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Milovic A, Duong JV, Barbour AG. The infection-tolerant white-footed deermouse tempers interferon responses to endotoxin in comparison to the mouse and rat. eLife 2024; 12:RP90135. [PMID: 38193896 PMCID: PMC10945503 DOI: 10.7554/elife.90135] [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] [Indexed: 01/10/2024] Open
Abstract
The white-footed deermouse Peromyscus leucopus, a long-lived rodent, is a key reservoir in North America for agents of several zoonoses, including Lyme disease, babesiosis, anaplasmosis, and a viral encephalitis. While persistently infected, this deermouse is without apparent disability or diminished fitness. For a model for inflammation elicited by various pathogens, the endotoxin lipopolysaccharide (LPS) was used to compare genome-wide transcription in blood by P. leucopus, Mus musculus, and Rattus norvegicus and adjusted for white cell concentrations. Deermice were distinguished from the mice and rats by LPS response profiles consistent with non-classical monocytes and alternatively-activated macrophages. LPS-treated P. leucopus, in contrast to mice and rats, also displayed little transcription of interferon-gamma and lower magnitude fold-changes in type 1 interferon-stimulated genes. These characteristics of P. leucopus were also noted in a Borrelia hermsii infection model. The phenomenon was associated with comparatively reduced transcription of endogenous retrovirus sequences and cytoplasmic pattern recognition receptors in the deermice. The results reveal a mechanism for infection tolerance in this species and perhaps other animal reservoirs for agents of human disease.
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Affiliation(s)
- Ana Milovic
- Department of Microbiology & Molecular Genetics, University of California, IrvineIrvineUnited States
| | - Jonathan V Duong
- Department of Microbiology & Molecular Genetics, University of California, IrvineIrvineUnited States
| | - Alan G Barbour
- Departments of Medicine, Microbiology & Molecular Genetics, and Ecology & Evolutionary Biology, University of California, IrvineIrvineUnited States
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Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye C, Dall'Era M, Yazdany J, Criswell L, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM. Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.567477. [PMID: 38076936 PMCID: PMC10705239 DOI: 10.1101/2023.11.27.567477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
There is an established yet unexplained link between interferon (IFN) and systemic lupus erythematosus (SLE). The expression of sequences derived from transposable elements (TEs) may contribute to production of type I IFNs and generation of autoantibodies. We profiled cell-sorted RNA-seq data (CD4+ T cells, CD14+ monocytes, CD19+ B cells, and NK cells) from PBMCs of 120 SLE patients and quantified TE expression identifying 27,135 TEs. We tested for differential TE expression across 10 SLE phenotypes including autoantibody production and disease activity and discovered 731 differentially expressed (DE) TEs whose effects were mostly cell-specific and phenotype-specific. DE TEs were enriched for specific families and viral genes encoded in TE sequences. Increased expression of DE TEs was associated with genes involved in antiviral activity such as LY6E, ISG15, TRIM22 and pathways such as interferon signaling. These findings suggest that expression of TEs contributes to activation of SLE-related mechanisms in a cell-specific manner, which can impact disease diagnostics and therapeutics.
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Milovic A, Duong JV, Barbour AG. The white-footed deermouse, an infection-tolerant reservoir for several zoonotic agents, tempers interferon responses to endotoxin in comparison to the mouse and rat. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543964. [PMID: 37745581 PMCID: PMC10515768 DOI: 10.1101/2023.06.06.543964] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The white-footed deermouse Peromyscus leucopus, a long-lived rodent, is a key reservoir for agents of several zoonoses, including Lyme disease. While persistently infected, this deermouse is without apparent disability or diminished fitness. For a model for inflammation elicited by various pathogens, the endotoxin lipopolysaccharide (LPS) was used to compare genome-wide transcription in blood by P. leucopus, Mus musculus and Rattus norvegicus and adjusted for white cell concentrations. Deermice were distinguished from the mice and rats by LPS response profiles consistent with non-classical monocytes and alternatively-activated macrophages. LPS-treated P. leucopus, in contrast to mice and rats, also displayed little transcription of interferon-gamma and lower magnitude fold-changes in type 1 interferon-stimulated genes. This was associated with comparatively reduced transcription of endogenous retrovirus sequences and cytoplasmic pattern recognition receptors in the deermice. The results reveal a mechanism for infection tolerance in this species and perhaps other animal reservoirs for agents of human disease.
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Affiliation(s)
- Ana Milovic
- Department of Microbiology & Molecular Genetics, University of California Irvine
| | - Jonathan V. Duong
- Department of Microbiology & Molecular Genetics, University of California Irvine
| | - Alan G. Barbour
- Departments of Medicine, Microbiology & Molecular Genetics, and Ecology & Evolutionary Biology, University of California Irvine
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Wang M, Song J, Gao C, Yu C, Qin C, Lang Y, Xu A, Liu Y, Feng W, Tang J, Zhang R. UHRF1 Deficiency Inhibits Alphaherpesvirus through Inducing RIG-I-IRF3-Mediated Interferon Production. J Virol 2023; 97:e0013423. [PMID: 36916938 PMCID: PMC10062162 DOI: 10.1128/jvi.00134-23] [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: 01/23/2023] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
Type I interferon (IFN-I) response plays a prominent role in innate immunity, which is frequently modulated during viral infection. Here, we report DNA methylation regulator UHRF1 as a potent negative regulator of IFN-I induction during alphaherpesvirus infection, whereas the viruses in turn regulates the transcriptional expression of UHRF1. Knockdown of UHRF1 in cells significantly increases interferon-β (IFN-β)-mediated gene transcription and viral inhibition against herpes simplex virus 1 (HSV1) and pseudorabies virus (PRV). Mechanistically, UHRF1 deficiency promotes IFN-I production by triggering dsRNA-sensing receptor RIG-I and activating IRF3 phosphorylation. Knockdown of UHRF1 in cells upregulates the accumulation of double-stranded RNA (dsRNA), including host endogenous retroviral sequence (ERV) transcripts, while the treatment of RNase III, known to specifically digest dsRNA, prevents IFN-β induction by siUHRF1. Furthermore, the double-knockdown assay of UHRF1 and DNA methyltransferase DNMT1 suggests that siUHRF1-mediated DNA demethylation may play an important role in dsRNA accumulation and subsequently IFN induction. These findings establish the essential role of UHRF1 in IFN-I-induced antiviral immunity and reveal UHRF1 as a potential antivrial target. IMPORTANCE Alphaherpesviruses can establish lifelong infections and cause many diseases in humans and animals, which rely partly on their interaction with IFN-mediated innate immune response. Using alphaherpesviruses PRV and HSV-1 as models, we identified an essential role of DNA methylation regulator UHRF1 in IFN-mediated immunity against virus replication, which unravels a novel mechanism employed by epigenetic factor to control IFN-mediated antiviral immune response and highlight UHRF1, which might be a potential target for antiviral drug development.
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Affiliation(s)
- Mengdong Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jingjing Song
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chao Gao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Cuilian Yu
- College of Laboratory Animal & Shandong Laboratory Animal Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Chao Qin
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yue Lang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Aotian Xu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yun Liu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wenhai Feng
- College of Biology, China Agricultural University, Beijing, China
| | - Jun Tang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Rui Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
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5
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Jin X, Li X, Guan F, Zhang J. Human Endogenous Retroviruses and Toll-Like Receptors. Viral Immunol 2023; 36:73-82. [PMID: 36251943 DOI: 10.1089/vim.2022.0090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are estimated to comprise ∼8% of the entire human genome, but the vast majority of them remain transcriptionally silent in most normal tissues due to accumulated mutations. However, HERVs can be frequently activated and detected in various tissues under certain conditions. Nucleic acids or proteins produced by HERVs can bind to pattern recognition receptors of immune cells or other cells and initiate an innate immune response, which may be involved in some pathogenesis of diseases, especially cancer and autoimmune diseases. In this review, we collect studies of the interaction between HERV elements and Toll-like receptors and attempt to provide an overview of their role in the immunopathological mechanisms of inflammatory and autoimmune diseases.
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Affiliation(s)
- Xinyi Jin
- Department of Laboratory Medicine, School of Medicine, Shaoxing University, Shaoxing, P.R. China
| | - Xueyuan Li
- Department of Laboratory Medicine, School of Medicine, Shaoxing University, Shaoxing, P.R. China
| | - Fang Guan
- Department of Laboratory Medicine, School of Medicine, Shaoxing University, Shaoxing, P.R. China
| | - Jianhua Zhang
- Department of Laboratory Medicine, School of Medicine, Shaoxing University, Shaoxing, P.R. China
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Mo G, Wei P, Hu B, Nie Q, Zhang X. Advances on genetic and genomic studies of ALV resistance. J Anim Sci Biotechnol 2022; 13:123. [PMID: 36217167 PMCID: PMC9550310 DOI: 10.1186/s40104-022-00769-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/14/2022] [Indexed: 12/01/2022] Open
Abstract
Avian leukosis (AL) is a general term for a variety of neoplastic diseases in avian caused by avian leukosis virus (ALV). No vaccine or drug is currently available for the disease. Therefore, the disease can result in severe economic losses in poultry flocks. Increasing the resistance of poultry to ALV may be one effective strategy. In this review, we provide an overview of the roles of genes associated with ALV infection in the poultry genome, including endogenous retroviruses, virus receptors, interferon-stimulated genes, and other immune-related genes. Furthermore, some methods and techniques that can improve ALV resistance in poultry are discussed. The objectives are willing to provide some valuable references for disease resistance breeding in poultry.
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Affiliation(s)
- Guodong Mo
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Ping Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, 530001, Guangxi, China
| | - Bowen Hu
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qinghua Nie
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China. .,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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Sahu S, Singh B, Kumar Rai A. Human endogenous retrovirus regulates the initiation and progression of cancers (Review). Mol Clin Oncol 2022; 17:143. [PMID: 36157315 PMCID: PMC9468830 DOI: 10.3892/mco.2022.2576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/22/2022] [Indexed: 11/05/2022] Open
Abstract
The expression of genes is altered in various diseases and is responsible for the disease's initiation, progression and pathology. Several other genes, predominantly inactivated, may become activated in a given condition and contribute to the initiation and progression of the disease. Similarly, human endogenous viruses (HERVs) are an incomplete, non-productive and inactive viral sequence present in the heterochromatin of the human genome, and are often referred to as junk DNA. HERVs were inserted into the host genome millions of years ago. However, they were silenced due to multiple mutations and recombination that occurred over time. However, their expression is increased in cancers due to either epigenetic or transcriptional dysregulation. Some of the HERVs having intact open reading frames have been reported to express virus-like particles, functional peptides and proteins involved in tumorigenesis. To summarize, there is involvement of different HERVs in the initiation and progression of several cancers. The present review aims to provide concise information on HERV and its involvement in the initiation and progression of multiple types of cancer.
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Affiliation(s)
- Srishti Sahu
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Uttar Pradesh 211004, India
| | - Bharat Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Uttar Pradesh 211004, India
| | - Ambak Kumar Rai
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Uttar Pradesh 211004, India
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Activation of lnc-ALVE1-AS1 inhibited ALV-J replication through triggering the TLR3 pathway in chicken macrophage like cell line. Vet Res Commun 2022; 47:431-443. [PMID: 35715584 DOI: 10.1007/s11259-022-09960-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/14/2022] [Indexed: 11/27/2022]
Abstract
Endogenous retroviruses (ERVs) are remnants of the historical retroviral infections, and their derived transcripts with viral signatures are important sources of long noncoding RNAs (lncRNAs). We have previously shown that the chicken ERV-derived lncRNA lnc-ALVE1-AS1 exerts antiviral innate immunity in chicken embryo fibroblasts. However, it is not clear whether this endogenous retroviral RNA has a similar function in immune cells. Here, we found that lnc-ALVE1-AS1 was persistently inhibited in chicken macrophages after avian leukosis virus subgroup J (ALV-J) infection. Furthermore, overexpression of lnc-ALVE1-AS1 significantly inhibited the replication of exogenous ALV-J, whereas knockdown of lnc-ALVE1-AS1 promoted the replication of ALV-J in chicken macrophages. This phenomenon is attributed to the induction of antiviral innate immunity by lnc-ALVE1-AS1 in macrophages, whereas knockdown of lnc-ALVE1-AS1 had the opposite effect. Mechanistically, lnc-ALVE1-AS1 can be sensed by the cytosolic pattern recognition receptor TLR3 and trigger the type I interferons response. The present study provides novel insights into the antiviral defense of ERV-derived lncRNAs in macrophages and offers new strategies for future antiviral solutions.
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9
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Matteucci C, Balestrieri E, Hurst TP, Magiorkinis G, Strick R. Editorial: Unravelling the Role of HERVs in Cancer: Insights and New Targets for Therapy. Front Oncol 2022; 12:874245. [PMID: 35359384 PMCID: PMC8963950 DOI: 10.3389/fonc.2022.874245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Claudia Matteucci
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
- *Correspondence: Claudia Matteucci,
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Tara Patricia Hurst
- Department of Life Sciences, School of Health Sciences, Birmingham City University, Birmingham, United Kingdom
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Reiner Strick
- Department of Gynaecology and Obstetrics, Laboratory for Molecular Medicine, University Hospital Erlangen, Erlangen, Germany
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10
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Lecuelle J, Favier L, Fraisse C, Lagrange A, Kaderbhai C, Boidot R, Chevrier S, Joubert P, Routy B, Truntzer C, Ghiringhelli F. MER4 endogenous retrovirus correlated with better efficacy of anti-PD1/PD-L1 therapy in non-small cell lung cancer. J Immunother Cancer 2022; 10:jitc-2021-004241. [PMID: 35277462 PMCID: PMC8919440 DOI: 10.1136/jitc-2021-004241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2022] [Indexed: 12/15/2022] Open
Abstract
Background Endogenous retroviruses (ERVs) are highly expressed in various cancer types and are associated with increased innate immune response and better efficacy of antiprogrammed death-1/ligand-1 (anti-PD1/PD-L1)-directed immune checkpoint inhibitors (ICI) in preclinical models. However, their role in human non-small cell lung cancer (NSCLC) remains unknown. Methods We conducted a retrospective study of patients receiving ICI for advanced NSCLC in two independent cohorts. ERV expression was determined by RNA sequencing. The primary endpoint was progression-free survival (PFS) under ICI. The secondary endpoint was overall survival (OS) from ICI initiation. We studied expression of 6205 ERVs. Multivariate Cox regression model with lasso penalty was estimated on the training set to select ERVs significantly associated with survival. The predictive power of these ERVs was compared with that of previously described transcriptomic signatures. Results We studied two independent cohorts of 89 and 70 patients, used as training and validation sets. Clinicopathological characteristics included 75% of patients with non-squamous NSCLC. We selected four ERVs significantly associated with PFS. Only high MER4 ERV was associated with better PFS and OS in both cohorts. From a biological point of view, high MER4 expression is associated with higher infiltration of eosinophils and inflammatory gene signatures, while low MER4 expression is associated with enrichment in metabolism and proliferation signatures. Adding MER4 to previously described transcriptomic signatures of response to ICI improved their predictive power. Conclusions MER4 ERV expression is useful to stratify risk and predict PFS and OS in patients treated with ICI for NSCLC. It also improves the predictive power of other known transcriptomic signatures.
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Affiliation(s)
- Julie Lecuelle
- Platform of Transfer in Biological Oncology, Georges-Francois Leclerc Cancer Center - UNICANCER, Dijon, Bourgogne-Franche-Comté, France
- UMR INSERM 1231, Dijon, Bourgogne-Franche-Comté, France
- Genomic and Immunotherapy Medical Institute, Dijon University Hospital, Dijon, Bourgogne-Franche-Comté, France
- University of Burgundy-Franche Comté, Dijon, Bourgogne-Franche-Comté, France
| | - Laure Favier
- Departmnt of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, Dijon, Bourgogne-Franche-Comté, France
| | - Cléa Fraisse
- Departmnt of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, Dijon, Bourgogne-Franche-Comté, France
| | - Aurélie Lagrange
- Departmnt of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, Dijon, Bourgogne-Franche-Comté, France
| | - Coureche Kaderbhai
- Departmnt of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, Dijon, Bourgogne-Franche-Comté, France
| | - Romain Boidot
- Department of Biopathology, Georges François Leclerc Cancer Center - UNICANCER, Dijon, Bourgogne-Franche-Comté, France
| | - Sandy Chevrier
- Department of Biopathology, Georges François Leclerc Cancer Center - UNICANCER, Dijon, Bourgogne-Franche-Comté, France
| | - Philippe Joubert
- Department of Pathology, Quebec Heart and Lung Institute Research Center, Quebec City, Quebec, Canada
| | - Bertrand Routy
- Department of Medicine Montréal, Division of Oncology, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
- Division of Hematology-Oncology, Centre Hospitalier de l'Université de Montréal (CHUM), Quebec City, Quebec, Canada
| | - Caroline Truntzer
- Platform of Transfer in Biological Oncology, Georges-Francois Leclerc Cancer Center - UNICANCER, Dijon, Bourgogne-Franche-Comté, France
- UMR INSERM 1231, Dijon, Bourgogne-Franche-Comté, France
- Genomic and Immunotherapy Medical Institute, Dijon University Hospital, Dijon, Bourgogne-Franche-Comté, France
- University of Burgundy-Franche Comté, Dijon, Bourgogne-Franche-Comté, France
| | - Francois Ghiringhelli
- Platform of Transfer in Biological Oncology, Georges-Francois Leclerc Cancer Center - UNICANCER, Dijon, Bourgogne-Franche-Comté, France
- UMR INSERM 1231, Dijon, Bourgogne-Franche-Comté, France
- Genomic and Immunotherapy Medical Institute, Dijon University Hospital, Dijon, Bourgogne-Franche-Comté, France
- University of Burgundy-Franche Comté, Dijon, Bourgogne-Franche-Comté, France
- Departmnt of Medical Oncology, Georges François Leclerc Cancer Center - UNICANCER, Dijon, Bourgogne-Franche-Comté, France
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Vitiello GAF, Ferreira WAS, Cordeiro de Lima VC, Medina TDS. Antiviral Responses in Cancer: Boosting Antitumor Immunity Through Activation of Interferon Pathway in the Tumor Microenvironment. Front Immunol 2021; 12:782852. [PMID: 34925363 PMCID: PMC8674309 DOI: 10.3389/fimmu.2021.782852] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/15/2021] [Indexed: 12/22/2022] Open
Abstract
In recent years, it became apparent that cancers either associated with viral infections or aberrantly expressing endogenous retroviral elements (EREs) are more immunogenic, exhibiting an intense intra-tumor immune cell infiltration characterized by a robust cytolytic apparatus. On the other hand, epigenetic regulation of EREs is crucial to maintain steady-state conditions and cell homeostasis. In line with this, epigenetic disruptions within steady-state cells can lead to cancer development and trigger the release of EREs into the cytoplasmic compartment. As such, detection of viral molecules by intracellular innate immune sensors leads to the production of type I and type III interferons that act to induce an antiviral state, thus restraining viral replication. This knowledge has recently gained momentum due to the possibility of triggering intratumoral activation of interferon responses, which could be used as an adjuvant to elicit strong anti-tumor immune responses that ultimately lead to a cascade of cytokine production. Accordingly, several therapeutic approaches are currently being tested using this rationale to improve responses to cancer immunotherapies. In this review, we discuss the immune mechanisms operating in viral infections, show evidence that exogenous viruses and endogenous retroviruses in cancer may enhance tumor immunogenicity, dissect the epigenetic control of EREs, and point to interferon pathway activation in the tumor milieu as a promising molecular predictive marker and immunotherapy target. Finally, we briefly discuss current strategies to modulate these responses within tumor tissues, including the clinical use of innate immune receptor agonists and DNA demethylating agents.
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Affiliation(s)
| | - Wallax Augusto Silva Ferreira
- Translational Immuno-Oncology Group, International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
- Laboratory of Cytogenomics and Environmental Mutagenesis, Environment Section (SAMAM), Evandro Chagas Institute, Ananindeua, Brazil
| | | | - Tiago da Silva Medina
- Translational Immuno-Oncology Group, International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil
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12
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Middlebrook EA, Stark DL, Cornwall DH, Kubinak JL, Potts WK. Deep Sequencing of MHC-Adapted Viral Lines Reveals Complex Recombinational Exchanges With Endogenous Retroviruses Leading to High-Frequency Variants. Front Genet 2021; 12:716623. [PMID: 34512727 PMCID: PMC8430262 DOI: 10.3389/fgene.2021.716623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/05/2021] [Indexed: 12/03/2022] Open
Abstract
Experimental evolution (serial passage) of Friend virus complex (FVC) in mice demonstrates phenotypic adaptation to specific host major histocompatibility complex (MHC) genotypes. These evolved viral lines show increased fitness and virulence in their host-genotype-of-passage, but display fitness and virulence tradeoffs when infecting unfamiliar host MHC genotypes. Here, we deep sequence these viral lines in an attempt to discover the genetic basis of FVC adaptation. The principal prediction for genotype-specific adaptation is that unique mutations would rise to high frequency in viral lines adapted to each host MHC genotype. This prediction was not supported by our sequencing data as most observed high-frequency variants were present in each of our independently evolved viral lines. However, using a multi-variate approach to measure divergence between viral populations, we show that populations of replicate evolved viral lines from the same MHC congenic mouse strain were more similar to one another than to lines derived from different MHC congenic mouse strains, suggesting that MHC genotype does predictably act on viral evolution in our model. Sequence analysis also revealed rampant recombination with endogenous murine leukemia virus sequences (EnMuLVs) that are encoded within the BALB/c mouse genome. The highest frequency variants in all six lines contained a 12 bp insertion from a recombinant EnMuLV source, suggesting such recombinants were either being favored by selection or were contained in a recombinational hotspot. Interestingly, they did not reach fixation, as if they are low fitness. The amount of background mutations linked to FVC/EnMuLV variable sites indicated that FVC/EnMuLV recombinants had not reached mutation selection equilibrium and thus, that EnMuLV sequences are likely continuously introgressing into the replicating viral population. These discoveries raise the question: is the expression of EnMuLV sequences in mouse splenocytes that permit recombination with exogenous FVC a pathogen or host adaptation?
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Affiliation(s)
- Earl A. Middlebrook
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Derek L. Stark
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
| | - Douglas H. Cornwall
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
- Department of Pathology, University of Utah, Salt Lake City, UT, United States
| | - Jason L. Kubinak
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Wayne K. Potts
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
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Panda A, Ganesan S. Genomic and Immunologic Correlates of Indoleamine 2,3-Dioxygenase Pathway Expression in Cancer. Front Genet 2021; 12:706435. [PMID: 34367262 PMCID: PMC8340027 DOI: 10.3389/fgene.2021.706435] [Citation(s) in RCA: 3] [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: 05/07/2021] [Accepted: 06/30/2021] [Indexed: 02/04/2023] Open
Abstract
Immune checkpoint blockade leads to unprecedented responses in many cancer types. An alternative method of unleashing anti-tumor immune response is to target immunosuppressive metabolic pathways like the indoleamine 2,3-dioxygenase (IDO) pathway. Despite promising results in Phase I/II clinical trials, an IDO-1 inhibitor did not show clinical benefit in a Phase III clinical trial. Since, a treatment can be quite effective in a specific subset without being effective in the whole cancer type, it is important to identify the subsets of cancers that may benefit from IDO-1 inhibitors. In this study, we looked for the genomic and immunologic correlates of IDO pathway expression in cancer using the Cancer Genome Atlas (TCGA) dataset. Strong CD8+ T-cell infiltration, high mutation burden, and expression of exogenous viruses [Epstein-Barr virus (EBV), Human papilloma virus (HPV), and Hepatitis C virus (HCV)] or endogenous retrovirus (ERV3-2) were associated with over-expression of IDO-1 in most cancer types, IDO-2 in many cancer types, and TDO-2 in a few cancer types. High mutation burden in ER+ HER2- breast cancer, and ERV3-2 expression in ER- HER2- and HER2+ breast, colon, and endometrial cancers were associated with over-expression of all three genes. These results may have important implications for guiding development clinical trials of IDO-1 inhibitors.
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Affiliation(s)
- Anshuman Panda
- Department of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Shridar Ganesan
- Department of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
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14
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Srinivasachar Badarinarayan S, Sauter D. Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections. J Virol 2021; 95:e02299-20. [PMID: 33883223 PMCID: PMC8315955 DOI: 10.1128/jvi.02299-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/30/2021] [Indexed: 01/15/2023] Open
Abstract
Long disregarded as junk DNA or genomic dark matter, endogenous retroviruses (ERVs) have turned out to represent important components of the antiviral immune response. These remnants of once-infectious retroviruses not only regulate cellular immune activation, but may even directly target invading viral pathogens. In this Gem, we summarize mechanisms by which retroviral fossils protect us from viral infections. One focus will be on recent advances in the role of ERVs as regulators of antiviral gene expression.
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MESH Headings
- Animals
- Endogenous Retroviruses/genetics
- Endogenous Retroviruses/physiology
- Enhancer Elements, Genetic
- Gene Expression Regulation
- Humans
- Immunity, Cellular
- Promoter Regions, Genetic
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Pattern Recognition/metabolism
- Receptors, Virus/antagonists & inhibitors
- Receptors, Virus/metabolism
- Retroelements
- Viral Proteins/metabolism
- Virion/metabolism
- Virus Diseases/genetics
- Virus Diseases/immunology
- Virus Diseases/virology
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Affiliation(s)
- Smitha Srinivasachar Badarinarayan
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Germany
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15
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Declerck K, Novo CP, Grielens L, Van Camp G, Suter A, Vanden Berghe W. Echinacea purpurea (L.) Moench treatment of monocytes promotes tonic interferon signaling, increased innate immunity gene expression and DNA repeat hypermethylated silencing of endogenous retroviral sequences. BMC Complement Med Ther 2021; 21:141. [PMID: 33980308 PMCID: PMC8114977 DOI: 10.1186/s12906-021-03310-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Background Herbal remedies of Echinacea purpurea tinctures are widely used today to reduce common cold respiratory tract infections. Methods Transcriptome, epigenome and kinome profiling allowed a systems biology level characterisation of genomewide immunomodulatory effects of a standardized Echinacea purpurea (L.) Moench extract in THP1 monocytes. Results Gene expression and DNA methylation analysis revealed that Echinaforce® treatment triggers antiviral innate immunity pathways, involving tonic IFN signaling, activation of pattern recognition receptors, chemotaxis and immunometabolism. Furthermore, phosphopeptide based kinome activity profiling and pharmacological inhibitor experiments with filgotinib confirm a key role for Janus Kinase (JAK)-1 dependent gene expression changes in innate immune signaling. Finally, Echinaforce® treatment induces DNA hypermethylation at intergenic CpG, long/short interspersed nuclear DNA repeat elements (LINE, SINE) or long termininal DNA repeats (LTR). This changes transcription of flanking endogenous retroviral sequences (HERVs), involved in an evolutionary conserved (epi) genomic protective response against viral infections. Conclusions Altogether, our results suggest that Echinaforce® phytochemicals strengthen antiviral innate immunity through tonic IFN regulation of pattern recognition and chemokine gene expression and DNA repeat hypermethylated silencing of HERVs in monocytes. These results suggest that immunomodulation by Echinaforce® treatment holds promise to reduce symptoms and duration of infection episodes of common cold corona viruses (CoV), Severe Acute Respiratory Syndrome (SARS)-CoV, and new occurring strains such as SARS-CoV-2, with strongly impaired interferon (IFN) response and weak innate antiviral defense. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-021-03310-5.
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Affiliation(s)
- Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Claudina Perez Novo
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Lisa Grielens
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, Department of Biomedical Sciences, University of Antwerp (UA) and University Hospital Antwerp (UZA), Antwerp, Belgium
| | | | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium.
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16
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Römer C. Viruses and Endogenous Retroviruses as Roots for Neuroinflammation and Neurodegenerative Diseases. Front Neurosci 2021; 15:648629. [PMID: 33776642 PMCID: PMC7994506 DOI: 10.3389/fnins.2021.648629] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
Many neurodegenerative diseases are associated with chronic inflammation in the brain and periphery giving rise to a continuous imbalance of immune processes. Next to inflammation markers, activation of transposable elements, including long intrespersed nuclear elements (LINE) elements and endogenous retroviruses (ERVs), has been identified during neurodegenerative disease progression and even correlated with the clinical severity of the disease. ERVs are remnants of viral infections in the human genome acquired during evolution. Upon activation, they produce transcripts and the phylogenetically youngest ones are still able to produce viral-like particles. In addition, ERVs can bind transcription factors and modulate immune response. Being between own and foreign, ERVs are reviewed in the context of viral infections of the central nervous system, in aging and neurodegenerative diseases. Moreover, this review tests the hypothesis that viral infection may be a trigger at the onset of neuroinflammation and that ERVs sustain the inflammatory imbalance by summarizing existing data of neurodegenerative diseases associated with viruses and/or ERVs.
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Affiliation(s)
- Christine Römer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, The Berlin Institute for Medical Systems Biology, Berlin, Germany
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17
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Díaz-Carballo D, Saka S, Acikelli AH, Homp E, Erwes J, Demmig R, Klein J, Schröer K, Malak S, D'Souza F, Noa-Bolaño A, Menze S, Pano E, Andrioff S, Teipel M, Dammann P, Klein D, Nasreen A, Tannapfel A, Grandi N, Tramontano E, Ochsenfarth C, Strumberg D. Enhanced antitumoral activity of TLR7 agonists via activation of human endogenous retroviruses by HDAC inhibitors. Commun Biol 2021; 4:276. [PMID: 33658617 PMCID: PMC7930250 DOI: 10.1038/s42003-021-01800-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 01/25/2021] [Indexed: 12/18/2022] Open
Abstract
In this work, we are reporting that "Shock and Kill", a therapeutic approach designed to eliminate latent HIV from cell reservoirs, is extrapolatable to cancer therapy. This is based on the observation that malignant cells express a spectrum of human endogenous retroviral elements (HERVs) which can be transcriptionally boosted by HDAC inhibitors. The endoretroviral gene HERV-V2 codes for an envelope protein, which resembles syncytins. It is significantly overexpressed upon exposure to HDAC inhibitors and can be effectively targeted by simultaneous application of TLR7/8 agonists, triggering intrinsic apoptosis. We demonstrated that this synergistic cytotoxic effect was accompanied by the functional disruption of the TLR7/8-NFκB, Akt/PKB, and Ras-MEK-ERK signalling pathways. CRISPR/Cas9 ablation of TLR7 and HERV-V1/V2 curtailed apoptosis significantly, proving the pivotal role of these elements in driving cell death. The effectiveness of this new approach was confirmed in ovarian tumour xenograft studies, revealing a promising avenue for future cancer therapies.
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Affiliation(s)
- David Díaz-Carballo
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany.
| | - Sahitya Saka
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Ali H Acikelli
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Ekaterina Homp
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Julia Erwes
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Rebecca Demmig
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Jacqueline Klein
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Katrin Schröer
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Sascha Malak
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Flevy D'Souza
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Adrien Noa-Bolaño
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Saskia Menze
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Emilio Pano
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Swetlana Andrioff
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Marc Teipel
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Philip Dammann
- Central Animal Laboratory, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Diana Klein
- Institute of Cell Biology, Cancer Research, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Amber Nasreen
- Visceral Surgery Department, Marien Hospital Herne, Ruhr University Bochum Medical School, Herne, Germany
| | | | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Crista Ochsenfarth
- Department of Anesthesia, Intensive Care, Pain and Palliative Medicine, Marien Hospital Herne, Ruhr-University Bochum Medical School, Herne, Germany
| | - Dirk Strumberg
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
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18
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Jönsson ME, Garza R, Sharma Y, Petri R, Södersten E, Johansson JG, Johansson PA, Atacho DA, Pircs K, Madsen S, Yudovich D, Ramakrishnan R, Holmberg J, Larsson J, Jern P, Jakobsson J. Activation of endogenous retroviruses during brain development causes an inflammatory response. EMBO J 2021; 40:e106423. [PMID: 33644903 PMCID: PMC8090857 DOI: 10.15252/embj.2020106423] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 01/09/2023] Open
Abstract
Endogenous retroviruses (ERVs) make up a large fraction of mammalian genomes and are thought to contribute to human disease, including brain disorders. In the brain, aberrant activation of ERVs is a potential trigger for an inflammatory response, but mechanistic insight into this phenomenon remains lacking. Using CRISPR/Cas9‐based gene disruption of the epigenetic co‐repressor protein Trim28, we found a dynamic H3K9me3‐dependent regulation of ERVs in proliferating neural progenitor cells (NPCs), but not in adult neurons. In vivo deletion of Trim28 in cortical NPCs during mouse brain development resulted in viable offspring expressing high levels of ERVs in excitatory neurons in the adult brain. Neuronal ERV expression was linked to activated microglia and the presence of ERV‐derived proteins in aggregate‐like structures. This study demonstrates that brain development is a critical period for the silencing of ERVs and provides causal in vivo evidence demonstrating that transcriptional activation of ERV in neurons results in an inflammatory response.
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Affiliation(s)
- Marie E Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Yogita Sharma
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Rebecca Petri
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Erik Södersten
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jenny G Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Pia A Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Diahann Am Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Karolina Pircs
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Sofia Madsen
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - David Yudovich
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
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19
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Sadeq S, Al-Hashimi S, Cusack CM, Werner A. Endogenous Double-Stranded RNA. Noncoding RNA 2021; 7:15. [PMID: 33669629 PMCID: PMC7930956 DOI: 10.3390/ncrna7010015] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
The birth of long non-coding RNAs (lncRNAs) is closely associated with the presence and activation of repetitive elements in the genome. The transcription of endogenous retroviruses as well as long and short interspersed elements is not only essential for evolving lncRNAs but is also a significant source of double-stranded RNA (dsRNA). From an lncRNA-centric point of view, the latter is a minor source of bother in the context of the entire cell; however, dsRNA is an essential threat. A viral infection is associated with cytoplasmic dsRNA, and endogenous RNA hybrids only differ from viral dsRNA by the 5' cap structure. Hence, a multi-layered defense network is in place to protect cells from viral infections but tolerates endogenous dsRNA structures. A first line of defense is established with compartmentalization; whereas endogenous dsRNA is found predominantly confined to the nucleus and the mitochondria, exogenous dsRNA reaches the cytoplasm. Here, various sensor proteins recognize features of dsRNA including the 5' phosphate group of viral RNAs or hybrids with a particular length but not specific nucleotide sequences. The sensors trigger cellular stress pathways and innate immunity via interferon signaling but also induce apoptosis via caspase activation. Because of its central role in viral recognition and immune activation, dsRNA sensing is implicated in autoimmune diseases and used to treat cancer.
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Affiliation(s)
| | | | | | - Andreas Werner
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (S.A.-H.); (C.M.C.)
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20
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Schust DJ, Bonney EA, Sugimoto J, Ezashi T, Roberts RM, Choi S, Zhou J. The Immunology of Syncytialized Trophoblast. Int J Mol Sci 2021; 22:ijms22041767. [PMID: 33578919 PMCID: PMC7916661 DOI: 10.3390/ijms22041767] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/02/2021] [Accepted: 02/06/2021] [Indexed: 02/06/2023] Open
Abstract
Multinucleate syncytialized trophoblast is found in three forms in the human placenta. In the earliest stages of pregnancy, it is seen at the invasive leading edge of the implanting embryo and has been called primitive trophoblast. In later pregnancy, it is represented by the immense, multinucleated layer covering the surface of placental villi and by the trophoblast giant cells found deep within the uterine decidua and myometrium. These syncytia interact with local and/or systemic maternal immune effector cells in a fine balance that allows for invasion and persistence of allogeneic cells in a mother who must retain immunocompetence for 40 weeks of pregnancy. Maternal immune interactions with syncytialized trophoblast require tightly regulated mechanisms that may differ depending on the location of fetal cells and their invasiveness, the nature of the surrounding immune effector cells and the gestational age of the pregnancy. Some specifically reflect the unique mechanisms involved in trophoblast cell–cell fusion (aka syncytialization). Here we will review and summarize several of the mechanisms that support healthy maternal–fetal immune interactions specifically at syncytiotrophoblast interfaces.
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Affiliation(s)
- Danny J. Schust
- Department of Obstetrics, Gynecology, University of Missouri School of Medicine, Columbia, MO 65202, USA; (T.E.); (R.M.R.); (S.C.); (J.Z.)
- Correspondence:
| | - Elizabeth A. Bonney
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Vermont College of Medicine, Burlington, VT 05405, USA;
| | - Jun Sugimoto
- Department of Obstetrics and Gynecology, Hiroshima University, Hiroshima 734-8551, Japan;
| | - Toshi Ezashi
- Department of Obstetrics, Gynecology, University of Missouri School of Medicine, Columbia, MO 65202, USA; (T.E.); (R.M.R.); (S.C.); (J.Z.)
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - R. Michael Roberts
- Department of Obstetrics, Gynecology, University of Missouri School of Medicine, Columbia, MO 65202, USA; (T.E.); (R.M.R.); (S.C.); (J.Z.)
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Sehee Choi
- Department of Obstetrics, Gynecology, University of Missouri School of Medicine, Columbia, MO 65202, USA; (T.E.); (R.M.R.); (S.C.); (J.Z.)
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jie Zhou
- Department of Obstetrics, Gynecology, University of Missouri School of Medicine, Columbia, MO 65202, USA; (T.E.); (R.M.R.); (S.C.); (J.Z.)
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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21
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Mikhalkevich N, O’Carroll IP, Tkavc R, Lund K, Sukumar G, Dalgard CL, Johnson KR, Li W, Wang T, Nath A, Iordanskiy S. Response of human macrophages to gamma radiation is mediated via expression of endogenous retroviruses. PLoS Pathog 2021; 17:e1009305. [PMID: 33556144 PMCID: PMC7895352 DOI: 10.1371/journal.ppat.1009305] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/19/2021] [Accepted: 01/11/2021] [Indexed: 01/11/2023] Open
Abstract
Ionizing radiation-induced tissue damage recruits monocytes into the exposed area where they are differentiated to macrophages. These implement phagocytic removal of dying cells and elicit an acute inflammatory response, but can also facilitate tumorigenesis due to production of anti-inflammatory cytokines. Using primary human monocyte-derived macrophages (MDMs) and the THP1 monocytic cell line, we demonstrate that gamma radiation triggers monocyte differentiation toward the macrophage phenotype with increased expression of type I interferons (IFN-I) and both pro- and anti-inflammatory macrophage activation markers. We found that these changes correlate with significantly upregulated expression of 622 retroelements from various groups, particularly of several clades of human endogenous retroviruses (HERVs). Elevated transcription was detected in both sense and antisense directions in the HERV subgroups tested, including the most genetically homogeneous clade HML-2. The level of antisense transcription was three- to five-fold higher than of the sense strand levels. Using a proximity ligation assay and immunoprecipitation followed by RNA quantification, we identified an increased amount of the dsRNA receptors MDA-5 and TLR3 bound to an equivalent number of copies of sense and antisense chains of HERVK HML-2 RNA. This binding triggered MAVS-associated signaling pathways resulting in increased expression of IFN-I and inflammation related genes that enhanced the cumulative inflammatory effect of radiation-induced senescence. HML-2 knockdown was accompanied with reduced expression and secretion of IFNα, pro-inflammatory (IL-1β, IL-6, CCL2, CCL3, CCL8, and CCL20) and anti-inflammatory (IL10) modulators in irradiated monocytes and MDMs. Taken together, our data indicate that radiation stress-induced HERV expression enhances the IFN-I and cytokine response and results in increased levels of pro-inflammatory modulators along with expression of anti-inflammatory factors associated with the macrophage tumorigenic phenotype. Ionizing radiation is a powerful stressogenic factor that induces massive cell damage. The signals released from radiation-damaged tissues recruit the monocytes, which are differentiated into macrophages that remove dying cells via phagocytosis and facilitate inflammation but can also contribute to tumorigenesis through anti-inflammatory and regenerative activities. The mechanism of this dual response of macrophages to irradiation is not fully understood. Using primary human macrophages and a monocytic cell line, we demonstrated that gamma radiation doses activate expression of various human endogenous retroviruses (HERVs). At the molecular level, we have shown that increased numbers of sense and antisense transcripts of tested HERV subgroups bind to double-stranded RNA receptors inducing the expression of type I interferons, multiple pro-inflammatory and some anti-inflammatory factors. At the phenotypic level, polarized macrophages exhibit a potent inflammatory response along with potentially tumorigenic characteristics. Our data suggest that endogenous retroviruses represent an important contributor of the macrophage-mediated inflammation in response to radiation-induced stress but may also indirectly influence tumorigenesis via biased macrophage polarization.
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Affiliation(s)
- Natallia Mikhalkevich
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Ina P. O’Carroll
- Department of Chemistry, United States Naval Academy, Annapolis, Maryland, United States of America
| | - Rok Tkavc
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Kateryna Lund
- Biomedical Instrumentation Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Gauthaman Sukumar
- The American Genome Center (TAGC), Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Clifton L. Dalgard
- The American Genome Center (TAGC), Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Kory R. Johnson
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tongguang Wang
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (AN); (SI)
| | - Sergey Iordanskiy
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- * E-mail: (AN); (SI)
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22
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El-Shehawi AM, Alotaibi SS, Elseehy MM. Genomic Study of COVID-19 Corona Virus Excludes Its Origin from Recombination or Characterized Biological Sources and Suggests a Role for HERVS in Its Wide Range Symptoms. CYTOL GENET+ 2021; 54:588-604. [PMID: 33487779 PMCID: PMC7810191 DOI: 10.3103/s0095452720060031] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 07/12/2019] [Accepted: 11/18/2020] [Indexed: 01/08/2023]
Abstract
The COVID-19 corona virus has become a world pandemic which started in December 2019 in Wuhan, China with no confirmed biological source. Various countries reported the genomic sequence of different isolates obtained from infected patients. This allowed us to obtain a number of 38 isolates of full genomic sequences. Alignment of nucleotide (nt) sequence was carried out using Clustal Omega multiple alignment service at the EBI website. Alignment of nt sequence and phylogenetic relationship revealed that the COVID-19 is a new viral strain and its biological source has not been yet detected. The expected orf pattern was different among isolates obtained from the same country or different countries as well as from SARS-CoV isolates or bats CoV suggesting different virus human interaction possibilities during infection and severity. All isolates had the main five orfs (1ab, S, M, N, E), whereas they differed in the expected accessory orfs. Being with the biological source of COVID-19 undetected, the role of human endogenous retrovirus (HERVs) in the regulation of the host cell gene expression or the encoding for products that could modulate COVID-19 infection and the spectrum of its symptoms is discussed.
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Affiliation(s)
- Ahmed M El-Shehawi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099 21944 Taif, Saudi Arabia.,Department of Genetics, Faculty of Agriculture, University of Alexandria, 21527 Alexandria, Egypt
| | - Saqer S Alotaibi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099 21944 Taif, Saudi Arabia
| | - Mona M Elseehy
- Department of Genetics, Faculty of Agriculture, University of Alexandria, 21527 Alexandria, Egypt
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23
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RNA-Seq Transcriptome Analysis Reveals Long Terminal Repeat Retrotransposon Modulation in Human Peripheral Blood Mononuclear Cells after In Vivo Lipopolysaccharide Injection. J Virol 2020; 94:JVI.00587-20. [PMID: 32669333 DOI: 10.1128/jvi.00587-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/07/2020] [Indexed: 12/30/2022] Open
Abstract
Human endogenous retroviruses (HERVs) and mammalian apparent long terminal repeat (LTR) retrotransposons (MaLRs) are retroviral sequences that integrated into germ line cells millions of years ago. Transcripts of these LTR retrotransposons are present in several tissues, and their expression is modulated in pathological conditions, although their function remains often far from being understood. Here, we focused on the HERV/MaLR expression and modulation in a scenario of immune system activation. We used a public data set of human peripheral blood mononuclear cells (PBMCs) RNA-Seq from 15 healthy participants to a clinical trial before and after exposure to lipopolysaccharide (LPS), for which we established an RNA-Seq workflow for the identification of expressed and modulated cellular genes and LTR retrotransposon elements.IMPORTANCE We described the HERV and MaLR transcriptome in PBMCs, finding that about 8.4% of the LTR retrotransposon loci were expressed and identifying the betaretrovirus-like HERVs as those with the highest percentage of expressed loci. We found 4,607 HERV and MaLR loci that were modulated as a result of in vivo stimulation with LPS. The HERV-H group showed the highest number of differentially expressed most intact proviruses. We characterized the HERV and MaLR loci as differentially expressed, checking their genomic context of insertion and observing a general colocalization with genes that are involved and modulated in the immune response, as a consequence of LPS stimulation. The analyses of HERV and MaLR expression and modulation show that these LTR retrotransposons are expressed in PBMCs and regulated in inflammatory settings. The similar regulation of HERVs/MaLRs and genes after LPS stimulation suggests possible interactions of LTR retrotransposons and the immune host response.
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24
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Liu CH, Grandi N, Palanivelu L, Tramontano E, Lin LT. Contribution of Human Retroviruses to Disease Development-A Focus on the HIV- and HERV-Cancer Relationships and Treatment Strategies. Viruses 2020; 12:E852. [PMID: 32759845 PMCID: PMC7472297 DOI: 10.3390/v12080852] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023] Open
Abstract
Animal retroviruses are known for their transforming potential, and this is also true for the ones hosted by humans, which have gathered expanding attention as one of the potent causative agents in various disease, including specific cancer types. For instance, Human T Lymphotropic virus (HTLV) is a well-studied class of oncoviruses causing T cell leukemia, while human immunodeficiency virus (HIV) leads to acquired immunodeficiency syndrome (AIDS), which is linked to a series of defining cancers including Kaposi sarcoma, certain types of non-Hodgkin lymphoma, and cervical cancer. Of note, in addition to these "modern" exogenous retroviruses, our genome harbors a staggering number of human endogenous retroviruses (HERVs). HERVs are the genetic remnants of ancient retroviral germline infection of human ancestors and are typically silenced in normal tissues due to inactivating mutations and sequence loss. While some HERV elements have been appropriated and contribute to human physiological functions, others can be reactivated through epigenetic dysregulations to express retroviral elements and promote carcinogenesis. Conversely, HERV replication intermediates or protein products can also serve as intrinsic pathogen-associated molecular patterns that cause the immune system to interpret it as an exogenous infection, thereby stimulating immune responses against tumors. As such, HERVs have also been targeted as a potential internal strategy to sensitize tumor cells for promising immunotherapies. In this review, we discuss the dynamic role of human retroviruses in cancer development, focusing on HIV and HERVs contribution. We also describe potential treatment strategies, including immunotherapeutic targeting of HERVs, inhibiting DNA methylation to expose HERV signatures, and the use of antiretroviral drugs against HIV and HERVs, which can be employed as prospective anti-cancer modalities.
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Affiliation(s)
- Ching-Hsuan Liu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, 09042 Cagliari, Italy; (N.G.); (E.T.)
| | - Lalitha Palanivelu
- International Master Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, 09042 Cagliari, Italy; (N.G.); (E.T.)
| | - Liang-Tzung Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
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25
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Gagliardi A, Porter VL, Zong Z, Bowlby R, Titmuss E, Namirembe C, Griner NB, Petrello H, Bowen J, Chan SK, Culibrk L, Darragh TM, Stoler MH, Wright TC, Gesuwan P, Dyer MA, Ma Y, Mungall KL, Jones SJM, Nakisige C, Novik K, Orem J, Origa M, Gastier-Foster JM, Yarchoan R, Casper C, Mills GB, Rader JS, Ojesina AI, Gerhard DS, Mungall AJ, Marra MA. Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade-specific epigenome and transcriptome landscapes. Nat Genet 2020; 52:800-810. [PMID: 32747824 PMCID: PMC7498180 DOI: 10.1038/s41588-020-0673-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 06/26/2020] [Indexed: 01/18/2023]
Abstract
Cervical cancer is the most common cancer affecting sub-Saharan African women and is prevalent among HIV-positive (HIV+) individuals. No comprehensive profiling of cancer genomes, transcriptomes or epigenomes has been performed in this population thus far. We characterized 118 tumors from Ugandan patients, of whom 72 were HIV+, and performed extended mutation analysis on an additional 89 tumors. We detected human papillomavirus (HPV)-clade-specific differences in tumor DNA methylation, promoter- and enhancer-associated histone marks, gene expression and pathway dysregulation. Changes in histone modification at HPV integration events were correlated with upregulation of nearby genes and endogenous retroviruses.
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Affiliation(s)
- Alessia Gagliardi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Vanessa L Porter
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zusheng Zong
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | | | - Nicholas B Griner
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Jay Bowen
- Nationwide Children's Hospital, Columbus, OH, USA
| | - Simon K Chan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Teresa M Darragh
- Department of Pathology, University of California at San Francisco, San Francisco, CA, USA
| | - Mark H Stoler
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Thomas C Wright
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maureen A Dyer
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Karen Novik
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | | | | | - Julie M Gastier-Foster
- Nationwide Children's Hospital, Columbus, OH, USA
- Departments of Pathology and Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Robert Yarchoan
- Office of HIV and AIDS Malignancy, National Cancer Institute, National Institues of Health, Bethesda, MD, USA
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Corey Casper
- Infectious Disease Research Institute, Seattle, WA, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Janet S Rader
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Akinyemi I Ojesina
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
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26
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Human Endogenous Retrovirus K in Cancer: A Potential Biomarker and Immunotherapeutic Target. Viruses 2020; 12:v12070726. [PMID: 32640516 PMCID: PMC7412025 DOI: 10.3390/v12070726] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/16/2022] Open
Abstract
In diseases where epigenetic mechanisms are changed, such as cancer, many genes show altered gene expression and inhibited genes become activated. Human endogenous retrovirus type K (HERV-K) expression is usually inhibited in normal cells from healthy adults. In tumor cells, however, HERV-K mRNA expression has been frequently documented to increase. Importantly, HERV-K-derived proteins can act as tumor-specific antigens, a class of neoantigens, and induce immune responses in different types of cancer. In this review, we describe the function of the HERV-K HML-2 subtype in carcinogenesis as biomarkers, and their potential as targets for cancer immunotherapy.
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27
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Mason AS, Lund AR, Hocking PM, Fulton JE, Burt DW. Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data. Mob DNA 2020; 11:22. [PMID: 32617122 PMCID: PMC7325683 DOI: 10.1186/s13100-020-00216-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022] Open
Abstract
Background Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. In chickens, endogenous Avian Leukosis Virus subgroup E (ALVE) expression has been associated with reductions in muscle growth rate and egg production, as well as providing the potential for novel recombinant viruses. However, ALVEs can remain in commercial stock due to their incomplete identification and association with desirable traits, such as ALVE21 and slow feathering. The availability of whole genome sequencing (WGS) data facilitates high-throughput identification and characterisation of these retroviral remnants. Results We have developed obsERVer, a new bioinformatic ERV identification pipeline which can identify ALVEs in WGS data without further sequencing. With this pipeline, 20 ALVEs were identified across eight elite layer lines from Hy-Line International, including four novel integrations and characterisation of a fast feathered phenotypic revertant that still contained ALVE21. These bioinformatically detected sites were subsequently validated using new high-throughput KASP assays, which showed that obsERVer was highly precise and exhibited a 0% false discovery rate. A further fifty-seven diverse chicken WGS datasets were analysed for their ALVE content, identifying a total of 322 integration sites, over 80% of which were novel. Like exogenous ALV, ALVEs show site preference for proximity to protein-coding genes, but also exhibit signs of selection against deleterious integrations within genes. Conclusions obsERVer is a highly precise and broadly applicable pipeline for identifying retroviral integrations in WGS data. ALVE identification in commercial layers has aided development of high-throughput diagnostic assays which will aid ALVE management, with the aim to eventually eradicate ALVEs from high performance lines. Analysis of non-commercial chicken datasets with obsERVer has revealed broad ALVE diversity and facilitates the study of the biological effects of these ERVs in wild and domesticated populations.
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Affiliation(s)
- Andrew S Mason
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK.,York Biomedical Research Institute, The Department of Biology, The University of York, York, YO10 5DD UK
| | - Ashlee R Lund
- Hy-Line International, 2583 240th Street, Dallas Center, Iowa, 50063 USA
| | - Paul M Hocking
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Janet E Fulton
- Hy-Line International, 2583 240th Street, Dallas Center, Iowa, 50063 USA
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK.,The University of Queensland, Brisbane, Queensland 4072 Australia
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28
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Bravo JI, Nozownik S, Danthi PS, Benayoun BA. Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation. Development 2020; 147:dev175786. [PMID: 32527937 PMCID: PMC10680986 DOI: 10.1242/dev.175786] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Our understanding of the molecular regulation of aging and age-related diseases is still in its infancy, requiring in-depth characterization of the molecular landscape shaping these complex phenotypes. Emerging classes of molecules with promise as aging modulators include transposable elements, circRNAs and the mitochondrial transcriptome. Analytical complexity means that these molecules are often overlooked, even though they exhibit strong associations with aging and, in some cases, may directly contribute to its progress. Here, we review the links between these novel factors and age-related phenotypes, and we suggest tools that can be easily incorporated into existing pipelines to better understand the aging process.
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Affiliation(s)
- Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Séverine Nozownik
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Magistère européen de Génétique, Université Paris Diderot-Paris 7, Paris 75014, France
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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29
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Pisano MP, Grandi N, Tramontano E. High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development. Viruses 2020; 12:E633. [PMID: 32545287 PMCID: PMC7354619 DOI: 10.3390/v12060633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 01/19/2023] Open
Abstract
Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. Their transcriptional activity is finely regulated in early developmental stages and their expression is modulated in different cell types and tissues. Such activity has an impact on human physiology and pathology that is only partially understood up to date. Novel high-throughput sequencing tools have recently allowed for a great advancement in elucidating the various HERV expression patterns in different tissues as well as the mechanisms controlling their transcription, and overall, have helped in gaining better insights in an all-inclusive understanding of the impact of HERVs in biology of the host.
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Affiliation(s)
- Maria Paola Pisano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
| | - Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, 09042 Cagliari, Italy
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30
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Mason AS, Miedzinska K, Kebede A, Bamidele O, Al-Jumaili AS, Dessie T, Hanotte O, Smith J. Diversity of endogenous avian leukosis virus subgroup E (ALVE) insertions in indigenous chickens. Genet Sel Evol 2020; 52:29. [PMID: 32487054 PMCID: PMC7268647 DOI: 10.1186/s12711-020-00548-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/26/2020] [Indexed: 12/05/2022] Open
Abstract
Background Avian leukosis virus subgroup E (ALVE) insertions are endogenous retroviruses (ERV) that are restricted to the domestic chicken and its wild progenitor. In commercial chickens, ALVE are known to have a detrimental effect on productivity and provide a source for recombination with exogenous retroviruses. The wider diversity of ALVE in non-commercial chickens and the role of these elements in ERV-derived immunity (EDI) are yet to be investigated. Results In total, 974 different ALVE were identified from 407 chickens sampled from village populations in Ethiopia, Iraq, and Nigeria, using the recently developed obsERVer bioinformatics identification pipeline. Eighty-eight percent of all identified ALVE were novel, bringing the known number of ALVE integrations to more than 1300 across all analysed chickens. ALVE content was highly lineage-specific and populations generally exhibited a large diversity of ALVE at low frequencies, which is typical for ERV involved in EDI. A significantly larger number of ALVE was found within or near coding regions than expected by chance, although a relative depletion of ALVE was observed within coding regions, which likely reflects selection against deleterious integrations. These effects were less pronounced than in previous analyses of chickens from commercial lines. Conclusions Identification of more than 850 novel ALVE has trebled the known diversity of these retroviral elements. This work provides the basis for future studies to fully quantify the role of ALVE in immunity against exogenous ALV, and development of programmes to improve the productivity and welfare of chickens in developing economies.
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Affiliation(s)
- Andrew S Mason
- The University of York, York, YO10 5DD, UK. .,The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Katarzyna Miedzinska
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Adebabay Kebede
- LiveGene-CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.,Addis Ababa University, Addis Ababa, Ethiopia
| | - Oladeji Bamidele
- African Chicken Genetic Gains, Department of Animal Sciences, Obafemi Awolowo, Ile Ife, Osun, Nigeria
| | - Ahmed S Al-Jumaili
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK.,University of Anbar, Ramadi, Anbar, Iraq
| | - Tadelle Dessie
- LiveGene-CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- LiveGene-CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.,School of Life Sciences, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK.,University of Anbar, Ramadi, Anbar, Iraq
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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31
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Panda A, Rosenfeld JA, Singer EA, Bhanot G, Ganesan S. Genomic and immunologic correlates of LAG-3 expression in cancer. Oncoimmunology 2020; 9:1756116. [PMID: 32923111 PMCID: PMC7458666 DOI: 10.1080/2162402x.2020.1756116] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 03/31/2020] [Indexed: 02/07/2023] Open
Abstract
Immune checkpoint blockade leads to unprecedented responses in many cancers. Although currently available agents mostly target the PD-1 and CTLA-4 pathways, agents targeting the immune checkpoint protein LAG-3 are under active clinical development, and early clinical data show that LAG-3 expression is a biomarker of response to LAG-3 blockade. To determine which cancers may benefit most from LAG-3 blockade, we performed a pan-cancer analysis of The Cancer Genome Atlas dataset to identify genomic and immunologic correlates of LAG-3 expression. High mutation burden, and expression of exogenous virus (EBV, HPV) or endogenous retrovirus (ERV3-2), were associated with overexpression of LAG-3 in multiple cancers. Although CD8+ T-cell marker (CD8A) and LAG-3 were strongly co-expressed with each other and with PD-L1 in most cancers, there were three notable exceptions: HPV+ head-neck squamous cell cancer, renal cell cancer, and glioblastoma. These results may have important implications for guiding development clinical trials of LAG-3 blockade.
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Affiliation(s)
- Anshuman Panda
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Jeffrey A. Rosenfeld
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Eric A. Singer
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Division of Urology, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Gyan Bhanot
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, USA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, USA
- Moores Cancer Center at UC San Diego Health, University of California at San Diego, La Jolla, CA, USA
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
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32
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Marasca F, Gasparotto E, Polimeni B, Vadalà R, Ranzani V, Bodega B. The Sophisticated Transcriptional Response Governed by Transposable Elements in Human Health and Disease. Int J Mol Sci 2020; 21:ijms21093201. [PMID: 32366056 PMCID: PMC7247572 DOI: 10.3390/ijms21093201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 01/15/2023] Open
Abstract
Transposable elements (TEs), which cover ~45% of the human genome, although firstly considered as “selfish” DNA, are nowadays recognized as driving forces in eukaryotic genome evolution. This capability resides in generating a plethora of sophisticated RNA regulatory networks that influence the cell type specific transcriptome in health and disease. Indeed, TEs are transcribed and their RNAs mediate multi-layered transcriptional regulatory functions in cellular identity establishment, but also in the regulation of cellular plasticity and adaptability to environmental cues, as occurs in the immune response. Moreover, TEs transcriptional deregulation also evolved to promote pathogenesis, as in autoimmune and inflammatory diseases and cancers. Importantly, many of these findings have been achieved through the employment of Next Generation Sequencing (NGS) technologies and bioinformatic tools that are in continuous improvement to overcome the limitations of analyzing TEs sequences. However, they are highly homologous, and their annotation is still ambiguous. Here, we will review some of the most recent findings, questions and improvements to study at high resolution this intriguing portion of the human genome in health and diseases, opening the scenario to novel therapeutic opportunities.
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Affiliation(s)
- Federica Marasca
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Erica Gasparotto
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Benedetto Polimeni
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Rebecca Vadalà
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
- Translational and Molecular Medicine, DIMET, University of Milan-Bicocca, 20900 Monza, Italy
| | - Valeria Ranzani
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Beatrice Bodega
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
- Correspondence:
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33
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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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Wolf D, Fiegl H, Zeimet AG, Wieser V, Marth C, Sprung S, Sopper S, Hartmann G, Reimer D, Boesch M. High RIG-I expression in ovarian cancer associates with an immune-escape signature and poor clinical outcome. Int J Cancer 2020; 146:2007-2018. [PMID: 31800094 PMCID: PMC7028124 DOI: 10.1002/ijc.32818] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/28/2019] [Accepted: 11/25/2019] [Indexed: 12/25/2022]
Abstract
Ovarian cancer (OC) is the most lethal gynecological malignancy, with platinum-based chemotherapy remaining the mainstay for adjuvant treatment after surgery. The lack of indication for immunotherapy may at least in part result from the lack of suitable biomarkers allowing stratification of potentially responding patients. In this monocentric study of 141 cases with OC, we used real-time quantitative PCR to assess the expression of retinoic acid-inducible gene-I (RIG-I) in primary tumor and healthy ovarian control tissues. RIG-I expression was correlated to various clinicopathological characteristics as well as to a set of molecular and immunological markers. The prognostic significance of RIG-I expression was queried in univariate and multivariate analyses and validated in an independent cohort. RIG-I was overexpressed in the cancerous ovary and correlated with a higher tumor grade. The more aggressive Type-II cancers and cancers with inactivating p53 mutations exhibited higher RIG-I expression. RIG-I levels were also elevated in cancers that recurred after remission or were platinum-refractory. Survival analyses disclosed RIG-I as an independent marker of poor outcome in OC. Continuative analyses revealed the molecular and immunological correlates of RIG-I expression in the tumor microenvironment, including interferon production and a distinct immune-regulatory signature involving checkpoint molecules (PD-L1/PD-1), the RNA-editing enzyme ADAR1 and the regulatory T cell-specific transcription factor FoxP3. We conclude that high RIG-I expression associates with poor outcome in OC, which is explainable by local immunosuppression in the tumor bed. RIG-I expression may inform checkpoint blockade and/or RIG-I agonistic targeting in a subset of high-risk OC patients.
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Affiliation(s)
- Dominik Wolf
- Internal Medicine VMedical University of InnsbruckInnsbruckAustria
- Medical Clinic III, Oncology, Hematology, Immuno‐Oncology and RheumatologyUniversity Clinic BonnBonnGermany
| | - Heidi Fiegl
- Department of Gynecology and ObstetricsMedical University of InnsbruckInnsbruckAustria
| | - Alain G. Zeimet
- Department of Gynecology and ObstetricsMedical University of InnsbruckInnsbruckAustria
| | - Verena Wieser
- Department of Gynecology and ObstetricsMedical University of InnsbruckInnsbruckAustria
| | - Christian Marth
- Department of Gynecology and ObstetricsMedical University of InnsbruckInnsbruckAustria
| | - Susanne Sprung
- Department of PathologyMedical University of InnsbruckInnsbruckAustria
| | - Sieghart Sopper
- Internal Medicine VMedical University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research InstituteInnsbruckAustria
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Clinical PharmacologyUniversity Clinic BonnBonnGermany
| | - Daniel Reimer
- Department of Gynecology and ObstetricsMedical University of InnsbruckInnsbruckAustria
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35
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Macchietto MG, Langlois RA, Shen SS. Virus-induced transposable element expression up-regulation in human and mouse host cells. Life Sci Alliance 2020; 3:3/2/e201900536. [PMID: 31964680 PMCID: PMC6977392 DOI: 10.26508/lsa.201900536] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/18/2022] Open
Abstract
Genome-wide transposon expression up-regulation in host cells regardless of virus, species, and host cell tissue types occurs early during viral infection and likely contributes to promoting the host innate immune response. Virus–host cell interactions initiate a host cell–defensive response during virus infection. How transposable elements in the host cell respond to viral stress at the molecular level remains largely unclear. By reanalyzing next generation sequencing data sets from dozens of virus infection studies from the Gene Expression Omnibus database, we found that genome-wide transposon expression up-regulation in host cells occurs near antiviral response genes and exists in all studies regardless of virus, species, and host cell tissue types. Some transposons were found to be up-regulated almost immediately upon infection and before increases in virus replication and significant increases in interferon β expression. These findings indicate that transposon up-regulation is a common phenomenon during virus infection in human and mouse and that early up-regulated transposons are part of the first wave response during virus infection.
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Affiliation(s)
| | - Ryan A Langlois
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Steven S Shen
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA .,Clinical Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
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36
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Endogenous Retroviruses Activity as a Molecular Signature of Neurodevelopmental Disorders. Int J Mol Sci 2019; 20:ijms20236050. [PMID: 31801288 PMCID: PMC6928979 DOI: 10.3390/ijms20236050] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are genetic elements resulting from relics of ancestral infection of germline cells, now recognized as cofactors in the etiology of several complex diseases. Here we present a review of findings supporting the role of the abnormal HERVs activity in neurodevelopmental disorders. The derailment of brain development underlies numerous neuropsychiatric conditions, likely starting during prenatal life and carrying on during subsequent maturation of the brain. Autism spectrum disorders, attention deficit hyperactivity disorders, and schizophrenia are neurodevelopmental disorders that arise clinically during early childhood or adolescence, currently attributed to the interplay among genetic vulnerability, environmental risk factors, and maternal immune activation. The role of HERVs in human embryogenesis, their intrinsic responsiveness to external stimuli, and the interaction with the immune system support the involvement of HERVs in the derailed neurodevelopmental process. Although definitive proofs that HERVs are involved in neurobehavioral alterations are still lacking, both preclinical models and human studies indicate that the abnormal expression of ERVs could represent a neurodevelopmental disorders-associated biological trait in affected individuals and their parents.
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37
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Rodrigues LS, da Silva Nali LH, Leal COD, Sabino EC, Lacerda EM, Kingdon CC, Nacul L, Romano CM. HERV-K and HERV-W transcriptional activity in myalgic encephalomyelitis/chronic fatigue syndrome. AUTOIMMUNITY HIGHLIGHTS 2019; 10:12. [PMID: 32257068 PMCID: PMC7065355 DOI: 10.1186/s13317-019-0122-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/09/2019] [Indexed: 02/08/2023]
Abstract
Background Chronic fatigue syndrome/myalgic encephalomyelitis (CFS/MS) is an incapacitating chronic disease that dramatically compromise the life quality. The CFS/ME pathogenesis is multifactorial, and it is believed that immunological, metabolic and environmental factors play a role. It is well documented an increased activity of Human endogenous retroviruses (HERVs) from different families in autoimmune and neurological diseases, making these elements good candidates for biomarkers or even triggers for such diseases. Methods Here the expression of Endogenous retroviruses K and W (HERV-K and HERV-W) was determined in blood from moderately and severely affected ME/CFS patients through real time PCR. Results HERV-K was overexpressed only in moderately affected individuals but HERV-W showed no difference. Conclusions This is the first report about HERV-K differential expression in moderate ME/CFS. Although the relationship between HERVs and ME/CFS has yet to be proven, the observation of this phenomenon deserves further attention.
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Affiliation(s)
- Lucas S Rodrigues
- 1Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP 05403-000 Brazil
| | - Luiz H da Silva Nali
- 1Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP 05403-000 Brazil.,2Pós-Graduação em Ciências da Saúde, Universidade Santo Amaro, São Paulo, Brazil
| | - Cibele O D Leal
- 1Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP 05403-000 Brazil
| | - Ester C Sabino
- 1Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP 05403-000 Brazil.,3Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Eliana M Lacerda
- 4Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Caroline C Kingdon
- 4Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Luis Nacul
- 4Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Camila M Romano
- 1Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, Rua Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP 05403-000 Brazil.,5Hospital das Clinicas HCFMUSP (LIM52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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38
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Balestrieri E, Cipriani C, Matteucci C, Benvenuto A, Coniglio A, Argaw-Denboba A, Toschi N, Bucci I, Miele MT, Grelli S, Curatolo P, Sinibaldi-Vallebona P. Children With Autism Spectrum Disorder and Their Mothers Share Abnormal Expression of Selected Endogenous Retroviruses Families and Cytokines. Front Immunol 2019; 10:2244. [PMID: 31616420 PMCID: PMC6775388 DOI: 10.3389/fimmu.2019.02244] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/04/2019] [Indexed: 12/31/2022] Open
Abstract
The Autism Spectrum Disorder (ASD) is a heterogeneous group of neurodevelopmental disorders, only clinically diagnosed since the lack of reliable biomarkers. Autism etiology is probably attributable to the combination of genetic vulnerability and environmental factors, and recently, maternal immune activation has been linked to derailed neurodevelopment, resulting in ASD in the offspring. Human endogenous retroviruses (HERVs) are relics of ancestral infections, stably integrated in the human DNA. Given the HERV persistence in the genome, some of HERVs have been co-opted for physiological functions during evolution, while their reactivation has been associated with several pathological conditions, including cancer, autoimmune, and neurological and psychiatric disorders. Particularly, due to their intrinsic responsiveness to external stimuli, HERVs can modulate the host immune response and in turn HERVs can be activated by the immune effectors. In previous works we demonstrated high expression levels of HERV-H in blood of autistic patients, closely related with the severity of the disease. Moreover, in a preclinical ASD model we proved changes of expression of several ERV families and cytokines from the intrauterine life to the adulthood, and across generations via maternal lineage. Here we analyzed the expression of HEMO and of selected HERVs and cytokines in blood from ASD patients and their parents and corresponding healthy controls, to look for a common molecular trait within family members. ASD patients and their mothers share altered expression of HERV-H and HEMO and of cytokines such as TNF-α, IFN-γ, IL-10. The multivariate regression models showed a mother-child association by HEMO activity and demonstrated in children and mothers an association between HERV-H and HEMO expression and, only in mothers, between HEMO, and TNF-α expression. Furthermore, high diagnostic performance for HERV-H and HEMO was found, suggesting their potential application for the identification of ASD children and their mothers. The present data support the involvement of HERVs in ASD and suggest HERVs and cytokines as ASD-associated traits. Since ASD is a heterogeneous group of neurodevelopmental disorders, a single determinant alone could be not enough to account for the complexity, and HERV/cytokines expression could be considered in a set of biomarkers, easily detectable in blood, and potentially useful for an early diagnosis.
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Affiliation(s)
- Emanuela Balestrieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Chiara Cipriani
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Claudia Matteucci
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Arianna Benvenuto
- Child Neurology and Psychiatry Unit, Systems Medicine Department, University Hospital Tor Vergata, Rome, Italy
| | - Antonella Coniglio
- Child Neurology and Psychiatry Unit, Systems Medicine Department, University Hospital Tor Vergata, Rome, Italy
| | | | - Nicola Toschi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Athinoula A. Martinos Center for Biomedical Imaging, Harvard Medical School, Boston, MA, United States
| | - Ilaria Bucci
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Martino Tony Miele
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, University Hospital Tor Vergata, Rome, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.,Institute of Translational Pharmacology, National Research Council, Rome, Italy
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39
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Bloom AC, Bender LH, Tiwary S, Pasquet L, Clark K, Jiang T, Xia Z, Morales-Kastresana A, Jones JC, Walters I, Terabe M, Berzofsky JA. Intratumorally delivered formulation, INT230-6, containing potent anticancer agents induces protective T cell immunity and memory. Oncoimmunology 2019; 8:e1625687. [PMID: 31646070 DOI: 10.1080/2162402x.2019.1625687] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 05/02/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
The benefits of anti-cancer agents extend beyond direct tumor killing. One aspect of cell death is the potential to release antigens that initiate adaptive immune responses. Here, a diffusion enhanced formulation, INT230-6, containing potent anti-cancer cytotoxic agents, was administered intratumorally into large (approx. 300mm3) subcutaneous murine Colon26 tumors. Treatment resulted in regression from baseline in 100% of the tumors and complete response in up to 90%. CD8+ or CD8+/CD4+ T cell double-depletion at treatment onset prevented complete responses, indicating a critical role of T cells in promoting complete tumor regression. Mice with complete response were protected from subcutaneous and intravenous re-challenge of Colon26 cells in a CD4+/CD8+ dependent manner. Thus, immunological T cell memory was induced by INT230-6. Colon26 tumors express the endogenous retroviral protein gp70 containing the CD8+ T-cell AH-1 epitope. AH-1-specific CD8+ T cells were detected in peripheral blood of tumor-bearing mice and their frequency increased 14 days after treatment onset. AH-1-specific CD8+ T cells were also significantly enriched in tumors of untreated mice. These cells had an activated phenotype and highly expressed Programmed cell-death protein-1 (PD-1) but did not lead to tumor regression. CD8+ T cell tumor infiltrate also increased 11 days after treatment. INT230-6 synergized with checkpoint blockade, inducing a complete remission of the primary tumors and shrinking of untreated contralateral tumors, which demonstrates not only a local but also systemic immunological effect of the combined therapy. Similar T-cell dependent inhibition of tumor growth was also found in an orthotopic 4T1 breast cancer model.
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Affiliation(s)
- Anja C Bloom
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Shweta Tiwary
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Lise Pasquet
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Katharine Clark
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Tianbo Jiang
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zheng Xia
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Jennifer C Jones
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Masaki Terabe
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jay A Berzofsky
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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Hurst TP, Aswad A, Karamitros T, Katzourakis A, Smith AL, Magiorkinis G. Interferon-Inducible Protein 16 (IFI16) Has a Broad-Spectrum Binding Ability Against ssDNA Targets: An Evolutionary Hypothesis for Antiretroviral Checkpoint. Front Microbiol 2019; 10:1426. [PMID: 31333597 PMCID: PMC6621918 DOI: 10.3389/fmicb.2019.01426] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/05/2019] [Indexed: 12/14/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are under genomic and epigenetic control but can be expressed in normal tissues, producing RNA transcripts some of which are translated. While it has not been demonstrated experimentally in modern humans, cDNA copies from HERV RNA (namely HERV-K HML-2 or HK2) were produced after the human-chimp split and until at least 250,000 years ago. We were interested in determining if such cDNA could be a ligand for pattern recognition receptors (PRRs) of the innate immune response. The AIM-2-like receptors for DNA, interferon-γ-inducible protein 16 (IFI16) and Cyclic GMP-AMP synthase (cGAS) were candidate PRRs. IFI16 can detect cDNA produced during HIV-1 replication, causing increased T cell death. While HIV-1 has emerged relatively recently as a human pathogen, the cDNA functionality of IFI16 could have been selected for during the course of human evolution. Here we present a novel hypothesis that the products of reverse transcription of HK2, which has been proliferating in the genome of human ancestors for 30 million years, could interact with IFI16. In support of our hypothesis, we provide preliminary data showing that IFI16 (but not cGAS) interacts with synthetic single-stranded HK2 oligos corresponding to the first product of reverse transcription. Further, we show that ssDNA detection by IFI16 has variability with respect to sequence features but is not dependent on strong secondary structures mimicking dsDNA. Among the HK2 oligos, IFI16 interacts more intensely with those derived from LTRs, suggesting these oligos have undetermined structural features that allow IFI16 to bind with greater affinity. Further, cells with stem cell features that naturally allow HK2 expression were found to express many components of the innate immune system including cGAS but not IFI16. Based on the presented preliminary data we further postulate another hypothesis: that the IFI16 functionality in human cells has been acting as "second-line" defense to control abnormal HK2 replication in somatic tissues. The absence of this protein in stem cells and a stem cell line could permit these cells to express HERVs which contribute to stem cell identity. Finally, we also comment on potential studies that could support or refute our hypothesis.
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Affiliation(s)
- Tara Patricia Hurst
- Department of Zoology, University of Oxford, Oxford, United Kingdom.,Department of Life Sciences, School of Health Sciences, Birmingham City University, Birmingham, United Kingdom
| | - Amr Aswad
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Timokratis Karamitros
- Department of Zoology, University of Oxford, Oxford, United Kingdom.,Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Adrian L Smith
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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41
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Neil JA, Cadwell K. The Intestinal Virome and Immunity. THE JOURNAL OF IMMUNOLOGY 2019; 201:1615-1624. [PMID: 30181300 DOI: 10.4049/jimmunol.1800631] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 05/21/2018] [Indexed: 12/12/2022]
Abstract
The composition of the human microbiome is considered a major source of interindividual variation in immunity and, by extension, susceptibility to diseases. Intestinal bacteria have been the major focus of research. However, diverse communities of viruses that infect microbes and the animal host cohabitate the gastrointestinal tract and collectively constitute the gut virome. Although viruses are typically investigated as pathogens, recent studies highlight a relationship between the host and animal viruses in the gut that is more akin to host-microbiome interactions and includes both beneficial and detrimental outcomes for the host. These viruses are likely sources of immune variation, both locally and extraintestinally. In this review, we describe the components of the gut virome, in particular mammalian viruses, and their ability to modulate host responses during homeostasis and disease.
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Affiliation(s)
- Jessica A Neil
- Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016; and Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Ken Cadwell
- Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016; and Department of Microbiology, New York University School of Medicine, New York, NY 10016
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42
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Misiak B, Ricceri L, Sąsiadek MM. Transposable Elements and Their Epigenetic Regulation in Mental Disorders: Current Evidence in the Field. Front Genet 2019; 10:580. [PMID: 31293617 PMCID: PMC6603224 DOI: 10.3389/fgene.2019.00580] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/04/2019] [Indexed: 12/30/2022] Open
Abstract
Transposable elements (TEs) are highly repetitive DNA sequences in the human genome that are the relics of previous retrotransposition events. Although the majority of TEs are transcriptionally inactive due to acquired mutations or epigenetic processes, around 8% of TEs exert transcriptional activity. It has been found that TEs contribute to somatic mosaicism that accounts for functional specification of various brain cells. Indeed, autonomous retrotransposition of long interspersed element-1 (LINE-1) sequences has been reported in the neural rat progenitor cells from the hippocampus, the human fetal brain and the human embryonic stem cells. Moreover, expression of TEs has been found to regulate immune-inflammatory responses, conditioning immunity against exogenous infections. Therefore, aberrant epigenetic regulation and expression of TEs emerged as a potential mechanism underlying the development of various mental disorders, including autism spectrum disorders (ASD), schizophrenia, bipolar disorder, major depression, and Alzheimer's disease (AD). Consequently, some studies revealed that expression of some sequences of human endogenous retroviruses (HERVs) appears only in a certain group of patients with mental disorders (especially those with schizophrenia, bipolar disorder, and ASD) but not in healthy controls. In addition, it has been found that expression of HERVs might be related to subclinical inflammation observed in mental disorders. In this article, we provide an overview of detrimental effects of transposition on the brain development and immune mechanisms with relevance to mental disorders. We show that transposition is not the only mechanism, explaining the way TEs might shape the phenotype of mental disorders. Other mechanisms include the regulation of gene expression and the impact on genomic stability. Next, we review current evidence from studies investigating expression and epigenetic regulation of specific TEs in various mental disorders. Most consistently, these studies indicate altered expression of HERVs and methylation of LINE-1 sequences in patients with ASD, schizophrenia, and mood disorders. However, the contribution of TEs to the etiology of AD is poorly documented. Future studies should further investigate the mechanisms linking epigenetic processes, specific TEs and the phenotype of mental disorders to disentangle causal associations.
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Affiliation(s)
- Błażej Misiak
- Department of Genetics, Wrocław Medical University, Wrocław, Poland
| | - Laura Ricceri
- Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
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43
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Feng M, Ren F, Zhou Y, Zhang N, Lu Q, Swevers L, Sun J. Correlation in Expression between LTR Retrotransposons and Potential Host Cis-Targets during Infection of Antherea pernyi with ApNPV Baculovirus. Viruses 2019; 11:v11050421. [PMID: 31064084 PMCID: PMC6563192 DOI: 10.3390/v11050421] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 05/04/2019] [Indexed: 12/14/2022] Open
Abstract
The published genome sequence of Antheraeayamamai (Saturnnidae) was used to construct a library of long terminal repeat (LTR)-retrotransposons that is representative of the wild silkmoth (Antherea) genus, and that includes 22,666 solo LTRs and 541 full-length LTRs. The LTR retrotransposons of Antheraeayamamai (AyLTRs) could be classified into the three canonical groups of Gypsy, Copia and Belpao. Eleven AyLTRs contained the env gene element, but the relationship with the env element of baculovirus, particularly A. yamamai and pernyi nucleopolyhedrovirus (AyNPV and ApNPV), was distant. A total of 251 “independent” full-length AyLTRs were identified that were located within 100 kb distance (downstream or upstream) of 406 neighboring genes in A. yamamai. Regulation of these genes might occur in cis by the AyLTRs, and the neighboring genes were found to be enriched in GO terms such as “response to stimulus”, and KEGG terms such as “mTOR signaling pathway” among others. Furthermore, the library of LTR-retrotransposons and the A. yamamai genome were used to identify and analyze the expression of LTR-retrotransposons and genes in ApNPV-infected and non-infected A. pernyi larval midguts, using raw data of a published transcriptome study. Our analysis demonstrates that 93 full-length LTR-retrotransposons are transcribed in the midgut of A. pernyi of which 12 significantly change their expression after ApNPV infection (differentially expressed LTR-retrotransposons or DELs). In addition, the expression of differentially expressed genes (DEGs) and neighboring DELs on the chromosome following ApNPV infection suggests the possibility of regulation of expression of DEGs by DELs through a cis mechanism, which will require experimental verification. When examined in more detail, it was found that genes involved in Notch signaling and stress granule (SG) formation were significantly up-regulated in ApNPV-infected A. pernyi larval midgut. Moreover, several DEGs in the Notch and SG pathways were found to be located in the neighborhood of particular DELs, indicating the possibility of DEG-DEL cross-regulation in cis for these two pathways.
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Affiliation(s)
- Min Feng
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research Demokritos, Aghia Paraskevi, Athens 15341, Greece.
| | - Feifei Ren
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Yaohong Zhou
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Nan Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Qiuyuan Lu
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research Demokritos, Aghia Paraskevi, Athens 15341, Greece.
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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Lai RW, Lu R, Danthi PS, Bravo JI, Goumba A, Sampathkumar NK, Benayoun BA. Multi-level remodeling of transcriptional landscapes in aging and longevity. BMB Rep 2019. [PMID: 30526773 PMCID: PMC6386224 DOI: 10.5483/bmbrep.2019.52.1.296] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and gene expression has been observed to be deregulated with aging. In this review, we discuss the current knowledge on the transcriptional alterations that have been described to occur with age in metazoans. First, we discuss age-related transcriptional changes in protein-coding genes, the expected functional impact of such changes, and how known pro-longevity interventions impact these changes. Second, we discuss the changes and impact of emerging aspects of transcription in aging, including age-related changes in splicing, lncRNAs and circRNAs. Third, we discuss the changes and potential impact of transcription of transposable elements with aging. Fourth, we highlight small ncRNAs and their potential impact on the regulation of aging phenotypes. Understanding the aging transcriptome will be key to identify important regulatory targets, and ultimately slow-down or reverse aging and extend healthy lifespan in humans.
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Affiliation(s)
- Rochelle W Lai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Ryan Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089; Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Alexandre Goumba
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089; USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089; USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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45
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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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Zheng W, Satta Y. Functional Evolution of Avian RIG-I-Like Receptors. Genes (Basel) 2018; 9:genes9090456. [PMID: 30213147 PMCID: PMC6162795 DOI: 10.3390/genes9090456] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/06/2018] [Accepted: 09/06/2018] [Indexed: 12/24/2022] Open
Abstract
RIG-I-like receptors (retinoic acid-inducible gene-I-like receptors, or RLRs) are family of pattern-recognition receptors for RNA viruses, consisting of three members: retinoic acid-inducible gene I (RIG-I), melanoma differentiation-associated gene 5 (MDA5) and laboratory of genetics and physiology 2 (LGP2). To understand the role of RLRs in bird evolution, we performed molecular evolutionary analyses on the coding genes of avian RLRs using filtered predicted coding sequences from 62 bird species. Among the three RLRs, conservation score and dN/dS (ratio of nonsynonymous substitution rate over synonymous substitution rate) analyses indicate that avian MDA5 has the highest conservation level in the helicase domain but a lower level in the caspase recruitment domains (CARDs) region, which differs from mammals; LGP2, as a whole gene, has a lower conservation level than RIG-I or MDA5. We found evidence of positive selection across all bird lineages in RIG-I and MDA5 but only on the stem lineage of Galliformes in LGP2, which could be related to the loss of RIG-I in Galliformes. Analyses also suggest that selection relaxation may have occurred in LGP2 during the middle of bird evolution and the CARDs region of MDA5 contains many positively selected sites, which might explain its conservation level. Spearman’s correlation test indicates that species-to-ancestor dN/dS of RIG-I shows a negative correlation with endogenous retroviral abundance in bird genomes, suggesting the possibility of interaction between immunity and endogenous retroviruses during bird evolution.
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Affiliation(s)
- Wanjing Zheng
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan.
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan.
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Grandi N, Tramontano E. Human Endogenous Retroviruses Are Ancient Acquired Elements Still Shaping Innate Immune Responses. Front Immunol 2018; 9:2039. [PMID: 30250470 PMCID: PMC6139349 DOI: 10.3389/fimmu.2018.02039] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/20/2018] [Indexed: 12/25/2022] Open
Abstract
About 8% of our genome is composed of sequences with viral origin, namely human Endogenous Retroviruses (HERVs). HERVs are relics of ancient infections that affected the primates' germ line along the last 100 million of years, and became stable elements at the interface between self and foreign DNA. Intriguingly, HERV co-evolution with the host led to the domestication of activities previously devoted to the retrovirus life cycle, providing novel cellular functions. For example, selected HERV envelope proteins have been coopted for pregnancy-related purposes, and proviral Long Terminal Repeats participate in the transcriptional regulation of various cellular genes. Given the HERV persistence in the host genome and its basal expression in most healthy tissues, it is reasonable that human defenses should prevent HERV-mediated immune activation. Despite this, HERVs and their products (including RNA, cytosolic DNA, and proteins) are still able to modulate and be influenced by the host immune system, fascinatingly suggesting a central role in the evolution and functioning of the human innate immunity. Indeed, HERV sequences had been major contributors in shaping and expanding the interferon network, dispersing inducible genes that have been occasionally domesticated in various mammalian lineages. Also the HERV integration within or near to genes encoding for critical immune factors has been shown to influence their activity, or to be responsible for their polymorphic variation in the human population, such as in the case of an HERV-K(HML10) provirus in the major histocompatibility complex region. In addition, HERV expressed products have been shown to modulate innate immunity effectors, being therefore often related on the one side to inflammatory and autoimmune disorders, while on the other side to the control of excessive immune activation through their immunosuppressive properties. Finally, HERVs have been proposed to establish a protective effect against exogenous infections. The present review summarizes the involvement of HERVs and their products in innate immune responses, describing how their intricate interplay with the first line of human defenses can actively contribute either to the host protection or to his damage, implying a subtle balance between the persistence of HERV expression and the maintenance of a basal immune alert.
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Affiliation(s)
- Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.,Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
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48
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Tartaglione AM, Cipriani C, Chiarotti F, Perrone B, Balestrieri E, Matteucci C, Sinibaldi-Vallebona P, Calamandrei G, Ricceri L. Early Behavioral Alterations and Increased Expression of Endogenous Retroviruses Are Inherited Across Generations in Mice Prenatally Exposed to Valproic Acid. Mol Neurobiol 2018; 56:3736-3750. [DOI: 10.1007/s12035-018-1328-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/22/2018] [Indexed: 12/12/2022]
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49
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Montesion M, Williams ZH, Subramanian RP, Kuperwasser C, Coffin JM. Promoter expression of HERV-K (HML-2) provirus-derived sequences is related to LTR sequence variation and polymorphic transcription factor binding sites. Retrovirology 2018; 15:57. [PMID: 30126415 PMCID: PMC6102855 DOI: 10.1186/s12977-018-0441-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 08/13/2018] [Indexed: 12/29/2022] Open
Abstract
Background Increased transcription of the human endogenous retrovirus group HERV-K (HML-2) is often seen during disease. Although the mechanism of its tissue-specific activation is unclear, research shows that LTR CpG hypomethylation alone is not sufficient to induce its promoter activity and that the transcriptional milieu of a malignant cell contributes, at least partly, to differential HML-2 expression. Results We analyzed the relationship between LTR sequence variation and promoter expression patterns in human breast cancer cell lines, finding them to be positively correlated. In particular, two proviruses (3q12.3 and 11p15.4) displayed increased activity in almost all tumorigenic cell lines sampled. Using a transcription factor binding site prediction algorithm, we identified two unique binding sites in each 5′ LTR that appeared to be associated with inducing promoter activity during neoplasia. Genomic analysis of the homologous proviruses in several non-human primates indicated post-integration genetic drift in two transcription factor binding sites, away from the ancestral sequence and towards the active form. Based on the sequences of 2504 individuals from the 1000 Genomes Project, the active form of the 11p15.4 site was found to be polymorphic within the human population, with an allele frequency of 51%, whereas the activating mutation in the 3q12.3 provirus was fixed in humans but not present in the orthologous provirus in chimpanzees or gorillas. Conclusions These data suggest that stage-specific transcription factors at least partly contribute to LTR promoter activity during transformation and that, in some cases, transcription factor binding site polymorphisms may be responsible for the differential HML-2 expression often seen between individuals. Electronic supplementary material The online version of this article (10.1186/s12977-018-0441-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meagan Montesion
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.,Foundation Medicine, Inc., Cambridge, MA, USA
| | - Zachary H Williams
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Ravi P Subramanian
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.,Excerpta Medica, New York, NY, USA
| | - Charlotte Kuperwasser
- Department of Developmental, Chemical, and Molecular Biology, Tufts University School of Medicine, Boston, MA, USA.,Raymond and Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, Boston, MA, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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50
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Wallace AD, Wendt GA, Barcellos LF, de Smith AJ, Walsh KM, Metayer C, Costello JF, Wiemels JL, Francis SS. To ERV Is Human: A Phenotype-Wide Scan Linking Polymorphic Human Endogenous Retrovirus-K Insertions to Complex Phenotypes. Front Genet 2018; 9:298. [PMID: 30154825 PMCID: PMC6102640 DOI: 10.3389/fgene.2018.00298] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
Approximately 8% of the human genome is comprised of endogenous retroviral insertions (ERVs) originating from historic retroviral integration into germ cells. The function of ERVs as regulators of gene expression is well established. Less well studied are insertional polymorphisms of ERVs and their contribution to the heritability of complex phenotypes. The most recent integration of ERV, HERV-K, is expressed in a range of complex human conditions from cancer to neurologic diseases. Using an in-house computational pipeline and whole-genome sequencing data from the diverse 1,000 Genomes Phase 3 population (n = 2,504), we identified 46 polymorphic HERV-K insertions that are tagged by adjacent single nucleotide polymorphisms (SNPs). To test the potential role of polymorphic HERV-K in the heritability of complex diseases, existing databases were queried for enrichment of established relationships between the HERV-K insertion-associated SNPs (hiSNPs), and tissue specific gene expression and disease phenotypes. Overall, hiSNPs for the 46 polymorphic HERV-K sites were statistically enriched (p < 1.0E-16) for eQTLs across 44 human tissues. Fifteen of the 46 HERV-K insertions had hiSNPs annotated in the EMBL-EBI GWAS Catalog and cumulatively associated with >100 phenotypes. Experimental factor ontology enrichment analysis suggests that polymorphic HERV-K specifically contribute to neurologic and immunologic disease phenotypes, including traits related to intra cranial volume (FDR 2.00E-09), Parkinson's disease (FDR 1.80E-09), and autoimmune diseases (FDR 1.80E-09). These results provide strong candidates for context-specific study of polymorphic HERV-K insertions in disease-related traits, serving as a roadmap for future studies of the heritability of complex disease.
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Affiliation(s)
- Amelia D Wallace
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - George A Wendt
- Division of Epidemiology, School of Community Health Sciences, University of Nevada, Reno, NV, United States
| | - Lisa F Barcellos
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Adam J de Smith
- Department of Epidemiology and Biostatistics, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Kyle M Walsh
- Department of Neurosurgery, Duke University, Durham, NC, United States
| | - Catherine Metayer
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Joseph F Costello
- Department of Neurosurgery, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurosurgery, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Stephen S Francis
- Division of Epidemiology, School of Community Health Sciences, University of Nevada, Reno, NV, United States.,Department of Epidemiology and Biostatistics, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
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