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Singh VK, Saini A, Kalsan M, Kumar N, Chandra R. Describing the Stem Cell Potency: The Various Methods of Functional Assessment and In silico Diagnostics. Front Cell Dev Biol 2016; 4:134. [PMID: 27921030 PMCID: PMC5118841 DOI: 10.3389/fcell.2016.00134] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/02/2016] [Indexed: 12/11/2022] Open
Abstract
Stem cells are defined by their capabilities to self-renew and give rise to various types of differentiated cells depending on their potency. They are classified as pluripotent, multipotent, and unipotent as demonstrated through their potential to generate the variety of cell lineages. While pluripotent stem cells may give rise to all types of cells in an organism, Multipotent and Unipotent stem cells remain restricted to the particular tissue or lineages. The potency of these stem cells can be defined by using a number of functional assays along with the evaluation of various molecular markers. These molecular markers include diagnosis of transcriptional, epigenetic, and metabolic states of stem cells. Many reports are defining the particular set of different functional assays, and molecular marker used to demonstrate the developmental states and functional capacities of stem cells. The careful evaluation of all these methods could help in generating standard identifying procedures/markers for them.
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Affiliation(s)
- Vimal K Singh
- Stem Cell Research Laboratory, Department of Biotechnology, Delhi Technological University Delhi, India
| | - Abhishek Saini
- Stem Cell Research Laboratory, Department of Biotechnology, Delhi Technological University Delhi, India
| | - Manisha Kalsan
- Stem Cell Research Laboratory, Department of Biotechnology, Delhi Technological University Delhi, India
| | - Neeraj Kumar
- Stem Cell Research Laboratory, Department of Biotechnology, Delhi Technological University Delhi, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi Delhi, India
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52
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duVerle DA, Yotsukura S, Nomura S, Aburatani H, Tsuda K. CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. BMC Bioinformatics 2016; 17:363. [PMID: 27620863 PMCID: PMC5020541 DOI: 10.1186/s12859-016-1175-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 08/11/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality reduction techniques, have been suggested to help infer and visualise the underlying structure of cell populations from single-cell expression levels, yet their models generally lack proper biological grounding and struggle at identifying complex differentiation paths. RESULTS Here we introduce cellTree: an R/Bioconductor package that uses a novel statistical approach, based on document analysis techniques, to produce tree structures outlining the hierarchical relationship between single-cell samples, while identifying latent groups of genes that can provide biological insights. CONCLUSIONS With cellTree, we provide experimentalists with an easy-to-use tool, based on statistically and biologically-sound algorithms, to efficiently explore and visualise single-cell RNA data. The cellTree package is publicly available in the online Bionconductor repository at: http://bioconductor.org/packages/cellTree/ .
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Affiliation(s)
- David A duVerle
- Graduate School of Frontier Sciences at the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Japan. .,Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, Japan.
| | - Sohiya Yotsukura
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Seitaro Nomura
- Genome Science Division, Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Laboratory of Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Tokyo, Japan
| | - Koji Tsuda
- Graduate School of Frontier Sciences at the University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Japan. .,Center for Materials Research by Information Integration, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Japan. .,Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, Japan.
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53
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Abstract
Embryonic pluripotency can be recapitulated in vitro by a spectrum of pluripotent stem cell states stabilized with different culture conditions. Their distinct spatiotemporal characteristics provide an unprecedented tool for the study of early human development. The newly unveiled ability of some stem cell types for crossing xeno-barriers will facilitate the generation of interspecies chimeric embryos from distant species, including humans. When combined with efficient zygote genome editing technologies, xenogeneic human pluripotent stem cells may also open new frontiers for regenerative medicine applications, including the possibility of generating human organs in animals via interspecies chimeric complementation.
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54
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Petropoulos S, Panula SP, Schell JP, Lanner F. Single-cell RNA sequencing: revealing human pre-implantation development, pluripotency and germline development. J Intern Med 2016; 280:252-64. [PMID: 27046137 DOI: 10.1111/joim.12493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Early human development is a dynamic, heterogeneous, complex and multidimensional process. During the first week, the single-cell zygote undergoes eight to nine rounds of cell division generating the multicellular blastocyst, which consists of hundreds of cells forming spatially organized embryonic and extra-embryonic tissues. At the level of transcription, degradation of maternal RNA commences at around the two-cell stage, coinciding with embryonic genome activation. Although numerous efforts have recently focused on delineating this process in humans, many questions still remain as thorough investigation has been limited by ethical issues, scarce availability of human embryos and the presence of minute amounts of DNA and RNA. In vitro cultures of embryonic stem cells provide some insight into early human development, but such studies have been confounded by analysis on a population level failing to appreciate cellular heterogeneity. Recent technical developments in single-cell RNA sequencing have provided a novel and powerful tool to explore the early human embryo in a systematic manner. In this review, we will discuss the advantages and disadvantages of the techniques utilized to specifically investigate human development and consider how the technology has yielded new insights into pre-implantation development, embryonic stem cells and the establishment of the germ line.
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Affiliation(s)
- S Petropoulos
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden.,Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - S P Panula
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| | - J P Schell
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| | - F Lanner
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
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55
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Tang WWC, Kobayashi T, Irie N, Dietmann S, Surani MA. Specification and epigenetic programming of the human germ line. Nat Rev Genet 2016; 17:585-600. [DOI: 10.1038/nrg.2016.88] [Citation(s) in RCA: 274] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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56
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Zhao XM, Cui LS, Hao HS, Wang HY, Zhao SJ, Du WH, Wang D, Liu Y, Zhu HB. Transcriptome analyses of inner cell mass and trophectoderm cells isolated by magnetic-activated cell sorting from bovine blastocysts using single cell RNA-seq. Reprod Domest Anim 2016; 51:726-35. [PMID: 27440443 DOI: 10.1111/rda.12737] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/21/2016] [Indexed: 12/31/2022]
Abstract
Research on bovine embryonic stem cells (bESCs) has been hampered because bESCs are cultured in conditions that are based on information obtained from culturing mouse and human inner cell mass (ICM) cells. The aim of this study was to compare gene expression in ICM and trophectoderm (TE) cell lineages of bovine embryos and to discuss the findings relative to information available for mice and humans. We separated a high-purity (>90%) ICM and TE from bovine blastocysts by magnetic-activated cell sorting and analysed their transcriptomes by single cell RNA-seq. Differentially expressed genes (DEGs) were assessed using Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) databases. Finally, qRT-PCR was performed to validate the RNA-seq results. From 207 DEGs identified (adjusted p ≤ .05; fold change ≥2), 159 and 48 had greater expression in the ICM and TE cells respectively. We validated 27 genes using qRT-PCR and found their expression patterns were mostly similar to those of RNA-seq, including 12 novel ICM-dominant (HNF4A, CCL24, FGFR4, IFITM3, PTCHD2, GJB5, FN1, KLK7, PRDM14, GRP, FGF19 and GCM1) and two novel TE-dominant (SLC10A1 and WNT4) genes. Bioinformatics analysis showed that these DEGs are involved in many important pathways, such as MAPK and cancer cell pathways, and these pathways have been shown to play essential roles in mouse and human ESCs in the self-renewal and pluripotent maintenance. As a conclusion, there were sufficient differences to allow us to conclude that the control of pluripotency in bovine ICM cells is species-specific.
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Affiliation(s)
- X-M Zhao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - L-S Cui
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - H-S Hao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - H-Y Wang
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - S-J Zhao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - W-H Du
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - D Wang
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Y Liu
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - H-B Zhu
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
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57
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Shahbazi MN, Jedrusik A, Vuoristo S, Recher G, Hupalowska A, Bolton V, Fogarty NNM, Campbell A, Devito L, Ilic D, Khalaf Y, Niakan KK, Fishel S, Zernicka-Goetz M. Self-organization of the human embryo in the absence of maternal tissues. Nat Cell Biol 2016; 18:700-708. [PMID: 27144686 PMCID: PMC5049689 DOI: 10.1038/ncb3347] [Citation(s) in RCA: 434] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 03/29/2016] [Indexed: 12/14/2022]
Abstract
Remodelling of the human embryo at implantation is indispensable for successful pregnancy. Yet it has remained mysterious because of the experimental hurdles that beset the study of this developmental phase. Here, we establish an in vitro system to culture human embryos through implantation stages in the absence of maternal tissues and reveal the key events of early human morphogenesis. These include segregation of the pluripotent embryonic and extra-embryonic lineages, and morphogenetic rearrangements leading to generation of a bilaminar disc, formation of a pro-amniotic cavity within the embryonic lineage, appearance of the prospective yolk sac, and trophoblast differentiation. Using human embryos and human pluripotent stem cells, we show that the reorganization of the embryonic lineage is mediated by cellular polarization leading to cavity formation. Together, our results indicate that the critical remodelling events at this stage of human development are embryo-autonomous, highlighting the remarkable and unanticipated self-organizing properties of human embryos.
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Affiliation(s)
- Marta N Shahbazi
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience; Downing Street, Cambridge, CB2 3DY, UK
| | - Agnieszka Jedrusik
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience; Downing Street, Cambridge, CB2 3DY, UK
| | - Sanna Vuoristo
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience; Downing Street, Cambridge, CB2 3DY, UK
| | - Gaelle Recher
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience; Downing Street, Cambridge, CB2 3DY, UK
| | - Anna Hupalowska
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience; Downing Street, Cambridge, CB2 3DY, UK
| | - Virginia Bolton
- Faculty of Life Sciences and Medicine, King's College London, Women's Health Academic Centre, Assisted Conception Unit, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Norah N M Fogarty
- Human Embryo and Stem Cell Laboratory, Francis Crick Institute, Mill Hill Laboratory, London, NW7 1AA, UK
| | - Alison Campbell
- CARE Fertility Group, John Webster House, 6 Lawrence Drive, Nottingham Business Park, Nottingham, NG8 6PZ, UK
| | - Liani Devito
- Faculty of Life Sciences and Medicine, King's College London, Women's Health Academic Centre, Assisted Conception Unit, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Dusko Ilic
- Faculty of Life Sciences and Medicine, King's College London, Women's Health Academic Centre, Assisted Conception Unit, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Yakoub Khalaf
- Faculty of Life Sciences and Medicine, King's College London, Women's Health Academic Centre, Assisted Conception Unit, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, Francis Crick Institute, Mill Hill Laboratory, London, NW7 1AA, UK
| | - Simon Fishel
- CARE Fertility Group, John Webster House, 6 Lawrence Drive, Nottingham Business Park, Nottingham, NG8 6PZ, UK
| | - Magdalena Zernicka-Goetz
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience; Downing Street, Cambridge, CB2 3DY, UK
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58
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Garg V, Morgani S, Hadjantonakis AK. Capturing Identity and Fate Ex Vivo: Stem Cells from the Mouse Blastocyst. Curr Top Dev Biol 2016; 120:361-400. [PMID: 27475857 DOI: 10.1016/bs.ctdb.2016.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During mouse preimplantation development, three molecularly, morphologically, and spatially distinct lineages are formed, the embryonic epiblast, the extraembryonic primitive endoderm, and the trophectoderm. Stem cell lines representing each of these lineages have now been derived and can be indefinitely maintained and expanded in culture, providing an unlimited source of material to study the interplay of tissue-specific transcription factors and signaling pathways involved in these fundamental cell fate decisions. Here we outline our current understanding of the derivation, maintenance, and properties of these in vitro stem cell models representing the preimplantation embryonic lineages.
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Affiliation(s)
- V Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, United States
| | - S Morgani
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - A-K Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, United States.
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59
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Ávila-González D, García-López G, García-Castro IL, Flores-Herrera H, Molina-Hernández A, Portillo W, Díaz NF. Capturing the ephemeral human pluripotent state. Dev Dyn 2016; 245:762-73. [PMID: 27004967 DOI: 10.1002/dvdy.24405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 12/22/2022] Open
Abstract
During human development, pluripotency is present only in early stages of development. This ephemeral cell potential can be captured in vitro by obtaining pluripotent stem cells (PSC) with self-renewal properties, the human embryonic stem cells (hESC). However, diverse studies suggest the existence of a plethora of human PSC (hPSC) that can be derived from both embryonic and somatic sources, depending on defined culture conditions, their spatial origin, and the genetic engineering used for reprogramming. This review will focus on hPSC, covering the conventional primed hESC, naïve-like hPSC that resemble the ground-state of development, region-selective PSC, and human induced PSC (hiPSC). We will analyze differences and similarities in their differentiation potential as well as in the molecular circuitry of pluripotency. Finally, we describe the need for human feeder cells to derive and maintain hPSC, because they could emulate the interaction of in vivo pluripotent cells with extraembryonic structures that support development. Developmental Dynamics 245:762-773, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Daniela Ávila-González
- Departamento de Biología Celular, Instituto Nacional de Perinatología, México D.F., México
| | - Guadalupe García-López
- Departamento de Biología Celular, Instituto Nacional de Perinatología, México D.F., México
| | | | - Héctor Flores-Herrera
- Departamento de Inmunobioquímica, Instituto Nacional de Perinatología, Lomas Virreyes, México D.F., México
| | | | - Wendy Portillo
- Departamento de Neurobiología Conductual y Cognitiva, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, México
| | - Néstor Fabián Díaz
- Departamento de Biología Celular, Instituto Nacional de Perinatología, México D.F., México
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60
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Self-organization of the in vitro attached human embryo. Nature 2016; 533:251-4. [DOI: 10.1038/nature17948] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/30/2016] [Indexed: 12/23/2022]
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61
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Van der Jeught M, Taelman J, Duggal G, Ghimire S, Lierman S, Chuva de Sousa Lopes SM, Deforce D, Deroo T, De Sutter P, Heindryckx B. Application Of Small Molecules Favoring Naïve Pluripotency during Human Embryonic Stem Cell Derivation. Cell Reprogram 2016; 17:170-80. [PMID: 26053517 DOI: 10.1089/cell.2014.0085] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In mice, inhibition of both the fibroblast growth factor (FGF) mitogen-activated protein kinase kinase/extracellular-signal regulated kinase (MEK/Erk) and the Wnt signaling inhibitor glycogen synthase-3β (GSK3β) enables the derivation of mouse embryonic stem cells (mESCs) from nonpermissive strains in the presence of leukemia inhibitory factor (LIF). Whereas mESCs are in an uncommitted naïve state, human embryonic stem cells (hESCs) represent a more advanced state, denoted as primed pluripotency. This burdens hESCs with a series of characteristics, which, in contrast to naïve ESCs, makes them not ideal for key applications such as cell-based clinical therapies and human disease modeling. In this study, different small molecule combinations were applied during human ESC derivation. Hereby, we aimed to sustain the naïve pluripotent state, by interfering with various key signaling pathways. First, we tested several combinations on existing, 2i (PD0325901 and CHIR99021)-derived mESCs. All combinations were shown to be equally adequate to sustain the expression of naïve pluripotency markers. Second, these conditions were tested during hESC derivation. Overall, the best results were observed in the presence of medium supplemented with 2i, LIF, and the noncanonical Wnt signaling agonist Wnt5A, alone and combined with epinephrine. In these conditions, outgrowths repeatedly showed an ESC progenitor-like morphology, starting from day 3. Culturing these "progenitor cells" did not result in stable, naïve hESC lines in the current conditions. Although Wnt5A could not promote naïve hESC derivation, we found that it was sustaining the conversion of established hESCs toward a more naïve state. Future work should aim to distinct the effects of the various culture formulations, including our Wnt5A-supplemented medium, reported to promote stable naïve pluripotency in hESCs.
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Affiliation(s)
- Margot Van der Jeught
- 1 Ghent Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital , 9000 Ghent, Belgium .,4 These authors contributed equally to this work
| | - Jasin Taelman
- 1 Ghent Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital , 9000 Ghent, Belgium .,4 These authors contributed equally to this work
| | - Galbha Duggal
- 1 Ghent Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital , 9000 Ghent, Belgium
| | - Sabitri Ghimire
- 1 Ghent Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital , 9000 Ghent, Belgium
| | - Sylvie Lierman
- 1 Ghent Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital , 9000 Ghent, Belgium
| | - Susana M Chuva de Sousa Lopes
- 1 Ghent Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital , 9000 Ghent, Belgium .,2 Department of Anatomy and Embryology, Leiden University Medical Center , 2300 Leiden, The Netherlands
| | - Dieter Deforce
- 3 Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University , 9000 Ghent, Belgium
| | - Tom Deroo
- 1 Ghent Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital , 9000 Ghent, Belgium
| | - Petra De Sutter
- 1 Ghent Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital , 9000 Ghent, Belgium
| | - Björn Heindryckx
- 1 Ghent Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital , 9000 Ghent, Belgium
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62
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Guo G, von Meyenn F, Santos F, Chen Y, Reik W, Bertone P, Smith A, Nichols J. Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass. Stem Cell Reports 2016; 6:437-446. [PMID: 26947977 PMCID: PMC4834040 DOI: 10.1016/j.stemcr.2016.02.005] [Citation(s) in RCA: 261] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 02/07/2016] [Accepted: 02/08/2016] [Indexed: 12/31/2022] Open
Abstract
Conventional generation of stem cells from human blastocysts produces a developmentally advanced, or primed, stage of pluripotency. In vitro resetting to a more naive phenotype has been reported. However, whether the reset culture conditions of selective kinase inhibition can enable capture of naive epiblast cells directly from the embryo has not been determined. Here, we show that in these specific conditions individual inner cell mass cells grow into colonies that may then be expanded over multiple passages while retaining a diploid karyotype and naive properties. The cells express hallmark naive pluripotency factors and additionally display features of mitochondrial respiration, global gene expression, and genome-wide hypomethylation distinct from primed cells. They transition through primed pluripotency into somatic lineage differentiation. Collectively these attributes suggest classification as human naive embryonic stem cells. Human counterparts of canonical mouse embryonic stem cells would argue for conservation in the phased progression of pluripotency in mammals. Karyotypically normal pluripotent stem cells derived from single human ICM cells Expanded lines retain anticipated molecular features of naive embryonic stem cells Consistency between ICM-derived and in vitro reset naive human pluripotent stem cells Presence of KLF17 protein in human ICM and naive stem cells
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Affiliation(s)
- Ge Guo
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | | | - Fatima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Yaoyao Chen
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Paul Bertone
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Austin Smith
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 4BG, UK.
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63
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Geens M, Seriola A, Barbé L, Santalo J, Veiga A, Dée K, Van Haute L, Sermon K, Spits C. Female human pluripotent stem cells rapidly lose X chromosome inactivation marks and progress to a skewed methylation pattern during culture. Mol Hum Reprod 2016; 22:285-98. [DOI: 10.1093/molehr/gaw004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/13/2016] [Indexed: 12/25/2022] Open
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Harvey AJ, Rathjen J, Gardner DK. Metaboloepigenetic Regulation of Pluripotent Stem Cells. Stem Cells Int 2015; 2016:1816525. [PMID: 26839556 PMCID: PMC4709785 DOI: 10.1155/2016/1816525] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/29/2015] [Indexed: 12/19/2022] Open
Abstract
The differentiation of pluripotent stem cells is associated with extensive changes in metabolism, as well as widespread remodeling of the epigenetic landscape. Epigenetic regulation is essential for the modulation of differentiation, being responsible for cell type specific gene expression patterns through the modification of DNA and histones, thereby establishing cell identity. Each cell type has its own idiosyncratic pattern regarding the use of specific metabolic pathways. Rather than simply being perceived as a means of generating ATP and building blocks for cell growth and division, cellular metabolism can directly influence cellular regulation and the epigenome. Consequently, the significance of nutrients and metabolites as regulators of differentiation is central to understanding how cells interact with their immediate environment. This review serves to integrate studies on pluripotent stem cell metabolism, and the regulation of DNA methylation and acetylation and identifies areas in which current knowledge is limited.
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Affiliation(s)
- Alexandra J. Harvey
- Stem Cells Australia, Parkville, VIC 3010, Australia
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Joy Rathjen
- Stem Cells Australia, Parkville, VIC 3010, Australia
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- School of Medicine, University of Tasmania, Hobart, TAS 7000, Australia
| | - David K. Gardner
- Stem Cells Australia, Parkville, VIC 3010, Australia
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
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Ji F, Hu AB. Hepatic differentiation of pluripotent stem cells. Shijie Huaren Xiaohua Zazhi 2015; 23:5101-5106. [DOI: 10.11569/wcjd.v23.i32.5101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pluripotent stem cell mainly contain two types: embryonic stem cell (ESC) and induced pluripotent stem cell (iPSC). Their hepatic differentiation and application in transplantation may make them serve as new seed cells for replacement therapy and become an effective adjunctive therapy for end-stage hepatic diseases. Recently, great progress has been made in the research of stem cell technology. For example, iPSCs can maintain pluripotency, and the application of iPSCs can avoid the ethical issues associated with the use of ESCs. The research of differentiation of stem cells has greatly shifted from differentiation into hepatic single-cell lineage to differentiation into liver tissues. All of these can improve the development of replacement therapy, and update the basic knowledge of ectogenesis of the liver.
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De Los Angeles A, Ferrari F, Xi R, Fujiwara Y, Benvenisty N, Deng H, Hochedlinger K, Jaenisch R, Lee S, Leitch HG, Lensch MW, Lujan E, Pei D, Rossant J, Wernig M, Park PJ, Daley GQ. Hallmarks of pluripotency. Nature 2015; 525:469-78. [PMID: 26399828 DOI: 10.1038/nature15515] [Citation(s) in RCA: 276] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/26/2015] [Indexed: 12/20/2022]
Abstract
Stem cells self-renew and generate specialized progeny through differentiation, but vary in the range of cells and tissues they generate, a property called developmental potency. Pluripotent stem cells produce all cells of an organism, while multipotent or unipotent stem cells regenerate only specific lineages or tissues. Defining stem-cell potency relies upon functional assays and diagnostic transcriptional, epigenetic and metabolic states. Here we describe functional and molecular hallmarks of pluripotent stem cells, propose a checklist for their evaluation, and illustrate how forensic genomics can validate their provenance.
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Affiliation(s)
- Alejandro De Los Angeles
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children's Hospital Boston, and Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Francesco Ferrari
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ruibin Xi
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.,School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China
| | - Yuko Fujiwara
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children's Hospital Boston, and Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Nissim Benvenisty
- Stem Cell Unit, Department of Genetics, Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Hongkui Deng
- College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Konrad Hochedlinger
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, Massachusetts 02114, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Soohyun Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Harry G Leitch
- Medical Research Council Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - M William Lensch
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children's Hospital Boston, and Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Ernesto Lujan
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
| | - Duanqing Pei
- South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Janet Rossant
- The Hospital for Sick Children Research Institute, Toronto, Ontario ON M5G 0A4, Canada
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - George Q Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children's Hospital Boston, and Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
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Zdravkovic T, Nazor KL, Larocque N, Gormley M, Donne M, Hunkapillar N, Giritharan G, Bernstein HS, Wei G, Hebrok M, Zeng X, Genbacev O, Mattis A, McMaster MT, Krtolica A, Valbuena D, Simón C, Laurent LC, Loring JF, Fisher SJ. Human stem cells from single blastomeres reveal pathways of embryonic or trophoblast fate specification. Development 2015; 142:4010-25. [PMID: 26483210 PMCID: PMC4712832 DOI: 10.1242/dev.122846] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 10/05/2015] [Indexed: 01/04/2023]
Abstract
Mechanisms of initial cell fate decisions differ among species. To gain insights into lineage allocation in humans, we derived ten human embryonic stem cell lines (designated UCSFB1-10) from single blastomeres of four 8-cell embryos and one 12-cell embryo from a single couple. Compared with numerous conventional lines from blastocysts, they had unique gene expression and DNA methylation patterns that were, in part, indicative of trophoblast competence. At a transcriptional level, UCSFB lines from different embryos were often more closely related than those from the same embryo. As predicted by the transcriptomic data, immunolocalization of EOMES, T brachyury, GDF15 and active β-catenin revealed differential expression among blastomeres of 8- to 10-cell human embryos. The UCSFB lines formed derivatives of the three germ layers and CDX2-positive progeny, from which we derived the first human trophoblast stem cell line. Our data suggest heterogeneity among early-stage blastomeres and that the UCSFB lines have unique properties, indicative of a more immature state than conventional lines.
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Affiliation(s)
- Tamara Zdravkovic
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kristopher L Nazor
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas Larocque
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew Gormley
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew Donne
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Nathan Hunkapillar
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Harold S Bernstein
- The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Grace Wei
- The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Diabetes Center, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthias Hebrok
- Diabetes Center, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Xianmin Zeng
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Olga Genbacev
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Aras Mattis
- The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Michael T McMaster
- The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Diana Valbuena
- Fundación Instituto Valenciano de Infertilidad (IVI), Parc Científic Universitat de València, 46980, Valencia, Spain
| | - Carlos Simón
- Fundación Instituto Valenciano de Infertilidad (IVI), Parc Científic Universitat de València, 46980, Valencia, Spain
| | - Louise C Laurent
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA Department of Reproductive Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeanne F Loring
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Susan J Fisher
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA Division of Maternal Fetal Medicine, University of California San Francisco, San Francisco, CA 94143, USA Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA The Eli & Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA Human Embryonic Stem Cell Program, University of California San Francisco, San Francisco, CA 94143, USA Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
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Qiu D, Ye S, Ruiz B, Zhou X, Liu D, Zhang Q, Ying QL. Klf2 and Tfcp2l1, Two Wnt/β-Catenin Targets, Act Synergistically to Induce and Maintain Naive Pluripotency. Stem Cell Reports 2015; 5:314-22. [PMID: 26321140 PMCID: PMC4618593 DOI: 10.1016/j.stemcr.2015.07.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 11/30/2022] Open
Abstract
Activation of Wnt/β-catenin signaling can induce both self-renewal and differentiation in naive pluripotent embryonic stem cells (ESCs). To gain insights into the mechanism by which Wnt/β-catenin regulates ESC fate, we screened and characterized its downstream targets. Here, we show that the self-renewal-promoting effect of Wnt/β-catenin signaling is mainly mediated by two of its downstream targets, Klf2 and Tfcp2l1. Forced expression of Klf2 and Tfcp2l1 can not only induce reprogramming of primed state pluripotency into naive state ESCs, but also is sufficient to maintain the naive pluripotent state of ESCs. Conversely, downregulation of Klf2 and Tfcp2l1 impairs ESC self-renewal mediated by Wnt/β-catenin signaling. Our study therefore establishes the pivotal role of Klf2 and Tfcp2l1 in mediating ESC self-renewal promoted by Wnt/β-catenin signaling. Klf2 and Tfcp2l1 are downstream targets of Wnt/β-catenin Klf2 and Tfcp2l1 overexpression maintains mESC self-renewal Downregulation of Klf2 and Tfcp2l1 impairs mESC self-renewal mediated by 2i KLF2 and TFCP2L1 promote reprogramming of EpiSCs to naive ESCs
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Affiliation(s)
- Dongbo Qiu
- Guangdong Provincial Key Laboratory of Liver Disease, Cell-Gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, PRC; Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, University of Southern California, Los Angeles, CA 90033, USA
| | - Shoudong Ye
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, University of Southern California, Los Angeles, CA 90033, USA; Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei 230601, PRC
| | - Bryan Ruiz
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, University of Southern California, Los Angeles, CA 90033, USA
| | - Xingliang Zhou
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, University of Southern California, Los Angeles, CA 90033, USA
| | - Dahai Liu
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei 230601, PRC
| | - Qi Zhang
- Guangdong Provincial Key Laboratory of Liver Disease, Cell-Gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, PRC
| | - Qi-Long Ying
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, University of Southern California, Los Angeles, CA 90033, USA.
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69
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Manor YS, Massarwa R, Hanna JH. Establishing the human naïve pluripotent state. Curr Opin Genet Dev 2015; 34:35-45. [PMID: 26291026 DOI: 10.1016/j.gde.2015.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 02/08/2023]
Abstract
Pluripotency is first assembled within the inner-cell-mass of developing pre-implantation blastocysts, and is gradually reconfigured and dismantled during early post-implantation development, before overt differentiation into somatic lineages ensues. This transition from pre-implantation to post-implantation pluripotent states, respectively referred to as naïve and primed, is accompanied by dramatic changes in molecular and functional characteristics. Remarkably, pluripotent states can be artificially preserved in a self-renewing state in vitro by continuous supplementation of a variety of exogenous cytokines and small molecule inhibitors. Different exogenous factors endow the cells with distinct configurations of pluripotency that have direct influence on stem cell characteristics both in mice and humans. Here we overview pluripotent states captured from rodents and humans under different growth conditions, and provide a conceptual framework for classifying pluripotent cell states on the basis of a combination of multiple characteristics that a pluripotent cell can simultaneously retain. We further highlight the complexity and dynamic nature of these artificially isolated in vitro pluripotent states in humans.
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Affiliation(s)
- Yair S Manor
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rada Massarwa
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Jacob H Hanna
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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70
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Krivega M, Essahib W, Van de Velde H. WNT3 and membrane-associated β-catenin regulate trophectoderm lineage differentiation in human blastocysts. Mol Hum Reprod 2015; 21:711-22. [DOI: 10.1093/molehr/gav036] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 06/22/2015] [Indexed: 12/29/2022] Open
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Van der Jeught M, O'Leary T, Duggal G, De Sutter P, Chuva de Sousa Lopes S, Heindryckx B. The post-inner cell mass intermediate: implications for stem cell biology and assisted reproductive technology. Hum Reprod Update 2015; 21:616-26. [PMID: 26089403 DOI: 10.1093/humupd/dmv028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 06/01/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Until recently, the temporal events that precede the generation of pluripotent embryonic stem cells (ESCs) and their equivalence with specific developmental stages in vivo was poorly understood. Our group has discovered the existence of a transient epiblast-like structure, coined the post-inner cell mass (ICM) intermediate or PICMI, that emerges before human ESC (hESCs) are established, which supports their primed nature (i.e. already showing some predispositions towards certain cell types) of pluripotency. METHODS The PICMI results from the progressive epithelialization of the ICM and it expresses a mixture of early and late epiblast markers, as well as some primordial germ cell markers. The PICMI is a closer progenitor of hESCs than the ICM and it can be seen as the first proof of why all existing hESCs, until recently, display a primed state of pluripotency. RESULTS Even though the pluripotent characteristics of ESCs differ from mouse (naïve) to human (primed), it has recently been shown in mice that a similar process of self-organization at the transition from ICM to (naïve) mouse ESCs (mESCs) transforms the amorphous ICM into a rosette of polarized epiblast cells, a mouse PICMI. The transient PICMI stage is therefore at the origin of both mESCs and hESCs. In addition, several groups have now reported the conversion from primed to the naïve (mESCs-like) hESCs, broadening the pluripotency spectrum and opening new opportunities for the use of pluripotent stem cells. CONCLUSIONS In this review, we discuss the recent discoveries of mouse and human transient states from ICM to ESCs and their relation towards the state of pluripotency in the eventual stem cells, being naïve or primed. We will now further investigate how these intermediate and/or different pluripotent stages may impact the use of human stem cells in regenerative medicine and assisted reproductive technology.
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Affiliation(s)
- Margot Van der Jeught
- Ghent Fertility and Stem Cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, Ghent 9000, Belgium
| | - Thomas O'Leary
- Ghent Fertility and Stem Cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, Ghent 9000, Belgium Present address: Coastal Fertility Specialists, 1375 Hospital Drive, Mt Pleasant, SC 29464, USA
| | - Galbha Duggal
- Ghent Fertility and Stem Cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, Ghent 9000, Belgium Present address: Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Petra De Sutter
- Ghent Fertility and Stem Cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, Ghent 9000, Belgium
| | - Susana Chuva de Sousa Lopes
- Ghent Fertility and Stem Cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, Ghent 9000, Belgium Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Björn Heindryckx
- Ghent Fertility and Stem Cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, Ghent 9000, Belgium
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Abstract
Mouse embryonic stem (ES) cells perpetuate in vitro the broad developmental potential of naïve founder cells in the preimplantation embryo. ES cells self-renew relentlessly in culture but can reenter embryonic development seamlessly, differentiating on schedule to form all elements of the fetus. Here we review the properties of these remarkable cells. Arising from the stability, homogeneity, and equipotency of ES cells, we consider the concept of a pluripotent ground state. We evaluate the authenticity of ES cells in relation to cells in the embryo and examine their utility for dissecting mechanisms that confer pluripotency and that execute fate choice. We summarize current knowledge of the transcription factor circuitry that governs the ES cell state and discuss the opportunity to expose molecular logic further through iterative computational modeling and experimentation. Finally, we present a perspective on unresolved questions, including the challenge of deriving ground state pluripotent stem cells from non-rodent species.
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Ghimire S, Heindryckx B, Van der Jeught M, Neupane J, O'Leary T, Lierman S, De Vos WH, Chuva de Sousa Lopes S, Deroo T, De Sutter P. Inhibition of transforming growth factor β signaling promotes epiblast formation in mouse embryos. Stem Cells Dev 2015; 24:497-506. [PMID: 25245024 DOI: 10.1089/scd.2014.0206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Early lineage segregation in preimplantation embryos and maintenance of pluripotency in embryonic stem cells (ESCs) are both regulated by specific signaling pathways. Small molecules have been shown to modulate these signaling pathways. We examined the influence of several small molecules and growth factors on second-lineage segregation of the inner cell mass toward hypoblast and epiblast lineage during mouse embryonic preimplantation development. We found that the second-lineage segregation is influenced by activation or inhibition of the transforming growth factor (TGF)β pathway. Inhibition of the TGFβ pathway from the two-cell, four-cell, and morula stages onward up to the blastocyst stage significantly increased the epiblast cell proliferation. The epiblast formed in the embryos in which TGFβ signaling was inhibited was fully functional as demonstrated by the potential of these epiblast cells to give rise to pluripotent ESCs. Conversely, activating the TGFβ pathway reduced epiblast formation. Inhibition of the glycogen synthase kinase (GSK)3 pathway and activation of bone morphogenetic protein 4 signaling reduced the formation of both epiblast and hypoblast cells. Activation of the protein kinase A pathway and of the Janus kinase/signal transducer and activator of transcription 3 pathway did not influence the second-lineage segregation in mouse embryos. The simultaneous inhibition of three pathways--TGFβ, GSK3β, and the fibroblast growth factor (FGF)/extracellular signal-regulated kinases (Erk)--significantly enhanced the proliferation of epiblast cells than that caused by inhibition of either TGFβ pathway alone or by combined inhibition of the GSK3β and FGF/Erk pathways only.
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Affiliation(s)
- Sabitri Ghimire
- 1 Ghent Fertility and Stem Cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital , Ghent, Belgium
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Duggal G, Heindryckx B, Warrier S, Taelman J, Van der Jeught M, Deforce D, Chuva de Sousa Lopes S, De Sutter P. Exogenous supplementation of Activin A enhances germ cell differentiation of human embryonic stem cells. Mol Hum Reprod 2015; 21:410-23. [PMID: 25634576 DOI: 10.1093/molehr/gav004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 01/26/2015] [Indexed: 01/15/2023] Open
Abstract
Human embryonic stem cells (hESCs) derived in the presence of Activin A (ActA) demonstrate an increased differentiation propensity toward the germ cell lineage. In addition, mouse epiblast stem cells and mouse epiblast-like cells are poised toward germ cell differentiation and are derived in the presence of ActA. We therefore investigated whether supplementation with ActA enhances in vitro hESC differentiation toward germ cell lineage. ActA up-regulated early primordial germ cell (PGC) genes STELLA/DPPA3 (developmental pluripotency associated 3) and tyrosine kinase receptor cKIT in both ActA-derived and standard-derived hESCs indicating its role in priming hESCs toward the PGC lineage. Indeed, ActA plus bone morphogenic protein 4 (BMP4) strongly increased germ cell differentiation potential of hESCs based on the high expression of late PGC markers DAZL (deleted in azoospermia-like) and VASA/DDX4 (DEAD-box polypeptide 4) at mRNA and protein level. Hence, the combination of ActA with BMP4 provides an additional boost for hESCs to develop into postmigratory germ cells. Together with increased VASA expression in the presence of ActA and BMP4, we also observed up-regulation of endoderm-specific genes GATA4 (GATA binding protein 4) and GATA6. Finally, we were able to further mature these in vitro-derived PGC-like cells (PGCLCs) by culturing them in in vitro maturation (IVM) medium, resulting in the formation of germ cell-like clusters and induction of meiotic gene expression. In conclusion, we demonstrate for the first time a synergism between ActA and BMP4 in facilitating germ cell-directed differentiation of hESCs, which is enhanced by extended culture in IVM medium, as shown by cytoplasmic VASA-expressing PGCLCs. We propose a novel relationship between the endoderm and germ cell lineage during hESC differentiation.
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Affiliation(s)
- Galbha Duggal
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Björn Heindryckx
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Sharat Warrier
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Jasin Taelman
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Margot Van der Jeught
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Susana Chuva de Sousa Lopes
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Petra De Sutter
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
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Huang G, Ye S, Zhou X, Liu D, Ying QL. Molecular basis of embryonic stem cell self-renewal: from signaling pathways to pluripotency network. Cell Mol Life Sci 2015; 72:1741-57. [PMID: 25595304 DOI: 10.1007/s00018-015-1833-2] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 12/17/2014] [Accepted: 01/08/2015] [Indexed: 12/18/2022]
Abstract
Embryonic stem cells (ESCs) can be maintained in culture indefinitely while retaining the capacity to generate any type of cell in the body, and therefore not only hold great promise for tissue repair and regeneration, but also provide a powerful tool for modeling human disease and understanding biological development. In order to fulfill the full potential of ESCs, it is critical to understand how ESC fate, whether to self-renew or to differentiate into specialized cells, is regulated. On the molecular level, ESC fate is controlled by the intracellular transcriptional regulatory networks that respond to various extrinsic signaling stimuli. In this review, we discuss and compare important signaling pathways in the self-renewal and differentiation of mouse, rat, and human ESCs with an emphasis on how these pathways integrate into ESC-specific transcription circuitries. This will be beneficial for understanding the common and conserved mechanisms that govern self-renewal, and for developing novel culture conditions that support ESC derivation and maintenance.
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Affiliation(s)
- Guanyi Huang
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, 230601, PR China
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76
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Abstract
Pluripotent cells in embryos are situated near the apex of the hierarchy of developmental potential. They are capable of generating all cell types of the mammalian body proper. Therefore, they are the exemplar of stem cells. In vivo, pluripotent cells exist transiently and become expended within a few days of their establishment. Yet, when explanted into artificial culture conditions, they can be indefinitely propagated in vitro as pluripotent stem cell lines. A host of transcription factors and regulatory genes are now known to underpin the pluripotent state. Nonetheless, how pluripotent cells are equipped with their vast multilineage differentiation potential remains elusive. Consensus holds that pluripotency transcription factors prevent differentiation by inhibiting the expression of differentiation genes. However, this does not explain the developmental potential of pluripotent cells. We have presented another emergent perspective, namely, that pluripotency factors function as lineage specifiers that enable pluripotent cells to differentiate into specific lineages, therefore endowing pluripotent cells with their multilineage potential. Here we provide a comprehensive overview of the developmental biology, transcription factors, and extrinsic signaling associated with pluripotent cells, and their accompanying subtypes, in vitro heterogeneity and chromatin states. Although much has been learned since the appreciation of mammalian pluripotency in the 1950s and the derivation of embryonic stem cell lines in 1981, we will specifically emphasize what currently remains unclear. However, the view that pluripotency factors capacitate differentiation, recently corroborated by experimental evidence, might perhaps address the long-standing question of how pluripotent cells are endowed with their multilineage differentiation potential.
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Affiliation(s)
- Kyle M. Loh
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
| | - Bing Lim
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
| | - Lay Teng Ang
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
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77
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Richter A, Valdimarsdottir L, Hrafnkelsdottir HE, Runarsson JF, Omarsdottir AR, Ward-van Oostwaard D, Mummery C, Valdimarsdottir G. BMP4 promotes EMT and mesodermal commitment in human embryonic stem cells via SLUG and MSX2. Stem Cells 2014; 32:636-48. [PMID: 24549638 DOI: 10.1002/stem.1592] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 10/08/2013] [Accepted: 10/12/2013] [Indexed: 01/05/2023]
Abstract
Bone morphogenetic proteins (BMPs) initiate differentiation in human embryonic stem cells (hESCs) but the exact mechanisms have not been fully elucidated. We demonstrate here that SLUG and MSX2, transcription factors involved in epithelial-mesenchymal transitions, essential features of gastrulation in development and tumor progression, are important mediators of BMP4-induced differentiation in hESCs. Phosphorylated Smad1/5/8 colocalized with the SLUG protein at the edges of hESC colonies where differentiation takes place. The upregulation of the BMP target SLUG was direct as shown by the binding of phosphorylated Smad1/5/8 to its promoter, which interrupted the formation of adhesion proteins, resulting in migration. Knockdown of SLUG by short hairpin RNA blocked these changes, confirming an important role for SLUG in BMP-mediated mesodermal differentiation. Furthermore, BMP4-induced MSX2 expression leads to mesoderm formation and then preferential differentiation toward the cardiovascular lineage.
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Affiliation(s)
- Anne Richter
- Department of Biochemistry and Molecular Biology, BioMedical Center, University of Iceland, Iceland
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78
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Ye S, Liu D, Ying QL. Signaling pathways in induced naïve pluripotency. Curr Opin Genet Dev 2014; 28:10-5. [PMID: 25173148 DOI: 10.1016/j.gde.2014.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/29/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
Abstract
Pluripotent stem cells have become powerful tools for both research and regenerative medicine. To date, however, only mouse and rat embryonic stem cells (ESCs)/induced pluripotent stem cells (iPSCs) have the ability to contribute to the formation of germline-competent chimeras. These stem cells are thus considered as 'naïve' pluripotent stem cells. Several signaling pathways have been identified to play a critical role in the induction and maintenance of this naïve pluripotent state. Understanding how these pathways induce and maintain naïve pluripotency will likely lead to the generation of germline-competent naïve ESCs/iPSCs from humans and animals phylogenetically close to humans.
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Affiliation(s)
- Shoudong Ye
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei 230601, PR China; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Dahai Liu
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei 230601, PR China
| | - Qi-Long Ying
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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79
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Payer B, Lee JT. Coupling of X-chromosome reactivation with the pluripotent stem cell state. RNA Biol 2014; 11:798-807. [PMID: 25137047 DOI: 10.4161/rna.29779] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
X-chromosome inactivation (XCI) in female mammals is a dramatic example of epigenetic gene regulation, which entails the silencing of an entire chromosome through a wide range of mechanisms involving noncoding RNAs, chromatin-modifications, and DNA-methylation. While XCI is associated with the differentiated cell state, it is reversed by X-chromosome reactivation (XCR) ex vivo in pluripotent stem cells and in vivo in the early mouse embryo and the germline. Critical in the regulation of XCI vs. XCR is the X-inactivation center, a multigene locus on the X-chromosome harboring several long noncoding RNA genes including, most prominently, Xist and Tsix. These genes, which sit at the top of the XCI hierarchy, are by themselves controlled by pluripotency factors, coupling XCR with the naïve pluripotent stem cell state. In this point-of-view article we review the latest findings regarding this intricate relationship between cell differentiation state and epigenetic control of the X-chromosome. In particular, we discuss the emerging picture of complex multifactorial regulatory mechanisms, ensuring both a fine-tuned and robust X-reactivation process.
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Affiliation(s)
- Bernhard Payer
- Howard Hughes Medical Institute; Department of Molecular Biology; Massachusetts General Hospital; Department of Genetics; Harvard Medical School; Boston, MA USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute; Department of Molecular Biology; Massachusetts General Hospital; Department of Genetics; Harvard Medical School; Boston, MA USA
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80
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Guo H, Zhu P, Yan L, Li R, Hu B, Lian Y, Yan J, Ren X, Lin S, Li J, Jin X, Shi X, Liu P, Wang X, Wang W, Wei Y, Li X, Guo F, Wu X, Fan X, Yong J, Wen L, Xie SX, Tang F, Qiao J. The DNA methylation landscape of human early embryos. Nature 2014; 511:606-10. [PMID: 25079557 DOI: 10.1038/nature13544] [Citation(s) in RCA: 643] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 05/30/2014] [Indexed: 12/23/2022]
Abstract
DNA methylation is a crucial element in the epigenetic regulation of mammalian embryonic development. However, its dynamic patterns have not been analysed at the genome scale in human pre-implantation embryos due to technical difficulties and the scarcity of required materials. Here we systematically profile the methylome of human early embryos from the zygotic stage through to post-implantation by reduced representation bisulphite sequencing and whole-genome bisulphite sequencing. We show that the major wave of genome-wide demethylation is complete at the 2-cell stage, contrary to previous observations in mice. Moreover, the demethylation of the paternal genome is much faster than that of the maternal genome, and by the end of the zygotic stage the genome-wide methylation level in male pronuclei is already lower than that in female pronuclei. The inverse correlation between promoter methylation and gene expression gradually strengthens during early embryonic development, reaching its peak at the post-implantation stage. Furthermore, we show that active genes, with the trimethylation of histone H3 at lysine 4 (H3K4me3) mark at the promoter regions in pluripotent human embryonic stem cells, are essentially devoid of DNA methylation in both mature gametes and throughout pre-implantation development. Finally, we also show that long interspersed nuclear elements or short interspersed nuclear elements that are evolutionarily young are demethylated to a milder extent compared to older elements in the same family and have higher abundance of transcripts, indicating that early embryos tend to retain higher residual methylation at the evolutionarily younger and more active transposable elements. Our work provides insights into the critical features of the methylome of human early embryos, as well as its functional relation to the regulation of gene expression and the repression of transposable elements.
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Affiliation(s)
- Hongshan Guo
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2]
| | - Ping Zhu
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China [3]
| | - Liying Yan
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China [3]
| | - Rong Li
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China [3]
| | - Boqiang Hu
- Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China
| | - Ying Lian
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Jie Yan
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Xiulian Ren
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Shengli Lin
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Junsheng Li
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Xiaohu Jin
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Xiaodan Shi
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Ping Liu
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Xiaoye Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Wei Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Xianlong Li
- Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China
| | - Fan Guo
- Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China
| | - Xinglong Wu
- Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China
| | - Xiaoying Fan
- Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China
| | - Jun Yong
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Lu Wen
- Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China
| | - Sunney X Xie
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Fuchou Tang
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Jie Qiao
- 1] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
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81
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Hough SR, Thornton M, Mason E, Mar JC, Wells CA, Pera MF. Single-cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cells. Stem Cell Reports 2014; 2:881-95. [PMID: 24936473 PMCID: PMC4050352 DOI: 10.1016/j.stemcr.2014.04.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 04/23/2014] [Accepted: 04/24/2014] [Indexed: 12/11/2022] Open
Abstract
Pluripotent stem cells display significant heterogeneity in gene expression, but whether this diversity is an inherent feature of the pluripotent state remains unknown. Single-cell gene expression analysis in cell subsets defined by surface antigen expression revealed that human embryonic stem cell cultures exist as a continuum of cell states, even under defined conditions that drive self-renewal. The majority of the population expressed canonical pluripotency transcription factors and could differentiate into derivatives of all three germ layers. A minority subpopulation of cells displayed high self-renewal capacity, consistently high transcripts for all pluripotency-related genes studied, and no lineage priming. This subpopulation was characterized by its expression of a particular set of intercellular signaling molecules whose genes shared common regulatory features. Our data support a model of an inherently metastable self-renewing population that gives rise to a continuum of intermediate pluripotent states, which ultimately become primed for lineage specification. Single-cell transcript profiles characteristic of distinct substates of pluripotency Prospective isolation of substate with high self-renewal, no lineage priming Self-renewing subpopulation marked by expression of specific ligands and receptors
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Affiliation(s)
- Shelley R Hough
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA ; University of Melbourne, Melbourne, 3010 VIC, Australia
| | - Matthew Thornton
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Elizabeth Mason
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, 4072 QLD, Australia
| | - Jessica C Mar
- Department of Systems and Computational Biology and Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Christine A Wells
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, 4072 QLD, Australia
| | - Martin F Pera
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA ; University of Melbourne, Walter and Eliza Hall Institute of Medical Research, Florey Institute of Neuroscience and Mental Health, Melbourne, 3010 VIC, Australia
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82
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Vossaert L, Meert P, Scheerlinck E, Glibert P, Van Roy N, Heindryckx B, De Sutter P, Dhaenens M, Deforce D. Identification of histone H3 clipping activity in human embryonic stem cells. Stem Cell Res 2014; 13:123-34. [PMID: 24874291 DOI: 10.1016/j.scr.2014.05.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/29/2014] [Accepted: 05/02/2014] [Indexed: 01/17/2023] Open
Abstract
Posttranslational histone modifications are essential features in epigenetic regulatory networks. One of these modifications has remained largely understudied: regulated histone proteolysis. In analogy to the histone H3 clipping during early mouse embryonic stem cell differentiation, we report for the first time that also in human embryonic stem cells this phenomenon takes place in the two different analyzed cell lines. Employing complementary techniques, different cleavage sites could be identified, namely A21, R26 and residue 31. The enzyme responsible for this cleavage is found to be a serine protease. The formation of cleaved H3 follows a considerably variable pattern, depending on the timeframe, culture conditions and culture media applied. Contrary to earlier findings on H3 clipping, our results disconnect the link between declining Oct4 expression and H3 cleavage.
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Affiliation(s)
- Liesbeth Vossaert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Paulien Meert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Ellen Scheerlinck
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Pieter Glibert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Nadine Van Roy
- Department of Medical Genetics, Ghent University, Ghent, Belgium
| | - Björn Heindryckx
- Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Petra De Sutter
- Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Maarten Dhaenens
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium.
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83
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Condic ML. Totipotency: what it is and what it is not. Stem Cells Dev 2014; 23:796-812. [PMID: 24368070 PMCID: PMC3991987 DOI: 10.1089/scd.2013.0364] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 12/23/2013] [Indexed: 02/03/2023] Open
Abstract
There is surprising confusion surrounding the concept of biological totipotency, both within the scientific community and in society at large. Increasingly, ethical objections to scientific research have both practical and political implications. Ethical controversy surrounding an area of research can have a chilling effect on investors and industry, which in turn slows the development of novel medical therapies. In this context, clarifying precisely what is meant by "totipotency" and how it is experimentally determined will both avoid unnecessary controversy and potentially reduce inappropriate barriers to research. Here, the concept of totipotency is discussed, and the confusions surrounding this term in the scientific and nonscientific literature are considered. A new term, "plenipotent," is proposed to resolve this confusion. The requirement for specific, oocyte-derived cytoplasm as a component of totipotency is outlined. Finally, the implications of twinning for our understanding of totipotency are discussed.
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Affiliation(s)
- Maureen L Condic
- Department of Neurobiology, School of Medicine, University of Utah , Salt Lake City, Utah
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84
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De Paepe C, Krivega M, Cauffman G, Geens M, Van de Velde H. Totipotency and lineage segregation in the human embryo. ACTA ACUST UNITED AC 2014; 20:599-618. [DOI: 10.1093/molehr/gau027] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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85
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The States of Pluripotency: Pluripotent Lineage Development in the Embryo and in the Dish. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/208067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The pluripotent cell lineage of the embryo comprises a series of temporally and functionally distinct intermediary cell states, the epiblast precursor cell of the newly formed blastocyst, the epiblast population of the inner cell mass, and the early and late epiblast of the postimplantation embryo, referred to here as early and late primitive ectoderm. Pluripotent cell populations representative of the embryonic populations can be formed in culture. Although multiple pluripotent cell states are now recognised, little is known about the signals and pathways that progress cells from the epiblast precursor cell to the late primitive ectoderm in the embryo or in culture. The characterisation of cell states is most advanced in mouse where conditions for culturing distinct pluripotent cell states are well established and embryonic material is accessible. This review will focus on the pluripotent cell states present during embryonic development in the mouse and what is known of the mechanisms that regulate the progression of the lineage from the epiblast precursor cell and the ground state of pluripotency to the late primitive ectoderm present immediately prior to cell differentiation.
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86
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Duggal G, Heindryckx B, Deroo T, De Sutter P. Use of pluripotent stem cells for reproductive medicine: are we there yet? Vet Q 2014; 34:42-51. [DOI: 10.1080/01652176.2014.891061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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87
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How should we assess the safety of IVF technologies? Reprod Biomed Online 2013; 27:710-21. [DOI: 10.1016/j.rbmo.2013.09.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/03/2013] [Accepted: 09/05/2013] [Indexed: 11/22/2022]
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88
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Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor. EMBO J 2013; 32:2561-74. [PMID: 23942233 PMCID: PMC3791366 DOI: 10.1038/emboj.2013.177] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/16/2013] [Indexed: 02/02/2023] Open
Abstract
Self-renewal of pluripotent mouse embryonic stem (ES) cells is sustained by the cytokine leukaemia inhibitory factor (LIF) acting through the transcription factor Stat3. Several targets of Stat3 have previously been identified, most notably the reprogramming factor Klf4. However, such factors are neither required nor sufficient for the potent effect of LIF. We took advantage of Stat3 null ES cells to confirm that Stat3 mediates the self-renewal response to LIF. Through comparative transcriptome analysis intersected with genome location data, we arrived at a set of candidate transcription factor effectors. Among these, Tfcp2l1 (also known as Crtr-1) was most abundant. Constitutive expression of Tfcp2l1 at levels similar to those induced by LIF effectively substituted for LIF or Stat3 in sustaining clonal self-renewal and pluripotency. Conversely, knockdown of Tfcp2l1 profoundly compromised responsiveness to LIF. We further found that Tfcp2l1 is both necessary and sufficient to direct molecular reprogramming of post-implantation epiblast stem cells to naïve pluripotency. These results establish Tfcp2l1 as the principal bridge between LIF/Stat3 input and the transcription factor core of naïve pluripotency.
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89
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Welling M, Geijsen N. Uncovering the true identity of naïve pluripotent stem cells. Trends Cell Biol 2013; 23:442-8. [DOI: 10.1016/j.tcb.2013.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/10/2013] [Accepted: 04/10/2013] [Indexed: 01/08/2023]
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90
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Duggal G, Heindryckx B, Warrier S, O'Leary T, Van der Jeught M, Lierman S, Vossaert L, Deroo T, Deforce D, Chuva de Sousa Lopes SM, De Sutter P. Influence of activin A supplementation during human embryonic stem cell derivation on germ cell differentiation potential. Stem Cells Dev 2013; 22:3141-55. [PMID: 23829223 DOI: 10.1089/scd.2013.0024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Human embryonic stem cells (hESCs) are more similar to "primed" mouse epiblast stem cells (mEpiSCs). mEpiSCs, which are derived in Activin A, show an increased propensity to form primordial germ cell (PGC)-like cells in response to bone morphogenic protein 4 (BMP4). Hence, we hypothesized that hESCs derived in the presence of Activin A may be more competent in differentiating towards PGC-like cells after supplementation with BMP4 compared to standard hESC lines. We were able to successfully derive two hESC lines in the presence of Activin A, which were pluripotent and showed higher base levels of STELLA and cKIT compared to standard hESC lines derived without Activin A addition. Furthermore, upon differentiation as embryoid bodies in the presence of BMP4, we observed upregulation of VASA at day 7, both at the transcript and protein level compared to standard hESC lines, which appeared to take longer time for PGC specification. Unlike other hESC lines, nuclear pSMAD2/3 presence confirmed that Activin signalling was switched on in Activin A-derived hESC lines. They were also responsive to BMP4 based on nuclear detection of pSMAD1/5/8 and showed endodermal differentiation as a result of GATA-6 expression. Hence, our results provide novel insights into the impact of hESC derivation in the presence of Activin A and its subsequent influence on germ cell differentiation potential in vitro.
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Affiliation(s)
- Galbha Duggal
- 1 Department for Reproductive Medicine, Ghent University Hospital , Ghent, Belgium
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91
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Embryonic stem cell self-renewal pathways converge on the transcription factor Tfcp2l1. EMBO J 2013; 32:2548-60. [PMID: 23942238 DOI: 10.1038/emboj.2013.175] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/16/2013] [Indexed: 11/08/2022] Open
Abstract
Mouse embryonic stem cell (mESC) self-renewal can be maintained by activation of the leukaemia inhibitory factor (LIF)/signal transducer and activator of transcription 3 (Stat3) signalling pathway or dual inhibition (2i) of glycogen synthase kinase 3 (Gsk3) and mitogen-activated protein kinase kinase (MEK). Several downstream targets of the pathways involved have been identified that when individually overexpressed can partially support self-renewal. However, none of these targets is shared among the involved pathways. Here, we show that the CP2 family transcription factor Tfcp2l1 is a common target in LIF/Stat3- and 2i-mediated self-renewal, and forced expression of Tfcp2l1 can recapitulate the self-renewal-promoting effect of LIF or either of the 2i components. In addition, Tfcp2l1 can reprogram post-implantation epiblast stem cells to naïve pluripotent ESCs. Tfcp2l1 upregulates Nanog expression and promotes self-renewal in a Nanog-dependent manner. We conclude that Tfcp2l1 is at the intersection of LIF- and 2i-mediated self-renewal pathways and plays a critical role in maintaining ESC identity. Our study provides an expanded understanding of the current model of ground-state pluripotency.
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92
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Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol 2013; 20:1131-9. [PMID: 23934149 DOI: 10.1038/nsmb.2660] [Citation(s) in RCA: 1116] [Impact Index Per Article: 101.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/05/2013] [Indexed: 12/15/2022]
Abstract
Measuring gene expression in individual cells is crucial for understanding the gene regulatory network controlling human embryonic development. Here we apply single-cell RNA sequencing (RNA-Seq) analysis to 124 individual cells from human preimplantation embryos and human embryonic stem cells (hESCs) at different passages. The number of maternally expressed genes detected in our data set is 22,687, including 8,701 long noncoding RNAs (lncRNAs), which represents a significant increase from 9,735 maternal genes detected previously by cDNA microarray. We discovered 2,733 novel lncRNAs, many of which are expressed in specific developmental stages. To address the long-standing question whether gene expression signatures of human epiblast (EPI) and in vitro hESCs are the same, we found that EPI cells and primary hESC outgrowth have dramatically different transcriptomes, with 1,498 genes showing differential expression between them. This work provides a comprehensive framework of the transcriptome landscapes of human early embryos and hESCs.
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93
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Hall VJ. Early development of the porcine embryo: the importance of cell signalling in development of pluripotent cell lines. Reprod Fertil Dev 2013; 25:94-102. [PMID: 23244832 DOI: 10.1071/rd12264] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Understanding the cell signalling events that govern cell renewal in porcine pluripotent cells may help improve culture conditions and allow for establishment of bona fide porcine embryonic stem cells (pESC) and stable porcine induced pluripotent stem cells (piPSC). This review investigates cell signalling in the porcine preimplantation embryo containing either the inner cell mass or epiblast, with particular emphasis on fibroblast growth factor, SMAD, WNT and Janus tyrosine kinases/signal transducers and activators of transcription signalling. It is clear that key differences exist in the cell signalling events that govern pluripotency in this species compared with similar embryonic stages in mouse and human. The fact that bona fide pESC have still not been produced and that piPSC cannot survive in culture following the silencing or downregulation of the reprogramming transgenes suggest that culture conditions are not optimal. Unravelling the factor/s that regulate pluripotency in porcine embryos will pave the way for future establishment of stable pluripotent stem cell lines.
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Affiliation(s)
- Vanessa Jane Hall
- University of Copenhagen, Faculty of Health and Medical Sciences, Department of Veterinary Clinical and Animal Sciences, Gronnegaardsvej 7, DK-1870 Frederiksberg C, Denmark.
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94
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Lessing D, Anguera MC, Lee JT. X chromosome inactivation and epigenetic responses to cellular reprogramming. Annu Rev Genomics Hum Genet 2013; 14:85-110. [PMID: 23662665 DOI: 10.1146/annurev-genom-091212-153530] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Reprogramming somatic cells to derive induced pluripotent stem cells (iPSCs) has provided a new method to model disease and holds great promise for regenerative medicine. Although genetically identical to their donor somatic cells, iPSCs undergo substantial changes in the epigenetic landscape during reprogramming. One such epigenetic process, X chromosome inactivation (XCI), has recently been shown to vary widely in human female iPSCs and embryonic stem cells (ESCs). XCI is a form of dosage compensation whose chief regulator is the noncoding RNA Xist. In mouse iPSCs and ESCs, Xist expression and XCI strictly correlate with the pluripotent state, but no such correlation exists in humans. Lack of XIST expression in human cells is linked to reduced developmental potential and an altered transcriptional profile, including upregulation of genes associated with cancer, which has therefore led to concerns about the safety of pluripotent stem cells for use in regenerative medicine. In this review, we describe how different states of XIST expression define three classes of female human pluripotent stem cells and explore progress in discovering the reasons for these variations and how they might be countered.
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Affiliation(s)
- Derek Lessing
- Howard Hughes Medical Institute, Department of Molecular Biology, and Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114; , ,
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95
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Defining the genomic signature of totipotency and pluripotency during early human development. PLoS One 2013; 8:e62135. [PMID: 23614026 PMCID: PMC3629124 DOI: 10.1371/journal.pone.0062135] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 03/19/2013] [Indexed: 11/25/2022] Open
Abstract
The genetic mechanisms governing human pre-implantation embryo development and the in vitro counterparts, human embryonic stem cells (hESCs), still remain incomplete. Previous global genome studies demonstrated that totipotent blastomeres from day-3 human embryos and pluripotent inner cell masses (ICMs) from blastocysts, display unique and differing transcriptomes. Nevertheless, comparative gene expression analysis has revealed that no significant differences exist between hESCs derived from blastomeres versus those obtained from ICMs, suggesting that pluripotent hESCs involve a new developmental progression. To understand early human stages evolution, we developed an undifferentiation network signature (UNS) and applied it to a differential gene expression profile between single blastomeres from day-3 embryos, ICMs and hESCs. This allowed us to establish a unique signature composed of highly interconnected genes characteristic of totipotency (61 genes), in vivo pluripotency (20 genes), and in vitro pluripotency (107 genes), and which are also proprietary according to functional analysis. This systems biology approach has led to an improved understanding of the molecular and signaling processes governing human pre-implantation embryo development, as well as enabling us to comprehend how hESCs might adapt to in vitro culture conditions.
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96
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O'Leary T, Heindryckx B, Lierman S, Van der Jeught M, Duggal G, De Sutter P, Chuva de Sousa Lopes SM. Derivation of human embryonic stem cells using a post–inner cell mass intermediate. Nat Protoc 2013; 8:254-64. [DOI: 10.1038/nprot.2012.157] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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97
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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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98
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Ooi J, Liu P. Pluripotency and its layers of complexity. CELL REGENERATION 2012; 1:7. [PMID: 25408870 PMCID: PMC4230502 DOI: 10.1186/2045-9769-1-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 08/02/2012] [Indexed: 12/15/2022]
Abstract
Pluripotency is depicted by a self-renewing state that can competently differentiate to form the three germ layers. Different stages of early murine development can be captured on a petri dish, delineating a spectrum of pluripotent states, ranging from embryonic stem cells, embryonic germ cells to epiblast stem cells. Anomalous cell populations displaying signs of pluripotency have also been uncovered, from the isolation of embryonic carcinoma cells to the derivation of induced pluripotent stem cells. Gaining insight into the molecular circuitry within these cell types enlightens us about the significance and contribution of each stage, hence deepening our understanding of vertebrate development. In this review, we aim to describe experimental milestones that led to the understanding of embryonic development and the conception of pluripotency. We also discuss attempts at exploring the realm of pluripotency with the identification of pluripotent stem cells within mouse teratocarcinomas and embryos, and the generation of pluripotent cells through nuclear reprogramming. In conclusion, we illustrate pluripotent cells derived from other organisms, including human derivatives, and describe current paradigms in the comprehension of human pluripotency.
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Affiliation(s)
- Jolene Ooi
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA UK ; Technology and Research, Agency for Science, 1 Fusionopolis Way, #20-10, Connexis North Tower, Kragujevac, 138632 Singapore
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA UK
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99
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Van der Jeught M, O'Leary T, Ghimire S, Lierman S, Duggal G, Versieren K, Deforce D, Chuva de Sousa Lopes S, Heindryckx B, De Sutter P. The combination of inhibitors of FGF/MEK/Erk and GSK3β signaling increases the number of OCT3/4- and NANOG-positive cells in the human inner cell mass, but does not improve stem cell derivation. Stem Cells Dev 2012; 22:296-306. [PMID: 22784186 DOI: 10.1089/scd.2012.0256] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In embryonic stem cell culture, small molecules can be used to alter key signaling pathways to promote self-renewal and inhibit differentiation. In mice, small-molecule inhibition of both the FGF/MEK/Erk and the GSK3β pathways during preimplantation development suppresses hypoblast formation, and this results in more pluripotent cells of the inner cell mass (ICM). In this study, we evaluated the effects of different small-molecule inhibitors of the FGF/MEK/Erk and GSK3β pathway on embryo preimplantation development, early lineage segregation, and subsequent embryonic stem cell derivation in the humans. We did not observe any effect on blastocyst formation, but small-molecule inhibition did affect the number of OCT3/4- and NANOG-positive cells in the human ICM. We found that combined inhibition of the FGF/MEK/Erk and GSK3β pathways by PD0325901 and CHIR99021, respectively, resulted in ICMs containing significantly more OCT3/4-positive cells. Inhibition of FGF/MEK/Erk alone as well as in combination with inhibition of GSK3β significantly increased the number of NANOG-positive cells in blastocysts possessing good-quality ICMs. Secondly, we verified the influence of this increased pluripotency after 2i culture on the efficiency of stem cell derivation. Similar human embryonic stem cell (hESC) derivation rates were observed after 2i compared to control conditions, resulting in 2 control hESC lines and 1 hESC line from an embryo cultured in 2i conditions. In conclusion, we demonstrated that FGF/MEK/Erk and GSK3β signaling increases the number of OCT3/4- and NANOG-positive cells in the human ICM, but does not improve stem cell derivation.
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Affiliation(s)
- Margot Van der Jeught
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, Ghent, Belgium.
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100
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Tracing the genesis of human embryonic stem cells. Nat Biotechnol 2012; 30:247-9. [PMID: 22398620 DOI: 10.1038/nbt.2139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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