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Kilroy JM, Leal AA, Henderson AJ. Chronic HIV Transcription, Translation, and Persistent Inflammation. Viruses 2024; 16:751. [PMID: 38793632 PMCID: PMC11125830 DOI: 10.3390/v16050751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
People with HIV exhibit persistent inflammation that correlates with HIV-associated comorbidities including accelerated aging, increased risk of cardiovascular disease, and neuroinflammation. Mechanisms that perpetuate chronic inflammation in people with HIV undergoing antiretroviral treatments are poorly understood. One hypothesis is that the persistent low-level expression of HIV proviruses, including RNAs generated from defective proviral genomes, drives the immune dysfunction that is responsible for chronic HIV pathogenesis. We explore factors during HIV infection that contribute to the generation of a pool of defective proviruses as well as how HIV-1 mRNA and proteins alter immune function in people living with HIV.
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Affiliation(s)
- Jonathan M. Kilroy
- Department of Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; (J.M.K.); (A.A.L.)
| | - Andrew A. Leal
- Department of Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; (J.M.K.); (A.A.L.)
| | - Andrew J. Henderson
- Department of Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; (J.M.K.); (A.A.L.)
- Department of Medicine and Virology, Immunology, Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
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2
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da Silva AL, Guedes BLM, Santos SN, Correa GF, Nardy A, Nali LHDS, Bachi ALL, Romano CM. Beyond pathogens: the intriguing genetic legacy of endogenous retroviruses in host physiology. Front Cell Infect Microbiol 2024; 14:1379962. [PMID: 38655281 PMCID: PMC11035796 DOI: 10.3389/fcimb.2024.1379962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
The notion that viruses played a crucial role in the evolution of life is not a new concept. However, more recent insights suggest that this perception might be even more expansive, highlighting the ongoing impact of viruses on host evolution. Endogenous retroviruses (ERVs) are considered genomic remnants of ancient viral infections acquired throughout vertebrate evolution. Their exogenous counterparts once infected the host's germline cells, eventually leading to the permanent endogenization of their respective proviruses. The success of ERV colonization is evident so that it constitutes 8% of the human genome. Emerging genomic studies indicate that endogenous retroviruses are not merely remnants of past infections but rather play a corollary role, despite not fully understood, in host genetic regulation. This review presents some evidence supporting the crucial role of endogenous retroviruses in regulating host genetics. We explore the involvement of human ERVs (HERVs) in key physiological processes, from their precise and orchestrated activities during cellular differentiation and pluripotency to their contributions to aging and cellular senescence. Additionally, we discuss the costs associated with hosting a substantial amount of preserved viral genetic material.
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Affiliation(s)
- Amanda Lopes da Silva
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Bruno Luiz Miranda Guedes
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Samuel Nascimento Santos
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | - Giovanna Francisco Correa
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ariane Nardy
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | | | - Andre Luis Lacerda Bachi
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | - Camila Malta Romano
- Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
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3
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Dopkins N, Nixon DF. Activation of human endogenous retroviruses and its physiological consequences. Nat Rev Mol Cell Biol 2024; 25:212-222. [PMID: 37872387 DOI: 10.1038/s41580-023-00674-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
Human endogenous retroviruses (HERVs) are abundant sequences that persist within the human genome as remnants of ancient retroviral infections. These sequences became fixed and accumulate mutations or deletions over time. HERVs have affected human evolution and physiology by providing a unique repertoire of coding and non-coding sequences to the genome. In healthy individuals, HERVs participate in immune responses, formation of syncytiotrophoblasts and cell-fate specification. In this Review, we discuss how endogenized retroviral motifs and regulatory sequences have been co-opted into human physiology and how they are tightly regulated. Infections and mutations can derail this regulation, leading to differential HERV expression, which may contribute to pathologies including neurodegeneration, pathological inflammation and oncogenesis. Emerging evidence demonstrates that HERVs are crucial to human health and represent an understudied facet of many diseases, and we therefore argue that investigating their fundamental properties could improve existing therapies and help develop novel therapeutic strategies.
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Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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4
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Cherkasova EA, Chen L, Childs RW. Mechanistic regulation of HERV activation in tumors and implications for translational research in oncology. Front Cell Infect Microbiol 2024; 14:1358470. [PMID: 38379771 PMCID: PMC10877039 DOI: 10.3389/fcimb.2024.1358470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Transcription of distinct loci of human endogenous retroviruses (HERVs) and in some cases, translation of these transcripts have been consistently observed in many types of cancer. It is still debated whether HERV activation serves as a trigger for carcinogenesis or rather occurs as a consequence of epigenetic alterations and other molecular sequelae that characterize cellular transformation. Here we review the known molecular and epigenetic mechanisms of HERV activation in cancer cells as well as its potential contribution to carcinogenesis. Further, we describe the use of HERV expression in cancer diagnostic and characterize the potential of HERV-derived antigens to serve as novel targets for cancer immunotherapy. We believe this review, which summarizes both what is known as well as unknown in this rapidly developing field, will boost interest in research on the therapeutic potential of targeting HERV elements in tumors and the impact of HERV activation in oncogenesis.
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Affiliation(s)
| | | | - Richard W. Childs
- Laboratory of Transplantation Immunotherapy, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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5
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Mantovani F, Kitsou K, Magiorkinis G. HERVs: Expression Control Mechanisms and Interactions in Diseases and Human Immunodeficiency Virus Infection. Genes (Basel) 2024; 15:192. [PMID: 38397182 PMCID: PMC10888493 DOI: 10.3390/genes15020192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/24/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are the result of retroviral infections acquired millions of years ago; nowadays, they compose around 8% of human DNA. Multiple mechanisms have been employed for endogenous retroviral deactivation, rendering replication and retrotransposition defective, while some of them have been co-opted to serve host evolutionary advantages. A pleiad of mechanisms retains the delicate balance of HERV expression in modern humans. Thus, epigenetic modifications, such as DNA and histone methylation, acetylation, deamination, chromatin remodeling, and even post-transcriptional control are recruited. In this review, we aim to summarize the main HERV silencing pathways, revisit paradigms of human disease with a HERV component, and emphasize the human immunodeficiency virus (HIV) and HERV interactions during HIV infection.
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Affiliation(s)
| | | | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (F.M.); (K.K.)
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Mantovani F, Kitsou K, Paraskevis D, Lagiou P, Magiorkinis G. The interaction of human immunodeficiency virus-1 and human endogenous retroviruses in patients (primary cell cultures) and cell line models. Microbiol Spectr 2023; 11:e0137923. [PMID: 37811936 PMCID: PMC10715072 DOI: 10.1128/spectrum.01379-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE In this work, we demonstrated that human immunodeficiency virus (HIV) infection leads to the modification of the human endogenous retrovirus (HERV) expression. Differential expression of multiple HERVs was found in peripheral blood mononuclear cells derived from HIV-infected patients compared to healthy donors and HIV-infected T cell cultures compared to non-infected. The effect of HIV presence on HERV expression appears to be more restricted in cells of monocytic origin, as only deregulation of HERV-W and HERV-K (HML-6) was found in these cell cultures after their infection with HIV. Multiple factors contribute to this aberrant HERV expression, and its levels appear to be modified in a time-dependent manner. Further studies and the development of optimized in vitro protocols are warranted to elucidate the interactions between HIV and HERVs in detail.
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Affiliation(s)
- Federica Mantovani
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantina Kitsou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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7
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Ko EJ, Kim MH, Kim DY, An H, Leem SH, Choi YH, Kim HS, Cha HJ. The Role of Human Endogenous Retrovirus (HERV)-K119 env in THP-1 Monocytic Cell Differentiation. Int J Mol Sci 2023; 24:15566. [PMID: 37958549 PMCID: PMC10648273 DOI: 10.3390/ijms242115566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
Human endogenous retrovirus (HERV)-K was reportedly inserted into the human genome millions of years ago and is closely related to various diseases, including cancer and immune regulation. In our previous studies, CRISPR-Cas9-enabled knockout (KO) of the HERV-K env gene was found to potentially reduce cell proliferation, cell migration, and invasion in colorectal and ovarian cancer cell lines. The immune response involves the migration and invasion of cells and is similar to cancer; however, in certain ways, it is completely unlike cancer. Therefore, we induced HERV-K119 env gene KO in THP-1, a monocytic cell that can be differentiated into a macrophage, to investigate the role of HERV-K119 env in immune regulation. Cell migration and invasion were noted to be significantly increased in HERV-K119 env KO THP-1 cells than in MOCK, and these results were contrary to those of cancer cells. To identify the underlying mechanism of HERV-K119 env KO in THP-1 cells, transcriptome analysis and cytokine array analysis were conducted. Semaphorin7A (SEMA7A), which induces the production of cytokines in macrophages and monocytic cells and plays an important role in immune effector cell activation during an inflammatory immune response, was significantly increased in HERV-K119 env KO THP-1 cells. We also found that HERV-K119 env KO THP-1 cells expressed various macrophage-specific surface markers, suggesting that KO of HERV-K119 env triggers the differentiation of THP-1 cells from monocytic cells into macrophages. In addition, analysis of the expression of M1 and M2 macrophage markers showed that M1 macrophage marker cluster of differentiation 32 (CD32) was significantly increased in HERV-K119 env KO cells. These results suggest that HERV-K119 env is implicated in the differentiation of monocytic cells into M1 macrophages and plays important roles in the immune response.
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Affiliation(s)
- Eun-Ji Ko
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Republic of Korea; (E.-J.K.); (M.-H.K.); (D.-Y.K.); (H.A.)
| | - Min-Hye Kim
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Republic of Korea; (E.-J.K.); (M.-H.K.); (D.-Y.K.); (H.A.)
- Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea;
| | - Do-Ye Kim
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Republic of Korea; (E.-J.K.); (M.-H.K.); (D.-Y.K.); (H.A.)
| | - Hyojin An
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Republic of Korea; (E.-J.K.); (M.-H.K.); (D.-Y.K.); (H.A.)
| | - Sun-Hee Leem
- Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea;
| | - Yung Hyun Choi
- Department of Biochemistry, College of Oriental Medicine, Dongeui University, Busan 47227, Republic of Korea;
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 49241, Republic of Korea;
| | - Hee-Jae Cha
- Departments of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Republic of Korea; (E.-J.K.); (M.-H.K.); (D.-Y.K.); (H.A.)
- Institute for Medical Science, Kosin University College of Medicine, Busan 49267, Republic of Korea
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8
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Costa B, Vale N. Exploring HERV-K (HML-2) Influence in Cancer and Prospects for Therapeutic Interventions. Int J Mol Sci 2023; 24:14631. [PMID: 37834078 PMCID: PMC10572383 DOI: 10.3390/ijms241914631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
This review investigates the intricate role of human endogenous retroviruses (HERVs) in cancer development and progression, explicitly focusing on HERV-K (HML-2). This paper sheds light on the latest research advancements and potential treatment strategies by examining the historical context of HERVs and their involvement in critical biological processes such as embryonic development, immune response, and disease progression. This review covers computational modeling for drug-target binding assessment, systems biology modeling for simulating HERV-K viral cargo dynamics, and using antiviral drugs to combat HERV-induced diseases. The findings presented in this review contribute to our understanding of HERV-mediated disease mechanisms and provide insights into future therapeutic approaches. They emphasize why HERV-K holds significant promise as a biomarker and a target.
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Affiliation(s)
- Bárbara Costa
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal
| | - Nuno Vale
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal
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Gimenez J, Spalloni A, Cappelli S, Ciaiola F, Orlando V, Buratti E, Longone P. TDP-43 Epigenetic Facets and Their Neurodegenerative Implications. Int J Mol Sci 2023; 24:13807. [PMID: 37762112 PMCID: PMC10530927 DOI: 10.3390/ijms241813807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/31/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
Since its initial involvement in numerous neurodegenerative pathologies in 2006, either as a principal actor or as a cofactor, new pathologies implicating transactive response (TAR) DNA-binding protein 43 (TDP-43) are regularly emerging also beyond the neuronal system. This reflects the fact that TDP-43 functions are particularly complex and broad in a great variety of human cells. In neurodegenerative diseases, this protein is often pathologically delocalized to the cytoplasm, where it irreversibly aggregates and is subjected to various post-translational modifications such as phosphorylation, polyubiquitination, and cleavage. Until a few years ago, the research emphasis has been focused particularly on the impacts of this aggregation and/or on its widely described role in complex RNA splicing, whether related to loss- or gain-of-function mechanisms. Interestingly, recent studies have strengthened the knowledge of TDP-43 activity at the chromatin level and its implication in the regulation of DNA transcription and stability. These discoveries have highlighted new features regarding its own transcriptional regulation and suggested additional mechanistic and disease models for the effects of TPD-43. In this review, we aim to give a comprehensive view of the potential epigenetic (de)regulations driven by (and driving) this multitask DNA/RNA-binding protein.
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Affiliation(s)
- Juliette Gimenez
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
| | - Alida Spalloni
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
| | - Sara Cappelli
- Molecular Pathology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy; (S.C.); (E.B.)
| | - Francesca Ciaiola
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
- Department of Systems Medicine, University of Roma Tor Vergata, 00133 Rome, Italy
| | - Valerio Orlando
- KAUST Environmental Epigenetics Program, Biological Environmental Sciences and Engineering Division BESE, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
| | - Emanuele Buratti
- Molecular Pathology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy; (S.C.); (E.B.)
| | - Patrizia Longone
- Molecular Neurobiology Laboratory, Experimental Neuroscience, IRCCS Fondazione Santa Lucia (FSL), 00143 Rome, Italy; (A.S.); (P.L.)
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10
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Li Z, Wang Q, Lv N, Xu G, Yang X, Zhu B. Genome-wide identification of endogenous retrovirus elements and their active transcription in mink genome. MLIFE 2023; 2:201-208. [PMID: 38817617 PMCID: PMC10989824 DOI: 10.1002/mlf2.12074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/12/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2024]
Abstract
Mammalian endogenous retroviruses (ERVs) are ancient retroviruses that have been integrated into genomes. ERVs were believed to be inactive until the discovery of ERV transcription in the mouse genome. However, the transcription level and function of ERV elements in mammalian genomes are not well understood. In this study, we performed the first genome-wide scanning of ERV loci in the American mink (Neogale vison) genome (NeoERV) followed by transcriptomic analysis to detect actively transcribed NeoERV elements. A total of 365,791 NeoERV loci were identified, and161,205 (44%) of these loci were found to be actively transcribed based on transcriptomic data from three types of tissues (amygdala, trachea and lung). More than one third of the actively transcribed NeoERV loci were tissue-specific. Furthermore, some of the active loci were associated with host gene transcription, and the level of NeoERV transcription was positively correlated with that of host genes, specifically when active loci were located in overlapped gene regions. An in-depth analysis of the envelope protein coding env gene showed that, in general, its transcription level was higher than that of NeoERVs, which is believed to be associated with host immunity.
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Affiliation(s)
- Zheng Li
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qing Wang
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- Jiangxi Science and Technology Normal UniversityNanchangChina
| | - Na Lv
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- Jinan Microecological Biomedicine Shandong LaboratoryJinanChina
| | - Guojin Xu
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Xuemei Yang
- Beijing Pediatric Research InstituteBeijingChina
| | - Baoli Zhu
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Jinan Microecological Biomedicine Shandong LaboratoryJinanChina
- Department of Pathogenic Biology, School of Basic Medical SciencesSouthwest Medical UniversityLuzhouChina
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Laine A, Wang X, Ni K, Smith SEB, Najjar R, Whitmore LS, Yacoub M, Bays A, Gale M, Mustelin T. Expression of Envelope Protein Encoded by Endogenous Retrovirus K102 in Rheumatoid Arthritis Neutrophils. Microorganisms 2023; 11:1310. [PMID: 37317284 PMCID: PMC10223813 DOI: 10.3390/microorganisms11051310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/13/2023] [Accepted: 05/14/2023] [Indexed: 06/16/2023] Open
Abstract
Many patients suffering from autoimmune diseases have autoantibodies against proteins encoded by genomic retroelements, suggesting that normal epigenetic silencing is insufficient to prevent the production of the encoded proteins for which immune tolerance appears to be limited. One such protein is the transmembrane envelope (Env) protein encoded by human endogenous retrovirus K (HERV-K). We reported recently that patients with rheumatoid arthritis (RA) have IgG autoantibodies that recognize Env. Here, we use RNA sequencing of RA neutrophils to analyze HERV-K expression and find that only two loci with an intact open-reading frame for Env, HERV-K102, and K108 are expressed, but only the former is increased in RA. In contrast, other immune cells express more K108 than K102. Patient autoantibodies recognized endogenously expressed Env in breast cancer cells and in RA neutrophils but not healthy controls. A monoclonal anti-Env antibody also detected Env on the surface of RA neutrophils but very little on the surface of other immune cells. We conclude that HERV-K102 is the locus that produces Env detectable on the surface of neutrophils in RA. The low levels of HERV-K108 transcripts may contribute only marginally to cell surface Env on neutrophils or other immune cells in some patients.
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Affiliation(s)
- Amanda Laine
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Xiaoxing Wang
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Kathryn Ni
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sarah E. B. Smith
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rayan Najjar
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Leanne S. Whitmore
- Center for Innate Immunity and Infectious Disease, Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Michael Yacoub
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Alison Bays
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Michael Gale
- Center for Innate Immunity and Infectious Disease, Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Center for Innate Immunity and Infectious Disease, Department of Immunology, University of Washington, Seattle, WA 98195, USA
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12
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Wang D, Gomes MT, Mo Y, Prohaska CC, Zhang L, Chelvanambi S, Clauss MA, Zhang D, Machado RF, Gao M, Bai Y. Human Endogenous Retrovirus, SARS-CoV-2, and HIV Promote PAH via Inflammation and Growth Stimulation. Int J Mol Sci 2023; 24:7472. [PMID: 37108634 PMCID: PMC10138839 DOI: 10.3390/ijms24087472] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a pulmonary vascular disease characterized by the progressive elevation of pulmonary arterial pressures. It is becoming increasingly apparent that inflammation contributes to the pathogenesis and progression of PAH. Several viruses are known to cause PAH, such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), human endogenous retrovirus K(HERV-K), and human immunodeficiency virus (HIV), in part due to acute and chronic inflammation. In this review, we discuss the connections between HERV-K, HIV, SARS-CoV-2, and PAH, to stimulate research regarding new therapeutic options and provide new targets for the treatment of the disease.
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Affiliation(s)
- Desheng Wang
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Marta T. Gomes
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Yanfei Mo
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Clare C. Prohaska
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Lu Zhang
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Sarvesh Chelvanambi
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthias A. Clauss
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Dongfang Zhang
- Department of Pharmacognosy, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Roberto F. Machado
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Mingqi Gao
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Yang Bai
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA
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13
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Angileri KM, Bagia NA, Feschotte C. Transposon control as a checkpoint for tissue regeneration. Development 2022; 149:dev191957. [PMID: 36440631 PMCID: PMC10655923 DOI: 10.1242/dev.191957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022]
Abstract
Tissue regeneration requires precise temporal control of cellular processes such as inflammatory signaling, chromatin remodeling and proliferation. The combination of these processes forms a unique microenvironment permissive to the expression, and potential mobilization of, transposable elements (TEs). Here, we develop the hypothesis that TE activation creates a barrier to tissue repair that must be overcome to achieve successful regeneration. We discuss how uncontrolled TE activity may impede tissue restoration and review mechanisms by which TE activity may be controlled during regeneration. We posit that the diversification and co-evolution of TEs and host control mechanisms may contribute to the wide variation in regenerative competency across tissues and species.
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Affiliation(s)
- Krista M. Angileri
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
| | - Nornubari A. Bagia
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
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14
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A Systems Biology Approach on the Regulatory Footprint of Human Endogenous Retroviruses (HERVs). Diseases 2022; 10:diseases10040098. [PMID: 36412592 PMCID: PMC9680359 DOI: 10.3390/diseases10040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are a family of endogenous retroviruses that comprise the ~8.93% of the human genome sequence, with a high proportion being human specific. The recent expansion of repeated HERV sequences has offered a framework for genetic and epigenetic innovation. In the current report, a systematic approach is implemented to catalogue regulatory elements within HERVs, as a roadmap to potential functions of HERV sequences in gene networks. ENCODE Project has offered a wealth of epigenetic data based on omics technologies. I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. On the one side, HERVs are in 1 out of 9 cCREs (>100.000 cCREs in total), dispersed within the genome and present in cis-regulatory regions of ~81% of human genes, as calculated following gene enrichment analysis. On the other side, promoter-associated HERV cCREs are present adjacent to (in a 200 bp window) the transcription start sites of 256 human genes. Regulatory network production, followed by centrality analysis led to the discovery of 90 core genes containing HERV-associated promoters. Pathway analysis on the core network genes and their immediate neighbors revealed a regulatory footprint that, among others, is associated with inflammation, chemokine signaling and response to viral infection. Collectively, these results support the concept that the expansion of regulatory sequences derived from HERVs is critical for epigenetic innovation that may have wired together genes into novel transcriptional networks with critical roles in cellular physiology and pathology.
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15
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Khadjinova AI, Wang X, Laine A, Ukadike K, Eckert M, Stevens A, Bengtsson AA, Lood C, Mustelin T. Autoantibodies against the envelope proteins of endogenous retroviruses K102 and K108 in patients with systemic lupus erythematosus correlate with active disease. Clin Exp Rheumatol 2022; 40:1306-1312. [PMID: 34665695 PMCID: PMC10695298 DOI: 10.55563/clinexprheumatol/2kg1d8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/09/2021] [Indexed: 11/13/2022]
Abstract
OBJECTIVES To determine if patients with systemic lupus erythematosus (SLE), a disease characterised by elevated type I interferons reminiscent of anti-viral immunity, have expression of human endogenous retrovirus K (HERV-K) proviruses capable of producing envelope (Env) protein, as well as associated autoantibodies against the Env protein. METHODS ELISAs were conducted with recombinant Env protein and sera from SLE patients with active (n=60) or inactive (n=49) disease, healthy controls (n=47), other rheumatic disorders (n=59), as well as plasma from paediatric lupus patients with active (n=30) or inactive (n=30) disease, and 17 healthy children. Antibody reactivity was evaluated for correlations with clinical and laboratory parameters of the patients. Expression of HERV-K transcripts were profiled in SLE leukocytes by RNA-Seq. RESULTS Both adult and paediatric SLE patients had autoantibodies against HERV-K Env with higher titres than healthy controls or patients with Sjögren's syndrome, small- or large-vessel vasculitis, or psoriatic arthritis. Transcripts from only two HERV-K loci capable of producing Env, HERV-K102 and -K108, were detected among the 10 expressed loci in SLE patients. CONCLUSIONS Our data reveal that HERV-K proviruses are expressed in SLE and that the HERV-K-encoded Env protein elicits an immune response in patients, particularly during active disease.
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Affiliation(s)
- Anastasia I Khadjinova
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Xiaoxing Wang
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Amanda Laine
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kennedy Ukadike
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mary Eckert
- Seattle Children's Hospital, Seattle, WA, USA
| | - Anne Stevens
- Seattle Children's Hospital and Seattle Children's Research Institute, Seattle, WA, and Jansen Research and Development LLC, Malvern, PA, USA
| | | | - Christian Lood
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA.
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16
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Boldyreva LV, Andreyeva EN, Pindyurin AV. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation. Mol Biol 2022. [DOI: 10.1134/s0026893322030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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High Expression of HERV-K (HML-2) Might Stimulate Interferon in COVID-19 Patients. Viruses 2022; 14:v14050996. [PMID: 35632738 PMCID: PMC9143815 DOI: 10.3390/v14050996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 12/15/2022] Open
Abstract
Background. Interferon is a marker of host antiviral immunity, which is disordered in COVID-19 patients. ERV can affect the secretion of interferon through the cGAS-STING pathway. In this study, we explored whether IFN-I and HERV-K (HML-2) were activated in COVID-19 patients and whether there was an interaction between them. Methods. We collected blood samples from COVID-19 patients and healthy controls. We first detected the expression of HERV-K (HML-2) gag, env, and pol genes and IFN-I-related genes between patients and healthy people by qPCR, synchronously detected VERO cells infected with SARS-CoV-2. Then, the chromosome distributions of highly expressed HERV-K (HML-2) gag, env, and pol genes were mapped by the next-generation sequencing results, and GO analysis was performed on the related genes. Results. We found that the HERV-K (HML-2) gag, env, and pol genes were highly expressed in COVID-19 patients and VERO cells infected with SARS-CoV-2. The interferon-related genes IFNB1, ISG15, and IFIT1 were also activated in COVID-19 patients, and GO analysis showed that HERV-K (HML-2) can regulate the secretion of interferon. Conclusions. The high expression of HERV-K (HML-2) might activate the increase of interferon in COVID-19 patients, proving that HERV-K does not only play a negative role in the human body.
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Abstract
Human endogenous retroviruses (HERVs) occupy approximately 8% of the human genome. HERVs, transcribed in early embryos, are epigenetically silenced in somatic cells, except under pathological conditions. HERV-K is thought to protect embryos from exogenous viral infection. However, uncontrolled HERV-K expression in somatic cells has been implicated in several diseases. Here, we show that SOX2, which plays a key role in maintaining the pluripotency of stem cells, is critical for HERV-K LTR5Hs. HERV-K undergoes retrotransposition within producer cells in the absence of Env expression. Furthermore, we identified new HERV-K integration sites in long-term culture of induced pluripotent stem cells that express SOX2. These results suggest that the strict dependence of HERV-K on SOX2 has allowed HERV-K to protect early embryos during evolution while limiting the potentially harmful effects of HERV-K retrotransposition on host genome integrity in these early embryos. IMPORTANCE Human endogenous retroviruses (HERVs) account for approximately 8% of the human genome; however, the physiological role of HERV-K remains unknown. This study found that HERV-K LTR5Hs and LTR5B were transactivated by SOX2, which is essential for maintaining and reestablishing pluripotency. HERV-K can undergo retrotransposition within producer cells without env expression, and new integration sites may affect cell proliferation. In induced pluripotent stem cells (iPSCs), genomic impairment due to HERV-K retrotransposition has been identified, but it is a rare event. Considering the retention of SOX2-responsive elements in the HERV-K long terminal repeat (LTR) for over 20 million years, we conclude that HERV-K may play important physiological roles in SOX2-expressing cells.
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19
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Randolph K, Hyder U, D’Orso I. KAP1/TRIM28: Transcriptional Activator and/or Repressor of Viral and Cellular Programs? Front Cell Infect Microbiol 2022; 12:834636. [PMID: 35281453 PMCID: PMC8904932 DOI: 10.3389/fcimb.2022.834636] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/03/2022] [Indexed: 01/01/2023] Open
Abstract
Several transcriptional and epigenetic regulators have been functionally linked to the control of viral and cellular gene expression programs. One such regulator is Krüppel-associated box (KRAB)-associated protein 1 (KAP1: also named TRIM28 or TIF1β), which has been extensively studied in the past three decades. Here we offer an up-to date review of its various functions in a diversity of contexts. We first summarize the discovery of KAP1 repression of endogenous retroviruses during development. We then deliberate evidence in the literature suggesting KAP1 is both an activator and repressor of HIV-1 transcription and discuss experimental differences and limitations of previous studies. Finally, we discuss KAP1 regulation of DNA and RNA viruses, and then expand on KAP1 control of cellular responses and immune functions. While KAP1 positive and negative regulation of viral and cellular transcriptional programs is vastly documented, our mechanistic understanding remains narrow. We thus propose that precision genetic tools to reveal direct KAP1 functions in gene regulation will be required to not only illuminate new biology but also provide the foundation to translate the basic discoveries from the bench to the clinics.
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20
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Wang X, Hefton A, Ni K, Ukadike KC, Bowen MA, Eckert M, Stevens A, Lood C, Mustelin T. Autoantibodies Against Unmodified and Citrullinated Human Endogenous Retrovirus K Envelope Protein in Patients With Rheumatoid Arthritis. J Rheumatol Suppl 2022; 49:26-35. [PMID: 34334364 PMCID: PMC8963793 DOI: 10.3899/jrheum.201492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2021] [Indexed: 01/03/2023]
Abstract
OBJECTIVE Autoantibodies against proteins encoded by human endogenous retrovirus K (HERV-K) have been reported in patients with rheumatoid arthritis (RA), but their relevance, if any, has remained unresolved. We revisited this question and tested if such autoantibodies may react with citrullinated epitopes on the envelope (Env) protein of HERV-K. METHODS Immunoblotting and ELISAs were conducted with unmodified Env protein and with Env citrullinated by protein arginine deiminase 4 (PAD4). Sera from 100 patients with RA, plasma from 32 patients with juvenile idiopathic arthritis (JIA), and healthy adult and pediatric controls were included. Antibody reactivity was evaluated for correlations with clinical and laboratory variables of the patients. RESULTS We replicated and expanded upon published data suggesting that patients with RA or JIA have autoantibodies against HERV-K Env, some with high titers. Anti-HERV-K antibodies correlated with cigarette smoking and with circulating myeloperoxidase-DNA complexes indicative of nonapoptotic neutrophil cell death. Further, most of the patients with RA, but not those with JIA, had autoantibodies that reacted more strongly with Env that was citrullinated by PAD4. These anticitrullinated Env autoantibodies correlated with seropositivity and tended to be higher in patients with erosive disease. CONCLUSION Our data suggest that anti-HERV-K immunity is elevated in RA and JIA and may have a connection with pathogenic protein citrullination in RA.
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Affiliation(s)
- Xiaoxing Wang
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Amanda Hefton
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Kathryn Ni
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Kennedy C. Ukadike
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Michael A. Bowen
- M.A. Bowen, PhD, Product and Process Development, Allogene Therapeutics, San Francisco, California
| | - Mary Eckert
- M. Eckert, BS, Seattle Children’s Research Institute, Seattle, Washington
| | - Anne Stevens
- A. Stevens, MD, Professor, Seattle Children’s Research Institute, Seattle, Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, Washington, and Janssen Research & Development, LLC, Wayne, Pennsylvania, USA
| | - Christian Lood
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Tomas Mustelin
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
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21
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Hale BG. Antiviral immunity triggered by infection-induced host transposable elements. Curr Opin Virol 2021; 52:211-216. [PMID: 34959082 DOI: 10.1016/j.coviro.2021.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022]
Abstract
Host silencing of transposable elements (TEs) is critical to prevent genome damage and inappropriate inflammation. However, new evidence suggests that a virus-infected host may re-activate TEs and co-opt them for antiviral defense. RNA-Seq and specialized bioinformatics have revealed the diversity of virus infections that induce TEs. Furthermore, studies with influenza virus have uncovered how infection-triggered changes to the SUMOylation of TRIM28, an epigenetic co-repressor, lead to TE de-repression. Importantly, there is a growing appreciation of how de-repressed TEs stimulate antiviral gene expression, either via cis-acting enhancer functions or via their recognition as viral mimetics by innate immune nucleic acid sensors (e.g. RIG-I, mda-5 and cGAS). Understanding how viruses trigger, and counteract, TE-based antiviral immunity should provide insights into pathogenic mechanisms.
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Affiliation(s)
- Benjamin G Hale
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland.
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22
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Rodríguez-Frías F, Quer J, Tabernero D, Cortese MF, Garcia-Garcia S, Rando-Segura A, Pumarola T. Microorganisms as Shapers of Human Civilization, from Pandemics to Even Our Genomes: Villains or Friends? A Historical Approach. Microorganisms 2021; 9:2518. [PMID: 34946123 PMCID: PMC8708650 DOI: 10.3390/microorganisms9122518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/23/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Universal history is characterized by continuous evolution, in which civilizations are born and die. This evolution is associated with multiple factors, among which the role of microorganisms is often overlooked. Viruses and bacteria have written or decisively contributed to terrible episodes of history, such as the Black Death in 14th century Europe, the annihilation of pre-Columbian American civilizations, and pandemics such as the 1918 Spanish flu or the current COVID-19 pandemic caused by the coronavirus SARS-CoV-2. Nevertheless, it is clear that we could not live in a world without these tiny beings. Endogenous retroviruses have been key to our evolution and for the regulation of gene expression, and the gut microbiota helps us digest compounds that we could not otherwise process. In addition, we have used microorganisms to preserve or prepare food for millennia and more recently to obtain drugs such as antibiotics or to develop recombinant DNA technologies. Due to the enormous importance of microorganisms for our survival, they have significantly influenced the population genetics of different human groups. This paper will review the role of microorganisms as "villains" who have been responsible for tremendous mortality throughout history but also as "friends" who help us survive and evolve.
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Affiliation(s)
- Francisco Rodríguez-Frías
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain;
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Maria Francesca Cortese
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Selene Garcia-Garcia
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Ariadna Rando-Segura
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain;
- Department of Microbiology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Tomas Pumarola
- Department of Microbiology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
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23
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Kitsou K, Iliopoulou M, Spoulou V, Lagiou P, Magiorkinis G. Viral Causality of Human Cancer and Potential Roles of Human Endogenous Retroviruses in the Multi-Omics Era: An Evolutionary Epidemiology Review. Front Oncol 2021; 11:687631. [PMID: 34778024 PMCID: PMC8586426 DOI: 10.3389/fonc.2021.687631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
Being responsible for almost 12% of cancers worldwide, viruses are among the oldest known and most prevalent oncogenic agents. The quality of the evidence for the in vivo tumorigenic potential of microorganisms varies, thus accordingly, viruses were classified in 4 evidence-based categories by the International Agency for Research on Cancer in 2009. Since then, our understanding of the role of viruses in cancer has significantly improved, firstly due to the emergence of high throughput sequencing technologies that allowed the “brute-force” recovery of unknown viral genomes. At the same time, multi-omics approaches unravelled novel virus-host interactions in stem-cell biology. We now know that viral elements, either exogenous or endogenous, have multiple sometimes conflicting roles in human pathophysiology and the development of cancer. Here we integrate emerging evidence on viral causality in human cancer from basic mechanisms to clinical studies. We analyze viral tumorigenesis under the scope of deep-in-time human-virus evolutionary relationships and critically comment on the evidence through the eyes of clinical epidemiology, firstly by reviewing recognized oncoviruses and their mechanisms of inducing tumorigenesis, and then by examining the potential role of integrated viruses in our genome in the process of carcinogenesis.
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Affiliation(s)
- Konstantina Kitsou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Immunobiology and Vaccinology Research Laboratory, First Department of Peadiatrics, "Aghia Sophia" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Iliopoulou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Vana Spoulou
- Immunobiology and Vaccinology Research Laboratory, First Department of Peadiatrics, "Aghia Sophia" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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Curty G, Iñiguez LP, Nixon DF, Soares MA, de Mulder Rougvie M. Hallmarks of Retroelement Expression in T-Cells Treated With HDAC Inhibitors. FRONTIERS IN VIROLOGY 2021. [DOI: 10.3389/fviro.2021.756635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A wide spectrum of drugs have been assessed as latency reversal agents (LRA) to reactivate HIV-1 from cellular reservoirs and aid in viral eradication strategies. Histone deacetylase inhibitors (HDACi) have been studied in vitro and in vivo as potential candidates for HIV-1 latency reversion. Suberoylanilide hydroxamic acid (SAHA) and romidepsin (RMD) are two HDACi able to reverse HIV latency, however studies of potential off-target effects on retroelement expression have been limited. Retroelements constitute a large portion of the human genome, and some are considered “fossil viruses” as they constitute remnants of ancient exogenous retroviruses infections. Retroelements are reactivated during certain disease conditions like cancer or during HIV-1 infection. In this study, we analyzed differential expression of retroelements using publicly available RNA-seq datasets (GSE102187 and GSE114883) obtained from uninfected CD4+, and HIV-1 latently infected CD4+ T-cells treated with HDACi (SAHA and RMD). We found a total of 712 and 1,380 differentially expressed retroelements in HIV-1 latently infected cells following a 24-h SAHA and RMD treatment, respectively. Furthermore, we found that 531 retroelement sequences (HERVs and L1) were differentially expressed under both HDACi treatments, while 1,030 HERV/L1 were exclusively regulated by each drug. Despite differences in specific HERV loci expression, the overall pattern at the HERV family level was similar for both treatments. We detected differential expression of full-length HERV families including HERV-K, HERV-W and HERV-H. Furthermore, we analyzed the link between differentially expressed retroelements and nearby immune genes. TRAF2 (TNF receptor) and GBP5 (inflammasome activator) were upregulated in HDACi treated samples and their expression was correlated with nearby HERV (MERV101_9q34.3) and L1 (L1FLnI_1p22.2k, L1FLnI_1p22.2j, L1FLnI_1p22.2i). Our findings suggest that HDACi have an off-target effect on the expression of retroelements and on the expression of immune associated genes in treated CD4+ T-cells. Furthermore, our data highlights the importance of exploring the interaction between HIV-1 and retroelement expression in LRA treated samples to understand their role and impact on “shock and kill” strategies and their potential use as reservoir biomarkers.
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25
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Tavakolian S, Goudarzi H, Moridi A, Faghihloo E. Analysing the HERV-K env, np9, rec and gag expression in cervical tissues. New Microbes New Infect 2021; 44:100936. [PMID: 34621524 PMCID: PMC8484807 DOI: 10.1016/j.nmni.2021.100936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Cervical cancer is considered to be the fourth common cancer. It is assumed that numerous risk factors, especially infectious ones, can have a detrimental effect on cervical cancer. In this study, we evaluated the expression of Herv-K env, np9, rec and gag in cervical tissues. After RNA extraction and cDNA sensitizing of 12 cervical cancer tissues and CIN3, 51 CIN1,2 and 18 normal ones, Herv-K env, np9, rec and gag were assessed using quantitative real-time PCR analysis. There was a decrease in the level of HERV-K env expression in cervical cancer and CIN 1-3 in compression with normal tissues. Cervical cancer and CIN3 indicated the most increase in expression. Meanwhile, we observed an increase in gag and rec expression in CIN 1,2; although cervical cancer and CIN 3 had a decrease in rec and gag expression, we did not report any changes in np expression. In conclusion, given the relationship between HERV-associated genes and cervical cancer, our study suggests that these genes can be useful for cancer diagnosis. However, further investigations are needed to provide a better perspective about the effectiveness of these genes in the diagnostic strategies of gastrointestinal cancer. These results are just an observation that could open a wider investigation to test the correlation between the expression of these genes and cervical cancer.
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Affiliation(s)
- S Tavakolian
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - H Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - A Moridi
- Clinical Research Development Center, Mahdiyeh Educational Hospital, Shahid Beheshti University Of Medical Sciences, Tehran, Iran
| | - E Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Li X, Guo Y, Li H, Huang X, Pei Z, Wang X, Liu Y, Jia L, Li T, Bao Z, Wang X, Han L, Han J, Li J, Li L. Infection by Diverse HIV-1 Subtypes Leads to Different Elevations in HERV-K Transcriptional Levels in Human T Cell Lines. Front Microbiol 2021; 12:662573. [PMID: 34079529 PMCID: PMC8165174 DOI: 10.3389/fmicb.2021.662573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
Human endogenous retroviruses (HERVs) make up ~8% of the human genome, and for millions of years, they have been subject to strict biological regulation. Many HERVs do not participate in normal physiological activities in the body. However, in some pathological conditions, they can be abnormally activated. For example, HIV infection can cause abnormal activation of HERVs, and under different infection conditions, HERV expression may be different. We observed significant differences in HERV-K transcription levels among HIV-1 subtype-infected individuals. The transcriptional levels in the HERV-K gag region were significantly increased in HIV-1 B subtype-infected patients, while the transcriptional levels in the HERV-K pol region were significantly increased in CRF01_AE and CRF07_BC subtype-infected patients. In vitro, the transcriptional levels of HEVR-K were increased 5-fold and 15-fold in MT2 cells transfected with two different HIV-1 strains (B and CRF01_AE, respectively). However, there was no significant difference in transcriptional levels among regions of HERV-K. When MT2 cells were infected with different subtypes of HIV-1 Tat proteins (B, CRF01_AE), which is constructed by lentiviruses, and the transcription levels of HERV-K were increased 4-fold and 2-fold, respectively. Thus, different subtypes of HIV-1 have different effects on HERV-K transcription levels, which may be caused by many factors, not only Tat protein.
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Affiliation(s)
- Xi Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yaolin Guo
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaofeng Huang
- The Second Medical Center, National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Zhichao Pei
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tianyi Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zuoyi Bao
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaorui Wang
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Key Laboratory of Infectious Disease Control and Prevention in Universities of Shandong, Jinan, China
| | - Leilei Han
- School of Public Health and Affiliated Shijiazhuang Fifth Hospital, North China University of Science and Technology, Tangshan, China
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Department of AIDS Research, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Gröger V, Emmer A, Staege MS, Cynis H. Endogenous Retroviruses in Nervous System Disorders. Pharmaceuticals (Basel) 2021; 14:ph14010070. [PMID: 33467098 PMCID: PMC7829834 DOI: 10.3390/ph14010070] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 02/06/2023] Open
Abstract
Human endogenous retroviruses (HERV) have been implicated in the pathogenesis of several nervous system disorders including multiple sclerosis and amyotrophic lateral sclerosis. The toxicity of HERV-derived RNAs and proteins for neuronal cells has been demonstrated. The involvement of HERV in the pathogenesis of currently incurable diseases might offer new treatment strategies based on the inhibition of HERV activities by small molecules or therapeutic antibodies.
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Affiliation(s)
- Victoria Gröger
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, 06120 Halle (Saale), Germany;
| | - Alexander Emmer
- Department of Neurology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Martin S. Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Correspondence: (M.S.S.); (H.C.); Tel.: +49-345-557-7280 (M.S.S.); +49-345-13142835 (H.C.)
| | - Holger Cynis
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology, 06120 Halle (Saale), Germany;
- Correspondence: (M.S.S.); (H.C.); Tel.: +49-345-557-7280 (M.S.S.); +49-345-13142835 (H.C.)
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28
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Srinivasachar Badarinarayan S, Shcherbakova I, Langer S, Koepke L, Preising A, Hotter D, Kirchhoff F, Sparrer KMJ, Schotta G, Sauter D. HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression. Nucleic Acids Res 2020; 48:10890-10908. [PMID: 33021676 PMCID: PMC7641743 DOI: 10.1093/nar/gkaa832] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
Although endogenous retroviruses (ERVs) are known to harbor cis-regulatory elements, their role in modulating cellular immune responses remains poorly understood. Using an RNA-seq approach, we show that several members of the ERV9 lineage, particularly LTR12C elements, are activated upon HIV-1 infection of primary CD4+ T cells. Intriguingly, HIV-1-induced ERVs harboring transcription start sites are primarily found in the vicinity of immunity genes. For example, HIV-1 infection activates LTR12C elements upstream of the interferon-inducible genes GBP2 and GBP5 that encode for broad-spectrum antiviral factors. Reporter assays demonstrated that these LTR12C elements drive gene expression in primary CD4+ T cells. In line with this, HIV-1 infection triggered the expression of a unique GBP2 transcript variant by activating a cryptic transcription start site within LTR12C. Furthermore, stimulation with HIV-1-induced cytokines increased GBP2 and GBP5 expression in human cells, but not in macaque cells that naturally lack the GBP5 gene and the LTR12C element upstream of GBP2. Finally, our findings suggest that GBP2 and GBP5 have already been active against ancient viral pathogens as they suppress the maturation of the extinct retrovirus HERV-K (HML-2). In summary, our findings uncover how human cells can exploit remnants of once-infectious retroviruses to regulate antiviral gene expression.
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Affiliation(s)
| | - Irina Shcherbakova
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
| | - Simon Langer
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Andrea Preising
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Gunnar Schotta
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
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29
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O'Carroll IP, Fan L, Kroupa T, McShane EK, Theodore C, Yates EA, Kondrup B, Ding J, Martin TS, Rein A, Wang YX. Structural Mimicry Drives HIV-1 Rev-Mediated HERV-K Expression. J Mol Biol 2020; 432:166711. [PMID: 33197463 DOI: 10.1016/j.jmb.2020.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 10/23/2022]
Abstract
Expression of the Human Endogenous Retrovirus Type K (HERV-K), the youngest and most active HERV, has been associated with various cancers and neurodegenerative diseases. As in all retroviruses, a fraction of HERV-K transcripts is exported from the nucleus in unspliced or incompletely spliced forms to serve as templates for translation of viral proteins. In a fraction of HERV-K loci (Type 2 proviruses), nuclear export of the unspliced HERV-K mRNA appears to be mediated by a cis-acting signal on the mRNA, the RcRE, and the protein Rec-these are analogous to the RRE-Rev system in HIV-1. Interestingly, the HIV-1 Rev protein is able to mediate the nuclear export of the HERV-K RcRE, contributing to elevated HERV-K expression in HIV-infected patients. We aimed to understand the structural basis for HIV Rev-HERV-K RcRE recognition. We examined the conformation of the RcRE RNA in solution using small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM). We found that the 433-nt long RcRE can assume folded or extended conformations as observed by AFM. SAXS analysis of a truncated RcRE variant revealed an "A"-shaped topological structure similar to the one previously reported for the HIV-1 RRE. The effect of the overall topology was examined using several deletion variants. SAXS and biochemical analyses demonstrated that the "A" shape is necessary for efficient Rev-RcRE complex formation in vitro and nuclear export activity in cell culture. The findings provide insight into the mechanism of HERV-K expression and a structural explanation for HIV-1 Rev-mediated expression of HERV-K in HIV-infected patients. IMPORTANCE: Expression of the human endogenous retrovirus type K (HERV-K) has been associated with various cancers and autoimmune diseases. Nuclear export of both HIV-1 and HERV-K mRNAs is dependent on the interaction between a small viral protein (Rev in HIV-1 and Rec in HERV-K) and a region on the mRNA (RRE in HIV-1 and RcRE in HERV-K). HIV-1 Rev is able to mediate the nuclear export of RcRE-containing HERV-K mRNAs, which contributes to elevated production of HERV-K proteins in HIV-infected patients. We report the solution conformation of the RcRE RNA-the first three-dimensional topological structure for a HERV molecule-and find that the RcRE resembles the HIV-1 nuclear export signal, RRE. The finding reveals the structural basis for the increased HERV-K expression observed in HIV-infected patients. Elevated HERV expression, mediated by HIV infection or other stressors, can have various HERV-related biological consequences. The findings provide structural insight for regulation of HERV-K expression.
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Affiliation(s)
- Ina P O'Carroll
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA.
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of the National Cancer Institute, Frederick, MD 21702, USA
| | - Tomáš Kroupa
- HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Erin K McShane
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA
| | - Christophe Theodore
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA
| | - Elizabeth A Yates
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA
| | - Benjamin Kondrup
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA
| | - Jienyu Ding
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Tyler S Martin
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA
| | - Alan Rein
- HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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30
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Mustelin T, Ukadike KC. How Retroviruses and Retrotransposons in Our Genome May Contribute to Autoimmunity in Rheumatological Conditions. Front Immunol 2020; 11:593891. [PMID: 33281822 PMCID: PMC7691656 DOI: 10.3389/fimmu.2020.593891] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/19/2020] [Indexed: 12/14/2022] Open
Abstract
More than 200 human disorders include various manifestations of autoimmunity. The molecular events that lead to these diseases are still incompletely understood and their causes remain largely unknown. Numerous potential triggers of autoimmunity have been proposed over the years, but very few of them have been conclusively confirmed or firmly refuted. Viruses have topped the lists of suspects for decades, and it seems that many viruses, including those of the Herpesviridae family, indeed can influence disease initiation and/or promote exacerbations by a number of mechanisms that include prolonged anti-viral immunity, immune subverting factors, and mechanisms, and perhaps “molecular mimicry”. However, no specific virus has yet been established as being truly causative. Here, we discuss a different, but perhaps mechanistically related possibility, namely that retrotransposons or retroviruses that infected us in the past and left a lasting copy of themselves in our genome still can provoke an escalating immune response that leads to autoimmune disease. Many of these loci still encode for retroviral proteins that have retained some, or all, of their original functions. Importantly, these endogenous proviruses cannot be eliminated by the immune system the way it can eliminate exogenous viruses. Hence, if not properly controlled, they may drive a frustrated and escalating chronic, or episodic, immune response to the point of a frank autoimmune disorder. Here, we discuss the evidence and the proposed mechanisms, and assess the therapeutic options that emerge from the current understanding of this field.
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Affiliation(s)
- Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Kennedy C Ukadike
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
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31
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Curty G, Beckerle GA, Iñiguez LP, Furler RL, de Carvalho PS, Marston JL, Champiat S, Heymann JJ, Ormsby CE, Reyes-Terán G, Soares MA, Nixon DF, Bendall ML, Leal FE, de Mulder Rougvie M. Human Endogenous Retrovirus Expression Is Upregulated in the Breast Cancer Microenvironment of HIV Infected Women: A Pilot Study. Front Oncol 2020; 10:553983. [PMID: 33194615 PMCID: PMC7649802 DOI: 10.3389/fonc.2020.553983] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/17/2020] [Indexed: 12/21/2022] Open
Abstract
In people living with HIV (PLWH), chronic inflammation can lead to cancer initiation and progression, besides driving a dysregulated and diminished immune responsiveness. HIV infection also leads to increased transcription of Human Endogenous Retroviruses (HERVs), which could increase an inflammatory environment and create a tumor growth suppressive environment with high expression of pro-inflammatory cytokines. In order to determine the impact of HIV infection to HERV expression on the breast cancer microenvironment, we sequenced total RNA from formalin-fixed paraffin-embedded (FFPE) breast cancer samples of women HIV-negative and HIV-positive for transcriptome and retrotranscriptome analyses. We performed RNA extraction from FFPE samples, library preparation and total RNA sequencing (RNA-seq). The RNA-seq analysis shows 185 differentially expressed genes: 181 host genes (178 upregulated and three downregulated) and four upregulated HERV transcripts in HIV-positive samples. We also explored the impact of HERV expression in its neighboring breast cancer development genes (BRCA1, CCND1, NBS1/NBN, RAD50, KRAS, PI3K/PIK3CA) and in long non-coding RNA expression (AC060780.1, also known as RP11-242D8.1). We found a significant positive association of HERV expression with RAD50 and with AC060780.1, which suggest a possible role of HERV in regulating breast cancer genes from PLWH with breast cancer. In addition, we found immune system, extracellular matrix organization and metabolic signaling genes upregulated in HIV-positive breast cancer. In conclusion, our findings provide evidence of transcriptional and retrotranscriptional changes in breast cancer from PLWH compared to non-HIV breast cancer, including dysregulation of HERVs, suggesting an indirect effect of the virus on the breast cancer microenvironment.
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Affiliation(s)
- Gislaine Curty
- Oncovirology Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Greta A Beckerle
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Luis P Iñiguez
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Robert L Furler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | | | - Jez L Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Stephane Champiat
- Drug Development Department (DITEP), Gustave Roussy, Paris-Saclay University, Villejuif, France
| | - Jonas J Heymann
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Christopher E Ormsby
- Center for Research in Infectious Diseases (CIENI), National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Center for Research in Infectious Diseases (CIENI), National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Marcelo A Soares
- Oncovirology Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Fabio E Leal
- Oncovirology Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Miguel de Mulder Rougvie
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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32
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Geis FK, Goff SP. Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview. Viruses 2020; 12:v12080884. [PMID: 32823517 PMCID: PMC7472088 DOI: 10.3390/v12080884] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Almost half of the human genome is made up of transposable elements (TEs), and about 8% consists of endogenous retroviruses (ERVs). ERVs are remnants of ancient exogenous retrovirus infections of the germ line. Most TEs are inactive and not detrimental to the host. They are tightly regulated to ensure genomic stability of the host and avoid deregulation of nearby gene loci. Histone-based posttranslational modifications such as H3K9 trimethylation are one of the main silencing mechanisms. Trim28 is one of the identified master regulators of silencing, which recruits most prominently the H3K9 methyltransferase Setdb1, among other factors. Sumoylation and ATP-dependent chromatin remodeling factors seem to contribute to proper localization of Trim28 to ERV sequences and promote Trim28 interaction with Setdb1. Additionally, DNA methylation as well as RNA-mediated targeting of TEs such as piRNA-based silencing play important roles in ERV regulation. Despite the involvement of ERV overexpression in several cancer types, autoimmune diseases, and viral pathologies, ERVs are now also appreciated for their potential positive role in evolution. ERVs can provide new regulatory gene elements or novel binding sites for transcription factors, and ERV gene products can even be repurposed for the benefit of the host.
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Affiliation(s)
- Franziska K. Geis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
| | - Stephen P. Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
- Correspondence: ; Tel.: +1-212-305-3794
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Salavatiha Z, Soleimani-Jelodar R, Jalilvand S. The role of endogenous retroviruses-K in human cancer. Rev Med Virol 2020; 30:1-13. [PMID: 32734655 DOI: 10.1002/rmv.2142] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022]
Abstract
It is known that human endogenous retroviruses (HERVs) constitute almost 8% of the human genome. Although the expression of HERVs from the human genome is tightly regulated, different exogenous and endogenous factors could trigger HERV activation. Aberrant expression of different HERVs may potentially cause a variety of diseases such as neurological and autoimmune diseases as well as cancer. It is suggested that HERV-K can induce cancer through different mechanisms that are discussed. The interplay between some tumor viruses and HERV-K seems to be a key player in progression of viral-associated cancers because elevated levels of Rec and Np9 proteins are observed in several cancers. The frequent over expression of HERV proteins and some specific antibodies in cancer cells could be considered as suitable prognostic and therapeutic biomarkers in diagnosis and treatment of cancers. The expression of HERV proteins in cancers and development of immune responses against them may also be used as targets for cancer immunotherapy. Further studies are warranted to evaluate the role of HERVs in cancer formation and use of different HERV proteins in developing new diagnostic and therapeutic approaches for cancer treatments.
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Affiliation(s)
- Zahra Salavatiha
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Rahim Soleimani-Jelodar
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Comprehensive Analysis of HERV Transcriptome in HIV+ Cells: Absence of HML2 Activation and General Downregulation of Individual HERV Loci. Viruses 2020; 12:v12040481. [PMID: 32340287 PMCID: PMC7232394 DOI: 10.3390/v12040481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 01/08/2023] Open
Abstract
Human endogenous retrovirus (HERV) expression is currently studied for its possible activation by HIV infection. In this context, the HERV-K(HML2) group is the most investigated: it has been proposed that HIV-1 infection can prompt HML2 transcription, and that HML2 proteins can affect HIV-1 replication, either complementing HIV or possibly influencing antiretroviral therapy. However, little information is available on the expression of other HERV groups in HIV infection. In the present study, we used a bioinformatics pipeline to investigate the transcriptional modulation of approximately 3250 well-characterized HERV loci, comparing their expression in a public RNA-seq profile, including a HIV-1-infected and a control T cell culture. In our pilot study, we found approximately 200 HERV loci belonging to 35 HERV groups that were expressed in one or both conditions, with transcripts per million (TPM) values from 1 to >500. Intriguingly, HML2 elements constituted only the 3% of expressed HERV loci, and in most cases (160) HERV expression was downregulated in the HIV-infected culture, showing from a 1- to 14-fold decrease as compared to uninfected cells. HERV transcriptome has been inferred de novo and employed to predict a total of about 950 HERV open reading frames (ORFs). These have been validated according to the coding potential and estimated abundance of the corresponding transcripts, leading to a set of 57 putative proteins potentially encoded by 23 HERV loci. Analysis showed that some individual loci have a coding potential that deserves further investigation. Among them, a HML6 provirus at locus 19q13.43 was predicted to produce a transcript showing the highest TPM among HERV-derived transcripts, being upregulated in HIV+ cells and inferred to produce Gag and Env puteins with possible biological activity.
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35
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Talotta R, Atzeni F, Laska MJ. Retroviruses in the pathogenesis of systemic lupus erythematosus: Are they potential therapeutic targets? Autoimmunity 2020; 53:177-191. [PMID: 32321325 DOI: 10.1080/08916934.2020.1755962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The pathogenesis of systemic lupus erythematosus (SLE) is characterised by the hyper-activation of immunologic pathways related to the antiviral response. Exogenous and endogenous retroviruses, by integrating their DNA templates in the host cell genome, may epigenetically control the transcription of genes involved in the immune response. Furthermore, their nucleic acids or neo-synthesized proteins could stimulate the sensor molecules placed upstream the inflammatory cascade. Exogenous retroviruses, like human immunodeficiency virus, have been associated to SLE-like manifestations or to a fair SLE diagnosis. In addition, there is some evidence confirming a pathogenic role of human endogenous retroviruses in SLE. In line with these data, the use of antiretroviral agents could represent an attractive opportunity in the future therapeutic algorithms of this disease, but studies are still missing.
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Affiliation(s)
- Rossella Talotta
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University Hospital "Gaetano Martino", Messina, Italy
| | - Fabiola Atzeni
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University Hospital "Gaetano Martino", Messina, Italy
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36
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DeMarino C, Cowen M, Pleet ML, Pinto DO, Khatkar P, Erickson J, Docken SS, Russell N, Reichmuth B, Phan T, Kuang Y, Anderson DM, Emelianenko M, Kashanchi F. Differences in Transcriptional Dynamics Between T-cells and Macrophages as Determined by a Three-State Mathematical Model. Sci Rep 2020; 10:2227. [PMID: 32042107 PMCID: PMC7010665 DOI: 10.1038/s41598-020-59008-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/17/2020] [Indexed: 12/18/2022] Open
Abstract
HIV-1 viral transcription persists in patients despite antiretroviral treatment, potentially due to intermittent HIV-1 LTR activation. While several mathematical models have been explored in the context of LTR-protein interactions, in this work for the first time HIV-1 LTR model featuring repressed, intermediate, and activated LTR states is integrated with generation of long (env) and short (TAR) RNAs and proteins (Tat, Pr55, and p24) in T-cells and macrophages using both cell lines and infected primary cells. This type of extended modeling framework allows us to compare and contrast behavior of these two cell types. We demonstrate that they exhibit unique LTR dynamics, which ultimately results in differences in the magnitude of viral products generated. One of the distinctive features of this work is that it relies on experimental data in reaction rate computations. Two RNA transcription rates from the activated promoter states are fit by comparison of experimental data to model predictions. Fitting to the data also provides estimates for the degradation/exit rates for long and short viral RNA. Our experimentally generated data is in reasonable agreement for the T-cell as well macrophage population and gives strong evidence in support of using the proposed integrated modeling paradigm. Sensitivity analysis performed using Latin hypercube sampling method confirms robustness of the model with respect to small parameter perturbations. Finally, incorporation of a transcription inhibitor (F07#13) into the governing equations demonstrates how the model can be used to assess drug efficacy. Collectively, our model indicates transcriptional differences between latently HIV-1 infected T-cells and macrophages and provides a novel platform to study various transcriptional dynamics leading to latency or activation in numerous cell types and physiological conditions.
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MESH Headings
- Anti-HIV Agents/pharmacology
- Anti-HIV Agents/therapeutic use
- Cell Line
- Drug Resistance, Viral/drug effects
- Drug Resistance, Viral/genetics
- Drug Resistance, Viral/immunology
- Gene Expression Regulation, Viral/immunology
- HIV Infections/blood
- HIV Infections/drug therapy
- HIV Infections/immunology
- HIV Long Terminal Repeat/genetics
- HIV-1/drug effects
- HIV-1/genetics
- HIV-1/immunology
- Humans
- Macrophages/immunology
- Macrophages/virology
- Models, Genetic
- Models, Immunological
- Primary Cell Culture
- RNA, Viral/genetics
- RNA, Viral/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/virology
- Transcription, Genetic/drug effects
- Transcription, Genetic/immunology
- Virus Replication/drug effects
- Virus Replication/genetics
- Virus Replication/immunology
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Affiliation(s)
- Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Maria Cowen
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Michelle L Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Daniel O Pinto
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Pooja Khatkar
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - James Erickson
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Steffen S Docken
- Department of Mathematics, University of California Davis, Davis, CA, USA
| | - Nicholas Russell
- Department of Mathematical Sciences, University of Delaware, Newark, DE, USA
| | - Blake Reichmuth
- Department of Mathematical Sciences, George Mason University, Fairfax, VA, USA
| | - Tin Phan
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA
| | - Yang Kuang
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA
| | - Daniel M Anderson
- Department of Mathematical Sciences, George Mason University, Fairfax, VA, USA.
| | - Maria Emelianenko
- Department of Mathematical Sciences, George Mason University, Fairfax, VA, USA.
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA.
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Gray LR, Jackson RE, Jackson PEH, Bekiranov S, Rekosh D, Hammarskjöld ML. HIV-1 Rev interacts with HERV-K RcREs present in the human genome and promotes export of unspliced HERV-K proviral RNA. Retrovirology 2019; 16:40. [PMID: 31842941 PMCID: PMC6916052 DOI: 10.1186/s12977-019-0505-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 12/07/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The HERV-K (HML-2) viruses are the youngest of the human endogenous retroviruses. They are present as several almost complete proviral copies and numerous fragments in the human genome. Many HERV-K proviruses express a regulatory protein Rec, which binds to an element present in HERV-K mRNAs called the RcRE. This interaction is necessary for the nucleo-cytoplasmic export and expression of HERV-K mRNAs that retain introns and plays a role analogous to that of Rev and the RRE in HIV replication. There are over 900 HERV-K RcREs distributed throughout the human genome. Thus, it was of interest to determine if Rev could functionally interact with selected RcRE elements that map either to HERV-K proviruses or human gene regions. This interaction would have the potential to alter the expression of both HERV-K mRNAs and cellular mRNAs during HIV-1 infection. RESULTS In this study we employed a combination of RNAseq, bioinformatics and cell-based functional assays. Potential RcREs were identified through a number of bioinformatic approaches. They were then tested for their ability to promote export and translation of a reporter mRNA with a retained intron in conjunction with Rev or Rec. Some of the selected elements functioned well with either Rev, Rec or both, whereas some showed little or no function. Rev function on individual RcREs varied and was also dependent on the Rev sequence. We also performed RNAseq on total and cytoplasmic RNA isolated from SupT1 cells expressing HIV Rev, with or without Tat, or HERV-K Rec. Proviral mRNA from three HERV-K loci (4p16.1b, 22q11.23 and most significantly 3q12.3) accumulated in the cytoplasm in the presence of Rev or Tat and Rev, but not Rec. Consistent with this, the 3' RcRE from 3q12.3 functioned well with HIV-Rev in our reporter assay. In contrast, this RcRE showed little or no function with Rec. CONCLUSIONS The HIV Rev protein can functionally interact with many RcREs present in the human genome, depending on the RcRE sequence, as well as the Rev sequence. This leads to export of some of the HERV-K proviral mRNAs and also has the potential to change the expression of non-viral genes.
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Affiliation(s)
- Laurie R Gray
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Rachel E Jackson
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Patrick E H Jackson
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, 22908, USA
| | - Stefan Bekiranov
- Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, 22908, USA
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Marie-Louise Hammarskjöld
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA.
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Abstract
PURPOSE OF THE REVIEW The aim of this review is to discuss recent data pointing at an involvement of human endogenous retroviruses (HERVs) in type 1 diabetes (T1D) onset and progression. RECENT FINDINGS The envelope protein of HERV-W family, named HERV-W-Env, was detected in pancreata from T1D patients and was shown to display pro-inflammatory properties and direct toxicity toward pancreatic beta cells. The etiopathogenesis of T1D remains elusive, even if conventional environmental viral infections have been recurrently involved. Nonetheless, a new category of pathogens may provide the missing link between genetic susceptibility and environmental factors long thought to contribute to T1D onset. A number of studies have now shown that HERV sequences, which are normally inactivated or repressed in the human genome, could be activated by environmental viruses. Thus, if similarly activated by viruses associated with T1D, disregarded HERV genes may underlie T1D genetic susceptibility. Moreover, once expressed, HERV elements may display broad pathogenic properties, which identify them as potential new therapeutic targets.
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Affiliation(s)
- Sandrine Levet
- GeNeuro Innovation, 60 avenue Rockefeller, 69008 Lyon, France
| | - B. Charvet
- GeNeuro Innovation, 60 avenue Rockefeller, 69008 Lyon, France
| | - A. Bertin
- Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, Université Lille, F-59000 Lille, France
| | - A. Deschaumes
- Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, Université Lille, F-59000 Lille, France
| | - H. Perron
- GeNeuro Innovation, 60 avenue Rockefeller, 69008 Lyon, France
- Laboratoire des déficits immunitaires, University of Lyon, Lyon, France
- Plan-les-Ouates, GeNeuro SA, Geneva, Switzerland
| | - D. Hober
- Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, Université Lille, F-59000 Lille, France
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39
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Kaplan MH, Kaminski M, Estes JM, Gitlin SD, Zahn J, Elder JT, Tejasvi T, Gensterblum E, Sawalha AH, McGowan JP, Dosik MH, Direskeneli H, Direskeneli GS, Adebamowo SN, Adebamowo CA, Sajadi M, Contreras-Galindo R. Structural variation of centromeric endogenous retroviruses in human populations and their impact on cutaneous T-cell lymphoma, Sézary syndrome, and HIV infection. BMC Med Genomics 2019; 12:58. [PMID: 31046767 PMCID: PMC6498702 DOI: 10.1186/s12920-019-0505-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/15/2019] [Indexed: 12/16/2022] Open
Abstract
Background Human Endogenous Retroviruses type K HML-2 (HK2) are integrated into 117 or more areas of human chromosomal arms while two newly discovered HK2 proviruses, K111 and K222, spread extensively in pericentromeric regions, are the first retroviruses discovered in these areas of our genome. Methods We use PCR and sequencing analysis to characterize pericentromeric K111 proviruses in DNA from individuals of diverse ethnicities and patients with different diseases. Results We found that the 5′ LTR-gag region of K111 proviruses is missing in certain individuals, creating pericentromeric instability. K111 deletion (−/− K111) is seen in about 15% of Caucasian, Asian, and Middle Eastern populations; it is missing in 2.36% of African individuals, suggesting that the −/− K111 genotype originated out of Africa. As we identified the −/−K111 genotype in Cutaneous T-cell lymphoma (CTCL) cell lines, we studied whether the −/−K111 genotype is associated with CTCL. We found a significant increase in the frequency of detection of the −/−K111 genotype in Caucasian patients with severe CTCL and/or Sézary syndrome (n = 35, 37.14%), compared to healthy controls (n = 160, 15.6%) [p = 0.011]. The −/−K111 genotype was also found to vary in HIV-1 infection. Although Caucasian healthy individuals have a similar frequency of detection of the −/− K111 genotype, Caucasian HIV Long-Term Non-Progressors (LTNPs) and/or elite controllers, have significantly higher detection of the −/−K111 genotype (30.55%; n = 36) than patients who rapidly progress to AIDS (8.5%; n = 47) [p = 0.0097]. Conclusion Our data indicate that pericentromeric instability is associated with more severe CTCL and/or Sézary syndrome in Caucasians, and appears to allow T-cells to survive lysis by HIV infection. These findings also provide new understanding of human evolution, as the −/−K111 genotype appears to have arisen out of Africa and is distributed unevenly throughout the world, possibly affecting the severity of HIV in different geographic areas. Electronic supplementary material The online version of this article (10.1186/s12920-019-0505-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mark H Kaplan
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mark Kaminski
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Judith M Estes
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Scott D Gitlin
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Joseph Zahn
- Division of Dermatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - James T Elder
- Division of Dermatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Trilokraj Tejasvi
- Division of Dermatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Elizabeth Gensterblum
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joseph Patrick McGowan
- Division of Infectious Diseases, The Feinstein Institute for Medical research, Manhasset, NY, 11030, USA
| | | | - Haner Direskeneli
- Division of Rheumatology, School of Medicine, Marmara University, Istanbul, Turkey
| | | | - Sally N Adebamowo
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Clement A Adebamowo
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Mohammad Sajadi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Rafael Contreras-Galindo
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA. .,Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.
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40
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Chan SM, Sapir T, Park SS, Rual JF, Contreras-Galindo R, Reiner O, Markovitz DM. The HERV-K accessory protein Np9 controls viability and migration of teratocarcinoma cells. PLoS One 2019; 14:e0212970. [PMID: 30818388 PMCID: PMC6394991 DOI: 10.1371/journal.pone.0212970] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/12/2019] [Indexed: 11/19/2022] Open
Abstract
Human endogenous retroviruses are remnants of ancient germline infections that make up approximately 8% of the modern human genome. The HERV-K (HML-2) family is one of the most recent entrants into the human germline, these viruses appear to be transcriptionally active, and HERV-K viral like particles (VLPs) are found in cell lines from a number of human malignancies. HERV-K VLPs were first found to be produced in teratocarcinoma cell lines, and since then teratocarcinoma has been thought of as the classical model for HERV-Ks, with the NCCIT teratocarcinoma cell line particularly known to produce VLPs. Treatment for teratocarcinoma has progressed since its discovery, with improved prognosis for patients. Since the introduction of platinum based therapy, first year survival has greatly improved even with disseminated disease; however, it is estimated that 20% to 30% of patients present with metastatic germ cell tumor relapse following initial treatments. Also, the toxicity associated with the use of chemotherapeutic agents used to treat germ cell tumors is still a major concern. In this study, we show that the depletion of the HERV-K accessory protein Np9 increases the sensitivity of NCCIT teratocarcinoma cells to bleomycin and cisplatin. While decreasing the expression of Np9 had only a modest effect on the baseline viability of the cells, the reduced expression of Np9 increased the sensitivity of the teratocarcinoma cells to environmental (serum starvation) and chemical (chemotherapeutic) stresses. Np9 is also essential to the migration of NCCIT teratocarcinoma cells: in a wound closure assay, reduced expression of Np9 resulted in cells migrating into the wound at a slower rate, whereas reintroduction of Np9 resulted in NCCIT cells migrating back into the wound in a manner similar to the control. These findings support the implication that the HERV-K accessory protein Np9 has oncogenic potential.
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Affiliation(s)
- Susana M. Chan
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tamar Sapir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sung-Soo Park
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jean-François Rual
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rafael Contreras-Galindo
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - David M. Markovitz
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Graduate Program in Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- Cancer Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
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41
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Broecker F, Moelling K. Evolution of Immune Systems From Viruses and Transposable Elements. Front Microbiol 2019; 10:51. [PMID: 30761103 PMCID: PMC6361761 DOI: 10.3389/fmicb.2019.00051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022] Open
Abstract
Virus-derived sequences and transposable elements constitute a substantial portion of many cellular genomes. Recent insights reveal the intimate evolutionary relationship between these sequences and various cellular immune pathways. At the most basic level, superinfection exclusion may be considered a prototypical virus-mediated immune system that has been described in both prokaryotes and eukaryotes. More complex immune mechanisms fully or partially derived from mobile genetic elements include CRISPR-Cas of prokaryotes and the RAG1/2 system of vertebrates, which provide immunological memory of foreign genetic elements and generate antibody and T cell receptor diversity, respectively. In this review, we summarize the current knowledge on the contribution of mobile genetic elements to the evolution of cellular immune pathways. A picture is emerging in which the various cellular immune systems originate from and are spread by viruses and transposable elements. Immune systems likely evolved from simple superinfection exclusion to highly complex defense strategies.
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Affiliation(s)
- Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Max Planck Institute for Molecular Genetics, Berlin, Germany
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42
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Chen J, Foroozesh M, Qin Z. Transactivation of human endogenous retroviruses by tumor viruses and their functions in virus-associated malignancies. Oncogenesis 2019; 8:6. [PMID: 30643113 PMCID: PMC6331641 DOI: 10.1038/s41389-018-0114-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/24/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023] Open
Abstract
Human endogenous retroviruses (HERVs), viral-associated sequences, are normal components of the human genome and account for 8–9% of our genome. These original provirus sequences can be transactivated to produce functional products. Several reactivated HERVs have been implicated in cancers and autoimmune diseases. An emerging body of literature supports a potential role of reactivated HERVs in viral diseases, in particular viral-associated neoplasms. Demystifying studies on the mechanism(s) of HERV reactivation could provide a new framework for the development of treatment and prevention strategies targeting virus-associated tumors. Although available data suggest that co-infection by other viruses, such as Kaposi’s Sarcoma-associated herpesvirus (KSHV) and Epstein–Barr virus (EBV), may be a crucial driving force to transactivate HERV boom, the mechanisms of action of viral infection-induced HERV transactivation and the contributions of HERVs to viral oncogenesis warrant further studies. Here, we review viral co-infection contributes to HERVs transactivation with focus on human viral infection associated oncogenesis and diseases, including the abilities of viral regulators involved in HERV reactivation, and physiological effects of viral infection response on HERV reactivation.
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Affiliation(s)
- Jungang Chen
- Department of Pathology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA
| | - Maryam Foroozesh
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, LA, 70125, USA
| | - Zhiqiang Qin
- Department of Pathology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA. .,Department of Pediatrics, East Hospital, Tongji University School of Medicine, 200120, Shanghai, China. .,Research Center for Translational Medicine and Key Laboratory of Arrhythmias, East Hospital, Tongji University School of Medicine, 200120, Shanghai, China.
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43
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Maze EA, Ham C, Kelly J, Ussher L, Almond N, Towers GJ, Berry N, Belshaw R. Variable Baseline Papio cynocephalus Endogenous Retrovirus (PcEV) Expression Is Upregulated in Acutely SIV-Infected Macaques and Correlated to STAT1 Expression in the Spleen. Front Immunol 2019; 10:901. [PMID: 31156613 PMCID: PMC6529565 DOI: 10.3389/fimmu.2019.00901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/08/2019] [Indexed: 01/12/2023] Open
Abstract
Retroviral replication leaves a DNA copy in the host cell chromosome, which over millions of years of infection of germline cells has led to 5% of the human genome sequence being comprised of endogenous retroviruses (ERVs), distributed throughout an estimated 100,000 loci. Over time these loci have accrued mutations such as premature stop codons that prevent continued replication. However, many loci remain both transcriptionally and translationally active and ERVs have been implicated in interacting with the host immune system. Using archived plasma and tissue samples from past macaque studies, experimentally infected with simian immunodeficiency virus (SIV), the expression of one macaque ERV in response to acute viral infection was explored together with a measure of the innate immune response. Specifically, RNA levels were determined for (a) Papio cynocephalus Endogenous Retrovirus (PcEV), an ERV (b) STAT1, a key gene in the interferon signaling pathway, and (c) SIV, an exogenous pathogen. Bioinformatic analysis of DNA sequences of the PcEV loci within the macaque reference genome revealed the presence of open reading frames (ORFs) consistent with potential protein expression but not ERV replication. Quantitative RT-PCR analysis of DNase-treated RNA extracts from plasma derived from acute SIV-infection detected PcEV RNA at low levels in 7 of 22 macaques. PcEV RNA levels were significantly elevated in PBMC and spleen samples recovered during acute SIV infection, but not in the thymus and lymph nodes. A strong positive correlation was identified between PcEV and STAT1 RNA levels in spleen samples recovered from SIV-positive macaques. One possibility is that SIV infection induces PcEV expression in infected lymphoid tissue that contributes to induction of an antiviral response.
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Affiliation(s)
- Emmanuel Atangana Maze
- School of Biomedical Sciences, Faculty of Medicine and Dentistry, University of Plymouth, Plymouth, United Kingdom.,Division of Infectious Disease Diagnostics, National Institute of Standards and Control (NIBSC), Potters Bar, United Kingdom
| | - Claire Ham
- Division of Infectious Disease Diagnostics, National Institute of Standards and Control (NIBSC), Potters Bar, United Kingdom
| | - Jack Kelly
- School of Biomedical Sciences, Faculty of Medicine and Dentistry, University of Plymouth, Plymouth, United Kingdom
| | - Lindsay Ussher
- School of Biomedical Sciences, Faculty of Medicine and Dentistry, University of Plymouth, Plymouth, United Kingdom
| | - Neil Almond
- Division of Infectious Disease Diagnostics, National Institute of Standards and Control (NIBSC), Potters Bar, United Kingdom
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Neil Berry
- Division of Infectious Disease Diagnostics, National Institute of Standards and Control (NIBSC), Potters Bar, United Kingdom
| | - Robert Belshaw
- School of Biomedical Sciences, Faculty of Medicine and Dentistry, University of Plymouth, Plymouth, United Kingdom
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44
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The Decrease in Human Endogenous Retrovirus-H Activity Runs in Parallel with Improvement in ADHD Symptoms in Patients Undergoing Methylphenidate Therapy. Int J Mol Sci 2018; 19:ijms19113286. [PMID: 30360480 PMCID: PMC6274708 DOI: 10.3390/ijms19113286] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 12/24/2022] Open
Abstract
Increasing scientific evidence demonstrated the deregulation of human endogenous retroviruses (HERVs) expression in complex diseases, such as cancer, autoimmune, psychiatric, and neurological disorders. The dynamic regulation of HERV activity and their responsiveness to a variety of environmental stimuli designate HERVs as genetic elements that could be modulated by drugs. Methylphenidate (MPH) is widely used in the treatment of attention deficit hyperactivity disorder (ADHD). The aim of this study was to evaluate the time course of human endogenous retrovirus H (HERV-H) expression in peripheral blood mononuclear cells (PBMCs) with respect to clinical response in ADHD patients undergoing MPH therapy. A fast reduction in HERV-H activity in ADHD patients undergoing MPH therapy was observed in parallel with an improvement in clinical symptoms. Moreover, when PBMCs from drug-naïve patients were cultured in vitro, HERV-H expression increased, while no changes in the expression levels were found in ADHD patients undergoing therapy. This suggests that MPH could affect the HERV-H activity and supports the hypothesis that high expression levels of HERV-H could be considered a distinctive trait of ADHD patients.
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45
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Garcia-Montojo M, Doucet-O'Hare T, Henderson L, Nath A. Human endogenous retrovirus-K (HML-2): a comprehensive review. Crit Rev Microbiol 2018; 44:715-738. [PMID: 30318978 DOI: 10.1080/1040841x.2018.1501345] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The human genome contains a large number of retroviral elements acquired over the process of evolution, some of which are specific to primates. However, as many of these are defective or silenced through epigenetic changes, they were historically considered "junk DNA" and their potential role in human physiology or pathological circumstances have been poorly studied. The most recently acquired, human endogenous retrovirus-K (HERV-K), has multiple copies in the human genome and some of them have complete open reading frames that are transcribed and translated, especially in early embryogenesis. Phylogenetically, HERV-K is considered a supergroup of viruses. One of the subtypes, termed HML-2, seems to be the most active and hence, it is the best studied. Aberrant expression of HML-2 in adult tissues has been associated with certain types of cancer and with neurodegenerative diseases. This review discusses the discovery of these viruses, their classification, structure, regulation and potential for replication, physiological roles, and their involvement in disease pathogenesis. Finally, it presents different therapeutic approaches being considered to target these viruses.
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Affiliation(s)
- Marta Garcia-Montojo
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Tara Doucet-O'Hare
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Lisa Henderson
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
| | - Avindra Nath
- a Section of Infections of the Nervous System , National Institute of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD , USA
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46
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Matteucci C, Balestrieri E, Argaw-Denboba A, Sinibaldi-Vallebona P. Human endogenous retroviruses role in cancer cell stemness. Semin Cancer Biol 2018; 53:17-30. [PMID: 30317035 DOI: 10.1016/j.semcancer.2018.10.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/30/2018] [Accepted: 10/05/2018] [Indexed: 12/18/2022]
Abstract
Cancer incidence and mortality, metastasis, drug resistance and recurrence are still the critical issues of oncological diseases. In this scenario, increasing scientific evidences demonstrate that the activation of human endogenous retroviruses (HERVs) is involved in the aggressiveness of tumors such as melanoma, breast, germ cell, renal, ovarian, liver and haematological cancers. In their dynamic regulation, HERVs have also proved to be important determinants of pluripotency in human embryonic stem cells (ESC) and of the reprogramming process of induced pluripotent stem cells (iPSCs). In many types of tumors, essential characteristics of aggressiveness have been associated with the achievement of stemness features, often accompanied with the identification of defined subpopulations, termed cancer stem cells (CSCs), which possess stem cell-like properties and sustain tumorigenesis. Indeed, CSCs show high self-renewal capacity with a peculiar potential in tumor initiation, progression, metastasis, heterogeneity, recurrence, radiotherapy and drug resistance. However, HERVs role in CSCs biology is still not fully elucidated. In this regard, CD133 is a widely recognized marker of CSCs, and our group demonstrated, for the first time, the requirement of HERV-K activation to expand and maintain a CD133+ melanoma cell subpopulation with stemness features in response to microenvironmental modifications. The review will discuss HERVs expression as cancer hallmark, with particular focus on their role in the regulation of cancer stemness features and the potential involvement as targets for therapy.
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Affiliation(s)
- Claudia Matteucci
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy.
| | - Emanuela Balestrieri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy
| | - Ayele Argaw-Denboba
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy; European Molecular Biology Laboratory (EMBL), Adriano Buzzati-Traverso Campus, Monterotondo, Rome, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier, 1, 00133, Rome, Italy; Institute of Translational Pharmacology, National Research Council, Via Fosso del Cavaliere, 100, 00133, Rome, Italy
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Dai L, Del Valle L, Miley W, Whitby D, Ochoa AC, Flemington EK, Qin Z. Transactivation of human endogenous retrovirus K (HERV-K) by KSHV promotes Kaposi's sarcoma development. Oncogene 2018; 37:4534-4545. [PMID: 29743595 PMCID: PMC6195842 DOI: 10.1038/s41388-018-0282-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/23/2018] [Accepted: 04/02/2018] [Indexed: 12/16/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of several human cancers such as Kaposi's sarcoma (KS), which represents the most common AIDS-associated malignancy that lacks effective treatment options. Despite its clear role in AIDS malignancies, the fact that only a small set of KSHV-infected patients will eventually develop these tumors implies that additional co-factors are required for the development of KSHV-related cancers. In the current study, we demonstrate for the first time that KSHV de novo infection or viral latent proteins are able to transactivate human endogenous retrovirus K (HERV-K) through a variety of cellular signaling pathways and transcriptional factors. Moreover, we found that HERV-K transactivation, particularly activation of its encoded oncogenic NP9 protein, plays an important role in KSHV pathogenesis and tumorigenesis in vitro and in vivo. Our data provide innovative insights into the mechanisms of HERV-K transactivation contributing to viral oncogenesis, which may represent a promising target for KS treatment.
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Affiliation(s)
- Lu Dai
- Department of Genetics, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, 1700 Tulane Avenue, New Orleans, LA, 70112, USA
- Department of Pediatrics, Research Center for Translational Medicine and Key Laboratory of Arrhythmias, East Hospital, Tongji University School of Medicine, 200120, Shanghai, China
| | - Luis Del Valle
- Department of Pathology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, 1700 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Wendell Miley
- Viral Oncology Section, AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, PO Box B, Frederick, MD, 21702, USA
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, PO Box B, Frederick, MD, 21702, USA
| | - Augusto C Ochoa
- Department of Pediatrics, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, 1700 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Erik K Flemington
- Department of Pathology, Tulane University Health Sciences Center, Tulane Cancer Center, 1700 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Zhiqiang Qin
- Department of Genetics, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, 1700 Tulane Avenue, New Orleans, LA, 70112, USA.
- Department of Pediatrics, Research Center for Translational Medicine and Key Laboratory of Arrhythmias, East Hospital, Tongji University School of Medicine, 200120, Shanghai, China.
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48
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Balestrieri E, Argaw-Denboba A, Gambacurta A, Cipriani C, Bei R, Serafino A, Sinibaldi-Vallebona P, Matteucci C. Human Endogenous Retrovirus K in the Crosstalk Between Cancer Cells Microenvironment and Plasticity: A New Perspective for Combination Therapy. Front Microbiol 2018; 9:1448. [PMID: 30013542 PMCID: PMC6036167 DOI: 10.3389/fmicb.2018.01448] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/11/2018] [Indexed: 12/24/2022] Open
Abstract
Abnormal activation of human endogenous retroviruses (HERVs) has been associated with several diseases such as cancer, autoimmunity, and neurological disorders. In particular, in cancer HERV activity and expression have been specifically associated with tumor aggressiveness and patient outcomes. Cancer cell aggressiveness is intimately linked to the acquisition of peculiar plasticity and heterogeneity based on cell stemness features, as well as on the crosstalk between cancer cells and the microenvironment. The latter is a driving factor in the acquisition of aggressive phenotypes, associated with metastasis and resistance to conventional cancer therapies. Remarkably, in different cell types and stages of development, HERV expression is mainly regulated by epigenetic mechanisms and is subjected to a very precise temporal and spatial regulation according to the surrounding microenvironment. Focusing on our research experience with HERV-K involvement in the aggressiveness and plasticity of melanoma cells, this perspective aims to highlight the role of HERV-K in the crosstalk between cancer cells and the tumor microenvironment. The implications for a combination therapy targeted at HERVs with standard approaches are discussed.
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Affiliation(s)
- Emanuela Balestrieri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | - Ayele Argaw-Denboba
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | - Alessandra Gambacurta
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | - Chiara Cipriani
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | - Roberto Bei
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Annalucia Serafino
- Institute of Translational Pharmacology, National Research Council, Rome, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy.,Institute of Translational Pharmacology, National Research Council, Rome, Italy
| | - Claudia Matteucci
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
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White CH, Beliakova-Bethell N, Lada SM, Breen MS, Hurst TP, Spina CA, Richman DD, Frater J, Magiorkinis G, Woelk CH. Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment. Front Immunol 2018; 9:603. [PMID: 29706951 PMCID: PMC5906534 DOI: 10.3389/fimmu.2018.00603] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/09/2018] [Indexed: 12/19/2022] Open
Abstract
The greatest obstacle to a cure for HIV is the provirus that integrates into the genome of the infected cell and persists despite antiretroviral therapy. A "shock and kill" approach has been proposed as a strategy for an HIV cure whereby drugs and compounds referred to as latency-reversing agents (LRAs) are used to "shock" the silent provirus into active replication to permit "killing" by virus-induced pathology or immune recognition. The LRA most utilized to date in clinical trials has been the histone deacetylase (HDAC) inhibitor-vorinostat. Potentially, pathological off-target effects of vorinostat may result from the activation of human endogenous retroviruses (HERVs), which share common ancestry with exogenous retroviruses including HIV. To explore the effects of HDAC inhibition on HERV transcription, an unbiased pharmacogenomics approach (total RNA-Seq) was used to evaluate HERV expression following the exposure of primary CD4+ T cells to a high dose of vorinostat. Over 2,000 individual HERV elements were found to be significantly modulated by vorinostat, whereby elements belonging to the ERVL family (e.g., LTR16C and LTR33) were predominantly downregulated, in contrast to LTR12 elements of the HERV-9 family, which exhibited the greatest signal, with the upregulation of 140 distinct elements. The modulation of three different LTR12 elements by vorinostat was confirmed by droplet digital PCR along a dose-response curve. The monitoring of LTR12 expression during clinical trials with vorinostat may be indicated to assess the impact of this HERV on the human genome and host immunity.
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Affiliation(s)
- Cory H. White
- Faculty of Medicine, University of Southampton, Southampton, Hants, United Kingdom
| | - Nadejda Beliakova-Bethell
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA, United States
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Steven M. Lada
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA, United States
| | - Michael S. Breen
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tara P. Hurst
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Celsa A. Spina
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA, United States
- Department of Pathology, University of California San Diego, La Jolla, CA, United States
| | - Douglas D. Richman
- San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA, United States
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
- Department of Pathology, University of California San Diego, La Jolla, CA, United States
| | - John Frater
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford, United Kingdom
| | | | - Christopher H. Woelk
- Faculty of Medicine, University of Southampton, Southampton, Hants, United Kingdom
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50
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Li H, Li L, Liu LR, Omange RW, Toledo N, Kashem MA, Hai Y, Liang B, Plummer FA, Luo M. Hypothetical endogenous SIV-like antigens in Mauritian cynomolgus macaques. Bioinformation 2018; 14:48-52. [PMID: 29618899 PMCID: PMC5879946 DOI: 10.6026/97320630014048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 01/24/2023] Open
Abstract
Simian immunodeficiency virus (SIV) infection of Mauritian cynomolgus macaques (MCMs) is an increasingly important nonhuman primate model for HIV vaccine research. We previously reported that in MCMs anti-SIV antibodies can be naturally developed without exogenous infection or vaccination, and that a vaccine targeting SIV protease cleavage sites (PCS) can cross-induce antibodies to non-PCS SIV antigens. We speculate that this is potentially caused by the existence of endogenous SIV-like antigens. External stimuli (such as environmental factors and vaccination) may induce expression of endogenous SIV-like antigens to elicit these antibodies. Database and mass spectrometry analyses were conducted to search for such antigens. We identified endogenous SIV-like DNA sequences in cynomolgus macaque genome and non-PCS peptide homologous to SIV Env protein in PBMCs of a PCS-vaccinated monkey. Our preliminary insights suggest that endogenous SIV-like antigens may be one of the possible reasons for the natural and cross-inducible SIV antibodies in MCMs.
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Affiliation(s)
- Hongzhao Li
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Lin Li
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
| | - Lewis R Liu
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Robert W Omange
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Nikki Toledo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Mohammad Abul Kashem
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Yan Hai
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Binhua Liang
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 3N4, Canada
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3L5, Canada
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