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Semsari H, Babaei E, Ranjkesh M, Esmaili N, Mallet F, Karimi A. Association of Human Endogenous Retrovirus-W (HERV-W) Copies with Pemphigus Vulgaris. Curr Mol Med 2024; 24:683-688. [PMID: 37078354 DOI: 10.2174/1566524023666230418114152] [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: 10/30/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 04/21/2023]
Abstract
BACKGROUND Pemphigus is classified as a group of chronic, recurrent, and potentially fatal bullous autoimmune diseases that leads to blisters and skin lesions resulting from IgG antibodies and the loss of cellular connections in the epidermis. Human endogenous retrovirus (HERV) sequences and their products (RNA, cytosolic DNA, and proteins) can modulate the immune system and contribute to autoimmunity. The extent to which, HERV-W env copies may be involved in the pathogenesis of pemphigus remains to be elucidated. AIM This study aimed to comparatively evaluate the relative levels of HERV-W env DNA copy numbers in the peripheral blood mononuclear cells (PBMCs) of pemphigus vulgaris patients and healthy controls. METHODS Thirty-one pemphigus patients and the corresponding age- and sex-matched healthy controls were included in the study. The relative levels of HERV-W env DNA copy numbers were then evaluated by qPCR using specific primers, in the PBMCs of the patients and controls. RESULTS Our results indicated that relative levels of HERV-W env DNA copy numbers in the patients were significantly higher than that in the controls (1.67±0.86 vs. 1.17±0.75; p = 0.02). There was also a significant difference between the HERV-W env copies of male and female patients (p = 0.001). Furthermore, there was no relationship between the HERV-W env copy number and disease onset (p = 0.19) . According to the obtained data, we could not find any relationship between the HERV-W env copy number and serum Dsg1(p=0.86) and Dsg3 (p=0.76) levels. CONCLUSION Our results indicated a positive link between the HERV-W env copies and pathogenesis of pemphigus. The association between clinical severity score and HERVW env copies in the PBMCs as a biomarker for pemphigus needs further studies.
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Affiliation(s)
- Hanieh Semsari
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Esmaeil Babaei
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Mohammadreza Ranjkesh
- Department of Dermatology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nafiseh Esmaili
- Autoimmune Bullous Diseases Research Center, Tehran University of Medical Sciences, Razi Hospital, Tehran, Iran
| | - François Mallet
- Joint Research Unit Hospices Civils de Lyon-bioMérieux, Lyon Sud Hospital, Pierre-Bénite, France
- EA 7426 Pathophysiology of Injury-Induced Immunosuppression, Edouard Herriot Hospital, University of Lyon1- Hospices Civils de Lyon-bioMérieux, 5 Place d'Arsonval, Lyon Cedex 3, Lyon, France
| | - Abbas Karimi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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2
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Switzer CH. Non-canonical nitric oxide signalling and DNA methylation: Inflammation induced epigenetic alterations and potential drug targets. Br J Pharmacol 2023. [PMID: 38116806 DOI: 10.1111/bph.16302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 12/21/2023] Open
Abstract
DNA methylation controls DNA accessibility to transcription factors and other regulatory proteins, thereby affecting gene expression and hence cellular identity and function. As epigenetic modifications control the transcriptome, epigenetic dysfunction is strongly associated with pathological conditions and ageing. The development of pharmacological agents that modulate the activity of major epigenetic proteins are in pre-clinical development and clinical use. However, recent publications have identified novel redox-based signalling pathways, and therefore novel drug targets, that may exert epigenetic effects. This review will discuss the recent developments in nitric oxide (NO) signalling on DNA methylation as well as potential epigenetic drug targets that have emerged from the intersection of inflammation/redox biology and epigenetic regulation.
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Affiliation(s)
- Christopher H Switzer
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
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Priščáková P, Svoboda M, Feketová Z, Hutník J, Repiská V, Gbelcová H, Gergely L. Syncytin-1, syncytin-2 and suppressyn in human health and disease. J Mol Med (Berl) 2023; 101:1527-1542. [PMID: 37855856 PMCID: PMC10697888 DOI: 10.1007/s00109-023-02385-6] [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: 03/24/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023]
Abstract
In this review, we summarized the results of experimental and clinical studies about three human endogenous retroviruses and their products-syncytin-1, syncytin-2, and suppressyn in human physiology and pathophysiology. We summed up the described connection with various pathological processes and diseases, mainly with pregnancy-induced hypertensive diseases such as preeclampsia, oncogenesis, gestational trophoblastic disease, and multiple sclerosis. Supposed mechanisms of action and the potential of clinical applications are also described.
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Affiliation(s)
- Petra Priščáková
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Michal Svoboda
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Zuzana Feketová
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Juraj Hutník
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Vanda Repiská
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Helena Gbelcová
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Lajos Gergely
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic.
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4
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Nevalainen T, Autio A, Hurme M. Human endogenous retroviruses of the HERV-K (HML-2) family are expressed in the brain of healthy individuals and modify the composition of the brain-infiltrating immune cells. Heliyon 2023; 9:e21283. [PMID: 37920490 PMCID: PMC10618496 DOI: 10.1016/j.heliyon.2023.e21283] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/10/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections in the human genome. RNA expression of individual HERVs has frequently been observed in various pathologic conditions, but some activity can also be seen in healthy individuals, e.g. in the blood. To quantitate the basal expression levels of HERVs in the brain, we now used high-throughput sequencing-based metagenomic analysis to characterize the expression profiles of the HERV-K (HML-2) family proviruses in different brain regions of healthy brain tissue. To this end, RNA-seq data from the Genotype-Tissue Expression (GTEx) project was used. The GTEx project is a public resource to study tissue-specific gene expression and regulation, consisting of a large selection of sequenced samples from different tissues. The GTEx data used in this study consisted of 378 samples taken from 13 brain regions from 55 individuals. The data demonstrated that out of 99 intact proviruses in the family 58 were expressed, but the expression profiles were highly divergent and there were no significant differences in the expression profiles between the various anatomic regions of the brain. It is known that the brain contains a variety of infiltrating immune cells, which are probably of great importance both in the normal defense mechanisms as well as in the various pathogenic processes. Digital cytometry (CIBERSORTx) was used to quantify the proportions of the infiltrating immune cells in the same brain samples. Six most abundant (>5 % of the total population) cell types were observed to be CD4 memory resting T cells, M0 macrophages, plasma cells, CD8 T cells, CD4 memory activated T cells, and monocytes. Analysis of the correlations between the individual HERVs and infiltrating cell types indicated that a cluster of 6 HERVs had a notable correlation signature between T cell type infiltrating cell proportions and HERV RNA expression intensity. The correlations between inflammatory type infiltrating cells were negative or weak. Taken together, these data indicate that the expression of HERVs is associated with a T cell type immunity.
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Affiliation(s)
- Tapio Nevalainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center (GEREC), Tampere, Finland
- Tampere University Hospital, Finland
| | - Arttu Autio
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center (GEREC), Tampere, Finland
| | - Mikko Hurme
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center (GEREC), Tampere, Finland
- Tampere University Hospital, Finland
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5
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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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Reviewing the Potential Links between Viral Infections and TDP-43 Proteinopathies. Int J Mol Sci 2023; 24:ijms24021581. [PMID: 36675095 PMCID: PMC9867397 DOI: 10.3390/ijms24021581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023] Open
Abstract
Transactive response DNA binding protein 43 kDa (TDP-43) was discovered in 2001 as a cellular factor capable to inhibit HIV-1 gene expression. Successively, it was brought to new life as the most prevalent RNA-binding protein involved in several neurological disorders, such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Despite the fact that these two research areas could be considered very distant from each other, in recent years an increasing number of publications pointed out the existence of a potentially important connection. Indeed, the ability of TDP-43 to act as an important regulator of all aspects of RNA metabolism makes this protein also a critical factor during expression of viral RNAs. Here, we summarize all recent observations regarding the involvement of TDP-43 in viral entry, replication and latency in several viruses that include enteroviruses (EVs), Theiler's murine encephalomyelitis virus (TMEV), human immunodeficiency virus (HIV), human endogenous retroviruses (HERVs), hepatitis B virus (HBV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), West Nile virus (WNV), and herpes simplex virus-2 (HSV). In particular, in this work, we aimed to highlight the presence of similarities with the most commonly studied TDP-43 related neuronal dysfunctions.
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Fan TJ, Cui J. Human Endogenous Retroviruses in Diseases. Subcell Biochem 2023; 106:403-439. [PMID: 38159236 DOI: 10.1007/978-3-031-40086-5_15] [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] [Indexed: 01/03/2024]
Abstract
Human endogenous retroviruses (HERVs), which are conserved sequences of ancient retroviruses, are widely distributed in the human genome. Although most HERVs have been rendered inactive by evolution, some have continued to exhibit important cytological functions. HERVs in the human genome perform dual functions: on the one hand, they are involved in important physiological processes such as placental development and immune regulation; on the other hand, their aberrant expression is closely associated with the pathological processes of several diseases, such as cancers, autoimmune diseases, and viral infections. HERVs can also regulate a variety of host cellular functions, including the expression of protein-coding genes and regulatory elements that have evolved from HERVs. Here, we present recent research on the roles of HERVs in viral infections and cancers, including the dysregulation of HERVs in various viral infections, HERV-induced epigenetic modifications of histones (such as methylation and acetylation), and the potential mechanisms of HERV-mediated antiviral immunity. We also describe therapies to improve the efficacy of vaccines and medications either by directly or indirectly targeting HERVs, depending on the HERV.
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Affiliation(s)
- Tian-Jiao Fan
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
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8
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Wieland L, Schwarz T, Engel K, Volkmer I, Krüger A, Tarabuko A, Junghans J, Kornhuber ME, Hoffmann F, Staege MS, Emmer A. Epstein-Barr Virus-Induced Genes and Endogenous Retroviruses in Immortalized B Cells from Patients with Multiple Sclerosis. Cells 2022; 11:cells11223619. [PMID: 36429047 PMCID: PMC9688211 DOI: 10.3390/cells11223619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Accepted: 11/06/2022] [Indexed: 11/18/2022] Open
Abstract
The immune pathogenesis of multiple sclerosis (MS) is thought to be triggered by environmental factors in individuals with an unfavorable genetic predisposition. Epstein-Barr virus (EBV) infection is a major risk factor for subsequent development of MS. Human endogenous retroviruses (HERVs) can be activated by EBV, and might be a missing link between an initial EBV infection and the later onset of MS. In this study, we investigated differential gene expression patterns in EBV-immortalized lymphoblastoid B cell lines (LCL) from MS-affected individuals (MSLCL) and controls by using RNAseq and qRT-PCR. RNAseq data from LCL mapped to the human genome and a virtual virus metagenome were used to identify possible biomarkers for MS or disease-relevant risk factors, e.g., the relapse rate. We observed that lytic EBNA-1 transcripts seemed to be negatively correlated with age leading to an increased expression in LCL from younger PBMC donors. Further, HERV-K (HML-2) GAG was increased upon EBV-triggered immortalization. Besides the well-known transactivation of HERV-K18, our results suggest that another six HERV loci are up-regulated upon stimulation with EBV. We identified differentially expressed genes in MSLCL, e.g., several HERV-K loci, ERVMER61-1 and ERV3-1, as well as genes associated with relapses. In summary, EBV induces genes and HERV in LCL that might be suitable as biomarkers for MS or the relapse risk.
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Affiliation(s)
- Lisa Wieland
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Tommy Schwarz
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Kristina Engel
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Ines Volkmer
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Anna Krüger
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Alexander Tarabuko
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jutta Junghans
- Department of Neurology, Martha-Maria Hospital Halle-Dölau, 06120 Halle (Saale), Germany
| | - Malte E. Kornhuber
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Frank Hoffmann
- Department of Neurology, Martha-Maria Hospital Halle-Dölau, 06120 Halle (Saale), Germany
| | - Martin S. Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Correspondence: ; Tel.: +49-34-5557-7280
| | - Alexander Emmer
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
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Ilse V, Scholz R, Wermann M, Naumann M, Staege MS, Roßner S, Cynis H. Immunogenicity of the Envelope Surface Unit of Human Endogenous Retrovirus K18 in Mice. Int J Mol Sci 2022; 23:ijms23158330. [PMID: 35955468 PMCID: PMC9369184 DOI: 10.3390/ijms23158330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 02/06/2023] Open
Abstract
The triggers for the development of multiple sclerosis (MS) have not been fully understood to date. One hypothesis proposes a viral etiology. Interestingly, viral proteins from human endogenous retroviruses (HERVs) may play a role in the pathogenesis of MS. Allelic variants of the HERV-K18 env gene represent a genetic risk factor for MS, and the envelope protein is considered to be an Epstein–Barr virus-trans-activated superantigen. To further specify a possible role for HERV-K18 in MS, the present study examined the immunogenicity of the purified surface unit (SU). HERV-K18(SU) induced envelope-specific plasma IgG in immunized mice and triggered proliferation of T cells isolated from these mice. It did not trigger phenotypic changes in a mouse model of experimental autoimmune encephalomyelitis. Further studies are needed to investigate the underlying mechanisms of HERV-K18 interaction with immune system regulators in more detail.
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Affiliation(s)
- Victoria Ilse
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.I.); (R.S.); (M.W.); (M.N.)
| | - Rebekka Scholz
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.I.); (R.S.); (M.W.); (M.N.)
| | - Michael Wermann
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.I.); (R.S.); (M.W.); (M.N.)
| | - Marcel Naumann
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.I.); (R.S.); (M.W.); (M.N.)
| | - Martin S. Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06097 Halle, Germany;
| | - Steffen Roßner
- Paul Flechsig Institute for Brain Research, Leipzig University, Liebigstraße 19, 04103 Leipzig, Germany;
| | - Holger Cynis
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, Weinbergweg 22, 06120 Halle, Germany; (V.I.); (R.S.); (M.W.); (M.N.)
- Correspondence: ; Tel.: +49-345-13142835; Fax: +49-345-13142801
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10
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The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology. Int J Mol Sci 2022; 23:ijms23105847. [PMID: 35628657 PMCID: PMC9148063 DOI: 10.3390/ijms23105847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) have been extensively studied for decades. In recent years, the introduction of whole-genome and whole-transcriptome approaches, as well as single-cell resolution techniques, provided a breakthrough that uncovered TE involvement in host gene expression regulation underlying multiple normal and pathological processes. Of particular interest is increased TE activity in neuronal tissue, and specifically in the hippocampus, that was repeatedly demonstrated in multiple experiments. On the other hand, numerous neuropathologies are associated with TE dysregulation. Here, we provide a comprehensive review of literature about the role of TEs in neurons published over the last three decades. The first chapter of the present review describes known mechanisms of TE interaction with host genomes in general, with the focus on mammalian and human TEs; the second chapter provides examples of TE exaptation in normal neuronal tissue, including TE involvement in neuronal differentiation and plasticity; and the last chapter lists TE-related neuropathologies. We sought to provide specific molecular mechanisms of TE involvement in neuron-specific processes whenever possible; however, in many cases, only phenomenological reports were available. This underscores the importance of further studies in this area.
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Shah AH, Govindarajan V, Doucet-O'Hare TT, Rivas S, Ampie L, DeMarino C, Banasavadi-Siddegowda YK, Zhang Y, Johnson KR, Almsned F, Gilbert MR, Heiss JD, Nath A. Differential expression of an endogenous retroviral element [HERV-K(HML-6)] is associated with reduced survival in glioblastoma patients. Sci Rep 2022; 12:6902. [PMID: 35477752 PMCID: PMC9046263 DOI: 10.1038/s41598-022-10914-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 04/04/2022] [Indexed: 11/09/2022] Open
Abstract
Comprising approximately 8% of our genome, Human Endogenous RetroViruses (HERVs) represent a class of germline retroviral infections that are regulated through epigenetic modifications. In cancer cells, which often have epigenetic dysregulation, HERVs have been implicated as potential oncogenic drivers. However, their role in gliomas is not known. Given the link between HERV expression in cancer cell lines and the distinct epigenetic dysregulation in gliomas, we utilized a tailored bioinformatic pipeline to characterize and validate the glioma retrotranscriptome and correlate HERV expression with locus-specific epigenetic modifications. We identified robust overexpression of multiple HERVs in our cell lines, including a retroviral transcript, HML-6, at 19q13.43b in glioblastoma cells. HERV expression inversely correlated with loci-specific DNA methylation. HML-6 contains an intact open reading frame encoding a small envelope protein, ERVK3-1. Increased expression of ERVK3-1 in GBM patients is associated with a poor prognosis independent of IDH-mutational status. Our results suggest that not only is HML-6 uniquely overexpressed in highly invasive cell lines and tissue samples, but also its gene product, ERVK3-1, may be associated with reduced survival in GBM patients. These results may have implications for both the tumor biology of GBM and the role of ERVK3-1 as a potential therapeutic target.
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Affiliation(s)
- Ashish H Shah
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA.
| | - Vaidya Govindarajan
- Department of Neurosurgery, University of Miami School of Medicine, Miami, FL, USA
| | - Tara T Doucet-O'Hare
- Center for Cancer Research (CCR), National Institutes of Health, National Cancer Institute (NCI), Neuro-Oncology Branch (NOB), Bethesda, MD, USA
| | - Sarah Rivas
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Leo Ampie
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Catherine DeMarino
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | | | - Yong Zhang
- Bioinformatics Section, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Kory R Johnson
- Bioinformatics Section, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Fahad Almsned
- Bioinformatics Section, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Mark R Gilbert
- Center for Cancer Research (CCR), National Institutes of Health, National Cancer Institute (NCI), Neuro-Oncology Branch (NOB), Bethesda, MD, USA
| | - John D Heiss
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
| | - Avindra Nath
- Surgical Neurology Branch, National Institutes of Health, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA
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Peze-Heidsieck E, Bonnifet T, Znaidi R, Ravel-Godreuil C, Massiani-Beaudoin O, Joshi RL, Fuchs J. Retrotransposons as a Source of DNA Damage in Neurodegeneration. Front Aging Neurosci 2022; 13:786897. [PMID: 35058771 PMCID: PMC8764243 DOI: 10.3389/fnagi.2021.786897] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023] Open
Abstract
The etiology of aging-associated neurodegenerative diseases (NDs), such as Parkinson’s disease (PD) and Alzheimer’s disease (AD), still remains elusive and no curative treatment is available. Age is the major risk factor for PD and AD, but the molecular link between aging and neurodegeneration is not fully understood. Aging is defined by several hallmarks, some of which partially overlap with pathways implicated in NDs. Recent evidence suggests that aging-associated epigenetic alterations can lead to the derepression of the LINE-1 (Long Interspersed Element-1) family of transposable elements (TEs) and that this derepression might have important implications in the pathogenesis of NDs. Almost half of the human DNA is composed of repetitive sequences derived from TEs and TE mobility participated in shaping the mammalian genomes during evolution. Although most TEs are mutated and no longer mobile, more than 100 LINE-1 elements have retained their full coding potential in humans and are thus retrotransposition competent. Uncontrolled activation of TEs has now been reported in various models of neurodegeneration and in diseased human brain tissues. We will discuss in this review the potential contribution of LINE-1 elements in inducing DNA damage and genomic instability, which are emerging pathological features in NDs. TEs might represent an important molecular link between aging and neurodegeneration, and a potential target for urgently needed novel therapeutic disease-modifying interventions.
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Affiliation(s)
- Eugenie Peze-Heidsieck
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Tom Bonnifet
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Rania Znaidi
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Olivia Massiani-Beaudoin
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Rajiv L Joshi
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
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13
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Durnaoglu S, Lee SK, Ahnn J. Human Endogenous Retroviruses as Gene Expression Regulators: Insights from Animal Models into Human Diseases. Mol Cells 2021; 44:861-878. [PMID: 34963103 PMCID: PMC8718366 DOI: 10.14348/molcells.2021.5016] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022] Open
Abstract
The human genome contains many retroviral elements called human endogenous retroviruses (HERVs), resulting from the integration of retroviruses throughout evolution. HERVs once were considered inactive junk because they are not replication-competent, primarily localized in the heterochromatin, and silenced by methylation. But HERVs are now clearly shown to actively regulate gene expression in various physiological and pathological conditions such as developmental processes, immune regulation, cancers, autoimmune diseases, and neurological disorders. Recent studies report that HERVs are activated in patients suffering from coronavirus disease 2019 (COVID-19), the current pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection. In this review, we describe internal and external factors that influence HERV activities. We also present evidence showing the gene regulatory activity of HERV LTRs (long terminal repeats) in model organisms such as mice, rats, zebrafish, and invertebrate models of worms and flies. Finally, we discuss several molecular and cellular pathways involving various transcription factors and receptors, through which HERVs affect downstream cellular and physiological events such as epigenetic modifications, calcium influx, protein phosphorylation, and cytokine release. Understanding how HERVs participate in various physiological and pathological processes will help develop a strategy to generate effective therapeutic approaches targeting HERVs.
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Affiliation(s)
- Serpen Durnaoglu
- Department of Life Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Sun-Kyung Lee
- Department of Life Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Joohong Ahnn
- Department of Life Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
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14
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Zarghami A, Li Y, Claflin SB, van der Mei I, Taylor BV. Role of environmental factors in multiple sclerosis. Expert Rev Neurother 2021; 21:1389-1408. [PMID: 34494502 DOI: 10.1080/14737175.2021.1978843] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Environmental factors play a significant role in the pathogenesis and progression of multiple sclerosis (MS), either acting alone or by interacting with other environmental or genetic factors. This cumulative exposure to external risk factors is highly complex and highly variable between individuals. AREAS COVERED We narratively review the current evidence on the role of environment-specific risk factors in MS onset and progression, as well as the effect of gene-environment interactions and the timing of exposure We have reviewed the latest literature, by Ovid Medline, retrieving the most recently published systematic reviews and/or meta-analyses and more recent studies not previously included in meta-analyses or systematic reviews. EXPERT OPINION There is some good evidence supporting the impact of some environmental risk factors in increasing the risk of developing MS. Tobacco smoking, low vitamin D levels and/or low sun exposure, Epstein Barr Virus (EBV) seropositivity and a history of infectious mononucleosis may increase the risk of developing MS. Additionally, there is some evidence that gene-smoking, gene-EBV, and smoking-EBV interactions additively affect the risk of MS onset. However, the evidence for a role of other environmental factors in MS progression is limited. Finally, there is some evidence that tobacco smoking, insufficient vitamin D levels and/or sun exposure have impacts on MS phenotypes and various markers of disease activity including relapse, disability progression and MRI findings. Clearly the effect of environmental factors on MS disease course is an area that requires significantly more research.
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Affiliation(s)
- Amin Zarghami
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Ying Li
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Suzi B Claflin
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Ingrid van der Mei
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Bruce V Taylor
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
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15
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Bello-Morales R, Andreu S, Ripa I, López-Guerrero JA. HSV-1 and Endogenous Retroviruses as Risk Factors in Demyelination. Int J Mol Sci 2021; 22:ijms22115738. [PMID: 34072259 PMCID: PMC8199333 DOI: 10.3390/ijms22115738] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/19/2022] Open
Abstract
Herpes simplex virus type 1 (HSV-1) is a neurotropic alphaherpesvirus that can infect the peripheral and central nervous systems, and it has been implicated in demyelinating and neurodegenerative processes. Transposable elements (TEs) are DNA sequences that can move from one genomic location to another. TEs have been linked to several diseases affecting the central nervous system (CNS), including multiple sclerosis (MS), a demyelinating disease of unknown etiology influenced by genetic and environmental factors. Exogenous viral transactivators may activate certain retrotransposons or class I TEs. In this context, several herpesviruses have been linked to MS, and one of them, HSV-1, might act as a risk factor by mediating processes such as molecular mimicry, remyelination, and activity of endogenous retroviruses (ERVs). Several herpesviruses have been involved in the regulation of human ERVs (HERVs), and HSV-1 in particular can modulate HERVs in cells involved in MS pathogenesis. This review exposes current knowledge about the relationship between HSV-1 and human ERVs, focusing on their contribution as a risk factor for MS.
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Affiliation(s)
- Raquel Bello-Morales
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (S.A.); (I.R.); (J.A.L.-G.)
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
- Correspondence:
| | - Sabina Andreu
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (S.A.); (I.R.); (J.A.L.-G.)
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
| | - Inés Ripa
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (S.A.); (I.R.); (J.A.L.-G.)
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
| | - José Antonio López-Guerrero
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain; (S.A.); (I.R.); (J.A.L.-G.)
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain
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16
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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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17
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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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18
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Glinsky GV. Genomics-Guided Drawing of Molecular and Pathophysiological Components of Malignant Regulatory Signatures Reveals a Pivotal Role in Human Diseases of Stem Cell-Associated Retroviral Sequences and Functionally-Active hESC Enhancers. Front Oncol 2021; 11:638363. [PMID: 33869024 PMCID: PMC8044830 DOI: 10.3389/fonc.2021.638363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/10/2021] [Indexed: 12/31/2022] Open
Abstract
Repetitive DNA sequences (repeats) colonized two-third of human genome and a majority of repeats comprised of transposable genetic elements (TE). Evolutionary distinct categories of TE represent nucleic acid sequences that are repeatedly copied from and pasted into chromosomes at multiple genomic locations and acquired a multitude of regulatory functions. Here, genomics-guided maps of stemness regulatory signatures were drawn to dissect the contribution of TE to clinical manifestations of malignant phenotypes of human cancers. From patients’ and physicians’ perspectives, the clinical definition of a tumor’s malignant phenotype could be restricted to the early diagnosis of sub-types of malignancies with the increased risk of existing therapy failure and high likelihood of death from cancer. It is the viewpoint from which the understanding of stemness and malignant regulatory signatures is considered in this contribution. Genomics-guided analyses of experimental and clinical observations revealed the pivotal role of human stem cell-associated retroviral sequences (SCARS) in the origin and pathophysiology of clinically-lethal malignancies. SCARS were defined as the evolutionary- and biologically-related family of genomic regulatory sequences, the principal physiological function of which is to create and maintain the stemness phenotype during human preimplantation embryogenesis. For cell differentiation to occur, SCARS expression must be silenced and SCARS activity remains repressed in most terminally-differentiated human cells which are destined to perform specialized functions in the human body. Epigenetic reprogramming, de-repression, and sustained activity of SCARS results in various differentiation-defective phenotypes. One of the most prominent tissue- and organ-specific clinical manifestations of sustained SCARS activities is diagnosed as a pathological condition defined by a consensus of morphological, molecular, and genetic examinations as the malignant growth. Here, contemporary evidence are acquired, analyzed, and reported defining both novel diagnostic tools and druggable molecular targets readily amenable for diagnosis and efficient therapeutic management of clinically-lethal malignancies. These diagnostic and therapeutic approaches are based on monitoring of high-fidelity molecular signals of continuing SCARS activities in conjunction with genomic regulatory networks of thousands’ functionally-active embryonic enhancers affecting down-stream phenotype-altering genetic loci. Collectively, reported herein observations support a model of SCARS-activation triggered singular source code facilitating the intracellular propagation and intercellular (systemic) dissemination of disease states in the human body.
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Affiliation(s)
- Gennadi V Glinsky
- Institute of Engineering in Medicine, University of California, San Diego, CA, United States.,Department of Functional & Translational Genomics, OncoSCAR, Inc., Portland, OR, United States
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19
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Römer C. Viruses and Endogenous Retroviruses as Roots for Neuroinflammation and Neurodegenerative Diseases. Front Neurosci 2021; 15:648629. [PMID: 33776642 PMCID: PMC7994506 DOI: 10.3389/fnins.2021.648629] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
Many neurodegenerative diseases are associated with chronic inflammation in the brain and periphery giving rise to a continuous imbalance of immune processes. Next to inflammation markers, activation of transposable elements, including long intrespersed nuclear elements (LINE) elements and endogenous retroviruses (ERVs), has been identified during neurodegenerative disease progression and even correlated with the clinical severity of the disease. ERVs are remnants of viral infections in the human genome acquired during evolution. Upon activation, they produce transcripts and the phylogenetically youngest ones are still able to produce viral-like particles. In addition, ERVs can bind transcription factors and modulate immune response. Being between own and foreign, ERVs are reviewed in the context of viral infections of the central nervous system, in aging and neurodegenerative diseases. Moreover, this review tests the hypothesis that viral infection may be a trigger at the onset of neuroinflammation and that ERVs sustain the inflammatory imbalance by summarizing existing data of neurodegenerative diseases associated with viruses and/or ERVs.
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Affiliation(s)
- Christine Römer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, The Berlin Institute for Medical Systems Biology, Berlin, Germany
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