharmacology, National Research Council, Via Fosso del Cavaliere 100, 00133, Rome, Italy
| | - Claudia Matteucci
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
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Abstract
Although genetic transfer between viruses and vertebrate hosts occurs less frequently than gene flow between bacteriophages and prokaryotes, it is extensive and has affected the evolution of both parties. With retroviruses, the integration of proviral DNA into chromosomal DNA can result in the activation of adjacent host gene expression and in the transduction of host transcripts into retroviral genomes as oncogenes. Yet in contrast to lysogenic phage, there is little evidence that viral oncogenes persist in a chain of natural transmission or that retroviral transduction is a significant driver of the horizontal spread of host genes. Conversely, integration of proviruses into the host germ line has generated endogenous retroviral genomes (ERV) in all vertebrate genomes sequenced to date. Some of these genomes retain potential infectivity and upon reactivation may transmit to other host species. During mammalian evolution, sequences of retroviral origin have been repurposed to serve host functions, such as the viral envelope glycoproteins crucial to the development of the placenta. Beyond retroviruses, DNA viruses with complex genomes have acquired numerous genes of host origin which influence replication, pathogenesis and immune evasion, while host species have accumulated germline sequences of both DNA and RNA viruses. A codicil is added on lateral transmission of cancer cells between hosts and on migration of host mitochondria into cancer cells.
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Affiliation(s)
- Robin A Weiss
- Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT, UK.
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Babaian A, Mager DL. Endogenous retroviral promoter exaptation in human cancer. Mob DNA 2016; 7:24. [PMID: 27980689 PMCID: PMC5134097 DOI: 10.1186/s13100-016-0080-x] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/11/2016] [Indexed: 12/13/2022] Open
Abstract
Cancer arises from a series of genetic and epigenetic changes, which result in abnormal expression or mutational activation of oncogenes, as well as suppression/inactivation of tumor suppressor genes. Aberrant expression of coding genes or long non-coding RNAs (lncRNAs) with oncogenic properties can be caused by translocations, gene amplifications, point mutations or other less characterized mechanisms. One such mechanism is the inappropriate usage of normally dormant, tissue-restricted or cryptic enhancers or promoters that serve to drive oncogenic gene expression. Dispersed across the human genome, endogenous retroviruses (ERVs) provide an enormous reservoir of autonomous gene regulatory modules, some of which have been co-opted by the host during evolution to play important roles in normal regulation of genes and gene networks. This review focuses on the “dark side” of such ERV regulatory capacity. Specifically, we discuss a growing number of examples of normally dormant or epigenetically repressed ERVs that have been harnessed to drive oncogenes in human cancer, a process we term onco-exaptation, and we propose potential mechanisms that may underlie this phenomenon.
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Affiliation(s)
- Artem Babaian
- Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3 Canada ; Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Dixie L Mager
- Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3 Canada ; Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
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48
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Shapiro JA. Exploring the read-write genome: mobile DNA and mammalian adaptation. Crit Rev Biochem Mol Biol 2016; 52:1-17. [DOI: 10.1080/10409238.2016.1226748] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
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49
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Göke J, Ng HH. CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome. EMBO Rep 2016; 17:1131-44. [PMID: 27402545 DOI: 10.15252/embr.201642743] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 06/20/2016] [Indexed: 12/25/2022] Open
Abstract
The human genome contains millions of fragments from retrotransposons-highly repetitive DNA sequences that were once able to "copy and paste" themselves to other regions in the genome. However, the majority of retrotransposons have lost this capacity through acquisition of mutations or through endogenous silencing mechanisms. Without this imminent threat of transposition, retrotransposons have the potential to act as a major source of genomic innovation. Indeed, large numbers of retrotransposons have been found to be active in specific contexts: as gene regulatory elements and promoters for protein-coding genes or long noncoding RNAs, among others. In this review, we summarise recent findings about retrotransposons, with implications in gene expression regulation, the expansion of gene isoform diversity and the generation of long noncoding RNAs. We highlight key examples that demonstrate their role in cellular identity and their versatility as markers of cell states, and we discuss how their dysregulation may contribute to the formation of and possibly therapeutic response in human cancers.
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Affiliation(s)
- Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Huck Hui Ng
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore Department of Biochemistry, National University of Singapore, Singapore Department of Biological Sciences, National University of Singapore, Singapore School of Biological Sciences, Nanyang Technological University, Singapore
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Hanke K, Hohn O, Bannert N. HERV-K(HML-2), a seemingly silent subtenant - but still waters run deep. APMIS 2016; 124:67-87. [PMID: 26818263 DOI: 10.1111/apm.12475] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/12/2015] [Indexed: 01/26/2023]
Abstract
A large proportion of the human genome consists of endogenous retroviruses, some of which are well preserved, showing transcriptional activity, and expressing retroviral proteins. The HERV-K(HML-2) family represents the most intact members of these elements, with some having open and intact reading frames for viral proteins and the ability to form virus-like particles. Although generally suppressed in most healthy tissues by a variety of epigenetic processes and antiviral mechanisms, there is evidence that some members of this family are (at least partly) still active - particularly in certain stem cells and various tumors. This raises the possibility of their involvement in tumor induction or in developmental processes. In recent years, many new insights into this fascinating field have been attained, and this review focuses on new discoveries about coevolutionary events and intracellular defense mechanisms against HERV-K(HML-2) activity. We also describe what might occur when these mechanisms fail or become modulated by viral proteins or other viruses and discuss the new vistas opened up by the reconstitution of ancestral viral proteins and even complete HML-2 viruses.
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Affiliation(s)
- Kirsten Hanke
- Department HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Oliver Hohn
- Department HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Norbert Bannert
- Department HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
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