1
|
Guo X, Zhao Y, You F. Identification and characterization of endogenous retroviruses upon SARS-CoV-2 infection. Front Immunol 2024; 15:1294020. [PMID: 38646531 PMCID: PMC11026653 DOI: 10.3389/fimmu.2024.1294020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/14/2024] [Indexed: 04/23/2024] Open
Abstract
Endogenous retroviruses (ERVs) derived from the long terminal repeat (LTR) family of transposons constitute a significant portion of the mammalian genome, with origins tracing back to ancient viral infections. Despite comprising approximately 8% of the human genome, the specific role of ERVs in the pathogenesis of COVID-19 remains unclear. In this study, we conducted a genome-wide identification of ERVs in human peripheral blood mononuclear cells (hPBMCs) and primary lung epithelial cells from monkeys and mice, both infected and uninfected with SARS-CoV-2. We identified 405, 283, and 206 significantly up-regulated transposable elements (TEs) in hPBMCs, monkeys, and mice, respectively. This included 254, 119, 68, and 28 ERVs found in hPBMCs from severe and mild COVID-19 patients, monkeys, and transgenic mice expressing the human ACE2 receptor (hACE2) and infected with SARS-CoV-2. Furthermore, analysis using the Genomic Regions Enrichment of Annotations Tool (GREAT) revealed certain parental genomic sequences of these up-regulated ERVs in COVID-19 patients may be involved in various biological processes, including histone modification and viral replication. Of particular interest, we identified 210 ERVs specifically up-regulated in the severe COVID-19 group. The genes associated with these differentially expressed ERVs were enriched in processes such as immune response activation and histone modification. HERV1_I-int: ERV1:LTR and LTR7Y: ERV1:LTR were highlighted as potential biomarkers for evaluating the severity of COVID-19. Additionally, validation of our findings using RT-qPCR in Bone Marrow-Derived Macrophages (BMDMs) from mice infected by HSV-1 and VSV provided further support to our results. This study offers insights into the expression patterns and potential roles of ERVs following viral infection, providing a valuable resource for future studies on ERVs and their interaction with SARS-CoV-2.
Collapse
|
2
|
Lee M, Ahmad SF, Xu J. Regulation and function of transposable elements in cancer genomes. Cell Mol Life Sci 2024; 81:157. [PMID: 38556602 PMCID: PMC10982106 DOI: 10.1007/s00018-024-05195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 04/02/2024]
Abstract
Over half of human genomic DNA is composed of repetitive sequences generated throughout evolution by prolific mobile genetic parasites called transposable elements (TEs). Long disregarded as "junk" or "selfish" DNA, TEs are increasingly recognized as formative elements in genome evolution, wired intimately into the structure and function of the human genome. Advances in sequencing technologies and computational methods have ushered in an era of unprecedented insight into how TE activity impacts human biology in health and disease. Here we discuss the current views on how TEs have shaped the regulatory landscape of the human genome, how TE activity is implicated in human cancers, and how recent findings motivate novel strategies to leverage TE activity for improved cancer therapy. Given the crucial role of methodological advances in TE biology, we pair our conceptual discussions with an in-depth review of the inherent technical challenges in studying repeats, specifically related to structural variation, expression analyses, and chromatin regulation. Lastly, we provide a catalog of existing and emerging assays and bioinformatic software that altogether are enabling the most sophisticated and comprehensive investigations yet into the regulation and function of interspersed repeats in cancer genomes.
Collapse
Affiliation(s)
- Michael Lee
- Department of Pediatrics, Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA.
| | - Syed Farhan Ahmad
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA
| | - Jian Xu
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA.
| |
Collapse
|
3
|
Moawad AS, Wang F, Zheng Y, Chen C, Saleh AA, Hou J, Song C. Evolution of Endogenous Retroviruses in the Subfamily of Caprinae. Viruses 2024; 16:398. [PMID: 38543763 PMCID: PMC10975924 DOI: 10.3390/v16030398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 05/23/2024] Open
Abstract
The interest in endogenous retroviruses (ERVs) has been fueled by their impact on the evolution of the host genome. In this study, we used multiple pipelines to conduct a de novo exploration and annotation of ERVs in 13 species of the Caprinae subfamily. Through analyses of sequence identity, structural organization, and phylogeny, we defined 28 ERV groups within Caprinae, including 19 gamma retrovirus groups and 9 beta retrovirus groups. Notably, we identified four recent and potentially active groups prevalent in the Caprinae genomes. Additionally, our investigation revealed that most long noncoding genes (lncRNA) and protein-coding genes (PC) contain ERV-derived sequences. Specifically, we observed that ERV-derived sequences were present in approximately 75% of protein-coding genes and 81% of lncRNA genes in sheep. Similarly, in goats, ERV-derived sequences were found in approximately 74% of protein-coding genes and 75% of lncRNA genes. Our findings lead to the conclusion that the majority of ERVs in the Caprinae genomes can be categorized as fossils, representing remnants of past retroviral infections that have become permanently integrated into the genomes. Nevertheless, the identification of the Cap_ERV_20, Cap_ERV_21, Cap_ERV_24, and Cap_ERV_25 groups indicates the presence of relatively recent and potentially active ERVs in these genomes. These particular groups may contribute to the ongoing evolution of the Caprinae genome. The identification of putatively active ERVs in the Caprinae genomes raises the possibility of harnessing them for future genetic marker development.
Collapse
Affiliation(s)
- Ali Shoaib Moawad
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Fengxu Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (F.W.); (J.H.)
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
| | - Ahmed A. Saleh
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria City 11865, Egypt
| | - Jian Hou
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (F.W.); (J.H.)
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
| |
Collapse
|
4
|
Fandiño S, Gomez-Lucia E, Benítez L, Doménech A. Comparison of Endogenous Alpharetroviruses (ALV-like) across Galliform Species: New Distant Proviruses. Microorganisms 2023; 12:86. [PMID: 38257913 PMCID: PMC10820513 DOI: 10.3390/microorganisms12010086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
The Genus Alpharetrovirus contains viruses pathogenic mainly for chickens, forming the Avian Sarcoma and Leukosis Virus group (ASLV). Cells of most Galliform species, besides chickens, contain genetic elements (endogenous retroviruses, ERVs) that could recombine with other alpharetroviruses or express proteins, complementing defective ASLV, which may successfully replicate and cause disease. However, they are quite unknown, and only ALV-F, from ring-necked pheasants, has been partially published. Upon scrutiny of 53 genomes of different avian species, we found Alpharetrovirus-like sequences only in 12 different Galliformes, including six full-length (7.4-7.6 Kbp) and 27 partial sequences. Phylogenetic studies of the regions studied (LTR, gag, pol, and env) consistently resulted in five almost identical clades containing the same ERVs: Clade I (presently known ASLVs); Clade II (Callipepla spp. ERVs); Clade IIIa (Phasianus colchicus ERVs); Clade IIIb (Alectoris spp. ERVs); and Clade IV (Centrocercus spp. ERVs). The low pol identity scores suggested that each of these Clades may be considered a different species. ORF analysis revealed that putatively encoded proteins would be very similar in length and domains to those of other alpharetroviruses and thus potentially functional. This will undoubtedly contribute to better understanding the biology of defective viruses, especially in wild Galliformes, their evolution, and the danger they may represent for other wild species and the poultry industry.
Collapse
Affiliation(s)
- Sergio Fandiño
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain; (S.F.); (A.D.)
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), C. de José Antonio Novais 12, 28040 Madrid, Spain;
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
| | - Esperanza Gomez-Lucia
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain; (S.F.); (A.D.)
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
| | - Laura Benítez
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), C. de José Antonio Novais 12, 28040 Madrid, Spain;
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
| | - Ana Doménech
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro s/n, 28040 Madrid, Spain; (S.F.); (A.D.)
- Research Group, “Animal Viruses” of Complutense University of Madrid, 28040 Madrid, Spain
| |
Collapse
|
5
|
Enriquez-Gasca R, Gould PA, Tunbak H, Conde L, Herrero J, Chittka A, Beck CR, Gifford R, Rowe HM. Co-option of endogenous retroviruses through genetic escape from TRIM28 repression. Cell Rep 2023; 42:112625. [PMID: 37294634 DOI: 10.1016/j.celrep.2023.112625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 04/04/2023] [Accepted: 05/23/2023] [Indexed: 06/11/2023] Open
Abstract
Endogenous retroviruses (ERVs) have rewired host gene networks. To explore the origins of co-option, we employed an active murine ERV, IAPEz, and an embryonic stem cell (ESC) to neural progenitor cell (NPC) differentiation model. Transcriptional silencing via TRIM28 maps to a 190 bp sequence encoding the intracisternal A-type particle (IAP) signal peptide, which confers retrotransposition activity. A subset of "escapee" IAPs (∼15%) exhibits significant genetic divergence from this sequence. Canonical repressed IAPs succumb to a previously undocumented demarcation by H3K9me3 and H3K27me3 in NPCs. Escapee IAPs, in contrast, evade repression in both cell types, resulting in their transcriptional derepression, particularly in NPCs. We validate the enhancer function of a 47 bp sequence within the U3 region of the long terminal repeat (LTR) and show that escapee IAPs convey an activating effect on nearby neural genes. In sum, co-opted ERVs stem from genetic escapees that have lost vital sequences required for both TRIM28 restriction and autonomous retrotransposition.
Collapse
Affiliation(s)
- Rocio Enriquez-Gasca
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK.
| | - Poppy A Gould
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Hale Tunbak
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6DD, UK
| | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6DD, UK
| | - Alexandra Chittka
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Christine R Beck
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, The Jackson Laboratory for Genomic Medicine, Connecticut, JAX CT, Farmington, CT 06032, USA
| | - Robert Gifford
- MRC-University of Glasgow Centre for Virus Research, Glasgow G611QH, UK
| | - Helen M Rowe
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK.
| |
Collapse
|
6
|
Zhou X, Xu Y, Ren S, Yang N, Sun Y, Yang Q, Zhang Y, Cai H, Deng W, Chen J, Chen D, Cao B, Qi H, Wang H, Lu J. Trophoblast PR-SET7 dysfunction induces viral mimicry response and necroptosis associated with recurrent miscarriage. Proc Natl Acad Sci U S A 2023; 120:e2216206120. [PMID: 37307441 DOI: 10.1073/pnas.2216206120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/16/2023] [Indexed: 06/14/2023] Open
Abstract
Recurrent miscarriage (RM) is a distressing pregnancy complication. While the etiology of RM remains unclear, growing evidence has indicated the relevance of trophoblast impairment to the pathogenesis of RM. PR-SET7 is the sole enzyme catalyzing monomethylation of H4K20 (H4K20me1) and has been implicated in many pathophysiological processes. However, how PR-SET7 functions in trophoblasts and its relevance to RM remain unknown. Here, we found that trophoblast-specific loss of Pr-set7 in mice led to defective trophoblasts, resulting in early embryonic loss. Mechanistic analysis revealed that PR-SET7 deficiency in trophoblasts derepressed endogenous retroviruses (ERVs), leading to double-stranded RNA stress and subsequent viral mimicry, which drove overwhelming interferon response and necroptosis. Further examination discovered that H4K20me1 and H4K20me3 mediated the inhibition of cell-intrinsic expression of ERVs. Importantly, dysregulation of PR-SET7 expression and the corresponding aberrant epigenetic modifications were observed in the placentas of RM. Collectively, our results demonstrate that PR-SET7 acts as an epigenetic transcriptional modulator essential for repressing ERVs in trophoblasts, ensuring normal pregnancy and fetal survival, which sheds new light on potential epigenetic causes contributing to RM.
Collapse
Affiliation(s)
- Xiaobo Zhou
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yingchun Xu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Shengnan Ren
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Ningjie Yang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Yang Sun
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Qibing Yang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Yue Zhang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Han Cai
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Wenbo Deng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Jingsi Chen
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Dunjin Chen
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Bin Cao
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Hongbo Qi
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Jinhua Lu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| |
Collapse
|
7
|
Liu J, Min S, Kim D, Park J, Park E, Koh Y, Shin DY, Kim TK, Byun JM, Yoon SS, Hong J. Epigenetic priming improves salvage chemotherapy in diffuse large B-cell lymphoma via endogenous retrovirus-induced cGAS-STING activation. Clin Epigenetics 2023; 15:75. [PMID: 37138342 PMCID: PMC10155448 DOI: 10.1186/s13148-023-01493-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Although most patients with diffuse large B-cell lymphoma (DLBCL) achieve complete remission after first-line rituximab-containing immunochemotherapy, up to 40% of patients relapse and require salvage therapy. Among those patients, a substantial proportion remain refractory to salvage therapy due to insufficient efficacy or intolerance of toxicities. A hypomethylating agent, 5-azacytidine, showed a chemosensitizing effect when primed before chemotherapy in lymphoma cell lines and newly diagnosed DLBCL patients. However, its potential to improve outcomes of salvage chemotherapy in DLBCL has not been investigated. RESULTS In this study, we demonstrated the mechanism of 5-azacytidine priming as a chemosensitizer in a platinum-based salvage regimen. This chemosensitizing effect was associated with endogenous retrovirus (ERV)-induced viral mimicry responses via the cGAS-STING axis. We found deficiency of cGAS impaired the chemosensitizing effect of 5-azacytidine. Furthermore, combining vitamin C and 5-azacytidine to synergistically activate STING could be a potential remedy for insufficient priming induced by 5-azacytidine alone. CONCLUSIONS Taken together, the chemosensitizing effect of 5-azacytidine could be exploited to overcome the limitations of the current platinum-containing salvage chemotherapy in DLBCL and the status of cGAS-STING has the potential to predict the efficacy of 5-azacytidine priming.
Collapse
Affiliation(s)
- Jun Liu
- College of Medicine, Zhejiang University, Hangzhou, China
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Suji Min
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dongchan Kim
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jihyun Park
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunchae Park
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youngil Koh
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Yeop Shin
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Tae Kon Kim
- Division of Hematology/Oncology, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ja Min Byun
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Junshik Hong
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
8
|
Gruchot J, Herrero F, Weber-Stadlbauer U, Meyer U, Küry P. Interplay between activation of endogenous retroviruses and inflammation as common pathogenic mechanism in neurological and psychiatric disorders. Brain Behav Immun 2023; 107:242-52. [PMID: 36270439 DOI: 10.1016/j.bbi.2022.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/21/2022] [Accepted: 10/13/2022] [Indexed: 12/05/2022] Open
Abstract
Human endogenous retroviruses (ERVs) are ancestorial retroviral elements that were integrated into our genome through germline infections and insertions during evolution. They have repeatedly been implicated in the aetiology and pathophysiology of numerous human disorders, particularly in those that affect the central nervous system. In addition to the known association of ERVs with multiple sclerosis and amyotrophic lateral sclerosis, a growing number of studies links the induction and expression of these retroviral elements with the onset and severity of neurodevelopmental and psychiatric disorders. Although these disorders differ in terms of overall disease pathology and causalities, a certain degree of (subclinical) chronic inflammation can be identified in all of them. Based on these commonalities, we discuss the bidirectional relationship between ERV expression and inflammation and highlight that numerous entry points to this reciprocal sequence of events exist, including initial infections with ERV-activating pathogens, exposure to non-infectious inflammatory stimuli, and conditions in which epigenetic silencing of ERV elements is disrupted.
Collapse
|
9
|
Calero-Layana M, López-Cruz C, Ocaña A, Tejera E, Armijos-Jaramillo V. Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes. PeerJ 2022; 10:e14431. [PMID: 36575684 PMCID: PMC9790151 DOI: 10.7717/peerj.14431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022] Open
Abstract
Background Endogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes: gag, pol, and env, each of which encodes viral proteins that can be conserved or not. ERVs have been observed in a wide range of vertebrate genomes and their functions are associated with viral silencing and gene regulation. Results In this work, we studied the evolutionary history of endogenous retroviruses associated with five human genes (INPP5B, DET1, PSMA1, USH2A, and MACROD2), which are located within intron sections. To verify the retroviral origin of the candidates, several approaches were used to detect and locate ERV elements. Both orthologous and paralogous genes were identified by Ensembl and then analyzed for ERV presence using RetroTector. A phylogenetic tree was reconstructed to identify the minimum time point of ERV acquisition. From that search, we detected ERVs throughout the primate lineage and in some other groups. Also, we identified the minimum origin of the ERVs from the parvorder Catarrhini to the Homininae subfamily. Conclusions With the data collected, and by observing the transcription factors annotated inside ERVs, we propose that these elements play a relevant role in gene expression regulation and they probably possess important features for tumorigenesis control.
Collapse
Affiliation(s)
- Melissa Calero-Layana
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador
| | - Carmen López-Cruz
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador
| | - Agustín Ocaña
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador
| | - Eduardo Tejera
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador,Grupo de Bio-Quimioinformática, Universidad de las Americas, Quito, Ecuador
| | - Vinicio Armijos-Jaramillo
- Ingeniería en Biotecnología. Facultad de Ingeniería y Ciencias Aplicadas, Universidad de las Americas, Quito, Ecuador,Grupo de Bio-Quimioinformática, Universidad de las Americas, Quito, Ecuador
| |
Collapse
|
10
|
Ai Z, Xiang X, Xiang Y, Szczerbinska I, Qian Y, Xu X, Ma C, Su Y, Gao B, Shen H, Bin Ramli MN, Chen D, Liu Y, Hao JJ, Ng HH, Zhang D, Chan YS, Liu W, Liang H. Krüppel-like factor 5 rewires NANOG regulatory network to activate human naive pluripotency specific LTR7Ys and promote naive pluripotency. Cell Rep 2022; 40:111240. [PMID: 36001968 DOI: 10.1016/j.celrep.2022.111240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/06/2022] [Accepted: 07/27/2022] [Indexed: 12/01/2022] Open
Abstract
Endogenous retroviruses (ERVs) have been reported to participate in pre-implantation development of mammalian embryos. In early human embryogenesis, different ERV sub-families are activated in a highly stage-specific manner. How the specificity of ERV activation is achieved remains largely unknown. Here, we demonstrate the mechanism of how LTR7Ys, the human morula-blastocyst-specific HERVH long terminal repeats, are activated by the naive pluripotency transcription network. We find that KLF5 interacts with and rewires NANOG to bind and regulate LTR7Ys; in contrast, the primed-specific LTR7s are preferentially bound by NANOG in the absence of KLF5. The specific activation of LTR7Ys by KLF5 and NANOG in pluripotent stem cells contributes to human-specific naive pluripotency regulation. KLF5-LTR7Y axis also promotes the expression of trophectoderm genes and contributes to the expanded cell potential toward extra-embryonic lineage. Our study suggests that HERVs are activated by cell-state-specific transcription machinery and promote stage-specific transcription network and cell potency.
Collapse
Affiliation(s)
- Zhipeng Ai
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Xinyu Xiang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Yangquan Xiang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Iwona Szczerbinska
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Yuli Qian
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Xiao Xu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Chenyang Ma
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Yaqi Su
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Bing Gao
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Hao Shen
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Muhammad Nadzim Bin Ramli
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Di Chen
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Yue Liu
- Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Jia-Jie Hao
- Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Huck Hui Ng
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117597, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798, Singapore
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.
| | - Yun-Shen Chan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China.
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China; Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310029, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Hongqing Liang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China.
| |
Collapse
|
11
|
Prieto-Oliveir P. H ERVs role in the pathogenesis, diagnosis or prognosis of aging diseases: A systematic review. Curr Mol Med 2022:CMM-EPUB-123964. [PMID: 35619278 DOI: 10.2174/1566524022666220525144135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 11/22/2022]
Abstract
HERVs are humans endogenous retroviruses, which represent about 8% of human genome, and have various physiological functions, specially in pregnancy, embryo development and placenta formation. However, their involvement in diseases is not well defined. Some studies observed changes in HERVs expression according to age. Therefore, the aim of this systematic review was to analyze their role in pathogenesis and usage of diagnosis or prognosis biomarkers in aging disorders. I performed a search on the Pubmed interface for papers published from January 1953 to june 1st 2021. There was inclusion of 45 articles, which matched the eligibility criteria and evaluated the following diseases: breast cancer, prostate cancer, amyotrophic lateral sclerosis (ALS), osteoarthritis, Alzheimer disease, immunosenescence, cognitive impairment, cataract, glaucoma and hypertension. In conclusion, the results suggested that HERVs play a role in the pathogenesis and can be used as biomarkers for diagnosis or prognosis of aging disorders.
Collapse
Affiliation(s)
- Paula Prieto-Oliveir
- Laboratory of Retrovirology, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, SP, Brazil
| |
Collapse
|
12
|
Yang B, Fang L, Gao Q, Xu C, Xu J, Chen ZX, Wang Y, Yang P. Species-specific KRAB-ZFPs function as repressors of retroviruses by targeting PBS regions. Proc Natl Acad Sci U S A 2022; 119:e2119415119. [PMID: 35259018 DOI: 10.1073/pnas.2119415119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Hosts often target the relatively conserved regions in rapidly mutating retroviruses to inhibit their replication. One of these regions is called a primer binding site (PBS), which has to be complementary to the host tRNA to initiate reverse transcription. By analyzing endogenous retroviral elements, we found that host cells use this sequence as a target in efforts to block the expression of viral elements. A specific type of zinc finger protein targets the PBS in a host genome, which not only inhibits the transcription of endogenous viruses but also inhibits the replication of exogenous retroviruses with the same PBS. Thus, our study sheds light on a strategy for searching for host restriction factors targeting retroviruses. Eukaryotic genomes harbor sequences derived from the chromosomal integration of ancient viruses, such as endogenous retroviruses (ERVs), which comprise 8% of the human genome. Like exogenous retroviruses, ERVs retain many common functional elements, including the corresponding DNA sequences of transfer RNA (tRNA) primer binding sites (PBSs), which are utilized for reverse transcription initiation by exogenous retroviruses. Here, through a medium-scale analysis of PBS loci positioned within ERVs, coupled with chromatin immunoprecipitation sequencing (ChIP-seq) of Kruppel-associated box zinc finger proteins (KRAB-ZFPs), we identified multiple ZFPs that specifically bind to different PBS loci. Among these, we focused on PBS-Lys, which is utilized by HIV-1, and identified its specific binding proteins to be mouse ZFP961 and human ZNF417/ZNF587. We found that these proteins not only repress ERV transcription but also inhibit retrovirus integration and transcription. Disruption of these ZFPs rendered cells more susceptible to HIV-1 infection. Thus, our research provides a methodology for identifying potential host factors that target retroviruses by ERVs.
Collapse
|
13
|
Mao J, Zhang Q, Wang Y, Zhuang Y, Xu L, Ma X, Guan D, Zhou J, Liu J, Wu X, Liang Q, Wang M, Cong Y. TERT activates endogenous retroviruses to promote an immunosuppressive tumour microenvironment. EMBO Rep 2022; 23:e52984. [PMID: 35107856 PMCID: PMC8982579 DOI: 10.15252/embr.202152984] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/29/2021] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Telomerase plays a pivotal role in tumorigenesis by both telomere-dependent and telomere-independent activities, although the underlying mechanisms are not completely understood. Using single-sample gene set enrichment analysis (ssGSEA) across 9,264 tumour samples, we observe that expression of telomerase reverse transcriptase (TERT) is closely associated with immunosuppressive signatures. We demonstrate that TERT can activate a subclass of endogenous retroviruses (ERVs) independent of its telomerase activity to form double-stranded RNAs (dsRNAs), which are sensed by the RIG-1/MDA5-MAVS signalling pathway and trigger interferon signalling in cancer cells. Furthermore, we show that TERT-induced ERV/interferon signalling stimulates the expression of chemokines, including CXCL10, which induces the infiltration of suppressive T-cell populations with increased percentage of CD4+ and FOXP3+ cells. These data reveal an unanticipated role for telomerase as a transcriptional activator of ERVs and provide strong evidence that TERT-mediated ERV/interferon signalling contributes to immune suppression in tumours.
Collapse
Affiliation(s)
- Jian Mao
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Qian Zhang
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Yaxiang Wang
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Yang Zhuang
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Lu Xu
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Xiaohe Ma
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Di Guan
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Junzhi Zhou
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Jiang Liu
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Xiaoying Wu
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Qian Liang
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Miao Wang
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| | - Yu‐Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang ProvinceHangzhou Normal University School of Basic Medical SciencesHangzhouChina
| |
Collapse
|
14
|
Grundy EE, Diab N, Chiappinelli KB. Transposable element regulation and expression in cancer. FEBS J 2021; 289:1160-1179. [PMID: 33471418 DOI: 10.1111/febs.15722] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/08/2021] [Accepted: 01/14/2021] [Indexed: 12/11/2022]
Abstract
Approximately 45% of the human genome is composed of transposable elements (TEs). Expression of these elements is tightly regulated during normal development. TEs may be expressed at high levels in embryonic stem cells but are epigenetically silenced in terminally differentiated cells. As part of the global 'epigenetic dysregulation' that cells undergo during transformation from normal to cancer, TEs can lose epigenetic silencing and become transcribed, and, in some cases, active. Here, we summarize recent advances detailing the consequences of TE activation in cancer and describe how these understudied residents of our genome can both aid tumorigenesis and potentially be harnessed for anticancer therapies.
Collapse
Affiliation(s)
- Erin E Grundy
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.,The GW Cancer Center, The George Washington University, Washington, DC, USA.,The Institute for Biomedical Sciences at The George Washington University, Washington, DC, USA
| | - Noor Diab
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.,The GW Cancer Center, The George Washington University, Washington, DC, USA
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.,The GW Cancer Center, The George Washington University, Washington, DC, USA
| |
Collapse
|
15
|
Elmer JL, Ferguson-Smith AC. Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans-Acting Modifiers. Viruses 2020; 12:E810. [PMID: 32727076 DOI: 10.3390/v12080810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Approximately 10 percent of the mouse genome consists of endogenous retroviruses (ERVs), relics of ancient retroviral infections that are classified based on their relatedness to exogenous retroviral genera. Because of the ability of ERVs to retrotranspose, as well as their cis-acting regulatory potential due to functional elements located within the elements, mammalian ERVs are generally subject to epigenetic silencing by DNA methylation and repressive histone modifications. The mobilisation and expansion of ERV elements is strain-specific, leading to ERVs being highly polymorphic between inbred mouse strains, hinting at the possibility of the strain-specific regulation of ERVs. In this review, we describe the existing evidence of mouse strain-specific epigenetic control of ERVs and discuss the implications of differential ERV regulation on epigenetic inheritance models. We consider Krüppel-associated box domain (KRAB) zinc finger proteins as likely candidates for strain-specific ERV modifiers, drawing on insights gained from the study of the strain-specific behaviour of transgenes. We conclude by considering the coevolution of KRAB zinc finger proteins and actively transposing ERV elements, and highlight the importance of cross-strain studies in elucidating the mechanisms and consequences of strain-specific ERV regulation.
Collapse
|
16
|
Skirmuntt EC, Escalera-Zamudio M, Teeling EC, Smith A, Katzourakis A. The Potential Role of Endogenous Viral Elements in the Evolution of Bats as Reservoirs for Zoonotic Viruses. Annu Rev Virol 2020; 7:103-119. [PMID: 32432980 DOI: 10.1146/annurev-virology-092818-015613] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Despite a small genome size, bats have comparable diversity of retroviral and non-retroviral endogenous sequences to other mammals. These include Class I and Class II retroviral sequences, foamy viruses, and deltaretroviruses, as well as filovirus, bornavirus, and parvovirus endogenous viral elements. Some of these endogenous viruses are sufficiently preserved in bat genomes to be expressed, with potential effects for host biology. It is clear that the bat immune system differs when compared with other mammals, yet the role that virus-derived endogenous elements may have played in the evolution of bat immunity is poorly understood. In this review, we discuss some of the bat-specific immune mechanisms that may have resulted in a virus-tolerant phenotype and link these to the long-standing virus-host coevolution that may have allowed a large diversity of endogenous retroviruses and other endogenous viral elements to colonize bat genomes. We also consider the possible effects of endogenization in the evolution of the bat immune system.
Collapse
Affiliation(s)
- Emilia C Skirmuntt
- Department of Zoology, University of Oxford, OX1 3PS Oxford, United Kingdom;
| | | | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Adrian Smith
- Department of Zoology, University of Oxford, OX1 3PS Oxford, United Kingdom;
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, OX1 3PS Oxford, United Kingdom;
| |
Collapse
|
17
|
Sznarkowska A, Mikac S, Pilch M. MHC Class I Regulation: The Origin Perspective. Cancers (Basel) 2020; 12:cancers12051155. [PMID: 32375397 PMCID: PMC7281430 DOI: 10.3390/cancers12051155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/27/2020] [Accepted: 05/03/2020] [Indexed: 12/11/2022] Open
Abstract
Viral-derived elements and non-coding RNAs that build up “junk DNA” allow for flexible and context-dependent gene expression. They are extremely dense in the MHC region, accounting for flexible expression of the MHC I, II, and III genes and adjusting the level of immune response to the environmental stimuli. This review brings forward the viral-mediated aspects of the origin and evolution of adaptive immunity and aims to link this perspective with the MHC class I regulation. The complex regulatory network behind MHC expression is largely controlled by virus-derived elements, both as binding sites for immune transcription factors and as sources of regulatory non-coding RNAs. These regulatory RNAs are imbalanced in cancer and associate with different tumor types, making them promising targets for diagnostic and therapeutic interventions.
Collapse
|
18
|
Kong Q, Quan X, Du J, Tai Y, Liu W, Zhang J, Zhang X, Mu Y, Liu Z. Endo-siRNAs regulate early embryonic development by inhibiting transcription of long terminal repeat sequence in pig†. Biol Reprod 2019; 100:1431-1439. [PMID: 30883641 DOI: 10.1093/biolre/ioz042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/21/2019] [Accepted: 03/16/2019] [Indexed: 11/12/2022] Open
Abstract
Activity of some endogenous retroviruses (ERVs) has been proven to be important for development of early mammalian embryo. However, abnormal activation of ERVs can also cause genetic diseases due to their ability to retrotranspose, so the regulatory mechanism to limit transcription of ERVs needs to be clarified. Endogenous small interfering RNA (endo-siRNA) has been reported to protect cells against transposable elements (TEs). Here, we determined the role of ERVs long terminal repeat sequences (LTRs) derived endo-siRNAs (LTR-siRNAs) on inhibition of the activity of ERVs during early embryonic development in pig. Seven most highly expressed LTR-siRNAs were identified in porcine zygote by high-throughput small RNA sequencing. We verified that the biogenesis of the LTR-siRNAs was DICER-dependent and they were generated from double-stranded RNA (dsRNA) formed by sense and antisense transcripts of LTRs. And, the expression of sense and antisense of LTRs might be due to the loss of DNA methylation at some LTR loci. Furthermore, we showed that the LTR-siRNAs could regulate early embryonic development by repression of LTRs expression at a post-transcriptional level. So, we propose here, during early embryonic development when epigenetic reprogramming occurs, the endo-siRNA pathway acts as a sophisticated balance of regulatory mechanism for ERV activity.
Collapse
Affiliation(s)
- Qingran Kong
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Xue Quan
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Jiawei Du
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Yurong Tai
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Wanxin Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Jiaming Zhang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Xiaolei Zhang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Yanshuang Mu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, Harbin, China
| |
Collapse
|
19
|
de Sousa-Pereira P, Abrantes J, Baldauf HM, Esteves PJ. Evolutionary studies on the betaretrovirus RERV-H in the Leporidae family reveal an endogenization in the ancestor of Oryctolagus, Bunolagus and Pentalagus at 9 million years ago. Virus Res 2017; 262:24-29. [PMID: 29208424 DOI: 10.1016/j.virusres.2017.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 12/01/2017] [Accepted: 12/01/2017] [Indexed: 01/31/2023]
Abstract
RERV-H was first identified in human tissues and mistaken for a human exogenous retrovirus. However, the integration sites carried by this virus showed that it was instead a European rabbit (Oryctolagus cuniculus) endogenous retrovirus. The first clones retrieved from European rabbit samples represented defective proviruses, although estimation of proviral copy numbers found in the European rabbit genome ranged from hundreds to thousands. Screening for the presence of RERV-H showed the absence of the virus in two other lagomorphs, pika (Ochotona) and hares (Lepus), which diverged from rabbits about 35 and 12 million years ago, respectively. Using a PCR-based approach, samples of seven different Lagomorph genera were tested for the presence of RERV-H. It was possible to amplify a proviral fragment corresponding to RNaseH from Oryctolagus, Bunolagus and Pentalagus genomic samples. The amplification of proviral DNA in species other than Oryctolagus revealed that this virus was endogenized in their common ancestor, roughly 9 million years ago. Using the European rabbit genome sequence OryCun2.0, it was possible to find multiple copies spread throughout the genome and several complete proviral genomes were retrieved. Some copies contained full open reading frames for all viral components. The lack of a complete genome in the other Lagomorph species did not allow further analyses of the provirus, although more deleterious mutations were found in Bunolagus and Pentalagus than in Oryctolagus RNaseH-amplified sequences. To what extent RERV-H and other endogenous viruses might have had an impact on the rabbit genome and its immune system remains elusive.
Collapse
Affiliation(s)
- Patricia de Sousa-Pereira
- InBIO - Research Network in Biodiversity and Evolutionary Biology, CIBIO, Campus de Vairão, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; Max von Pettenkofer-Institute for Virology, Ludwig-Maximilians-University Munich, Munich, Germany.
| | - Joana Abrantes
- InBIO - Research Network in Biodiversity and Evolutionary Biology, CIBIO, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
| | - Hanna-Mari Baldauf
- Max von Pettenkofer-Institute for Virology, Ludwig-Maximilians-University Munich, Munich, Germany.
| | - Pedro José Esteves
- InBIO - Research Network in Biodiversity and Evolutionary Biology, CIBIO, Campus de Vairão, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal.
| |
Collapse
|
20
|
Sistiaga-Poveda M, Larruskain A, Mateo-Abad M, Jugo BM. Lack of association between polymorphic copies of endogenous Jaagsiekte sheep retrovirus (enJSRVs) and Ovine Pulmonary Adenocarcinoma. Vet Microbiol 2016; 185:49-55. [PMID: 26931391 DOI: 10.1016/j.vetmic.2016.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/18/2016] [Accepted: 01/25/2016] [Indexed: 10/22/2022]
Abstract
Ovine Pulmonary Adenocarcinoma (OPA) is a retrovirus-induced lung tumor of sheep, goat and mouflon, and its etiologic agent, Jaagsiekte sheep retrovirus (JSRV) is the only virus known to cause a naturally occurred lung adenocarcinoma. The oncogenic JSRV has several endogenous counterparts termed enJSRVs, some of which have been shown to interfere with JSRV replication at early and late stages of the retroviral cycle inhibiting JSRV exit from the cell, and thus, protecting sheep against the infection. In this work, Latxa sheep breed animals were classified depending on the presence/absence of OPA-characteristic clinical lesions in the lung. Using a PCR genotyping method and a logistic regression-based association study, five polymorphic enJSRV copies were analyzed in 49 OPA positive sheep and 124 control individuals. Our results showed that the frequency of the provirus enJSRV-16 is much higher in Latxa sheep breed than in other breeds, suggesting a recent proliferation of this provirus in the studied breed. However, no polymorphic enJSRV was found to be statistically associated with the susceptibility/resistance to OPA development.
Collapse
Affiliation(s)
- Maialen Sistiaga-Poveda
- Genetics, Physical Anthropology and Animal Physiology Department, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Amaia Larruskain
- Genetics, Physical Anthropology and Animal Physiology Department, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Maider Mateo-Abad
- Applied Mathematics, Statistics and Operative Research Department, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Begoña M Jugo
- Genetics, Physical Anthropology and Animal Physiology Department, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain.
| |
Collapse
|
21
|
Tan X, Xu X, Elkenani M, Smorag L, Zechner U, Nolte J, Engel W, Pantakani DK. Zfp819, a novel KRAB-zinc finger protein, interacts with KAP1 and functions in genomic integrity maintenance of mouse embryonic stem cells. Stem Cell Res 2013; 11:1045-59. [DOI: 10.1016/j.scr.2013.07.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 07/09/2013] [Accepted: 07/22/2013] [Indexed: 01/12/2023] Open
|