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Matsumoto S, Tanaka S. Wnt signaling activation confers a syncytiotrophoblast progenitor state on trophoblast stem cells of cynomolgus monkey†. Biol Reprod 2024; 111:1262-1281. [PMID: 39223948 PMCID: PMC11647102 DOI: 10.1093/biolre/ioae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/08/2024] [Accepted: 09/03/2024] [Indexed: 09/04/2024] Open
Abstract
Trophoblast stem cells, derived from the trophectoderm of the blastocyst, are used as an in vitro model to reveal the mechanisms underlying placentation in mammals. In humans, suitable culture conditions for trophoblast stem cell derivation have recently been established. The established human trophoblast stem cells differentiate efficiently toward two trophoblast subtypes: syncytiotrophoblasts and extravillous trophoblasts. However, the efficiency of differentiation is lower in macaque trophoblast stem cells than in human trophoblast stem cells. Here, we demonstrate that the activation of Wnt signaling downregulated the expression of inhibitory G protein and induced trophoblastic lineage switching to the syncytiotrophoblast progenitor state. The treatment of macaque trophoblast stem cells with a GSK-3 inhibitor, CHIR99021, upregulated syncytiotrophoblast progenitor markers and enhanced proliferation. Under the Wnt signaling-activated conditions, macaque trophoblast stem cells effectively differentiated to syncytiotrophoblasts upon dibutyryl cyclic AMP (dbcAMP) and forskolin treatment. RNA-seq analyses revealed the downregulation of inhibitory G protein, which may make macaque trophoblast stem cells responsive to forskolin. Interestingly, this lineage switching appeared to be reversible as the macaque trophoblast stem cells lost responsiveness to forskolin upon the removal of CHIR99021. The ability to regulate the direction of macaque trophoblast stem cell differentiation would be advantageous in elucidating the mechanisms underlying placentation in non-human primates.
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Affiliation(s)
- Shoma Matsumoto
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Satoshi Tanaka
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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2
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Baker JC. Placental Evolution: Innovating How to Feed Babies. Annu Rev Genet 2024; 58:391-408. [PMID: 39227137 DOI: 10.1146/annurev-genet-111523-102135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
The evolution of the placenta was transformative. It changed how offspring are fed during gestation from depositing all the resources into an egg to continually supplying resources throughout gestation. Placental evolution is infinitely complex, with many moving parts, but at the core it is driven by a conflict over resources between the mother and the baby, which sets up a Red Queen race, fueling rapid diversification of morphological, cellular, and genetic forms. Placentas from even closely related species are highly divergent in form and function, and many cellular processes are distinct. If we could extract the entirety of genomic information for placentas across all species, including the many hundreds that have evolved in fish and reptiles, we could find their shared commonality, and that would tell us which of the many pieces really matter. We do not have this information, but we do have clues. Convergent evolution mechanisms were repeatedly used in the placenta, including the intense selective pressure to co-opt an envelope protein to build a multinucleated syncytium, the use of the same hormones and structural proteins in placentas derived from separate embryonic origins that arose hundreds of millions of years apart, and the co-option of endogenous retroviruses to form capsids as a way of transport and as mutagens to form new enhancers. As a result, the placental genome is the Wild West of biology, set up to rapidly change, adapt, and innovate. This ability to adapt facilitated the evolution of big babies with big brains and will continue to support offspring and their mothers in our ever-changing global environment.
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Affiliation(s)
- Julie C Baker
- Department of Genetics, Stanford University, Stanford, California, USA;
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Caldwell A, Yang L, Scheef EA, Kaur A, Coyne CB. Comparative analysis of rhesus macaque and human placental organoids highlights evolutionary differences in placentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.11.617873. [PMID: 39416122 PMCID: PMC11482954 DOI: 10.1101/2024.10.11.617873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Throughout evolution, the placenta has diversified in both structure and cellular composition while maintaining its fundamental function. Trophoblasts are fetal-derived cells responsible for nourishing and protecting the developing fetus and are a universal component of all placentas. While primate placentas exhibit many shared morphological features, species-specific differences in gene expression remain largely unexplored, primarily due to the lack of suitable in vitro models. To address this gap, we developed organoids from rhesus macaque placentas, including trophoblast and maternal-derived decidua types, and compared them with organoids derived from human placentas. We performed comparative single-cell RNA sequencing to delineate shared and distinct transcriptional signatures between rhesus macaque and human trophoblasts. We further defined the differentiation trajectories leading to the multinucleated syncytiotrophoblast, highlighting both shared and unique transcriptional signatures between rhesus macaque and human placentas. This work establishes novel in vitro models of the non-human primate placenta and characterizes distinct trophoblast gene profiles in rhesus macaques and humans, providing insights into interspecies variations in placental biology.
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Wang YN, Chen XL, Yang J, Gong XX, Zhang HF, Zhang YM, Zeng DF, Chen PS, Chen HB. Reduced syncytin-1 regulates trophoblast invasion and apoptosis in preeclampsia. Placenta 2024; 155:32-41. [PMID: 39121585 DOI: 10.1016/j.placenta.2024.07.311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/08/2024] [Accepted: 07/28/2024] [Indexed: 08/12/2024]
Abstract
INTRODUCTION Preeclampsia is a pregnancy-specific disorder characterized by de novo development of hypertension and proteinuria over 20 weeks gestation that has been associated with the dysfunction of trophoblasts. Current evidence suggests that syncytin-1 plays an important role in the non-fusogenic biological activity of trophoblasts, except for specific fusogenic function. However, the underlying mechanism remains unclear. METHODS The expression and location of syncytin-1 in normal and the late-onset preeclampsia placentas were detected by quantitative real-time PCR, western blotting and immunofluorescence. Morphological and apoptosis analysis were processed in placentas. The ex vivo extravillous explant culture model was used to explore the effect of syncytin-1 on EVT outgrowths. Real-time quantitative PCR and immunoblotting were used to calculate syncytin-1 levels in the trophoblast cells before and after syncytin-1 knockdown or overexpression. CCK-8 assay was used to detect the cell viability. TUNEL staining and immunoblotting were processed in trophoblast cells. Transwell assays and wound healing assays were utilize to assess the invasion and migration of trophoblastic cells. Conditional knockout of syncytin-a mouse model was conducted to present the change of placentas in vivo. The ex vivo extravillous explant culture model was used to explore the effect of syncytin-1 on EVT outgrowths. Western blotting was used to identify the key proteins of PI3K/Akt pathways and invasion-related proteins in trophoblast cells. RESULTS AND DISCUSSION Here, reduced syncytin-1 was identified in the late-onset preeclampsia placentas. Reduced syncytin-1 may attenuates the EMT process by promoting apoptosis, inhibiting proliferation and invasion by suppressed PI3K/Akt pathway in trophoblast cells. Our findings provide novel insights into the non-fusogenic biological function of reduced syncytin-1 that may be involves in the pathogenesis of preeclampsia.
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Affiliation(s)
- Ya-Nan Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Shantou University Medical College, China; Department of Histology and Embryology, Shantou University Medical College, China
| | - Xue-Ling Chen
- Department of Histology and Embryology, Shantou University Medical College, China
| | - Ju Yang
- Department of Histology and Embryology, Shantou University Medical College, China
| | - Xing-Xing Gong
- Department of Histology and Embryology, Shantou University Medical College, China
| | - Hai-Feng Zhang
- Department of Histology and Embryology, Shantou University Medical College, China
| | - Yan-Mei Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Shantou University Medical College, China
| | - Dan-Feng Zeng
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Shantou University Medical College, China
| | - Pei-Shan Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Shantou University Medical College, China.
| | - Hai-Bin Chen
- Department of Histology and Embryology, Shantou University Medical College, China
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Pramono D, Sugimoto K, Kimura T, Miyake A, Nishigaki K. Characterization of the endogenous retrovirus-derived placenta-specific soluble protein EnvV-Fca from domestic cats. FEBS Lett 2024; 598:1792-1806. [PMID: 38604984 DOI: 10.1002/1873-3468.14873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 04/13/2024]
Abstract
Endogenous retroviruses (ERVs) are remnants of ancestral viruses in the host genome. The present study identified the expression of a defective retroviral env gene belonging to the ERV group V member Env (EnvV) in Felis catus (EnvV-Fca). EnV-Fca was specifically detected in the placental trophoblast syncytiotrophobic layer and expressed as a secreted protein in cultured cells. Genetic analyses indicated that EnvV2 genes are widely present in vertebrates and are under purifying selection among carnivores, suggesting a potential benefit for the host. This study suggests that birds, bats, and rodents carrying EnvV2 may play significant roles as intermediate vectors in spreading or cross-transmitting viruses among species. Our findings provide valuable insights into the evolution of ERV in vertebrate hosts.
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Affiliation(s)
- Didik Pramono
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Japan
| | - Kenji Sugimoto
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Japan
| | - Tohru Kimura
- The Joint Graduate School of Veterinary Medicine, Yamaguchi University, Japan
| | - Ariko Miyake
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Japan
| | - Kazuo Nishigaki
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Japan
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Toudic C, Maurer M, St-Pierre G, Xiao Y, Bannert N, Lafond J, Rassart É, Sato S, Barbeau B. Galectin-1 Modulates the Fusogenic Activity of Placental Endogenous Retroviral Envelopes. Viruses 2023; 15:2441. [PMID: 38140682 PMCID: PMC10747188 DOI: 10.3390/v15122441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Syncytin-1 and -2 are glycoproteins encoded by human endogenous retrovirus (hERV) that, through their fusogenic properties, are needed for the formation of the placental syncytiotrophoblast. Previous studies suggested that these proteins, in addition to the EnvP(b) envelope protein, are also involved in other cell fusion events. Since galectin-1 is a β-galactoside-binding protein associated with cytotrophoblast fusion during placental development, we previously tested its effect on Syncytin-mediated cell fusion and showed that this protein differently modulates the fusogenic potential of Syncytin-1 and -2. Herein, we were interested in comparing the impact of galectin-1 on hERV envelope proteins in different cellular contexts. Using a syncytium assay, we first demonstrated that galectin-1 increased the fusion of Syncytin-2- and EnvP(b)-expressing cells. We then tested the infectivity of Syncytin-1 and -2 vs. VSV-G-pseudotyped viruses toward Cos-7 and various human cell lines. In the presence of galectin-1, infection of Syncytin-2-pseudotyped viruses augmented for all cell lines. In contrast, the impact of galectin-1 on the infectivity of Syncytin-1-pseudotyped viruses varied, being cell- and dose-dependent. In this study, we report the functional associations between three hERV envelope proteins and galectin-1, which should provide information on the fusogenic activity of these proteins in the placenta and other biological and pathological processes.
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Affiliation(s)
- Caroline Toudic
- Département des Sciences Biologiques and Centre d’excellence en Recherche sur les Maladies Orphelines-Fondation Courtois, Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada; (C.T.); (Y.X.); (J.L.); (É.R.)
| | - Maike Maurer
- Robert-Koch Institute, 13353 Berlin, Germany; (M.M.); (N.B.)
| | - Guillaume St-Pierre
- Glycobiology and Bioimaging Laboratory, Research Centre for Infectious Diseases and Axe Maladies Infectieuses et Immunitaires, Laval University, Quebec City, QC G1V 0A6, Canada; (G.S.-P.); (S.S.)
| | - Yong Xiao
- Département des Sciences Biologiques and Centre d’excellence en Recherche sur les Maladies Orphelines-Fondation Courtois, Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada; (C.T.); (Y.X.); (J.L.); (É.R.)
| | - Norbert Bannert
- Robert-Koch Institute, 13353 Berlin, Germany; (M.M.); (N.B.)
| | - Julie Lafond
- Département des Sciences Biologiques and Centre d’excellence en Recherche sur les Maladies Orphelines-Fondation Courtois, Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada; (C.T.); (Y.X.); (J.L.); (É.R.)
| | - Éric Rassart
- Département des Sciences Biologiques and Centre d’excellence en Recherche sur les Maladies Orphelines-Fondation Courtois, Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada; (C.T.); (Y.X.); (J.L.); (É.R.)
| | - Sachiko Sato
- Glycobiology and Bioimaging Laboratory, Research Centre for Infectious Diseases and Axe Maladies Infectieuses et Immunitaires, Laval University, Quebec City, QC G1V 0A6, Canada; (G.S.-P.); (S.S.)
| | - Benoit Barbeau
- Département des Sciences Biologiques and Centre d’excellence en Recherche sur les Maladies Orphelines-Fondation Courtois, Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada; (C.T.); (Y.X.); (J.L.); (É.R.)
- Regroupement Intersectoriel de Recherche en Santé de l’Université du Québec, Montréal, QC H2X 1E3, Canada
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7
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Priščáková P, Svoboda M, Feketová Z, Hutník J, Repiská V, Gbelcová H, Gergely L. Syncytin-1, syncytin-2 and suppressyn in human health and disease. J Mol Med (Berl) 2023; 101:1527-1542. [PMID: 37855856 PMCID: PMC10697888 DOI: 10.1007/s00109-023-02385-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023]
Abstract
In this review, we summarized the results of experimental and clinical studies about three human endogenous retroviruses and their products-syncytin-1, syncytin-2, and suppressyn in human physiology and pathophysiology. We summed up the described connection with various pathological processes and diseases, mainly with pregnancy-induced hypertensive diseases such as preeclampsia, oncogenesis, gestational trophoblastic disease, and multiple sclerosis. Supposed mechanisms of action and the potential of clinical applications are also described.
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Affiliation(s)
- Petra Priščáková
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Michal Svoboda
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Zuzana Feketová
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Juraj Hutník
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Vanda Repiská
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Helena Gbelcová
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic
| | - Lajos Gergely
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University Bratislava, Sasinkova 4, Bratislava, 811 08, Slovak Republic.
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8
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Shimode S. Acquisition and Exaptation of Endogenous Retroviruses in Mammalian Placenta. Biomolecules 2023; 13:1482. [PMID: 37892164 PMCID: PMC10604696 DOI: 10.3390/biom13101482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Endogenous retroviruses (ERVs) are retrovirus-like sequences that were previously integrated into the host genome. Although most ERVs are inactivated by mutations, deletions, or epigenetic regulation, some remain transcriptionally active and impact host physiology. Several ERV-encoded proteins, such as Syncytins and Suppressyn, contribute to placenta acquisition, a crucial adaptation in mammals that protects the fetus from external threats and other risks while enabling the maternal supply of oxygen, nutrients, and antibodies. In primates, Syncytin-1 and Syncytin-2 facilitate cell-cell fusion for placental formation. Suppressyn is the first ERV-derived protein that inhibits cell fusion by binding to ASCT2, the receptor for Syncytin-1. Furthermore, Syncytin-2 likely inserted into the genome of the common ancestor of Anthropoidea, whereas Syncytin-1 and Suppressyn likely inserted into the ancestor of catarrhines; however, they were inactivated in some lineages, suggesting that multiple exaptation events had occurred. This review discusses the role of ERV-encoded proteins, particularly Syncytins and Suppressyn, in placental development and function, focusing on the integration of ERVs into the host genome and their contribution to the genetic mechanisms underlying placentogenesis. This review provides valuable insights into the molecular and genetic aspects of placentation, potentially shedding light on broader evolutionary and physiological processes in mammals.
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Affiliation(s)
- Sayumi Shimode
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan;
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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9
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Yu M, Hu X, Pan Z, Du C, Jiang J, Zheng W, Cai H, Wang Y, Deng W, Wang H, Lu J, Sun MA, Cao B. Endogenous retrovirus-derived enhancers confer the transcriptional regulation of human trophoblast syncytialization. Nucleic Acids Res 2023; 51:4745-4759. [PMID: 36864754 PMCID: PMC10250217 DOI: 10.1093/nar/gkad109] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 03/04/2023] Open
Abstract
Endogenous retroviruses (ERVs) have been proposed as a driving force for the evolution of the mammalian placenta, however, the contribution of ERVs to placental development and the underlying regulatory mechanism remain largely elusive. A key process of placental development is the formation of multinucleated syncytiotrophoblasts (STBs) in direct contact with maternal blood, through which constitutes the maternal-fetal interface critical for nutrient allocation, hormone production and immunological modulation during pregnancy. We delineate that ERVs profoundly rewire the transcriptional program of trophoblast syncytialization. Here, we first determined the dynamic landscape of bivalent ERV-derived enhancers with dual occupancy of H3K27ac and H3K9me3 in human trophoblast stem cells (hTSCs). We further demonstrated that enhancers overlapping several ERV families tend to exhibit increased H3K27ac and reduced H3K9me3 occupancy in STBs relative to hTSCs. Particularly, bivalent enhancers derived from the Simiiformes-specific MER50 transposons were linked to a cluster of genes important for STB formation. Importantly, deletions of MER50 elements adjacent to several STB genes, including MFSD2A and TNFAIP2, significantly attenuated their expression concomitant to compromised syncytium formation. Together, we propose that ERV-derived enhancers, MER50 specifically, fine-tune the transcriptional networks accounting for human trophoblast syncytialization, which sheds light on a novel ERV-mediated regulatory mechanism underlying placental development.
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Affiliation(s)
- Miao Yu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian361002, China
| | - Xiaoqian Hu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian361002, China
| | - Zihang Pan
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian361002, China
| | - Cui Du
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu225009, China
| | - Jing Jiang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu225009, China
| | - Wanshan Zheng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian361002, China
| | - Han Cai
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian361002, China
| | - Yinan Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian361002, China
| | - Wenbo Deng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian361002, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian361002, China
| | - Jinhua Lu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian361002, China
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Bin Cao
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian361002, China
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10
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Taylor AS, Tinning H, Ovchinnikov V, Edge J, Smith W, Pullinger AL, Sutton RA, Constantinides B, Wang D, Forbes K, Forde N, O'Connell MJ. A burst of genomic innovation at the origin of placental mammals mediated embryo implantation. Commun Biol 2023; 6:459. [PMID: 37100852 PMCID: PMC10133327 DOI: 10.1038/s42003-023-04809-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 04/05/2023] [Indexed: 04/28/2023] Open
Abstract
The origin of embryo implantation in mammals ~148 million years ago was a dramatic shift in reproductive strategy, yet the molecular changes that established mammal implantation are largely unknown. Although progesterone receptor signalling predates the origin of mammals and is highly conserved in, and critical for, successful mammal pregnancy, it alone cannot explain the origin and subsequent diversity of implantation strategies throughout the placental mammal radiation. MiRNAs are known to be flexible and dynamic regulators with a well-established role in the pathophysiology of mammal placenta. We propose that a dynamic core microRNA (miRNA) network originated early in placental mammal evolution, responds to conserved mammal pregnancy cues (e.g. progesterone), and facilitates species-specific responses. Here we identify 13 miRNA gene families that arose at the origin of placental mammals and were subsequently retained in all descendent lineages. The expression of these miRNAs in response to early pregnancy molecules is regulated in a species-specific manner in endometrial epithelia of species with extreme implantation strategies (i.e. bovine and human). Furthermore, this set of miRNAs preferentially target proteins under positive selective pressure on the ancestral eutherian lineage. Discovery of this core embryo implantation toolkit and specifically adapted proteins helps explain the origin and evolution of implantation in mammals.
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Affiliation(s)
- Alysha S Taylor
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Haidee Tinning
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
| | - Vladimir Ovchinnikov
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Jessica Edge
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
| | - William Smith
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
- Leeds Fertility, Leeds Teaching Hospitals NHS Trust, York Road, Seacroft, Leeds, LS14 6UH, UK
| | - Anna L Pullinger
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
| | - Ruth A Sutton
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
| | - Bede Constantinides
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Dapeng Wang
- LeedsOmics, University of Leeds, Leeds, LS2 9JT, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Karen Forbes
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
| | - Niamh Forde
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK.
| | - Mary J O'Connell
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
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11
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Shoji H, Kitao K, Miyazawa T, Nakagawa S. Potentially reduced fusogenicity of syncytin-2 in New World monkeys. FEBS Open Bio 2023; 13:459-467. [PMID: 36647789 PMCID: PMC9989925 DOI: 10.1002/2211-5463.13555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Syncytin-2 is a membrane fusion protein involved in placenta development that is derived from the endogenous retrovirus envelope gene acquired in the common ancestral lineage of New World and Old World monkeys (OWMs). It is known that syncytin-2 is conserved between apes and OWMs, suggesting its functional importance; however, syncytin-2 of common marmosets (Callithrix jacchus) exhibits lower fusogenic activity than those of humans and OWMs in human cell lines. To obtain insight into the functional diversity of syncytin-2 genes in primates, we examined the syncytin-2 gene in New World monkeys (NWMs). We experimentally evaluated the cell fusion ability of syncytin-2 in humans, C. jacchus, and tufted capuchins (Sapajus apella). We found that the cell fusion ability of S. apella was lower than that of human syncytin-2. Chimeric syncytin-2 constructs revealed that the amino acid differences in the surface unit of S. apella syncytin-2 were responsible for the weak cell fusion activity. In addition, genomic sequence analyses of syncytin-2 revealed that the open reading frames (ORFs) of syncytin-2 were highly conserved in seven apes and 22 OWMs; however, the syncytin-2 ORFs of three of 12 NWM species were truncated. Our results suggest that syncytin-2 in several NWMs may be of less importance than in OWMs and apes, and other syncytin-like genes may be required for placental development in various NWM species.
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Affiliation(s)
- Hiyori Shoji
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University, Japan
| | - Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
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12
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Matsumoto S, Okamura E, Muto M, Ema M. Similarities and differences in placental development between humans and cynomolgus monkeys. Reprod Med Biol 2023; 22:e12522. [PMID: 37377753 PMCID: PMC10292683 DOI: 10.1002/rmb2.12522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Background The placenta is an extraembryonic organ, which is essential to maintain a normal pregnancy. However, placental development in humans is poorly understood because of technical and ethical reasons. Methods We analyzed the anatomical localization of each trophoblastic subtype in the cynomolgus monkey placenta by immunohistochemistry in the early second trimester. Histological differences among the mouse, cynomolgus monkey, and human placenta were compared. The PubMed database was used to search for studies on placentation in rodents and primates. Main findings The anatomical structures and subtypes of the placenta in cynomolgus monkeys are highly similar to those in humans, with the exception of fewer interstitial extravillous trophoblasts in cynomolgus monkeys. Conclusion The cynomolgus monkey appears to be a good animal model to investigate human placentation.
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Affiliation(s)
- Shoma Matsumoto
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Eiichi Okamura
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Masanaga Muto
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life ScienceShiga University of Medical ScienceOtsuJapan
- Institute for the Advanced Study of Human Biology (WPI‐ASHBi)Kyoto UniversityKyotoJapan
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13
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Simpson J, Kozak CA, Boso G. Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders. PLoS Genet 2022; 18:e1010458. [PMID: 36240227 PMCID: PMC9604959 DOI: 10.1371/journal.pgen.1010458] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/26/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
Endogenous retroviruses (ERVs) found in vertebrate genomes are remnants of retroviral invasions of their ancestral species. ERVs thus represent molecular fossil records of ancient retroviruses and provide a unique opportunity to study viral-host interactions, including cross-species transmissions, in deep time. While most ERVs contain the mutated remains of the original retrovirus, on rare occasions evolutionary selection pressures lead to the co-option/exaptation of ERV genes for a host function. Here, we report the identification of two ancient related non-orthologous ERV env genes, ARTenvV and CARenvV, that are preserved with large open reading frames (ORFs) in the mammalian orders Artiodactyla and Carnivora, respectively, but are not found in other mammals. These Env proteins lack a transmembrane motif, but phylogenetic analyses show strong sequence preservation and positive selection of the env surface ORF in their respective orders, and transcriptomic analyses show a broad tissue expression pattern for both ARTenvV and CARenvV, suggesting that these genes may be exapted for a host function. Multiple lines of evidence indicate that ARTenvV and CARenvV were derived from an ancient ancestral exogenous gamma-like retrovirus that was independently endogenized in two mammalian orders more than 60 million years ago, which roughly coincides with the K-Pg mass extinction event and subsequent mammalian diversification. Thus, these findings identify the oldest known retroviral cross-ordinal transmission of a gamma-like retrovirus with no known extant infectious counterpart in mammals, and the first discovery of the convergent co-option of an ERV gene derived from the same ancestral retrovirus in two different mammalian orders.
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Affiliation(s)
- J’Zaria Simpson
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Christine A. Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Guney Boso
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
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14
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Modzelewski AJ, Gan Chong J, Wang T, He L. Mammalian genome innovation through transposon domestication. Nat Cell Biol 2022; 24:1332-1340. [PMID: 36008480 PMCID: PMC9729749 DOI: 10.1038/s41556-022-00970-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/27/2022] [Indexed: 01/13/2023]
Abstract
Since the discovery of transposons, their sheer abundance in host genomes has puzzled many. While historically viewed as largely harmless 'parasitic' DNAs during evolution, transposons are not a mere record of ancient genome invasion. Instead, nearly every element of transposon biology has been integrated into host biology. Here we review how host genome sequences introduced by transposon activities provide raw material for genome innovation and document the distinct evolutionary path of each species.
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Affiliation(s)
- Andrew J Modzelewski
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, CA, USA
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Johnny Gan Chong
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, CA, USA
| | - Ting Wang
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Lin He
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, CA, USA.
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15
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Imakawa K, Kusama K, Kaneko-Ishino T, Nakagawa S, Kitao K, Miyazawa T, Ishino F. Endogenous Retroviruses and Placental Evolution, Development, and Diversity. Cells 2022; 11:cells11152458. [PMID: 35954303 PMCID: PMC9367772 DOI: 10.3390/cells11152458] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
The main roles of placentas include physical protection, nutrient and oxygen import, export of gasses and fetal waste products, and endocrinological regulation. In addition to physical protection of the fetus, the placentas must provide immune protection throughout gestation. These basic functions are well-conserved; however, placentas are undoubtedly recent evolving organs with structural and cellular diversities. These differences have been explained for the last two decades through co-opting genes and gene control elements derived from transposable elements, including endogenous retroviruses (ERVs). However, the differences in placental structures have not been explained or characterized. This manuscript addresses the sorting of ERVs and their integration into the mammalian genomes and provides new ways to explain why placental structures have diverged.
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Affiliation(s)
- Kazuhiko Imakawa
- Research Institute of Agriculture, Tokai University, Kumamoto 862-8652, Japan
- Correspondence: ; Tel.: +81-96-386-2652
| | - Kazuya Kusama
- Department of Endocrine Pharmacology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | | | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Nakagawa 259-1193, Japan
| | - Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Fumitoshi Ishino
- Institute of Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
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16
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Renaud SJ, Jeyarajah MJ. How trophoblasts fuse: an in-depth look into placental syncytiotrophoblast formation. Cell Mol Life Sci 2022; 79:433. [PMID: 35859055 PMCID: PMC11072895 DOI: 10.1007/s00018-022-04475-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/07/2022] [Accepted: 07/06/2022] [Indexed: 11/24/2022]
Abstract
In humans, cell fusion is restricted to only a few cell types under normal conditions. In the placenta, cell fusion is a critical process for generating syncytiotrophoblast: the giant multinucleated trophoblast lineage containing billions of nuclei within an interconnected cytoplasm that forms the primary interface separating maternal blood from fetal tissue. The unique morphology of syncytiotrophoblast ensures that nutrients and gases can be efficiently transferred between maternal and fetal tissue while simultaneously restricting entry of potentially damaging substances and maternal immune cells through intercellular junctions. To maintain integrity of the syncytiotrophoblast layer, underlying cytotrophoblast progenitor cells terminate their capability for self-renewal, upregulate expression of genes needed for differentiation, and then fuse into the overlying syncytium. These processes are disrupted in a variety of obstetric complications, underscoring the importance of proper syncytiotrophoblast formation for pregnancy health. Herein, an overview of key mechanisms underlying human trophoblast fusion and syncytiotrophoblast development is discussed.
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Affiliation(s)
- Stephen J Renaud
- Department of Anatomy and Cell Biology and Children's Health Research Institute, University of Western Ontario, London, ON, N6A5C1, Canada.
| | - Mariyan J Jeyarajah
- Department of Anatomy and Cell Biology and Children's Health Research Institute, University of Western Ontario, London, ON, N6A5C1, Canada
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17
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Convergent evolution of antiviral machinery derived from endogenous retrovirus truncated envelope genes in multiple species. Proc Natl Acad Sci U S A 2022; 119:e2114441119. [PMID: 35749360 PMCID: PMC9245640 DOI: 10.1073/pnas.2114441119] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Host genetic resistance to viral infection controls the pathogenicity and epidemic dynamics of infectious diseases. Refrex-1 is a restriction factor against feline leukemia virus subgroup D (FeLV-D) and an endogenous retrovirus (ERV) in domestic cats (ERV-DC). Refrex-1 is encoded by a subset of ERV-DC loci with truncated envelope genes and secreted from cells as a soluble protein. Here, we identified the copper transporter CTR1 as the entry receptor for FeLV-D and genotype I ERV-DCs. We also identified CTR1 as a receptor for primate ERVs from crab-eating macaques and rhesus macaques, which were found in a search of intact envelope genes capable of forming infectious viruses. Refrex-1 counteracted infection by FeLV-D and ERV-DCs via competition for the entry receptor CTR1; the antiviral effects extended to primate ERVs with CTR1-dependent entry. Furthermore, truncated ERV envelope genes found in chimpanzee, bonobo, gorilla, crab-eating macaque, and rhesus macaque genomes could also block infection by feline and primate retroviruses. Genetic analyses showed that these ERV envelope genes were acquired in a species- or genus-specific manner during host evolution. These results indicated that soluble envelope proteins could suppress retroviral infection across species boundaries, suggesting that they function to control retroviral spread. Our findings revealed that several mammalian species acquired antiviral machinery from various ancient retroviruses, leading to convergent evolution for host defense.
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18
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Boso G, Fleck K, Carley S, Liu Q, Buckler-White A, Kozak CA. The Oldest Co-opted gag Gene of a Human Endogenous Retrovirus Shows Placenta-Specific Expression and Is Upregulated in Diffuse Large B-Cell Lymphomas. Mol Biol Evol 2021; 38:5453-5471. [PMID: 34410386 PMCID: PMC8662612 DOI: 10.1093/molbev/msab245] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Vertebrate genomes contain endogenous retroviruses (ERVs) that represent remnants of past germline infections by ancient retroviruses. Despite comprising 8% of the human genome, the human ERVs (HERVs) do not encode a replication competent retrovirus. However, some HERV genes have been co-opted to serve host functions, most notably the viral envelope-derived syncytins involved in placentation. Here, we identify the oldest HERV intact gag gene with an open reading frame, gagV1. Its provirus contains an intact env, envV1, and the first open reading frame found in an HERV gag leader, pre-gagV1, which encodes a novel protein. This HERV is linked to a related gag gene, gagV3, and these three genes all show patterns of evolutionary conservation in primates. gagV1 and pre-gagV1 orthologs are present in all simian primate lineages indicating that this HERV entered the germline of the common simian primate ancestor at least 43 Ma, whereas gagV3 is found in Old and New World monkeys. gagV1 and gagV3 have undergone recurrent gene conversion events and positive selection. Expression of gagV1, gagV3, and pre-gagV1 is restricted to the placenta in humans and macaques suggesting co-option for placenta-specific host functions. Transcriptomic analysis of human tumors also found upregulated levels of gagV1 transcripts in diffuse large B-cell lymphomas. These findings suggest that these HERV-V genes may be useful markers for the most common type of non-Hodgkin's lymphoma and that they may have contributed to the successive domestications of env and gag genes in eutherians involved in the ongoing ERV-driven evolution of the placenta.
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Affiliation(s)
- Guney Boso
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Katherine Fleck
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Samuel Carley
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Qingping Liu
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Alicia Buckler-White
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Christine A Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
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19
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Kitao K, Nakagawa S, Miyazawa T. An ancient retroviral RNA element hidden in mammalian genomes and its involvement in co-opted retroviral gene regulation. Retrovirology 2021; 18:36. [PMID: 34753509 PMCID: PMC8579622 DOI: 10.1186/s12977-021-00580-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/22/2021] [Indexed: 01/19/2023] Open
Abstract
Background Retroviruses utilize multiple unique RNA elements to control RNA processing and translation. However, it is unclear what functional RNA elements are present in endogenous retroviruses (ERVs). Gene co-option from ERVs sometimes entails the conservation of viral cis-elements required for gene expression, which might reveal the RNA regulation in ERVs. Results Here, we characterized an RNA element found in ERVs consisting of three specific sequence motifs, called SPRE. The SPRE-like elements were found in different ERV families but not in any exogenous viral sequences examined. We observed more than a thousand of copies of the SPRE-like elements in several mammalian genomes; in human and marmoset genomes, they overlapped with lineage-specific ERVs. SPRE was originally found in human syncytin-1 and syncytin-2. Indeed, several mammalian syncytin genes: mac-syncytin-3 of macaque, syncytin-Ten1 of tenrec, and syncytin-Car1 of Carnivora, contained the SPRE-like elements. A reporter assay revealed that the enhancement of gene expression by SPRE depended on the reporter genes. Mutation of SPRE impaired the wild-type syncytin-2 expression while the same mutation did not affect codon-optimized syncytin-2, suggesting that SPRE activity depends on the coding sequence. Conclusions These results indicate multiple independent invasions of various mammalian genomes by retroviruses harboring SPRE-like elements. Functional SPRE-like elements are found in several syncytin genes derived from these retroviruses. This element may facilitate the expression of viral genes, which were suppressed due to inefficient codon frequency or repressive elements within the coding sequences. These findings provide new insights into the long-term evolution of RNA elements and molecular mechanisms of gene expression in retroviruses. Supplementary Information The online version contains supplementary material available at 10.1186/s12977-021-00580-2.
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Affiliation(s)
- Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan.
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20
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Zhou X, Sam TW, Lee AY, Leung D. Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations. Nat Commun 2021; 12:6462. [PMID: 34753915 PMCID: PMC8578388 DOI: 10.1038/s41467-021-26630-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 10/14/2021] [Indexed: 12/27/2022] Open
Abstract
Polymorphic integrations of endogenous retroviruses (ERVs) have been previously detected in mouse and human genomes. While most are inert, a subset can influence the activity of the host genes. However, the molecular mechanism underlying how such elements affect the epigenome and transcriptome and their roles in driving intra-specific variation remain unclear. Here, by utilizing wildtype murine embryonic stem cells (mESCs) derived from distinct genetic backgrounds, we discover a polymorphic MMERGLN (GLN) element capable of regulating H3K27ac enrichment and transcription of neighboring loci. We demonstrate that this polymorphic element can enhance the neighboring Klhdc4 gene expression in cis, which alters the activity of downstream stress response genes. These results suggest that the polymorphic ERV-derived cis-regulatory element contributes to differential phenotypes from stimuli between mouse strains. Moreover, we identify thousands of potential polymorphic ERVs in mESCs, a subset of which show an association between proviral activity and nearby chromatin states and transcription. Overall, our findings elucidate the mechanism of how polymorphic ERVs can shape the epigenome and transcriptional networks that give rise to phenotypic divergence between individuals.
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Affiliation(s)
- Xuemeng Zhou
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China
| | - Tsz Wing Sam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China
| | - Ah Young Lee
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China
| | - Danny Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China. .,Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China.
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21
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Rosenkrantz JL, Gaffney JE, Roberts VHJ, Carbone L, Chavez SL. Transcriptomic analysis of primate placentas and novel rhesus trophoblast cell lines informs investigations of human placentation. BMC Biol 2021; 19:127. [PMID: 34154587 PMCID: PMC8218487 DOI: 10.1186/s12915-021-01056-7] [Citation(s) in RCA: 7] [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: 09/08/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Proper placentation, including trophoblast differentiation and function, is essential for the health and well-being of both the mother and baby throughout pregnancy. Placental abnormalities that occur during the early stages of development are thought to contribute to preeclampsia and other placenta-related pregnancy complications. However, relatively little is known about these stages in humans due to obvious ethical and technical limitations. Rhesus macaques are considered an ideal surrogate for studying human placentation, but the unclear translatability of known human placental markers and lack of accessible rhesus trophoblast cell lines can impede the use of this animal model. RESULTS Here, we performed a cross-species transcriptomic comparison of human and rhesus placenta and determined that while the majority of human placental marker genes (HPGs) were similarly expressed, 952 differentially expressed genes (DEGs) were identified between the two species. Functional enrichment analysis of the 447 human-upregulated DEGs, including ADAM12, ERVW-1, KISS1, LGALS13, PAPPA2, PGF, and SIGLEC6, revealed over-representation of genes implicated in preeclampsia and other pregnancy disorders. Additionally, to enable in vitro functional studies of early placentation, we generated and thoroughly characterized two highly pure first trimester telomerase (TERT) immortalized rhesus trophoblast cell lines (iRP-D26 and iRP-D28A) that retained crucial features of isolated primary trophoblasts. CONCLUSIONS Overall, our findings help elucidate the molecular translatability between human and rhesus placenta and reveal notable expression differences in several HPGs and genes implicated in pregnancy complications that should be considered when using the rhesus animal model to study normal and pathological human placentation.
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Affiliation(s)
- Jimi L. Rosenkrantz
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 USA
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
| | - Jessica E. Gaffney
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
| | - Victoria H. J. Roberts
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
| | - Lucia Carbone
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006 USA
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239 USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239 USA
| | - Shawn L. Chavez
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 USA
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
- Department of Obstetrics and Gynecology, Oregon Health and Science University School of Medicine, Portland, OR 97239 USA
- Department of Biomedical Engineering, Oregon Health and Science University School of Medicine, Portland, OR 97239 USA
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22
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Abstract
Significant advances have been observed in the field of cell biology, with numerous studies exploring the molecular genetic pathways that have contributed to species evolution and disease development. The current study adds to the existing body of research evidence by reviewing information related to the role of leftover viruses and/or viral remnants in human physiology. To explore leftover viruses, their incorporation, and their roles in human physiology. The study entailed conducting a systematic search in the PsycINFO, PubMed, Web of Science, and CINAHL databases to locate articles related to the topic of investigation. The search terms included “leftovers,” “viruses,” “genome sequences,” “transposable elements,” “immune response,” and “evolution.” Additional articles were selected from the references of the studies identified in the electronic databases. Evidence showed that both retroviruses and nonretroviruses can be integrated into the human germline via various mechanisms. The role of leftover viruses in human physiology has been explored by studying the activation of human retroviral genes in the human placenta, RNA transfer between neurons through virus-like particles, and RNA transfer through extracellular vesicles. Research evidence suggested that leftover viruses play key roles in human physiology. A more complete understanding of the underlying pathways may provide an avenue for studying human evolution and allow researchers to determine the pathogenesis of some viral infections. Evidence obtained in this review shows that leftover viruses may be incorporated into the human genome. Retroviral genes are critical for the development of different parts of the body, such as the placenta in mammals.
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Affiliation(s)
- Borros Arneth
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, University Hospital of the Universities of Giessen and Marburg UKGM, Justus Liebig University Giessen, Feulgenstr. 12, 35392, Giessen, Germany.
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23
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Díaz-Carballo D, Saka S, Acikelli AH, Homp E, Erwes J, Demmig R, Klein J, Schröer K, Malak S, D'Souza F, Noa-Bolaño A, Menze S, Pano E, Andrioff S, Teipel M, Dammann P, Klein D, Nasreen A, Tannapfel A, Grandi N, Tramontano E, Ochsenfarth C, Strumberg D. Enhanced antitumoral activity of TLR7 agonists via activation of human endogenous retroviruses by HDAC inhibitors. Commun Biol 2021; 4:276. [PMID: 33658617 PMCID: PMC7930250 DOI: 10.1038/s42003-021-01800-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 01/25/2021] [Indexed: 12/18/2022] Open
Abstract
In this work, we are reporting that "Shock and Kill", a therapeutic approach designed to eliminate latent HIV from cell reservoirs, is extrapolatable to cancer therapy. This is based on the observation that malignant cells express a spectrum of human endogenous retroviral elements (HERVs) which can be transcriptionally boosted by HDAC inhibitors. The endoretroviral gene HERV-V2 codes for an envelope protein, which resembles syncytins. It is significantly overexpressed upon exposure to HDAC inhibitors and can be effectively targeted by simultaneous application of TLR7/8 agonists, triggering intrinsic apoptosis. We demonstrated that this synergistic cytotoxic effect was accompanied by the functional disruption of the TLR7/8-NFκB, Akt/PKB, and Ras-MEK-ERK signalling pathways. CRISPR/Cas9 ablation of TLR7 and HERV-V1/V2 curtailed apoptosis significantly, proving the pivotal role of these elements in driving cell death. The effectiveness of this new approach was confirmed in ovarian tumour xenograft studies, revealing a promising avenue for future cancer therapies.
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Affiliation(s)
- David Díaz-Carballo
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany.
| | - Sahitya Saka
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Ali H Acikelli
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Ekaterina Homp
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Julia Erwes
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Rebecca Demmig
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Jacqueline Klein
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Katrin Schröer
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Sascha Malak
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Flevy D'Souza
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Adrien Noa-Bolaño
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Saskia Menze
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Emilio Pano
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Swetlana Andrioff
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Marc Teipel
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
| | - Philip Dammann
- Central Animal Laboratory, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Diana Klein
- Institute of Cell Biology, Cancer Research, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Amber Nasreen
- Visceral Surgery Department, Marien Hospital Herne, Ruhr University Bochum Medical School, Herne, Germany
| | | | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Crista Ochsenfarth
- Department of Anesthesia, Intensive Care, Pain and Palliative Medicine, Marien Hospital Herne, Ruhr-University Bochum Medical School, Herne, Germany
| | - Dirk Strumberg
- Ruhr University Bochum, Faculty of Medicine, Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, Herne, Germany
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24
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Abstract
Three versions of syncytiotrophoblast exist in the human placenta: an invasive type associated with the implanting conceptus, non-invasive villous type of definitive placenta, and placental bed giant cells. Syncytins are encoded by modified env genes of endogenous retroviruses (ERV), but how they contribute functionally to placental syncytial structures is unclear. A minimum of eight genes (ERVW1, ERVFRD-1, ERVV-1, ERVV-2, ERVH48-1, ERVMER34-1, ERV3-1, & ERVK13-1) encoding syncytin family members are expressed in human trophoblast, the majority from implantation to term. ERVW1 (Syncytin 1) and ERVFRD-1 (Syncytin 2) are considered the major fusogens, but, when the expression of their genes is analyzed by single cell RNAseq in first trimester placenta, their transcripts are distinctly patterned and also differ from those of their proposed binding partners, SLC1A5 and MFSD2A, respectively. ERVRH48-1 (suppressyn or SUPYN) and ERVMER34-1 are probable negative regulators of fusion and co-expressed, primarily in cytotrophoblast. The remaining genes and their products have been little studied. Syncytin expression is a feature of placental development in almost all eutherian mammals studied, in at least one marsupial, and in viviparous lizards, which lack the trophoblast lineage. Their expression has been inferred to be essential for pregnancy success in the mouse. All the main human ERV genes arose following independent retroviral insertion events, none of which trace back to the divergence of eutherians and metatherians (marsupials). While syncytins may be crucial for placental development, it seems unlikely that they helped orchestrate the divergence of eutherians and marsupials.
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Mulholland CB, Nishiyama A, Ryan J, Nakamura R, Yiğit M, Glück IM, Trummer C, Qin W, Bartoschek MD, Traube FR, Parsa E, Ugur E, Modic M, Acharya A, Stolz P, Ziegenhain C, Wierer M, Enard W, Carell T, Lamb DC, Takeda H, Nakanishi M, Bultmann S, Leonhardt H. Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals. Nat Commun 2020; 11:5972. [PMID: 33235224 PMCID: PMC7686362 DOI: 10.1038/s41467-020-19603-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.
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Affiliation(s)
- Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Joel Ryan
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Merve Yiğit
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ivo M Glück
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael D Bartoschek
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Franziska R Traube
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Edris Parsa
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London, UK
| | - Aishwarya Acharya
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Paul Stolz
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Christoph Ziegenhain
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Thomas Carell
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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26
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Structure of the Receptor Binding Domain of EnvP(b)1, an Endogenous Retroviral Envelope Protein Expressed in Human Tissues. mBio 2020; 11:mBio.02772-20. [PMID: 33203760 PMCID: PMC7683403 DOI: 10.1128/mbio.02772-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Organisms can access genetic and functional novelty by capturing viral elements within their genomes, where they can evolve to drive new cellular or organismal processes. We demonstrate that a retroviral envelope gene, EnvP(b)1, has been maintained and its fusion activity preserved for 40 to 71 million years. It is expressed as a protein in multiple healthy human tissues. We determined the structure of its inferred receptor binding domain and compared it with the same domain in modern viruses. We found a common conserved architecture that underlies the varied receptor binding activity of divergent Env genes. The modularity and versatility of this domain may underpin the evolutionary success of this clade of fusogens. EnvP(b)1 is an endogenous retroviral envelope gene found in human and other primate genomes. We report EnvP(b)1 sequences in primate genomes consistent with an integration event between 40 and 71 million years ago. Using a highly specific polyclonal antiserum raised against the putative receptor binding domain (RBD) of human EnvP(b)1, we detected expression in human placenta, ovaries, and thymus. We found that EnvP(b)1 is proteolytically processed, and using cell-cell fusion assays in multiple primate cell lines, we demonstrated that extant EnvP(b)1 proteins from a variety of primate genomes are fusogenic. This work supports the idea that EnvP(b)1 is under purifying selection and its fusogenic activity has been maintained for over 40 million years. We determined the structure of the RBD of human EnvP(b)1, which defines structural similarities with extant leukemia viruses, despite little sequence conservation. This structure highlights a common scaffold from which novel receptor binding specificities likely evolved. The evolutionary plasticity of this domain may underlie the diversity of related Envs in circulating viruses.
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27
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Liu CH, Grandi N, Palanivelu L, Tramontano E, Lin LT. Contribution of Human Retroviruses to Disease Development-A Focus on the HIV- and HERV-Cancer Relationships and Treatment Strategies. Viruses 2020; 12:E852. [PMID: 32759845 PMCID: PMC7472297 DOI: 10.3390/v12080852] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023] Open
Abstract
Animal retroviruses are known for their transforming potential, and this is also true for the ones hosted by humans, which have gathered expanding attention as one of the potent causative agents in various disease, including specific cancer types. For instance, Human T Lymphotropic virus (HTLV) is a well-studied class of oncoviruses causing T cell leukemia, while human immunodeficiency virus (HIV) leads to acquired immunodeficiency syndrome (AIDS), which is linked to a series of defining cancers including Kaposi sarcoma, certain types of non-Hodgkin lymphoma, and cervical cancer. Of note, in addition to these "modern" exogenous retroviruses, our genome harbors a staggering number of human endogenous retroviruses (HERVs). HERVs are the genetic remnants of ancient retroviral germline infection of human ancestors and are typically silenced in normal tissues due to inactivating mutations and sequence loss. While some HERV elements have been appropriated and contribute to human physiological functions, others can be reactivated through epigenetic dysregulations to express retroviral elements and promote carcinogenesis. Conversely, HERV replication intermediates or protein products can also serve as intrinsic pathogen-associated molecular patterns that cause the immune system to interpret it as an exogenous infection, thereby stimulating immune responses against tumors. As such, HERVs have also been targeted as a potential internal strategy to sensitize tumor cells for promising immunotherapies. In this review, we discuss the dynamic role of human retroviruses in cancer development, focusing on HIV and HERVs contribution. We also describe potential treatment strategies, including immunotherapeutic targeting of HERVs, inhibiting DNA methylation to expose HERV signatures, and the use of antiretroviral drugs against HIV and HERVs, which can be employed as prospective anti-cancer modalities.
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Affiliation(s)
- Ching-Hsuan Liu
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, 09042 Cagliari, Italy; (N.G.); (E.T.)
| | - Lalitha Palanivelu
- International Master Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, 09042 Cagliari, Italy; (N.G.); (E.T.)
| | - Liang-Tzung Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
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28
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Nishihara H. Retrotransposons spread potential cis-regulatory elements during mammary gland evolution. Nucleic Acids Res 2020; 47:11551-11562. [PMID: 31642473 PMCID: PMC7145552 DOI: 10.1093/nar/gkz1003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 12/18/2022] Open
Abstract
Acquisition of cis-elements is a major driving force for rewiring a gene regulatory network. Several kinds of transposable elements (TEs), mostly retrotransposons that propagate via a copy-and-paste mechanism, are known to possess transcription factor binding motifs and have provided source sequences for enhancers/promoters. However, it remains largely unknown whether retrotransposons have spread the binding sites of master regulators of morphogenesis and accelerated cis-regulatory expansion involved in common mammalian morphological features during evolution. Here, I demonstrate that thousands of binding sites for estrogen receptor α (ERα) and three related pioneer factors (FoxA1, GATA3 and AP2γ) that are essential regulators of mammary gland development arose from a spreading of the binding motifs by retrotransposons. The TE-derived functional elements serve primarily as distal enhancers and are enriched around genes associated with mammary gland morphogenesis. The source TEs occurred via a two-phased expansion consisting of mainly L2/MIR in a eutherian ancestor and endogenous retrovirus 1 (ERV1) in simian primates and murines. Thus the build-up of potential sources for cis-elements by retrotransposons followed by their frequent utilization by the host (co-option/exaptation) may have a general accelerating effect on both establishing and diversifying a gene regulatory network, leading to morphological innovation.
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Affiliation(s)
- Hidenori Nishihara
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-S2-17, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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29
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Matsumoto S, Porter CJ, Ogasawara N, Iwatani C, Tsuchiya H, Seita Y, Chang YW, Okamoto I, Saitou M, Ema M, Perkins TJ, Stanford WL, Tanaka S. Establishment of macaque trophoblast stem cell lines derived from cynomolgus monkey blastocysts. Sci Rep 2020; 10:6827. [PMID: 32321940 PMCID: PMC7176671 DOI: 10.1038/s41598-020-63602-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/02/2020] [Indexed: 12/23/2022] Open
Abstract
The placenta forms a maternal-fetal junction that supports many physiological functions such as the supply of nutrition and exchange of gases and wastes. Establishing an in vitro culture model of human and non-human primate trophoblast stem/progenitor cells is important for investigating the process of early placental development and trophoblast differentiation. In this study, we have established five trophoblast stem cell (TSC) lines from cynomolgus monkey blastocysts, named macTSC #1-5. Fibroblast growth factor 4 (FGF4) enhanced proliferation of macTSCs, while other exogenous factors were not required to maintain their undifferentiated state. macTSCs showed a trophoblastic gene expression profile and trophoblast-like DNA methylation status and also exhibited differentiation capacity towards invasive trophoblast cells and multinucleated syncytia. In a xenogeneic chimera assay, these stem cells contributed to trophectoderm (TE) development in the chimeric blastocysts. macTSC are the first primate trophoblast cell lines whose proliferation is promoted by FGF4. These cell lines provide a valuable in vitro culture model to analyze the similarities and differences in placental development between human and non-human primates.
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Affiliation(s)
- Shoma Matsumoto
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Toky, 113-8657, Japan
| | | | - Naomi Ogasawara
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Toky, 113-8657, Japan
| | - Chizuru Iwatani
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Sciences, Shiga University of Medical Sciences, Shiga, 520-2192, Japan
| | - Hideaki Tsuchiya
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Sciences, Shiga University of Medical Sciences, Shiga, 520-2192, Japan
| | - Yasunari Seita
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Sciences, Shiga University of Medical Sciences, Shiga, 520-2192, Japan
| | - Yu-Wei Chang
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Ikuhiro Okamoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.,Japan Science and Technology (JST), Exploratory Research for Advanced Technology (ERATO), Kyoto, Japan.,Institute for Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.,Institute for Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto, 606-8507, Japan
| | - Masatsugu Ema
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan.,Institute for Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | | | - William L Stanford
- The Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, K1H 8M5, Canada
| | - Satoshi Tanaka
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Toky, 113-8657, Japan.
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30
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Lv B, An Q, Zeng Q, Zhang X, Lu P, Wang Y, Zhu X, Ji Y, Fan G, Xue Z. Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptuses. PLoS Biol 2019; 17:e3000187. [PMID: 31596842 PMCID: PMC6802852 DOI: 10.1371/journal.pbio.3000187] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/21/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022] Open
Abstract
Multipotent trophoblasts undergo dynamic morphological movement and cellular differentiation after conceptus implantation to generate placenta. However, the mechanism controlling trophoblast development and differentiation during peri-implantation development in human remains elusive. In this study, we modeled human conceptus peri-implantation development from blastocyst to early postimplantation stages by using an in vitro coculture system and profiled the transcriptome of 476 individual trophoblast cells from these conceptuses. We revealed the genetic networks regulating peri-implantation trophoblast development. While determining when trophoblast differentiation happens, our bioinformatic analysis identified T-box transcription factor 3 (TBX3) as a key regulator for the differentiation of cytotrophoblast (CT) into syncytiotrophoblast (ST). The function of TBX3 in trophoblast differentiation is then validated by a loss-of-function experiment. In conclusion, our results provided a valuable resource to study the regulation of trophoblasts development and differentiation during human peri-implantation development.
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Affiliation(s)
- Bo Lv
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Qin An
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, State of California, United States of America
| | - Qiao Zeng
- Center of Reproductive Medicine of Ji’an Maternal and Child Health Hospital, Ji’an, Jiangxi, China
| | - Xunyi Zhang
- Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, China
| | - Ping Lu
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Yanqiu Wang
- Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, China
| | - Xianmin Zhu
- Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yazhong Ji
- Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, China
- * E-mail: (ZX); (GF); (YJ)
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, State of California, United States of America
- * E-mail: (ZX); (GF); (YJ)
| | - Zhigang Xue
- Department of Regenerative Medicine, School of Medicine, Tongji University, Shanghai, China
- Reproductive Medicine Center, Tongji Hospital, Tongji University, Shanghai, China
- * E-mail: (ZX); (GF); (YJ)
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31
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Toudic C, Vargas A, Xiao Y, St-Pierre G, Bannert N, Lafond J, Rassart É, Sato S, Barbeau B. Galectin-1 interacts with the human endogenous retroviral envelope protein syncytin-2 and potentiates trophoblast fusion in humans. FASEB J 2019; 33:12873-12887. [PMID: 31499012 DOI: 10.1096/fj.201900107r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Syncytin (Syn)-2 is an important fusogenic protein that contributes to the formation of the placental syncytiotrophoblast. Galectin (Gal)-1, a soluble lectin, is also involved in trophoblast cell fusion and modulates the interaction of certain retroviral envelopes with their cellular receptor. This study aimed to investigate the association between Syn-2 and Gal-1 during human trophoblast cell fusion. This association was evaluated in vitro on primary villous cytotrophoblasts (vCTBs) and cell lines using recombinant Gal-1 and Syn-2-pseudotyped viruses. Using lactose, a Gal antagonist, and Gal-1-specific small interfering RNA (siRNA) transfections, we confirmed the implication of Gal-1 in vCTBs and BeWo cell fusion, although RT-PCR and ELISA analyses suggested that Gal-1 alone did not induce syncytialization. Infection assays showed a specific and significant effect of Gal-1 on the infectivity of Syn-2-pseudotyped viruses that depended on the expression of major facilitator superfamily domain-containing 2A (MFSD2a). Moreover, Gal-3, another placental Gal, did not modulate the infectivity of Syn-2-positive viruses, strengthening the specific association between Gal-1 and Syn-2. Interestingly, Gal-1 significantly reduced the infectivity of Syn-1-pseudotyped viruses, suggesting the opposite effects of Gal-1 on Syn-1 and -2. Finally, coimmunoprecipitation experiments showed a glycan-dependent interaction between Syn-2-bearing virions and Gal-1. We conclude that Gal-1 specifically interacts with Syn-2 and possibly regulates Syn-2/MFSD2a interaction during syncytialization of trophoblastic cells.-Toudic, C., Vargas, A., Xiao, Y., St-Pierre, G., Bannert, N., Lafond, J., Rassart, É., Sato, S., Barbeau, B. Galectin-1 interacts with the human endogenous retroviral envelope protein syncytin-2 and potentiates trophoblast fusion in humans.
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Affiliation(s)
- Caroline Toudic
- Département des Sciences Biologiques, Centre de Recherche BioMed, Université du Quebec à Montréal, Montreal, Quebec, Canada
| | - Amandine Vargas
- Département des Sciences Biologiques, Centre de Recherche BioMed, Université du Quebec à Montréal, Montreal, Quebec, Canada
| | - Yong Xiao
- Département des Sciences Biologiques, Centre de Recherche BioMed, Université du Quebec à Montréal, Montreal, Quebec, Canada
| | - Guillaume St-Pierre
- Glycobiology and Bioimaging Laboratory, Research Centre for Infectious Diseases, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
| | | | - Julie Lafond
- Département des Sciences Biologiques, Centre de Recherche BioMed, Université du Quebec à Montréal, Montreal, Quebec, Canada
| | - Éric Rassart
- Département des Sciences Biologiques, Centre de Recherche BioMed, Université du Quebec à Montréal, Montreal, Quebec, Canada
| | - Sachiko Sato
- Glycobiology and Bioimaging Laboratory, Research Centre for Infectious Diseases, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
| | - Benoit Barbeau
- Département des Sciences Biologiques, Centre de Recherche BioMed, Université du Quebec à Montréal, Montreal, Quebec, Canada
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Kwak YT, Muralimanoharan S, Gogate AA, Mendelson CR. Human Trophoblast Differentiation Is Associated With Profound Gene Regulatory and Epigenetic Changes. Endocrinology 2019; 160:2189-2203. [PMID: 31294776 PMCID: PMC6821221 DOI: 10.1210/en.2019-00144] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022]
Abstract
Defective placental implantation and vascularization with accompanying hypoxia contribute to preeclampsia (PE), a leading cause of maternal and neonatal morbidity and mortality. Genetic and epigenetic mechanisms underlying differentiation of proliferative cytotrophoblasts (CytTs) to multinucleated syncytiotrophoblast (SynT) are incompletely defined. The SynT performs key functions in nutrient and gas exchange, hormone production, and protection of the fetus from rejection by the maternal immune system. In this study, we used chromatin immunoprecipitation sequencing of midgestation human trophoblasts before CytT and after SynT differentiation in primary culture to analyze changes in binding of RNA polymerase II (Pol II) and of active and repressive histone marks during SynT differentiation. Our findings reveal that increased Pol II binding to promoters of a subset of genes during trophoblast differentiation was closely correlated with active histone marks. This gene set was enriched in those controlling immune response and immune modulation, including interferon-induced tetratricopeptide repeat and placenta-specific glycoprotein gene family members. By contrast, genes downregulated during SynT differentiation included proinflammatory transcription factors ERG1, cFOS, and cJUN, as well as members of the NR4A orphan nuclear receptor subfamily, NUR77, NURR1, and NOR1. Downregulation of proinflammatory transcription factors upon SynT differentiation was associated with decreased promoter enrichment of endogenous H3K27Ac and H3K9Ac and enhanced binding of H3K9me3 and histone deacetylase 1. However, promoter enrichment of H3K27me3 was low in both CytT and SynT and was not altered with changes in gene expression. These findings provide important insight into mechanisms underlying human trophoblast differentiation and may identify therapeutic targets for placental disorders, such as PE.
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Affiliation(s)
- Youn-Tae Kwak
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas
- North Texas March of Dimes Birth Defects Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Sribalasubashini Muralimanoharan
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas
- North Texas March of Dimes Birth Defects Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Aishwarya A Gogate
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Carole R Mendelson
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas
- North Texas March of Dimes Birth Defects Center, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas
- Correspondence: Carole R. Mendelson, PhD, Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390. E-mail:
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Skirmuntt EC, Katzourakis A. The evolution of endogenous retroviral envelope genes in bats and their potential contribution to host biology. Virus Res 2019; 270:197645. [PMID: 31271763 DOI: 10.1016/j.virusres.2019.197645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 12/22/2022]
Abstract
Bats are the primary reservoirs and carriers of a wide range of viruses of unknown infectivity and pathogenic potential. Some of those if transmitted to other species can cause enormous economic losses in agriculture, and mortality in humans. Bats can be persistently infected with viruses while not showing any symptoms of disease, despite having high virus titre levels in their tissues and shedding virions for months or years after primary infection. It has been suggested that the lack of symptoms of viral infections and low mortality rate in bats might be due to immune adaptations that result from their long-term co-evolution with viruses. In this study, we screened all publicly available bat genomes from six bat families within which we have identified several envelope sequences of retroviral origin (gammaretroviruses). We analysed the identified sequences with Bayesian methods and maximum-likelihood inference to generate a phylogenetic tree with additional reference sequences of known endogenous and exogenous viral envelope genes. We also identified groups of orthologous viral envelopes and analysed them to determine if any of them might be an EVE (endogenous virus element) with an EDI (EVE- derived immunity) function or a candidate for a bat syncytin gene, which is an endogenized viral envelope, mostly known from its function in placentation in animals. Our study shows that bat genomes contain a substantial number of large, intact envelopes with open reading frames, which were found clustering closely on a phylogenetic tree reconstruction with syncytin sequences of other species. That might indicate that such sequences are good candidates for further bat-syncytin/EDI search.
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Affiliation(s)
- Emilia Cecylia Skirmuntt
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK.
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Kitao K, Tanikaga T, Miyazawa T. Identification of a post-transcriptional regulatory element in the human endogenous retroviral syncytin-1. J Gen Virol 2019; 100:662-668. [PMID: 30794119 DOI: 10.1099/jgv.0.001238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Retroviral transcripts have cis-acting elements that interact with host and viral proteins to enable efficient nuclear export and/or translation; however, it is poorly understood whether the transcripts of human endogenous retroviral genes retain such elements. Here, we show that human syncytin-1, which is derived from human endogenous retrovirus W, requires a 3' untranslated region (3'UTR) for efficient gene expression and retains a post-transcriptional regulatory element (named SPRE). The insertion of SPRE markedly increased a reporter gene (human immunodeficiency virus type 1 Gag) expression without affecting the amounts of nuclear or cytoplasmic transcript. Deletion analysis identified a required sequence for SPRE activity, and the prediction of the RNA secondary structure demonstrated a common secondary structure found among active SPRE sequences. Another human syncytin, syncytin-2, also requires a 3'UTR for efficient gene expression. These data provide insights into post-transcriptional regulation in endogenous retroviral gene expression.
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Affiliation(s)
- Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takamasa Tanikaga
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
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35
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Capture of a Hyena-Specific Retroviral Envelope Gene with Placental Expression Associated in Evolution with the Unique Emergence among Carnivorans of Hemochorial Placentation in Hyaenidae. J Virol 2019; 93:JVI.01811-18. [PMID: 30463979 DOI: 10.1128/jvi.01811-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/15/2018] [Indexed: 12/30/2022] Open
Abstract
Capture of retroviral envelope genes from endogenous retroviruses has played a role in the evolution of mammals, with evidence for the involvement of these genes in the formation of the maternofetal interface of the placenta. It has been shown that the diversity of captured genes is likely to be responsible for the diversity of placental structures, ranging from poorly invasive (epitheliochorial) to highly invasive (hemochorial), with an intermediate state (endotheliochorial) as found in carnivorans. The latter recapitulate part of this evolution, with the hyena being the sole carnivoran with a hemochorial placenta. In this study, we performed RNA sequencing on hyena placental transcripts and searched for endogenous retroviral envelope genes that have been captured specifically in the Hyaenidae clade and are not found in any other carnivoran. We identified an envelope gene that is expressed in the placenta at the level of the maternofetal interface, as evidenced by in situ hybridization/immunohistochemistry. The gene entry is coincidental with the emergence of the Hyaenidae clade 30 million years ago (Mya), being found at the same genomic locus in all 4 extant hyena species. Its coding sequence has further been maintained during all of Hyaenidae evolution. It is not found in any of the 30 other carnivorans-both Felidae and Canidae-that we screened. This envelope protein does not disclose any fusogenic activity in ex vivo assays, at variance with the syncytin-Car1 gene, which is found in all carnivorans, including the hyena, in which it is still present, transcriptionally active in the placenta, and fusogenic. Together, the present results illustrate the permanent renewal of placenta-specific genes by retroviral capture and de facto provide a candidate gene for the endotheliochorial to hemochorial transition of Hyaenidae among carnivorans.IMPORTANCE The placenta is the most diverse organ among mammals, due in part to stochastic capture of retroviral envelope genes. In carnivorans, capture of syncytin-Car1 took place 80 Mya. It is fusogenic, expressed at the syncytialized placental maternofetal interface, and conserved among all carnivorans, consistent with their shared endotheliochorial placenta. Hyenas are a remarkable exception, with a highly invasive hemochorial placenta, as found in humans, where disruption of maternal blood vessels results in maternal blood bathing the syncytial maternofetal interface. In this study, we identified a retroviral envelope gene capture and exaptation that took place about 30 Mya and is coincident with the emergence of the Hyaenidae, being conserved in all extant hyena species. It is expressed at the maternofetal interface in addition to the shared syncytin-Car1 gene. This new env gene, not present in any other carnivoran, is a likely candidate to be responsible for the specific structure of the hyena placenta.
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Syrett CM, Sierra I, Berry CL, Beiting D, Anguera MC. Sex-Specific Gene Expression Differences Are Evident in Human Embryonic Stem Cells and During In Vitro Differentiation of Human Placental Progenitor Cells. Stem Cells Dev 2018; 27:1360-1375. [PMID: 29993333 DOI: 10.1089/scd.2018.0081] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The placenta is a short-lived tissue required for embryonic growth and survival, and it is fetal derived. Fetal sex influences gestation, and many sexual dimorphic diseases have origins in utero. There is sex-biased gene expression in third-trimester human placentas, yet the origin of sex-specific expression is unknown. Here, we used an in vitro differentiation model to convert human embryonic stem cells (hESCs) into trophoblastic progenitor cells of the first-trimester placenta, which will eventually become mature extravillous trophoblasts and syncytiotrophoblasts. We observed significant sex differences in transcriptomic profiles of hESCs and trophoblastic progenitors, and also with the differentiation process itself. Male cells had higher dosage of X/Y gene pairs relative to female samples, supporting functions for Y-linked genes beyond spermatogenesis in the hESCs and in the early placenta. Female-specific differentiation altered the expression of several thousand genes compared with male cells, and female cells specifically upregulated numerous autosomal genes with known roles in trophoblast function. Sex-biased upregulation of cellular pathways during trophoblast differentiation was also evident. This study is the first to identify sex differences in trophoblastic progenitor cells of the first-trimester human placenta, and reveal early origins for sexual dimorphism.
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Affiliation(s)
- Camille M Syrett
- 1 Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Isabel Sierra
- 1 Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Corbett L Berry
- 2 Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Daniel Beiting
- 2 Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Montserrat C Anguera
- 1 Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
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Lu X, Wang R, Zhu C, Wang H, Lin HY, Gu Y, Cross JC, Wang H. Fine-Tuned and Cell-Cycle-Restricted Expression of Fusogenic Protein Syncytin-2 Maintains Functional Placental Syncytia. Cell Rep 2018; 21:1150-1159. [PMID: 29091755 DOI: 10.1016/j.celrep.2017.10.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/12/2017] [Accepted: 10/04/2017] [Indexed: 10/18/2022] Open
Abstract
Many types of multinucleated cells (syncytia) generated by cell-cell fusion are post-mitotic, but it remains unclear how this state is maintained and why. Here, we utilized the fluorescent ubiquitination-based cell-cycle indicator (Fucci) reporter system to show that human placental trophoblast cells were all in the G0 phase before they fuse. Expression of the fusogenic protein (fusogen) Syncytin-2 was confined to G0 cells. Overexpression of Syncytin-2 in cycling cells overrode the cell-cycle restriction and enabled fusion of cells in the S/G2/M phases but resulted in the unstable syncytia retaining mitotic features. The Syncytin-2-induced syncytia were functionally compromised with respect to pathogen defense and hormone secretion. We found that, during trophoblast fusion, the cell-cycle inhibitor p21 interacted with the GCM1 transcription factor, and this complex bound to the promoter of Syncytin-2 and promoted its transcription. These findings demonstrate that G0-restricted Syncytin-2 expression is a prerequisite for development of functional post-mitotic syncytia.
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Affiliation(s)
- Xiaoyin Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng Zhu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haibin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hai-Yan Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Gu
- The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - James C Cross
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T1S 1A2, Canada; Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, AB T1S 1A2, Canada; Department of Obstetrics and Gynecology, University of Calgary, Calgary, AB T1S 1A2, Canada; Department of Medical Genetics, University of Calgary, Calgary, AB T1S 1A2, Canada.
| | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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38
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Euphyllophyte Paleoviruses Illuminate Hidden Diversity and Macroevolutionary Mode of Caulimoviridae. J Virol 2018; 92:JVI.02043-17. [PMID: 29491164 DOI: 10.1128/jvi.02043-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 02/16/2018] [Indexed: 12/29/2022] Open
Abstract
Endogenous viral elements (paleoviruses) provide "molecular fossils" for studying the deep history and macroevolution of viruses. Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms, but little is known about EPRVs in earlier-branching plants. Here we use a large-scale phylogenomic approach to investigate the diversity and macroevolution of plant pararetroviruses (formally known as Caulimoviridae). We uncover an unprecedented and unappreciated diversity of EPRVs within the genomes of gymnosperms and ferns. The known angiosperm viruses constitute only a minor part of the Caulimoviridae diversity. By characterizing the distribution of EPRVs, we show that no major euphyllophyte lineages escape the activity of Caulimoviridae, raising the possibility that many exogenous Caulimoviridae remain to be discovered in euphyllophytes. We find that the copy numbers of EPRVs are generally high, suggesting that EPRVs might define a unique group of repetitive elements and represent important components of euphyllophyte genomes. Evolutionary analyses suggest an ancient origin of Caulimoviridae and at least three independent origins of Caulimoviridae in angiosperms. Our findings reveal the remarkable diversity of Caulimoviridae and have important implications for understanding the origin and macroevolution of plant pararetroviruses.IMPORTANCE Few viruses have been documented in plants outside angiosperms. Viruses can occasionally integrate into host genomes, forming endogenous viral elements (EVEs). Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms. In this study, we performed comprehensive comparative and phylogenetic analyses of EPRVs and found that EPRVs are present in the genomes of gymnosperms and ferns. We identified numerous EPRVs in gymnosperm and fern genomes, revealing an unprecedented depth in the diversity of plant pararetroviruses. Plant pararetroviruses mainly underwent cross-species transmission, and angiosperm pararetroviruses arose at least three times. Our study provides novel insights into the diversity and macroevolution of plant pararetroviruses.
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Grandi N, Tramontano E. HERV Envelope Proteins: Physiological Role and Pathogenic Potential in Cancer and Autoimmunity. Front Microbiol 2018; 9:462. [PMID: 29593697 PMCID: PMC5861771 DOI: 10.3389/fmicb.2018.00462] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/27/2018] [Indexed: 12/29/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are relics of ancient infections accounting for about the 8% of our genome. Despite their persistence in human DNA led to the accumulation of mutations, HERVs are still contributing to the human transcriptome, and a growing number of findings suggests that their expression products may have a role in various diseases. Among HERV products, the envelope proteins (Env) are currently highly investigated for their pathogenic properties, which could likely be participating to several disorders with complex etiology, particularly in the contexts of autoimmunity and cancer. In fact, HERV Env proteins have been shown, on the one side, to trigger both innate and adaptive immunity, prompting inflammatory, cytotoxic and apoptotic reactions; and, on the other side, to prevent the immune response activation, presenting immunosuppressive properties and acting as immune downregulators. In addition, HERV Env proteins have been shown to induce abnormal cell-cell fusion, possibly contributing to tumor development and metastasizing processes. Remarkably, even highly defective HERV env genes and alternative env splicing variants can provide further mechanisms of pathogenesis. A well-known example is the HERV-K(HML2) env gene that, depending on the presence or the absence of a 292-bp deletion, can originate two proteins of different length (Np9 and Rec) proposed to have oncogenic properties. The understanding of their involvement in complex pathological disorders made HERV Env proteins potential targets for therapeutic interventions. Of note, a monoclonal antibody directed against a HERV-W Env is currently under clinical trial as therapeutic approach for multiple sclerosis, representing the first HERV-based treatment. The present review will focus on the current knowledge of the HERV Env expression, summarizing its role in human physiology and its possible pathogenic effects in various cancer and autoimmune disorders. It moreover analyzes HERV Env possible exploitation for the development of innovative therapeutic strategies.
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Affiliation(s)
- Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
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40
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Abstract
Cell-cell fusion is essential for fertilization and organ development. Dedicated proteins known as fusogens are responsible for mediating membrane fusion. However, until recently, these proteins either remained unidentified or were poorly understood at the mechanistic level. Here, we review how fusogens surmount multiple energy barriers to mediate cell-cell fusion. We describe how early preparatory steps bring membranes to a distance of ∼10 nm, while fusogens act in the final approach between membranes. The mechanical force exerted by cell fusogens and the accompanying lipidic rearrangements constitute the hallmarks of cell-cell fusion. Finally, we discuss the relationship between viral and eukaryotic fusogens, highlight a classification scheme regrouping a superfamily of fusogens called Fusexins, and propose new questions and avenues of enquiry.
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Affiliation(s)
- Javier M Hernández
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Benjamin Podbilewicz
- Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
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41
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Vršanský P, OruŘinský R, Aristov D, Wei DD, Vidlička Ľ, Ren D. Temporary deleterious mass mutations relate to originations of cockroach families. Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0096] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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42
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Jangam D, Feschotte C, Betrán E. Transposable Element Domestication As an Adaptation to Evolutionary Conflicts. Trends Genet 2017; 33:817-831. [PMID: 28844698 DOI: 10.1016/j.tig.2017.07.011] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 12/26/2022]
Abstract
Transposable elements (TEs) are selfish genetic units that typically encode proteins that enable their proliferation in the genome and spread across individual hosts. Here we review a growing number of studies that suggest that TE proteins have often been co-opted or 'domesticated' by their host as adaptations to a variety of evolutionary conflicts. In particular, TE-derived proteins have been recurrently repurposed as part of defense systems that protect prokaryotes and eukaryotes against the proliferation of infectious or invasive agents, including viruses and TEs themselves. We argue that the domestication of TE proteins may often be the only evolutionary path toward the mitigation of the cost incurred by their own selfish activities.
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Affiliation(s)
- Diwash Jangam
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA; Present address: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
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43
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Frank JA, Feschotte C. Co-option of endogenous viral sequences for host cell function. Curr Opin Virol 2017; 25:81-89. [PMID: 28818736 DOI: 10.1016/j.coviro.2017.07.021] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/13/2017] [Accepted: 07/23/2017] [Indexed: 01/26/2023]
Abstract
Eukaryotic genomes are littered with sequences of diverse viral origins, termed endogenous viral elements (EVEs). Here we used examples primarily drawn from mammalian endogenous retroviruses to document how the influx of EVEs has provided a source of prefabricated coding and regulatory sequences that were formerly utilized for viral infection and replication, but have been occasionally repurposed for cellular function. While EVE co-option has benefited a variety of host biological functions, there appears to be a disproportionate contribution to immunity and antiviral defense. The mammalian embryo and placenta offer opportunistic routes of viral transmission to the next host generation and as such they represent hotbeds for EVE cooption. Based on these observations, we propose that EVE cooption is initially driven as a mean to mitigate conflicts between host and viruses, which in turn acts as a stepping-stone toward the evolution of cellular innovations serving host physiology and development.
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Affiliation(s)
- John A Frank
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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44
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Abstract
Viruses must establish an intimate relationship with their hosts and vectors in order to infect, replicate, and disseminate; hence, viruses can be considered as symbionts with their hosts. Symbiotic relationships encompass different lifestyles, including antagonistic (or pathogenic, the most well-studied lifestyle for viruses), commensal (probably the most common lifestyle), and mutualistic (important beneficial partners). Symbiotic relationships can shape the evolution of the partners in a holobiont, and placing viruses in this context provides an important framework for understanding virus-host relationships and virus ecology. Although antagonistic relationships are thought to lead to coevolution, this is not always clear in virus-host interactions, and impacts on evolution may be complex. Commensalism implies a hitchhiking role for viruses-selfish elements just along for the ride. Mutualistic relationships have been described in detail in the past decade, and they reveal how important viruses are in considering host ecology. Ultimately, symbiosis can lead to symbiogenesis, or speciation through fusion, and the presence of large amounts of viral sequence in the genomes of everything from bacteria to humans, including some important functional genes, illustrates the significance of viral symbiogenesis in the evolution of all life on Earth.
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Affiliation(s)
- Marilyn J Roossinck
- Center for Infectious Disease Dynamics, Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Edelio R Bazán
- Center for Infectious Disease Dynamics, Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania 16802;
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45
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HEMO, an ancestral endogenous retroviral envelope protein shed in the blood of pregnant women and expressed in pluripotent stem cells and tumors. Proc Natl Acad Sci U S A 2017; 114:E6642-E6651. [PMID: 28739914 DOI: 10.1073/pnas.1702204114] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Capture of retroviral envelope genes is likely to have played a role in the emergence of placental mammals, with evidence for multiple, reiterated, and independent capture events occurring in mammals, and be responsible for the diversity of present day placental structures. Here, we uncover a full-length endogenous retrovirus envelope protein, dubbed HEMO [human endogenous MER34 (medium-reiteration-frequency-family-34) ORF], with unprecedented characteristics, because it is actively shed in the blood circulation in humans via specific cleavage of the precursor envelope protein upstream of the transmembrane domain. At variance with previously identified retroviral envelope genes, its encoding gene is found to be transcribed from a unique CpG-rich promoter not related to a retroviral LTR, with sites of expression including the placenta as well as other tissues and rather unexpectedly, stem cells as well as reprogrammed induced pluripotent stem cells (iPSCs), where the protein can also be detected. We provide evidence that the associated retroviral capture event most probably occurred >100 Mya before the split of Laurasiatheria and Euarchontoglires, with the identified retroviral envelope gene encoding a full-length protein in all simians under purifying selection and with similar shedding capacity. Finally, a comprehensive screen of the expression of the gene discloses high transcript levels in several tumor tissues, such as germ cell, breast, and ovarian tumors, with in the latter case, evidence for a histotype dependence and specific protein expression in clear-cell carcinoma. Altogether, the identified protein could constitute a "stemness marker" of the normal cell and a possible target for immunotherapeutic approaches in tumors.
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46
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Meyer TJ, Rosenkrantz JL, Carbone L, Chavez SL. Endogenous Retroviruses: With Us and against Us. Front Chem 2017; 5:23. [PMID: 28439515 PMCID: PMC5384584 DOI: 10.3389/fchem.2017.00023] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/20/2017] [Indexed: 12/13/2022] Open
Abstract
Mammalian genomes are scattered with thousands of copies of endogenous retroviruses (ERVs), mobile genetic elements that are relics of ancient retroviral infections. After inserting copies into the germ line of a host, most ERVs accumulate mutations that prevent the normal assembly of infectious viral particles, becoming trapped in host genomes and unable to leave to infect other cells. While most copies of ERVs are inactive, some are transcribed and encode the proteins needed to generate new insertions at novel loci. In some cases, old copies are removed via recombination and other mechanisms. This creates a shifting landscape of ERV copies within host genomes. New insertions can disrupt normal expression of nearby genes via directly inserting into key regulatory elements or by containing regulatory motifs within their sequences. Further, the transcriptional silencing of ERVs via epigenetic modification may result in changes to the epigenetic regulation of adjacent genes. In these ways, ERVs can be potent sources of regulatory disruption as well as genetic innovation. Here, we provide a brief review of the association between ERVs and gene expression, especially as observed in pre-implantation development and placentation. Moreover, we will describe how disruption of the regulated mechanisms of ERVs may impact somatic tissues, mostly in the context of human disease, including cancer, neurodegenerative disorders, and schizophrenia. Lastly, we discuss the recent discovery that some ERVs may have been pressed into the service of their host genomes to aid in the innate immune response to exogenous viral infections.
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Affiliation(s)
- Thomas J Meyer
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science UniversityPortland, OR, USA
| | - Jimi L Rosenkrantz
- Department of Molecular and Medical Genetics, Oregon Health & Science UniversityPortland, OR, USA.,Division of Reproductive & Developmental Sciences, Oregon National Primate Research CenterPortland, OR, USA
| | - Lucia Carbone
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science UniversityPortland, OR, USA.,Department of Molecular and Medical Genetics, Oregon Health & Science UniversityPortland, OR, USA.,Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science UniversityPortland, OR, USA
| | - Shawn L Chavez
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research CenterPortland, OR, USA.,Departments of Obstetrics and Gynecology and Physiology and Pharmacology, Oregon Health & Science University School of MedicinePortland, OR, USA
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Cotton JA, Steinbiss S, Yokoi T, Tsai IJ, Kikuchi T. An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus. Sci Rep 2016; 6:39749. [PMID: 28004836 PMCID: PMC5177903 DOI: 10.1038/srep39749] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/28/2016] [Indexed: 12/26/2022] Open
Abstract
Recently, nematode viruses infecting Caenorhabditis elegans have been reported from the family Nodaviridae, the first nematode viruses described. Here, we report the observation of a novel endogenous viral element (EVE) in the genome of Bursaphelenchus xylophilus, a plant parasitic nematode unrelated to other nematodes from which viruses have been characterised. This element derives from a different clade of nodaviruses to the previously reported nematode viruses. This represents the first endogenous nodavirus sequence, the first nematode endogenous viral element, and significantly extends our knowledge of the potential diversity of the Nodaviridae. A search for endogenous elements related to the Nodaviridae did not reveal any elements in other available nematode genomes. Further surveillance for endogenous viral elements is warranted as our knowledge of nematode genome diversity, and in particular of free-living nematodes, expands.
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Affiliation(s)
- James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sascha Steinbiss
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Toshiro Yokoi
- Forestry and Forest Products Research Institute, Tsukuba 305-8687, Japan
| | - Isheng J Tsai
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan.,Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Taisei Kikuchi
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Forestry and Forest Products Research Institute, Tsukuba 305-8687, Japan.,Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
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Genome-Wide Screening of Retroviral Envelope Genes in the Nine-Banded Armadillo (Dasypus novemcinctus, Xenarthra) Reveals an Unfixed Chimeric Endogenous Betaretrovirus Using the ASCT2 Receptor. J Virol 2016; 90:8132-49. [PMID: 27384664 DOI: 10.1128/jvi.00483-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/24/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Retroviruses enter host cells through the interaction of their envelope (Env) protein with a cell surface receptor, which triggers the fusion of viral and cellular membranes. The sodium-dependent neutral amino acid transporter ASCT2 is the common receptor of the large RD114 retrovirus interference group, whose members display frequent env recombination events. Germ line retrovirus infections have led to numerous inherited endogenous retroviruses (ERVs) in vertebrate genomes, which provide useful insights into the coevolutionary history of retroviruses and their hosts. Rare ERV-derived genes display conserved viral functions, as illustrated by the fusogenic syncytin env genes involved in placentation. Here, we searched for functional env genes in the nine-banded armadillo (Dasypus novemcinctus) genome and identified dasy-env1.1, which clusters with RD114 interference group env genes and with two syncytin genes sharing ASCT2 receptor usage. Using ex vivo pseudotyping and cell-cell fusion assays, we demonstrated that the Dasy-Env1.1 protein is fusogenic and can use both human and armadillo ASCT2s as receptors. This gammaretroviral env gene belongs to a provirus with betaretrovirus-like features, suggesting acquisition through recombination. Provirus insertion was found in several Dasypus species, where it has not reached fixation, whereas related family members integrated before diversification of the genus Dasypus >12 million years ago (Mya). This newly described ERV lineage is potentially useful as a population genetic marker. Our results extend the usage of ASCT2 as a retrovirus receptor to the mammalian clade Xenarthra and suggest that the acquisition of an ASCT2-interacting env gene is a major selective force driving the emergence of numerous chimeric viruses in vertebrates. IMPORTANCE Retroviral infection is initiated by the binding of the viral envelope glycoprotein to a host cell receptor(s), triggering membrane fusion. Ancient germ line infections have generated numerous endogenous retroviruses (ERVs) in nearly all vertebrate genomes. Here, we report a previously uncharacterized ERV lineage from the genome of a xenarthran species, the nine-banded armadillo (Dasypus novemcinctus). It entered the Dasypus genus >12 Mya, with one element being inserted more recently in some Dasypus species, where it could serve as a useful marker for population genetics. This element exhibits an env gene, acquired by recombination events, with conserved viral fusogenic properties through binding to ASCT2, a receptor used by a wide range of recombinant retroviruses infecting other vertebrate orders. This specifies the ASCT2 transporter as a successful receptor for ERV endogenization and suggests that ASCT2-binding env acquisition events have favored the emergence of numerous chimeric viruses in a wide range of species.
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Soygur B, Sati L. The role of syncytins in human reproduction and reproductive organ cancers. Reproduction 2016; 152:R167-78. [PMID: 27486264 DOI: 10.1530/rep-16-0031] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 08/01/2016] [Indexed: 12/29/2022]
Abstract
Human life begins with sperm and oocyte fusion. After fertilization, various fusion events occur during human embryogenesis and morphogenesis. For example, the fusion of trophoblastic cells constitutes a key process for normal placental development. Fusion in the placenta is facilitated by syncytin 1 and syncytin 2. These syncytins arose from retroviral sequences that entered the primate genome 25 million and more than 40 million years ago respectively. About 8% of the human genome consists of similar human endogenous retroviral (HERVs) sequences. Many are inactive because of mutations or deletions. However, the role of the few that remain transcriptionally active has not been fully elucidated. Syncytin proteins maintain cell-cell fusogenic activity based on ENV: gene-mediated viral cell entry. In this review, we summarize how syncytins and their receptors are involved in fusion events during human reproduction. The significance of syncytins in tumorigenesis is also discussed.
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Affiliation(s)
- Bikem Soygur
- Department of Histology and EmbryologyAkdeniz University School of Medicine, Antalya, Turkey
| | - Leyla Sati
- Department of Histology and EmbryologyAkdeniz University School of Medicine, Antalya, Turkey
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50
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McLysaght A, Hurst LD. Open questions in the study of de novo genes: what, how and why. Nat Rev Genet 2016; 17:567-78. [PMID: 27452112 DOI: 10.1038/nrg.2016.78] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The study of de novo protein-coding genes is maturing from the ad hoc reporting of individual cases to the systematic analysis of extensive genomic data from several species. We identify three key challenges for this emerging field: understanding how best to identify de novo genes, how they arise and why they spread. We highlight the intellectual challenges of understanding how a de novo gene becomes integrated into pre-existing functions and becomes essential. We suggest that, as with protein sequence evolution, antagonistic co-evolution may be key to de novo gene evolution, particularly for new essential genes and new cancer-associated genes.
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Affiliation(s)
- Aoife McLysaght
- The Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset BA2 7AY, UK
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