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Agostinho de Sousa J, Wong CW, Dunkel I, Owens T, Voigt P, Hodgson A, Baker D, Schulz EG, Reik W, Smith A, Rostovskaya M, von Meyenn F. Epigenetic dynamics during capacitation of naïve human pluripotent stem cells. SCIENCE ADVANCES 2023; 9:eadg1936. [PMID: 37774033 PMCID: PMC10541016 DOI: 10.1126/sciadv.adg1936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are of fundamental relevance in regenerative medicine. Naïve hPSCs hold promise to overcome some of the limitations of conventional (primed) hPSCs, including recurrent epigenetic anomalies. Naïve-to-primed transition (capacitation) follows transcriptional dynamics of human embryonic epiblast and is necessary for somatic differentiation from naïve hPSCs. We found that capacitated hPSCs are transcriptionally closer to postimplantation epiblast than conventional hPSCs. This prompted us to comprehensively study epigenetic and related transcriptional changes during capacitation. Our results show that CpG islands, gene regulatory elements, and retrotransposons are hotspots of epigenetic dynamics during capacitation and indicate possible distinct roles of specific epigenetic modifications in gene expression control between naïve and primed hPSCs. Unexpectedly, PRC2 activity appeared to be dispensable for the capacitation. We find that capacitated hPSCs acquire an epigenetic state similar to conventional hPSCs. Significantly, however, the X chromosome erosion frequently observed in conventional female hPSCs is reversed by resetting and subsequent capacitation.
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Affiliation(s)
- João Agostinho de Sousa
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | - Chee-Wai Wong
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
| | - Ilona Dunkel
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Thomas Owens
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Philipp Voigt
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Adam Hodgson
- School of Biosciences, The Julia Garnham Centre, University of Sheffield, S10 2TN Sheffield, UK
| | - Duncan Baker
- Sheffield Diagnostic Genetics Services, Sheffield Children’s NHS Foundation Trust, S5 7AU Sheffield, UK
| | - Edda G. Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1QR, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Altos Labs Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Austin Smith
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Living Systems Institute, University of Exeter, EX4 4QD Exeter, UK
| | - Maria Rostovskaya
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, 8603 Schwerzenbach, Switzerland
- Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, SE1 9RT London, UK
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7
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Loaeza-Loaeza J, Cerecedo-Castillo AJ, Rodríguez-Ruiz HA, Castro-Coronel Y, Del Moral-Hernández O, Recillas-Targa F, Hernández-Sotelo D. DNMT3B overexpression downregulates genes with CpG islands, common motifs, and transcription factor binding sites that interact with DNMT3B. Sci Rep 2022; 12:20839. [PMID: 36460706 PMCID: PMC9718745 DOI: 10.1038/s41598-022-24186-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022] Open
Abstract
DNA methylation is a key epigenetic modification to regulate gene expression in mammalian cells. Abnormal DNA methylation in gene promoters is common across human cancer types. DNMT3B is the main de novo methyltransferase enhanced in several primary tumors. How de novo methylation is established in genes related to cancer is poorly understood. CpG islands (CGIs), common sequences, and transcription factors (TFs) that interact with DNMT3B have been associated with abnormal de novo methylation. We initially identified cis elements associated with DNA methylation to investigate the contribution of DNMT3B overexpression to the deregulation of its possible target genes in an epithelial cell model. In a set of downregulated genes (n = 146) from HaCaT cells with DNMT3B overexpression, we found CGI, common sequences, and TFs Binding Sites that interact with DNMT3B (we called them P-down-3B). PPL1, VAV3, IRF1, and BRAF are P-down-3B genes that are downregulated and increased their methylation in DNMT3B presence. Together these findings suggest that methylated promoters aberrantly have some cis elements that could conduce de novo methylation by DNMT3B.
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Affiliation(s)
- Jaqueline Loaeza-Loaeza
- grid.412856.c0000 0001 0699 2934Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070 Chilpancingo, Guerrero Mexico
| | - Angel Josué Cerecedo-Castillo
- grid.9486.30000 0001 2159 0001Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Hugo Alberto Rodríguez-Ruiz
- grid.412856.c0000 0001 0699 2934Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070 Chilpancingo, Guerrero Mexico
| | - Yaneth Castro-Coronel
- grid.412856.c0000 0001 0699 2934Laboratorio de Citopatología e Inmunohistoquímica, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070 Chilpancingo, Guerrero Mexico
| | - Oscar Del Moral-Hernández
- grid.412856.c0000 0001 0699 2934Laboratorio de Virus y Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070 Chilpancingo, Guerrero Mexico
| | - Félix Recillas-Targa
- grid.9486.30000 0001 2159 0001Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Daniel Hernández-Sotelo
- grid.412856.c0000 0001 0699 2934Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070 Chilpancingo, Guerrero Mexico
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8
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Leitão E, Schröder C, Parenti I, Dalle C, Rastetter A, Kühnel T, Kuechler A, Kaya S, Gérard B, Schaefer E, Nava C, Drouot N, Engel C, Piard J, Duban-Bedu B, Villard L, Stegmann APA, Vanhoutte EK, Verdonschot JAJ, Kaiser FJ, Tran Mau-Them F, Scala M, Striano P, Frints SGM, Argilli E, Sherr EH, Elder F, Buratti J, Keren B, Mignot C, Héron D, Mandel JL, Gecz J, Kalscheuer VM, Horsthemke B, Piton A, Depienne C. Systematic analysis and prediction of genes associated with monogenic disorders on human chromosome X. Nat Commun 2022; 13:6570. [PMID: 36323681 PMCID: PMC9630267 DOI: 10.1038/s41467-022-34264-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Disease gene discovery on chromosome (chr) X is challenging owing to its unique modes of inheritance. We undertook a systematic analysis of human chrX genes. We observe a higher proportion of disorder-associated genes and an enrichment of genes involved in cognition, language, and seizures on chrX compared to autosomes. We analyze gene constraints, exon and promoter conservation, expression, and paralogues, and report 127 genes sharing one or more attributes with known chrX disorder genes. Using machine learning classifiers trained to distinguish disease-associated from dispensable genes, we classify 247 genes, including 115 of the 127, as having high probability of being disease-associated. We provide evidence of an excess of variants in predicted genes in existing databases. Finally, we report damaging variants in CDK16 and TRPC5 in patients with intellectual disability or autism spectrum disorders. This study predicts large-scale gene-disease associations that could be used for prioritization of X-linked pathogenic variants.
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Affiliation(s)
- Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Christopher Schröder
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ilaria Parenti
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Carine Dalle
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Agnès Rastetter
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Theresa Kühnel
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Sabine Kaya
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Bénédicte Gérard
- Unité de Génétique Moléculaire, IGMA, Hôpitaux Universitaire de Strasbourg, Strasbourg, France
| | - Elise Schaefer
- Service de Génétique Médicale, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Caroline Nava
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
| | - Nathalie Drouot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France
- Université de Strasbourg, Illkirch, 67400, France
| | - Camille Engel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France
- Université de Strasbourg, Illkirch, 67400, France
| | - Juliette Piard
- Centre de Génétique Humaine, CHU Besançon, Besançon, France
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement, Université de Bourgogne-Franche-Comté, Dijon, France
| | | | - Laurent Villard
- Aix-Marseille University, INSERM, MMG, UMR-S 1251, Faculté de médecine, Marseille, France
- Département de Génétique Médicale, APHM, Hôpital d'Enfants de La Timone, Marseille, France
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Els K Vanhoutte
- Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Job A J Verdonschot
- Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, The Netherlands
- Cardiovascular Research Institute (CARIM), Departments of Cardiology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Frédéric Tran Mau-Them
- INSERM UMR1231, Equipe Génétique des Anomalies du Développement, Université de Bourgogne-Franche-Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Suzanna G M Frints
- Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, The Netherlands
- Department of Genetics and Cell Biology, Faculty of Health Medicine Life Sciences, Maastricht University Medical Center+, Maastricht University, Maastricht, The Netherlands
| | - Emanuela Argilli
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Fikret Elder
- UF de Génomique du Développement, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France
| | - Julien Buratti
- UF de Génomique du Développement, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France
| | - Boris Keren
- UF de Génomique du Développement, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France
| | - Cyril Mignot
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013, Paris, France
- APHP, Sorbonne Université, Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière and Hôpital Trousseau, Paris, France
| | - Delphine Héron
- APHP, Sorbonne Université, Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière and Hôpital Trousseau, Paris, France
| | - Jean-Louis Mandel
- Unité de Génétique Moléculaire, IGMA, Hôpitaux Universitaire de Strasbourg, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France
- Université de Strasbourg, Illkirch, 67400, France
| | - Jozef Gecz
- School of Medicine, The University of Adelaide, Adelaide, 5005, SA, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5006, Australia
- South Australian Health and Medical Research Institute, The University of Adelaide, Adelaide, 5005, SA, Australia
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Amélie Piton
- Unité de Génétique Moléculaire, IGMA, Hôpitaux Universitaire de Strasbourg, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France
- Université de Strasbourg, Illkirch, 67400, France
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
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