651
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Nityanandam A, Baldwin KK. Advances in reprogramming-based study of neurologic disorders. Stem Cells Dev 2015; 24:1265-83. [PMID: 25749371 DOI: 10.1089/scd.2015.0044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The technology to convert adult human non-neural cells into neural lineages, through induced pluripotent stem cells (iPSCs), somatic cell nuclear transfer, and direct lineage reprogramming or transdifferentiation has progressed tremendously in recent years. Reprogramming-based approaches aimed at manipulating cellular identity have enormous potential for disease modeling, high-throughput drug screening, cell therapy, and personalized medicine. Human iPSC (hiPSC)-based cellular disease models have provided proof of principle evidence of the validity of this system. However, several challenges remain before patient-specific neurons produced by reprogramming can provide reliable insights into disease mechanisms or be efficiently applied to drug discovery and transplantation therapy. This review will first discuss limitations of currently available reprogramming-based methods in faithfully and reproducibly recapitulating disease pathology. Specifically, we will address issues such as culture heterogeneity, interline and inter-individual variability, and limitations of two-dimensional differentiation paradigms. Second, we will assess recent progress and the future prospects of reprogramming-based neurologic disease modeling. This includes three-dimensional disease modeling, advances in reprogramming technology, prescreening of hiPSCs and creating isogenic disease models using gene editing.
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Affiliation(s)
- Anjana Nityanandam
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Kristin K Baldwin
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California
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652
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Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells. Proc Natl Acad Sci U S A 2015; 112:4666-71. [PMID: 25825768 DOI: 10.1073/pnas.1502855112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
NANOG (from Irish mythology Tír na nÓg) transcription factor plays a central role in maintaining pluripotency, cooperating with OCT4 (also known as POU5F1 or OCT3/4), SOX2, and other pluripotency factors. Although the physiological roles of the NANOG protein have been extensively explored, biochemical and biophysical properties in relation to its structural analysis are poorly understood. Here we determined the crystal structure of the human NANOG homeodomain (hNANOG HD) bound to an OCT4 promoter DNA, which revealed amino acid residues involved in DNA recognition that are likely to be functionally important. We generated a series of hNANOG HD alanine substitution mutants based on the protein-DNA interaction and evolutionary conservation and determined their biological activities. Some mutant proteins were less stable, resulting in loss or decreased affinity for DNA binding. Overexpression of the orthologous mouse NANOG (mNANOG) mutants failed to maintain self-renewal of mouse embryonic stem cells without leukemia inhibitory factor. These results suggest that these residues are critical for NANOG transcriptional activity. Interestingly, one mutant, hNANOG L122A, conversely enhanced protein stability and DNA-binding affinity. The mNANOG L122A, when overexpressed in mouse embryonic stem cells, maintained their expression of self-renewal markers even when retinoic acid was added to forcibly drive differentiation. When overexpressed in epiblast stem cells or human induced pluripotent stem cells, the L122A mutants enhanced reprogramming into ground-state pluripotency. These findings demonstrate that structural and biophysical information on key transcriptional factors provides insights into the manipulation of stem cell behaviors and a framework for rational protein engineering.
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653
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Nashun B, Hill PWS, Hajkova P. Reprogramming of cell fate: epigenetic memory and the erasure of memories past. EMBO J 2015; 34:1296-308. [PMID: 25820261 PMCID: PMC4491992 DOI: 10.15252/embj.201490649] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/18/2015] [Indexed: 12/24/2022] Open
Abstract
Cell identity is a reflection of a cell type-specific gene expression profile, and consequently, cell type-specific transcription factor networks are considered to be at the heart of a given cellular phenotype. Although generally stable, cell identity can be reprogrammed in vitro by forced changes to the transcriptional network, the most dramatic example of which was shown by the induction of pluripotency in somatic cells by the ectopic expression of defined transcription factors alone. Although changes to cell fate can be achieved in this way, the efficiency of such conversion remains very low, in large part due to specific chromatin signatures constituting an epigenetic barrier to the transcription factor-mediated reprogramming processes. Here we discuss the two-way relationship between transcription factor binding and chromatin structure during cell fate reprogramming. We additionally explore the potential roles and mechanisms by which histone variants, chromatin remodelling enzymes, and histone and DNA modifications contribute to the stability of cell identity and/or provide a permissive environment for cell fate change during cellular reprogramming.
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Affiliation(s)
- Buhe Nashun
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Peter W S Hill
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Petra Hajkova
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
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654
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Feng W, Dai Y, Mou L, Cooper DKC, Shi D, Cai Z. The potential of the combination of CRISPR/Cas9 and pluripotent stem cells to provide human organs from chimaeric pigs. Int J Mol Sci 2015; 16:6545-56. [PMID: 25807262 PMCID: PMC4394547 DOI: 10.3390/ijms16036545] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/11/2015] [Accepted: 03/16/2015] [Indexed: 12/26/2022] Open
Abstract
Clinical organ allotransplantation is limited by the availability of deceased human donors. However, the transplantation of human organs produced in other species would provide an unlimited number of organs. The pig has been identified as the most suitable source of organs for humans as organs of any size would be available. Genome editing by RNA-guided endonucleases, also known as clustered regularly interspaced short palindromic repeat (CRISPR/Cas9), in combination with induced pluripotent stem cells (iPSC), may have the potential to enable the creation of human organs from genetically-modified chimaeric pigs. These could potentially provide an unlimited supply of organs that would not be rejected by the recipient's immune system. However, substantial research is needed to prove that this approach will work. Genetic modification of chimaeric pigs could also provide useful models for developing therapies for various human diseases, especially in relation to drug development.
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Affiliation(s)
- Wanyou Feng
- Shenzhen Key Laboratory of Xenotransplantaton, State and Local Joint Cancer Genome Clinical Application of Key Technology Laboratory, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China.
| | - Yifan Dai
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 210029, China.
| | - Lisha Mou
- Shenzhen Key Laboratory of Xenotransplantaton, State and Local Joint Cancer Genome Clinical Application of Key Technology Laboratory, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China.
| | - David K C Cooper
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA.
| | - Deshun Shi
- State Key Laboratory of Conservation & Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China.
| | - Zhiming Cai
- Shenzhen Key Laboratory of Xenotransplantaton, State and Local Joint Cancer Genome Clinical Application of Key Technology Laboratory, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China.
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655
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Abstract
In recent years, there has been much interest in the prospect of generating and using human stem cells that exhibit a state of naïve pluripotency. Such a pluripotent state might be functionally confirmed by assessing the chimeric contribution of these cells to non-human blastocysts. Furthermore, the generation of naïve human pluripotent stem cells in vitro could lead to the creation of chimeric animal models that can facilitate the study of human development and disease. However, these lines of research raise thorny ethical concerns about the moral status of such chimeric animals. Here, I call attention to these ethical barbs and suggest a way in which to proceed cautiously.
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Affiliation(s)
- Insoo Hyun
- Department of Bioethics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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656
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Ebina W, Rossi DJ. Transcription factor-mediated reprogramming toward hematopoietic stem cells. EMBO J 2015; 34:694-709. [PMID: 25712209 DOI: 10.15252/embj.201490804] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
De novo generation of human hematopoietic stem cells (HSCs) from renewable cell types has been a long sought-after but elusive goal in regenerative medicine. Paralleling efforts to guide pluripotent stem cell differentiation by manipulating developmental cues, substantial progress has been made recently toward HSC generation via combinatorial transcription factor (TF)-mediated fate conversion, a paradigm established by Yamanaka's induction of pluripotency in somatic cells by mere four TFs. This review will integrate the recently reported strategies to directly convert a variety of starting cell types toward HSCs in the context of hematopoietic transcriptional regulation and discuss how these findings could be further developed toward the ultimate generation of therapeutic human HSCs.
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Affiliation(s)
- Wataru Ebina
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA Department of Pediatrics, Harvard Medical School, Boston, MA, USA Harvard Stem Cell Institute, Cambridge, MA, USA
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657
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Abstract
In September 2014, over 100 scientists from around the globe gathered at Wotton House near London for the Company of Biologists' workshop 'From Stem Cells to Human Development'. The workshop covered diverse aspects of human development, from the earliest stages of embryogenesis to differentiation of mature cell types of all three germ layers from pluripotent cells. In this Meeting Review, we summarise some of the exciting data presented at the workshop and draw together the main themes that emerged.
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Affiliation(s)
- Alexander Medvinsky
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
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658
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Abstract
Lessons learned from conserved vertebrate developmental pathways have catalyzed rapid advances in pluripotent stem cell differentiation towards therapeutically relevant cell types. The most highly conserved phases of development are associated with the early patterning of the body plan - the so-called phylotypic stage. Both prior to and after this stage there is much more divergence across species. Developmental differences between human and mouse at the blastocyst and early post-implantation stages might help explain the differences among the different stem cell lines derived from these embryos. A better understanding of these early stages of human development will aid our ability to generate and manipulate human stem cells and their derivatives.
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Affiliation(s)
- Janet Rossant
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, Ontario, Canada M5G OA4 Department of Molecular Genetics, University of Toronto, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, Ontario, Canada M5G OA4
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659
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Huang SXL, Green MD, de Carvalho AT, Mumau M, Chen YW, D'Souza SL, Snoeck HW. The in vitro generation of lung and airway progenitor cells from human pluripotent stem cells. Nat Protoc 2015; 10:413-25. [PMID: 25654758 DOI: 10.1038/nprot.2015.023] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Lung and airway epithelial cells generated in vitro from human pluripotent stem cells (hPSCs) have applications in regenerative medicine, modeling of lung disease, drug screening and studies of human lung development. Here we describe a strategy for directed differentiation of hPSCs into developmental lung progenitors, and their subsequent differentiation into predominantly distal lung epithelial cells. The protocol entails four stages that recapitulate lung development, and it takes ∼50 d. First, definitive endoderm (DE) is induced in the presence of high concentrations of activin A. Subsequently, lung-biased anterior foregut endoderm (AFE) is specified by sequential inhibition of bone morphogenetic protein (BMP), transforming growth factor-β (TGF-β) and Wnt signaling. AFE is then ventralized by applying Wnt, BMP, fibroblast growth factor (FGF) and retinoic acid (RA) signaling to obtain lung and airway progenitors. Finally, these are further differentiated into more mature epithelial cells types using Wnt, FGF, cAMP and glucocorticoid agonism. This protocol is conducted in defined conditions, it does not involve genetic manipulation of the cells and it results in cultures in which the majority of the cells express markers of various lung and airway epithelial cells, with a predominance of cells identifiable as functional type II alveolar epithelial cells.
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Affiliation(s)
- Sarah X L Huang
- 1] Columbia Center for Translational Immunology, Columbia University Medical Center, New York, New York, USA. [2] Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Michael D Green
- 1] Columbia Center for Translational Immunology, Columbia University Medical Center, New York, New York, USA. [2] Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Ana Toste de Carvalho
- 1] Columbia Center for Translational Immunology, Columbia University Medical Center, New York, New York, USA. [2] Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Melanie Mumau
- 1] Columbia Center for Translational Immunology, Columbia University Medical Center, New York, New York, USA. [2] Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Ya-Wen Chen
- 1] Columbia Center for Translational Immunology, Columbia University Medical Center, New York, New York, USA. [2] Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Sunita L D'Souza
- Department of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Experimental Therapeutic Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hans-Willem Snoeck
- 1] Columbia Center for Translational Immunology, Columbia University Medical Center, New York, New York, USA. [2] Department of Medicine, Columbia University Medical Center, New York, New York, USA. [3] Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, USA
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660
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Barakat TS, Ghazvini M, de Hoon B, Li T, Eussen B, Douben H, van der Linden R, van der Stap N, Boter M, Laven JS, Galjaard RJ, Grootegoed JA, de Klein A, Gribnau J. Stable X chromosome reactivation in female human induced pluripotent stem cells. Stem Cell Reports 2015; 4:199-208. [PMID: 25640760 PMCID: PMC4325229 DOI: 10.1016/j.stemcr.2014.12.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 12/22/2014] [Accepted: 12/27/2014] [Indexed: 01/01/2023] Open
Abstract
In placental mammals, balanced expression of X-linked genes is accomplished by X chromosome inactivation (XCI) in female cells. In humans, random XCI is initiated early during embryonic development. To investigate whether reprogramming of female human fibroblasts into induced pluripotent stem cells (iPSCs) leads to reactivation of the inactive X chromosome (Xi), we have generated iPSC lines from fibroblasts heterozygous for large X-chromosomal deletions. These fibroblasts show completely skewed XCI of the mutated X chromosome, enabling monitoring of X chromosome reactivation (XCR) and XCI using allele-specific single-cell expression analysis. This approach revealed that XCR is robust under standard culture conditions, but does not prevent reinitiation of XCI, resulting in a mixed population of cells with either two active X chromosomes (Xas) or one Xa and one Xi. This mixed population of XaXa and XaXi cells is stabilized in naive human stem cell medium, allowing expansion of clones with two Xas. Robust X chromosome reactivation in human iPSCs with large X-chromosomal deletions Female human iPSCs with two active X chromosomes Expansion of human iPSCs with two active X chromosomes in naive human stem cell medium
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Affiliation(s)
- Tahsin Stefan Barakat
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Mehrnaz Ghazvini
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands; Erasmus Stem Cell and Regenerative Medicine Institute, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Bas de Hoon
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands; Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Tracy Li
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands; Erasmus Stem Cell and Regenerative Medicine Institute, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Bert Eussen
- Department of Clinical Genetics, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Hannie Douben
- Department of Clinical Genetics, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Reinier van der Linden
- Erasmus Stem Cell and Regenerative Medicine Institute, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Nathalie van der Stap
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands; Erasmus Stem Cell and Regenerative Medicine Institute, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Marjan Boter
- Department of Clinical Genetics, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Joop S Laven
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Robert-Jan Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - J Anton Grootegoed
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 CE Rotterdam, the Netherlands.
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661
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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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662
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Dynamic switching of active promoter and enhancer domains regulates Tet1 and Tet2 expression during cell state transitions between pluripotency and differentiation. Mol Cell Biol 2015; 35:1026-42. [PMID: 25582196 DOI: 10.1128/mcb.01172-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Tet 5-methylcytosine dioxygenases catalyze DNA demethylation by producing 5-hydroxymethylcytosine and further oxidized products. Tet1 and Tet2 are highly expressed in mouse pluripotent cells and downregulated to different extents in somatic cells, but the transcriptional mechanisms are unclear. Here we defined the promoter and enhancer domains in Tet1 and Tet2. Within a 15-kb "superenhancer" of Tet1, there are two transcription start sites (TSSs) with different activation patterns during development. A 6-kb promoter region upstream of the distal TSS is highly active in naive pluripotent cells, autonomously reports Tet1 expression in a transgenic system, and rapidly undergoes DNA methylation and silencing upon differentiation in cultured cells and native epiblast. A second TSS downstream, associated with a constitutively weak CpG-rich promoter, is activated by a neighboring enhancer in naive embryonic stem cells (ESCs) and primed epiblast-like cells (EpiLCs). Tet2 has a CpG island promoter with pluripotency-independent activity and an ESC-specific distal intragenic enhancer; the latter is rapidly downregulated in EpiLCs. Our study reveals distinct modes of transcriptional regulation at Tet1 and Tet2 during cell state transitions of early development. New transgenic reporters using Tet1 and Tet2 cis-regulatory domains may serve to distinguish nuanced changes in pluripotent states and the underlying epigenetic variations.
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663
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Fort A, Yamada D, Hashimoto K, Koseki H, Carninci P. Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming. Cell Cycle 2015; 14:1148-55. [PMID: 25664506 PMCID: PMC4613594 DOI: 10.4161/15384101.2014.988031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/08/2014] [Accepted: 01/07/2015] [Indexed: 01/07/2023] Open
Abstract
Identification of functionally relevant differences between induced pluripotent stem cells (iPSC) and reference embryonic stem cells (ESC) remains a central question for therapeutic applications. Differences in gene expression between iPSC and ESC have been examined by microarray and more recently with RNA-SEQ technologies. We here report an in depth analyses of nuclear and cytoplasmic transcriptomes, using the CAGE (cap analysis of gene expression) technology, for 5 iPSC clones derived from mouse lymphocytes B and 3 ESC lines. This approach reveals nuclear transcriptomes significantly more complex in ESC than in iPSC. Hundreds of yet not annotated putative non-coding RNAs and enhancer-associated transcripts specifically transcribed in ESC have been detected and supported with epigenetic and chromatin-chromatin interactions data. We identified super-enhancers transcriptionally active specifically in ESC and associated with genes implicated in the maintenance of pluripotency. Similarly, we detected non-coding transcripts of yet unknown function being regulated by ESC specific super-enhancers. Taken together, these results demonstrate that current protocols of iPSC reprogramming do not trigger activation of numerous cis-regulatory regions. It thus reinforces the need for already suggested deeper monitoring of the non-coding transcriptome when characterizing iPSC clones. Such differences in regulatory transcript expression may indeed impact their potential for clinical applications.
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Affiliation(s)
- Alexandre Fort
- Division of Genomic Technologies; RIKEN Center for Life Science Technologies; Yokohama, Japan
- Present address: Department of Genetic Medicine and Development; University of Geneva Medical School; Geneva, Switzerland
| | - Daisuke Yamada
- Laboratory for Developmental Genetics; RIKEN Center for Integrative Medical Sciences; Yokohama, Japan
| | - Kosuke Hashimoto
- Division of Genomic Technologies; RIKEN Center for Life Science Technologies; Yokohama, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics; RIKEN Center for Integrative Medical Sciences; Yokohama, Japan
| | - Piero Carninci
- Division of Genomic Technologies; RIKEN Center for Life Science Technologies; Yokohama, Japan
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664
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Geula S, Moshitch-Moshkovitz S, Dominissini D, Mansour AA, Kol N, Salmon-Divon M, Hershkovitz V, Peer E, Mor N, Manor YS, Ben-Haim MS, Eyal E, Yunger S, Pinto Y, Jaitin DA, Viukov S, Rais Y, Krupalnik V, Chomsky E, Zerbib M, Maza I, Rechavi Y, Massarwa R, Hanna S, Amit I, Levanon EY, Amariglio N, Stern-Ginossar N, Novershtern N, Rechavi G, Hanna JH. Stem cells. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation. Science 2015; 347:1002-6. [PMID: 25569111 DOI: 10.1126/science.1261417] [Citation(s) in RCA: 1155] [Impact Index Per Article: 128.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Naïve and primed pluripotent states retain distinct molecular properties, yet limited knowledge exists on how their state transitions are regulated. Here, we identify Mettl3, an N(6)-methyladenosine (m(6)A) transferase, as a regulator for terminating murine naïve pluripotency. Mettl3 knockout preimplantation epiblasts and naïve embryonic stem cells are depleted for m(6)A in mRNAs, yet are viable. However, they fail to adequately terminate their naïve state and, subsequently, undergo aberrant and restricted lineage priming at the postimplantation stage, which leads to early embryonic lethality. m(6)A predominantly and directly reduces mRNA stability, including that of key naïve pluripotency-promoting transcripts. This study highlights a critical role for an mRNA epigenetic modification in vivo and identifies regulatory modules that functionally influence naïve and primed pluripotency in an opposing manner.
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Affiliation(s)
- Shay Geula
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon Moshitch-Moshkovitz
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dan Dominissini
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Abed AlFatah Mansour
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Nitzan Kol
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mali Salmon-Divon
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Vera Hershkovitz
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eyal Peer
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nofar Mor
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yair S Manor
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Moshe Shay Ben-Haim
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Eyal
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sharon Yunger
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yishay Pinto
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - Sergey Viukov
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yoach Rais
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Vladislav Krupalnik
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Elad Chomsky
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Mirie Zerbib
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Itay Maza
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Rechavi
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rada Massarwa
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Suhair Hanna
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. The Department of Pediatrics and the Pediatric Immunology Unit, Rambam Medical Center, and the B. Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Ido Amit
- The Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Ninette Amariglio
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel. Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Noam Stern-Ginossar
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Novershtern
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Gideon Rechavi
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Jacob H Hanna
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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665
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Dean W. Cellular Reprogramming in Basic and Applied Biomedicine: The Dawn of Regenerative Medicine. Methods Mol Biol 2015; 1330:3-13. [PMID: 26621584 DOI: 10.1007/978-1-4939-2848-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fertilization triggers a cascade of cellular and molecular events restoring the totipotent state and the potential for all cell types. However, the program quickly directs differentiation and cellular commitment. Under the genetic and epigenetic control of this process, Waddington likened this to a three-dimensional landscape where cells could not ascend the slope or traverse once canalized thus leading to cell fate decisions and the progressive restriction of cellular potency. But this is not the only possible outcome at least experimentally. Somatic cell nuclear transfer and overexpression of key transcription factors to generate induced pluripotent cells have challenged this notion. The return to pluripotency and the reinstatement of plasticity and heterogeneity once thought to be the exclusive remit of the developing embryo can now be replicated in vitro. The following chapter introduces some of these ideas and suggests that the fundamental principles learned may constitute the first step toward the opportunity for specific tissue renewal and replacement in healthy aging and the treatment of chronic diseases-the age of regenerative medicine.
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Affiliation(s)
- Wendy Dean
- Epigenetics Programme, The Babraham Institute, Babraham Hall, Babraham Research Campus, Cambridgeshire, CB22 3AT, UK.
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666
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Abstract
Recent studies link changes in energy metabolism with the fate of pluripotent stem cells (PSCs). Safe use of PSC derivatives in regenerative medicine requires an enhanced understanding and control of factors that optimize in vitro reprogramming and differentiation protocols. Relative shifts in metabolism from naïve through "primed" pluripotent states to lineage-directed differentiation place variable demands on mitochondrial biogenesis and function for cell types with distinct energetic and biosynthetic requirements. In this context, mitochondrial respiration, network dynamics, TCA cycle function, and turnover all have the potential to influence reprogramming and differentiation outcomes. Shifts in cellular metabolism affect enzymes that control epigenetic configuration, which impacts chromatin reorganization and gene expression changes during reprogramming and differentiation. Induced PSCs (iPSCs) may have utility for modeling metabolic diseases caused by mutations in mitochondrial DNA, for which few disease models exist. Here, we explore key features of PSC energy metabolism research in mice and man and the impact this work is starting to have on our understanding of early development, disease modeling, and potential therapeutic applications.
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Affiliation(s)
- Tara Teslaa
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Michael A Teitell
- Molecular Biology Institute, University of California, Los Angeles, CA, USA Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA Department of Bioengineering, University of California, Los Angeles, CA, USA Department of Pediatrics, University of California, Los Angeles, CA, USA California NanoSystems Institute, University of California, Los Angeles, CA, USA Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
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667
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Abstract
In mice, three pluripotent stem cell lines have been established from different stage of developing embryo, which are embryonic stem (ES) cell, post-implantation epiblast stem cell (EpiSC), and embryonic germ (EG) cell. ES cell and EG cell share many common features including factor requirement, colony morphology, and gene expression pattern. On the other hand, EpiSC needs different external signal inputs, exhibits flattened colony morphology, and a different set of gene expression patterns. In addition, the germ line competency of EpiSCs is still unclear. To distinguish the differences between them, they are defined by the words "naïve" and "primed" pluripotent cells, respectively. This article introduces how pluripotent stem cell lines are established in culture, and how much those cells in vitro are similar or relevant to their in vivo origin and the knowledge about transcription factors to support this state.
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668
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Abstract
Devising a cell culture method that maintains human pluripotent stem cells (PSCs) in a state similar to naive mouse embryonic stem cells (ESCs) has been a much sought after goal in recent years. Here I consider the historical background to this quest and ask why it is considered consequential.
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Affiliation(s)
- Martin F Pera
- University of Melbourne, Florey Institute of Neuroscience and Mental Health, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3010, Australia.
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669
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Honsho K, Hirose M, Hatori M, Yasmin L, Izu H, Matoba S, Togayachi S, Miyoshi H, Sankai T, Ogura A, Honda A. Naïve-like conversion enhances the difference in innate in vitro differentiation capacity between rabbit ES cells and iPS cells. J Reprod Dev 2014; 61:13-9. [PMID: 25345855 PMCID: PMC4354226 DOI: 10.1262/jrd.2014-098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/17/2014] [Indexed: 01/27/2023] Open
Abstract
Quality evaluation of pluripotent stem cells using appropriate animal models needs to be improved for human regenerative medicine. Previously, we demonstrated that although the in vitro neural differentiating capacity of rabbit induced pluripotent stem cells (iPSCs) can be mitigated by improving their baseline level of pluripotency, i.e., by converting them into the so-called "naïve-like" state, the effect after such conversion of rabbit embryonic stem cells (ESCs) remains to be elucidated. Here we found that naïve-like conversion enhanced the differences in innate in vitro differentiation capacity between ESCs and iPSCs. Naïve-like rabbit ESCs exhibited several features indicating pluripotency, including the capacity for teratoma formation. They differentiated into mature oligodendrocytes much more effectively (3.3-7.2 times) than naïve-like iPSCs. This suggests an inherent variation in differentiation potential in vitro among PSC lines. When naïve-like ESCs were injected into preimplantation rabbit embryos, although they contributed efficiently to forming the inner cell mass of blastocysts, no chimeric pups were obtained. Thus, in vitro neural differentiation following naïve-like conversion is a promising option for determining the quality of PSCs without the need to demonstrate chimeric contribution. These results provide an opportunity to evaluate which pluripotent stem cells or treatments are best suited for therapeutic use.
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Affiliation(s)
- Kimiko Honsho
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
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670
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Huang K, Maruyama T, Fan G. The naive state of human pluripotent stem cells: a synthesis of stem cell and preimplantation embryo transcriptome analyses. Cell Stem Cell 2014; 15:410-415. [PMID: 25280217 PMCID: PMC5507179 DOI: 10.1016/j.stem.2014.09.014] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here we use a systems biology approach to comprehensively assess the conservation of gene networks in naive pluripotent stem cells (PSCs) with preimplantation embryos. While gene networks in murine naive and primed pluripotent states are reproducible across data sets, different sources of human stem cells display high degrees of variation, partly reflecting disparities in culture conditions. Finally, naive gene networks between human and mouse PSCs are not well conserved and better resemble their respective blastocysts.
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Affiliation(s)
- Kevin Huang
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
| | - Toru Maruyama
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
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