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da Silva Santos R, Pascoalino Pinheiro D, Gustavo Hirth C, Barbosa Bezerra MJ, Joyce de Lima Silva-Fernandes I, Andréa da Silva Oliveira F, Viana de Holanda Barros M, Silveira Ramos E, A. Moura A, Filho ODMM, Pessoa C, Miranda Furtado CL. Hypomethylation at H19DMR in penile squamous cell carcinoma is not related to HPV infection. Epigenetics 2024; 19:2305081. [PMID: 38245880 PMCID: PMC10802203 DOI: 10.1080/15592294.2024.2305081] [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: 08/09/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Penile squamous cell carcinoma (SCC) is a rare and aggressive tumour mainly related to lifestyle behaviour and human papillomavirus (HPV) infection. Environmentally induced loss of imprinting (LOI) at the H19 differentially methylated region (H19DMR) is associated with many cancers in the early events of tumorigenesis and may be involved in the pathogenesis of penile SCC. We sought to evaluate the DNA methylation pattern at H19DMR and its association with HPV infection in men with penile SCC by bisulfite sequencing (bis-seq). We observed an average methylation of 32.2% ± 11.6% at the H19DMR of penile SCC and did not observe an association between the p16INK4a+ (p = 0.59) and high-risk HPV+ (p = 0.338) markers with methylation level. The average methylation did not change according to HPV positive for p16INK4a+ or hrHPV+ (35.4% ± 10%) and negative for both markers (32.4% ± 10.1%) groups. As the region analysed has a binding site for the CTCF protein, the hypomethylation at the surrounding CpG sites might alter its insulator function. In addition, there was a positive correlation between intense polymorphonuclear cell infiltration and hypomethylation at H19DMR (p = 0.035). Here, we report that hypomethylation at H19DMR in penile SCC might contribute to tumour progression and aggressiveness regardless of HPV infection.
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Affiliation(s)
- Renan da Silva Santos
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | | | | | | | | | - Maisa Viana de Holanda Barros
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Ester Silveira Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Arlindo A. Moura
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Animal Science, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Odorico de Moraes Manoel Filho
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Claudia Pessoa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Cristiana Libardi Miranda Furtado
- Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Experimental Biology Center, University of Fortaleza, Fortaleza, Ceará, Brazil
- Graduate Program in Medical Sciences, Universidade de Fortaleza, Fortaleza, Ceará, Brazil
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2
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Smith LC, Paredes LA, Sampaio RV, Nociti RP, Therrien J, Meirelles FV. Haploid embryos and embryonic stem cells to produce offspring with predetermined parental genomes in cattle. Anim Reprod 2024; 21:e20240030. [PMID: 39175994 PMCID: PMC11340792 DOI: 10.1590/1984-3143-ar2024-0030] [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: 03/18/2024] [Accepted: 05/13/2024] [Indexed: 08/24/2024] Open
Abstract
Selection strategies are performed post-fertilization when the random combination of paternal and maternal genomes has already occurred. It would be greatly advantageous to eliminate meiotic uncertainty by selecting genetically superior gametes before fertilization. To achieve this goal, haploid embryonic cells and embryonic stem cell lineages could be derived, genotyped, and used to substitute gametes. On the paternal side, androgenetic development can be achieved by removing the maternal chromosomes from the oocyte before or after fertilization. We have shown that once developed into an embryo, haploid cells can be removed for genotyping and, if carrying the selected genome, be used to replace sperm at fertilization. A similar strategy can be used on the maternal side by activating the oocyte parthenogenetically and using some embryonic cells for genotyping while the remaining are used to produce diploid embryos by fertilization. Placed together, both androgenetic and parthenogenetic haploid cells that have been genotyped to identify optimal genomes can be used to produce offspring with predetermined genomes. Successes and problems in developing such a breeding platform to achieve this goal are described and discussed below.
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Affiliation(s)
- Lawrence Charles Smith
- Centre de Recherche en Reproduction et Fértilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
- Laboratório de Morfofisiologia Molecular e Desenvolvimento, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo – USP, Pirassununga, SP, Brasil
| | - Luis Aguila Paredes
- Laboratory of Reproduction, Centre of Reproductive Biotechnology – CEBIOR-BIOREN, Faculty of Agriculture and Environmental Sciences, Universidad de la Frontera, Temuco, Chile
| | - Rafael Vilar Sampaio
- Centre de Recherche en Reproduction et Fértilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Ricardo Perecin Nociti
- Centre de Recherche en Reproduction et Fértilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Jacinthe Therrien
- Centre de Recherche en Reproduction et Fértilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Flavio Vieira Meirelles
- Laboratório de Morfofisiologia Molecular e Desenvolvimento, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo – USP, Pirassununga, SP, Brasil
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3
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Aguila L, Nociti RP, Sampaio RV, Therrien J, Meirelles FV, Felmer RN, Smith LC. Haploid androgenetic development of bovine embryos reveals imbalanced WNT signaling and impaired cell fate differentiation†. Biol Reprod 2023; 109:821-838. [PMID: 37788061 DOI: 10.1093/biolre/ioad124] [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: 02/09/2023] [Revised: 08/09/2023] [Accepted: 09/11/2023] [Indexed: 10/04/2023] Open
Abstract
Haploid embryos have contributed significantly to our understanding of the role of parental genomes in development and can be applied to important biotechnology for human and animal species. However, development to the blastocyst stage is severely hindered in bovine haploid androgenetic embryos (hAE). To further our understanding of such developmental arrest, we performed a comprehensive comparison of the transcriptomic profile of morula-stage embryos, which were validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) of transcripts associated with differentiation in haploid and biparental embryos. Among numerous disturbances, results showed that pluripotency pathways, especially the wingless-related integration site (WNT) signaling, were particularly unbalanced in hAE. Moreover, transcript levels of KLF4, NANOG, POU5F1, SOX2, CDX2, CTNNBL1, AXIN2, and GSK3B were noticeably altered in hAE, suggesting disturbance of pluripotency and canonical WNT pathways. To evaluate the role of WNT on hAE competence, we exposed early Day-5 morula stage embryos to the GSK3B inhibitor CHIR99021. Although no alterations were observed in pluripotency and WNT-related transcripts, exposure to CHIR99021 improved their ability to reach the blastocysts stage, confirming the importance of the WNT pathway in the developmental outcome of bovine hAE.
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Affiliation(s)
- Luis Aguila
- Centre de Recherche en Reproduction et Fértilité (CRRF), Département de biomédecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
- Laboratory of Reproduction, Centre of Reproductive Biotechnology (CEBIOR-BIOREN), Faculty of Agriculture and Forestry, Universidad de La Frontera, Temuco, Chile
| | - Ricardo P Nociti
- Centre de Recherche en Reproduction et Fértilité (CRRF), Département de biomédecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, São Paulo, Brazil
| | - Rafael V Sampaio
- Centre de Recherche en Reproduction et Fértilité (CRRF), Département de biomédecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
| | - Jacinthe Therrien
- Centre de Recherche en Reproduction et Fértilité (CRRF), Département de biomédecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
| | - Flavio V Meirelles
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, São Paulo, Brazil
| | - Ricardo N Felmer
- Laboratory of Reproduction, Centre of Reproductive Biotechnology (CEBIOR-BIOREN), Faculty of Agriculture and Forestry, Universidad de La Frontera, Temuco, Chile
| | - Lawrence C Smith
- Centre de Recherche en Reproduction et Fértilité (CRRF), Département de biomédecine vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
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4
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Wilkinson AL, Zorzan I, Rugg-Gunn PJ. Epigenetic regulation of early human embryo development. Cell Stem Cell 2023; 30:1569-1584. [PMID: 37858333 DOI: 10.1016/j.stem.2023.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Studies of mammalian development have advanced our understanding of the genetic, epigenetic, and cellular processes that orchestrate embryogenesis and have uncovered new insights into the unique aspects of human embryogenesis. Recent studies have now produced the first epigenetic maps of early human embryogenesis, stimulating new ideas about epigenetic reprogramming, cell fate control, and the potential mechanisms underpinning developmental plasticity in human embryos. In this review, we discuss these new insights into the epigenetic regulation of early human development and the importance of these processes for safeguarding development. We also highlight unanswered questions and key challenges that remain to be addressed.
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Affiliation(s)
| | - Irene Zorzan
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
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5
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Sarel-Gallily R, Keshet G, Kinreich S, Haim-Abadi G, Benvenisty N. EpiTyping: analysis of epigenetic aberrations in parental imprinting and X-chromosome inactivation using RNA-seq. Nat Protoc 2023; 18:3881-3917. [PMID: 37914783 DOI: 10.1038/s41596-023-00898-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/28/2023] [Indexed: 11/03/2023]
Abstract
Human pluripotent stem cells (hPSCs) hold a central role in studying human development, in disease modeling and in regenerative medicine. These cells not only acquire genetic modifications when kept in culture, but they may also harbor epigenetic aberrations, mainly involving parental imprinting and X-chromosome inactivation. Here we present a detailed bioinformatic protocol for detecting such aberrations using RNA sequencing data. We provide a pipeline designed to process and analyze RNA sequencing data for the identification of abnormal biallelic expression of imprinted genes, and thus detect loss of imprinting. Furthermore, we show how to differentiate among X-chromosome inactivation, full activation and aberrant erosion of X chromosome in female hPSCs. In addition to providing bioinformatic tools, we discuss the impact of such epigenetic variations in hPSCs on their utility for various purposes. This pipeline can be used by any user with basic understanding of the Linux command line. It is available on GitHub as a software container ( https://github.com/Gal-Keshet/EpiTyping ) and produces reliable results in 1-4 d.
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Affiliation(s)
- Roni Sarel-Gallily
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gal Keshet
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Shay Kinreich
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Guy Haim-Abadi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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6
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Lo EKW, Velazquez JJ, Peng D, Kwon C, Ebrahimkhani MR, Cahan P. Platform-agnostic CellNet enables cross-study analysis of cell fate engineering protocols. Stem Cell Reports 2023; 18:1721-1742. [PMID: 37478860 PMCID: PMC10444577 DOI: 10.1016/j.stemcr.2023.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/23/2023] Open
Abstract
Optimization of cell engineering protocols requires standard, comprehensive quality metrics. We previously developed CellNet, a computational tool to quantitatively assess the transcriptional fidelity of engineered cells compared with their natural counterparts, based on bulk-derived expression profiles. However, this platform and others were limited in their ability to compare data from different sources, and no current tool makes it easy to compare new protocols with existing state-of-the-art protocols in a standardized manner. Here, we utilized our prior application of the top-scoring pair transformation to build a computational platform, platform-agnostic CellNet (PACNet), to address both shortcomings. To demonstrate the utility of PACNet, we applied it to thousands of samples from over 100 studies that describe dozens of protocols designed to produce seven distinct cell types. We performed an in-depth examination of hepatocyte and cardiomyocyte protocols to identify the best-performing methods, characterize the extent of intra-protocol and inter-lab variation, and identify common off-target signatures, including a surprising neural/neuroendocrine signature in primary liver-derived organoids. We have made PACNet available as an easy-to-use web application, allowing users to assess their protocols relative to our database of reference engineered samples, and as open-source, extensible code.
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Affiliation(s)
- Emily K W Lo
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeremy J Velazquez
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Da Peng
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chulan Kwon
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mo R Ebrahimkhani
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.
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7
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Lu Z, Li J, Lu Y, Li L, Wang W, Zhang C, Xu L, Nie Y, Gao C, Bian X, Liu Z, Wang GZ, Sun Q. Cynomolgus-rhesus hybrid macaques serve as a platform for imprinting studies. Innovation (N Y) 2023; 4:100436. [PMID: 37215523 PMCID: PMC10196704 DOI: 10.1016/j.xinn.2023.100436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
Genomic imprinting can lead to allele-specific expression (ASE), where one allele is preferentially expressed more than the other. Perturbations in genomic imprinting or ASE genes have been widely observed across various neurological disorders, notably autism spectrum disorder (ASD). In this study, we crossed rhesus cynomolgus monkeys to produce hybrid monkeys and established a framework to evaluate their allele-specific gene expression patterns using the parental genomes as a reference. Our proof-of-concept analysis of the hybrid monkeys identified 353 genes with allele-biased expression in the brain, enabling us to determine the chromosomal locations of ASE clusters. Importantly, we confirmed a significant enrichment of ASE genes associated with neuropsychiatric disorders, including ASD, highlighting the potential of hybrid monkey models in advancing our understanding of genomic imprinting.
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Affiliation(s)
- Zongyang Lu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Jie Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Lu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ling Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Wei Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chenchen Zhang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Libing Xu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanhong Nie
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Changshan Gao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyan Bian
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiang Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
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8
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Keshet G, Bar S, Sarel-Gallily R, Yanuka O, Benvenisty N, Eldar-Geva T. Differentiation of uniparental human embryonic stem cells into granulosa cells reveals a paternal contribution to gonadal development. Stem Cell Reports 2023; 18:817-828. [PMID: 37001516 PMCID: PMC10147827 DOI: 10.1016/j.stemcr.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 04/03/2023] Open
Abstract
Genomic imprinting underlies the mammalian requirement for sexual reproduction. Nonetheless, the relative contribution of the two parental genomes during human development is not fully understood. Specifically, a fascinating question is whether the formation of the gonad, which holds the ability to reproduce, depends on equal contribution from both parental genomes. Here, we differentiated androgenetic and parthenogenetic human pluripotent stem cells (hPSCs) into ovarian granulosa-like cells (GLCs). We show that in contrast to biparental and androgenetic cells, parthenogenetic hPSCs present a reduced capacity to differentiate into GLCs. We further identify the paternally expressed gene IGF2 as the most upregulated imprinted gene upon differentiation. Remarkably, while IGF2 knockout androgenetic cells fail to differentiate into GLCs, the differentiation of parthenogenetic cells supplemented with IGF2 is partly rescued. Thus, our findings unravel a surprising essentiality of genes that are only expressed from the paternal genome to the development of the female reproductive system.
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Affiliation(s)
- Gal Keshet
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel.
| | - Shiran Bar
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Roni Sarel-Gallily
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Ofra Yanuka
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel.
| | - Talia Eldar-Geva
- Reproductive Endocrinology and Genetics Unit, Division of Obstetrics and Gynecology, Shaare Zedek Medical Center, Jerusalem, Israel; The Hebrew University School of Medicine, Jerusalem, Israel.
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9
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Chao Y, Qin Y, Zou X, Wang X, Hu C, Xia F, Zou C. Promising therapeutic aspects in human genetic imprinting disorders. Clin Epigenetics 2022; 14:146. [PMID: 36371218 PMCID: PMC9655922 DOI: 10.1186/s13148-022-01369-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon of monoallelic gene expression pattern depending on parental origin. In humans, congenital imprinting disruptions resulting from genetic or epigenetic mechanisms can cause a group of diseases known as genetic imprinting disorders (IDs). Genetic IDs involve several distinct syndromes sharing homologies in terms of genetic etiologies and phenotypic features. However, the molecular pathogenesis of genetic IDs is complex and remains largely uncharacterized, resulting in a lack of effective therapeutic approaches for patients. In this review, we begin with an overview of the genomic and epigenomic molecular basis of human genetic IDs. Notably, we address ethical aspects as a priority of employing emerging techniques for therapeutic applications in human IDs. With a particular focus, we delineate the current field of emerging therapeutics for genetic IDs. We briefly summarize novel symptomatic drugs and highlight the key milestones of new techniques and therapeutic programs as they stand today which can offer highly promising disease-modifying interventions for genetic IDs accompanied by various challenges.
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Affiliation(s)
- Yunqi Chao
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Yifang Qin
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Xinyi Zou
- grid.13402.340000 0004 1759 700XZhejiang University City College, Hangzhou, 310015 Zhejiang China
| | - Xiangzhi Wang
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Chenxi Hu
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Fangling Xia
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Chaochun Zou
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
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10
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Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta. Proc Natl Acad Sci U S A 2022; 119:e2211073119. [PMID: 36161909 DOI: 10.1073/pnas.2211073119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mammalian sex chromosomes encode homologous X/Y gene pairs that were retained on the Y chromosome in males and escape X chromosome inactivation (XCI) in females. Inferred to reflect X/Y pair dosage sensitivity, monosomy X is a leading cause of miscarriage in humans with near full penetrance. This phenotype is shared with many other mammals but not the mouse, which offers sophisticated genetic tools to generate sex chromosomal aneuploidy but also tolerates its developmental impact. To address this critical gap, we generated X-monosomic human induced pluripotent stem cells (hiPSCs) alongside otherwise isogenic euploid controls from male and female mosaic samples. Phased genomic variants in these hiPSC panels enable systematic investigation of X/Y dosage-sensitive features using in vitro models of human development. Here, we demonstrate the utility of these validated hiPSC lines to test how X/Y-linked gene dosage impacts a widely used model for human syncytiotrophoblast development. While these isogenic panels trigger a GATA2/3- and TFAP2A/C-driven trophoblast gene circuit irrespective of karyotype, differential expression implicates monosomy X in altered levels of placental genes and in secretion of placental growth factor (PlGF) and human chorionic gonadotropin (hCG). Remarkably, weighted gene coexpression network modules that significantly reflect these changes are also preserved in first-trimester chorionic villi and term placenta. Our results suggest monosomy X may skew trophoblast cell type composition and function, and that the combined haploinsufficiency of the pseudoautosomal region likely plays a key role in these changes.
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11
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CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles. Sci Rep 2022; 12:15525. [PMID: 36109624 PMCID: PMC9477841 DOI: 10.1038/s41598-022-19782-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Cis-natural antisense transcripts (cis-NATs) are transcribed from the same genomic locus as their partner gene but from the opposite DNA strand and overlap with the partner gene transcript. Here, we developed a simple and convenient program termed CCIVR (comprehensive cis-NATs identifier via RNA-seq data) that comprehensively identifies all kinds of cis-NATs based on genome annotation with expression data obtained from RNA-seq. Using CCIVR with genome databases, we demonstrated total cis-NAT pairs from 11 model organisms. CCIVR analysis with RNA-seq data from parthenogenetic and androgenetic embryonic stem cells identified well-known imprinted cis-NAT pair, KCNQ1/KCNQ1OT1, ensuring the availability of CCIVR. Finally, CCIVR identified cis-NAT pairs that demonstrate inversely correlated expression upon TGFβ stimulation including cis-NATs that functionally repress their partner genes by introducing epigenetic alteration in the promoters of partner genes. Thus, CCIVR facilitates the investigation of structural characteristics and functions of cis-NATs in numerous processes in various species.
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12
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Pluripotent Core in Bovine Embryos: A Review. Animals (Basel) 2022; 12:ani12081010. [PMID: 35454256 PMCID: PMC9032358 DOI: 10.3390/ani12081010] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/31/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Early development in mammals is characterized by the ability of each cell to produce a complete organism plus the extraembryonic, or placental, cells, defined as pluripotency. During subsequent development, pluripotency is lost, and cells begin to differentiate to a particular cell fate. This review summarizes the current knowledge of pluripotency features of bovine embryos cultured in vitro, focusing on the core of pluripotency genes (OCT4, NANOG, SOX2, and CDX2), and main chemical strategies for controlling pluripotent networks during early development. Finally, we discuss the applicability of manipulating pluripotency during the morula to blastocyst transition in cattle species.
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13
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Edwards MM, Zuccaro MV, Sagi I, Ding Q, Vershkov D, Benvenisty N, Egli D, Koren A. Delayed DNA replication in haploid human embryonic stem cells. Genome Res 2021; 31:2155-2169. [PMID: 34810218 PMCID: PMC8647822 DOI: 10.1101/gr.275953.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
Abstract
Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X Chromosome in haploids, consistent with the lack of X-Chromosome inactivation. We also identified 21 autosomal regions that had delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also underreplicated in polyploid placental cells. The same delays were observed in female ESCs with two active X Chromosomes, suggesting that increased X-Chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.
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Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Michael V Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Ido Sagi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dan Vershkov
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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14
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Generation of developmentally competent oocytes and fertile mice from parthenogenetic embryonic stem cells. Protein Cell 2021; 12:947-964. [PMID: 34845589 PMCID: PMC8674391 DOI: 10.1007/s13238-021-00865-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/20/2021] [Indexed: 12/11/2022] Open
Abstract
Parthenogenetic embryos, created by activation and diploidization of oocytes, arrest at mid-gestation for defective paternal imprints, which impair placental development. Also, viable offspring has not been obtained without genetic manipulation from parthenogenetic embryonic stem cells (pESCs) derived from parthenogenetic embryos, presumably attributable to their aberrant imprinting. We show that an unlimited number of oocytes can be derived from pESCs and produce healthy offspring. Moreover, normal expression of imprinted genes is found in the germ cells and the mice. pESCs exhibited imprinting consistent with exclusively maternal lineage, and higher X-chromosome activation compared to female ESCs derived from the same mouse genetic background. pESCs differentiated into primordial germ cell-like cells (PGCLCs) and formed oocytes following in vivo transplantation into kidney capsule that produced fertile pups and reconstituted ovarian endocrine function. The transcriptome and methylation of imprinted and X-linked genes in pESC-PGCLCs closely resembled those of in vivo produced PGCs, consistent with efficient reprogramming of methylation and genomic imprinting. These results demonstrate that amplification of germ cells through parthenogenesis faithfully maintains maternal imprinting, offering a promising route for deriving functional oocytes and having potential in rebuilding ovarian endocrine function.
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15
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Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells. Nat Commun 2021; 12:6718. [PMID: 34795250 PMCID: PMC8602306 DOI: 10.1038/s41467-021-26949-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
In mammals, imprinted genes are regulated by differentially methylated regions (DMRs) that are inherited from germ cells, leading to monoallelic expression in accordance with parent-of-origin. Yet, it is largely unknown how imprinted DMRs are maintained in human embryos despite global DNA demethylation following fertilization. Here, we explored the mechanisms involved in imprinting regulation by employing human parthenogenetic embryonic stem cells (hpESCs), which lack paternal alleles. We show that although global loss of DNA methylation in hpESCs affects most imprinted DMRs, many paternally-expressed genes (PEGs) remain repressed. To search for factors regulating PEGs, we performed a genome-wide CRISPR/Cas9 screen in haploid hpESCs. This revealed ATF7IP as an essential repressor of a set of PEGs, which we further show is also required for silencing sperm-specific genes. Our study reinforces an important role for histone modifications in regulating imprinted genes and suggests a link between parental imprinting and germ cell identity. Genetic imprinting ensures monoallelic gene expression critical for normal embryonic development. Here the authors take advantage of human haploid parthenogenic embryonic stem cells lacking paternal alleles to identify, by genome-wide screening, factors involved in the regulation of imprinted genes.
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16
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Chu C, Zhang W, Kang Y, Si C, Ji W, Niu Y, Zhang Y. Analysis of developmental imprinting dynamics in primates using SNP-free methods to identify imprinting defects in cloned placenta. Dev Cell 2021; 56:2826-2840.e7. [PMID: 34619096 DOI: 10.1016/j.devcel.2021.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022]
Abstract
Our knowledge of genomic imprinting in primates is lagging behind that of mice largely because of the difficulties of allelic analyses in outbred animals. To understand imprinting dynamics in primates, we profiled transcriptomes, DNA methylomes, and H3K27me3 in uniparental monkey embryos. We further developed single-nucleotide-polymorphism (SNP)-free methods, TARSII and CARSII, to identify germline differentially methylated regions (DMRs) in somatic tissues. Our comprehensive analyses showed that allelic DNA methylation, but not H3K27me3, is a major mark that correlates with paternal-biasedly expressed genes (PEGs) in uniparental monkey embryos. Interestingly, primate germline DMRs are different from PEG-associated DMRs in early embryos and are enriched in placenta. Strikingly, most placenta-specific germline DMRs are lost in placenta of cloned monkeys. Collectively, our study establishes SNP-free germline DMR identification methods, defines developmental imprinting dynamics in primates, and demonstrates imprinting defects in cloned monkey placenta, which provides important clues for improving primate cloning.
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Affiliation(s)
- Chu Chu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Wenhao Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Yu Kang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Chenyang Si
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA.
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17
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Xu J, Shu Y, Yao G, Zhang Y, Niu W, Zhang Y, Ma X, Jin H, Zhang F, Shi S, Wang Y, Song W, Dai S, Cheng L, Zhang X, Xie W, Hsueh AJ, Sun Y. Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition. Genome Res 2021; 31:1519-1530. [PMID: 34330789 PMCID: PMC8415376 DOI: 10.1101/gr.273318.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 07/22/2021] [Indexed: 11/24/2022]
Abstract
Uniparental embryos derived from only the mother (gynogenetic [GG]) or the father (androgenetic [AG]) are unique models for studying genomic imprinting and parental contributions to embryonic development. Human parthenogenetic embryos can be obtained following artificial activation of unfertilized oocytes, but the production of AG embryos by injection of two sperm into one denucleated oocyte leads to an extra centriole, resulting in multipolar spindles, abnormal cell division, and developmental defects. Here, we improved androgenote production by transferring the male pronucleus from one zygote into another haploid androgenote to prevent extra centrioles and successfully generated human diploid AG embryos capable of developing into blastocysts with an identifiable inner cell mass (ICM) and trophectoderm (TE). The GG embryos were also generated. The zygotic genome was successfully activated in both the AG and GG embryos. DNA methylome analysis showed that the GG blastocysts partially retain the oocyte transcription-dependent methylation pattern, whereas the AG blastocyst methylome showed more extensive demethylation. The methylation states of most known imprinted differentially methylated regions (DMRs) were recapitulated in the AG and GG blastocysts. Novel candidate imprinted DMRs were also identified. The production of uniparental human embryos followed by transcriptome and methylome analysis is valuable for identifying parental contributions and epigenome memory transitions during early human development.
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Affiliation(s)
- Jiawei Xu
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Yimin Shu
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Guidong Yao
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenbin Niu
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Yile Zhang
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Xueshan Ma
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Haixia Jin
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Fuli Zhang
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Senlin Shi
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Yang Wang
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Wenyan Song
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Shanjun Dai
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Luyao Cheng
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Xiangyang Zhang
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Aaron J Hsueh
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Yingpu Sun
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000 China
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18
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Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nat Commun 2021; 12:3804. [PMID: 34155196 PMCID: PMC8217501 DOI: 10.1038/s41467-021-23510-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 04/30/2021] [Indexed: 02/06/2023] Open
Abstract
In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation. In most mammals, imprinted genes contain epigenetic marks that differ in each parental genome and control their parent-of-origin-specific expression. Here, the authors map imprinted genes in mouse preimplantation embryos and find that imprinted gene expression in blastocysts is mainly dependent on Polycomb-mediated H3K27me3-associated gene silencing.
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Affiliation(s)
- Laura Santini
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Florian Halbritter
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fabian Titz-Teixeira
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Toru Suzuki
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Maki Asami
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Xiaoyan Ma
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Julia Ramesmayer
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Andreas Lackner
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Nick Warr
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell, UK
| | - Florian Pauler
- Institute for Science and Technology Austria, Klosterneuburg, Austria
| | - Simon Hippenmeyer
- Institute for Science and Technology Austria, Klosterneuburg, Austria
| | - Ernest Laue
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Andreas Beyer
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Anthony C F Perry
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath, UK.
| | - Martin Leeb
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria.
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19
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Aguila L, Suzuki J, Hill ABT, García M, de Mattos K, Therrien J, Smith LC. Dysregulated Gene Expression of Imprinted and X-Linked Genes: A Link to Poor Development of Bovine Haploid Androgenetic Embryos. Front Cell Dev Biol 2021; 9:640712. [PMID: 33869192 PMCID: PMC8044962 DOI: 10.3389/fcell.2021.640712] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/25/2021] [Indexed: 11/13/2022] Open
Abstract
Mammalian uniparental embryos are efficient models for genome imprinting research and allow studies on the contribution of the paternal and maternal genomes to early embryonic development. In this study, we analyzed different methods for production of bovine haploid androgenetic embryos (hAE) to elucidate the causes behind their poor developmental potential. Results indicate that hAE can be efficiently generated by using intracytoplasmic sperm injection and oocyte enucleation at telophase II. Although androgenetic haploidy does not disturb early development up to around the 8-cell stage, androgenetic development is disturbed after the time of zygote genome activation and hAE that reach the morula stage are less capable to reach the blastocyst stage of development. Karyotypic comparisons to parthenogenetic- and ICSI-derived embryos excluded chromosomal segregation errors as causes of the developmental constraints of hAE. However, analysis of gene expression indicated abnormal levels of transcripts for key long non-coding RNAs involved in X chromosome inactivation and genomic imprinting of the KCNQ1 locus, suggesting an association with X chromosome and some imprinted loci. Moreover, transcript levels of methyltransferase 3B were significantly downregulated, suggesting potential anomalies in hAE establishing de novo methylation. Finally, the methylation status of imprinted control regions for XIST and KCNQ1OT1 genes remained hypomethylated in hAE at the morula and blastocyst stages, confirming their origin from spermatozoa. Thus, our results exclude micromanipulation and chromosomal abnormalities as major factors disturbing the normal development of bovine haploid androgenotes. In addition, although the cause of the arrest remains unclear, we have shown that the inefficient development of haploid androgenetic bovine embryos to develop to the blastocyst stage is associated with abnormal expression of key factors involved in X chromosome activity and genomic imprinting.
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Affiliation(s)
| | | | | | | | | | | | - Lawrence C. Smith
- Département de Biomédecine Vétérinaire, Centre de Recherche en Reproduction Et Fertilité, Université de Montreal, Saint-Hyacinthe, QC, Canada
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20
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Cahan P, Cacchiarelli D, Dunn SJ, Hemberg M, de Sousa Lopes SMC, Morris SA, Rackham OJL, Del Sol A, Wells CA. Computational Stem Cell Biology: Open Questions and Guiding Principles. Cell Stem Cell 2021; 28:20-32. [PMID: 33417869 PMCID: PMC7799393 DOI: 10.1016/j.stem.2020.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Computational biology is enabling an explosive growth in our understanding of stem cells and our ability to use them for disease modeling, regenerative medicine, and drug discovery. We discuss four topics that exemplify applications of computation to stem cell biology: cell typing, lineage tracing, trajectory inference, and regulatory networks. We use these examples to articulate principles that have guided computational biology broadly and call for renewed attention to these principles as computation becomes increasingly important in stem cell biology. We also discuss important challenges for this field with the hope that it will inspire more to join this exciting area.
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Affiliation(s)
- Patrick Cahan
- Institute for Cell Engineering, Department of Biomedical Engineering, Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy d Department of Translational Medicine, University of Naples "Federico II," Naples, Italy
| | - Sara-Jane Dunn
- DeepMind, 14-18 Handyside Street, London N1C 4DN, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | | | - Samantha A Morris
- Department of Developmental Biology, Department of Genetics, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Owen J L Rackham
- Centre for Computational Biology and The Program for Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Belvaux 4366, Luxembourg; CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Christine A Wells
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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21
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Zuccaro MV, Xu J, Mitchell C, Marin D, Zimmerman R, Rana B, Weinstein E, King RT, Palmerola KL, Smith ME, Tsang SH, Goland R, Jasin M, Lobo R, Treff N, Egli D. Allele-Specific Chromosome Removal after Cas9 Cleavage in Human Embryos. Cell 2020; 183:1650-1664.e15. [PMID: 33125898 DOI: 10.1016/j.cell.2020.10.025] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/02/2020] [Accepted: 10/14/2020] [Indexed: 12/24/2022]
Abstract
Correction of disease-causing mutations in human embryos holds the potential to reduce the burden of inherited genetic disorders and improve fertility treatments for couples with disease-causing mutations in lieu of embryo selection. Here, we evaluate repair outcomes of a Cas9-induced double-strand break (DSB) introduced on the paternal chromosome at the EYS locus, which carries a frameshift mutation causing blindness. We show that the most common repair outcome is microhomology-mediated end joining, which occurs during the first cell cycle in the zygote, leading to embryos with non-mosaic restoration of the reading frame. Notably, about half of the breaks remain unrepaired, resulting in an undetectable paternal allele and, after mitosis, loss of one or both chromosomal arms. Correspondingly, Cas9 off-target cleavage results in chromosomal losses and hemizygous indels because of cleavage of both alleles. These results demonstrate the ability to manipulate chromosome content and reveal significant challenges for mutation correction in human embryos.
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Affiliation(s)
- Michael V Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Jia Xu
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA
| | - Carl Mitchell
- Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Diego Marin
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA
| | | | - Bhavini Rana
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA; Department of Molecular Biosciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854, USA
| | - Everett Weinstein
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Rebeca T King
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Katherine L Palmerola
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Morgan E Smith
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Stephen H Tsang
- Columbia University Stem Cell Initiative, New York, NY 10032, USA; Departments of Ophthalmology, Pathology & Cell Biology, Columbia University. New York, NY, 10032, USA
| | - Robin Goland
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Rogerio Lobo
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Nathan Treff
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA; Department of Molecular Biosciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA.
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22
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Precise allele-specific genome editing by spatiotemporal control of CRISPR-Cas9 via pronuclear transplantation. Nat Commun 2020; 11:4593. [PMID: 32929070 PMCID: PMC7490392 DOI: 10.1038/s41467-020-18391-y] [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: 01/19/2020] [Accepted: 08/13/2020] [Indexed: 01/04/2023] Open
Abstract
Gene-targeted animal models that are generated by injecting Cas9 and sgRNAs into zygotes are often accompanied by undesired double-strand break (DSB)-induced byproducts and random biallelic targeting due to uncontrollable Cas9 targeting activity. Here, we establish a parental allele-specific gene-targeting (Past-CRISPR) method, based on the detailed observation that pronuclear transfer-mediated cytoplasmic dilution can effectively terminate Cas9 activity. We apply this method in embryos to efficiently target the given parental alleles of a gene of interest and observed little genomic mosaicism because of the spatiotemporal control of Cas9 activity. This method allows us to rapidly explore the function of individual parent-of-origin effects and to construct animal models with a single genomic change. More importantly, Past-CRISPR could also be used for therapeutic applications or disease model construction. Injecting Cas9 and gRNA into an animal zygote often produces mosaicism and random biallelic targeting. Here, the authors use pronuclear transfer to reduce mosaicism and selectively target parental alleles.
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23
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Aizawa E, Wutz A. From Mother or Father: Uniparental Embryos Uncover Parent-of-Origin Effects in Humans. Cell Stem Cell 2020; 25:587-589. [PMID: 31703767 DOI: 10.1016/j.stem.2019.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In mammals, both parents make unique contributions to the offspring and maternal and paternal genomes are required for development. Two recent papers in Cell Stem Cell (Leng et al., 2019; Sagi et al., 2019) study uniparental embryos and uniparental embryonic stem cells to interrogate parent-of-origin effects in human embryogenesis.
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Affiliation(s)
- Eishi Aizawa
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, HPL E12, Otto-Stern-Weg 7, 8049 Zurich, Switzerland
| | - Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, HPL E12, Otto-Stern-Weg 7, 8049 Zurich, Switzerland.
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24
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Li X, Li MJ, Yang Y, Bai Y. Effects of reprogramming on genomic imprinting and the application of pluripotent stem cells. Stem Cell Res 2019; 41:101655. [PMID: 31734645 DOI: 10.1016/j.scr.2019.101655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/27/2019] [Accepted: 11/08/2019] [Indexed: 12/11/2022] Open
Abstract
Pluripotent stem cells are considered to be the ideal candidates for cell-based therapies in humans. In this regard, both nuclear transfer embryonic stem (ntES) cells and induced pluripotent stem (iPS) cells are particularly advantageous because patient-specific autologous ntES and iPS cells can avoid immunorejection and other side effects that may be present in the allogenic pluripotent stem cells derived from unrelated sources. However, they have been found to contain deleterious genetic and epigenetic changes that may hinder their therapeutic applications. Indeed, deregulation of genomic imprinting has been frequently observed in reprogrammed ntES and iPS cells. We will survey the recent studies on genomic imprinting in pluripotent stem cells, particularly in iPS cells. In a previous study published about six years ago, genomic imprinting was found to be variably lost in mouse iPS clones. Intriguingly, de novo DNA methylation also occurred at the previously unmethylated imprinting control regions (ICRs) in a high percentage of iPS clones. These unexpected results were confirmed by a recent independent study with a similar approach. Since dysregulation of genomic imprinting can cause many human diseases including cancer and neurological disorders, these recent findings on genomic imprinting in reprogramming may have some implications for therapeutic applications of pluripotent stem cells.
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Affiliation(s)
- Xiajun Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Max Jiahua Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yang Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yun Bai
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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