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Topham JT, Titmuss E, Pleasance ED, Williamson LM, Karasinska JM, Culibrk L, Lee MKC, Mendis S, Denroche RE, Jang GH, Kalloger SE, Wong HL, Moore RA, Mungall AJ, O'Kane GM, Knox JJ, Gallinger S, Loree JM, Mager DL, Laskin J, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Endogenous Retrovirus Transcript Levels Are Associated with Immunogenic Signatures in Multiple Metastatic Cancer Types. Mol Cancer Ther 2020; 19:1889-1897. [PMID: 32518206 DOI: 10.1158/1535-7163.mct-20-0094] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/28/2020] [Accepted: 06/04/2020] [Indexed: 11/16/2022]
Abstract
Next-generation sequencing of solid tumors has revealed variable signatures of immunogenicity across tumors, but underlying molecular characteristics driving such variation are not fully understood. Although expression of endogenous retrovirus (ERV)-containing transcripts can provide a source of tumor-specific neoantigen in some cancer models, associations between ERV levels and immunogenicity across different types of metastatic cancer are not well established. We performed bioinformatics analysis of genomic, transcriptomic, and clinical data across an integrated cohort of 199 patients with metastatic breast, colorectal, and pancreatic ductal adenocarcinoma tumors. Within each cancer type, we identified a subgroup of viral mimicry tumors in which increased ERV levels were coupled with transcriptional signatures of autonomous antiviral response and immunogenicity. In addition, viral mimicry colorectal and pancreatic tumors showed increased expression of DNA demethylation gene TET2 Taken together, these data demonstrate the existence of an ERV-associated viral mimicry phenotype across three distinct metastatic cancer types, while indicating links between ERV abundance, epigenetic dysregulation, and immunogenicity.
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Affiliation(s)
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Erin D Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | | | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Michael K C Lee
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Shehara Mendis
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | | | - Gun-Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Steve E Kalloger
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hui-Li Wong
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Grainne M O'Kane
- University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer J Knox
- University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan M Loree
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Dixie L Mager
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Anatomic Pathology, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, British Columbia, Canada. .,Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Hsu K, Lee YK, Chew A, Chiu S, Lim D, Greenhalgh DG, Cho K. Inherently variable responses to glucocorticoid stress among endogenous retroviruses isolated from 23 mouse strains. Biochim Biophys Acta Mol Basis Dis 2016; 1863:2594-2600. [PMID: 27816520 DOI: 10.1016/j.bbadis.2016.10.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/28/2016] [Accepted: 10/27/2016] [Indexed: 10/20/2022]
Abstract
Active participation of endogenous retroviruses (ERVs) in disease processes has been exemplified by the finding that the HERV (human ERV)-W envelope protein is involved in the pathogenesis of multiple sclerosis, an autoimmune disease. We also demonstrated that injury-elicited stressors alter the expression of murine ERVs (MuERVs), both murine leukemia virus-type and mouse mammary tumor virus (MMTV)-type (MMTV-MuERV). In this study, to evaluate MMTV-MuERVs' responses to stress (e.g., injury, infection)-elicited systemic glucocorticoid (GC) levels, we examined the GC-stress response of 64 MMTV-MuERV promoters isolated from the genomes of 23 mouse strains. All 64 promoters responded to treatment with a synthetic GC, dexamethasone (DEX), at a wide range from a 0.6- to 85.7-fold increase in reporter activity compared to no treatment. An analysis of the 10 lowest and 10 highest DEX responders revealed specific promoter elements exclusively present in either the three lowest or the two highest responders. Each promoter had a unique profile of transcription regulatory elements and the glucocorticoid response element (GRE) was identified in all promoters with the number of GREs ranging from 2 to 7. The three lowest DEX responders were the only promoters with two GREs. The findings from this study suggest that certain MMTV-MuERVs are more responsive to stress-elicited systemic GC elevation compared to the others. The mouse strain-specific genomic MMTV-MuERV profiles and individual MMTV-MuERVs' differential responses to GC-stress might explain, at least in part, the variable inflammatory responses to injury and/or infection, often observed among different mouse strains. This article is part of a Special Issue entitled: Immune and Metabolic Alterations in Trauma and Sepsis edited by Dr. Raghavan Raju.
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Affiliation(s)
- Karen Hsu
- Burn Research, Shriners Hospitals for Children Northern California, Davis, Sacramento, CA 95817, USA
| | - Young-Kwan Lee
- Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - Alex Chew
- Burn Research, Shriners Hospitals for Children Northern California, Davis, Sacramento, CA 95817, USA
| | - Sophia Chiu
- Burn Research, Shriners Hospitals for Children Northern California, Davis, Sacramento, CA 95817, USA
| | - Debora Lim
- Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - David G Greenhalgh
- Burn Research, Shriners Hospitals for Children Northern California, Davis, Sacramento, CA 95817, USA; Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - Kiho Cho
- Burn Research, Shriners Hospitals for Children Northern California, Davis, Sacramento, CA 95817, USA; Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA.
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3
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Naveira H, Bello X, Abal-Fabeiro JL, Maside X. Evidence for the persistence of an active endogenous retrovirus (ERVE) in humans. Genetica 2014; 142:451-60. [PMID: 25192754 DOI: 10.1007/s10709-014-9789-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 08/26/2014] [Indexed: 02/02/2023]
Abstract
Transposable elements (TEs) account for nearly half (44 %) of the human genome. However, their overall activity has been steadily declining over the past 35-50 million years, so that <0.05 % of TEs are presumably still "alive" (potentially transposable) in human populations. All the active elements are retrotransposons, either autonomous (LINE-1 and possibly the endogenous retrovirus ERVK), or non-autonomous (Alu and SVA, whose transposition is dependent on the LINE-1 enzymatic machinery). Here we show that a lineage of the endogenous retrovirus ERVE was recently engaged in ectopic recombination events and may have at least one potentially fully functional representative, initially reported as a novel retrovirus isolated from blood cells of a Chinese patient with chronic myeloid leukemia, which bears signals of positive selection on its envelope region. Altogether, there is strong evidence that ERVE should be included in the short list of potentially active TEs, and we give clues on how to identify human specific insertions of this element that are likely to be segregating in some of our populations.
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MESH Headings
- Animals
- Base Sequence
- Endogenous Retroviruses/classification
- Endogenous Retroviruses/genetics
- Evolution, Molecular
- Gene Products, env/chemistry
- Gene Products, env/genetics
- Genome, Human/genetics
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Models, Molecular
- Molecular Sequence Data
- Phylogeny
- Protein Structure, Tertiary
- Retroelements/genetics
- Selection, Genetic
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Horacio Naveira
- Grupo de Investigación en Bioloxía Evolutiva, Departamento de Bioloxía Celular e Molecular, Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, 15071, A Coruña, Spain,
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Lee KH, Rah H, Green T, Lee YK, Lim D, Nemzek J, Wahl W, Greenhalgh D, Cho K. Divergent and dynamic activity of endogenous retroviruses in burn patients and their inflammatory potential. Exp Mol Pathol 2014; 96:178-87. [PMID: 24509167 DOI: 10.1016/j.yexmp.2014.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 02/02/2014] [Indexed: 10/25/2022]
Abstract
Genes constitute ~3% of the human genome, whereas human endogenous retroviruses (HERVs) represent ~8%. We examined post-burn HERV expression in patients' blood cells, and the inflammatory potentials of the burn-associated HERVs were evaluated. Buffy coat cells, collected at various time points from 11 patients, were screened for the expression of eight HERV families, and we identified their divergent expression profiles depending on patient, HERV, and time point. The population of expressed HERV sequences was patient-specific, suggesting HERVs' inherent genomic polymorphisms and/or differential expression potentials depending on characteristics of patients and courses of injury response. Some HERVs were shared among the patients, while the others were divergent. Interestingly, one burn-associated HERV gag gene from a patient's genome induced IL-6, IL-1β, Ptgs-2, and iNOS. These findings demonstrate that injury stressors initiate divergent HERV responses depending on patient, HERV, and disease course and implicate HERVs as genetic elements contributing to polymorphic injury pathophysiology.
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Affiliation(s)
- Kang-Hoon Lee
- Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - HyungChul Rah
- Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - Tajia Green
- Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA
| | - Young-Kwan Lee
- Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - Debora Lim
- Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - Jean Nemzek
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI 48109-0614, USA
| | - Wendy Wahl
- Department of Surgery, Saint Joseph Mercy Health System, Ann Arbor, MI 48106, USA
| | - David Greenhalgh
- Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - Kiho Cho
- Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA; Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA.
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Pathological and evolutionary implications of retroviruses as mobile genetic elements. Genes (Basel) 2013; 4:573-82. [PMID: 24705263 PMCID: PMC3927575 DOI: 10.3390/genes4040573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/27/2013] [Accepted: 10/08/2013] [Indexed: 11/17/2022] Open
Abstract
Retroviruses, a form of mobile genetic elements, have important roles in disease and primate evolution. Exogenous retroviruses, such as human immunodeficiency virus (HIV), have significant pathological implications that have created a massive public health challenge in recent years. Endogenous retroviruses (ERVs), which are the primary focus of this review, can also be pathogenic, as well as being beneficial to a host in some cases. Furthermore, retroviruses may have played a key role in primate evolution that resulted in the incorporation of these elements into the human genome. Retroviruses are mobile genetic elements that have important roles in disease and primate evolution. We will further discuss the pathogenic potential of retroviruses, including their role in cancer biology, and will briefly summarize their evolutionary implications.
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Lee YJ, Jeong BH, Park JB, Kwon HJ, Kim YS, Kwak IS. The prevalence of human endogenous retroviruses in the plasma of major burn patients. Burns 2013; 39:1200-5. [PMID: 23339865 DOI: 10.1016/j.burns.2012.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 11/20/2012] [Accepted: 12/19/2012] [Indexed: 10/27/2022]
Abstract
BACKGROUND Approximately 8% of the human genome is composed of retroviral sequences, which are known as human endogenous retroviruses (HERVs) and, have been implicated in both health status and disease. Recently, indirect evidence for a possible role of retroviral elements in the systemic response to stress signals has been provided by several studies. In the present study, we sought to evaluate the relationship between HERVs and major burn in humans. METHOD We investigated the prevalence of HERV families by reverse transcriptase PCR (RT-PCR) in cell-free plasma samples from patients with burns and from normal individuals. RESULTS Different prevalences of HERV families were observed in the plasma samples from the burn patient group and normal group. Compared with the prevalences of HERV-W and HERV-K in the normal group, in the burn patient group, the prevalence of HERV-W was significantly lower (P<0.001), but the prevalence of HERV-K was higher (P=0.059). CONCLUSIONS Our study of the prevalences of HERVs revealed that the activation of certain HERV families may be influenced not only by burns but also by the initial treatments that were used to address these injuries.
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Affiliation(s)
- Yun-Jung Lee
- Ilsong Institute of Life Science, Hallym University, Anyang, Gyeonggi-do 431-060, Republic of Korea
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Lee KH, Lim D, Green T, Greenhalgh D, Cho K. Injury-elicited stressors alter endogenous retrovirus expression in lymphocytes depending on cell type and source lymphoid organ. BMC Immunol 2013; 14:2. [PMID: 23289855 PMCID: PMC3562510 DOI: 10.1186/1471-2172-14-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 12/11/2012] [Indexed: 11/10/2022] Open
Abstract
Background Murine leukemia virus-type endogenous retroviruses (MuLV-ERVs) constitute ~10% of the mouse genome and are associated with various pathophysiologic processes. In this study, we examined whether MuLV-ERVs’ response to burn-elicited stressors is specific for certain lymphocyte populations and/or locations of lymphoid organ. Results B- and T-cells, which were sorted from nine lymphoid organs of C57BL/6J mice after burn, were subjected to MuLV-ERV expression analyses. Overall, the post-burn MuLV-ERV expression pattern was dependent on lymphocyte type, time after injury, location of lymphoid organ, and MuLV-ERV type. For instance, the MuLV-ERV expression in T-cells from the thymus and three cervical lymph nodes decreased at 3 hours post-burn while the expression of some MuLV-ERVs was augmented in B-cells derived from the mesenteric lymph node. The MuLV-ERV U3 sequences population of the burn-24 hours group was less diverse in comparison to the no burn and burn-3 hours groups. In addition, it was apparent that at the 24 hours time point, the U3 populations of B-cells from both no burn and burn groups were less heterogeneous than the T-cells’ U3 populations. Using the U3 sequences, some of which were isolated only from specific experimental groups (B- vs. T-cells; no burn vs. burn), as probes, 51 putative MuLV-ERVs, including 16 full-length proviruses, were mapped followed by characterization of their biologic properties. Conclusion MuLV-ERVs’ response to burn-elicited stressors may be differentially controlled depending on lymphocyte type, location of lymphoid organ, MuLV-ERV type, and stress duration.
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Affiliation(s)
- Kang-Hoon Lee
- Department of Surgery, Burn Research, Shriners Hospitals for Children Northern California, University of California, Davis, Sacramento, CA 95817, USA
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Kao D, Hsu K, Chiu S, Tu V, Chew A, Lee KH, Lee YK, Kwon DN, Greenhalgh DG, Cho K. ERE database: a database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome. Genomics 2012; 100:157-61. [PMID: 22691267 DOI: 10.1016/j.ygeno.2012.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 05/31/2012] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
Abstract
Endogenous retroviral elements (EREs), a family of transposable elements, constitute a substantial fraction of mammalian genomes. It is expected that profiles of the ERE sequences and their genomic locations are unique for each individual. Comprehensive characterization of the EREs' genomic locations and their biological properties is essential for understanding their roles in the pathophysiology of the host. In this study, we identified and mapped putative EREs (a total of 111 endogenous retroviruses [ERVs] and 488 solo long terminal repeats [sLTRs]) within the C57BL/6J mouse genome. The biological properties of individual ERE isolates (both ERVs and sLTRs) were then characterized in the following aspects: transcription potential, tropism trait, coding potential, recombination event, integration age, and primer binding site for replication. In addition, a suite of database management system programs was developed to organize and update the data acquired from current and future studies and to make the data accessible via internet.
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Affiliation(s)
- Damian Kao
- Burn Research, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA
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Tropism, cytotoxicity, and inflammatory properties of two envelope genes of murine leukemia virus type-endogenous retroviruses of C57BL/6J mice. Mediators Inflamm 2011; 2011:509604. [PMID: 21772664 PMCID: PMC3134291 DOI: 10.1155/2011/509604] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Accepted: 03/09/2011] [Indexed: 12/16/2022] Open
Abstract
Envelope (env) proteins of certain endogenous retroviruses (ERVs) participate in various pathophysiological processes. In this study, we characterized pathophysiologic properties of two murine leukemia virus-type ERV (MuLV-ERV) env genes cloned from the ovary of C57BL/6J mice. The two env genes (named ENVOV1 and ENVOV2), with 1,926 bp coding region, originated from two MuLV-ERV loci on chromosomes 8 and 18, respectively. ENVOV1 and ENVOV2 were ~75 kDa and predominantly expressed on the cell membrane. They were capable of producing pseudotype murine leukemia virus virions. Tropism trait and infectivity of ENVOV2 were similar to the polytropic env; however, ENVOV1 had very low level of infectivity. Overexpression of ENVOV2, but not ENVOV1, exerted cytotoxic effects and induced expression of COX-2, IL-1β, IL-6, and iNOS. These findings suggest that the ENVOV1 and ENVOV2 are capable of serving as an env protein for virion assembly, and they exert differential cytotoxicity and modulation of inflammatory mediators.
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Kwon DN, Lee YK, Greenhalgh DG, Cho K. Lipopolysaccharide stress induces cell-type specific production of murine leukemia virus type-endogenous retroviral virions in primary lymphoid cells. J Gen Virol 2010; 92:292-300. [PMID: 20965985 PMCID: PMC3081078 DOI: 10.1099/vir.0.023416-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Some murine-endogenous retroviruses, making up ∼10 % of the mouse genome, are induced during the course of experimental sepsis in which lipopolysaccharide (LPS), a pathogenic component of gram-negative bacteria, often plays a critical role. In this study, we investigated whether LPS stress induces the production of murine leukemia virus type-endogenous retrovirus (MuLV-ERV) virions in primary lymphoid cells. LPS treatment of cells (single-cell suspensions and sorted B- and T-cells) isolated from seven lymphoid organs of C57BL/6J mice resulted in a differential increase in the production of MuLV-ERV virions in most cells examined. Interestingly, among the 34 unique MuLV-ERV U3 sequences cloned from the viral genomic RNAs, the nuclear respiratory factor 1 (transcription factor) element was present only in the 20 U3 sequences that were derived from the LPS-induced MuLV-ERV U3 bands. Using the U3 sequences as a probe, 55 putative MuLV-ERV loci were mapped onto the C57BL/6J mouse genome and 15 of them retained full coding potential. Furthermore, one full-length recombinant MuLV-ERV originating from a locus on chromosome 13 was determined to be responsive to LPS stress. The findings from this study suggest that LPS stress differentially activates MuLV-ERV virion production in lymphoid organs in a cell type- and MuLV-ERV-specific manner. Further investigation is needed to define the role of MuLV-ERVs in the LPS signalling pathway(s) in general, as well as in the pathogenesis of sepsis.
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Affiliation(s)
- Deug-Nam Kwon
- Burn Research, Shriners Hospitals for Children Northern California and Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
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11
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Moon HJ, Kim HK, Park SJ, Lee CS, Song DS, Kang BK, Park BK. Comparison of the age-related porcine endogenous retrovirus (PERV)expression using duplex RT-PCR. J Vet Sci 2010; 10:317-22. [PMID: 19934597 PMCID: PMC2807268 DOI: 10.4142/jvs.2009.10.4.317] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Porcine endogenous retroviruses (PERVs) are members of family Retroviridae, genus Gamma retrovirus, and transmitted by both horizontally and vertically like other endogenous retroviruses (ERVs). PERV was initially described in the 1970s having inserted its gene in the host genome of different pig breeds, and three classes, PERV-A, PERV-B, and PERV-C are known. The therapeutic use of living cells, tissues, and organs from animals called xenotransplantation might relieve the limited supply of allografts in the treatment of organ dysfunction. Because of ethical considerations, compatible organ sizes, and physiology, the pig has been regarded as an alternative source for xenotransplantation. Sensitive duplex reverse transcription-polymerase chain reaction protocols for simultaneously detecting PERV gag mRNA and porcine glyceraldehydes 3-phosphate dehydrogenase mRNA in one tube was established. To compare the age-related PERV expression patterns of the lung, liver, spleen, kidney, heart, and pancreas in commercial pigs, 20 pigs from four age groups (5 heads each in 10 days-, 40 days-, 70 days-, and 110 days-old, respectively) were used in this study. The expression patterns of PERV were statistically different among age groups in lung, liver, and kidney (ANOVA, p < 0.05). These data may support in the selection of appropriate donor pigs expressing low levels of PERV mRNA.
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Affiliation(s)
- Hyoung Joon Moon
- Department of Veterinary Medicine Virology Lab, College of Veterinary Medicine and BK21 Program for Veterinary Science, Seoul National University, Seoul 151-742, Korea
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Belancio VP, Deininger PL, Roy-Engel AM. LINE dancing in the human genome: transposable elements and disease. Genome Med 2009; 1:97. [PMID: 19863772 PMCID: PMC2784310 DOI: 10.1186/gm97] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Transposable elements (TEs) have been consistently underestimated in their contribution to genetic instability and human disease. TEs can cause human disease by creating insertional mutations in genes, and also contributing to genetic instability through non-allelic homologous recombination and introduction of sequences that evolve into various cis-acting signals that alter gene expression. Other outcomes of TE activity, such as their potential to cause DNA double-strand breaks or to modulate the epigenetic state of chromosomes, are less fully characterized. The currently active human transposable elements are members of the non-LTR retroelement families, LINE-1, Alu (SINE), and SVA. The impact of germline insertional mutagenesis by TEs is well established, whereas the rate of post-insertional TE-mediated germline mutations and all forms of somatic mutations remain less well quantified. The number of human diseases discovered to be associated with non-allelic homologous recombination between TEs, and particularly between Alu elements, is growing at an unprecedented rate. Improvement in the technology for detection of such events, as well as the mounting interest in the research and medical communities in resolving the underlying causes of the human diseases with unknown etiology, explain this increase. Here, we focus on the most recent advances in understanding of the impact of the active human TEs on the stability of the human genome and its relevance to human disease.
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Affiliation(s)
- Victoria P Belancio
- Department of Structural and Cellular Biology, School of Medicine, Tulane Cancer Center and Tulane Center for Aging, Tulane University, SL-49 1430 Tulane Ave, New Orleans, LA 70112, USA.
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Carré-Eusèbe D, Coudouel N, Magre S. OVEX1, a novel chicken endogenous retrovirus with sex-specific and left-right asymmetrical expression in gonads. Retrovirology 2009; 6:59. [PMID: 19534790 PMCID: PMC2717909 DOI: 10.1186/1742-4690-6-59] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Accepted: 06/17/2009] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND In chickens, as in most birds, female gonad morphogenesis is asymmetrical. Gonads appear first rather similarly, but only the left one undergoes full differentiation and gives rise to a functional ovary. The right gonad, in which the cortex does not develop, remains restricted to the medulla and finally regresses. Opportunity was taken of this left-right asymmetry to perform a suppression subtractive hybridization screening to select for transcripts preferentially expressed in the developing left ovary as compared to the right one, and thus identify genes that are potentially involved in the process of ovarian differentiation. RESULTS One of these transcripts, named Ovex1 according to its expression profile, corresponds to an endogenous retrovirus that has not been previously characterized. It is transcribed as full-length and singly spliced mRNAs and contains three uninterrupted open reading frames coding potentially for proteins with homology to Gag and Pro-Pol retroviral polyproteins and a third protein showing only a weak similarity with Env glycoproteins. Ovex1 is severely degenerated; it is devoid of typical long terminal repeats and displays some evidence of recombination. An orthologous Ovex1 locus was identified in the genome of zebra finch, a member of a different bird order, and similar sequences were detected in turkey, guinea fowl, and duck DNA. The relationship between these sequences follows the bird phylogeny, suggesting vertical transmission of the endogenous retrovirus for more than 100 million years. Ovex1 is transcribed in chicken gonads with a sex-dependent and left-right asymmetrical pattern. It is first expressed in the cortex of the left indifferent gonads of both sexes. Expression is transient in the left testis and absent in the right one. In developing ovaries, Ovex1 transcription increases sharply in the left cortex and is weakly detected in the medulla. After folliculogenesis, Ovex1-expressing cells constitute the follicular granulosa cell layer. Ovex1 expression highlights a striking desquamation process that leads to profound cortical remodeling associated with follicle morphogenesis. CONCLUSION Evidence for a selection pressure at the protein level suggests that this endogenous retrovirus, expressed in the ovarian supporting cell lineage, might play an active role in bird ovarian physiology.
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Affiliation(s)
- Danièle Carré-Eusèbe
- Endocrinologie et Génétique de la Reproduction et du Développement, INSERM, U782, 32 rue des Carnets, F-92140, Clamart – France
- Univ. Paris-Sud, UMR-S0782, Clamart, F-92140
| | - Noëlline Coudouel
- Physiologie de l'Axe Gonadotrope, Unité de Biologie Fonctionnelle et Adaptative (BFA), Univ. PARIS 7 – CNRS, 4 rue MA Lagroua Weill-Hallé, 75205 Paris CEDEX 13 – France
| | - Solange Magre
- Physiologie de l'Axe Gonadotrope, Unité de Biologie Fonctionnelle et Adaptative (BFA), Univ. PARIS 7 – CNRS, 4 rue MA Lagroua Weill-Hallé, 75205 Paris CEDEX 13 – France
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Flockerzi A, Ruggieri A, Frank O, Sauter M, Maldener E, Kopper B, Wullich B, Seifarth W, Müller-Lantzsch N, Leib-Mösch C, Meese E, Mayer J. Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome Project. BMC Genomics 2008; 9:354. [PMID: 18664271 PMCID: PMC2525661 DOI: 10.1186/1471-2164-9-354] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Accepted: 07/29/2008] [Indexed: 12/14/2022] Open
Abstract
Background A significant proportion of the human genome is comprised of human endogenous retroviruses (HERVs). HERV transcripts are found in every human tissue. Expression of proviruses of the HERV-K(HML-2) family has been associated with development of human tumors, in particular germ cell tumors (GCT). Very little is known about transcriptional activity of individual HML-2 loci in human tissues, though. Results By employing private nucleotide differences between loci, we assigned ~1500 HML-2 cDNAs to individual HML-2 loci, identifying, in total, 23 transcriptionally active HML-2 proviruses. Several loci are active in various human tissue types. Transcription levels of some HML-2 loci appear higher than those of other loci. Several HML-2 Rec-encoding loci are expressed in GCT and non-GCT tissues. A provirus on chromosome 22q11.21 appears strongly upregulated in pathologic GCT tissues and may explain high HML-2 Gag protein levels in GCTs. Presence of Gag and Env antibodies in GCT patients is not correlated with activation of individual loci. HML-2 proviruses previously reported capable of forming an infectious HML-2 variant are transcriptionally active in germ cell tissue. Our study furthermore shows that Expressed Sequence Tag (EST) data are insufficient to describe transcriptional activity of HML-2 and other HERV loci in tissues of interest. Conclusion Our, to date, largest-scale study reveals in greater detail expression patterns of individual HML-2 loci in human tissues of clinical interest. Moreover, large-scale, specialized studies are indicated to better comprehend transcriptional activity and regulation of HERVs. We thus emphasize the need for a specialized HERV Transcriptome Project.
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Affiliation(s)
- Aline Flockerzi
- Department of Human Genetics, Medical Faculty, University of Saarland, Homburg, Germany.
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