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Lima-Junior DS, Krishnamurthy SR, Bouladoux N, Collins N, Han SJ, Chen EY, Constantinides MG, Link VM, Lim AI, Enamorado M, Cataisson C, Gil L, Rao I, Farley TK, Koroleva G, Attig J, Yuspa SH, Fischbach MA, Kassiotis G, Belkaid Y. Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota. Cell 2021; 184:3794-3811.e19. [PMID: 34166614 PMCID: PMC8381240 DOI: 10.1016/j.cell.2021.05.020] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 04/10/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023]
Abstract
The microbiota plays a fundamental role in regulating host immunity. However, the processes involved in the initiation and regulation of immunity to the microbiota remain largely unknown. Here, we show that the skin microbiota promotes the discrete expression of defined endogenous retroviruses (ERVs). Keratinocyte-intrinsic responses to ERVs depended on cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes protein (STING) signaling and promoted the induction of commensal-specific T cells. Inhibition of ERV reverse transcription significantly impacted these responses, resulting in impaired immunity to the microbiota and its associated tissue repair function. Conversely, a lipid-enriched diet primed the skin for heightened ERV- expression in response to commensal colonization, leading to increased immune responses and tissue inflammation. Together, our results support the idea that the host may have co-opted its endogenous virome as a means to communicate with the exogenous microbiota, resulting in a multi-kingdom dialog that controls both tissue homeostasis and inflammation.
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Affiliation(s)
- Djalma S Lima-Junior
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas Collins
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seong-Ji Han
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erin Y Chen
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Michael G Constantinides
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIH Center for Human Immunology, Bethesda, MD 20896, USA
| | - Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michel Enamorado
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christophe Cataisson
- In Vitro Pathogenesis Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Louis Gil
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Indira Rao
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Taylor K Farley
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, UK
| | | | - Jan Attig
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| | - Stuart H Yuspa
- In Vitro Pathogenesis Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael A Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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52
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Tokuyama M, Gunn BM, Venkataraman A, Kong Y, Kang I, Rakib T, Townsend MJ, Costenbader KH, Alter G, Iwasaki A. Antibodies against human endogenous retrovirus K102 envelope activate neutrophils in systemic lupus erythematosus. J Exp Med 2021; 218:212176. [PMID: 34019642 PMCID: PMC8144942 DOI: 10.1084/jem.20191766] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/08/2021] [Accepted: 04/23/2021] [Indexed: 01/03/2023] Open
Abstract
Neutrophil activation and the formation of neutrophil extracellular traps (NETs) are hallmarks of innate immune activation in systemic lupus erythematosus (SLE). Here we report that the expression of an endogenous retrovirus (ERV) locus ERV-K102, encoding an envelope protein, was significantly elevated in SLE patient blood and correlated with autoantibody levels and higher interferon status. Induction of ERV-K102 in SLE negatively correlated with the expression of epigenetic silencing factors. Anti-ERV-K102 IgG levels in SLE plasma correlated with higher interferon stimulated gene expression, and further promoted enhanced neutrophil phagocytosis of ERV-K102 envelope protein through immune complex formation. Finally, phagocytosis of ERV-K102 immune complexes resulted in the formation of NETs consisting of DNA, neutrophil elastase, and citrullinated histone H3. Together, we identified an immunostimulatory ERV-K envelope protein that in an immune complex with SLE IgG is capable of activating neutrophils.
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Affiliation(s)
- Maria Tokuyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Bronwyn M Gunn
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA
| | - Arvind Venkataraman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Yong Kong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Insoo Kang
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT
| | - Tasfia Rakib
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | | | | | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT.,Howard Hughes Medical Institute, Chevy Chase, MD
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53
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Multiple Infiltration and Cross-Species Transmission of Foamy Viruses across the Paleozoic to the Cenozoic Era. J Virol 2021; 95:e0048421. [PMID: 33910951 DOI: 10.1128/jvi.00484-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Foamy viruses (FVs) are complex retroviruses that can infect humans and other animals. In this study, by integrating transcriptomic and genomic data, we discovered 412 FVs from 6 lineages in amphibians, which significantly increased the known set of FVs in amphibians. Among these lineages, salamander FVs maintained a coevolutionary pattern with their hosts that could be dated back to the Paleozoic era, while in contrast, frog FVs were much more likely acquired from cross-species (class-level) transmission in the Cenozoic era. In addition, we found that three distinct FV lineages had integrated into the genome of a salamander. Unexpectedly, we identified a lineage of endogenous FVs in caecilians that expressed all complete major genes, demonstrating the potential existence of an exogenous form of FV outside of mammals. Our discovery of rare phenomena in amphibian FVs has significantly increased our understanding of the macroevolution of the complex retrovirus. IMPORTANCE Foamy viruses (FVs) represent, more so than other viruses, the best model of coevolution between a virus and a host. This study represents the largest investigation so far of amphibian FVs and reveals 412 FVs of 6 distinct lineages from three major orders of amphibians. Besides a coevolutionary pattern, cross-species and repeated infections were also observed during the evolution of amphibian FVs. Remarkably, expressed FVs including a potential exogenous form were discovered, suggesting that active FVs might be underestimated in nature. These findings revealed that the multiple origins and complex evolution of amphibian FVs started from the Paleozoic era.
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54
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Wang J, Han GZ. A Sister Lineage of Sampled Retroviruses Corroborates the Complex Evolution of Retroviruses. Mol Biol Evol 2021; 38:1031-1039. [PMID: 33249491 PMCID: PMC7947760 DOI: 10.1093/molbev/msaa272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The origin and deep history of retroviruses remain mysterious and contentious, largely because the diversity of retroviruses is incompletely understood. Here, we report the discovery of lokiretroviruses, a novel major lineage of retroviruses, within the genomes of a wide range of vertebrates (at least 137 species), including lampreys, ray-finned fishes, lobe-finned fishes, amphibians, and reptiles. Lokiretroviruses share a similar genome architecture with known retroviruses, but display some unique features. Interestingly, lokiretrovirus Env proteins share detectable similarity with fusion glycoproteins of viruses within the Mononegavirales order, blurring the boundary between retroviruses and negative sense single-stranded RNA viruses. Phylogenetic analyses based on reverse transcriptase demonstrate that lokiretroviruses are sister to all the retroviruses sampled to date, providing a crucial nexus for studying the deep history of retroviruses. Comparing congruence between host and virus phylogenies suggests lokiretroviruses mainly underwent cross-species transmission. Moreover, we find that retroviruses replaced their ribonuclease H and integrase domains multiple times during their evolutionary course, revealing the importance of domain shuffling in the evolution of retroviruses. Overall, our findings greatly expand our views of the diversity of retroviruses, and provide novel insights into the origin and complex evolutionary history of retroviruses.
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Affiliation(s)
- Jianhua Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
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55
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SMARCB1 deletion in atypical teratoid rhabdoid tumors results in human endogenous retrovirus K (HML-2) expression. Sci Rep 2021; 11:12893. [PMID: 34145313 PMCID: PMC8213802 DOI: 10.1038/s41598-021-92223-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022] Open
Abstract
Atypical Teratoid Rhabdoid Tumor (AT/RT) is a rare pediatric central nervous system cancer often characterized by deletion or mutation of SMARCB1, a tumor suppressor gene. In this study, we found that SMARCB1 regulates Human Endogenous Retrovirus K (HERV-K, subtype HML-2) expression. HML-2 is a repetitive element scattered throughout the human genome, encoding several intact viral proteins that have been associated with stem cell maintenance and tumorigenesis. We found HML-2 env expression in both the intracellular and extracellular compartments in all AT/RT cell lines (n = 4) and in 95% of AT/RT patient tissues (n = 37) evaluated. SMARCB1 knock-down in neural stem cells (NSCs) led to an upregulation of HML-2 transcription. We found that SMARCB1 binds adjacent to the HML-2 promoter, repressing its transcription via chromatin immunoprecipitation; restoration of SMARCB1 expression in AT/RT cell lines significantly downregulated HML-2 expression. Further, targeted downregulation of HML-2 transcription via CRISPR-dCas9 coupled with suppressor proteins led to cellular dispersion, decreased proliferation, and cell death in vitro. HML-2 knock-down with shRNA, siRNA, and CRISPR-dCas9 significantly decreased Ras expression as measured by qRT-PCR, suggesting that HML-2 modulates MAPK/ERK signaling in AT/RT cells. Overexpression of NRAS was sufficient to restore cellular proliferation, and MYC, a transcription factor downstream of NRAS, was bound to the HERV-K LTR significantly more in the absence of SMARCB1 expression in AT/RT cells. We show a mechanism by which these undifferentiated tumors remain pluripotent, and we demonstrate that their formation is aided by aberrant HML-2 activation, which is dependent on SMARCB1 and its interaction with MYC.
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56
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Karlik E, Gurbuz O, Yildiz Y, Gozukirmizi N. Endogenous retrovirus HERV-K6 and HERV-K11 polymorphisms’ analyses in head and neck squamous cell carcinoma patients. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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57
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Stephenson T, Speight N, Low WY, Woolford L, Tearle R, Hemmatzadeh F. Molecular Diagnosis of Koala Retrovirus (KoRV) in South Australian Koalas ( Phascolarctos cinereus). Animals (Basel) 2021; 11:ani11051477. [PMID: 34065572 PMCID: PMC8161083 DOI: 10.3390/ani11051477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/06/2021] [Accepted: 05/16/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Koala retrovirus (KoRV) is a significant threat to koalas across Australia. Koalas in northern koala populations (from New South Wales and Queensland) have KoRV inserted into their DNA and inherited to their offspring. Southern koala populations (from Victoria and South Australia) have KoRV infection spread through close contact of koalas. As such, there are koalas within South Australia that are not infected with KoRV. Accurate diagnosis of the infection of each koala is therefore fundamental for disease studies. Previous studies have shown differences in prevalence of different KoRV genes in the Mount Lofty Ranges Koala population; therefore, clarification is necessary. This study uses a large cohort (n = 216) and defines the diagnostic regions of the KoRV genome within the South Australian population. Using multiple molecular techniques, it demonstrates strong evidence for two clear groupings of koalas: KoRV positive and KoRV negative. Within this study, a population of 41% were shown to be KoRV positive and 57% were KoRV negative, with 2% inconclusive. This differentiation is of great importance when examining the clinical importance of KoRV infection within southern koalas. Abstract Koala retrovirus, a recent discovery in Australian koalas, is endogenised in 100% of northern koalas but has lower prevalence in southern populations, with lower proviral and viral loads, and an undetermined level of endogenisation. KoRV has been associated with lymphoid neoplasia, e.g., lymphoma. Recent studies have revealed high complexity in southern koala retroviral infections, with a need to clarify what constitutes positive and negative cases. This study aimed to define KoRV infection status in Mount Lofty Ranges koalas in South Australia using RNA-seq and proviral analysis (n = 216). The basis for positivity of KoRV was deemed the presence of central regions of the KoRV genome (gag 2, pol, env 1, and env 2) and based on this, 41% (89/216) koalas were positive, 57% (124/216) negative, and 2% inconclusive. These genes showed higher expression in lymph node tissue from KoRV positive koalas with lymphoma compared with other KoRV positive koalas, which showed lower, fragmented expression. Terminal regions (LTRs, partial gag, and partial env) were present in SA koalas regardless of KoRV status, with almost all (99.5%, 215/216) koalas positive for gag 1 by proviral PCR. Further investigation is needed to understand the differences in KoRV infection in southern koala populations.
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Affiliation(s)
- Tamsyn Stephenson
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (N.S.); (L.W.); (F.H.)
- Correspondence:
| | - Natasha Speight
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (N.S.); (L.W.); (F.H.)
| | - Wai Yee Low
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (W.Y.L.); (R.T.)
| | - Lucy Woolford
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (N.S.); (L.W.); (F.H.)
- Veterinary Diagnostics Laboratory, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia
| | - Rick Tearle
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (W.Y.L.); (R.T.)
| | - Farhid Hemmatzadeh
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (N.S.); (L.W.); (F.H.)
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58
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Human Endogenous Retroviruses as Biomedicine Markers. Virol Sin 2021; 36:852-858. [PMID: 33905075 DOI: 10.1007/s12250-021-00387-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 03/15/2021] [Indexed: 11/27/2022] Open
Abstract
Human endogenous retroviruses (HERVs) were formed via ancient integration of exogenous retroviruses into the human genome and are considered to be viral "fossils". The human genome is embedded with a considerable amount of HERVs, witnessing the long-term evolutionary history of the viruses and the host. Most HERVs have lost coding capability during selection but still function in terms of HERV-mediated regulation of host gene expression. In this review, we summarize the roles of HERV activation in response to viral infections and diseases, and emphasize the potential use of HERVs as biomedicine markers in the early diagnosis of diseases such as cancer, which provides a new perspective for the clinical application of HERVs.
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59
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Wang J, Han GZ. Frequent Retroviral Gene Co-option during the Evolution of Vertebrates. Mol Biol Evol 2021; 37:3232-3242. [PMID: 32667990 DOI: 10.1093/molbev/msaa180] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Endogenous retroviruses are ubiquitous in the vertebrate genomes. On occasion, hosts recruited retroviral genes to mediate their own biological functions, a process formally known as co-option or exaptation. Much remains unknown about the extent of retroviral gene co-option in vertebrates, although more than ten retroviral gene co-option events have been documented. Here, we use a phylogenomic approach to analyze more than 700 vertebrate genomes to uncover retroviral gene co-option taking place during the evolution of vertebrates. We identify a total of 177 independent retroviral gene co-option events in vertebrates, a majority of which have not been reported previously. Among these retroviral gene co-option events, 93 and 84 involve gag and env genes, respectively. More than 78.0% (138 out of 177) of retroviral gene co-option occurred within mammals. The gag and env co-option events share a generally similar temporal pattern with less frequent retroviral gene co-option identified in the deep branches, suggesting that retroviral gene co-option might have not been maintained for very long time periods. Moreover, we find co-opted retroviral genes are subject to different selection pressure, implying potentially diverse cellular functionality. Our study provides a comprehensive picture of co-opted retroviral genes during the evolution of vertebrates and has implications in understanding the ancient evolution of vertebrate-retrovirus interaction.
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Affiliation(s)
- Jianhua Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
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60
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Hol JA, Diets IJ, de Krijger RR, van den Heuvel-Eibrink MM, Jongmans MC, Kuiper RP. TRIM28 variants and Wilms' tumour predisposition. J Pathol 2021; 254:494-504. [PMID: 33565090 PMCID: PMC8252630 DOI: 10.1002/path.5639] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/22/2021] [Accepted: 02/05/2021] [Indexed: 12/11/2022]
Abstract
TRIM28 was recently identified as a Wilms' tumour (WT) predisposition gene, with germline pathogenic variants identified in around 1% of isolated and 8% of familial WT cases. TRIM28 variants are associated with epithelial WT, but the presence of other tumour components or anaplasia does not exclude the presence of a germline or somatic TRIM28 variant. In children with WT, TRIM28 acts as a classical tumour suppressor gene, with both alleles generally disrupted in the tumour. Therefore, loss of TRIM28 (KAP1/TIF1beta) protein expression in tumour tissue by immunohistochemistry is an effective strategy to identify patients carrying pathogenic TRIM28 variants. TRIM28 is a ubiquitously expressed corepressor that binds transcription factors in a context‐, species‐, and cell‐type‐specific manner to control the expression of genes and transposable elements during embryogenesis and cellular differentiation. In this review, we describe the inheritance patterns, histopathological and clinical features of TRIM28‐associated WT, as well as potential underlying mechanisms of tumourigenesis during embryonic kidney development. Recognizing germline TRIM28 variants in patients with WT can enable counselling, genetic testing, and potential early detection of WT in other children in the family. A further exploration of TRIM28‐associated WT will help to unravel the diverse and complex mechanisms underlying WT development. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Janna A Hol
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Marjolijn Cj Jongmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht/Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht/Wilhelmina Children's Hospital, Utrecht, The Netherlands
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61
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Fulton JE, Mason AS, Wolc A, Arango J, Settar P, Lund AR, Burt DW. The impact of endogenous Avian Leukosis Viruses (ALVE) on production traits in elite layer lines. Poult Sci 2021; 100:101121. [PMID: 33975038 PMCID: PMC8131724 DOI: 10.1016/j.psj.2021.101121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/26/2021] [Accepted: 02/26/2021] [Indexed: 11/28/2022] Open
Abstract
Avian Leukosis Virus subgroup E (ALVE) integrations are endogenous retroviral elements found in the chicken genome. The presence of ALVE has been reported to have negative impacts on multiple traits, including egg production and body weight. The recent development of rapid, inexpensive and specific ALVE detection methods has facilitated their characterization in elite commercial egg production lines across multiple generations. The presence of 20 ALVE was examined in 8 elite lines, from 3 different breeds. Seventeen of these ALVE (85%) were informative and found to be segregating in at least one of the lines. To test for an association between specific ALVE inserts and traits, a large genotype by phenotype study was undertaken. Genotypes were obtained for 500 to 1500 males per line, and the phenotypes used were sire-daughter averages. Phenotype data were analyzed by line with a linear model that included the effects of generation, ALVE genotype and their interaction. If genotype effect was significant, the number of ALVE copies was fitted as a regression to estimate additive ALVE gene substitution effect. Significant associations between the presence of specific ALVE inserts and 18 commercially relevant performance and egg quality traits, including egg production, egg weight and albumen height, were observed. When an ALVE was segregating in more than one line, these associations did not always have the same impact (negative, positive or none) in each line. It is hypothesized that the presence of ALVE in the chicken genome may influence production traits by 3 mechanisms: viral protein production may modulate the immune system and impact overall production performance (virus effect); insertional mutagenesis caused by viral integration may cause direct gene alterations or affect gene regulation (gene effect); or the integration site may be within or adjacent to a quantitative trait region which impacts a performance trait (linkage disequilibrium, marker effect).
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Affiliation(s)
- Janet E Fulton
- Department of Research and Development, Hy-Line International, Dallas Center, IA 50063, USA.
| | - Andrew S Mason
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology and The York Biomedical Research Institute, The University of York, York, YO10 5DD, United Kingdom
| | - Anna Wolc
- Department of Research and Development, Hy-Line International, Dallas Center, IA 50063, USA; Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Jesus Arango
- Department of Research and Development, Hy-Line International, Dallas Center, IA 50063, USA
| | - Petek Settar
- Department of Research and Development, Hy-Line International, Dallas Center, IA 50063, USA
| | - Ashlee R Lund
- Department of Research and Development, Hy-Line International, Dallas Center, IA 50063, USA
| | - David W Burt
- The University of Queensland, Brisbane, Queensland, 4072, Australia
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62
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Abstract
Exogenous retroviruses are RNA viruses that require reverse transcription for their replication. Among these viruses, human immunodeficiency virus (HIV) is infectious to humans and causes the development of acquired immune deficiency syndrome (AIDS). There are also endogenous retroelements that require reverse transcription for their retrotransposition, among which the type 1 long interspersed element (LINE-1) is the only type of retroelement that can replicate autonomously. It was once believed that retroviruses like HIV and retroelements like LINE-1 share similarities in processes such as reverse transcription and integration. Accordingly, many HIV suppressors are also potent LINE-1 inhibitors. However, in many cases, one suppressor uses two or more distinct mechanisms to repress HIV and LINE-1. In this review, we discuss some of these suppressors, focusing on their alternative mechanisms opposing the replication of HIV and LINE-1. Based on the differences in HIV and LINE-1 activity, the subcellular localization of these suppressors, and the impact of LINE-1 retrotransposition on human cells, we propose possible reasons for the inhibition of HIV and LINE-1 through different pathways by these suppressors, with the hope of accelerating future studies in associated research fields.
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Affiliation(s)
- Juan Du
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, China.,Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, First Hospital of Jilin University, Changchun, China
| | - Ke Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, China.,Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, First Hospital of Jilin University, Changchun, China
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63
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Quigley BL, Wedrowicz F, Hogan F, Timms P. Phylogenetic and geographical analysis of a retrovirus during the early stages of endogenous adaptation and exogenous spread in a new host. Mol Ecol 2020; 30:2626-2640. [PMID: 33219558 PMCID: PMC8246579 DOI: 10.1111/mec.15735] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/14/2020] [Accepted: 11/06/2020] [Indexed: 12/26/2022]
Abstract
Most retroviral endogenization and host adaptation happened in the distant past, with the opportunity to study these processes as they occurred lost to time. An exception exists with the discovery that koala retrovirus (KoRV) has recently begun its endogenization into the koala (Phascolarctos cinereus) genome. What makes this opportunity remarkable is the fact that Northern Australian koalas appear to be undergoing endogenization with one KoRV subtype (KoRV‐A), while all subtypes (KoRV‐A‐I) coexist exogenously, and Southern Australian koalas appear to carry all KoRV subtypes as an exogenous virus. To understand the distribution and relationship of all KoRV variants in koalas, the proviral KoRV envelope gene receptor binding domain was assessed across the koala's natural range. Examination of KoRV subtype‐specific proviral copy numbers per cell found that KoRV‐A proviral integration levels were consistent with endogenous incorporation in Northern Australia (southeast Queensland and northeast New South Wales) while revealing lower levels of KoRV‐A proviral integration (suggestive of exogenous incorporation) in southern regions (southeast New South Wales and Victoria). Phylogeographical analysis indicated that several major KoRV‐A variants were distributed uniformly across the country, while non‐KoRV‐A variants appeared to have undergone lineage diversification in geographically distinct regions. Further analysis of the major KoRV‐A variants revealed a distinct shift in variant proportions in southeast New South Wales, suggesting this as the geographical region where KoRV‐A transitions from being predominantly endogenous to exogenous in Australian koalas. Collectively, these findings advance both our understanding of KoRV in koalas and of retroviral endogenization and diversification in general. see also the Perspective by Elliott S. Chiu and Roderick B. Gagne.
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Affiliation(s)
- Bonnie L Quigley
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Faye Wedrowicz
- School of Science, Psychology and Sport, Federation University Australia, Churchill, Vic., Australia
| | - Fiona Hogan
- School of Science, Psychology and Sport, Federation University Australia, Churchill, Vic., Australia
| | - Peter Timms
- Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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Fambrini M, Usai G, Vangelisti A, Mascagni F, Pugliesi C. The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations. Genesis 2020; 58:e23399. [DOI: 10.1002/dvg.23399] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
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Gözen I, Dommersnes P. Biological lipid nanotubes and their potential role in evolution. THE EUROPEAN PHYSICAL JOURNAL. SPECIAL TOPICS 2020; 229:2843-2862. [PMID: 33224439 PMCID: PMC7666715 DOI: 10.1140/epjst/e2020-000130-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
The membrane of cells and organelles are highly deformable fluid interfaces, and can take on a multitude of shapes. One distinctive and particularly interesting property of biological membranes is their ability to from long and uniform nanotubes. These nanoconduits are surprisingly omnipresent in all domains of life, from archaea, bacteria, to plants and mammals. Some of these tubes have been known for a century, while others were only recently discovered. Their designations are different in different branches of biology, e.g. they are called stromule in plants and tunneling nanotubes in mammals. The mechanical transformation of flat membranes to tubes involves typically a combination of membrane anchoring and external forces, leading to a pulling action that results in very rapid membrane nanotube formation - micrometer long tubes can form in a matter of seconds. Their radius is set by a mechanical balance of tension and bending forces. There also exists a large class of membrane nanotubes that form due to curvature inducing molecules. It seems plausible that nanotube formation and functionality in plants and animals may have been inherited from their bacterial ancestors during endosymbiotic evolution. Here we attempt to connect observations of nanotubes in different branches of biology, and outline their similarities and differences with the aim of providing a perspective on their joint functions and evolutionary origin.
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Affiliation(s)
- Irep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318 Norway
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0315 Norway
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, 412 96 Sweden
| | - Paul Dommersnes
- Department of Physics, Norwegian University of Science and Technology, Hoegskoleringen 5, 7491 Trondheim, Norway
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66
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Saini SK, Ørskov AD, Bjerregaard AM, Unnikrishnan A, Holmberg-Thydén S, Borch A, Jensen KV, Anande G, Bentzen AK, Marquard AM, Tamhane T, Treppendahl MB, Gang AO, Dufva IH, Szallasi Z, Ternette N, Pedersen AG, Eklund AC, Pimanda J, Grønbæk K, Hadrup SR. Human endogenous retroviruses form a reservoir of T cell targets in hematological cancers. Nat Commun 2020; 11:5660. [PMID: 33168830 PMCID: PMC7653045 DOI: 10.1038/s41467-020-19464-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 10/10/2020] [Indexed: 01/03/2023] Open
Abstract
Human endogenous retroviruses (HERV) form a substantial part of the human genome, but mostly remain transcriptionally silent under strict epigenetic regulation, yet can potentially be reactivated by malignant transformation or epigenetic therapies. Here, we evaluate the potential for T cell recognition of HERV elements in myeloid malignancies by mapping transcribed HERV genes and generating a library of 1169 potential antigenic HERV-derived peptides predicted for presentation by 4 HLA class I molecules. Using DNA barcode-labeled MHC-I multimers, we find CD8+ T cell populations recognizing 29 HERV-derived peptides representing 18 different HERV loci, of which HERVH-5, HERVW-1, and HERVE-3 have more profound responses; such HERV-specific T cells are present in 17 of the 34 patients, but less frequently in healthy donors. Transcriptomic analyses reveal enhanced transcription of the HERVs in patients; meanwhile DNA-demethylating therapy causes a small and heterogeneous enhancement in HERV transcription without altering T cell recognition. Our study thus uncovers T cell recognition of HERVs in myeloid malignancies, thereby implicating HERVs as potential targets for immunotherapeutic therapies.
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Affiliation(s)
- Sunil Kumar Saini
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andreas Due Ørskov
- Department of Haematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Anne-Mette Bjerregaard
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ashwin Unnikrishnan
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- Prince of Wales Clinical School, UNSW, Sydney, NSW, 2052, Australia
| | - Staffan Holmberg-Thydén
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Haematology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Annie Borch
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kathrine Valentini Jensen
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Govardhan Anande
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- Prince of Wales Clinical School, UNSW, Sydney, NSW, 2052, Australia
| | - Amalie Kai Bentzen
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andrea Marion Marquard
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tripti Tamhane
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Anne Ortved Gang
- Department of Haematology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Inge Høgh Dufva
- Department of Haematology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Zoltan Szallasi
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicola Ternette
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anders Gorm Pedersen
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aron Charles Eklund
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - John Pimanda
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- Prince of Wales Clinical School, UNSW, Sydney, NSW, 2052, Australia
- Haematology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Randwick, NSW, 2031, Australia
| | - Kirsten Grønbæk
- Department of Haematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark.
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Chelkha N, Levasseur A, La Scola B, Colson P. Host-virus interactions and defense mechanisms for giant viruses. Ann N Y Acad Sci 2020; 1486:39-57. [PMID: 33090482 DOI: 10.1111/nyas.14469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/28/2020] [Accepted: 07/26/2020] [Indexed: 12/26/2022]
Abstract
Giant viruses, with virions larger than 200 nm and genomes larger than 340 kilobase pairs, modified the now outdated perception of the virosphere. With virions now reported reaching up to 1.5 μm in size and genomes of up to 2.5 Mb encoding components shared with cellular life forms, giant viruses exhibit a complexity similar to microbes, such as bacteria and archaea. Here, we review interactions of giant viruses with their hosts and defense strategies of giant viruses against their hosts and coinfecting microorganisms or virophages. We also searched by comparative genomics for homologies with proteins described or suspected to be involved in defense mechanisms. Our search reveals that natural immunity and apoptosis seem to be crucial components of the host defense against giant virus infection. Conversely, giant viruses possess methods of hijacking host functions to counteract cellular antiviral responses. In addition, giant viruses may encode other unique and complex pathways to manipulate the host machinery and eliminate other competing microorganisms. Notably, giant viruses have evolved defense mechanisms against their virophages and they might trigger defense systems against other viruses through sequence integration. We anticipate that comparative genomics may help identifying genes involved in defense strategies of both giant viruses and their hosts.
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Affiliation(s)
- Nisrine Chelkha
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
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68
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Wilson KD, Ameen M, Guo H, Abilez OJ, Tian L, Mumbach MR, Diecke S, Qin X, Liu Y, Yang H, Ma N, Gaddam S, Cunningham NJ, Gu M, Neofytou E, Prado M, Hildebrandt TB, Karakikes I, Chang HY, Wu JC. Endogenous Retrovirus-Derived lncRNA BANCR Promotes Cardiomyocyte Migration in Humans and Non-human Primates. Dev Cell 2020; 54:694-709.e9. [PMID: 32763147 PMCID: PMC7529962 DOI: 10.1016/j.devcel.2020.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/03/2020] [Accepted: 07/11/2020] [Indexed: 01/04/2023]
Abstract
Transposable elements (TEs) comprise nearly half of the human genome and are often transcribed or exhibit cis-regulatory properties with unknown function in specific processes such as heart development. In the case of endogenous retroviruses (ERVs), a TE subclass, experimental interrogation is constrained as many are primate-specific or human-specific. Here, we use primate pluripotent stem-cell-derived cardiomyocytes that mimic fetal cardiomyocytes in vitro to discover hundreds of ERV transcripts from the primate-specific MER41 family, some of which are regulated by the cardiogenic transcription factor TBX5. The most significant of these are located within BANCR, a long non-coding RNA (lncRNA) exclusively expressed in primate fetal cardiomyocytes. Functional studies reveal that BANCR promotes cardiomyocyte migration in vitro and ventricular enlargement in vivo. We conclude that recently evolved TE loci such as BANCR may represent potent de novo developmental regulatory elements that can be interrogated with species-matching pluripotent stem cell models.
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Affiliation(s)
- Kitchener D Wilson
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Mohamed Ameen
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Cancer Biology, Stanford University, Stanford, CA 94305, USA
| | - Hongchao Guo
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Oscar J Abilez
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Lei Tian
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Sebastian Diecke
- Berlin Institute of Health, Max Delbrück Center, and DZHK (German Center for Cardiovascular Research), Berlin, Germany
| | - Xulei Qin
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Yonggang Liu
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Huaxiao Yang
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Ning Ma
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Sadhana Gaddam
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Mingxia Gu
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Evgenios Neofytou
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Maricela Prado
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Thomas B Hildebrandt
- Wildlife Reproduction Medicine, Freie University and Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Joseph C Wu
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Departments of Medicine and Radiology, Stanford University, Stanford, CA 94305, USA.
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69
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Li Z, Hua X, Serra-Cardona A, Xu X, Gan S, Zhou H, Yang WS, Chen CL, Xu RM, Zhang Z. DNA polymerase α interacts with H3-H4 and facilitates the transfer of parental histones to lagging strands. SCIENCE ADVANCES 2020; 6:eabb5820. [PMID: 32923642 PMCID: PMC7449674 DOI: 10.1126/sciadv.abb5820] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/14/2020] [Indexed: 05/03/2023]
Abstract
How parental histones, the carriers of epigenetic modifications, are deposited onto replicating DNA remains poorly understood. Here, we describe the eSPAN method (enrichment and sequencing of protein-associated nascent DNA) in mouse embryonic stem (ES) cells and use it to detect histone deposition onto replicating DNA strands with a relatively small number of cells. We show that DNA polymerase α (Pol α), which synthesizes short primers for DNA synthesis, binds histone H3-H4 preferentially. A Pol α mutant defective in histone binding in vitro impairs the transfer of parental H3-H4 to lagging strands in both yeast and mouse ES cells. Last, dysregulation of both coding genes and noncoding endogenous retroviruses is detected in mutant ES cells defective in parental histone transfer. Together, we report an efficient eSPAN method for analysis of DNA replication-linked processes in mouse ES cells and reveal the mechanism of Pol α in parental histone transfer.
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Affiliation(s)
- Zhiming Li
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Albert Serra-Cardona
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xiaowei Xu
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Songlin Gan
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Zhou
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Wen-Si Yang
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-long Chen
- Curie Institute, PSL Research University, CNRS UMR 3244, F-75005, Paris, France
- Sorbonne University, F-75005 Paris, France
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
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70
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van der Kuyl AC, Berkhout B. Viruses in the reproductive tract: On their way to the germ line? Virus Res 2020; 286:198101. [PMID: 32710926 DOI: 10.1016/j.virusres.2020.198101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 01/13/2023]
Abstract
Studies of vertebrate genomes have indicated that all species contain in their chromosomes stretches of DNA with sequence similarity to viral genomes. How such 'endogenous' viral elements (EVEs) ended up in host genomes is usually explained in general terms such as 'they entered the germ line at some point during evolution'. This seems a correct statement, but is also rather imprecise. The vast number of endogenous viral sequences suggest that common routes to the 'germ line' may exist, as relying on chance alone may not easily explain the abundance of EVEs in modern mammalian genomes. An increasing number of virus types have been detected in human semen and a growing number of studies have reported on viral infections that cause male infertility or subfertility and on viral infections that threaten in vitro fertilisation practices. Thus, it is timely to survey the pathway(s) that viruses can use to gain access to the human germ line. Embryo transfer and semen quality studies in livestock form another source of relevant information because virus infection during reproduction is clearly unwanted, as is the case for the human situation. In this review, studies on viruses in the male and female reproductive tract and in the early embryo will be discussed to propose a plausible viral route to the mammalian germ line.
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Affiliation(s)
- Antoinette Cornelia van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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71
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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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Kuriyama K, Tabara M, Moriyama H, Kanazawa A, Koiwa H, Takahashi H, Fukuhara T. Disturbance of floral colour pattern by activation of an endogenous pararetrovirus, petunia vein clearing virus, in aged petunia plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:497-511. [PMID: 32100385 PMCID: PMC7496347 DOI: 10.1111/tpj.14728] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/04/2020] [Indexed: 05/22/2023]
Abstract
White areas of star-type bicolour petals of petunia (Petunia hybrida) are caused by post-transcriptional gene silencing (PTGS) of the key enzyme of anthocyanin biosynthesis. We observed blotched flowers and a vein-clearing symptom in aged petunia plants. To determine the cause of blotched flowers, we focused on an endogenous pararetrovirus, petunia vein clearing virus (PVCV), because this virus may have a suppressor of PTGS (VSR). Transcripts and episomal DNAs derived from proviral PVCVs accumulated in aged plants, indicating that PVCV was activated as the host plant aged. Furthermore, DNA methylation of CG and CHG sites in the promoter region of proviral PVCV decreased in aged plants, suggesting that poor maintenance of DNA methylation activates PVCV. In parallel, de novo DNA methylation of CHH sites in its promoter region was also detected. Therefore, both activation and inactivation of PVCV occurred in aged plants. The accumulation of PVCV transcripts and episomal DNAs in blotched regions and the detection of VSR activity support a mechanism in which suppression of PTGS by PVCV causes blotched flowers.
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Affiliation(s)
- Kazunori Kuriyama
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Midori Tabara
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Hiromitsu Moriyama
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Akira Kanazawa
- Research Faculty of AgricultureHokkaido UniversityKita 9, Nishi 9, Kita‐kuSapporo060‐8589Japan
| | - Hisashi Koiwa
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Department of Horticultural SciencesTexas A&M UniversityCollege StationTX77843USA
| | - Hideki Takahashi
- Graduate School of Agricultural ScienceTohoku University468‐1, Aramaki‐Aza‐AobaSendai980‐0845Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
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Yap MW, Young GR, Varnaite R, Morand S, Stoye JP. Duplication and divergence of the retrovirus restriction gene Fv1 in Mus caroli allows protection from multiple retroviruses. PLoS Genet 2020; 16:e1008471. [PMID: 32525879 PMCID: PMC7313476 DOI: 10.1371/journal.pgen.1008471] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 06/23/2020] [Accepted: 05/13/2020] [Indexed: 12/29/2022] Open
Abstract
Viruses and their hosts are locked in an evolutionary race where resistance to infection is acquired by the hosts while viruses develop strategies to circumvent these host defenses. Forming one arm of the host defense armory are cell autonomous restriction factors like Fv1. Originally described as protecting laboratory mice from infection by murine leukemia virus (MLV), Fv1s from some wild mice have also been found to restrict non-MLV retroviruses, suggesting an important role in the protection against viruses in nature. We surveyed the Fv1 genes of wild mice trapped in Thailand and characterized their restriction activities against a panel of retroviruses. An extra copy of the Fv1 gene, named Fv7, was found on chromosome 6 of three closely related Asian species of mice: Mus caroli, M. cervicolor, and M. cookii. The presence of flanking repeats suggested it arose by LINE-mediated retroduplication within their most recent common ancestor. A high degree of natural variation was observed in both Fv1 and Fv7 and, on top of positive selection at certain residues, insertions and deletions were present that changed the length of the reading frames. These genes exhibited a range of restriction phenotypes, with activities directed against gamma-, spuma-, and lentiviruses. It seems likely, at least in the case of M. caroli, that the observed gene duplication may expand the breadth of restriction beyond the capacity of Fv1 alone and that one or more such viruses have recently driven or continue to drive the evolution of the Fv1 and Fv7 genes.
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Affiliation(s)
| | | | | | - Serge Morand
- Centre National de la Recherche Scientifique-Centre de coopération
Internationale en Recherche Agronomique pour le Développement Animal et Gestion
Intégrée des Risques, Faculty of Veterinary Technology, Kasetsart University,
Bangkok, Thailand
| | - Jonathan P. Stoye
- The Francis Crick Institute, London, United Kingdom
- Faculty of Medicine, Imperial College London, London, United
Kingdom
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74
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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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75
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Abstract
Bats are reservoirs of emerging viruses that are highly pathogenic to other mammals, including humans. Despite the diversity and abundance of bat viruses, to date they have not been shown to harbor exogenous retroviruses. Here we report the discovery and characterization of a group of koala retrovirus-related (KoRV-related) gammaretroviruses in Australian and Asian bats. These include the Hervey pteropid gammaretrovirus (HPG), identified in the scat of the Australian black flying fox (Pteropus alecto), which is the first reproduction-competent retrovirus found in bats. HPG is a close relative of KoRV and the gibbon ape leukemia virus (GALV), with virion morphology and Mn2+-dependent virion-associated reverse transcriptase activity typical of a gammaretrovirus. In vitro, HPG is capable of infecting bat and human cells, but not mouse cells, and displays a similar pattern of cell tropism as KoRV-A and GALV. Population studies reveal the presence of HPG and KoRV-related sequences in several locations across northeast Australia, as well as serologic evidence for HPG in multiple pteropid bat species, while phylogenetic analysis places these bat viruses as the basal group within the KoRV-related retroviruses. Taken together, these results reveal bats to be important reservoirs of exogenous KoRV-related gammaretroviruses.
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76
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Watanabe T, Kawaoka Y. Villains or heroes? The raison d'être of viruses. Clin Transl Immunology 2020; 9:e01114. [PMID: 32099651 PMCID: PMC7029637 DOI: 10.1002/cti2.1114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 12/21/2022] Open
Abstract
The relationship between humans and viruses has a long history. Since the first identification of viruses in the 19th century, we have considered them to be 'pathogens' and have studied their mechanisms of replication and pathogenicity to combat the diseases that they cause. However, the relationships between hosts and viruses are various and virus infections do not necessarily cause diseases in their hosts. Rather, recent studies have shown that viral infections sometimes have beneficial effects on the biological functions and/or evolution of hosts. Here, we provide some insight into the positive side of viruses.
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Affiliation(s)
- Tokiko Watanabe
- Division of VirologyDepartment of Microbiology and ImmunologyInstitute of Medical ScienceUniversity of TokyoTokyoJapan
| | - Yoshihiro Kawaoka
- Division of VirologyDepartment of Microbiology and ImmunologyInstitute of Medical ScienceUniversity of TokyoTokyoJapan
- Department of Pathobiological SciencesSchool of Veterinary MedicineUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Special PathogensInternational Research Center for Infectious DiseasesInstitute of Medical ScienceUniversity of TokyoTokyoJapan
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77
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Percharde M, Sultana T, Ramalho-Santos M. What Doesn't Kill You Makes You Stronger: Transposons as Dual Players in Chromatin Regulation and Genomic Variation. Bioessays 2020; 42:e1900232. [PMID: 32053231 DOI: 10.1002/bies.201900232] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/10/2020] [Indexed: 12/22/2022]
Abstract
Transposable elements (TEs) are sequences currently or historically mobile, and are present across all eukaryotic genomes. A growing interest in understanding the regulation and function of TEs has revealed seemingly dichotomous roles for these elements in evolution, development, and disease. On the one hand, many gene regulatory networks owe their organization to the spread of cis-elements and DNA binding sites through TE mobilization during evolution. On the other hand, the uncontrolled activity of transposons can generate mutations and contribute to disease, including cancer, while their increased expression may also trigger immune pathways that result in inflammation or senescence. Interestingly, TEs have recently been found to have novel essential functions during mammalian development. Here, the function and regulation of TEs are discussed, with a focus on LINE1 in mammals. It is proposed that LINE1 is a beneficial endogenous dual regulator of gene expression and genomic diversity during mammalian development, and that both of these functions may be detrimental if deregulated in disease contexts.
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Affiliation(s)
- Michelle Percharde
- MRC London Institute of Medical Sciences (LMS), London, W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Tania Sultana
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5T 3L9, Ontario, Canada
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5T 3L9, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Ontario, Canada
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78
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Tatkiewicz W, Dickie J, Bedford F, Jones A, Atkin M, Kiernan M, Maze EA, Agit B, Farnham G, Kanapin A, Belshaw R. Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines. Mob DNA 2020; 11:9. [PMID: 32055257 PMCID: PMC7007669 DOI: 10.1186/s13100-020-0204-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/14/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The cell-surface attachment protein (Env) of the HERV-K(HML-2) lineage of endogenous retroviruses is a potentially attractive tumour-associated antigen for anti-cancer immunotherapy. The human genome contains around 100 integrated copies (called proviruses or loci) of the HERV-K(HML-2) virus and we argue that it is important for therapy development to know which and how many of these contribute to protein expression, and how this varies across tissues. We measured relative provirus expression in HERV-K(HML-2), using enriched RNA-Seq analysis with both short- and long-read sequencing, in three Mantle Cell Lymphoma cell lines (JVM2, Granta519 and REC1). We also confirmed expression of the Env protein in two of our cell lines using Western blotting, and analysed provirus expression data from all other relevant published studies. RESULTS Firstly, in both our and other reanalysed studies, approximately 10% of the transcripts mapping to HERV-K(HML-2) came from Env-encoding proviruses. Secondly, in one cell line the majority of the protein expression appears to come from one provirus (12q14.1). Thirdly, we find a strong tissue-specific pattern of provirus expression. CONCLUSIONS A possible dependency of Env expression on a single provirus, combined with the earlier observation that this provirus is not present in all individuals and a general pattern of tissue-specific expression among proviruses, has serious implications for future HERV-K(HML-2)-targeted immunotherapy. Further research into HERV-K(HML-2) as a possible tumour-associated antigen in blood cancers requires a more targeted, proteome-based, screening protocol that will consider these polymorphisms within HERV-K(HML-2). We include a plan (and necessary alignments) for such work.
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Affiliation(s)
- Witold Tatkiewicz
- Peninsula Medical School, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - James Dickie
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Franchesca Bedford
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Alexander Jones
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Mark Atkin
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Michele Kiernan
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Emmanuel Atangana Maze
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Bora Agit
- Peninsula Medical School, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Garry Farnham
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
| | - Alexander Kanapin
- Department of Oncology, University of Oxford, Oxford, UK
- Current address: Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Robert Belshaw
- School of Biomedical Sciences, Faculty of Health: Medicine, Dentistry and Human Sciences, University of Plymouth, Plymouth, UK
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Abstract
Interferon-induced transmembrane (IFITM) proteins are encoded by many vertebrate species and exhibit antiviral activities against a wide range of viruses. IFITM3, when present in virus-producing cells, reduces the fusion potential of HIV-1 virions, but the mechanism is poorly understood. To define the breadth and mechanistic basis for the antiviral activity of IFITM3, we took advantage of a murine leukemia virus (MLV)-based pseudotyping system. By carefully controlling amounts of IFITM3 and envelope protein (Env) in virus-producing cells, we found that IFITM3 potently inhibits MLV infectivity when Env levels are limiting. Loss of infectivity was associated with defective proteolytic processing of Env and lysosomal degradation of the Env precursor. Ecotropic and xenotropic variants of MLV Env, as well as HIV-1 Env and vesicular stomatitis virus glycoprotein (VSV-G), are sensitive to IFITM3, whereas Ebola glycoprotein is resistant, suggesting that IFITM3 selectively inactivates certain viral glycoproteins. Furthermore, endogenous IFITM3 in human and murine cells negatively regulates MLV Env abundance. However, we found that the negative impact of IFITM3 on virion infectivity is greater than its impact on decreasing Env incorporation, suggesting that IFITM3 may impair Env function, as well as reduce the amount of Env in virions. Finally, we demonstrate that loss of virion infectivity mediated by IFITM3 is reversed by the expression of glycoGag, a murine retrovirus accessory protein previously shown to antagonize the antiviral activity of SERINC proteins. Overall, we show that IFITM3 impairs virion infectivity by regulating Env quantity and function but that enhanced Env expression and glycoGag confer viral resistance to IFITM3.IMPORTANCE The viral envelope glycoprotein, known as "Env" in Retroviridae, is found on the virion surface and facilitates virus entry into cells by mediating cell attachment and fusion. Env is a major structural component of retroviruses and is targeted by all arms of the immune response, including adaptive and innate immunity. Less is known about how cell-intrinsic immunity prevents retrovirus replication at the level of individual cells. Here, we show that cellular IFITM3 and IFITM2 inhibit the fusion potential of retroviral virions by inhibiting Env protein via a two-pronged mechanism. IFITM proteins inhibit Env abundance in cells and also impair its function when levels are low. The posttranslational block of retroviral Env function by IFITM proteins is likely to impede both exogenous and endogenous retrovirus replication. In support of a relevant role for IFITM3 in retrovirus control, the retroviral accessory protein glycoGag counteracts IFITM3 function to promote virus infectivity.
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80
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Acton O, Grant T, Nicastro G, Ball NJ, Goldstone DC, Robertson LE, Sader K, Nans A, Ramos A, Stoye JP, Taylor IA, Rosenthal PB. Structural basis for Fullerene geometry in a human endogenous retrovirus capsid. Nat Commun 2019; 10:5822. [PMID: 31862888 PMCID: PMC6925226 DOI: 10.1038/s41467-019-13786-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/28/2019] [Indexed: 01/09/2023] Open
Abstract
The HML2 (HERV-K) group constitutes the most recently acquired family of human endogenous retroviruses, with many proviruses less than one million years old. Many maintain intact open reading frames and provirus expression together with HML2 particle formation are observed in early stage human embryo development and are associated with pluripotency as well as inflammatory disease, cancers and HIV-1 infection. Here, we reconstruct the core structural protein (CA) of an HML2 retrovirus, assemble particles in vitro and employ single particle cryogenic electron microscopy (cryo-EM) to determine structures of four classes of CA Fullerene shell assemblies. These icosahedral and capsular assemblies reveal at high-resolution the molecular interactions that allow CA to form both pentamers and hexamers and show how invariant pentamers and structurally plastic hexamers associate to form the unique polyhedral structures found in retroviral cores.
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Affiliation(s)
- Oliver Acton
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Tim Grant
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Neil J Ball
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David C Goldstone
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Laura E Robertson
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Kasim Sader
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Thermo Fisher Scientific Materials and Structural Analysis, Eindhoven, Netherlands
| | - Andrea Nans
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andres Ramos
- Division of Molecular Structure, MRC National Institute for Medical Research, London, NW7 1AA, UK
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Jonathan P Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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81
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Gray LR, Jackson RE, Jackson PEH, Bekiranov S, Rekosh D, Hammarskjöld ML. HIV-1 Rev interacts with HERV-K RcREs present in the human genome and promotes export of unspliced HERV-K proviral RNA. Retrovirology 2019; 16:40. [PMID: 31842941 PMCID: PMC6916052 DOI: 10.1186/s12977-019-0505-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 12/07/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The HERV-K (HML-2) viruses are the youngest of the human endogenous retroviruses. They are present as several almost complete proviral copies and numerous fragments in the human genome. Many HERV-K proviruses express a regulatory protein Rec, which binds to an element present in HERV-K mRNAs called the RcRE. This interaction is necessary for the nucleo-cytoplasmic export and expression of HERV-K mRNAs that retain introns and plays a role analogous to that of Rev and the RRE in HIV replication. There are over 900 HERV-K RcREs distributed throughout the human genome. Thus, it was of interest to determine if Rev could functionally interact with selected RcRE elements that map either to HERV-K proviruses or human gene regions. This interaction would have the potential to alter the expression of both HERV-K mRNAs and cellular mRNAs during HIV-1 infection. RESULTS In this study we employed a combination of RNAseq, bioinformatics and cell-based functional assays. Potential RcREs were identified through a number of bioinformatic approaches. They were then tested for their ability to promote export and translation of a reporter mRNA with a retained intron in conjunction with Rev or Rec. Some of the selected elements functioned well with either Rev, Rec or both, whereas some showed little or no function. Rev function on individual RcREs varied and was also dependent on the Rev sequence. We also performed RNAseq on total and cytoplasmic RNA isolated from SupT1 cells expressing HIV Rev, with or without Tat, or HERV-K Rec. Proviral mRNA from three HERV-K loci (4p16.1b, 22q11.23 and most significantly 3q12.3) accumulated in the cytoplasm in the presence of Rev or Tat and Rev, but not Rec. Consistent with this, the 3' RcRE from 3q12.3 functioned well with HIV-Rev in our reporter assay. In contrast, this RcRE showed little or no function with Rec. CONCLUSIONS The HIV Rev protein can functionally interact with many RcREs present in the human genome, depending on the RcRE sequence, as well as the Rev sequence. This leads to export of some of the HERV-K proviral mRNAs and also has the potential to change the expression of non-viral genes.
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Affiliation(s)
- Laurie R Gray
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Rachel E Jackson
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Patrick E H Jackson
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, 22908, USA
| | - Stefan Bekiranov
- Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, 22908, USA
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Marie-Louise Hammarskjöld
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA.
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82
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Chen Y, Wei X, Zhang G, Holmes EC, Cui J. Identification and evolution of avian endogenous foamy viruses. Virus Evol 2019; 5:vez049. [PMID: 31777663 PMCID: PMC6875641 DOI: 10.1093/ve/vez049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A history of long-term co-divergence means that foamy viruses (family Retroviridae) provide an ideal framework to understanding virus-host evolution over extended time periods. Endogenous foamy viruses (EndFVs) are rare, and to date have only been described in a limited number of mammals, amphibians, reptiles and fish genomes. By screening 414 avian genomes we identified EndFVs in two bird species: the Maguari Stork (Ciconia maguari) and the Oriental Stork (Ciconia boyciana). Analyses of phylogenetic relationships, genome structures and flanking sequences revealed a single origin of EndFVs in Ciconia species. In addition, the marked incongruence between the virus and host phylogenies suggested that this integration event occurred independently in birds. In sum, by providing evidence that birds can be infected with foamy viruses, we fill the last major gap in the taxonomic distribution of foamy viruses and their animal hosts.
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Affiliation(s)
- Yicong Chen
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoman Wei
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Jie Cui
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
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83
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Watanabe T, Suzuki N, Tomonaga K, Sawa H, Matsuura Y, Kawaguchi Y, Takahashi H, Nagasaki K, Kawaoka Y. Neo-virology: The raison d'etre of viruses. Virus Res 2019; 274:197751. [PMID: 31520652 DOI: 10.1016/j.virusres.2019.197751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/07/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
Given that approximately 1031 virus particles exist on Earth and all of them are parasitic in living organisms, it is not hard to imagine how virus infection might affect the physiology of hosts and their ecosystems. However, traditional virology research tends to focus on viral pathogenicity or the individual pathogenic viruses; hence, the significance of viruses and viral-mediated processes in the global ecosystem has been poorly understood. To identify the previously unrecognized "raison d'etre of viruses" in nature, we established a research community, designated as the 'Neo-virology' consortium. In this consortium, we define a virus as a component of the global ecosystem and our aim is to elucidate its key roles in host organisms, that is, the intra-host ecosystem.
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Affiliation(s)
- Tokiko Watanabe
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Nobuhiro Suzuki
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Keizo Tomonaga
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Hirofumi Sawa
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Yoshiharu Matsuura
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Yasushi Kawaguchi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Hideki Takahashi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Keizo Nagasaki
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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84
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Karimi A, Sheervalilou R, Kahroba H. A New Insight on Activation of Human Endogenous Retroviruses (HERVs) in Malignant Melanoma upon Exposure to CuSO4. Biol Trace Elem Res 2019; 191:70-74. [PMID: 30539386 DOI: 10.1007/s12011-018-1605-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
Abstract
Human endogenous retroviruses (HERVs) are semi-conserved subtypes of long-terminal repeats containing retrotransposons that constitute approximately 8% of the genome. Under pathological conditions, the expression of HERVs is also affected by epigenetic modifications. The extent to which the activation of human endogenous retroviruses can be influenced upon exposure to copper remains to be evaluated. Thus, the present study was designed to evaluate the effects of CuSO4 administration on the transcriptional activity of three HERV families (H, K, and W) in human malignant melanoma cells. For this purpose, following the determination of less cytotoxic concentrations of copper sulfate, the human skin malignant melanoma SK-MEL-37 cells were treated with 25, 50, and 75 μM CuSO4 for 96 h. Then, mRNA expression of env gene of HERV-H, HERV-K, and HERV-W was evaluated by qPCR. According to the results, 96-h treatment of SK-MEL-37 cells with 75 μM CuSO4 could significantly downregulate HERV-H evn expression (P < 0.05). Moreover, exposure of 25 μM copper significantly upregulated the expression of HERV-K env (P < 0.05). Regarding HERV-W env, the expression level increased significantly in all treated concentrations (P < 0.05). It seems that the expression change was decreased in both HERV-W and HERV-K by increasing doses. The study results demonstrated that copper exposure to melanoma cells might promote tumor growth by inducing HERVs and/or control tumor development by decreasing the activation of HERVs in defined levels of copper. According to the findings of this study, copper might exert a binary effect on malignant melanoma.
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Affiliation(s)
- Abbas Karimi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Golgasht St., Tabriz, East Azerbaijan, 5166614756, Iran.
| | - Roghayeh Sheervalilou
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Golgasht St., Tabriz, East Azerbaijan, 5166614756, Iran
| | - Houman Kahroba
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Golgasht St., Tabriz, East Azerbaijan, 5166614756, Iran
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85
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An endogenous retroviral element exerts an antiviral innate immune function via the derived lncRNA lnc-ALVE1-AS1. Antiviral Res 2019; 170:104571. [PMID: 31374219 DOI: 10.1016/j.antiviral.2019.104571] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/27/2019] [Accepted: 07/29/2019] [Indexed: 11/24/2022]
Abstract
Endogenous retroviruses (ERVs) constitute an important component of animal and human genomes and are usually silenced by epigenetic mechanisms in adult cells. Although ERVs were recently reported to be linked to early development, tumorigenesis and autoimmune disease, their impacts on antiviral innate immunity and the underlying mechanisms have not been elucidated. Here, we provide the first direct evidence of an endogenous retroviral element affecting antiviral innate immunity via its derived antisense long non-coding RNA (lncRNA). We found that an antisense lncRNA, which is called lnc-ALVE1-AS1 and is transcribed from the endogenous avian leukosis virus in chromosome 1 (ALVE1), distinctly inhibited the entry and replication of exogenous retroviruses in chicken embryonic fibroblasts (CEFs). This behaviour is at least in part attributed to the induction of an antiviral innate immune pathway by ALVE1 activation, suggesting that an activated endogenous retroviral element may induce antiviral defence responses via its derived antisense lncRNA. We also found that lnc-ALVE1-AS1 mediated these effects by activating the TLR3 signalling in the cytoplasm. Our results provide novel insights into the antiviral innate immune function of ERVs, suggesting that ERVs may play an important role in antiviral defences and provide new strategies for the development of new vaccines.
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86
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Coudert AE, Redelsperger F, Chabbi-Achengli Y, Vernochet C, Marty C, Decrouy X, Heidmann T, de Vernejoul MC, Dupressoir A. Role of the captured retroviral envelope syncytin-B gene in the fusion of osteoclast and giant cell precursors and in bone resorption, analyzed ex vivo and in vivo in syncytin-B knockout mice. Bone Rep 2019; 11:100214. [PMID: 31360740 PMCID: PMC6637224 DOI: 10.1016/j.bonr.2019.100214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/09/2019] [Indexed: 12/23/2022] Open
Abstract
Syncytin-A and -B are envelope genes of retroviral origin that have been captured in evolution for a role in placentation. They trigger cell-cell fusion and were shown to be essential for the formation of the syncytiotrophoblast layer during mouse placenta formation. Syncytin-A and -B expression has been described in other tissues and their highly fusogenic properties suggested that they might be involved in the fusion of other cell types. Here, taking advantage of mice knocked out for syncytin-B, SynB-/- mice, we investigated the potential role of syncytin-B in the fusion of cells from the monocyte/macrophage lineage into multinucleated osteoclasts (OCs) -in bone- or multinucleated giant cells -in soft tissues. In ex vivo experiments, a significant reduction in fusion index and in the number of multinucleated OCs and giant cells was observed as soon as Day3 in SynB-/- as compared to wild-type cell cultures. Interestingly, the number of nuclei per multinucleated OC or giant cell remained unchanged. These results, together with the demonstration that syncytin-B expression is maximal in the first 2 days of OC differentiation, argue for syncytin-B playing a role in the fusion of OC and giant cell mononucleated precursors, at initial stages. Finally, ex vivo, the observed reduction in multinucleated OC number had no impact on the expression of OC differentiation markers, and a dentin resorption assay did not evidence any difference in the osteoclastic resorption activity, suggesting that syncytin-B is not required for OC activity. In vivo, syncytin-B was found to be expressed in the periosteum of embryos at embryonic day 16.5, where TRAP-positive cells were observed. Yet, in adults, no significant reduction in OC number or alteration in bone phenotype was observed in SynB-/- mice. In addition, SynB-/- mice did not show any change in the number of foreign body giant cells (FBGCs) that formed in response to implantation of foreign material, as compared to wild-type mice. Altogether the results suggest that in addition to its essential role in placenta formation, syncytin-B plays a role in OCs and macrophage fusion; yet it is not essential in vivo for OC and FBGC formation, or maintenance of bone homeostasis, at least under the conditions tested.
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Affiliation(s)
- Amélie E Coudert
- BIOSCAR, Unité Mixte de Recherche 1132, Institut National de la Santé et de la Recherche Médicale, Hôpital Lariboisière, Paris 75010, France.,Laboratoire de Physiopathologie Orale Moléculaire, INSERM U1138, Centre de recherche des Cordeliers, UFR d'Odontologie Garancire, Université Paris Diderot, Paris 75006, France
| | - François Redelsperger
- Unité Physiologie et Pathologie Moléculaires des Rétrovirus Endogènes et Infectieux, Unité Mixte de Recherche 9196, Centre National de la Recherche Scientifique, Gustave Roussy, Villejuif, 94805, and Université Paris-Sud, Orsay, 91405, France
| | - Yasmine Chabbi-Achengli
- BIOSCAR, Unité Mixte de Recherche 1132, Institut National de la Santé et de la Recherche Médicale, Hôpital Lariboisière, Paris 75010, France
| | - Cécile Vernochet
- Unité Physiologie et Pathologie Moléculaires des Rétrovirus Endogènes et Infectieux, Unité Mixte de Recherche 9196, Centre National de la Recherche Scientifique, Gustave Roussy, Villejuif, 94805, and Université Paris-Sud, Orsay, 91405, France
| | - Caroline Marty
- BIOSCAR, Unité Mixte de Recherche 1132, Institut National de la Santé et de la Recherche Médicale, Hôpital Lariboisière, Paris 75010, France
| | - Xavier Decrouy
- Inserm, U955, Plateforme d'imagerie, Créteil, 9400, France and Université Paris Est, Faculté de médecine, Créteil, 94000, France
| | - Thierry Heidmann
- Unité Physiologie et Pathologie Moléculaires des Rétrovirus Endogènes et Infectieux, Unité Mixte de Recherche 9196, Centre National de la Recherche Scientifique, Gustave Roussy, Villejuif, 94805, and Université Paris-Sud, Orsay, 91405, France
| | - Marie-Christine de Vernejoul
- BIOSCAR, Unité Mixte de Recherche 1132, Institut National de la Santé et de la Recherche Médicale, Hôpital Lariboisière, Paris 75010, France
| | - Anne Dupressoir
- Unité Physiologie et Pathologie Moléculaires des Rétrovirus Endogènes et Infectieux, Unité Mixte de Recherche 9196, Centre National de la Recherche Scientifique, Gustave Roussy, Villejuif, 94805, and Université Paris-Sud, Orsay, 91405, France
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87
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Convergent Co-option of the Retroviral gag Gene during the Early Evolution of Mammals. J Virol 2019; 93:JVI.00542-19. [PMID: 31068420 DOI: 10.1128/jvi.00542-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/30/2019] [Indexed: 12/30/2022] Open
Abstract
Endogenous retroviruses, records of past retroviral infections, are ubiquitous in vertebrate genomes. On occasion, vertebrate hosts have co-opted retroviral genes for their own biological functions. Here, we perform a phylogenomic survey of retroviral gag gene homologs within vertebrate genomes and identify two ancient co-opted retroviral gag genes, designated wucaishi1 (wcs1) and wucaishi2 (wcs2), in mammals. Conserved synteny and evolutionary analyses suggest that the wcs1 and wcs2 co-options occurred before the origin of modern placental mammals (∼100 million years ago) and before the origin of modern marsupials (∼80 million years ago), respectively. We found that the wcs genes were lost or pseudogenized multiple times during the evolutionary course of mammals. While the wcs1 gene is mainly subject to negative selection in placental mammals (except in Perissodactyla), the wcs2 gene underwent positive selection in marsupials. Moreover, analyses of transcriptome-sequencing (RNA-seq) data suggest that the wcs1 and the wcs2 genes are expressed in a wide range of tissues. The convergent wcs co-option in mammals implies the retroviral gag gene might have been repurposed more frequently than previously thought.IMPORTANCE Retroviruses occasionally can infect host germ lines, forming endogenous retroviruses. Vertebrates, in turn, recruited retroviral genes for their own biological functions, a process formally known as co-option or exaptation. To date, co-opted retroviral gag genes have rarely been reported. In this study, we identified two co-opted retroviral gag genes, designated wucaishi1 (wcs1) and wucaishi2 (wcs2), in mammals. The co-option of wcs1 and wcs2 occurred before the origin of modern placentals and before the origin of modern marsupials, respectively. Our study indicates that retroviral gag gene co-option might have occurred more frequently than previously thought during the evolutionary course of vertebrates.
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88
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Nahas MR, Stroopinsky D, Rosenblatt J, Cole L, Pyzer AR, Anastasiadou E, Sergeeva A, Ephraim A, Washington A, Orr S, McMasters M, Weinstock M, Jain S, Leaf RK, Ghiasuddin H, Rahimian M, Liegel J, Molldrem JJ, Slack F, Kufe D, Avigan D. Hypomethylating agent alters the immune microenvironment in acute myeloid leukaemia (AML) and enhances the immunogenicity of a dendritic cell/AML vaccine. Br J Haematol 2019; 185:679-690. [PMID: 30828801 PMCID: PMC6590084 DOI: 10.1111/bjh.15818] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukaemia (AML) is a lethal haematological malignancy characterized by an immunosuppressive milieu in the tumour microenvironment (TME) that fosters disease growth and therapeutic resistance. Hypomethylating agents (HMAs) demonstrate clinical efficacy in AML patients and exert immunomodulatory activities. In the present study, we show that guadecitabine augments both antigen processing and presentation, resulting in increased AML susceptibility to T cell-mediated killing. Exposure to HMA results in the activation of the endogenous retroviral pathway with concomitant downstream amplification of critical mediators of inflammation. In an immunocompetent murine leukaemia model, guadecitabine negatively regulates inhibitory accessory cells in the TME by decreasing PD-1 (also termed PDCD1) expressing T cells and reducing AML-mediated expansion of myeloid-derived suppressor cells. Therapy with guadecitabine results in enhanced leukaemia-specific immunity, as manifested by increased CD4 and CD8 cells targeting syngeneic leukaemia cells. We have previously reported that vaccination with AML/dendritic cell fusions elicits the expansion of leukaemia-specific T cells and protects against disease relapse. In the present study, we demonstrate that vaccination in conjunction with HMA therapy results in enhanced anti-leukaemia immunity and survival. The combination of a novel personalized dendritic cell/AML fusion vaccine and an HMA has therapeutic potential, and a clinical trial investigating this combination is planned.
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MESH Headings
- Animals
- Antineoplastic Agents, Immunological/immunology
- Antineoplastic Agents, Immunological/pharmacology
- Azacitidine/analogs & derivatives
- Azacitidine/immunology
- Azacitidine/pharmacology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cancer Vaccines/immunology
- Cell Line, Tumor
- DNA Methylation/drug effects
- Dendritic Cells/immunology
- Disease Models, Animal
- Down-Regulation/drug effects
- Down-Regulation/immunology
- Humans
- Immunity, Cellular/drug effects
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/immunology
- Mice, Inbred C57BL
- Neoplasm Transplantation
- Programmed Cell Death 1 Receptor/metabolism
- Retroviridae/immunology
- Tumor Microenvironment/immunology
- Virus Activation/immunology
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Affiliation(s)
- Myrna R Nahas
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Dina Stroopinsky
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jacalyn Rosenblatt
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Leandra Cole
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Athalia R Pyzer
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Eleni Anastasiadou
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Anna Sergeeva
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adam Ephraim
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Abigail Washington
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shira Orr
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Matthew Weinstock
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Salvia Jain
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Rebecca K Leaf
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Haider Ghiasuddin
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Maryam Rahimian
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jessica Liegel
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Frank Slack
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Donald Kufe
- Dana-Farber Cancer Institute, Department of Medical Oncology, Boston, MA
| | - David Avigan
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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89
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Chang YH, Keegan RM, Prazak L, Dubnau J. Cellular labeling of endogenous retrovirus replication (CLEVR) reveals de novo insertions of the gypsy retrotransposable element in cell culture and in both neurons and glial cells of aging fruit flies. PLoS Biol 2019; 17:e3000278. [PMID: 31095565 PMCID: PMC6541305 DOI: 10.1371/journal.pbio.3000278] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/29/2019] [Accepted: 05/03/2019] [Indexed: 12/11/2022] Open
Abstract
Evidence is rapidly mounting that transposable element (TE) expression and replication may impact biology more widely than previously thought. This includes potential effects on normal physiology of somatic tissues and dysfunctional impacts in diseases associated with aging, such as cancer and neurodegeneration. Investigation of the biological impact of mobile elements in somatic cells will be greatly facilitated by the use of donor elements that are engineered to report de novo events in vivo. In multicellular organisms, reporter constructs demonstrating engineered long interspersed nuclear element (LINE-1; L1) mobilization have been in use for quite some time, and strategies similar to L1 retrotransposition reporter assays have been developed to report replication of Ty1 elements in yeast and mouse intracisternal A particle (IAP) long terminal repeat (LTR) retrotransposons in cultivated cells. We describe a novel approach termed cellular labeling of endogenous retrovirus replication (CLEVR), which reports replication of the gypsy element within specific cells in vivo in Drosophila. The gypsy-CLEVR reporter reveals gypsy replication both in cell culture and in individual neurons and glial cells of the aging adult fly. We also demonstrate that the gypsy-CLEVR replication rate is increased when the short interfering RNA (siRNA) silencing system is genetically disrupted. This CLEVR strategy makes use of universally conserved features of retroviruses and should be widely applicable to other LTR retrotransposons, endogenous retroviruses (ERVs), and exogenous retroviruses.
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Affiliation(s)
- Yung-Heng Chang
- Department of Anesthesiology, Stony Brook School of Medicine, Stony Brook, New York, United States of America
| | - Richard M. Keegan
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
| | - Lisa Prazak
- Biology, Farmingdale State College, Farmingdale, New York, United States of America
| | - Josh Dubnau
- Department of Anesthesiology, Stony Brook School of Medicine, Stony Brook, New York, United States of America
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
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90
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Nowak-Sliwinska P, Scapozza L, Ruiz i Altaba A. Drug repurposing in oncology: Compounds, pathways, phenotypes and computational approaches for colorectal cancer. Biochim Biophys Acta Rev Cancer 2019; 1871:434-454. [PMID: 31034926 PMCID: PMC6528778 DOI: 10.1016/j.bbcan.2019.04.005] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 02/08/2023]
Abstract
The strategy of using existing drugs originally developed for one disease to treat other indications has found success across medical fields. Such drug repurposing promises faster access of drugs to patients while reducing costs in the long and difficult process of drug development. However, the number of existing drugs and diseases, together with the heterogeneity of patients and diseases, notably including cancers, can make repurposing time consuming and inefficient. The key question we address is how to efficiently repurpose an existing drug to treat a given indication. As drug efficacy remains the main bottleneck for overall success, we discuss the need for machine-learning computational methods in combination with specific phenotypic studies along with mechanistic studies, chemical genetics and omics assays to successfully predict disease-drug pairs. Such a pipeline could be particularly important to cancer patients who face heterogeneous, recurrent and metastatic disease and need fast and personalized treatments. Here we focus on drug repurposing for colorectal cancer and describe selected therapeutics already repositioned for its prevention and/or treatment as well as potential candidates. We consider this review as a selective compilation of approaches and methodologies, and argue how, taken together, they could bring drug repurposing to the next level.
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Affiliation(s)
- Patrycja Nowak-Sliwinska
- School of Pharmaceutical Sciences, University of Geneva and University of Lausanne, Geneva, Switzerland; Translational Research Center in Oncohaematology, University of Geneva, Rue Michel Servet 1, 1211 Geneva 4, Switzerland.
| | - Leonardo Scapozza
- School of Pharmaceutical Sciences, University of Geneva and University of Lausanne, Geneva, Switzerland
| | - Ariel Ruiz i Altaba
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Geneva 4, Switzerland
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91
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Gagnier L, Belancio VP, Mager DL. Mouse germ line mutations due to retrotransposon insertions. Mob DNA 2019; 10:15. [PMID: 31011371 PMCID: PMC6466679 DOI: 10.1186/s13100-019-0157-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/01/2019] [Indexed: 12/24/2022] Open
Abstract
Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans.
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Affiliation(s)
- Liane Gagnier
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
| | - Victoria P. Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - Dixie L. Mager
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
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92
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Investigation of somatic single nucleotide variations in human endogenous retrovirus elements and their potential association with cancer. PLoS One 2019; 14:e0213770. [PMID: 30934003 PMCID: PMC6443178 DOI: 10.1371/journal.pone.0213770] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 02/28/2019] [Indexed: 11/19/2022] Open
Abstract
Human endogenous retroviruses (HERVs) have been investigated for potential links with human cancer. However, the distribution of somatic nucleotide variations in HERV elements has not been explored in detail. This study aims to identify HERV elements with an over-representation of somatic mutations (hot spots) in cancer patients. Four HERV elements with mutation hotspots were identified that overlap with exons of four human protein coding genes. These hotspots were identified based on the significant over-representation (p<8.62e-4) of non-synonymous single-nucleotide variations (nsSNVs). These genes are TNN (HERV-9/LTR12), OR4K15 (HERV-IP10F/LTR10F), ZNF99 (HERV-W/HERV17/LTR17), and KIR2DL1 (MST/MaLR). In an effort to identify mutations that effect survival, all nsSNVs were further evaluated and it was found that kidney cancer patients with mutation C2270G in ZNF99 have a significantly lower survival rate (hazard ratio = 2.6) compared to those without it. Among HERV elements in the human non-protein coding regions, we found 788 HERVs with significantly elevated numbers of somatic single-nucleotide variations (SNVs) (p<1.60e-5). From this category the top three HERV elements with significantly over-represented SNVs are HERV-H/LTR7, HERV-9/LTR12 and HERV-L/MLT2. Majority of the SNVs in these 788 HERV elements are located in three DNA functional groups: long non-coding RNAs (lncRNAs) (60%), introns (22.2%) and transcriptional factor binding sites (TFBS) (14.8%). This study provides a list of mutational hotspots in HERVs, which could potentially be used as biomarkers and therapeutic targets.
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93
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Li W, Lin L, Malhotra R, Yang L, Acharya R, Poss M. A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations. PLoS Comput Biol 2019; 15:e1006564. [PMID: 30921327 PMCID: PMC6456218 DOI: 10.1371/journal.pcbi.1006564] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 04/09/2019] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Human Endogenous Retrovirus type K (HERV-K) is the only HERV known to be insertionally polymorphic; not all individuals have a retrovirus at a specific genomic location. It is possible that HERV-Ks contribute to human disease because people differ in both number and genomic location of these retroviruses. Indeed viral transcripts, proteins, and antibody against HERV-K are detected in cancers, auto-immune, and neurodegenerative diseases. However, attempts to link a polymorphic HERV-K with any disease have been frustrated in part because population prevalence of HERV-K provirus at each polymorphic site is lacking and it is challenging to identify closely related elements such as HERV-K from short read sequence data. We present an integrated and computationally robust approach that uses whole genome short read data to determine the occupation status at all sites reported to contain a HERV-K provirus. Our method estimates the proportion of fixed length genomic sequence (k-mers) from whole genome sequence data matching a reference set of k-mers unique to each HERV-K locus and applies mixture model-based clustering of these values to account for low depth sequence data. Our analysis of 1000 Genomes Project Data (KGP) reveals numerous differences among the five KGP super-populations in the prevalence of individual and co-occurring HERV-K proviruses; we provide a visualization tool to easily depict the proportion of the KGP populations with any combination of polymorphic HERV-K provirus. Further, because HERV-K is insertionally polymorphic, the genome burden of known polymorphic HERV-K is variable in humans; this burden is lowest in East Asian (EAS) individuals. Our study identifies population-specific sequence variation for HERV-K proviruses at several loci. We expect these resources will advance research on HERV-K contributions to human diseases. Human Endogenous Retrovirus type K (HERV-K) is the youngest of retrovirus families in the human genome and is the only group of endogenous retroviruses that has polymorphic members; a locus containing a HERV-K can be occupied in one individual but empty in others. HERV-Ks could contribute to disease risk or pathogenesis but linking one of the known polymorphic HERV-K to a specific disease has been difficult. We develop an easy to use method that reveals the considerable variation existing among global populations in the prevalence of individual and co-occurring polymorphic HERV-K, and in the number of HERV-K that any individual has in their genome. Our study provides a reference of diversity for the currently known polymorphic HERV-K in global populations and tools needed to determine the profile of all known polymorphic HERV-K in the genome of any patient population.
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Affiliation(s)
- Weiling Li
- The School of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, PA, United States of America
| | - Lin Lin
- Department of Statistics, The Pennsylvania State University, University Park, PA, United States of America
| | - Raunaq Malhotra
- The School of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, PA, United States of America
| | - Lei Yang
- Department of Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Raj Acharya
- The School of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, PA, United States of America
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, United States of America
| | - Mary Poss
- Department of Biology, The Pennsylvania State University, University Park, PA, United States of America
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States of America
- * E-mail:
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94
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Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, Kidd JM. Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology 2019; 16:6. [PMID: 30845962 PMCID: PMC6407205 DOI: 10.1186/s12977-019-0468-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 01/20/2023] Open
Abstract
Background Vertebrate genomes contain a record of retroviruses that invaded the germlines of ancestral hosts and are passed to offspring as endogenous retroviruses (ERVs). ERVs can impact host function since they contain the necessary sequences for expression within the host. Dogs are an important system for the study of disease and evolution, yet no substantiated reports of infectious retroviruses in dogs exist. Here, we utilized Illumina whole genome sequence data to assess the origin and evolution of a recently active gammaretroviral lineage in domestic and wild canids. Results We identified numerous recently integrated loci of a canid-specific ERV-Fc sublineage within Canis, including 58 insertions that were absent from the reference assembly. Insertions were found throughout the dog genome including within and near gene models. By comparison of orthologous occupied sites, we characterized element prevalence across 332 genomes including all nine extant canid species, revealing evolutionary patterns of ERV-Fc segregation among species as well as subpopulations. Conclusions Sequence analysis revealed common disruptive mutations, suggesting a predominant form of ERV-Fc spread by trans complementation of defective proviruses. ERV-Fc activity included multiple circulating variants that infected canid ancestors from the last 20 million to within 1.6 million years, with recent bursts of germline invasion in the sublineage leading to wolves and dogs. Electronic supplementary material The online version of this article (10.1186/s12977-019-0468-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia V Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Abigail S Jarosz
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Robert J Gifford
- Centre for Virus Research, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Malika L Day
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Ave., Ann Arbor, MI, 48109, USA
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95
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Mage RG, Esteves PJ, Rader C. Rabbit models of human diseases for diagnostics and therapeutics development. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:99-104. [PMID: 30339876 PMCID: PMC6364550 DOI: 10.1016/j.dci.2018.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/07/2018] [Accepted: 10/11/2018] [Indexed: 05/03/2023]
Abstract
This review presents some examples of studies using the European rabbit (Oryctolagus cuniculus) that have led to, and continue to, contribute to advancement of understanding of human diseases as well as therapeutics development. In addition, we tabulate FDA-approved rabbit polyclonal and rabbit monoclonal antibodies (mAbs) that are used for diagnostic applications, as well as an overview of some "humanized" or otherwise altered rabbit mAbs that are in initial phase I, II, or advanced to phase III clinical trials. Information about endogenous retriviruses learned from studies of rabbits and other members of the order Lagomorpha are summarized as this knowledge now applies to new therapeutics being developed for several human diseases including Multiple Sclerosis, Type 1 Diabetes and Cancer.
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Affiliation(s)
- Rose G Mage
- Laboratory of Immune System Biology, NIAID, NIH, Bldg 10 11N311, 10 Center Drive, Bethesda, MD, 20892-1892, USA.
| | - Pedro J Esteves
- CIBIO, InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal; Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
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96
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Wei X, Chen Y, Duan G, Holmes EC, Cui J. A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses. Virus Evol 2019; 5:vez001. [PMID: 30838130 PMCID: PMC6393741 DOI: 10.1093/ve/vez001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Endogenous retroviruses (ERVs) represent host genomic 'fossils' of ancient viruses. Foamy viruses, including those that form endogenous copies, provide strong evidence for virus-host co-divergence across the vertebrate phylogeny. Endogenous foamy viruses (EFVs) have previously been discovered in mammals, amphibians, and fish. Here we report a novel endogenous foamy virus, termed ERV-Spuma-Spu, in genome of the tuatara (Sphenodon punctatus), an endangered reptile species endemic to New Zealand. Phylogenetic analyses revealed that foamy viruses have likely co-diverged with their hosts over many millions of years. The discovery of ERV-Spuma-Spu fills a major gap in the fossil record of foamy viruses and provides important insights into the early evolution of retroviruses.
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Affiliation(s)
- Xiaoman Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yicong Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guangqian Duan
- University of Chinese Academy of Sciences, Beijing, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Jie Cui
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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97
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Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups. Genes (Basel) 2019; 10:genes10020162. [PMID: 30791656 PMCID: PMC6410134 DOI: 10.3390/genes10020162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 01/04/2023] Open
Abstract
Retroviruses have invaded vertebrate hosts for millions of years and left an extensive endogenous retrovirus (ERV) record in the host genomes, which provides a remarkable source for an evolutionary perspective on retrovirus-host associations. Here we identified ERV variation across whole-genomes from two chicken lines, derived from a common founder population subjected to 50 years of bi-directional selection on body weight, and a distantly related domestic chicken line as a comparison outgroup. Candidate ERV loci, where at least one of the chicken lines indicated distinct differences, were analyzed for adjacent host genomic landscapes, selective sweeps, and compared by sequence associations to reference assembly ERVs in phylogenetic analyses. Current data does not support selection acting on specific ERV loci in the domestic chicken lines, as determined by presence inside selective sweeps or composition of adjacent host genes. The varying ERV records among the domestic chicken lines associated broadly across the assembly ERV phylogeny, indicating that the observed insertion differences result from pre-existing and segregating ERV loci in the host populations. Thus, data suggest that the observed differences between the host lineages are best explained by substantial standing ERV variation within host populations, and indicates that even truncated, presumably old, ERVs have not yet become fixed in the host population.
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98
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Gorillas have been infected with the HERV-K (HML-2) endogenous retrovirus much more recently than humans and chimpanzees. Proc Natl Acad Sci U S A 2019; 116:1337-1346. [PMID: 30610173 DOI: 10.1073/pnas.1814203116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human endogenous retrovirus-K (HERV-K) human mouse mammary tumor virus-like 2 (HML-2) is the most recently active endogenous retrovirus group in humans, and the only group with human-specific proviruses. HML-2 expression is associated with cancer and other diseases, but extensive searches have failed to reveal any replication-competent proviruses in humans. However, HML-2 proviruses are found throughout the catarrhine primates, and it is possible that they continue to infect some species today. To investigate this possibility, we searched for gorilla-specific HML-2 elements using both in silico data mining and targeted deep-sequencing approaches. We identified 150 gorilla-specific integrations, including 31 2-LTR proviruses. Many of these proviruses have identical LTRs, and are insertionally polymorphic, consistent with very recent integration. One identified provirus has full-length ORFs for all genes, and thus could potentially be replication-competent. We suggest that gorillas may still harbor infectious HML-2 virus and could serve as a model for understanding retrovirus evolution and pathogenesis in humans.
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99
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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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100
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Bergallo M, Daprà V, Ponti R, Quaglino P, Novelli M, Fava P, Montanari P, Calvi C, Galliano I, Fierro M. HERV-E expression in peripheral mononuclear cells of patients with psoriasis. Ital J Dermatol Venerol 2018; 156:42-45. [PMID: 30251805 DOI: 10.23736/s2784-8671.18.06133-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Psoriasis is a common inflammatory skin disease characterized by uncontrolled proliferation of keratinocytes and recruitment of T lymphocytes into the skin. Possible triggers for psoriasis have been attributed to drugs or pathogens such as bacteria and possibly virus. Human endogenous retroviruses (HERVs) might play a role in triggering these antiviral immune responses, since the role of HERVs in the pathogenesis of autoimmune diseases has generated considerable interest. Some studies have also reported an association of HERV-E and psoriasis. None of them investigate the HERV-E expression in peripheral blood of psoriasis. All these considerations have prompted us to perform a survey for HERV-E expression in PBMC from psoriatic patients. METHODS Peripheral blood mononuclear cells from 69 psoriatic patients were analyzed. Total RNA was extracted and amplified with reverse transcription polymerase chain reaction. Results were compared with those obtained in a cohort of 20 healthy donors. RESULTS HERV E was expressed in all samples analyzed but the level of expression was much lower in the psoriasis that in HC P<0.0001. CONCLUSIONS The reasons for the unexpected, low levels of HERV expression in psoriatic patients are unclear and might be in part a consequence of antiviral defense mechanisms.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy -
| | - Valentina Daprà
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy
| | - Renata Ponti
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Pietro Quaglino
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Mauro Novelli
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paolo Fava
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy
| | - Cristina Calvi
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy
| | - Mariateresa Fierro
- Section of Dermatology, Department of Medical Sciences, University of Turin, Turin, Italy
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