1
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Abalde S, Tellgren-Roth C, Heintz J, Vinnere Pettersson O, Jondelius U. The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes. Front Genet 2023; 14:1244493. [PMID: 37829276 PMCID: PMC10565955 DOI: 10.3389/fgene.2023.1244493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Background: Xenacoelomorpha is a marine clade of microscopic worms that is an important model system for understanding the evolution of key bilaterian novelties, such as the excretory system. Nevertheless, Xenacoelomorpha genomics has been restricted to a few species that either can be cultured in the lab or are centimetres long. Thus far, no genomes are available for Nemertodermatida, one of the group's main clades and whose origin has been dated more than 400 million years ago. Methods: DNA was extracted from a single specimen and sequenced with HiFi following the PacBio Ultra-Low DNA Input protocol. After genome assembly, decontamination, and annotation, the genome quality was benchmarked using two acoel genomes and one Illumina genome as reference. The gene content of three cnidarians, three acoelomorphs, four deuterostomes, and eight protostomes was clustered in orthogroups to make inferences of gene content evolution. Finally, we focused on the genes related to the ultrafiltration excretory system to compare patterns of presence/absence and gene architecture among these clades. Results: We present the first nemertodermatid genome sequenced from a single specimen of Nemertoderma westbladi. Although genome contiguity remains challenging (N50: 60 kb), it is very complete (BUSCO: 80.2%, Metazoa; 88.6%, Eukaryota) and the quality of the annotation allows fine-detail analyses of genome evolution. Acoelomorph genomes seem to be relatively conserved in terms of the percentage of repeats, number of genes, number of exons per gene and intron size. In addition, a high fraction of genes present in both protostomes and deuterostomes are absent in Acoelomorpha. Interestingly, we show that all genes related to the excretory system are present in Xenacoelomorpha except Osr, a key element in the development of these organs and whose acquisition seems to be interconnected with the origin of the specialised excretory system. Conclusion: Overall, these analyses highlight the potential of the Ultra-Low Input DNA protocol and HiFi to generate high-quality genomes from single animals, even for relatively large genomes, making it a feasible option for sequencing challenging taxa, which will be an exciting resource for comparative genomics analyses.
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Affiliation(s)
- Samuel Abalde
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Christian Tellgren-Roth
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Julia Heintz
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Ulf Jondelius
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
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2
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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: 2.0] [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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3
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Nakka K, Hachmer S, Mokhtari Z, Kovac R, Bandukwala H, Bernard C, Li Y, Xie G, Liu C, Fallahi M, Megeney LA, Gondin J, Chazaud B, Brand M, Zha X, Ge K, Dilworth FJ. JMJD3 activated hyaluronan synthesis drives muscle regeneration in an inflammatory environment. Science 2022; 377:666-669. [PMID: 35926054 DOI: 10.1126/science.abm9735] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Muscle stem cells (MuSCs) reside in a specialized niche that ensures their regenerative capacity. Although we know that innate immune cells infiltrate the niche in response to injury, it remains unclear how MuSCs adapt to this altered environment for initiating repair. Here, we demonstrate that inflammatory cytokine signaling from the regenerative niche impairs the ability of quiescent MuSCs to reenter the cell cycle. The histone H3 lysine 27 (H3K27) demethylase JMJD3, but not UTX, allowed MuSCs to overcome inhibitory inflammation signaling by removing trimethylated H3K27 (H3K27me3) marks at the Has2 locus to initiate production of hyaluronic acid, which in turn established an extracellular matrix competent for integrating signals that direct MuSCs to exit quiescence. Thus, JMJD3-driven hyaluronic acid synthesis plays a proregenerative role that allows MuSC adaptation to inflammation and the initiation of muscle repair.
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Affiliation(s)
- Kiran Nakka
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Sarah Hachmer
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Zeinab Mokhtari
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Radmila Kovac
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hina Bandukwala
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Clara Bernard
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS 5261, INSERM U1315, Université de Lyon, Lyon, France
| | - Yuefeng Li
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Guojia Xie
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chengyu Liu
- Transgenic Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Magid Fallahi
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Lynn A Megeney
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Julien Gondin
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS 5261, INSERM U1315, Université de Lyon, Lyon, France
| | - Bénédicte Chazaud
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS 5261, INSERM U1315, Université de Lyon, Lyon, France
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,LIFE Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Xiaohui Zha
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,LIFE Research Institute, University of Ottawa, Ottawa, ON, Canada
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4
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Andrews SV, Yang IJ, Froehlich K, Oskotsky T, Sirota M. Large-scale placenta DNA methylation integrated analysis reveals fetal sex-specific differentially methylated CpG sites and regions. Sci Rep 2022; 12:9396. [PMID: 35672357 PMCID: PMC9174475 DOI: 10.1038/s41598-022-13544-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/17/2022] [Indexed: 11/14/2022] Open
Abstract
Although male–female differences in placental structure and function have been observed, little is understood about their molecular underpinnings. Here, we present a mega-analysis of 14 publicly available placenta DNA methylation (DNAm) microarray datasets to identify individual CpGs and regions associated with fetal sex. In the discovery dataset of placentas from full term pregnancies (N = 532 samples), 5212 CpGs met genome-wide significance (p < 1E−8) and were enriched in pathways such as keratinization (FDR p-value = 7.37E−14), chemokine activity (FDR p-value = 1.56E−2), and eosinophil migration (FDR p-value = 1.83E−2). Nine differentially methylated regions were identified (fwerArea < 0.1) including a region in the promoter of ZNF300 that showed consistent differential DNAm in samples from earlier timepoints in pregnancy and appeared to be driven predominately by effects in the trophoblast cell type. We describe the largest study of fetal sex differences in placenta DNAm performed to date, revealing genes and pathways characterizing sex-specific placenta function and health outcomes later in life.
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Affiliation(s)
- Shan V Andrews
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Irene J Yang
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA.,Dougherty Valley High School, San Ramon, CA, USA
| | - Karolin Froehlich
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA. .,Department of Pediatrics, UCSF, San Francisco, CA, USA.
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, UCSF, San Francisco, CA, USA. .,Department of Pediatrics, UCSF, San Francisco, CA, USA.
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5
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Kozlov AP. Mammalian tumor-like organs. 1. The role of tumor-like normal organs and atypical tumor organs in the evolution of development (carcino-evo-devo). Infect Agent Cancer 2022; 17:2. [PMID: 35012580 PMCID: PMC8751115 DOI: 10.1186/s13027-021-00412-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Earlier I hypothesized that hereditary tumors might participate in the evolution of multicellular organisms. I formulated the hypothesis of evolution by tumor neofunctionalization, which suggested that the evolutionary role of hereditary tumors might consist in supplying evolving multicellular organisms with extra cell masses for the expression of evolutionarily novel genes and the origin of new cell types, tissues, and organs. A new theory—the carcino-evo-devo theory—has been developed based on this hypothesis. Main text My lab has confirmed several non-trivial predictions of this theory. Another non-trivial prediction is that evolutionarily new organs if they originated from hereditary tumors or tumor-like structures, should recapitulate some tumor features in their development. This paper reviews the tumor-like features of evolutionarily novel organs. It turns out that evolutionarily new organs such as the eutherian placenta, mammary gland, prostate, the infantile human brain, and hoods of goldfishes indeed have many features of tumors. I suggested calling normal organs, which have many tumor features, the tumor-like organs. Conclusion Tumor-like organs might originate from hereditary atypical tumor organs and represent the part of carcino-evo-devo relationships, i.e., coevolution of normal and neoplastic development. During subsequent evolution, tumor-like organs may lose the features of tumors and the high incidence of cancer and become normal organs without (or with almost no) tumor features.
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Affiliation(s)
- A P Kozlov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3, Gubkina Street, Moscow, Russia, 117971. .,Peter the Great St. Petersburg Polytechnic University, 29, Polytekhnicheskaya Street, St. Petersburg, Russia, 195251.
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6
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Hao Y, Lee HJ, Baraboo M, Burch K, Maurer T, Somarelli JA, Conant GC. Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation. Genome Biol Evol 2021; 12:35-47. [PMID: 32053193 PMCID: PMC7144826 DOI: 10.1093/gbe/evaa026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2020] [Indexed: 12/12/2022] Open
Abstract
It has long been challenging to uncover the molecular mechanisms behind striking morphological innovations such as mammalian pregnancy. We studied the power of a robust comparative orthology pipeline based on gene synteny to address such problems. We inferred orthology relations between human genes and genes from each of 43 other vertebrate genomes, resulting in ∼18,000 orthologous pairs for each genome comparison. By identifying genes that first appear coincident with origin of the placental mammals, we hypothesized that we would define a subset of the genome enriched for genes that played a role in placental evolution. We thus pinpointed orthologs that appeared before and after the divergence of eutherian mammals from marsupials. Reinforcing previous work, we found instead that much of the genetic toolkit of mammalian pregnancy evolved through the repurposing of preexisting genes to new roles. These genes acquired regulatory controls for their novel roles from a group of regulatory genes, many of which did in fact originate at the appearance of the eutherians. Thus, orthologs appearing at the origin of the eutherians are enriched in functions such as transcriptional regulation by Krüppel-associated box-zinc-finger proteins, innate immune responses, keratinization, and the melanoma-associated antigen protein class. Because the cellular mechanisms of invasive placentae are similar to those of metastatic cancers, we then used our orthology inferences to explore the association between placenta invasion and cancer metastasis. Again echoing previous work, we find that genes that are phylogenetically older are more likely to be implicated in cancer development.
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Affiliation(s)
- Yue Hao
- Bioinformatics Research Center, North Carolina State University
| | - Hyuk Jin Lee
- Division of Biological Sciences, University of Missouri-Columbia
| | | | | | | | - Jason A Somarelli
- Duke Cancer Institute, Duke University Medical Center.,Department of Medicine, Duke University School of Medicine
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University.,Division of Animal Sciences, University of Missouri-Columbia.,Program in Genetics, North Carolina State University.,Department of Biological Sciences, North Carolina State University
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7
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Franchini LF. Genetic Mechanisms Underlying Cortical Evolution in Mammals. Front Cell Dev Biol 2021; 9:591017. [PMID: 33659245 PMCID: PMC7917222 DOI: 10.3389/fcell.2021.591017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
The remarkable sensory, motor, and cognitive abilities of mammals mainly depend on the neocortex. Thus, the emergence of the six-layered neocortex in reptilian ancestors of mammals constitutes a fundamental evolutionary landmark. The mammalian cortex is a columnar epithelium of densely packed cells organized in layers where neurons are generated mainly in the subventricular zone in successive waves throughout development. Newborn cells move away from their site of neurogenesis through radial or tangential migration to reach their specific destination closer to the pial surface of the same or different cortical area. Interestingly, the genetic programs underlying neocortical development diversified in different mammalian lineages. In this work, I will review several recent studies that characterized how distinct transcriptional programs relate to the development and functional organization of the neocortex across diverse mammalian lineages. In some primates such as the anthropoids, the neocortex became extremely large, especially in humans where it comprises around 80% of the brain. It has been hypothesized that the massive expansion of the cortical surface and elaboration of its connections in the human lineage, has enabled our unique cognitive capacities including abstract thinking, long-term planning, verbal language and elaborated tool making capabilities. I will also analyze the lineage-specific genetic changes that could have led to the modification of key neurodevelopmental events, including regulation of cell number, neuronal migration, and differentiation into specific phenotypes, in order to shed light on the evolutionary mechanisms underlying the diversity of mammalian brains including the human brain.
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Affiliation(s)
- Lucía Florencia Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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8
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Florke Gee RR, Chen H, Lee AK, Daly CA, Wilander BA, Fon Tacer K, Potts PR. Emerging roles of the MAGE protein family in stress response pathways. J Biol Chem 2020; 295:16121-16155. [PMID: 32921631 PMCID: PMC7681028 DOI: 10.1074/jbc.rev120.008029] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
The melanoma antigen (MAGE) proteins all contain a MAGE homology domain. MAGE genes are conserved in all eukaryotes and have expanded from a single gene in lower eukaryotes to ∼40 genes in humans and mice. Whereas some MAGEs are ubiquitously expressed in tissues, others are expressed in only germ cells with aberrant reactivation in multiple cancers. Much of the initial research on MAGEs focused on exploiting their antigenicity and restricted expression pattern to target them with cancer immunotherapy. Beyond their potential clinical application and role in tumorigenesis, recent studies have shown that MAGE proteins regulate diverse cellular and developmental pathways, implicating them in many diseases besides cancer, including lung, renal, and neurodevelopmental disorders. At the molecular level, many MAGEs bind to E3 RING ubiquitin ligases and, thus, regulate their substrate specificity, ligase activity, and subcellular localization. On a broader scale, the MAGE genes likely expanded in eutherian mammals to protect the germline from environmental stress and aid in stress adaptation, and this stress tolerance may explain why many cancers aberrantly express MAGEs Here, we present an updated, comprehensive review on the MAGE family that highlights general characteristics, emphasizes recent comparative studies in mice, and describes the diverse functions exerted by individual MAGEs.
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Affiliation(s)
- Rebecca R Florke Gee
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Helen Chen
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anna K Lee
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christina A Daly
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Benjamin A Wilander
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Klementina Fon Tacer
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; School of Veterinary Medicine, Texas Tech University, Amarillo, Texas, USA.
| | - Patrick Ryan Potts
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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9
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Heger P, Zheng W, Rottmann A, Panfilio KA, Wiehe T. The genetic factors of bilaterian evolution. eLife 2020; 9:e45530. [PMID: 32672535 PMCID: PMC7535936 DOI: 10.7554/elife.45530] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo-Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship.
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Affiliation(s)
- Peter Heger
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Wen Zheng
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Anna Rottmann
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, Cologne Biocenter, University of CologneCologneGermany
- School of Life Sciences, University of Warwick, Gibbet Hill CampusCoventryUnited Kingdom
| | - Thomas Wiehe
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
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10
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McCartney AM, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez-Rodriguez J, Prado-Martinez J, Creevey CJ, Aspden JL, McInerney JO, Marques-Bonet T, O'Connell MJ. Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human. Genome Biol Evol 2020; 11:2678-2690. [PMID: 31400206 PMCID: PMC6764479 DOI: 10.1093/gbe/evz163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 12/14/2022] Open
Abstract
Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. We use Sequence Similarity Networks and species level comparisons of great ape genomes to identify 45 new genes that have emerged by transcriptional readthrough, that is, transcription-derived gene fusion. For 35 of these putative gene fusions, we have been able to assess available RNAseq data to determine whether there are reads that map to each breakpoint. A total of 29 of the putative gene fusions had annotated transcripts (9/29 of which are human-specific). We carried out RT-qPCR in a range of human tissues (placenta, lung, liver, brain, and testes) and found that 23 of the putative gene fusion events were expressed in at least one tissue. Examining the available ribosome foot-printing data, we find evidence for translation of three of the fused genes in human. Finally, we find enrichment for transcription-derived gene fusions in regions of known segmental duplication in human. Together, our results implicate chromosomal structural variation brought about by segmental duplication with the emergence of novel transcripts and translated protein products.
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Affiliation(s)
- Ann M McCartney
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
| | - Edel M Hyland
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Institute for Global Food Security, Queens University Belfast, United Kingdom
| | - Paul Cormican
- Teagasc Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland
| | - Raymond J Moran
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
| | - Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland
| | - Kate D Lee
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,School of Biological Sciences, University of Auckland, New Zealand.,School of Fundamental Sciences, Massey University, New Zealand
| | | | - Javier Prado-Martinez
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Christopher J Creevey
- Institute for Global Food Security, Queens University Belfast, United Kingdom.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom
| | - James O McInerney
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL, United Kingdom.,School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, NG7 2RD, United Kingdom
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain.,NAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.,Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom.,School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, NG7 2RD, United Kingdom
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11
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Guijarro-Clarke C, Holland PWH, Paps J. Widespread patterns of gene loss in the evolution of the animal kingdom. Nat Ecol Evol 2020; 4:519-523. [PMID: 32094540 DOI: 10.1038/s41559-020-1129-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 01/28/2020] [Indexed: 11/09/2022]
Abstract
The animal kingdom shows an astonishing diversity, the product of over 550 million years of animal evolution. The current wealth of genome sequence data offers an opportunity to better understand the genomic basis of this diversity. Here we analyse a sampling of 102 whole genomes including >2.6 million protein sequences. We infer major genomic patterns associated with the variety of animal forms from the superphylum to phylum level. We show that a remarkable amount of gene loss occurred during the evolution of two major groups of bilaterian animals, Ecdysozoa and Deuterostomia, and further loss in several deuterostome lineages. Deuterostomes and protostomes also show large genome novelties. At the phylum level, flatworms, nematodes and tardigrades show the largest reduction of gene complement, alongside gene novelty. These findings paint a picture of evolution in the animal kingdom in which reductive evolution at the protein-coding level played a major role in shaping genome composition.
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Affiliation(s)
| | | | - Jordi Paps
- School of Biological Sciences, University of Essex, Colchester, UK. .,Department of Zoology, University of Oxford, Oxford, UK. .,School of Biological Sciences, University of Bristol, Bristol, UK.
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12
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The Origin of Land Plants Is Rooted in Two Bursts of Genomic Novelty. Curr Biol 2020; 30:530-536.e2. [DOI: 10.1016/j.cub.2019.11.090] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/15/2019] [Accepted: 11/29/2019] [Indexed: 12/22/2022]
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13
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Kozlov AP. The Role of Heritable Tumors in Evolution of Development: a New Theory of Carcino-evo-devo. Acta Naturae 2019; 11:65-72. [PMID: 31993236 PMCID: PMC6977963 DOI: 10.32607/20758251-2019-11-4-65-72] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/06/2019] [Indexed: 02/04/2023] Open
Abstract
The hypothesis of evolution by tumor neofunctionalization (the "main hypothesis") describes the possible role of hereditary tumors in evolution. The present article examines the relationship of the main hypothesis to other biological theories. As shown in this paper, the main hypothesis does not contradict to the existing biological theories, but fills the lacunas between them and explains some unexplained (or not completely understood) questions. Common features of embryonic development and tumorigenesis are described by several recognized theories. Similarities between normal development and tumorigenesis suggest that tumors could participate in the evolution of ontogenesis and in the origin of new cell types, tissues and organs. A wide spectrum of non-trivial explanations and non-trivial predictions in different fields of biology, suggested by the main hypothesis, is an indication of its fundamental nature and the potential to become a new biological theory, a theory of the role of tumors in evolution of development, or carcino-evo-devo.
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Affiliation(s)
- A. P. Kozlov
- Vavilov Institute of General Genetics RAS, Moscow, 119333 Russia Biomedical Center, Research Institute of Ultrapure Biologicals and Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251 Russia
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14
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Moon JM, Capra JA, Abbot P, Rokas A. Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation. Bioessays 2019; 41:e1900072. [PMID: 31373044 DOI: 10.1002/bies.201900072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/03/2019] [Indexed: 11/05/2022]
Abstract
Novel regulatory elements that enabled expression of pre-existing immune genes in reproductive tissues and novel immune genes with pregnancy-specific roles in eutherians have shaped the evolution of mammalian pregnancy by facilitating the emergence of novel mechanisms for immune regulation over its course. Trade-offs arising from conflicting fitness effects on reproduction and host defenses have further influenced the patterns of genetic variation of these genes. These three mechanisms (novel regulatory elements, novel immune genes, and trade-offs) played a pivotal role in refining the regulation of maternal immune systems during pregnancy in eutherians, likely facilitating the establishment of prolonged direct maternal-fetal contact in eutherians without causing immunological rejection of the genetically distinct fetus.
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Affiliation(s)
- Jiyun M Moon
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, 37235, USA.,Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Patrick Abbot
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.,Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, 37235, USA.,Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37235, USA
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15
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Fon Tacer K, Montoya MC, Oatley MJ, Lord T, Oatley JM, Klein J, Ravichandran R, Tillman H, Kim M, Connelly JP, Pruett-Miller SM, Bookout AL, Binshtock E, Kamiński MM, Potts PR. MAGE cancer-testis antigens protect the mammalian germline under environmental stress. SCIENCE ADVANCES 2019; 5:eaav4832. [PMID: 31149633 PMCID: PMC6541465 DOI: 10.1126/sciadv.aav4832] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 04/17/2019] [Indexed: 05/17/2023]
Abstract
Ensuring robust gamete production even in the face of environmental stress is of utmost importance for species survival, especially in mammals that have low reproductive rates. Here, we describe a family of genes called melanoma antigens (MAGEs) that evolved in eutherian mammals and are normally restricted to expression in the testis (http://MAGE.stjude.org) but are often aberrantly activated in cancer. Depletion of Mage-a genes disrupts spermatogonial stem cell maintenance and impairs repopulation efficiency in vivo. Exposure of Mage-a knockout mice to genotoxic stress or long-term starvation that mimics famine in nature causes defects in spermatogenesis, decreased testis weights, diminished sperm production, and reduced fertility. Last, human MAGE-As are activated in many cancers where they promote fuel switching and growth of cells. These results suggest that mammalian-specific MAGE genes have evolved to protect the male germline against environmental stress, ensure reproductive success under non-optimal conditions, and are hijacked by cancer cells.
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Affiliation(s)
- Klementina Fon Tacer
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Marhiah C. Montoya
- Clinical & Translational Science Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Departments of Pediatrics, Microbiology and Immunology, Carver College of Medicine, University of Iowa, IA, USA
| | - Melissa J. Oatley
- Center for Reproductive Biology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Tessa Lord
- Center for Reproductive Biology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Jon M. Oatley
- Center for Reproductive Biology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Jonathon Klein
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Ramya Ravichandran
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Heather Tillman
- Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - MinSoo Kim
- Departments of Internal Medicine and Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jon P. Connelly
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | - Angie L. Bookout
- Department of Internal Medicine, Division of Hypothalamic Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emily Binshtock
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Marcin M. Kamiński
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Patrick Ryan Potts
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Corresponding author.
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16
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Paps J. What Makes an Animal? The Molecular Quest for the Origin of the Animal Kingdom. Integr Comp Biol 2018; 58:654-665. [DOI: 10.1093/icb/icy036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jordi Paps
- School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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17
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Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty. Nat Commun 2018; 9:1730. [PMID: 29712911 PMCID: PMC5928047 DOI: 10.1038/s41467-018-04136-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/28/2018] [Indexed: 12/03/2022] Open
Abstract
Understanding the emergence of the Animal Kingdom is one of the major challenges of modern evolutionary biology. Many genomic changes took place along the evolutionary lineage that gave rise to the Metazoa. Recent research has revealed the role that co-option of old genes played during this transition, but the contribution of genomic novelty has not been fully assessed. Here, using extensive genome comparisons between metazoans and multiple outgroups, we infer the minimal protein-coding genome of the first animal, in addition to other eukaryotic ancestors, and estimate the proportion of novelties in these ancient genomes. Contrary to the prevailing view, this uncovers an unprecedented increase in the extent of genomic novelty during the origin of metazoans, and identifies 25 groups of metazoan-specific genes that are essential across the Animal Kingdom. We argue that internal genomic changes were as important as external factors in the emergence of animals. Animals, the Metazoa, co-opted numerous unicellular genes in their transition to multicellularity. Here, the authors use phylogenomic analyses to infer the genome composition of the ancestor of extant animals and show there was also a burst of novel gene groups associated with this transition.
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