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An interview with Peter Rugg-Gunn. Development 2024; 151:dev204218. [PMID: 38995119 DOI: 10.1242/dev.204218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Peter Rugg-Gunn is a Group Leader and Head of Public Engagement at the Babraham Institute in Cambridge, UK, interested in the epigenome during early human development. Peter is scientific lead of the Human Developmental Biology Initiative (HDBI), a member of the Scientific and Clinical Advances Advisory Committee of the Human Fertilisation and Embryology Authority (HFEA), and is active in UK and international efforts to establish guidance in stem cell-based embryo models. We spoke to Peter about his career path, his interest in public dialogue and his role as an Editor for Development.
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Martini P, Sales G, Diamante L, Perrera V, Colantuono C, Riccardo S, Cacchiarelli D, Romualdi C, Martello G. BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes. Commun Biol 2022; 5:146. [PMID: 35177756 PMCID: PMC8854590 DOI: 10.1038/s42003-022-03087-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Genomic imprinting and X chromosome inactivation (XCI) are two prototypical epigenetic mechanisms whereby a set of genes is expressed mono-allelically in order to fine-tune their expression levels. Defects in genomic imprinting have been observed in several neurodevelopmental disorders, in a wide range of tumours and in induced pluripotent stem cells (iPSCs). Single Nucleotide Variants (SNVs) are readily detectable by RNA-sequencing allowing the determination of whether imprinted or X-linked genes are aberrantly expressed from both alleles, although standardised analysis methods are still missing. We have developed a tool, named BrewerIX, that provides comprehensive information about the allelic expression of a large, manually-curated set of imprinted and X-linked genes. BrewerIX does not require programming skills, runs on a standard personal computer, and can analyze both bulk and single-cell transcriptomes of human and mouse cells directly from raw sequencing data. BrewerIX confirmed previous observations regarding the bi-allelic expression of some imprinted genes in naive pluripotent cells and extended them to preimplantation embryos. BrewerIX also identified misregulated imprinted genes in breast cancer cells and in human organoids and identified genes escaping XCI in human somatic cells. We believe BrewerIX will be useful for the study of genomic imprinting and XCI during development and reprogramming, and for detecting aberrations in cancer, iPSCs and organoids. Due to its ease of use to non-computational biologists, its implementation could become standard practice during sample assessment, thus raising the robustness and reproducibility of future studies.
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Affiliation(s)
- Paolo Martini
- Department of Biology, University of Padova, Padua, Italy
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Gabriele Sales
- Department of Biology, University of Padova, Padua, Italy
| | - Linda Diamante
- Department of Molecular Medicine, Medical School, University of Padova, Padua, Italy
| | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padova, Padua, Italy
- International School for Advanced Studies (SISSA/ISAS), Trieste, 34136, Italy
| | - Chiara Colantuono
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Sara Riccardo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy
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Picerno A, Stasi A, Franzin R, Curci C, di Bari I, Gesualdo L, Sallustio F. Why stem/progenitor cells lose their regenerative potential. World J Stem Cells 2021; 13:1714-1732. [PMID: 34909119 PMCID: PMC8641024 DOI: 10.4252/wjsc.v13.i11.1714] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/26/2021] [Accepted: 10/31/2021] [Indexed: 02/06/2023] Open
Abstract
Nowadays, it is clear that adult stem cells, also called as tissue stem cells, play a central role to repair and maintain the tissue in which they reside by their self-renewal ability and capacity of differentiating into distinct and specialized cells. As stem cells age, their renewal ability declines and their capacity to maintain organ homeostasis and regeneration is impaired. From a molecular perspective, these changes in stem cells properties can be due to several types of cell intrinsic injury and DNA aberrant alteration (i.e epigenomic profile) as well as changes in the tissue microenviroment, both into the niche and by systemic circulating factors. Strikingly, it has been suggested that aging-induced deterioration of stem cell functions may play a key role in the pathophysiology of the various aging-associated disorders. Therefore, understanding how resident stem cell age and affects near and distant tissues is fundamental. Here, we examine the current knowledge about aging mechanisms in several kinds of adult stem cells under physiological and pathological conditions and the principal aging-related changes in number, function and phenotype that determine the loss of tissue renewal properties. Furthermore, we examine the possible cell rejuvenation strategies. Stem cell rejuvenation may reverse the aging phenotype and the discovery of effective methods for inducing and differentiating pluripotent stem cells for cell replacement therapies could open up new possibilities for treating age-related diseases.
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Affiliation(s)
- Angela Picerno
- Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Alessandra Stasi
- Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Rossana Franzin
- Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Claudia Curci
- Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Ighli di Bari
- Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Loreto Gesualdo
- Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, Bari 70124, Italy
| | - Fabio Sallustio
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, Bari 70124, Italy
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Keshet G, Benvenisty N. Large-scale analysis of imprinting in naive human pluripotent stem cells reveals recurrent aberrations and a potential link to FGF signaling. Stem Cell Reports 2021; 16:2520-2533. [PMID: 34597600 PMCID: PMC8514966 DOI: 10.1016/j.stemcr.2021.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 01/21/2023] Open
Abstract
Genomic imprinting is a parent-of-origin dependent monoallelic expression of genes. Previous studies showed that conversion of primed human pluripotent stem cells (hPSCs) into naive pluripotency is accompanied by genome-wide loss of methylation that includes imprinted loci. However, the extent of aberrant biallelic expression of imprinted genes is still unknown. Here, we analyze loss of imprinting (LOI) in a large cohort of both bulk and single-cell RNA sequencing samples of naive and primed hPSCs. We show that naive hPSCs exhibit high levels of non-random LOI, with bias toward paternally methylated imprinting control regions. Importantly, we show that different protocols used for the primed to naive conversion led to different extents of LOI, tightly correlated to FGF signaling. This analysis sheds light on the process of LOI occurring during the conversion to naive pluripotency and highlights the importance of these events when modeling disease and development or when utilizing the cells for therapy.
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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 91904, 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 91904, Israel.
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Nishino K, Takasawa K, Okamura K, Arai Y, Sekiya A, Akutsu H, Umezawa A. Identification of an epigenetic signature in human induced pluripotent stem cells using a linear machine learning model. Hum Cell 2020; 34:99-110. [PMID: 33047283 PMCID: PMC7788050 DOI: 10.1007/s13577-020-00446-3] [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] [Received: 06/24/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022]
Abstract
The use of human induced pluripotent stem cells (iPSCs), used as an alternative to human embryonic stem cells (ESCs), is a potential solution to challenges, such as immune rejection, and does not involve the ethical issues concerning the use of ESCs in regenerative medicine, thereby enabling developments in biological research. However, comparative analyses from previous studies have not indicated any specific feature that distinguishes iPSCs from ESCs. Therefore, in this study, we established a linear classification-based learning model to distinguish among ESCs, iPSCs, embryonal carcinoma cells (ECCs), and somatic cells on the basis of their DNA methylation profiles. The highest accuracy achieved by the learned models in identifying the cell type was 94.23%. In addition, the epigenetic signature of iPSCs, which is distinct from that of ESCs, was identified by component analysis of the learned models. The iPSC-specific regions with methylation fluctuations were abundant on chromosomes 7, 8, 12, and 22. The method developed in this study can be utilized with comprehensive data and widely applied to many aspects of molecular biology research.
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Affiliation(s)
- Koichiro Nishino
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan. .,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan.
| | - Ken Takasawa
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yoshikazu Arai
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Asato Sekiya
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Hidenori Akutsu
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akihiro Umezawa
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
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Choi NY, Bang JS, Park YS, Lee M, Hwang HS, Ko K, Myung SC, Tapia N, Schöler HR, Kim GJ, Ko K. Generation of human androgenetic induced pluripotent stem cells. Sci Rep 2020; 10:3614. [PMID: 32109236 PMCID: PMC7046633 DOI: 10.1038/s41598-020-60363-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/10/2020] [Indexed: 11/09/2022] Open
Abstract
In humans, parthenogenesis and androgenesis occur naturally in mature cystic ovarian teratomas and androgenetic complete hydatidiform moles (CHM), respectively. Our previous study has reported human parthenogenetic induced pluripotent stem cells from ovarian teratoma-derived fibroblasts and screening of imprinted genes using genome-wide DNA methylation analysis. However, due to the lack of the counterparts of uniparental cells, identification of new imprinted differentially methylated regions has been limited. CHM are inherited from only the paternal genome. In this study, we generated human androgenetic induced pluripotent stem cells (AgHiPSCs) from primary androgenetic fibroblasts derived from CHM. To investigate the pluripotency state of AgHiPSCs, we analyzed their cellular and molecular characteristics. We tested the DNA methylation status of imprinted genes using bisulfite sequencing and demonstrated the androgenetic identity of AgHiPSCs. AgHiPSCs might be an attractive alternative source of human androgenetic embryonic stem cells. Furthermore, AgHiPSCs can be used in regenerative medicine, for analysis of genomic imprinting, to study imprinting-related development, and for disease modeling in humans.
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Affiliation(s)
- Na Young Choi
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, 05029, Republic of Korea
- Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jin Seok Bang
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, 05029, Republic of Korea
- Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, 05029, Republic of Korea
| | - Yo Seph Park
- Department of Stem Cell Research, TJC Life Research and Development Center, TJC Life, Seoul, 06698, Republic of Korea
| | - Minseong Lee
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, 05029, Republic of Korea
- Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, 05029, Republic of Korea
| | - Han Sung Hwang
- Department of Obstetrics and Gynecology, Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, 05030, Republic of Korea
| | - Kisung Ko
- Department of Medicine, College of Medicine, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Soon Chul Myung
- Department of Urology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Natalia Tapia
- Institute of Biomedicine of Valencia, Spanish National Research Council, Jaime Roig 11, 46010, Valencia, Spain
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149, Münster, Germany
- Medical Faculty, University of Münster, 48149, Münster, Germany
| | - Gwang Jun Kim
- Department of Obstetrics and Gynecology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Kinarm Ko
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, 05029, Republic of Korea.
- Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, 05029, Republic of Korea.
- Research Institute of Medical Science, Konkuk University, Seoul, 05029, Republic of Korea.
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Goodwin J, Laslett AL, Rugg-Gunn PJ. The application of cell surface markers to demarcate distinct human pluripotent states. Exp Cell Res 2020; 387:111749. [PMID: 31790696 PMCID: PMC6983944 DOI: 10.1016/j.yexcr.2019.111749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/17/2019] [Accepted: 11/27/2019] [Indexed: 01/24/2023]
Abstract
Recent advances in human pluripotent stem cell (hPSC) research have uncovered different subpopulations within stem cell cultures and have captured a range of pluripotent states that hold distinct molecular and functional properties. At the two ends of the pluripotency spectrum are naïve and primed hPSC, whereby naïve hPSC grown in stringent conditions recapitulate features of the preimplantation human embryo, and the conventionally grown primed hPSC align closer to the early postimplantation embryo. Investigating these cell types will help to define the mechanisms that control early development and should provide new insights into stem cell properties such as cell identity, differentiation and reprogramming. Monitoring cell surface marker expression provides a valuable approach to resolve complex cell populations, to directly compare between cell types, and to isolate viable cells for functional experiments. This review discusses the discovery and applications of cell surface markers to study human pluripotent cell types with a particular focus on the transitions between naïve and primed states. Highlighted areas for future study include the potential functions for the identified cell surface proteins in pluripotency, the production of new high-quality monoclonal antibodies to naïve-specific protein epitopes and the use of cell surface markers to characterise subpopulations within pluripotent states.
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Affiliation(s)
- Jacob Goodwin
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Andrew L Laslett
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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Distinct Imprinting Signatures and Biased Differentiation of Human Androgenetic and Parthenogenetic Embryonic Stem Cells. Cell Stem Cell 2019; 25:419-432.e9. [DOI: 10.1016/j.stem.2019.06.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 03/17/2019] [Accepted: 06/18/2019] [Indexed: 12/11/2022]
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Bar S, Benvenisty N. Epigenetic aberrations in human pluripotent stem cells. EMBO J 2019; 38:embj.2018101033. [PMID: 31088843 DOI: 10.15252/embj.2018101033] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are being increasingly utilized worldwide in investigating human development, and modeling and discovering therapies for a wide range of diseases as well as a source for cellular therapy. Yet, since the first isolation of human embryonic stem cells (hESCs) 20 years ago, followed by the successful reprogramming of human-induced pluripotent stem cells (hiPSCs) 10 years later, various studies shed light on abnormalities that sometimes accumulate in these cells in vitro Whereas genetic aberrations are well documented, epigenetic alterations are not as thoroughly discussed. In this review, we highlight frequent epigenetic aberrations found in hPSCs, including alterations in DNA methylation patterns, parental imprinting, and X chromosome inactivation. We discuss the potential origins of these abnormalities in hESCs and hiPSCs, survey the different methods for detecting them, and elaborate on their potential consequences for the different utilities of hPSCs.
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Affiliation(s)
- Shiran Bar
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Nissim Benvenisty
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
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Perrera V, Martello G. How Does Reprogramming to Pluripotency Affect Genomic Imprinting? Front Cell Dev Biol 2019; 7:76. [PMID: 31143763 PMCID: PMC6521591 DOI: 10.3389/fcell.2019.00076] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/18/2019] [Indexed: 01/14/2023] Open
Abstract
Human induced Pluripotent Stem Cells (hiPSCs) have the capacity to generate a wide range of somatic cells, thus representing an ideal tool for regenerative medicine. Patient-derived hiPSCs are also used for in vitro disease modeling and drug screenings. Several studies focused on the identification of DNA mutations generated, or selected, during the derivation of hiPSCs, some of which are known to drive cancer formation. Avoiding such stable genomic aberrations is paramount for successful use of hiPSCs, but it is equally important to ensure that their epigenetic information is correct, given the critical role of epigenetics in transcriptional regulation and its involvement in a plethora of pathologic conditions. In this review we will focus on genomic imprinting, a prototypical epigenetic mechanism whereby a gene is expressed in a parent-of-origin specific manner, thanks to the differential methylation of specific DNA sequences. Conventional hiPSCs are thought to be in a pluripotent state primed for differentiation. They display a hypermethylated genome with an unexpected loss of DNA methylation at imprinted loci. Several groups recently reported the generation of hiPSCs in a more primitive developmental stage, called naïve pluripotency. Naïve hiPSCs share several features with early human embryos, such as a global genome hypomethylation, which is also accompanied by a widespread loss of DNA methylation at imprinted loci. Given that loss of imprinting has been observed in genetic developmental disorders as well as in a wide range of cancers, it is fundamental to make sure that hiPSCs do not show such epigenetic aberrations. We will discuss what specific imprinted genes, associated with human pathologies, have been found commonly misregulated in hiPSCs and suggest strategies to effectively detect and avoid such undesirable epigenetic abnormalities.
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Affiliation(s)
- Valentina Perrera
- Department of Molecular Medicine, School of Medicine and Surgery, University of Padova, Padua, Italy
| | - Graziano Martello
- Department of Molecular Medicine, School of Medicine and Surgery, University of Padova, Padua, Italy
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Analysis of the Paternally-Imprinted DLK1-MEG3 and IGF2-H19 Tandem Gene Loci in NT2 Embryonal Carcinoma Cells Identifies DLK1 as a Potential Therapeutic Target. Stem Cell Rev Rep 2019; 14:823-836. [PMID: 29980981 DOI: 10.1007/s12015-018-9838-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The paternally-imprinted genes insulin-like growth factor 2 (IGF2), H19, delta-like homologue 1 (DLK1), and maternally-expressed gene 3 (MEG3) are expressed from the tandem gene loci IGF2-H19 and DLK1-MEG3, which play crucial roles in initiating embryogenesis and development. The erasure of imprinting (EOI) at differentially methylated regions (DMRs) which regulate the expression of these genes maintains the developmental quiescence of primordial germ cells (PGCs) migrating through the embryo proper during embryogenesis and prevents them from forming teratomas. To address the potential involvement of the IGF2-H19 and DLK1-MEG3 loci in the pathogenesis of embryonal carcinoma (EC), we investigated their genomic imprinting at DMRs in the human PGC-derived EC cell line NTera-2 (NT2). We observed EOI at the IGF2-H19 locus and, somewhat to our surprise, a loss of imprinting (LOI) at the DLK1-MEG3 locus. As a result, NT2 cells express imprinted gene ratios from these loci such that there are i) low levels of the proliferation-promoting IGF2 relative to ii) high levels of the proliferation-inhibiting long noncoding RNA (lncRNA) H19 and iii) high levels of proliferation-promoting DLK1 relative to iv) low levels of the proliferation-inhibiting lncRNA MEG3. Consistent with this pattern of expression, the knockdown of DLK1 mRNA by shRNA resulted in decreased in vitro cell proliferation and in vivo tumor growth as well as decreased in vivo organ seeding by NT2 cells. Furthermore, treatment of NT2 cells with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-azaD) inhibited their proliferation. This inhibition was accompanied by changes in expression of both tandem gene sets: a decrease in the expression of DLK1 and upregulation of the proliferation-inhibiting lncRNA MEG3, and at the same time upregulation of IGF2 and downregulation of the lncRNA H19. These results suggest that the DLK1-MEG3 locus, and not the IGF2-H19 locus, drives the tumorigenicity of NT2 cells. Based on these results, we identified DLK1 as a novel treatment target for EC that could be downregulated by 5-azaD.
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Nishino K, Arai Y, Takasawa K, Toyoda M, Yamazaki-Inoue M, Sugawara T, Akutsu H, Nishimura K, Ohtaka M, Nakanishi M, Umezawa A. Epigenetic-scale comparison of human iPSCs generated by retrovirus, Sendai virus or episomal vectors. Regen Ther 2018; 9:71-78. [PMID: 30525077 PMCID: PMC6222281 DOI: 10.1016/j.reth.2018.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 11/30/2022] Open
Abstract
Human induced pluripotent stem cells (iPSCs) are established by introducing several reprogramming factors, such as OCT3/4, SOX2, KLF4, c-MYC. Because of their pluripotency and immortality, iPSCs are considered to be a powerful tool for regenerative medicine. To date, iPSCs have been established all over the world by various gene delivery methods. All methods induced high-quality iPSCs, but epigenetic analysis of abnormalities derived from differences in the gene delivery methods has not yet been performed. Here, we generated genetically matched human iPSCs from menstrual blood cells by using three kinds of vectors, i.e., retrovirus, Sendai virus, and episomal vectors, and compared genome-wide DNA methylation profiles among them. Although comparison of aberrant methylation revealed that iPSCs generated by Sendai virus vector have lowest number of aberrant methylation sites among the three vectors, the iPSCs generated by non-integrating methods did not show vector-specific aberrant methylation. However, the differences between the iPSC lines were determined to be the number of random aberrant hypermethylated regions compared with embryonic stem cells. These random aberrant hypermethylations might be a cause of the differences in the properties of each of the iPSC lines.
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Affiliation(s)
- Koichiro Nishino
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Yoshikazu Arai
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Ken Takasawa
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Masashi Toyoda
- Research Team for Geriatric Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Mayu Yamazaki-Inoue
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tohru Sugawara
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hidenori Akutsu
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Ken Nishimura
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | | | - Mahito Nakanishi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Akihiro Umezawa
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
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Mai Q, Mai X, Huang X, Zhang D, Huang K, Zhou C. Imprinting Status in Two Human Parthenogenetic Embryonic Stem Cell Lines: Analysis of 63 Imprinted Gene Expression Levels in Undifferentiated and Early Differentiated Stages. Stem Cells Dev 2018; 27:430-439. [PMID: 29402175 DOI: 10.1089/scd.2017.0247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human parthenogenetic embryonic stem cells (hPESCs) represent a source of histocompatible tissues for transplantation and carry two copies of the maternal genome, but lack the paternal genome. In this study, we selected 63 known human imprinted genes to investigate the imprinting status of hPESC. The expression level of these genes, including 27 maternally and 36 paternally imprinted were illustrated in hPESC and human embryonic stem cells (hESCs) derived from fertilized embryo lines. The expression activity changes of these genes were analyzed in undifferentiated and early differentiated hPESC lines. In addition, the methylation status of four differentially methylated regions (DMRs) of the imprinted genes was analyzed in undifferentiated and early differentiated hPESC and hESC lines. As a result, we found that all the maternally imprinted genes were expressed at similar levels in the undifferentiated hPESC lines and the hESC lines, except ZNF264 and ATP10A. Twenty-one analyzed paternal imprinted genes were expressed at the same level in two separated hPESC lines as well as compared with the hESC lines, whereas 15 other paternal imprinted genes were significantly downregulated or inactivated in hPESC lines as compared with the hESC line. During prolonged passage, the expression levels of the majority of imprinted genes remained stable in two hPESC lines. The four DMRs, including PEG3/ZIM2 (DMRs), SNURF/SNRPN DMRs, and KVDMR1 DMRs are highly methylated in the genes of two undifferentiated hPESCs and its embryonic bodies (EBs), whereas the genes of the undifferentiated hESCs and its EBs are half methylated. During the early differentiation stage, the imprinted genes showed the same expression trend and the expression levels of H19, IGF2, SLC22A2, SLC22A3/SLC22A18, and CPA4 were significantly upregulated in both hPESC lines. As conclusion, hPESCs show a substantial degree of epigenetic stability with respect to some imprinted genes.
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Affiliation(s)
- Qingyun Mai
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Xiuyun Mai
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China .,2 Reproductive Medical Center , Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xin Huang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Dan Zhang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Kejun Huang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Canquan Zhou
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
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14
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Takahashi Y, Wu J, Suzuki K, Martinez-Redondo P, Li M, Liao HK, Wu MZ, Hernández-Benítez R, Hishida T, Shokhirev MN, Esteban CR, Sancho-Martinez I, Belmonte JCI. Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells. Science 2018; 356:503-508. [PMID: 28473583 DOI: 10.1126/science.aag3260] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 12/12/2016] [Accepted: 04/06/2017] [Indexed: 12/31/2022]
Abstract
CpG islands (CGIs) are primarily promoter-associated genomic regions and are mostly unmethylated within highly methylated mammalian genomes. The mechanisms by which CGIs are protected from de novo methylation remain elusive. Here we show that insertion of CpG-free DNA into targeted CGIs induces de novo methylation of the entire CGI in human pluripotent stem cells (PSCs). The methylation status is stably maintained even after CpG-free DNA removal, extensive passaging, and differentiation. By targeting the DNA mismatch repair gene MLH1 CGI, we could generate a PSC model of a cancer-related epimutation. Furthermore, we successfully corrected aberrant imprinting in induced PSCs derived from an Angelman syndrome patient. Our results provide insights into how CpG-free DNA induces de novo CGI methylation and broaden the application of targeted epigenome editing for a better understanding of human development and disease.
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Affiliation(s)
- Yuta Takahashi
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.,Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8577, Japan
| | - Jun Wu
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.,Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos, N° 135 Guadalupe 30107, Murcia, Spain
| | - Keiichiro Suzuki
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Paloma Martinez-Redondo
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mo Li
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.,King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Hsin-Kai Liao
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Min-Zu Wu
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.,Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos, N° 135 Guadalupe 30107, Murcia, Spain
| | - Reyna Hernández-Benítez
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.,King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Maxim Nikolaievich Shokhirev
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Concepcion Rodriguez Esteban
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ignacio Sancho-Martinez
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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15
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Human Long Noncoding RNA Regulation of Stem Cell Potency and Differentiation. Stem Cells Int 2017; 2017:6374504. [PMID: 28951743 PMCID: PMC5603141 DOI: 10.1155/2017/6374504] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/12/2017] [Accepted: 08/02/2017] [Indexed: 12/15/2022] Open
Abstract
Because of their capability of differentiation into lineage-specific cells, stem cells are an attractive therapeutic modality in regenerative medicine. To develop an effective stem cell-based therapeutic strategy with predictable results, deeper understanding of the underlying molecular mechanisms of stem cell differentiation and/or pluripotency maintenance is required. Thus, reviewing the key factors involved in the transcriptional and epigenetic regulation of stem cell differentiation and maintenance is important. Accumulating data indicate that long noncoding RNAs (lncRNAs) mediate numerous biological processes, including stem cell differentiation and maintenance. Here, we review recent findings on the human lncRNA regulation of stem cell potency and differentiation. Although the clinical implication of these lncRNAs is only beginning to be elucidated, it is anticipated that lncRNAs will become important therapeutic targets in the near future.
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16
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Bar S, Schachter M, Eldar-Geva T, Benvenisty N. Large-Scale Analysis of Loss of Imprinting in Human Pluripotent Stem Cells. Cell Rep 2017; 19:957-968. [DOI: 10.1016/j.celrep.2017.04.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/01/2017] [Accepted: 04/06/2017] [Indexed: 12/30/2022] Open
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17
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A G-quadruplex structure at the 5' end of the H19 coding region regulates H19 transcription. Sci Rep 2017; 8:45815. [PMID: 28367967 PMCID: PMC5377947 DOI: 10.1038/srep45815] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 03/06/2017] [Indexed: 12/15/2022] Open
Abstract
The H19 gene, one of the best known imprinted genes, encodes a long non-coding RNA that regulates cell proliferation and differentiation. H19 RNA is widely expressed in embryonic tissues, but its expression is restricted in only a few tissues after birth. However, regulation of H19 gene expression remains poorly understood outside the context of genomic imprinting. Here we identified evolutionarily conserved guanine (G)-rich repeated motifs at the 5′ end of the H19 coding region that are consistent with theoretically deduced G-quadruplex sequences. Circular dichroism spectroscopy and electrophoretic mobility shift assays with G-quadruplex-specific ligands revealed that the G-rich motif, located immediately downstream of the transcription start site (TSS), forms a G-quadruplex structure in vitro. By using a series of mutant forms of H19 harboring deletion or G-to-A substitutions, we found that the H19-G-quadruplex regulates H19 gene expression. We further showed that transcription factors Sp1 and E2F1 were associated with the H19-G-quadruplex to either suppress or promote the H19 transcription, respectively. Moreover, H19 expression during differentiation of mouse embryonic stem cells appears to be regulated by a genomic H19 G-quadruplex. These results demonstrate that the G-quadruplex structure immediately downstream of the TSS functions as a novel regulatory element for H19 gene expression.
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18
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Kyriakides O, Halliwell JA, Andrews PW. Acquired Genetic and Epigenetic Variation in Human Pluripotent Stem Cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 163:187-206. [PMID: 29071402 DOI: 10.1007/10_2017_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human pluripotent stem cells (hPSCs) can acquire non-random genomic variation during culture. Some of these changes are common in tumours and confer a selective growth advantage in culture. Additionally, there is evidence that reprogramming of human induced pluripotent stem cells (hiPSCs) introduces mutations. This poses a challenge to both the safety of clinical applications and the reliability of basic research using hPSCs carrying genomic variation. A number of methods are available for monitoring the genomic integrity of hPSCs, and a balance between practicality and sensitivity must be considered in choosing the appropriate methods for each use of hPSCs. Adjusting protocols by which hPSCs are derived and cultured is an evolving process that is important in minimising acquired genomic variation. Assessing genetic variation for its potential impact is becoming increasingly important as techniques to detect genome-wide variation improve.
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Affiliation(s)
- O Kyriakides
- Centre for Stem Cell Biology, Department Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - J A Halliwell
- Centre for Stem Cell Biology, Department Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - P W Andrews
- Centre for Stem Cell Biology, Department Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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19
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20
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Stanurova J, Neureiter A, Hiber M, de Oliveira Kessler H, Stolp K, Goetzke R, Klein D, Bankfalvi A, Klump H, Steenpass L. Angelman syndrome-derived neurons display late onset of paternal UBE3A silencing. Sci Rep 2016; 6:30792. [PMID: 27484051 PMCID: PMC4971516 DOI: 10.1038/srep30792] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/02/2016] [Indexed: 01/21/2023] Open
Abstract
Genomic imprinting is an epigenetic phenomenon resulting in parent-of-origin-specific gene expression that is regulated by a differentially methylated region. Gene mutations or failures in the imprinting process lead to the development of imprinting disorders, such as Angelman syndrome. The symptoms of Angelman syndrome are caused by the absence of functional UBE3A protein in neurons of the brain. To create a human neuronal model for Angelman syndrome, we reprogrammed dermal fibroblasts of a patient carrying a defined three-base pair deletion in UBE3A into induced pluripotent stem cells (iPSCs). In these iPSCs, both parental alleles are present, distinguishable by the mutation, and express UBE3A. Detailed characterization of these iPSCs demonstrated their pluripotency and exceptional stability of the differentially methylated region regulating imprinted UBE3A expression. We observed strong induction of SNHG14 and silencing of paternal UBE3A expression only late during neuronal differentiation, in vitro. This new Angelman syndrome iPSC line allows to study imprinted gene regulation on both parental alleles and to dissect molecular pathways affected by the absence of UBE3A protein.
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Affiliation(s)
- Jana Stanurova
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Anika Neureiter
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Michaela Hiber
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Hannah de Oliveira Kessler
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Kristin Stolp
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Roman Goetzke
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstr. 20, 52074 Aachen, Germany
| | - Diana Klein
- Institute for Cell Biology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Agnes Bankfalvi
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Hannes Klump
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
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21
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Nishizawa M, Chonabayashi K, Nomura M, Tanaka A, Nakamura M, Inagaki A, Nishikawa M, Takei I, Oishi A, Tanabe K, Ohnuki M, Yokota H, Koyanagi-Aoi M, Okita K, Watanabe A, Takaori-Kondo A, Yamanaka S, Yoshida Y. Epigenetic Variation between Human Induced Pluripotent Stem Cell Lines Is an Indicator of Differentiation Capacity. Cell Stem Cell 2016; 19:341-54. [PMID: 27476965 DOI: 10.1016/j.stem.2016.06.019] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 05/26/2016] [Accepted: 06/28/2016] [Indexed: 12/23/2022]
Abstract
Variation in the differentiation capacity of induced pluripotent stem cells (iPSCs) to specific lineages is a significant concern for their use in clinical applications and disease modeling. To identify factors that affect differentiation capacity, we performed integration analyses between hematopoietic differentiation performance and molecular signatures such as gene expression, DNA methylation, and chromatin status, using 35 human iPSC lines and four ESC lines. Our analyses revealed that hematopoietic commitment of PSCs to hematopoietic precursors correlates with IGF2 expression level, which in turn depends on signaling-dependent chromatin accessibility at mesendodermal genes. Maturation capacity for conversion of PSC-derived hematopoietic precursors to mature blood associates with the amount and pattern of DNA methylation acquired during reprogramming. Our study therefore provides insight into the molecular features that determine the differential capacities seen among human iPSC lines and, through the predictive potential of this information, highlights a way to select optimal iPSCs for clinical applications.
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Affiliation(s)
- Masatoshi Nishizawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Kazuhisa Chonabayashi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Masaki Nomura
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Azusa Tanaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Masahiro Nakamura
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Azusa Inagaki
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Misato Nishikawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Ikue Takei
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Akiko Oishi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Koji Tanabe
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Mari Ohnuki
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Hidaka Yokota
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Michiyo Koyanagi-Aoi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Keisuke Okita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Akira Watanabe
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan; Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
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22
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Wianny F, Blachère T, Godet M, Guillermas R, Cortay V, Bourillot PY, Lefèvre A, Savatier P, Dehay C. Epigenetic status of H19/IGF2 and SNRPN imprinted genes in aborted and successfully derived embryonic stem cell lines in non-human primates. Stem Cell Res 2016; 16:557-67. [DOI: 10.1016/j.scr.2016.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 03/04/2016] [Accepted: 03/07/2016] [Indexed: 12/20/2022] Open
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23
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DNA methylation dynamics in human induced pluripotent stem cells. Hum Cell 2016; 29:97-100. [PMID: 27083573 DOI: 10.1007/s13577-016-0139-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 03/22/2016] [Indexed: 12/18/2022]
Abstract
Indeed human induced pluripotent stem cells (hiPSCs) are considered to be powerful tools in regenerative medicine. To enable the use of hiPSCs in the field of regenerative medicine, it is necessary to understand the mechanisms of reprogramming during the transformation of somatic cells into hiPSCs. Genome-wide epigenetic modification constitutes a critical event in the generation of iPSCs. In other words, to analyze epigenetic changes in iPSCs means to elucidate reprogramming processes. We have established a large number of hiPSCs derived from various human tissues and have obtained their DNA methylation profiles. Comparison analyses indicated that the epigenetic patterns of various hiPSCs, irrespective of their source tissue, were very similar to one another and were similar to those of human embryonic stem cells (hESCs). However, the profiles of hiPSCs and hESCs exhibited epigenetic differences, which were caused by random aberrant hypermethylation at early passages. Interestingly, continuous passaging of the hiPSCs diminished the differences between DNA methylation profiles of hiPSCs and hESCs. The number of aberrant DNA methylation regions may thus represent a useful epigenetic index for evaluating hiPSCs in the context of therapeutic applications.
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24
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Burns AJ, Goldstein AM, Newgreen DF, Stamp L, Schäfer KH, Metzger M, Hotta R, Young HM, Andrews PW, Thapar N, Belkind-Gerson J, Bondurand N, Bornstein JC, Chan WY, Cheah K, Gershon MD, Heuckeroth RO, Hofstra RMW, Just L, Kapur RP, King SK, McCann CJ, Nagy N, Ngan E, Obermayr F, Pachnis V, Pasricha PJ, Sham MH, Tam P, Vanden Berghe P. White paper on guidelines concerning enteric nervous system stem cell therapy for enteric neuropathies. Dev Biol 2016; 417:229-51. [PMID: 27059883 DOI: 10.1016/j.ydbio.2016.04.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 03/29/2016] [Accepted: 04/02/2016] [Indexed: 12/22/2022]
Abstract
Over the last 20 years, there has been increasing focus on the development of novel stem cell based therapies for the treatment of disorders and diseases affecting the enteric nervous system (ENS) of the gastrointestinal tract (so-called enteric neuropathies). Here, the idea is that ENS progenitor/stem cells could be transplanted into the gut wall to replace the damaged or absent neurons and glia of the ENS. This White Paper sets out experts' views on the commonly used methods and approaches to identify, isolate, purify, expand and optimize ENS stem cells, transplant them into the bowel, and assess transplant success, including restoration of gut function. We also highlight obstacles that must be overcome in order to progress from successful preclinical studies in animal models to ENS stem cell therapies in the clinic.
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Affiliation(s)
- Alan J Burns
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Allan M Goldstein
- Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Donald F Newgreen
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville 3052, Victoria, Australia
| | - Lincon Stamp
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Karl-Herbert Schäfer
- University of Applied Sciences, Kaiserlautern, Germany; Clinic of Pediatric Surgery, University Hospital Mannheim, University Heidelberg, Germany
| | - Marco Metzger
- Fraunhofer-Institute Interfacial Engineering and Biotechnology IGB Translational Centre - Würzburg branch and University Hospital Würzburg - Tissue Engineering and Regenerative Medicine (TERM), Würzburg, Germany
| | - Ryo Hotta
- Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Heather M Young
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peter W Andrews
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Nikhil Thapar
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Jaime Belkind-Gerson
- Division of Gastroenterology, Hepatology and Nutrition, Massachusetts General Hospital for Children, Harvard Medical School, Boston, USA
| | - Nadege Bondurand
- INSERM U955, 51 Avenue du Maréchal de Lattre de Tassigny, F-94000 Créteil, France; Université Paris-Est, UPEC, F-94000 Créteil, France
| | - Joel C Bornstein
- Department of Physiology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Wood Yee Chan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Kathryn Cheah
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong
| | - Michael D Gershon
- Department of Pathology and Cell Biology, Columbia University, New York 10032, USA
| | - Robert O Heuckeroth
- Department of Pediatrics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Perelman School of Medicine at the University of Pennsylvania, Abramson Research Center, Philadelphia, PA 19104, USA
| | - Robert M W Hofstra
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lothar Just
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Germany
| | - Raj P Kapur
- Department of Pathology, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Sebastian K King
- Department of Paediatric and Neonatal Surgery, The Royal Children's Hospital, Melbourne, Australia
| | - Conor J McCann
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Nandor Nagy
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Elly Ngan
- Department of Surgery, The University of Hong Kong, Hong Kong
| | - Florian Obermayr
- Department of Pediatric Surgery and Pediatric Urology, University Children's Hospital Tübingen, D-72076 Tübingen, Germany
| | | | | | - Mai Har Sham
- Department of Biochemistry, The University of Hong Kong, Hong Kong
| | - Paul Tam
- Department of Surgery, The University of Hong Kong, Hong Kong
| | - Pieter Vanden Berghe
- Laboratory for Enteric NeuroScience (LENS), TARGID, University of Leuven, Belgium
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25
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Noncoding RNAs in Tumor Epithelial-to-Mesenchymal Transition. Stem Cells Int 2016; 2016:2732705. [PMID: 26989421 PMCID: PMC4773551 DOI: 10.1155/2016/2732705] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 01/20/2016] [Indexed: 12/21/2022] Open
Abstract
Epithelial-derived tumor cells acquire the capacity for epithelial-to-mesenchymal transition (EMT), which enables them to invade adjacent tissues and/or metastasize to distant organs. Cancer metastasis is the main cause of cancer-related death. Molecular mechanisms involved in the switch from an epithelial phenotype to mesenchymal status are complicated and are controlled by a variety of signaling pathways. Recently, a set of noncoding RNAs (ncRNAs), including miRNAs and long noncoding RNAs (lncRNAs), were found to modulate gene expressions at either transcriptional or posttranscriptional levels. These ncRNAs are involved in EMT through their interplay with EMT-related transcription factors (EMT-TFs) and EMT-associated signaling. Reciprocal regulatory interactions between lncRNAs and miRNAs further increase the complexity of the regulation of gene expression and protein translation. In this review, we discuss recent findings regarding EMT-regulating ncRNAs and their associated signaling pathways involved in cancer progression.
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26
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Avior Y, Sagi I, Benvenisty N. Pluripotent stem cells in disease modelling and drug discovery. Nat Rev Mol Cell Biol 2016; 17:170-82. [DOI: 10.1038/nrm.2015.27] [Citation(s) in RCA: 413] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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27
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Canham MA, Van Deusen A, Brison DR, De Sousa PA, Downie J, Devito L, Hewitt ZA, Ilic D, Kimber SJ, Moore HD, Murray H, Kunath T. The Molecular Karyotype of 25 Clinical-Grade Human Embryonic Stem Cell Lines. Sci Rep 2015; 5:17258. [PMID: 26607962 PMCID: PMC4660465 DOI: 10.1038/srep17258] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/27/2015] [Indexed: 12/22/2022] Open
Abstract
The application of human embryonic stem cell (hESC) derivatives to regenerative medicine is now becoming a reality. Although the vast majority of hESC lines have been derived for research purposes only, about 50 lines have been established under Good Manufacturing Practice (GMP) conditions. Cell types differentiated from these designated lines may be used as a cell therapy to treat macular degeneration, Parkinson’s, Huntington’s, diabetes, osteoarthritis and other degenerative conditions. It is essential to know the genetic stability of the hESC lines before progressing to clinical trials. We evaluated the molecular karyotype of 25 clinical-grade hESC lines by whole-genome single nucleotide polymorphism (SNP) array analysis. A total of 15 unique copy number variations (CNVs) greater than 100 kb were detected, most of which were found to be naturally occurring in the human population and none were associated with culture adaptation. In addition, three copy-neutral loss of heterozygosity (CN-LOH) regions greater than 1 Mb were observed and all were relatively small and interstitial suggesting they did not arise in culture. The large number of available clinical-grade hESC lines with defined molecular karyotypes provides a substantial starting platform from which the development of pre-clinical and clinical trials in regenerative medicine can be realised.
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Affiliation(s)
- Maurice A Canham
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, UK
| | - Amy Van Deusen
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, UK
| | - Daniel R Brison
- Department of Reproductive Medicine, St. Mary's Hospital, Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Paul A De Sousa
- Roslin Cells Limited, Nine Edinburgh BioQuarter, Edinburgh, UK.,Centre for Clinical Brain Sciences and MRC Centre for Regenerative Medicine, The University of Edinburgh, UK
| | - Janet Downie
- Roslin Cells Limited, Nine Edinburgh BioQuarter, Edinburgh, UK
| | - Liani Devito
- Stem Cell Laboratories, Guy's Assisted Conception Unit, Division of Women's Health, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Zoe A Hewitt
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, UK
| | - Dusko Ilic
- Stem Cell Laboratories, Guy's Assisted Conception Unit, Division of Women's Health, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Susan J Kimber
- Faculty of Life Sciences, The University of Manchester, Manchester, UK
| | - Harry D Moore
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, UK
| | - Helen Murray
- Roslin Cells Limited, Nine Edinburgh BioQuarter, Edinburgh, UK
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, UK
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28
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Liu WQ, Li JL, Wang J, He WY, Va L, Sheng XM, Wu BL, Sun XF. Genetic Evaluation of Copy Number Variations, Loss of Heterozygosity, and Single-Nucleotide Variant Levels in Human Embryonic Stem Cells With or Without Skewed X Chromosome Inactivation. Stem Cells Dev 2015; 24:1779-92. [DOI: 10.1089/scd.2014.0463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Wei-Qiang Liu
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Jie-Liang Li
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jian Wang
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Wen-Yin He
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Lip Va
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Xiao-Ming Sheng
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Bai-Lin Wu
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Xiao-Fang Sun
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
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29
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Xie P, Sun Y, Ouyang Q, Hu L, Tan Y, Zhou X, Xiong B, Zhang Q, Yuan D, Pan Y, Liu T, Liang P, Lu G, Lin G. Physiological oxygen prevents frequent silencing of the DLK1-DIO3 cluster during human embryonic stem cells culture. Stem Cells 2014; 32:391-401. [PMID: 24123616 DOI: 10.1002/stem.1558] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 07/28/2013] [Accepted: 08/25/2013] [Indexed: 12/18/2022]
Abstract
Genetic and epigenetic alterations are observed in long-term culture (>30 passages) of human embryonic stem cells (hESCs); however, little information is available in early cultures. Through a large-scale gene expression analysis between initial-passage hESCs (ihESCs, <10 passages) and early-passage hESCs (ehESCs, 20-30 passages) of 12 hESC lines, we found that the DLK1-DIO3 gene cluster was normally expressed and showed normal methylation pattern in ihESC, but was frequently silenced after 20 passages. Both the DLK1-DIO3 active status in ihESCs and the inactive status in ehESCs were inheritable during differentiation. Silencing of the DLK1-DIO3 cluster did not seem to compromise the multilineage differentiation ability of hESCs, but was associated with reduced DNA damage-induced apoptosis in ehESCs and their differentiated hepatocyte-like cell derivatives, possibly through attenuation of the expression and phosphorylation of p53. Furthermore, we demonstrated that 5% oxygen, instead of the commonly used 20% oxygen, is required for preserving the expression of the DLK1-DIO3 cluster. Overall, the data suggest that active expression of the DLK1-DIO3 cluster represents a new biomarker for epigenetic stability of hESCs and indicates the importance of using a proper physiological oxygen level during the derivation and culture of hESCs.
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Affiliation(s)
- Pingyuan Xie
- Institute of Reproductive & Stem Cell Engineering, Central South University, Changsha, China; Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Changsha, China
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30
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Abstract
The precise, temporal order of gene expression during development is critical to ensure proper lineage commitment, cell fate determination, and ultimately, organogenesis. Epigenetic regulation of chromatin structure is fundamental to the activation or repression of genes during embryonic development. In recent years, there has been an explosion of research relating to various modes of epigenetic regulation, such as DNA methylation, post-translational histone tail modifications, noncoding RNA control of chromatin structure, and nucleosome remodeling. Technological advances in genome-wide epigenetic profiling and pluripotent stem cell differentiation have been primary drivers for elucidating the epigenetic control of cellular identity during development and nuclear reprogramming. Not only do epigenetic mechanisms regulate transcriptional states in a cell-type-specific manner but also they establish higher order genomic topology and nuclear architecture. Here, we review the epigenetic control of pluripotency and changes associated with pluripotent stem cell differentiation. We focus on DNA methylation, DNA demethylation, and common histone tail modifications. Finally, we briefly discuss epigenetic heterogeneity among pluripotent stem cell lines and the influence of epigenetic patterns on genome topology.
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Affiliation(s)
- Michael J Boland
- From the Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Kristopher L Nazor
- From the Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Jeanne F Loring
- From the Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037.
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31
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Grybek V, Aubry L, Maupetit-Méhouas S, Le Stunff C, Denis C, Girard M, Linglart A, Silve C. Methylation and transcripts expression at the imprinted GNAS locus in human embryonic and induced pluripotent stem cells and their derivatives. Stem Cell Reports 2014; 3:432-43. [PMID: 25241742 PMCID: PMC4266011 DOI: 10.1016/j.stemcr.2014.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 07/04/2014] [Accepted: 07/07/2014] [Indexed: 02/06/2023] Open
Abstract
Data from the literature indicate that genomic imprint marks are disturbed in human pluripotent stem cells (PSCs). GNAS is an imprinted locus that produces one biallelic (Gsα) and four monoallelic (NESP55, GNAS-AS1, XLsα, and A/B) transcripts due to differential methylation of their promoters (DMR). To document imprinting at the GNAS locus in PSCs, we studied GNAS locus DMR methylation and transcript (NESP55, XLsα, and A/B) expression in human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) derived from two human fibroblasts and their progenies. Results showed that (1) methylation at the GNAS locus DMRs is DMR and cell line specific, (2) changes in allelic transcript expression can be independent of a change in allele-specific DNA methylation, and (3) interestingly, methylation at A/B DMR is correlated with A/B transcript expression. These results indicate that these models are valuable to study the mechanisms controlling GNAS methylation, factors involved in transcript expression, and possibly mechanisms involved in the pathophysiology of pseudohypoparathyroidism type 1B. GNAS locus methylation is DMR and cell line specific in human pluripotent stem cells Allelic transcript expression can be independent of allele-specific DNA methylation A/B transcript expression, a key for PHP1B, is correlated with A/B DMR methylation
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Affiliation(s)
- Virginie Grybek
- INSERM U986, Hôpital Bicêtre, Le Kremlin Bicêtre 94276, France
| | - Laetitia Aubry
- UEVE UMR 861, I-Stem, AFM, Evry 91030, France; INSERM UMR 861, I-Stem, AFM, Evry 91030, France
| | | | | | - Cécile Denis
- CECS, I-Stem, AFM, Institute for Stem Cell Therapy and Exploration of Monogenic Diseases, Evry 91030, France
| | - Mathilde Girard
- CECS, I-Stem, AFM, Institute for Stem Cell Therapy and Exploration of Monogenic Diseases, Evry 91030, France
| | - Agnès Linglart
- INSERM U986, Hôpital Bicêtre, Le Kremlin Bicêtre 94276, France; Service d'Endocrinologie Pédiatrique, Hôpital Bicêtre-AP-HP, Le Kremlin Bicêtre 94276, France; Centre de Référence des Maladies Rares du Métabolisme Phospho-Calcique Hôpital Bicêtre, Le Kremlin Bicêtre 94276, France
| | - Caroline Silve
- INSERM U986, Hôpital Bicêtre, Le Kremlin Bicêtre 94276, France; Centre de Référence des Maladies Rares du Métabolisme Phospho-Calcique Hôpital Bicêtre, Le Kremlin Bicêtre 94276, France; Laboratoire de Biochimie Hormonale et Génétique, Hôpital Bichat Claude Bernard-AP-HP, Paris 75018, France.
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32
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Variable allelic expression of imprinted genes in human pluripotent stem cells during differentiation into specialized cell types in vitro. Biochem Biophys Res Commun 2014; 446:493-8. [DOI: 10.1016/j.bbrc.2014.02.141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 02/28/2014] [Indexed: 12/27/2022]
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33
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Josephson R. Molecular cytogenetics: making it safe for human embryonic stem cells to enter the clinic. Expert Rev Mol Diagn 2014; 7:395-406. [PMID: 17620047 DOI: 10.1586/14737159.7.4.395] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Regenerative therapies based on transplantation of cells derived from human embryonic stem cells (hESC) are currently being prepared for clinical trials. Unfortunately, recent evidence indicates that many kinds of changes can occur to hESC during expansion in culture, and alterations to the growth control mechanisms may be required to establish hESC lines at all. Changes in the genome and epigenome can affect the validity of in vitro and animal studies, and put transplant recipients at increased risk of cancer. New molecular cytogenetic technologies enable us to examine the whole human genome with ever-finer resolution. This review describes several techniques for whole-genome analysis and the information they can provide about hESC lines. Adoption of high-resolution genotyping into routine characterization may prevent highly discouraging clinical outcomes.
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34
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Yang H, Liu Z, Ma Y, Zhong C, Yin Q, Zhou C, Shi L, Cai Y, Zhao H, Wang H, Tang F, Wang Y, Zhang C, Liu XY, Lai D, Jin Y, Sun Q, Li J. Generation of haploid embryonic stem cells from Macaca fascicularis monkey parthenotes. Cell Res 2013; 23:1187-200. [PMID: 23856644 PMCID: PMC3790242 DOI: 10.1038/cr.2013.93] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/22/2013] [Accepted: 06/03/2013] [Indexed: 12/19/2022] Open
Abstract
Recent success in the derivation of haploid embryonic stem cells (haESCs) from mouse via parthenogenesis and androgenesis has enabled genetic screening in mammalian cells and generation of gene-modified animals. However, whether haESCs can be derived from primates remains unknown. Here, we report the derivation of haESCs from parthenogenetic blastocysts of Macaca fascicularis monkeys. These cells, termed as PG-haESCs, are pluripotent and can differentiate to cells of three embryonic germ layers in vitro or in vivo. Interestingly, the haploidy of one monkey PG-haESC line (MPH1) is more stable compared with that of the other one (MPH2), as shown by the existence of haploid cells for more than 140 days without fluorescence-activated cell sorting (FACS) enrichment of haploid cells. Importantly, transgenic monkey PG-haESC lines can be generated by lentivirus- and piggyBac transposon-mediated gene transfer. Moreover, genetic screening is feasible in monkey PG-haESCs. Our results demonstrate that PG-haESCs can be generated from monkeys, providing an ideal tool for genetic analyses in primates.
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Affiliation(s)
- Hui Yang
- Group of Epigenetic Reprogramming, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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35
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Abstract
Genomic imprinting is an epigenetic phenomenon in which either the paternal or the maternal allele of imprinted genes is expressed in somatic cells. It is unique to eutherian mammals, marsupials, and flowering plants. It is absolutely required for normal mammalian development. Dysregulation of genomic imprinting can cause a variety of human diseases. About 150 imprinted genes have been identified so far in mammals and many of them are clustered such that they are coregulated by a cis-acting imprinting control region, called the ICR. One hallmark of the ICR is that it contains a germ line-derived differentially methylated region that is methylated on the paternal chromosome or on the maternal chromosome. The DNA methylation imprint is reset in the germ line and differential methylation at an ICR is restored upon fertilization. The DNA methylation imprint is resistant to a genome-wide demethylation process in early embryos and is stably maintained in postimplantation embryos. Maintenance of the DNA methylation imprint is dependent on two distinct maternal effect genes (Zfp57 and PGC7/Stella). In germ cells, around midgestation, the DNA methylation imprint is erased and undergoes another round of the DNA methylation imprint cycle that includes erasure, resetting, restoration, and maintenance of differential DNA methylation.
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Affiliation(s)
- Xiajun Li
- Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, USA.
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36
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The Intersection of Genetics and Epigenetics: Reactivation of Mammalian LINE-1 Retrotransposons by Environmental Injury. ENVIRONMENTAL EPIGENOMICS IN HEALTH AND DISEASE 2013. [DOI: 10.1007/978-3-642-23380-7_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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37
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Nguyen HT, Geens M, Spits C. Genetic and epigenetic instability in human pluripotent stem cells. Hum Reprod Update 2012; 19:187-205. [PMID: 23223511 DOI: 10.1093/humupd/dms048] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND There is an increasing body of evidence that human pluripotent stem cells (hPSCs) are prone to (epi)genetic instability during in vitro culture. This review aims at giving a comprehensive overview of the current knowledge on culture-induced (epi)genetic alterations in hPSCs and their phenotypic consequences. METHODS Combinations of the following key words were applied as search criteria: human induced pluripotent stem cells and human embryonic stem cells in combination with malignancy, tumorigenicity, X inactivation, mitochondrial mutations, genomic integrity, chromosomal abnormalities, culture adaptation, aneuploidy and CD30. Only studies in English, on hPSCs and focused on (epi)genomic integrity were included. Further manuscripts were added from cross-references. RESULTS Numerous (epi)genetic aberrations have been detected in hPSCs. Recurrent genetic alterations give a selective advantage in culture to the altered cells leading to overgrowth of abnormal, culture-adapted cells. The functional effects of these alterations are not yet fully understood, but suggest a (pre)malignant transformation of abnormal cells with decreased differentiation and increased proliferative capacity. CONCLUSIONS Given the high degree of (epi)genetic alterations reported in the literature and altered phenotypic characteristics of the abnormal cells, controlling for the (epi)genetic integrity of hPSCs before any clinical application is an absolute necessity.
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Affiliation(s)
- H T Nguyen
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090 Jette, Brussels, Belgium
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38
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Kashir J, Jones C, Child T, Williams SA, Coward K. Viability Assessment for Artificial Gametes: The Need for Biomarkers of Functional Competency1. Biol Reprod 2012; 87:114. [DOI: 10.1095/biolreprod.112.103853] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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39
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Harvey AJ, Mao S, Lalancette C, Krawetz SA, Brenner CA. Transcriptional differences between rhesus embryonic stem cells generated from in vitro and in vivo derived embryos. PLoS One 2012; 7:e43239. [PMID: 23028448 PMCID: PMC3445581 DOI: 10.1371/journal.pone.0043239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 07/18/2012] [Indexed: 01/16/2023] Open
Abstract
Numerous studies have focused on the transcriptional signatures that underlie the maintenance of embryonic stem cell (ESC) pluripotency. However, it remains unclear whether ESC retain transcriptional aberrations seen in in vitro cultured embryos. Here we report the first global transcriptional profile comparison between ESC generated from either in vitro cultured or in vivo derived primate embryos by microarray analysis. Genes involved in pluripotency, oxygen regulation and the cell cycle were downregulated in rhesus ESC generated from in vitro cultured embryos (in vitro ESC). Significantly, several gene differences are similarly downregulated in preimplantation embryos cultured in vitro, which have been associated with long term developmental consequences and disease predisposition. This data indicates that prior to derivation, embryo quality may influence the molecular signature of ESC lines, and may differentially impact the physiology of cells prior to or following differentiation.
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Affiliation(s)
- Alexandra J Harvey
- Department of Physiology, Wayne State University, Detroit, Michigan, United States of America.
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40
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Lund RJ, Närvä E, Lahesmaa R. Genetic and epigenetic stability of human pluripotent stem cells. Nat Rev Genet 2012; 13:732-44. [PMID: 22965355 DOI: 10.1038/nrg3271] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Studies using high-resolution genome-wide approaches have recently reported that genomic and epigenomic alterations frequently accumulate in human pluripotent cells. Detailed characterization of these changes is crucial for understanding the impact of these alterations on self-renewal and proliferation, and particularly on the developmental and malignant potential of the cells. Such knowledge is required for the optimized and safe use of pluripotent cells for therapeutic purposes, such as regenerative cellular therapies using differentiated derivatives of pluripotent cells.In this Review, we summarize the current knowledge of the genomic and epigenomic stability of pluripotent human cells and the implications for stem cell research.
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Affiliation(s)
- Riikka J Lund
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FIN-20520 Turku, Finland
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41
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Ahmad R, Wolber W, Eckardt S, Koch P, Schmitt J, Semechkin R, Geis C, Heckmann M, Brüstle O, McLaughlin JK, Sirén AL, Müller AM. Functional neuronal cells generated by human parthenogenetic stem cells. PLoS One 2012; 7:e42800. [PMID: 22880113 PMCID: PMC3412801 DOI: 10.1371/journal.pone.0042800] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 07/11/2012] [Indexed: 12/21/2022] Open
Abstract
Parent of origin imprints on the genome have been implicated in the regulation of neural cell type differentiation. The ability of human parthenogenetic (PG) embryonic stem cells (hpESCs) to undergo neural lineage and cell type-specific differentiation is undefined. We determined the potential of hpESCs to differentiate into various neural subtypes. Concurrently, we examined DNA methylation and expression status of imprinted genes. Under culture conditions promoting neural differentiation, hpESC-derived neural stem cells (hpNSCs) gave rise to glia and neuron-like cells that expressed subtype-specific markers and generated action potentials. Analysis of imprinting in hpESCs and in hpNSCs revealed that maternal-specific gene expression patterns and imprinting marks were generally maintained in PG cells upon differentiation. Our results demonstrate that despite the lack of a paternal genome, hpESCs generate proliferating NSCs that are capable of differentiation into physiologically functional neuron-like cells and maintain allele-specific expression of imprinted genes. Thus, hpESCs can serve as a model to study the role of maternal and paternal genomes in neural development and to better understand imprinting-associated brain diseases.
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Affiliation(s)
- Ruhel Ahmad
- Institute for Medical Radiation and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, Würzburg, Germany
| | - Wanja Wolber
- Department of Neurosurgery, University of Würzburg, Würzburg, Germany
| | - Sigrid Eckardt
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Philipp Koch
- Institute of Reconstructive Neurobiology, Life and Brain Center, University of Bonn and Hertie Foundation, Bonn, Germany
| | - Jessica Schmitt
- Institute for Medical Radiation and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, Würzburg, Germany
| | - Ruslan Semechkin
- International Stem Cell Corporation, Oceanside, California, United States of America
| | - Christian Geis
- Department of Neurology, University of Würzburg, Germany
| | | | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, Life and Brain Center, University of Bonn and Hertie Foundation, Bonn, Germany
| | - John K. McLaughlin
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Anna-Leena Sirén
- Department of Neurosurgery, University of Würzburg, Würzburg, Germany
| | - Albrecht M. Müller
- Institute for Medical Radiation and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, Würzburg, Germany
- * E-mail:
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42
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Epigenetic stability of human pluripotent stem cells. Epigenomics 2012. [DOI: 10.1017/cbo9780511777271.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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43
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Anguera MC, Sadreyev R, Zhang Z, Szanto A, Payer B, Sheridan SD, Kwok S, Haggarty SJ, Sur M, Alvarez J, Gimelbrant A, Mitalipova M, Kirby JE, Lee JT. Molecular signatures of human induced pluripotent stem cells highlight sex differences and cancer genes. Cell Stem Cell 2012; 11:75-90. [PMID: 22770242 PMCID: PMC3587778 DOI: 10.1016/j.stem.2012.03.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 12/10/2011] [Accepted: 03/08/2012] [Indexed: 11/25/2022]
Abstract
Although human induced pluripotent stem cells (hiPSCs) have enormous potential in regenerative medicine, their epigenetic variability suggests that some lines may not be suitable for human therapy. There are currently few benchmarks for assessing quality. Here we show that X-inactivation markers can be used to separate hiPSC lines into distinct epigenetic classes and that the classes are phenotypically distinct. Loss of XIST expression is strongly correlated with upregulation of X-linked oncogenes, accelerated growth rate in vitro, and poorer differentiation in vivo. Whereas differences in X-inactivation potential result in epigenetic variability of female hiPSC lines, male hiPSC lines generally resemble each other and do not overexpress the oncogenes. Neither physiological oxygen levels nor HDAC inhibitors offer advantages to culturing female hiPSC lines. We conclude that female hiPSCs may be epigenetically less stable in culture and caution that loss of XIST may result in qualitatively less desirable stem cell lines.
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Affiliation(s)
- Montserrat C. Anguera
- Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan Sadreyev
- Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Zhaoqing Zhang
- SAB Biosciences, Qiagen, 6951 Executive Way, Suite 100, Frederick, MD 21703, USA
| | - Attila Szanto
- Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Bernhard Payer
- Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Steven D. Sheridan
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Showming Kwok
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephen J. Haggarty
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Mriganka Sur
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jason Alvarez
- Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Alexander Gimelbrant
- Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Maisam Mitalipova
- Whitehead Institute for Biomedical Sciences, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - James E. Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Jeannie T. Lee
- Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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44
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Yang H, Shi L, Wang BA, Liang D, Zhong C, Liu W, Nie Y, Liu J, Zhao J, Gao X, Li D, Xu GL, Li J. Generation of genetically modified mice by oocyte injection of androgenetic haploid embryonic stem cells. Cell 2012; 149:605-17. [PMID: 22541431 DOI: 10.1016/j.cell.2012.04.002] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/21/2012] [Accepted: 04/04/2012] [Indexed: 12/22/2022]
Abstract
Haploid cells are amenable for genetic analysis. Recent success in the derivation of mouse haploid embryonic stem cells (haESCs) via parthenogenesis has enabled genetic screening in mammalian cells. However, successful generation of live animals from these haESCs, which is needed to extend the genetic analysis to the organism level, has not been achieved. Here, we report the derivation of haESCs from androgenetic blastocysts. These cells, designated as AG-haESCs, partially maintain paternal imprints, express classical ESC pluripotency markers, and contribute to various tissues, including the germline, upon injection into diploid blastocysts. Strikingly, live mice can be obtained upon injection of AG-haESCs into MII oocytes, and these mice bear haESC-carried genetic traits and develop into fertile adults. Furthermore, gene targeting via homologous recombination is feasible in the AG-haESCs. Our results demonstrate that AG-haESCs can be used as a genetically tractable fertilization agent for the production of live animals via injection into oocytes.
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Affiliation(s)
- Hui Yang
- Group of Epigenetic Reprogramming, State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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45
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Sun B, Ito M, Mendjan S, Ito Y, Brons IGM, Murrell A, Vallier L, Ferguson-Smith AC, Pedersen RA. Status of genomic imprinting in epigenetically distinct pluripotent stem cells. Stem Cells 2012; 30:161-8. [PMID: 22109880 DOI: 10.1002/stem.793] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mouse epiblast stem cells (EpiSCs) derived from postimplantation embryos are developmentally and functionally different from embryonic stem cells (ESCs) generated from blastocysts. EpiSCs require Activin A and FGF2 signaling for self-renewal, similar to human ESCs (hESCs), while mouse ESCs require LIF and BMP4. Unlike ESCs, EpiSCs have undergone X-inactivation, similar to the tendency of hESCs. The shared self-renewal and X-inactivation properties of EpiSCs and hESCs suggest that they have an epigenetic state distinct from ESCs. This hypothesis predicts that EpiSCs would have monoallelic expression of most imprinted genes, like that observed in hESCs. Here, we confirm this prediction. By contrast, we find that mouse induced pluripotent stem cells (iPSCs) tend to lose imprinting similar to mouse ESCs. These findings reveal that iPSCs have an epigenetic status associated with their pluripotent state rather than their developmental origin. Our results also reinforce the view that hESCs and EpiSCs are in vitro counterparts, sharing an epigenetic status distinct from ESCs and iPSCs.
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Affiliation(s)
- Bowen Sun
- The Anne McLaren Laboratory for Regenerative Medicine, Department of Surgery, University of Cambridge, Cambridge, United Kingdom
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46
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Tsai AG, Chen DM, Lin M, Hsieh JCF, Okitsu CY, Taghva A, Shibata D, Hsieh CL. Heterogeneity and randomness of DNA methylation patterns in human embryonic stem cells. DNA Cell Biol 2012; 31:893-907. [PMID: 22277069 DOI: 10.1089/dna.2011.1477] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA methylation has been proposed to be important in many biological processes and is the subject of intense study. Traditional bisulfite genomic sequencing allows detailed high-resolution methylation pattern analysis of each molecule with haplotype information across a few hundred bases at each locus, but lacks the capacity to gather voluminous data. Although recent technological developments are aimed at assessing DNA methylation patterns in a high-throughput manner across the genome, the haplotype information cannot be accurately assembled when the sequencing reads are short or when each hybridization target only includes one or two cytosine-phosphate-guanine (CpG) sites. Whether a distinct and nonrandom DNA methylation pattern is present at a given locus is difficult to discern without the haplotype information, and the DNA methylation patterns are much less apparent because the data are often obtained only as methylation frequencies at each CpG site with some of these methods. It would facilitate the interpretation of data obtained from high-throughput bisulfite sequencing if the loci with nonrandom DNA methylation patterns could be distinguished from those that are randomly methylated. In this study, we carried out traditional genomic bisulfite sequencing using the normal diploid human embryonic stem (hES) cell lines, and utilized Hamming distance analysis to evaluate the existence of a distinct and nonrandom DNA methylation pattern at each locus studied. Our findings suggest that Hamming distance is a simple, quick, and useful tool to identify loci with nonrandom DNA methylation patterns and may be utilized to discern links between biological changes and DNA methylation patterns in the high-throughput bisulfite sequencing data sets.
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Affiliation(s)
- Albert G Tsai
- Department of Biochemistry and Molecular Biology, Norris Cancer Center, University of Southern California, Los Angeles, California 90033, USA
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47
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Taubenschmid J, Weitzer G. Mechanisms of cardiogenesis in cardiovascular progenitor cells. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 293:195-267. [PMID: 22251563 PMCID: PMC7615846 DOI: 10.1016/b978-0-12-394304-0.00012-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Self-renewing cells of the vertebrate heart have become a major subject of interest in the past decade. However, many researchers had a hard time to argue against the orthodox textbook view that defines the heart as a postmitotic organ. Once the scientific community agreed on the existence of self-renewing cells in the vertebrate heart, their origin was again put on trial when transdifferentiation, dedifferentiation, and reprogramming could no longer be excluded as potential sources of self-renewal in the adult organ. Additionally, the presence of self-renewing pluripotent cells in the peripheral blood challenges the concept of tissue-specific stem and progenitor cells. Leaving these unsolved problems aside, it seems very desirable to learn about the basic biology of this unique cell type. Thus, we shall here paint a picture of cardiovascular progenitor cells including the current knowledge about their origin, basic nature, and the molecular mechanisms guiding proliferation and differentiation into somatic cells of the heart.
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Affiliation(s)
- Jasmin Taubenschmid
- Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
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48
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Li SSL. Characterization and gene expression profiling of five human embryonic stem cell lines derived in Taiwan. Methods Mol Biol 2012; 873:127-49. [PMID: 22528352 DOI: 10.1007/978-1-61779-794-1_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Human embryonic stem cell (hESC) lines have been derived from the inner cell mass of blastocysts. Five hESC lines have been derived from 32 discarded blastocysts in Taiwan, and these lines have since been continuously cultured on mitotically inactivated mouse embryonic fibroblasts as feeder in the hESC medium for more than 44 passages and underwent freezing/thawing processes. All of five hESC lines expressed characteristic undifferentiated hESC markers such as SSEA-4, TRA-1-81, alkaline phosphatase, TERT, transcription factors POU5F1 (OCT4), and NANOG. The hESC lines T1 and T3 possess normal female karyotypes, whereas lines T4 and T5 are normal male, but line T2 is male trisomy 12 (47XY,+12). The hESC lines T1, T2, T3, and T5 were able to produce teratomas in SCID mice, and line T4 could only form embryoid bodies in vitro. Global gene expression profiles of single colonies of these five hESC lines were analyzed using Affymetrix human genome U133 plus 2.0 GeneChip. The results showed that 4,145 transcripts, including 19% of unknown functions, were detected in all five hESC lines. Comparison of the 4,145 genes commonly expressed in the five hESC lines with those genes expressed in teratoma produced by hESC line T1 and placenta revealed 40 genes exclusively expressed in all five hESC lines. These 40 genes include the previously reported stemness genes such as POU5F1 (OCT4), NANOG, TDGF1 (CRIPTO), SALL4, LECT1, and BUB1 responsible for self-renewal and pluripotent differentiation. The global gene expression analysis also indicated that the TGFβ/activin branch components inhibin BC, ACVR2A, ACVR1 (ALK2), TGFBR1 (ALK5), and SMAD2 were found to be highly expressed in undifferentiated states of these five hESC lines and decreased upon differentiation. The epigenetic states and expression of 32 known imprinted genes in these five hESC lines and/or differentiated derivatives were also investigated. In short, the hESC nature of these five hESC lines is supported by the undifferentiated state, extensive renewal capacity, and pluripotency, including the ability to form teratomas and/or embryoid bodies; and these cell lines will be useful for research on human embryonic stem cell biology and drug development/toxicity testing. The epigenetic states and expression of imprinted genes in hESC lines should be thoroughly studied after extended culture and upon differentiation in order to understand epigenetic stability in hESC lines before their clinical applications.
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Affiliation(s)
- Steven Shoei-Lung Li
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
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49
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Lee S, Kim J, Park TJ, Shin Y, Lee SY, Han YM, Kang S, Park HS. The effects of the physical properties of culture substrates on the growth and differentiation of human embryonic stem cells. Biomaterials 2011; 32:8816-29. [DOI: 10.1016/j.biomaterials.2011.07.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/16/2011] [Indexed: 12/19/2022]
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50
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Amps K, Andrews PW, Anyfantis G, Armstrong L, Avery S, Baharvand H, Baker J, Baker D, Munoz MB, Beil S, Benvenisty N, Ben-Yosef D, Biancotti JC, Bosman A, Brena RM, Brison D, Caisander G, Camarasa MV, Chen J, Chiao E, Choi YM, Choo ABH, Collins D, Colman A, Crook JM, Daley GQ, Dalton A, De Sousa PA, Denning C, Downie J, Dvorak P, Montgomery KD, Feki A, Ford A, Fox V, Fraga AM, Frumkin T, Ge L, Gokhale PJ, Golan-Lev T, Gourabi H, Gropp M, Lu G, Hampl A, Harron K, Healy L, Herath W, Holm F, Hovatta O, Hyllner J, Inamdar MS, Irwanto AK, Ishii T, Jaconi M, Jin Y, Kimber S, Kiselev S, Knowles BB, Kopper O, Kukharenko V, Kuliev A, Lagarkova MA, Laird PW, Lako M, Laslett AL, Lavon N, Lee DR, Lee JE, Li C, Lim LS, Ludwig TE, Ma Y, Maltby E, Mateizel I, Mayshar Y, Mileikovsky M, Minger SL, Miyazaki T, Moon SY, Moore H, Mummery C, Nagy A, Nakatsuji N, Narwani K, Oh SKW, Oh SK, Olson C, Otonkoski T, Pan F, Park IH, Pells S, Pera MF, Pereira LV, Qi O, Raj GS, Reubinoff B, Robins A, Robson P, Rossant J, Salekdeh GH, Schulz TC, Sermon K, Sheik Mohamed J, Shen H, Sherrer E, Sidhu K, Sivarajah S, Skottman H, Spits C, Stacey GN, Strehl R, Strelchenko N, Suemori H, Sun B, Suuronen R, Takahashi K, Tuuri T, Venu P, Verlinsky Y, Ward-van Oostwaard D, Weisenberger DJ, Wu Y, Yamanaka S, Young L, Zhou Q. Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol 2011; 29:1132-44. [PMID: 22119741 PMCID: PMC3454460 DOI: 10.1038/nbt.2051] [Citation(s) in RCA: 417] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 10/26/2011] [Indexed: 02/07/2023]
Abstract
The International Stem Cell Initiative analyzed 125 human embryonic stem (ES) cell lines and 11 induced pluripotent stem (iPS) cell lines, from 38 laboratories worldwide, for genetic changes occurring during culture. Most lines were analyzed at an early and late passage. Single-nucleotide polymorphism (SNP) analysis revealed that they included representatives of most major ethnic groups. Most lines remained karyotypically normal, but there was a progressive tendency to acquire changes on prolonged culture, commonly affecting chromosomes 1, 12, 17 and 20. DNA methylation patterns changed haphazardly with no link to time in culture. Structural variants, determined from the SNP arrays, also appeared sporadically. No common variants related to culture were observed on chromosomes 1, 12 and 17, but a minimal amplicon in chromosome 20q11.21, including three genes expressed in human ES cells, ID1, BCL2L1 and HM13, occurred in >20% of the lines. Of these genes, BCL2L1 is a strong candidate for driving culture adaptation of ES cells.
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Affiliation(s)
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- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, UK
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