1
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Lee M, Ahmad SF, Xu J. Regulation and function of transposable elements in cancer genomes. Cell Mol Life Sci 2024; 81:157. [PMID: 38556602 PMCID: PMC10982106 DOI: 10.1007/s00018-024-05195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 04/02/2024]
Abstract
Over half of human genomic DNA is composed of repetitive sequences generated throughout evolution by prolific mobile genetic parasites called transposable elements (TEs). Long disregarded as "junk" or "selfish" DNA, TEs are increasingly recognized as formative elements in genome evolution, wired intimately into the structure and function of the human genome. Advances in sequencing technologies and computational methods have ushered in an era of unprecedented insight into how TE activity impacts human biology in health and disease. Here we discuss the current views on how TEs have shaped the regulatory landscape of the human genome, how TE activity is implicated in human cancers, and how recent findings motivate novel strategies to leverage TE activity for improved cancer therapy. Given the crucial role of methodological advances in TE biology, we pair our conceptual discussions with an in-depth review of the inherent technical challenges in studying repeats, specifically related to structural variation, expression analyses, and chromatin regulation. Lastly, we provide a catalog of existing and emerging assays and bioinformatic software that altogether are enabling the most sophisticated and comprehensive investigations yet into the regulation and function of interspersed repeats in cancer genomes.
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Affiliation(s)
- Michael Lee
- Department of Pediatrics, Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA.
| | - Syed Farhan Ahmad
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA
| | - Jian Xu
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA.
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2
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Le Breton A, Bettencourt MP, Gendrel AV. Navigating the brain and aging: exploring the impact of transposable elements from health to disease. Front Cell Dev Biol 2024; 12:1357576. [PMID: 38476259 PMCID: PMC10927736 DOI: 10.3389/fcell.2024.1357576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that constitute on average 45% of mammalian genomes. Their presence and activity in genomes represent a major source of genetic variability. While this is an important driver of genome evolution, TEs can also have deleterious effects on their hosts. A growing number of studies have focused on the role of TEs in the brain, both in physiological and pathological contexts. In the brain, their activity is believed to be important for neuronal plasticity. In neurological and age-related disorders, aberrant activity of TEs may contribute to disease etiology, although this remains unclear. After providing a comprehensive overview of transposable elements and their interactions with the host, this review summarizes the current understanding of TE activity within the brain, during the aging process, and in the context of neurological and age-related conditions.
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Affiliation(s)
| | | | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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3
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Liang B, Yan T, Wei H, Zhang D, Li L, Liu Z, Li W, Zhang Y, Jiang N, Meng Q, Jiang G, Hu Y, Leng J. HERVK-mediated regulation of neighboring genes: implications for breast cancer prognosis. Retrovirology 2024; 21:4. [PMID: 38388382 PMCID: PMC10885364 DOI: 10.1186/s12977-024-00636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/18/2024] [Indexed: 02/24/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are the remnants of ancient retroviral infections integrated into the human genome. Although most HERVs are silenced or rendered inactive by various regulatory mechanisms, they retain the potential to influence the nearby genes. We analyzed the regulatory map of 91 HERV-Ks on neighboring genes in human breast cancer and investigated the impact of HERV-Ks on the tumor microenvironment (TME) and prognosis of breast cancer. Nine RNA-seq datasets were obtained from GEO and NCBI SRA. Differentially expressed genes and HERV-Ks were analyzed using DESeq2. Validation of high-risk prognostic candidate genes using TCGA data. These included Overall survival (multivariate Cox regression model), immune infiltration analysis (TIMER), tumor mutation burden (maftools), and drug sensitivity analysis (GSCA). A total of 88 candidate genes related to breast cancer prognosis were screened, of which CD48, SLAMF7, SLAMF1, IGLL1, IGHA1, and LRRC8A were key genes. Functionally, these six key genes were significantly enriched in some immune function-related pathways, which may be associated with poor prognosis for breast cancer (p = 0.00016), and the expression levels of these genes were significantly correlated with the sensitivity of breast cancer treatment-related drugs. Mechanistically, they may influence breast cancer development by modulating the infiltration of various immune cells into the TME. We further experimentally validated these genes to confirm the results obtained from bioinformatics analysis. This study represents the first report on the regulatory potential of HERV-K in the neighboring breast cancer genome. We identified three key HERV-Ks and five neighboring genes that hold promise as novel targets for future interventions and treatments for breast cancer.
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Affiliation(s)
- Boying Liang
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Nanning, China
| | - Tengyue Yan
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning, China
| | - Huilin Wei
- School of Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Die Zhang
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning, China
| | - Lanxiang Li
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zengjing Liu
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Wen Li
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Yuluan Zhang
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Nili Jiang
- School of Institute of Life Sciences, Guangxi Medical University, Nanning, China
| | - Qiuxia Meng
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Guiyang Jiang
- Genomic Experimental Center, Guangxi Medical University, Nanning, China
| | - Yanling Hu
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Collaborative Innovation Centre of Regenerative Medicine and Medical Bioresource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning, China.
- School of Institute of Life Sciences, Guangxi Medical University, Nanning, China.
- Genomic Experimental Center, Guangxi Medical University, Nanning, China.
| | - Jing Leng
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Guangxi Key Laboratory of Translational Medicine for Treating High-Incidence Infectious Diseases with Integrative Medicine, Nanning, China.
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4
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Takahashi Ueda M. Retrotransposon-derived transcripts and their functions in immunity and disease. Genes Genet Syst 2024; 98:305-319. [PMID: 38199240 DOI: 10.1266/ggs.23-00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024] Open
Abstract
Retrotransposons, which account for approximately 42% of the human genome, have been increasingly recognized as "non-self" pathogen-associated molecular patterns (PAMPs) due to their virus-like sequences. In abnormal conditions such as cancer and viral infections, retrotransposons that are aberrantly expressed due to impaired epigenetic suppression display PAMPs, leading to their recognition by pattern recognition receptors (PRRs) of the innate immune system and triggering inflammation. This viral mimicry mechanism has been observed in various human diseases, including aging and autoimmune disorders. However, recent evidence suggests that retrotransposons possess highly regulated immune reactivity and play important roles in the development and function of the immune system. In this review, I discuss a wide range of retrotransposon-derived transcripts, their role as targets in immune recognition, and the diseases associated with retrotransposon activity. Furthermore, I explore the implications of chimeric transcripts formed between retrotransposons and known gene mRNAs, which have been previously underestimated, for the increase of immune-related gene isoforms and their influence on immune function. Retrotransposon-derived transcripts have profound and multifaceted effects on immune system function. The aim of this comprehensive review is to provide a better understanding of the complex relationship between retrotransposon transcripts and immune defense.
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Affiliation(s)
- Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University
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5
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Abstract
Retrotransposons are transposable elements that are transposed via transcription and reverse transcription. Their copies have accumulated in the genome of mammals, occupying approximately 40% of mammalian genomic mass. These copies are often involved in numerous phenomena, such as chromatin spatial organization, gene expression, development and disease, and have been recognized as a driving force in evolution. Different organisms have gained specific retrotransposon subfamilies and retrotransposed copies, such as hundreds of Mus-specific subfamilies with diverse sequences and genomic locations. Despite this complexity, basic information is still necessary for present-day genomic and epigenomic studies. Herein, we describe the characteristics of each subfamily of Mus-specific retrotransposons in terms of sequence structure, phylogenetic relationships, evolutionary age, and preference for A or B compartments of chromatin.
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Affiliation(s)
- Masaki Kawase
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University
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Mottaghinia S, Stenzel S, Tsangaras K, Nikolaidis N, Laue M, Müller K, Hölscher H, Löber U, McEwen GK, Donnellan SC, Rowe KC, Aplin KP, Goffinet C, Greenwood AD. A recent gibbon ape leukemia virus germline integration in a rodent from New Guinea. Proc Natl Acad Sci U S A 2024; 121:e2220392121. [PMID: 38305758 PMCID: PMC10861895 DOI: 10.1073/pnas.2220392121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 11/30/2023] [Indexed: 02/03/2024] Open
Abstract
Germline colonization by retroviruses results in the formation of endogenous retroviruses (ERVs). Most colonization's occurred millions of years ago. However, in the Australo-Papuan region (Australia and New Guinea), several recent germline colonization events have been discovered. The Wallace Line separates much of Southeast Asia from the Australo-Papuan region restricting faunal and pathogen dispersion. West of the Wallace Line, gibbon ape leukemia viruses (GALVs) have been isolated from captive gibbons. Two microbat species from China appear to have been infected naturally. East of Wallace's Line, the woolly monkey virus (a GALV) and the closely related koala retrovirus (KoRV) have been detected in eutherians and marsupials in the Australo-Papuan region, often vertically transmitted. The detected vertically transmitted GALV-like viruses in Australo-Papuan fauna compared to sporadic horizontal transmission in Southeast Asia and China suggest the GALV-KoRV clade originates in the former region and further models of early-stage genome colonization may be found. We screened 278 samples, seven bat and one rodent family endemic to the Australo-Papuan region and bat and rodent species found on both sides of the Wallace Line. We identified two rodents (Melomys) from Australia and Papua New Guinea and no bat species harboring GALV-like retroviruses. Melomys leucogaster from New Guinea harbored a genomically complete replication-competent retrovirus with a shared integration site among individuals. The integration was only present in some individuals of the species indicating this retrovirus is at the earliest stages of germline colonization of the Melomys genome, providing a new small wild mammal model of early-stage genome colonization.
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Affiliation(s)
- Saba Mottaghinia
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
- Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieure de Lyon, LyonF-69007, France
| | - Saskia Stenzel
- Institute of Virology Charité–Universitätsmedizin Berlin, BerlinD-10117, Germany
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, LiverpoolL3 5QA, United Kingdom
| | - Kyriakos Tsangaras
- Department of Life and Health Sciences, University of Nicosia, NicosiaCY-2417, Cyprus
| | - Nikolas Nikolaidis
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA92834-6850
| | - Michael Laue
- Advanced Light and Electron Microscopy (ZBS 4), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, BerlinD-13353, Germany
| | - Karin Müller
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
| | - Henriette Hölscher
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
| | - Ulrike Löber
- Max-Delbrük Center for Molecular Medicine Helmholtz Association, Berlin13125, Germany
| | - Gayle K. McEwen
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
| | | | - Kevin C. Rowe
- Sciences Department, Museums Victoria, Melbourne, VIC3001, Australia
| | - Ken P. Aplin
- South Australian Museum, North Terrace, Adelaide SA5000, Australia
| | - Christine Goffinet
- Institute of Virology Charité–Universitätsmedizin Berlin, BerlinD-10117, Germany
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, LiverpoolL3 5QA, United Kingdom
| | - Alex D. Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
- School of Veterinary Medicine, Freie Universität Berlin, Berlin14163, Germany
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Hullahalli K, Dailey KG, Hasegawa Y, Johnson WE, Waldor MK. Reverse transcriptase inhibitors prevent liver abscess formation during Escherichia coli bloodstream infection. Proc Natl Acad Sci U S A 2024; 121:e2319162121. [PMID: 38227662 PMCID: PMC10823173 DOI: 10.1073/pnas.2319162121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024] Open
Abstract
The presence of bacteria in the bloodstream is associated with severe clinical outcomes. In mice, intravenous inoculation of Escherichia coli can lead to the formation of macroscopic abscesses in the liver. Abscesses are regions of severe necrosis and consist of millions of bacteria surrounded by inflammatory immune cells. Liver abscess susceptibility varies widely across strains of mice, but the host factors governing this variation are unknown. Here, we profiled hepatic transcriptomes in mice with varying susceptibility to liver abscess formation. We found that transcripts from endogenous retroviruses (ERVs) are robustly induced in the liver by E. coli infection and ERV expression positively correlates with the frequency of abscess formation. Hypothesizing that ERV-encoded reverse transcriptase may generate cytoplasmic DNA and heighten inflammatory responses, we tested whether nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) influence abscess formation. Strikingly, a single NRTI dose administered immediately following E. coli inoculation prevented abscess formation, leading to a concomitant 100,000-fold reduction in bacterial burden. We provide evidence that NRTIs inhibit abscess formation by preventing the tissue necrosis that facilitates bacterial replication. Together, our findings suggest that endogenous reverse transcriptases drive inflammatory responses during bacterial bloodstream infection to drive abscess formation. The high efficacy of NRTIs in preventing abscess formation suggests that the consequences of reverse transcription on inflammation should be further examined, particularly in infectious diseases where inflammation drives negative clinical outcomes, such as sepsis.
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Affiliation(s)
- Karthik Hullahalli
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Disease, Brigham and Women’s Hospital, Boston, MA02115
| | - Katherine G. Dailey
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Disease, Brigham and Women’s Hospital, Boston, MA02115
| | - Yuko Hasegawa
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Disease, Brigham and Women’s Hospital, Boston, MA02115
| | | | - Matthew K. Waldor
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Disease, Brigham and Women’s Hospital, Boston, MA02115
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Cocozza F, Martin‐Jaular L, Lippens L, Di Cicco A, Arribas YA, Ansart N, Dingli F, Richard M, Merle L, Jouve San Roman M, Poullet P, Loew D, Lévy D, Hendrix A, Kassiotis G, Joliot A, Tkach M, Théry C. Extracellular vesicles and co-isolated endogenous retroviruses from murine cancer cells differentially affect dendritic cells. EMBO J 2023; 42:e113590. [PMID: 38073509 PMCID: PMC10711651 DOI: 10.15252/embj.2023113590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023] Open
Abstract
Cells secrete extracellular vesicles (EVs) and non-vesicular extracellular (nano)particles (NVEPs or ENPs) that may play a role in intercellular communication. Tumor-derived EVs have been proposed to induce immune priming of antigen presenting cells or to be immuno-suppressive agents. We suspect that such disparate functions are due to variable compositions in EV subtypes and ENPs. We aimed to characterize the array of secreted EVs and ENPs of murine tumor cell lines. Unexpectedly, we identified virus-like particles (VLPs) from endogenous murine leukemia virus in preparations of EVs produced by many tumor cells. We established a protocol to separate small EVs from VLPs and ENPs. We compared their protein composition and analyzed their functional interaction with target dendritic cells. ENPs were poorly captured and did not affect dendritic cells. Small EVs specifically induced dendritic cell death. A mixed large/dense EV/VLP preparation was most efficient to induce dendritic cell maturation and antigen presentation. Our results call for systematic re-evaluation of the respective proportions and functions of non-viral EVs and VLPs produced by murine tumors and their contribution to tumor progression.
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Affiliation(s)
- Federico Cocozza
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
- Université de ParisParisFrance
| | - Lorena Martin‐Jaular
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
- Institut Curie Centre de RechercheCurieCoreTech Extracellular VesiclesParisFrance
| | - Lien Lippens
- Laboratory of Experimental Cancer Research, Department of Human Structure and RepairGhent University, and Cancer Research Institute GhentGhentBelgium
| | - Aurelie Di Cicco
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico‐chimie CurieParisFrance
- Institut Curie, PSL Research University, CNRS UMR144, Cell and Tissue Imaging Facility (PICT‐IBiSA)ParisFrance
| | - Yago A Arribas
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
| | - Nicolas Ansart
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
| | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse ProtéomiqueParisFrance
| | - Michael Richard
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse ProtéomiqueParisFrance
| | - Louise Merle
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
| | | | - Patrick Poullet
- Institut Curie, Bioinformatics core facility (CUBIC), INSERM U900, PSL Research University, Mines Paris TechParisFrance
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse ProtéomiqueParisFrance
| | - Daniel Lévy
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico‐chimie CurieParisFrance
- Institut Curie, PSL Research University, CNRS UMR144, Cell and Tissue Imaging Facility (PICT‐IBiSA)ParisFrance
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and RepairGhent University, and Cancer Research Institute GhentGhentBelgium
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute and Department of Medicine, Faculty of MedicineImperial CollegeLondonUK
| | - Alain Joliot
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
| | - Mercedes Tkach
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
| | - Clotilde Théry
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
- Institut Curie Centre de RechercheCurieCoreTech Extracellular VesiclesParisFrance
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Dubowsky M, Theunissen F, Carr JM, Rogers ML. The Molecular Link Between TDP-43, Endogenous Retroviruses and Inflammatory Neurodegeneration in Amyotrophic Lateral Sclerosis: a Potential Target for Triumeq, an Antiretroviral Therapy. Mol Neurobiol 2023; 60:6330-6345. [PMID: 37450244 PMCID: PMC10533598 DOI: 10.1007/s12035-023-03472-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease (MND), is a progressive neurological disorder, characterised by the death of upper and lower motor neurons. The aetiology of ALS remains unknown, and treatment options are limited. Endogenous retroviruses (ERVs), specifically human endogenous retrovirus type K (HERV-K), have been proposed to be involved in the propagation of neurodegeneration in ALS. ERVs are genomic remnants of ancient viral infection events, with most being inactive and not retaining the capacity to encode a fully infectious virus. However, some ERVs retain the ability to be activated and transcribed, and ERV transcripts have been found to be elevated within the brain tissue of MND patients. A hallmark of ALS pathology is altered localisation of the transactive response (TAR) DNA binding protein 43 kDa (TDP-43), which is normally found within the nucleus of neuronal and glial cells and is involved in RNA regulation. In ALS, TDP-43 aggregates within the cytoplasm and facilitates neurodegeneration. The involvement of ERVs in ALS pathology is thought to occur through TDP-43 and neuroinflammatory mediators. In this review, the proposed involvement of TDP-43, HERV-K and immune regulators on the onset and progression of ALS will be discussed. Furthermore, the evidence supporting a therapy based on targeting ERVs in ALS will be reviewed.
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Affiliation(s)
- Megan Dubowsky
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia.
| | - Frances Theunissen
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - Jillian M Carr
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - Mary-Louise Rogers
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
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10
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Sun X, Zhang T, Tong B, Cheng L, Jiang W, Sun Y. POGZ suppresses 2C transcriptional program and retrotransposable elements. Cell Rep 2023; 42:112867. [PMID: 37494184 DOI: 10.1016/j.celrep.2023.112867] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/23/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
The POGZ gene has been found frequently mutated in neurodevelopmental disorders (NDDs) such as autism spectrum disorder (ASD) and intellectual disability (ID). We have recently shown that POGZ maintains mouse embryonic stem cells (ESCs). However, the exact mechanisms remain unclear. Here, we show that POGZ plays an important role in the maintenance of ESCs by silencing Dux and endogenous retroviruses (ERVs). POGZ maintains a silent chromatin state at Dux and ERVs by associating with and recruiting TRIM28 and SETDB1, and its loss leads to decreased levels of H3K9me3/H4K20me3, resulting in up-regulation of 2C transcripts and ESC transition to a 2C-like state. POGZ suppresses different classes of ERVs through direct (IAPEy, the intracisternal A-type particle elements) and indirect regulation (MERVL). Activation of POGZ-bound ERVs is associated with up-regulation of nearby neural disease genes such as Serpina3m. Our findings provide important insights into understanding the disease mechanism caused by POGZ dysfunction.
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Affiliation(s)
- Xiaoyun Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Tianzhe Zhang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan 430071, China
| | - Bei Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Linxi Cheng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan 430071, China
| | - Yuhua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, P.R. China; Hubei Hongshan Laboratory, Wuhan 430070, P.R. China.
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11
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Kobayashi M, Kanbe F, Ishii R, Tsubouchi H, Hirai K, Miyasaka Y, Ohno T, Oda H, Ikeda S, Katoh H, Ichiyanagi K, Ishikawa A, Murai A, Horio F. C3H/HeNSlc mouse with low phospholipid transfer protein expression showed dyslipidemia. Sci Rep 2023; 13:13813. [PMID: 37620514 PMCID: PMC10449841 DOI: 10.1038/s41598-023-40917-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
High serum levels of triglycerides (TG) and low levels of high-density lipoprotein cholesterol (HDL-C) increase the risk of coronary heart disease in humans. Herein, we first reported that the C3H/HeNSlc (C3H-S) mouse, a C3H/HeN-derived substrain, is a novel model for dyslipidemia. C3H-S showed hypertriglyceridemia and low total cholesterol (TC), HDL-C, and phospholipid (PL) concentrations. To identify the gene locus causing dyslipidemia in C3H-S, we performed genetic analysis. In F2 intercrosses between C3H-S mice and strains with normal serum lipids, the locus associated with serum lipids was identified as 163-168 Mb on chromosome 2. The phospholipid transfer protein (Pltp) gene was a candidate gene within this locus. Pltp expression and serum PLTP activity were markedly lower in C3H-S mice. Pltp expression was negatively correlated with serum TG and positively correlated with serum TC and HDL-C in F2 mice. Genome sequencing analysis revealed that an endogenous retrovirus (ERV) sequence called intracisternal A particle was inserted into intron 12 of Pltp in C3H-S. These results suggest that ERV insertion within Pltp causes aberrant splicing, leading to reduced Pltp expression in C3H-S. This study demonstrated the contribution of C3H-S to our understanding of the relationship between TG, TC, and PL metabolism via PLTP.
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Affiliation(s)
- Misato Kobayashi
- Department of Nutritional Sciences, Nagoya University of Arts and Sciences, 57 Takenoyama, Iwasaki-Cho, Nisshin, Aichi, 470-0196, Japan.
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan.
| | - Fumi Kanbe
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Reika Ishii
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Hiroki Tsubouchi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Kana Hirai
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Yuki Miyasaka
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, Aichi, Japan
| | - Tamio Ohno
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, Aichi, Japan
| | - Hiroaki Oda
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Saiko Ikeda
- Department of Nutritional Sciences, Nagoya University of Arts and Sciences, 57 Takenoyama, Iwasaki-Cho, Nisshin, Aichi, 470-0196, Japan
| | - Hirokazu Katoh
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Kenji Ichiyanagi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Akira Ishikawa
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Atsushi Murai
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Fumihiko Horio
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
- Department of Life Studies and Environmental Science, Nagoya Women's University, Aichi, Japan
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12
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Felley-Bosco E. Exploring the Expression of the «Dark Matter» of the Genome in Mesothelioma for Potentially Predictive Biomarkers for Prognosis and Immunotherapy. Cancers (Basel) 2023; 15:cancers15112969. [PMID: 37296931 DOI: 10.3390/cancers15112969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Recent high-throughput RNA sequencing technologies have confirmed that a large part of the non-coding genome is transcribed. The priority for further investigations is nevertheless generally given in cancer to coding sequences, due to the obvious interest of finding therapeutic targets. In addition, several RNA-sequencing pipelines eliminate repetitive sequences, which are difficult to analyze. In this review, we shall focus on endogenous retroviruses. These sequences are remnants of ancestral germline infections by exogenous retroviruses. These sequences represent 8% of human genome, meaning four-fold the fraction of the genome encoding for proteins. These sequences are generally mostly repressed in normal adult tissues, but pathological conditions lead to their de-repression. Specific mesothelioma-associated endogenous retrovirus expression and their association to clinical outcome is discussed.
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Affiliation(s)
- Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, Zürich University Hospital, 8091 Zurich, Switzerland
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13
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Osipovich AB, Dudek KD, Trinh LT, Kim LH, Shrestha S, Cartailler JP, Magnuson MA. ZFP92, a KRAB domain zinc finger protein enriched in pancreatic islets, binds to B1/Alu SINE transposable elements and regulates retroelements and genes. PLoS Genet 2023; 19:e1010729. [PMID: 37155670 PMCID: PMC10166502 DOI: 10.1371/journal.pgen.1010729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/02/2023] [Indexed: 05/10/2023] Open
Abstract
Repressive KRAB domain-containing zinc-finger proteins (KRAB-ZFPs) are abundant in mammalian genomes and contribute both to the silencing of transposable elements (TEs) and to the regulation of developmental stage- and cell type-specific gene expression. Here we describe studies of zinc finger protein 92 (Zfp92), an X-linked KRAB-ZFP that is highly expressed in pancreatic islets of adult mice, by analyzing global Zfp92 knockout (KO) mice. Physiological, transcriptomic and genome-wide chromatin binding studies indicate that the principal function of ZFP92 in mice is to bind to and suppress the activity of B1/Alu type of SINE elements and modulate the activity of surrounding genomic entities. Deletion of Zfp92 leads to changes in expression of select LINE and LTR retroelements and genes located in the vicinity of ZFP92-bound chromatin. The absence of Zfp92 leads to altered expression of specific genes in islets, adipose and muscle that result in modest sex-specific alterations in blood glucose homeostasis, body mass and fat accumulation. In islets, Zfp92 influences blood glucose concentration in postnatal mice via transcriptional effects on Mafb, whereas in adipose and muscle, it regulates Acacb, a rate-limiting enzyme in fatty acid metabolism. In the absence of Zfp92, a novel TE-Capn11 fusion transcript is overexpressed in islets and several other tissues due to de-repression of an IAPez TE adjacent to ZFP92-bound SINE elements in intron 3 of the Capn11 gene. Together, these studies show that ZFP92 functions both to repress specific TEs and to regulate the transcription of specific genes in discrete tissues.
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Affiliation(s)
- Anna B. Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Karrie D. Dudek
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Linh T. Trinh
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Lily H. Kim
- College of Arts and Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Shristi Shrestha
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jean-Philippe Cartailler
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Mark A. Magnuson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
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14
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Lin CW, Ellegood J, Tamada K, Miura I, Konda M, Takeshita K, Atarashi K, Lerch JP, Wakana S, McHugh TJ, Takumi T. An old model with new insights: endogenous retroviruses drive the evolvement toward ASD susceptibility and hijack transcription machinery during development. Mol Psychiatry 2023; 28:1932-1945. [PMID: 36882500 PMCID: PMC10575786 DOI: 10.1038/s41380-023-01999-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 03/09/2023]
Abstract
The BTBR T+Itpr3tf/J (BTBR/J) strain is one of the most valid models of idiopathic autism, serving as a potent forward genetics tool to dissect the complexity of autism. We found that a sister strain with an intact corpus callosum, BTBR TF/ArtRbrc (BTBR/R), showed more prominent autism core symptoms but moderate ultrasonic communication/normal hippocampus-dependent memory, which may mimic autism in the high functioning spectrum. Intriguingly, disturbed epigenetic silencing mechanism leads to hyperactive endogenous retrovirus (ERV), a mobile genetic element of ancient retroviral infection, which increases de novo copy number variation (CNV) formation in the two BTBR strains. This feature makes the BTBR strain a still evolving multiple-loci model toward higher ASD susceptibility. Furthermore, active ERV, analogous to virus infection, evades the integrated stress response (ISR) of host defense and hijacks the transcriptional machinery during embryonic development in the BTBR strains. These results suggest dual roles of ERV in the pathogenesis of ASD, driving host genome evolution at a long-term scale and managing cellular pathways in response to viral infection, which has immediate effects on embryonic development. The wild-type Draxin expression in BTBR/R also makes this substrain a more precise model to investigate the core etiology of autism without the interference of impaired forebrain bundles as in BTBR/J.
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Affiliation(s)
- Chia-Wen Lin
- Laboratory for Mental Biology, RIKEN Brain Science Institute, Wako, 351-0198, Saitama, Japan
- Laboratory for Circuit and Behavioral Physiology, RIKEN Center for Brain Science, Wako, 351-0198, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Chuo, 650-0017, Kobe, Japan
| | - Jacob Ellegood
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, M5T 3H7, Canada
| | - Kota Tamada
- Laboratory for Mental Biology, RIKEN Brain Science Institute, Wako, 351-0198, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Chuo, 650-0017, Kobe, Japan
| | - Ikuo Miura
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Mikiko Konda
- Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku, 160-8582, Tokyo, Japan
| | - Kozue Takeshita
- Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku, 160-8582, Tokyo, Japan
| | - Koji Atarashi
- Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku, 160-8582, Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Tsurumi, 230-0045, Yokohama, Japan
| | - Jason P Lerch
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, M5T 3H7, Canada
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, Oxfordshire, OX39DU, UK
| | - Shigeharu Wakana
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Thomas J McHugh
- Laboratory for Circuit and Behavioral Physiology, RIKEN Center for Brain Science, Wako, 351-0198, Saitama, Japan
| | - Toru Takumi
- Laboratory for Mental Biology, RIKEN Brain Science Institute, Wako, 351-0198, Saitama, Japan.
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Chuo, 650-0017, Kobe, Japan.
- RIKEN Center for Biosystems Dynamics Research, Chuo, 650-0047, Kobe, Japan.
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15
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Abstract
Our defenses against infection rely on the ability of the immune system to distinguish invading pathogens from self. This task is exceptionally challenging, if not seemingly impossible, in the case of retroviruses that have integrated almost seamlessly into the host. This review examines the limits of innate and adaptive immune responses elicited by endogenous retroviruses and other retroelements, the targets of immune recognition, and the consequences for host health and disease. Contrary to theoretical expectation, endogenous retroelements retain substantial immunogenicity, which manifests most profoundly when their epigenetic repression is compromised, contributing to autoinflammatory and autoimmune disease and age-related inflammation. Nevertheless, recent evidence suggests that regulated immune reactivity to endogenous retroelements is integral to immune system development and function, underpinning cancer immunosurveillance, resistance to infection, and responses to the microbiota. Elucidation of the interaction points with endogenous retroelements will therefore deepen our understanding of immune system function and contribution to disease.
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Affiliation(s)
- George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, United Kingdom;
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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16
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Daradoumis J, Ragonnaud E, Skandorff I, Nielsen KN, Bermejo AV, Andersson AM, Schroedel S, Thirion C, Neukirch L, Holst PJ. An Endogenous Retrovirus Vaccine Encoding an Envelope with a Mutated Immunosuppressive Domain in Combination with Anti-PD1 Treatment Eradicates Established Tumours in Mice. Viruses 2023; 15:v15040926. [PMID: 37112906 PMCID: PMC10141008 DOI: 10.3390/v15040926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Endogenous retroviruses (ERVs) account for 8% of our genome, and, although they are usually silent in healthy tissues, they become reactivated and expressed in pathological conditions such as cancer. Several studies support a functional role of ERVs in tumour development and progression, specifically through their envelope (Env) protein, which contains a region described as an immunosuppressive domain (ISD). We have previously shown that targeting of the murine ERV (MelARV) Env using virus-like vaccine (VLV) technology, consisting of an adenoviral vector encoding virus-like particles (VLPs), induces protection against small tumours in mice. Here, we investigate the potency and efficacy of a novel MelARV VLV with a mutated ISD (ISDmut) that can modify the properties of the adenoviral vaccine-encoded Env protein. We show that the modification of the vaccine's ISD significantly enhanced T-cell immunogenicity in both prime and prime-boost vaccination regimens. The modified VLV in combination with an α-PD1 checkpoint inhibitor (CPI) exhibited excellent curative efficacy against large established colorectal CT26 tumours in mice. Furthermore, only ISDmut-vaccinated mice that survived CT26 challenge were additionally protected against rechallenge with a triple-negative breast cancer cell line (4T1), showing that our modified VLV provides cross-protection against different tumour types expressing ERV-derived antigens. We envision that translating these findings and technology into human ERVs (HERVs) could provide new treatment opportunities for cancer patients with unmet medical needs.
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Affiliation(s)
- Joana Daradoumis
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Emeline Ragonnaud
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Isabella Skandorff
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | | | - Amaia Vergara Bermejo
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Anne-Marie Andersson
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | | | | | - Lasse Neukirch
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Peter Johannes Holst
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
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17
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Bao H, Yan J, Huang J, Deng W, Zhang C, Liu C, Huang A, Zhang Q, Xiong Y, Wang Q, Wu H, Hou L. Activation of endogenous retrovirus triggers microglial immuno-inflammation and contributes to negative emotional behaviors in mice with chronic stress. J Neuroinflammation 2023; 20:37. [PMID: 36793064 PMCID: PMC9933381 DOI: 10.1186/s12974-023-02724-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND The "missing" link of complex and multifaceted interplay among endogenous retroviruses (ERVs) transcription, chronic immuno-inflammation, and the development of psychiatric disorders is still far from being completely clarified. The present study was aimed to investigate the mechanism of protective role of inhibiting ERVs on reversing microglial immuno-inflammation in basolateral amygdala (BLA) in chronic stress-induced negative emotional behaviors in mice. METHODS Male C57BL/6 mice were exposed to chronic unpredictable mild stress (CUMS) for 6 w. Negative emotional behaviors were comprehensively investigated to identify the susceptible mice. Microglial morphology, ERVs transcription, intrinsic nucleic acids sensing response, and immuno-inflammation in BLA were assessed. RESULTS Mice with chronic stress were presented as obviously depressive- and anxiety-like behaviors, and accompanied with significant microglial morphological activation, murine ERVs genes MuERV-L, MusD, and IAP transcription, cGAS-IFI16-STING pathway activation, NF-κB signaling pathway priming, as well as NLRP3 inflammasome activation in BLA. Antiretroviral therapy, pharmacological inhibition of reverse transcriptases, as well as knocking-down the ERVs transcriptional regulation gene p53 significantly inhibited microglial ERVs transcription and immuno-inflammation in BLA, as well as improved the chronic stress-induced negative emotional behaviors. CONCLUSIONS Our results provided an innovative therapeutic approach that targeting ERVs-associated microglial immuno-inflammation may be beneficial to the patients with psychotic disorders.
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Affiliation(s)
- Han Bao
- grid.12955.3a0000 0001 2264 7233Department of Anesthesiology, School of Medicine, Xiang’an Hospital of Xiamen University, Xiamen University, No. 2000, East of Xiang’an Rd, Xiamen, 361102 China
| | - Jinqi Yan
- grid.452438.c0000 0004 1760 8119Department of Critical Care Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061 China
| | - Jiancheng Huang
- grid.12955.3a0000 0001 2264 7233Department of Anesthesiology, School of Medicine, Xiang’an Hospital of Xiamen University, Xiamen University, No. 2000, East of Xiang’an Rd, Xiamen, 361102 China
| | - Wenjuan Deng
- grid.12955.3a0000 0001 2264 7233Department of Anesthesiology, School of Medicine, Xiang’an Hospital of Xiamen University, Xiamen University, No. 2000, East of Xiang’an Rd, Xiamen, 361102 China
| | - Ce Zhang
- grid.12955.3a0000 0001 2264 7233Department of Anesthesiology, School of Medicine, Xiang’an Hospital of Xiamen University, Xiamen University, No. 2000, East of Xiang’an Rd, Xiamen, 361102 China
| | - Cong Liu
- grid.12955.3a0000 0001 2264 7233Department of Anesthesiology, School of Medicine, Xiang’an Hospital of Xiamen University, Xiamen University, No. 2000, East of Xiang’an Rd, Xiamen, 361102 China
| | - Ailing Huang
- grid.12955.3a0000 0001 2264 7233Department of Anesthesiology, School of Medicine, Xiang’an Hospital of Xiamen University, Xiamen University, No. 2000, East of Xiang’an Rd, Xiamen, 361102 China
| | - Qiao Zhang
- grid.12955.3a0000 0001 2264 7233Department of Anesthesiology, School of Medicine, Xiang’an Hospital of Xiamen University, Xiamen University, No. 2000, East of Xiang’an Rd, Xiamen, 361102 China
| | - Ying Xiong
- grid.12955.3a0000 0001 2264 7233Department of Anesthesiology, School of Medicine, Xiang’an Hospital of Xiamen University, Xiamen University, No. 2000, East of Xiang’an Rd, Xiamen, 361102 China
| | - Qiang Wang
- Department of Anesthesiology, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, West of Yanta Rd, Xi'an, 710061, China.
| | - Huanghui Wu
- Translational Research Institute of Brain and Brain-Like Intelligence, School of Medicine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, 200434, China. .,Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, No.1279, Sanmen Rd, Shanghai, 200434, China.
| | - Lichao Hou
- Department of Anesthesiology, School of Medicine, Xiang'an Hospital of Xiamen University, Xiamen University, No. 2000, East of Xiang'an Rd, Xiamen, 361102, China.
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18
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Herrero F, Mueller FS, Gruchot J, Küry P, Weber-Stadlbauer U, Meyer U. Susceptibility and resilience to maternal immune activation are associated with differential expression of endogenous retroviral elements. Brain Behav Immun 2023; 107:201-214. [PMID: 36243285 DOI: 10.1016/j.bbi.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/26/2022] [Accepted: 10/09/2022] [Indexed: 12/05/2022] Open
Abstract
Endogenous retroviruses (ERVs) are ancestorial retroviral elements that were integrated into the mammalian genome through germline infections and insertions during evolution. While increased ERV expression has been repeatedly implicated in psychiatric and neurodevelopmental disorders, recent evidence suggests that aberrant endogenous retroviral activity may contribute to biologically defined subgroups of psychotic disorders with persisting immunological dysfunctions. Here, we explored whether ERV expression is altered in a mouse model of maternal immune activation (MIA), a transdiagnostic environmental risk factor of psychiatric and neurodevelopmental disorders. MIA was induced by maternal administration of poly(I:C) on gestation day 12 in C57BL/6N mice. Murine ERV transcripts were quantified in the placentae and fetal brains shortly after poly(I:C)-induced MIA, as well as in adult offspring that were stratified according to their behavioral profiles. We found that MIA increased and reduced levels of class II ERVs and syncytins, respectively, in placentae and fetal brain tissue. We also revealed abnormal ERV expression in MIA-exposed offspring depending on whether they displayed overt behavioral anomalies or not. Taken together, our findings provide a proof of concept that an inflammatory stimulus, even when initiated in prenatal life, has the potential of altering ERV expression across fetal to adult stages of development. Moreover, our data highlight that susceptibility and resilience to MIA are associated with differential ERV expression, suggesting that early-life exposure to inflammatory factors may play a role in determining disease susceptibility by inducing persistent alterations in the expression of endogenous retroviral elements.
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Affiliation(s)
- Felisa Herrero
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Flavia S Mueller
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Joel Gruchot
- Department of Neurology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Patrick Küry
- Department of Neurology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Ulrike Weber-Stadlbauer
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Urs Meyer
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.
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19
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Gruchot J, Herrero F, Weber-Stadlbauer U, Meyer U, Küry P. Interplay between activation of endogenous retroviruses and inflammation as common pathogenic mechanism in neurological and psychiatric disorders. Brain Behav Immun 2023; 107:242-52. [PMID: 36270439 DOI: 10.1016/j.bbi.2022.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/21/2022] [Accepted: 10/13/2022] [Indexed: 12/05/2022] Open
Abstract
Human endogenous retroviruses (ERVs) are ancestorial retroviral elements that were integrated into our genome through germline infections and insertions during evolution. They have repeatedly been implicated in the aetiology and pathophysiology of numerous human disorders, particularly in those that affect the central nervous system. In addition to the known association of ERVs with multiple sclerosis and amyotrophic lateral sclerosis, a growing number of studies links the induction and expression of these retroviral elements with the onset and severity of neurodevelopmental and psychiatric disorders. Although these disorders differ in terms of overall disease pathology and causalities, a certain degree of (subclinical) chronic inflammation can be identified in all of them. Based on these commonalities, we discuss the bidirectional relationship between ERV expression and inflammation and highlight that numerous entry points to this reciprocal sequence of events exist, including initial infections with ERV-activating pathogens, exposure to non-infectious inflammatory stimuli, and conditions in which epigenetic silencing of ERV elements is disrupted.
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20
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Devaux CA, Pontarotti P, Nehari S, Raoult D. 'Cannibalism' of exogenous DNA sequences: The ancestral form of adaptive immunity which entails recognition of danger. Front Immunol 2022; 13:989707. [PMID: 36618387 PMCID: PMC9816338 DOI: 10.3389/fimmu.2022.989707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Adaptive immunity is a sophisticated form of immune response capable of retaining the molecular memory of a very great diversity of target antigens (epitopes) as non-self. It is capable of reactivating itself upon a second encounter with an immunoglobulin or T-cell receptor antigen-binding site with a known epitope that had previously primed the host immune system. It has long been considered that adaptive immunity is a highly evolved form of non-self recognition that appeared quite late in speciation and complemented a more generalist response called innate immunity. Innate immunity offers a relatively non-specific defense (although mediated by sensors that could specifically recognize virus or bacteria compounds) and which does not retain a memory of the danger. But this notion of recent acquisition of adaptive immunity is challenged by the fact that another form of specific recognition mechanisms already existed in prokaryotes that may be able to specifically auto-protect against external danger. This recognition mechanism can be considered a primitive form of specific (adaptive) non-self recognition. It is based on the fact that many archaea and bacteria use a genome editing system that confers the ability to appropriate viral DNA sequences allowing prokaryotes to prevent host damage through a mechanism very similar to adaptive immunity. This is indistinctly called, 'endogenization of foreign DNA' or 'viral DNA predation' or, more pictorially 'DNA cannibalism'. For several years evidence has been accumulating, highlighting the crucial role of endogenization of foreign DNA in the fundamental processes related to adaptive immunity and leading to a change in the dogma that adaptive immunity appeared late in speciation.
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Affiliation(s)
- Christian A. Devaux
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France,Department of Biological Sciences, Centre National de la Recherche Scientifique, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France,*Correspondence: Christian A. Devaux,
| | - Pierre Pontarotti
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France,Department of Biological Sciences, Centre National de la Recherche Scientifique, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Sephora Nehari
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France
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21
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Arez M, Eckersley-maslin M, Klobučar T, von Gilsa Lopes J, Krueger F, Mupo A, Raposo AC, Oxley D, Mancino S, Gendrel A, Bernardes de Jesus B, da Rocha ST. Imprinting fidelity in mouse iPSCs depends on sex of donor cell and medium formulation. Nat Commun 2022; 13. [PMID: 36114205 PMCID: PMC9481624 DOI: 10.1038/s41467-022-33013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Reprogramming of somatic cells into induced Pluripotent Stem Cells (iPSCs) is a major leap towards personalised approaches to disease modelling and cell-replacement therapies. However, we still lack the ability to fully control the epigenetic status of iPSCs, which is a major hurdle for their downstream applications. Epigenetic fidelity can be tracked by genomic imprinting, a phenomenon dependent on DNA methylation, which is frequently perturbed in iPSCs by yet unknown reasons. To try to understand the causes underlying these defects, we conducted a thorough imprinting analysis using IMPLICON, a high-throughput method measuring DNA methylation levels, in multiple female and male murine iPSC lines generated under different experimental conditions. Our results show that imprinting defects are remarkably common in iPSCs, but their nature depends on the sex of donor cells and their response to culture conditions. Imprints in female iPSCs resist the initial genome-wide DNA demethylation wave during reprogramming, but ultimately cells accumulate hypomethylation defects irrespective of culture medium formulations. In contrast, imprinting defects on male iPSCs depends on the experimental conditions and arise during reprogramming, being mitigated by the addition of vitamin C (VitC). Our findings are fundamental to further optimise reprogramming strategies and generate iPSCs with a stable epigenome. Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) is associated with epigenetic alterations. Here the authors assess DNA methylation in detail in multiple female and male mouse iPSC lines generated with different protocols and find that defects depend on the sex of donor cells and can be partially mitigated by Vitamin C.
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22
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Asimi V, Sampath Kumar A, Niskanen H, Riemenschneider C, Hetzel S, Naderi J, Fasching N, Popitsch N, Du M, Kretzmer H, Smith ZD, Weigert R, Walther M, Mamde S, Meierhofer D, Wittler L, Buschow R, Timmermann B, Cisse II, Ameres SL, Meissner A, Hnisz D. Hijacking of transcriptional condensates by endogenous retroviruses. Nat Genet 2022. [PMID: 35864192 DOI: 10.1038/s41588-022-01132-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 05/26/2022] [Indexed: 12/20/2022]
Abstract
Most endogenous retroviruses (ERVs) in mammals are incapable of retrotransposition; therefore, why ERV derepression is associated with lethality during early development has been a mystery. Here, we report that rapid and selective degradation of the heterochromatin adapter protein TRIM28 triggers dissociation of transcriptional condensates from loci encoding super-enhancer (SE)-driven pluripotency genes and their association with transcribed ERV loci in murine embryonic stem cells. Knockdown of ERV RNAs or forced expression of SE-enriched transcription factors rescued condensate localization at SEs in TRIM28-degraded cells. In a biochemical reconstitution system, ERV RNA facilitated partitioning of RNA polymerase II and the Mediator coactivator into phase-separated droplets. In TRIM28 knockout mouse embryos, single-cell RNA-seq analysis revealed specific depletion of pluripotent lineages. We propose that coding and noncoding nascent RNAs, including those produced by retrotransposons, may facilitate ‘hijacking’ of transcriptional condensates in various developmental and disease contexts. TRIM28 depletion in embryonic stem cells disconnects transcriptional condensates from super-enhancers, which is rescued by knockdown of endogenous retroviruses.
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23
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BERGALLO M, LOIACONO E, GALLIANO I, MONTANARI P, PERUZZI L, TOVO PA, COPPO R. HERV-K and W expression in peripheral mononuclear cells of children with Henoch-Schönlein purpura and relation with TLR activation. Minerva Pediatr (Torino) 2022; 74:421-427. [DOI: 10.23736/s2724-5276.17.04717-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Grace BE, Backlund CM, Morgan DM, Kang BH, Singh NK, Huisman BD, Rappazzo CG, Moynihan KD, Maiorino L, Dobson CS, Kyung T, Gordon KS, Holec PV, Mbah OCT, Garafola D, Wu S, Love JC, Wittrup KD, Irvine DJ, Birnbaum ME. Identification of Highly Cross-Reactive Mimotopes for a Public T Cell Response in Murine Melanoma. Front Immunol 2022; 13:886683. [PMID: 35812387 PMCID: PMC9260506 DOI: 10.3389/fimmu.2022.886683] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
While immune checkpoint blockade results in durable responses for some patients, many others have not experienced such benefits. These treatments rely upon reinvigorating specific T cell-antigen interactions. However, it is often unknown what antigens are being recognized by T cells or how to potently induce antigen-specific responses in a broadly applicable manner. Here, we characterized the CD8+ T cell response to a murine model of melanoma following combination immunotherapy to determine the basis of tumor recognition. Sequencing of tumor-infiltrating T cells revealed a repertoire of highly homologous TCR sequences that were particularly expanded in treated mice and which recognized an antigen from an endogenous retrovirus. While vaccination against this peptide failed to raise a protective T cell response in vivo, engineered antigen mimotopes induced a significant expansion of CD8+ T cells cross-reactive to the original antigen. Vaccination with mimotopes resulted in killing of antigen-loaded cells in vivo yet showed modest survival benefit in a prophylactic vaccine paradigm. Together, this work demonstrates the identification of a dominant tumor-associated antigen and generation of mimotopes which can induce robust functional T cell responses that are cross-reactive to the endogenous antigen across multiple individuals.
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Affiliation(s)
- Beth E. Grace
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Coralie M. Backlund
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Duncan M. Morgan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Byong H. Kang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Nishant K. Singh
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Brooke D. Huisman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - C. Garrett Rappazzo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Kelly D. Moynihan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Laura Maiorino
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Connor S. Dobson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Taeyoon Kyung
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Khloe S. Gordon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Patrick V. Holec
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | - Daniel Garafola
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Shengwei Wu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - J. Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - K. Dane Wittrup
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Darrell J. Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Michael E. Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
- *Correspondence: Michael E. Birnbaum,
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Padeken J, Methot SP, Gasser SM. Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat Rev Mol Cell Biol 2022. [PMID: 35562425 DOI: 10.1038/s41580-022-00483-w] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 12/14/2022]
Abstract
Heterochromatin is characterized by dimethylated or trimethylated histone H3 Lys9 (H3K9me2 or H3K9me3, respectively) and is found at transposable elements, satellite repeats and genes, where it ensures their transcriptional silencing. The histone methyltransferases (HMTs) that methylate H3K9 — in mammals Suppressor of variegation 3–9 homologue 1 (SUV39H1), SUV39H2, SET domain bifurcated 1 (SETDB1), SETDB2, G9A and G9A-like protein (GLP) — and the ‘readers’ of H3K9me2 or H3K9me3 are highly conserved and show considerable redundancy. Despite their redundancy, genetic ablation or mistargeting of an individual H3K9 methyltransferase can correlate with impaired cell differentiation, loss of tissue identity, premature aging and/or cancer. In this Review, we discuss recent advances in understanding the roles of the known H3K9-specific HMTs in ensuring transcriptional homeostasis during tissue differentiation in mammals. We examine the effects of H3K9-methylation-dependent gene repression in haematopoiesis, muscle differentiation and neurogenesis in mammals, and compare them with mechanistic insights obtained from the study of model organisms, notably Caenorhabditis elegans and Drosophila melanogaster. In all these organisms, H3K9-specific HMTs have both unique and redundant roles that ensure the maintenance of tissue integrity by restricting the binding of transcription factors to lineage-specific promoters and enhancer elements. Histone H3 Lys9 (H3K9)-methylated heterochromatin ensures transcriptional silencing of repetitive elements and genes, and its deregulation leads to impaired cell and tissue identity, premature aging and cancer. Recent studies in mammals clarified the roles H3K9-specific histone methyltransferases in ensuring transcriptional homeostasis during tissue differentiation.
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26
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Gualdrini F, Polletti S, Simonatto M, Prosperini E, Pileri F, Natoli G. H3K9 trimethylation in active chromatin restricts the usage of functional CTCF sites in SINE B2 repeats. Genes Dev 2022; 36:414-432. [PMID: 35361678 PMCID: PMC9067402 DOI: 10.1101/gad.349282.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/16/2022] [Indexed: 12/23/2022]
Abstract
Here, Gualdrini et al. found that loss of H3K9me3 caused by SETDB1 depletion was associated with increased recruitment of CTCF to >1600 DNA binding motifs contained within SINE B2 repeats, a previously unidentified target of SETDB1-mediated repression. Their findings suggest a role for H3K9me3 in restraining genomic distribution and activity of CTCF, influencing chromatin organization and gene regulation. Six methyltransferases divide labor in establishing genomic profiles of histone H3 lysine 9 methylation (H3K9me), an epigenomic modification controlling constitutive heterochromatin, gene repression, and silencing of retroelements. Among them, SETDB1 is recruited to active chromatin domains to silence the expression of endogenous retroviruses. In the context of experiments aimed at determining the impact of SETDB1 on stimulus-inducible gene expression in macrophages, we found that loss of H3K9me3 caused by SETDB1 depletion was associated with increased recruitment of CTCF to >1600 DNA binding motifs contained within SINE B2 repeats, a previously unidentified target of SETDB1-mediated repression. CTCF is an essential regulator of chromatin folding that restrains DNA looping by cohesin, thus creating boundaries among adjacent topological domains. Increased CTCF binding to SINE B2 repeats enhanced insulation at hundreds of sites and increased loop formation within topological domains containing lipopolysaccharide-inducible genes, which correlated with their impaired regulation in response to stimulation. These data indicate a role of H3K9me3 in restraining genomic distribution and activity of CTCF, with an impact on chromatin organization and gene regulation.
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Affiliation(s)
- Francesco Gualdrini
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Sara Polletti
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Marta Simonatto
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Elena Prosperini
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Francesco Pileri
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Gioacchino Natoli
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
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27
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Fontes F, Rocha S, Sánchez R, Pessina P, Sebastian M, Benavides F, Breijo M. Detection of high antibodies titers against rat leukemia virus in an outbreak of reproductive disorders and lymphomas in Wistar rats. Lab Anim 2022; 56:437-445. [PMID: 35360996 DOI: 10.1177/00236772221085356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Young female Wistar rats from a specific pathogen free breeding colony presented an outbreak of infertility along with neurological symptoms and malignant lymphomas. We evaluated the presence and the potential role of the rat leukemia virus (RaLV) in the disease because these clinical signs could be compatible with a retrovirus. RaLV is a mammalian type C endogenous retrovirus initially isolated from in vitro Sprague-Dawley rat embryo cultures. There are no reports of clinical disease in rats associated with this virus, and little is known about its interaction with the host. Using reverse transcription polymerase chain reaction and enzyme-linked immunosorbent assay, we studied the synthesis of the viral particles and the development of an immune response against the virus in this rat colony. The results showed that healthy and diseased Wistar rats synthetized viral RNA but only diseased animals developed a detectable immune response against RaLV envelop protein. Furthermore, rats with lymphomas tended to have higher titers of antibodies against RaLV epitopes than those with infertility or neurological symptoms. The results suggest that increases in the RaLV infectious particle loads could be involved in the development of lymphomas in young rats. The potential causes of RaLV reactivation are discussed.
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Affiliation(s)
- Florencia Fontes
- Unidad de Reactivos y Biomodelos de Experimentación, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Sergio Rocha
- Unidad de Reactivos y Biomodelos de Experimentación, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rosina Sánchez
- Laboratorio de Análisis Clínicos, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - Paula Pessina
- Laboratorio de Análisis Clínicos, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - Manu Sebastian
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, USA
| | - Fernando Benavides
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, USA
| | - Martín Breijo
- Unidad de Reactivos y Biomodelos de Experimentación, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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28
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Jayewickreme R, Mao T, Philbrick W, Kong Y, Treger RS, Lu P, Rakib T, Dong H, Dang-Lawson M, Guild WA, Lau TJ, Iwasaki A, Tokuyama M. Endogenous Retroviruses Provide Protection Against Vaginal HSV-2 Disease. Front Immunol 2022; 12:758721. [PMID: 35058919 PMCID: PMC8764156 DOI: 10.3389/fimmu.2021.758721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
Endogenous retroviruses (ERVs) are genomic sequences that originated from retroviruses and are present in most eukaryotic genomes. Both beneficial and detrimental functions are attributed to ERVs, but whether ERVs contribute to antiviral immunity is not well understood. Here, we used herpes simplex virus type 2 (HSV-2) infection as a model and found that Toll-like receptor 7 (Tlr7 -/-) deficient mice that have high systemic levels of infectious ERVs are protected from intravaginal HSV-2 infection and disease, compared to wildtype C57BL/6 mice. We deleted the endogenous ecotropic murine leukemia virus (Emv2) locus on the Tlr7 -/- background (Emv2 -/- Tlr7 -/-) and found that Emv2 -/- Tlr7 -/- mice lose protection against HSV-2 infection. Intravaginal application of purified ERVs from Tlr7-/- mice prior to HSV-2 infection delays disease in both wildtype and highly susceptible interferon-alpha receptor-deficient (Ifnar1- /-) mice. However, intravaginal ERV treatment did not protect Emv2-/-Tlr7-/- mice from HSV-2 disease, suggesting that the protective mechanism mediated by exogenous ERV treatment may differ from that of constitutively and systemically expressed ERVs in Tlr7-/- mice. We did not observe enhanced type I interferon (IFN-I) signaling in the vaginal tissues from Tlr7-/- mice, and instead found enrichment in genes associated with extracellular matrix organization. Together, our results revealed that constitutive and/or systemic expression of ERVs protect mice against vaginal HSV-2 infection and delay disease.
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Affiliation(s)
- Radeesha Jayewickreme
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States
| | - William Philbrick
- Department of Internal Medicine, Section of Endocrinology, Yale School of Medicine, New Haven, CT, United States
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT, United States
| | - Rebecca S Treger
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States
| | - Tasfia Rakib
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States
| | - Huiping Dong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States
| | - May Dang-Lawson
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - W Austin Guild
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Tatiana J Lau
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States.,Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Maria Tokuyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States.,Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
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29
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Huang Y, Xu F, Mei S, Liu X, Zhao F, Wei L, Fan Z, Hu Y, Wang L, Ai B, Cen S, Liang C, Guo F. MxB inhibits long interspersed element type 1 retrotransposition. PLoS Genet 2022; 18:e1010034. [PMID: 35171907 PMCID: PMC8849481 DOI: 10.1371/journal.pgen.1010034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/12/2022] [Indexed: 12/13/2022] Open
Abstract
Long interspersed element type 1 (LINE-1, also L1 for short) is the only autonomously transposable element in the human genome. Its insertion into a new genomic site may disrupt the function of genes, potentially causing genetic diseases. Cells have thus evolved a battery of mechanisms to tightly control LINE-1 activity. Here, we report that a cellular antiviral protein, myxovirus resistance protein B (MxB), restricts the mobilization of LINE-1. This function of MxB requires the nuclear localization signal located at its N-terminus, its GTPase activity and its ability to form oligomers. We further found that MxB associates with LINE-1 protein ORF1p and promotes sequestration of ORF1p to G3BP1-containing cytoplasmic granules. Since knockdown of stress granule marker proteins G3BP1 or TIA1 abolishes MxB inhibition of LINE-1, we conclude that MxB engages stress granule components to effectively sequester LINE-1 proteins within the cytoplasmic granules, thus hindering LINE-1 from accessing the nucleus to complete retrotransposition. Thus, MxB protein provides one mechanism for cells to control the mobility of retroelements. Retrotransposons occupy more than 40% of human genome, and have co-evolved with humans for millions of years. Long interspersed element type 1 (LINE-1, or L1) is the only retrotransposon that is able to jump to a new locus. LINE-1 retrotransposition causes genome instability, and is associated with genetic diseases including autoimmune diseases and cancer. To suppress this genome toxicity caused by LINE-1, humans have developed multi-layered mechanisms to control LINE-1 activity. MxB has been previously shown to inhibit LINE-1 mobility, thus contributing to host restriction of LINE-1. Here, we further demonstrate that MxB effectively restricts LINE-1 retrotransposition by sequestering LINE-1 ribonucleoprotein (RNP) within the cytoplasmic stress granules, thus guards genome stability. Hence our data attribute the restriction function of MxB to sequestering LINE-1 RNP to stress granules.
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Affiliation(s)
- Yu Huang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Shan Mei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xiaoman Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Fei Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liang Wei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Zhangling Fan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yamei Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liming Wang
- Department of Medical Oncology, Beijing Hospital, Beijing, P. R. China
| | - Bin Ai
- Department of Medical Oncology, Beijing Hospital, Beijing, P. R. China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Chen Liang
- McGill Centre for Viral Diseases, Lady Davis Institute, Jewish General Hospital, Montreal, Canada
- * E-mail: (CL); (FG)
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- * E-mail: (CL); (FG)
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Chandrasekaran S, Espeso-Gil S, Loh YE, Javidfar B, Kassim B, Zhu Y, Zhang Y, Dong Y, Bicks LK, Li H, Rajarajan P, Peter CJ, Sun D, Agullo-Pascual E, Iskhakova M, Estill M, Lesch BJ, Shen L, Jiang Y, Akbarian S. Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansions. Nat Commun 2021; 12:7243. [PMID: 34903713 DOI: 10.1038/s41467-021-26862-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 10/27/2021] [Indexed: 01/16/2023] Open
Abstract
Regulatory mechanisms associated with repeat-rich sequences and chromosomal conformations in mature neurons remain unexplored. Here, we map cell-type specific chromatin domain organization in adult mouse cerebral cortex and report strong enrichment of Endogenous Retrovirus 2 (ERV2) repeat sequences in the neuron-specific heterochromatic B2NeuN+ megabase-scaling subcompartment. Single molecule long-read sequencing and comparative Hi-C chromosomal contact mapping in wild-derived SPRET/EiJ (Mus spretus) and laboratory inbred C57BL/6J (Mus musculus) reveal neuronal reconfigurations tracking recent ERV2 expansions in the murine germline, with significantly higher B2NeuN+ contact frequencies at sites with ongoing insertions in Mus musculus. Neuronal ablation of the retrotransposon silencer Kmt1e/Setdb1 triggers B2NeuN+ disintegration and rewiring with open chromatin domains enriched for cellular stress response genes, along with severe neuroinflammation and proviral assembly with infiltration of dendrites . We conclude that neuronal megabase-scale chromosomal architectures include an evolutionarily adaptive heterochromatic organization which, upon perturbation, results in transcriptional dysregulation and unleashes ERV2 proviruses with strong neuronal tropism.
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Navarro PA, Wang F, Pimentel R, Robinson LG Jr, Berteli TS, Keefe DL. Zidovudine inhibits telomere elongation, increases the transposable element LINE-1 copy number and compromises mouse embryo development. Mol Biol Rep 2021; 48:7767-73. [PMID: 34669125 DOI: 10.1007/s11033-021-06788-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 09/17/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE Millions of pregnant, HIV-infected women take reverse transcriptase inhibitors, such as zidovudine (azidothymidine or AZT), during pregnancy. Reverse transcription plays important roles in early development, including regulation of telomere length (TL) and activity of transposable elements (TE). So we evaluated the effects of AZT on embryo development, TL, and copy number of an active TE, Long Interspersed Nuclear Element 1 (LINE-1), during early development in a murine model. DESIGN Experimental study. METHODS In vivo fertilized mouse zygotes from B6C3F1/B6D2F1 mice were cultured for 48 h in KSOM with no AZT (n = 45), AZT 1 μM (n = 46) or AZT 10 μM (n = 48). TL was measured by single-cell quantitative PCR (SC-pqPCR) and LINE-1 copy number by qPCR. The percentage of morulas at 48 h, TL and LINE-1 copy number were compared among groups. RESULTS Exposure to AZT 1 μM or 10 μM significantly impairs early embryo development. TL elongates from oocyte to control embryos. TL in AZT 1 μM embryos is shorter than in control embryos. LINE-1 copy number is significantly lower in oocytes than control embryos. AZT 1 μM increases LINE-1 copy number compared to oocytes controls, and AZT 10 μM embryos. CONCLUSION AZT at concentrations approaching those used to prevent perinatal HIV transmission compromises mouse embryo development, prevents telomere elongation and increases LINE-1 copy number after 48 h treatment. The impact of these effects on the trajectory of aging of children exposed to AZT early during development deserves further investigation.
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32
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Yang L, Malhotra R, Chikhi R, Elleder D, Kaiser T, Rong J, Medvedev P, Poss M. Recombination marks the evolutionary dynamics of a recently endogenized retrovirus. Mol Biol Evol 2021; 38:5423-5436. [PMID: 34480565 PMCID: PMC8662619 DOI: 10.1093/molbev/msab252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
All vertebrate genomes have been colonized by retroviruses along their evolutionary trajectory. Although endogenous retroviruses (ERVs) can contribute important physiological functions to contemporary hosts, such benefits are attributed to long-term coevolution of ERV and host because germline infections are rare and expansion is slow, and because the host effectively silences them. The genomes of several outbred species including mule deer (Odocoileus hemionus) are currently being colonized by ERVs, which provides an opportunity to study ERV dynamics at a time when few are fixed. We previously established the locus-specific distribution of cervid ERV (CrERV) in populations of mule deer. In this study, we determine the molecular evolutionary processes acting on CrERV at each locus in the context of phylogenetic origin, genome location, and population prevalence. A mule deer genome was de novo assembled from short- and long-insert mate pair reads and CrERV sequence generated at each locus. We report that CrERV composition and diversity have recently measurably increased by horizontal acquisition of a new retrovirus lineage. This new lineage has further expanded CrERV burden and CrERV genomic diversity by activating and recombining with existing CrERV. Resulting interlineage recombinants then endogenize and subsequently expand. CrERV loci are significantly closer to genes than expected if integration were random and gene proximity might explain the recent expansion of one recombinant CrERV lineage. Thus, in mule deer, retroviral colonization is a dynamic period in the molecular evolution of CrERV that also provides a burst of genomic diversity to the host population.
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Affiliation(s)
- Lei Yang
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Raunaq Malhotra
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Rayan Chikhi
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Daniel Elleder
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 1083, 14220, Czech Republic Vídeňská Prague
| | - Theodora Kaiser
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jesse Rong
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Paul Medvedev
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mary Poss
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA
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Wedekind MF, Miller KE, Chen CY, Wang PY, Hutzen BJ, Currier MA, Nartker B, Roberts RD, Boon L, Conner J, LaHaye S, Kelly BJ, Gordon D, White P, Mardis ER, Cripe TP. Endogenous retrovirus envelope as a tumor-associated immunotherapeutic target in murine osteosarcoma. iScience 2021; 24:102759. [PMID: 34278266 PMCID: PMC8267546 DOI: 10.1016/j.isci.2021.102759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/12/2021] [Accepted: 06/18/2021] [Indexed: 01/04/2023] Open
Abstract
Osteosarcoma remains one of the deadliest cancers in pediatrics and young adults. We administered two types of immunotherapies, oncolytic virotherapy and immune checkpoint inhibition, to two murine osteosarcoma models and observed divergent results. Mice bearing F420 showed no response, whereas those with K7M2 showed prolonged survival in response to combination therapy. K7M2 had higher expression of immune-related genes and higher baseline immune cell infiltrates, but there were no significant differences in tumor mutational burden or predicted MHC class I binding of nonsynonymous mutations. Instead, we found several mouse endogenous retrovirus sequences highly expressed in K7M2 compared with F420. T cell tetramer staining for one of them, gp70, was detected in mice with K7M2 but not F420, suggesting that endogenous retrovirus proteins are targets for the anti-tumor immune reaction. Given prior observations of endogenous retrovirus expression in human osteosarcomas, our findings may be translatable to human disease.
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Affiliation(s)
- Mary Frances Wedekind
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
- Division of Hematology/Oncology/Blood and Marrow Transplantation, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Katherine E. Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Chun-Yu Chen
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
| | - Pin-Yi Wang
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
| | - Brian J. Hutzen
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
| | - Mark A. Currier
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
| | - Brooke Nartker
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
| | - Ryan D. Roberts
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
- Division of Hematology/Oncology/Blood and Marrow Transplantation, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Louis Boon
- Polpharma Biologics, Utrecht, the Netherlands
| | | | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Benjamin J. Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - David Gordon
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Timothy P. Cripe
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, 700 Children's Drive Columbus, OH 43205, USA
- Division of Hematology/Oncology/Blood and Marrow Transplantation, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
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34
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Mangiavacchi A, Liu P, Della Valle F, Orlando V. New insights into the functional role of retrotransposon dynamics in mammalian somatic cells. Cell Mol Life Sci 2021; 78:5245-5256. [PMID: 33990851 PMCID: PMC8257530 DOI: 10.1007/s00018-021-03851-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/31/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022]
Abstract
Retrotransposons are genetic elements present across all eukaryotic genomes. While their role in evolution is considered as a potentially beneficial natural source of genetic variation, their activity is classically considered detrimental due to their potentially harmful effects on genome stability. However, studies are increasingly shedding light on the regulatory function and beneficial role of somatic retroelement reactivation in non-pathological contexts. Here, we review recent findings unveiling the regulatory potential of retrotransposons, including their role in noncoding RNA transcription, as modulators of mammalian transcriptional and epigenome landscapes. We also discuss technical challenges in deciphering the multifaceted activity of retrotransposable elements, highlighting an unforeseen central role of this neglected portion of the genome both in early development and in adult life.
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Affiliation(s)
- Arianna Mangiavacchi
- Biological Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Peng Liu
- Biological Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Francesco Della Valle
- Biological Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Valerio Orlando
- Biological Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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35
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Scheller M, Ludwig AK, Göllner S, Rohde C, Krämer S, Stäble S, Janssen M, Müller JA, He L, Bäumer N, Arnold C, Gerß J, Schönung M, Thiede C, Niederwieser C, Niederwieser D, Serve H, Berdel WE, Thiem U, Hemmerling I, Leuschner F, Plass C, Schlesner M, Zaugg J, Milsom MD, Trumpp A, Pabst C, Lipka DB, Müller-Tidow C. Hotspot DNMT3A mutations in clonal hematopoiesis and acute myeloid leukemia sensitize cells to azacytidine via viral mimicry response. Nat Cancer 2021; 2:527-544. [PMID: 35122024 DOI: 10.1038/s43018-021-00213-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/19/2021] [Indexed: 02/04/2023]
Abstract
Somatic mutations in DNA methyltransferase 3A (DNMT3A) are among the most frequent alterations in clonal hematopoiesis (CH) and acute myeloid leukemia (AML), with a hotspot in exon 23 at arginine 882 (DNMT3AR882). Here, we demonstrate that DNMT3AR882H-dependent CH and AML cells are specifically susceptible to the hypomethylating agent azacytidine (AZA). Addition of AZA to chemotherapy prolonged AML survival solely in individuals with DNMT3AR882 mutations, suggesting its potential as a predictive marker for AZA response. AML and CH mouse models confirmed AZA susceptibility specifically in DNMT3AR882H-expressing cells. Hematopoietic stem cells (HSCs) and progenitor cells expressing DNMT3AR882H exhibited cell autonomous viral mimicry response as a result of focal DNA hypomethylation at retrotransposon sequences. Administration of AZA boosted hypomethylation of retrotransposons specifically in DNMT3AR882H-expressing cells and maintained elevated levels of canonical interferon-stimulated genes (ISGs), thus leading to suppressed protein translation and increased apoptosis.
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Affiliation(s)
- Marina Scheller
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany. .,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany.
| | - Anne Kathrin Ludwig
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Stefanie Göllner
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian Rohde
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Stephen Krämer
- Bioinformatics and Omics Data Analytics Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Sina Stäble
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Maike Janssen
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - James-Arne Müller
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Lixiazi He
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nicole Bäumer
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Christian Arnold
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Joachim Gerß
- Institute of Biostatistics and Clinical Research, WWU Münster, Münster, Germany
| | - Maximilian Schönung
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Christian Thiede
- Department of Medicine, University Hospital Dresden, Dresden, Germany
| | - Christian Niederwieser
- Interdisziplinäre Klinik und Poliklinik für Stammzelltransplantation, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | | | - Hubert Serve
- Department of Medicine II, University of Frankfurt, Frankfurt, Germany
| | - Wolfgang E Berdel
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Ulrich Thiem
- Geriatrics and Gerontology, University of Hamburg, Hamburg, Germany
| | - Inga Hemmerling
- Department of Medicine, Cardiology, University Hospital of Heidelberg, Heidelberg, Germany
| | - Florian Leuschner
- Department of Medicine, Cardiology, University Hospital of Heidelberg, Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Judith Zaugg
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Michael D Milsom
- Division of Experimental Hematology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Caroline Pabst
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Daniel B Lipka
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany. .,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany. .,National Center for Tumor Diseases (NCT), Heidelberg, Germany.
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Chen C, Wang X, Zong W, D'Alessandro E, Giosa D, Guo Y, Mao J, Song C. Genetic Diversity and Population Structures in Chinese Miniature Pigs Revealed by SINE Retrotransposon Insertion Polymorphisms, a New Type of Genetic Markers. Animals (Basel) 2021; 11:1136. [PMID: 33921134 DOI: 10.3390/ani11041136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/08/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Our previous studies suggested that the short interspersed nuclear element (SINE) retrotransposon insertion polymorphisms (RIPs), as a new type of molecular marker developed very recently, are ideal molecular markers and have the potential to be used for population genetic analysis and molecular breeding in pigs and possibly it can be extended to other livestock animals as well. However, no report is available for the application of SINE RIPs in population genetic analysis in livestock, including pigs. Here, we evaluated 30 SINE RIPs in several indigenous Chinese miniature pig breeds, including three subpopulations of Bama pigs (BM-cov, BM-clo, and BM-inb). BM-cov is a subpopulation conserved in the national conservation farm, and BM-clo is a closed population maintained over 30 years with only 2 boars and 14 sows imported from its original area, while BM-inb herd is an 18 generation continuous inbreeding line based on the BM-clo population. To our knowledge, it is the first time to report the genetic diversity, breed differentiation, and population structures for these populations by using SINE RIPs, and which suggests the feasibility of SINE RIPs in pig genetic analysis. Abstract RIPs have been developed as effective genetic markers and popularly applied for genetic analysis in plants, but few reports are available for domestic animals. Here, we established 30 new molecular markers based on the SINE RIPs, and applied them for population genetic analysis in seven Chinese miniature pigs. The data revealed that the closed herd (BM-clo), inbreeding herd (BM-inb) of Bama miniature pigs were distinctly different from the BM-cov herds in the conservation farm, and other miniature pigs (Wuzhishan, Congjiang Xiang, Tibetan, and Mingguang small ear). These later five miniature pig breeds can further be classified into two clades based on a phylogenetic tree: one included BM-cov and Wuzhishan, the other included Congjiang Xiang, Tibetan, and Mingguang small ear, which was well-supported by structure analysis. The polymorphic information contents estimated by using SINE RIPs are lower than the predictions based on microsatellites. Overall, the genetic distances and breed-relationships between these populations revealed by 30 SINE RIPs generally agree with their evolutions and geographic distributions. We demonstrated the potential of SINE RIPs as new genetic markers for genetic monitoring and population structure analysis in pigs, which can even be extended to other livestock animals.
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37
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Apakupakul K, Deem SL, Maqsood R, Sithiyopasakul P, Wang D, Lim ES. Endogenization of a Prosimian Retrovirus during Lemur Evolution. Viruses 2021; 13:383. [PMID: 33673677 DOI: 10.3390/v13030383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 02/23/2021] [Indexed: 01/08/2023] Open
Abstract
Studies of viruses that coevolved with lemurs provide an opportunity to understand the basal traits of primate viruses and provide an evolutionary context for host-virus interactions. Germline integration of endogenous retroviruses (ERVs) are fossil evidence of past infections. Hence, characterization of novel ERVs provides insight into the ancient precursors of extant viruses and the evolutionary history of their hosts. Here, we report the discovery of a novel endogenous retrovirus present in the genome of a lemur, Coquerel's sifaka (Propithecus coquereli). Using next-generation sequencing, we identified and characterized the complete genome sequence of a retrovirus, named prosimian retrovirus 1 (PSRV1). Phylogenetic analyses indicate that PSRV1 is a gamma-type betaretrovirus basal to the other primate betaretroviruses and most closely related to simian retroviruses. Molecular clock analysis of PSRV1 long terminal repeat (LTR) sequences estimated the time of endogenization within 4.56 MYA (± 2.4 MYA), placing it after the divergence of Propithecus species. These results indicate that PSRV1 is an important milestone of lemur evolution during the radiation of the Propithecus genus. These findings may have implications for both human and animal health in that the acquisition of a gamma-type env gene within an endogenized betaretrovirus could facilitate a cross-species jump between vertebrate class hosts.
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McEwen GK, Alquezar-Planas DE, Dayaram A, Gillett A, Tarlinton R, Mongan N, Chappell KJ, Henning J, Tan M, Timms P, Young PR, Roca AL, Greenwood AD. Retroviral integrations contribute to elevated host cancer rates during germline invasion. Nat Commun 2021; 12:1316. [PMID: 33637755 PMCID: PMC7910482 DOI: 10.1038/s41467-021-21612-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/01/2021] [Indexed: 12/16/2022] Open
Abstract
Repeated retroviral infections of vertebrate germlines have made endogenous retroviruses ubiquitous features of mammalian genomes. However, millions of years of evolution obscure many of the immediate repercussions of retroviral endogenisation on host health. Here we examine retroviral endogenisation during its earliest stages in the koala (Phascolarctos cinereus), a species undergoing germline invasion by koala retrovirus (KoRV) and affected by high cancer prevalence. We characterise KoRV integration sites (IS) in tumour and healthy tissues from 10 koalas, detecting 1002 unique IS, with hotspots of integration occurring in the vicinity of known cancer genes. We find that tumours accumulate novel IS, with proximate genes over-represented for cancer associations. We detect dysregulation of genes containing IS and identify a highly-expressed transduced oncogene. Our data provide insights into the tremendous mutational load suffered by the host during active retroviral germline invasion, a process repeatedly experienced and overcome during the evolution of vertebrate lineages.
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Affiliation(s)
- Gayle K McEwen
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - David E Alquezar-Planas
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Anisha Dayaram
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Institute for Neurophysiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Amber Gillett
- Australia Zoo Wildlife Hospital, Beerwah, QLD, Australia
| | - Rachael Tarlinton
- Faculty of Medicine and Health Sciences, University of Nottingham, Leicestershire, UK
| | - Nigel Mongan
- Faculty of Medicine and Health Sciences, University of Nottingham, Leicestershire, UK
| | - Keith J Chappell
- School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Joerg Henning
- School of Veterinary Science, University of Queensland, Brisbane, QLD, Australia
| | - Milton Tan
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Peter Timms
- Genecology Research Center, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Paul R Young
- School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
- Department of Veterinary Medicine, Freie Universität, Berlin, Germany.
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Schriek P, Liu H, Ching AC, Huang P, Gupta N, Wilson KR, Tsai M, Yan Y, Macri CF, Dagley LF, Infusini G, Webb AI, Mcwilliam HE, Ishido S, Mintern JD, Villadangos JA. Physiological substrates and ontogeny-specific expression of the ubiquitin ligases MARCH1 and MARCH8. Current Research in Immunology 2021; 2:218-28. [PMID: 35492398 PMCID: PMC9040089 DOI: 10.1016/j.crimmu.2021.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
MARCH1 and MARCH8 are ubiquitin ligases that control the expression and trafficking of critical immunoreceptors. Understanding of their function is hampered by three major knowledge gaps: (i) it is unclear which cell types utilize these ligases; (ii) their level of redundancy is unknown; and (iii) most of their putative substrates have been described in cell lines, often overexpressing MARCH1 or MARCH8, and it is unclear which substrates are regulated by either ligase in vivo. Here we address these questions by systematically analyzing the immune cell repertoire of MARCH1- or MARCH8-deficient mice, and applying unbiased proteomic profiling of the plasma membrane of primary cells to identify MARCH1 and MARCH8 substrates. Only CD86 and MHC II were unequivocally identified as immunoreceptors regulated by MARCH1 and MARCH8, but each ligase carried out its function in different tissues. MARCH1 regulated MHC II and CD86 in professional and “atypical” antigen presenting cells of hematopoietic origin, including neutrophils, eosinophils and monocytes. MARCH8 only operated in non-hematopoietic cells, such as thymic and alveolar epithelial cells. Our results establish the tissue-specific functions of MARCH1 and MARCH8 in regulation of immune receptor expression and reveal that the range of cells constitutively endowed with antigen-presentation capacity is wider than generally appreciated.
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Takaya T, Nihashi Y, Ono T, Kagami H. Transcription of Endogenous Retrovirus Group K Members and Their Neighboring Genes in Chicken Skeletal Muscle Myoblasts. J Poult Sci 2021; 58:79-87. [PMID: 33927561 DOI: 10.2141/jpsa.0200021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscle myoblasts are myogenic precursor cells that generate myofibers during muscle development and growth. We recently reported that broiler myoblasts, compared to layer myoblasts, proliferate and differentiate more actively and promptly into myocytes, which corresponds well with the muscle phenotype of broilers. Furthermore, RNA sequencing (RNA-seq) revealed that numerous genes are differentially expressed between layer and broiler myoblasts during myogenic differentiation. Based on the RNA-seq data, we herein report that chicken myoblasts transcribe endogenous retrovirus group K member (ERVK) genes. In total, 16 ERVKs were highly expressed in layer myoblasts and two (termed BrK1 and BrK2) were significantly induced in broiler myoblasts. These transcribed ERVKs had a total of 182 neighboring genes within ±100 kb on the chromosomes, of which 40% were concentrated within ±10 kb of the ERVKs. We further investigated whether the transcription of ERVKs affects the expression of their neighboring genes. BrK1 had two neighboring genes; LOC107052719 was overlapping with BrK1 and downregulated in the broiler myoblasts, and FAM19A2 was upregulated in the broiler myoblasts as well as BrK1. BrK2 had 14 neighboring genes, and only one gene, LOC772243, was differentially expressed between layer and broiler myoblasts. LOC772243 was overlapping with BrK2 and suppressed in the broiler myoblasts. These data indicate that the transcription of ERVKs may impact the expression of their neighboring genes in chicken myoblasts.
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Abstract
Endogenous retroviruses (ERVs) serve as markers of ancient viral infections and provide invaluable insight into host and viral evolution. ERVs have been exapted to assist in performing basic biological functions, including placentation, immune modulation, and oncogenesis. A subset of ERVs share high nucleotide similarity to circulating horizontally transmitted exogenous retrovirus (XRV) progenitors. In these cases, ERV-XRV interactions have been documented and include (a) recombination to result in ERV-XRV chimeras, (b) ERV induction of immune self-tolerance to XRV antigens, (c) ERV antigen interference with XRV receptor binding, and (d) interactions resulting in both enhancement and restriction of XRV infections. Whereas the mechanisms governing recombination and immune self-tolerance have been partially determined, enhancement and restriction of XRV infection are virus specific and only partially understood. This review summarizes interactions between six unique ERV-XRV pairs, highlighting important ERV biological functions and potential evolutionary histories in vertebrate hosts.
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Affiliation(s)
- Elliott S Chiu
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA; ,
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA; ,
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Blazhko N, Vyshegurov S, Donchenko A, Shatokhin K, Ryabinina V, Plotnikov K, Khodakova A, Pashkovskiy S. Genotypes diversity of env gene of Bovine leukemia virus in Western Siberia. BMC Genet 2020; 21:70. [PMID: 33092552 DOI: 10.1186/s12863-020-00874-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 06/23/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND This study describes the biodiversity and properties of Bovine leukemia virus in Western Siberia. This paper explores the effect of different genotypes of the env gene of the cattle leukemia virus on hematological parameters of infected animals. The researchers focused on exploring the polymorphism of the env gene and, in doing so, discovered the new genotypes Ia and Ib, which differ from genotype I. Several hypotheses on the origin of the different genotypes in Siberia are discussed. RESULTS We obtained varying length of the restriction fragments for genotypes I. Additionally using restrictase Hae III were received fragments was named genotype Ia, and genotype Ib. There are 2.57 ± 0.55% (20 out of 779) samples of genotype Ib which does not differ significantly from 1% (χ2 = 2.46). Other genotypes were observed in the cattle of Siberia as wild type genotypes (their frequency varied from 17.84 to 32.73%). The maximum viral load was observed in animals with the II and IV viral genotypes (1000-1400 viral particles per 1000 healthy cells), and the minimum viral load was observed animals with genotype Ib (from 700 to 900 viral particles per 1000 healthy cells). CONCLUSIONS The probability of the direct introduction of genotype II from South America to Siberia is extremely small and it is more likely that the strain originated independently in an autonomous population with its distribution also occurring independently. A new variety of genotype I (Ib) was found, which can be both a neoplasm and a relict strain.
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Chen F, Zhang W, Xie D, Gao T, Dong Z, Lu X. Histone chaperone FACT represses retrotransposon MERVL and MERVL-derived cryptic promoters. Nucleic Acids Res 2020; 48:10211-10225. [PMID: 32894293 PMCID: PMC7544220 DOI: 10.1093/nar/gkaa732] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Endogenous retroviruses (ERVs) were usually silenced by various histone modifications on histone H3 variants and respective histone chaperones in embryonic stem cells (ESCs). However, it is still unknown whether chaperones of other histones could repress ERVs. Here, we show that H2A/H2B histone chaperone FACT plays a critical role in silencing ERVs and ERV-derived cryptic promoters in ESCs. Loss of FACT component Ssrp1 activated MERVL whereas the re-introduction of Ssrp1 rescued the phenotype. Additionally, Ssrp1 interacted with MERVL and suppressed cryptic transcription of MERVL-fused genes. Remarkably, Ssrp1 interacted with and recruited H2B deubiquitinase Usp7 to Ssrp1 target genes. Suppression of Usp7 caused similar phenotypes as loss of Ssrp1. Furthermore, Usp7 acted by deubiquitinating H2Bub and thereby repressed the expression of MERVL-fused genes. Taken together, our study uncovers a unique mechanism by which FACT complex silences ERVs and ERV-derived cryptic promoters in ESCs.
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Affiliation(s)
- Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Dan Xie
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Tingting Gao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Zhiqiang Dong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Life Sciences, Nankai University, Tianjin 300307, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
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44
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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: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Elmer JL, Ferguson-Smith AC. Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans-Acting Modifiers. Viruses 2020; 12:E810. [PMID: 32727076 DOI: 10.3390/v12080810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Approximately 10 percent of the mouse genome consists of endogenous retroviruses (ERVs), relics of ancient retroviral infections that are classified based on their relatedness to exogenous retroviral genera. Because of the ability of ERVs to retrotranspose, as well as their cis-acting regulatory potential due to functional elements located within the elements, mammalian ERVs are generally subject to epigenetic silencing by DNA methylation and repressive histone modifications. The mobilisation and expansion of ERV elements is strain-specific, leading to ERVs being highly polymorphic between inbred mouse strains, hinting at the possibility of the strain-specific regulation of ERVs. In this review, we describe the existing evidence of mouse strain-specific epigenetic control of ERVs and discuss the implications of differential ERV regulation on epigenetic inheritance models. We consider Krüppel-associated box domain (KRAB) zinc finger proteins as likely candidates for strain-specific ERV modifiers, drawing on insights gained from the study of the strain-specific behaviour of transgenes. We conclude by considering the coevolution of KRAB zinc finger proteins and actively transposing ERV elements, and highlight the importance of cross-strain studies in elucidating the mechanisms and consequences of strain-specific ERV regulation.
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Rebollo R, Galvão-Ferrarini M, Gagnier L, Zhang Y, Ferraj A, Beck CR, Lorincz MC, Mager DL. Inter-Strain Epigenomic Profiling Reveals a Candidate IAP Master Copy in C3H Mice. Viruses 2020; 12:v12070783. [PMID: 32708087 PMCID: PMC7411935 DOI: 10.3390/v12070783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
Insertions of endogenous retroviruses cause a significant fraction of mutations in inbred mice but not all strains are equally susceptible. Notably, most new Intracisternal A particle (IAP) ERV mutagenic insertions have occurred in C3H mice. We show here that strain-specific insertional polymorphic IAPs accumulate faster in C3H/HeJ mice, relative to other sequenced strains, and that IAP transcript levels are higher in C3H/HeJ embryonic stem (ES) cells compared to other ES cells. To investigate the mechanism for high IAP activity in C3H mice, we identified 61 IAP copies in C3H/HeJ ES cells enriched with H3K4me3 (a mark of active promoters) and, among those tested, all are unmethylated in C3H/HeJ ES cells. Notably, 13 of the 61 are specific to C3H/HeJ and are members of the non-autonomous 1Δ1 IAP subfamily that is responsible for nearly all new insertions in C3H. One copy is full length with intact open reading frames and hence potentially capable of providing proteins in trans to other 1Δ1 elements. This potential “master copy” is present in other strains, including 129, but its 5’ long terminal repeat (LTR) is methylated in 129 ES cells. Thus, the unusual IAP activity in C3H may be due to reduced epigenetic repression coupled with the presence of a master copy.
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Affiliation(s)
- Rita Rebollo
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BC V5Z1L3, Canada; (L.G.); (Y.Z.)
- University of Lyon, INSA-Lyon, INRA, BF2i, UMR0203, F-69621 Villeurbanne, France;
- Correspondence: (R.R.); (D.L.M.)
| | | | - Liane Gagnier
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BC V5Z1L3, Canada; (L.G.); (Y.Z.)
| | - Ying Zhang
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BC V5Z1L3, Canada; (L.G.); (Y.Z.)
| | - Ardian Ferraj
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA; (A.F.); (C.R.B.)
| | - Christine R. Beck
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA; (A.F.); (C.R.B.)
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Matthew C. Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T1Z3, Canada;
| | - Dixie L. Mager
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BC V5Z1L3, Canada; (L.G.); (Y.Z.)
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T1Z3, Canada;
- Correspondence: (R.R.); (D.L.M.)
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Abstract
Mammalian fertilization begins with the fusion of two specialized gametes, followed by major epigenetic remodeling leading to the formation of a totipotent embryo. During the development of the pre-implantation embryo, precise reprogramming progress is a prerequisite for avoiding developmental defects or embryonic lethality, but the underlying molecular mechanisms remain elusive. For the past few years, unprecedented breakthroughs have been made in mapping the regulatory network of dynamic epigenomes during mammalian early embryo development, taking advantage of multiple advances and innovations in low-input genome-wide chromatin analysis technologies. The aim of this review is to highlight the most recent progress in understanding the mechanisms of epigenetic remodeling during early embryogenesis in mammals, including DNA methylation, histone modifications, chromatin accessibility and 3D chromatin organization.
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48
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Sznarkowska A, Mikac S, Pilch M. MHC Class I Regulation: The Origin Perspective. Cancers (Basel) 2020; 12:cancers12051155. [PMID: 32375397 PMCID: PMC7281430 DOI: 10.3390/cancers12051155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/27/2020] [Accepted: 05/03/2020] [Indexed: 12/11/2022] Open
Abstract
Viral-derived elements and non-coding RNAs that build up “junk DNA” allow for flexible and context-dependent gene expression. They are extremely dense in the MHC region, accounting for flexible expression of the MHC I, II, and III genes and adjusting the level of immune response to the environmental stimuli. This review brings forward the viral-mediated aspects of the origin and evolution of adaptive immunity and aims to link this perspective with the MHC class I regulation. The complex regulatory network behind MHC expression is largely controlled by virus-derived elements, both as binding sites for immune transcription factors and as sources of regulatory non-coding RNAs. These regulatory RNAs are imbalanced in cancer and associate with different tumor types, making them promising targets for diagnostic and therapeutic interventions.
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49
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Dai YD, Dias P, Margosiak A, Marquardt K, Bashratyan R, Hu WY, Haskins K, Evans LH. Endogenous retrovirus Gag antigen and its gene variants are unique autoantigens expressed in the pancreatic islets of non-obese diabetic mice. Immunol Lett 2020; 223:62-70. [PMID: 32335144 DOI: 10.1016/j.imlet.2020.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 12/16/2022]
Abstract
Endogenous retrovirus (ERV) are remnants of ancient retroviruses that have been incorporated into the genome and evidence suggests that they may play a role in the etiology of T1D. We previously identified a murine leukemia retrovirus-like ERV whose Env and Gag antigens are involved in autoimmune responses in non-obese diabetic (NOD) mice. In this study, we show that the Gag antigen is present in the islet stromal cells. Although Gag gene transcripts were present, Gag protein was not detected in diabetes-resistant mice. Cloning and sequencing analysis of individual Gag genes revealed that NOD islets express Gag gene variants with complete open-reading frames (ORFs), in contrast to the diabetes-resistant mice, whose islet Gag gene transcripts are mostly non-ORFs. Importantly, the ORFs obtained from the NOD islets are extremely heterogenous, coding for various mutants that are absence in the genome. We further show that Gag antigens are stimulatory for autoreactive T cells and identified one islet-expressing Gag variant that contains an altered peptide ligand capable of inducing IFN-gamma release by the T cells. The data highlight a unique retrovirus-like factor in the islets of the NOD mouse strain, which may participate in key events triggering autoimmunity and T1D.
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Affiliation(s)
- Yang D Dai
- Biomedical Research Institute of Southern California, Oceanside, CA, USA; Department of Immunology, Scripps Research, San Diego, CA, USA.
| | - Peter Dias
- Biomedical Research Institute of Southern California, Oceanside, CA, USA
| | - Amanda Margosiak
- Biomedical Research Institute of Southern California, Oceanside, CA, USA
| | | | | | | | - Kathryn Haskins
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Denver, CO, USA
| | - Leonard H Evans
- Laboratory of Persistent Viral Diseases, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
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50
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Dembny P, Newman AG, Singh M, Hinz M, Szczepek M, Krüger C, Adalbert R, Dzaye O, Trimbuch T, Wallach T, Kleinau G, Derkow K, Richard BC, Schipke C, Scheidereit C, Stachelscheid H, Golenbock D, Peters O, Coleman M, Heppner FL, Scheerer P, Tarabykin V, Ruprecht K, Izsvák Z, Mayer J, Lehnardt S. Human endogenous retrovirus HERV-K(HML-2) RNA causes neurodegeneration through Toll-like receptors. JCI Insight 2020; 5:131093. [PMID: 32271161 DOI: 10.1172/jci.insight.131093] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/04/2020] [Indexed: 01/27/2023] Open
Abstract
Although human endogenous retroviruses (HERVs) represent a substantial proportion of the human genome and some HERVs, such as HERV-K(HML-2), are reported to be involved in neurological disorders, little is known about their biological function. We report that RNA from an HERV-K(HML-2) envelope gene region binds to and activates human Toll-like receptor (TLR) 8, as well as murine Tlr7, expressed in neurons and microglia, thereby causing neurodegeneration. HERV-K(HML-2) RNA introduced into the cerebrospinal fluid (CSF) of either C57BL/6 wild-type mice or APPPS1 mice, a mouse model for Alzheimer's disease (AD), resulted in neurodegeneration and microglia accumulation. Tlr7-deficient mice were protected against neurodegenerative effects but were resensitized toward HERV-K(HML-2) RNA when neurons ectopically expressed murine Tlr7 or human TLR8. Transcriptome data sets of human AD brain samples revealed a distinct correlation of upregulated HERV-K(HML-2) and TLR8 RNA expression. HERV-K(HML-2) RNA was detectable more frequently in CSF from individuals with AD compared with controls. Our data establish HERV-K(HML-2) RNA as an endogenous ligand for species-specific TLRs 7/8 and imply a functional contribution of human endogenous retroviral transcripts to neurodegenerative processes, such as AD.
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Affiliation(s)
- Paul Dembny
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Andrew G Newman
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Manvendra Singh
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Michael Hinz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Michal Szczepek
- Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and BIH, Berlin, Germany
| | - Christina Krüger
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | | | - Omar Dzaye
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Department of Radiology.,Department of Neuroradiology
| | | | - Thomas Wallach
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Gunnar Kleinau
- Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and BIH, Berlin, Germany
| | - Katja Derkow
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | | | - Carola Schipke
- Department of Psychiatry and Psychotherapy, and.,Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and BIH.,German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Claus Scheidereit
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Harald Stachelscheid
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, BIH, Berlin-Brandenburg Center for Regenerative Therapies, Berlin, Germany
| | - Douglas Golenbock
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Oliver Peters
- Department of Psychiatry and Psychotherapy, and.,Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and BIH.,German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Michael Coleman
- Babraham Institute and John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, United Kingdom
| | - Frank L Heppner
- NeuroCure Cluster of Excellence.,Department of Neuropathology.,German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Patrick Scheerer
- Institute for Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and BIH, Berlin, Germany.,German Centre for Cardiovascular Research, partner site Berlin, Berlin, Germany
| | - Victor Tarabykin
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Klemens Ruprecht
- Department of Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and BIH, Berlin, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Jens Mayer
- Institute of Human Genetics, Universität des Saarlandes, Hamburg, Germany
| | - Seija Lehnardt
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Department of Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and BIH, Berlin, Germany
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