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Conrad JV, Meyer S, Ramesh PS, Neira JA, Rusteika M, Mamott D, Duffin B, Bautista M, Zhang J, Hiles E, Higgins EM, Steill J, Freeman J, Ni Z, Liu S, Ungrin M, Rancourt D, Clegg DO, Stewart R, Thomson JA, Chu LF. Efficient derivation of transgene-free porcine induced pluripotent stem cells enables in vitro modeling of species-specific developmental timing. Stem Cell Reports 2023; 18:2328-2343. [PMID: 37949072 PMCID: PMC10724057 DOI: 10.1016/j.stemcr.2023.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023] Open
Abstract
Sus scrofa domesticus (pig) has served as a superb large mammalian model for biomedical studies because of its comparable physiology and organ size to humans. The derivation of transgene-free porcine induced pluripotent stem cells (PiPSCs) will, therefore, benefit the development of porcine-specific models for regenerative biology and its medical applications. In the past, this effort has been hampered by a lack of understanding of the signaling milieu that stabilizes the porcine pluripotent state in vitro. Here, we report that transgene-free PiPSCs can be efficiently derived from porcine fibroblasts by episomal vectors along with microRNA-302/367 using optimized protocols tailored for this species. PiPSCs can be differentiated into derivatives representing the primary germ layers in vitro and can form teratomas in immunocompromised mice. Furthermore, the transgene-free PiPSCs preserve intrinsic species-specific developmental timing in culture, known as developmental allochrony. This is demonstrated by establishing a porcine in vitro segmentation clock model that, for the first time, displays a specific periodicity at ∼3.7 h, a timescale recapitulating in vivo porcine somitogenesis. We conclude that the transgene-free PiPSCs can serve as a powerful tool for modeling development and disease and developing transplantation strategies. We also anticipate that they will provide insights into conserved and unique features on the regulations of mammalian pluripotency and developmental timing mechanisms.
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Affiliation(s)
- J Vanessa Conrad
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Susanne Meyer
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Pranav S Ramesh
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Jaime A Neira
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Margaret Rusteika
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Daniel Mamott
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Bret Duffin
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Monica Bautista
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Jue Zhang
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Emily Hiles
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Eve M Higgins
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - John Steill
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jack Freeman
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Zijian Ni
- Department of Statistics, University of Wisconsin, Madison, WI 53706, USA
| | - Shiying Liu
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mark Ungrin
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Derrick Rancourt
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Dennis O Clegg
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Li-Fang Chu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
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2
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Lasry R, Maoz N, Cheng AW, Yom Tov N, Kulenkampff E, Azagury M, Yang H, Ople C, Markoulaki S, Faddah DA, Makedonski K, Orzech D, Sabag O, Jaenisch R, Buganim Y. Complex haploinsufficiency in pluripotent cells yields somatic cells with DNA methylation abnormalities and pluripotency induction defects. Stem Cell Reports 2023; 18:2174-2189. [PMID: 37832543 PMCID: PMC10679652 DOI: 10.1016/j.stemcr.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
A complete knockout of a single key pluripotency gene may drastically affect embryonic stem cell function and epigenetic reprogramming. In contrast, elimination of only one allele of a single pluripotency gene is mostly considered harmless to the cell. To understand whether complex haploinsufficiency exists in pluripotent cells, we simultaneously eliminated a single allele in different combinations of two pluripotency genes (i.e., Nanog+/-;Sall4+/-, Nanog+/-;Utf1+/-, Nanog+/-;Esrrb+/- and Sox2+/-;Sall4+/-). Although these double heterozygous mutant lines similarly contribute to chimeras, fibroblasts derived from these systems show a significant decrease in their ability to induce pluripotency. Tracing the stochastic expression of Sall4 and Nanog at early phases of reprogramming could not explain the seen delay or blockage. Further exploration identifies abnormal methylation around pluripotent and developmental genes in the double heterozygous mutant fibroblasts, which could be rescued by hypomethylating agent or high OSKM levels. This study emphasizes the importance of maintaining two intact alleles for pluripotency induction.
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Affiliation(s)
- Rachel Lasry
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Noam Maoz
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Albert W Cheng
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nataly Yom Tov
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Elisabeth Kulenkampff
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Meir Azagury
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Hui Yang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Cora Ople
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Styliani Markoulaki
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dina A Faddah
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kirill Makedonski
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Dana Orzech
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Ofra Sabag
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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3
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Déjosez M, Marin A, Hughes GM, Morales AE, Godoy-Parejo C, Gray JL, Qin Y, Singh AA, Xu H, Juste J, Ibáñez C, White KM, Rosales R, Francoeur NJ, Sebra RP, Alcock D, Volkert TL, Puechmaille SJ, Pastusiak A, Frost SDW, Hiller M, Young RA, Teeling EC, García-Sastre A, Zwaka TP. Bat pluripotent stem cells reveal unusual entanglement between host and viruses. Cell 2023; 186:957-974.e28. [PMID: 36812912 PMCID: PMC10085545 DOI: 10.1016/j.cell.2023.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/06/2022] [Accepted: 01/09/2023] [Indexed: 02/23/2023]
Abstract
Bats are distinctive among mammals due to their ability to fly, use laryngeal echolocation, and tolerate viruses. However, there are currently no reliable cellular models for studying bat biology or their response to viral infections. Here, we created induced pluripotent stem cells (iPSCs) from two species of bats: the wild greater horseshoe bat (Rhinolophus ferrumequinum) and the greater mouse-eared bat (Myotis myotis). The iPSCs from both bat species showed similar characteristics and had a gene expression profile resembling that of cells attacked by viruses. They also had a high number of endogenous viral sequences, particularly retroviruses. These results suggest that bats have evolved mechanisms to tolerate a large load of viral sequences and may have a more intertwined relationship with viruses than previously thought. Further study of bat iPSCs and their differentiated progeny will provide insights into bat biology, virus host relationships, and the molecular basis of bats' special traits.
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Affiliation(s)
- Marion Déjosez
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Paratus Sciences, 430 East 29th Street, Suite 600, New York, NY 10016, USA
| | - Arturo Marin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Ireland
| | - Ariadna E Morales
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany; Faculty of Biosciences, Goethe University, Max-von-Laue-Str, 60438 Frankfurt, Germany
| | - Carlos Godoy-Parejo
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Jonathan L Gray
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Yiren Qin
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Arun A Singh
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Hui Xu
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Javier Juste
- Estación biológica de doñana (CSIC), Avda. Américo Vespucio 26, Seville 41092, Spain; CIBER Epidemiology and Public Health, CIBERESP, Madrid, Spain
| | - Carlos Ibáñez
- Estación biológica de doñana (CSIC), Avda. Américo Vespucio 26, Seville 41092, Spain
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute for Genomics, New York, NY, USA
| | - Dominic Alcock
- School of Biology and Environmental Science, University College Dublin, Ireland
| | - Thomas L Volkert
- Paratus Sciences, 430 East 29th Street, Suite 600, New York, NY 10016, USA
| | | | - Andrzej Pastusiak
- Microsoft Premonition, Microsoft Building 99, 14820 NE 36th Street, Redmond, WA 98052, USA
| | - Simon D W Frost
- Microsoft Premonition, Microsoft Building 99, 14820 NE 36th Street, Redmond, WA 98052, USA; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany; Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany; Faculty of Biosciences, Goethe University, Max-von-Laue-Str, 60438 Frankfurt, Germany
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Ireland.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular and Cell-Based Medicine and the Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Thomas P Zwaka
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Paratus Sciences, 430 East 29th Street, Suite 600, New York, NY 10016, USA.
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4
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Conod A, Silvano M, Ruiz I Altaba A. On the origin of metastases: Induction of pro-metastatic states after impending cell death via ER stress, reprogramming, and a cytokine storm. Cell Rep 2022; 38:110490. [PMID: 35263600 DOI: 10.1016/j.celrep.2022.110490] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/07/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
How metastatic cells arise is unclear. Here, we search for the induction of recently characterized pro-metastatic states as a surrogate for the origin of metastasis. Since cell-death-inducing therapies can paradoxically promote metastasis, we ask if such treatments induce pro-metastatic states in human colon cancer cells. We find that post-near-death cells acquire pro-metastatic states (PAMEs) and form distant metastases in vivo. These PAME ("let's go" in Greek) cells exhibit a multifactorial cytokine storm as well as signs of enhanced endoplasmic reticulum (ER) stress and nuclear reprogramming, requiring CXCL8, INSL4, IL32, PERK-CHOP, and NANOG. PAMEs induce neighboring tumor cells to become PAME-induced migratory cells (PIMs): highly migratory cells that re-enact the storm and enhance PAME migration. Metastases are thus proposed to originate from the induction of pro-metastatic states through intrinsic and extrinsic cues in a pro-metastatic tumoral ecosystem, driven by an impending cell-death experience involving ER stress modulation, metastatic reprogramming, and paracrine recruitment via a cytokine storm.
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Affiliation(s)
- Arwen Conod
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marianna Silvano
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ariel Ruiz I Altaba
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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5
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Vojtek M, Zhang J, Sun J, Zhang M, Chambers I. Differential repression of Otx2 underlies the capacity of NANOG and ESRRB to induce germline entry. Stem Cell Reports 2021; 17:35-42. [PMID: 34971561 PMCID: PMC8758940 DOI: 10.1016/j.stemcr.2021.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/03/2022] Open
Abstract
Primordial germ cells (PGCs) arise from cells of the post-implantation epiblast in response to cytokine signaling. PGC development can be recapitulated in vitro by differentiating epiblast-like cells (EpiLCs) into PGC-like cells (PGCLCs) through cytokine exposure. Interestingly, the cytokine requirement for PGCLC induction can be bypassed by enforced expression of the transcription factor (TF) NANOG. However, the underlying mechanisms are not fully elucidated. Here, we show that NANOG mediates Otx2 downregulation in the absence of cytokines and that this is essential for PGCLC induction by NANOG. Moreover, the direct NANOG target gene Esrrb, which can substitute for several NANOG functions, does not downregulate Otx2 when overexpressed in EpiLCs and cannot promote PGCLC specification. However, expression of ESRRB in Otx2+/− EpiLCs rescues emergence of PGCLCs. This study illuminates the interplay of TFs occurring at the earliest stages of PGC specification. NANOG overexpression induces cytokine-free PGCLC specification by repressing Otx2 Enforced OTX2 expression prevents NANOG-induced germline entry ESRRB overexpression cannot repress Otx2 or induce cytokine-free germline entry Otx2 heterozygosity enables ESRRB to induce cytokine-free PGCLC specification
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Affiliation(s)
- Matúš Vojtek
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, Scotland
| | - Jingchao Zhang
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, Scotland
| | - Juanjuan Sun
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China; Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China
| | - Man Zhang
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, Scotland; Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China; The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China.
| | - Ian Chambers
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, Scotland.
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6
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Human ES Cell Culture Conditions Fail to Preserve the Mouse Epiblast State. Stem Cells Int 2021; 2021:8818356. [PMID: 33828592 PMCID: PMC8004371 DOI: 10.1155/2021/8818356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/11/2020] [Accepted: 01/24/2021] [Indexed: 11/17/2022] Open
Abstract
Mouse embryonic stem cells (mESCs) and mouse epiblast stem cells (mEpiSCs) are the pluripotent stem cells (PSCs), derived from the inner cell mass (ICM) of preimplantation embryos at embryonic day 3.5 (E3.5) and postimplantation embryos at E5.5-E7.5, respectively. Depending on their environment, PSCs can exist in the so-called naïve (ESCs) or primed (EpiSCs) states. Exposure to EpiSC or human ESC (hESC) culture condition can convert mESCs towards an EpiSC-like state. Here, we show that the undifferentiated epiblast state is however not stabilized in a sustained manner when exposing mESCs to hESC or EpiSC culture condition. Rather, prolonged exposure to EpiSC condition promotes a transition to a primitive streak- (PS-) like state via an unbiased epiblast-like intermediate. We show that the Brachyury-positive PS-like state is likely promoted by endogenous WNT signaling, highlighting a possible species difference between mouse epiblast-like stem cells and human Embryonic Stem Cells.
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7
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Heterogeneity in old fibroblasts is linked to variability in reprogramming and wound healing. Nature 2019; 574:553-558. [PMID: 31645721 DOI: 10.1038/s41586-019-1658-5] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/05/2019] [Indexed: 02/06/2023]
Abstract
Age-associated chronic inflammation (inflammageing) is a central hallmark of ageing1, but its influence on specific cells remains largely unknown. Fibroblasts are present in most tissues and contribute to wound healing2,3. They are also the most widely used cell type for reprogramming to induced pluripotent stem (iPS) cells, a process that has implications for regenerative medicine and rejuvenation strategies4. Here we show that fibroblast cultures from old mice secrete inflammatory cytokines and exhibit increased variability in the efficiency of iPS cell reprogramming between mice. Variability between individuals is emerging as a feature of old age5-8, but the underlying mechanisms remain unknown. To identify drivers of this variability, we performed multi-omics profiling of fibroblast cultures from young and old mice that have different reprogramming efficiencies. This approach revealed that fibroblast cultures from old mice contain 'activated fibroblasts' that secrete inflammatory cytokines, and that the proportion of activated fibroblasts in a culture correlates with the reprogramming efficiency of that culture. Experiments in which conditioned medium was swapped between cultures showed that extrinsic factors secreted by activated fibroblasts underlie part of the variability between mice in reprogramming efficiency, and we have identified inflammatory cytokines, including TNF, as key contributors. Notably, old mice also exhibited variability in wound healing rate in vivo. Single-cell RNA-sequencing analysis identified distinct subpopulations of fibroblasts with different cytokine expression and signalling in the wounds of old mice with slow versus fast healing rates. Hence, a shift in fibroblast composition, and the ratio of inflammatory cytokines that they secrete, may drive the variability between mice in reprogramming in vitro and influence wound healing rate in vivo. This variability may reflect distinct stochastic ageing trajectories between individuals, and could help in developing personalized strategies to improve iPS cell generation and wound healing in elderly individuals.
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8
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Zhang M, Leitch HG, Tang WWC, Festuccia N, Hall-Ponsele E, Nichols J, Surani MA, Smith A, Chambers I. Esrrb Complementation Rescues Development of Nanog-Null Germ Cells. Cell Rep 2019; 22:332-339. [PMID: 29320730 PMCID: PMC5775501 DOI: 10.1016/j.celrep.2017.12.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 11/15/2017] [Accepted: 12/17/2017] [Indexed: 12/24/2022] Open
Abstract
The transcription factors (TFs) Nanog and Esrrb play important roles in embryonic stem cells (ESCs) and during primordial germ-cell (PGC) development. Esrrb is a positively regulated direct target of NANOG in ESCs that can substitute qualitatively for Nanog function in ESCs. Whether this functional substitution extends to the germline is unknown. Here, we show that germline deletion of Nanog reduces PGC numbers 5-fold at midgestation. Despite this quantitative depletion, Nanog-null PGCs can complete germline development in contrast to previous findings. PGC-like cell (PGCLC) differentiation of Nanog-null ESCs is also impaired, with Nanog-null PGCLCs showing decreased proliferation and increased apoptosis. However, induced expression of Esrrb restores PGCLC numbers as efficiently as Nanog. These effects are recapitulated in vivo: knockin of Esrrb to Nanog restores PGC numbers to wild-type levels and results in fertile adult mice. These findings demonstrate that Esrrb can replace Nanog function in germ cells. Germline deletion of Nanog reduces PGC numbers but does not abolish PGC development Without Nanog, PGCLCs form ineffectively with less proliferation and more apoptosis The Nanog target gene Esrrb can rescue PGCLC differentiation of Nanog−/− ESCs Knockin of Esrrb at the Nanog locus restores PGC development efficiency
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Affiliation(s)
- Man Zhang
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, Scotland
| | - Harry G Leitch
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, United Kingdom.
| | - Walfred W C Tang
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Physiology, Development and Neuroscience, Downing Street, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Nicola Festuccia
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, Scotland
| | - Elisa Hall-Ponsele
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, Scotland
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, United Kingdom; Department of Physiology, Development and Neuroscience, Downing Street, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 1QN, United Kingdom; Department of Physiology, Development and Neuroscience, Downing Street, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Austin Smith
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, United Kingdom; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, Scotland.
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9
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Hu B, Zheng L, Long C, Song M, Li T, Yang L, Zuo Y. EmExplorer: a database for exploring time activation of gene expression in mammalian embryos. Open Biol 2019; 9:190054. [PMID: 31164042 PMCID: PMC6597754 DOI: 10.1098/rsob.190054] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding early development offers a striking opportunity to investigate genetic disease, stem cell and assisted reproductive technology. Recent advances in high-throughput sequencing technology have led to the rising influx of omics data, which have rapidly boosted our understanding of mammalian developmental mechanisms. Here, we review the database EmExplorer (a database for exploring time activation of gene expression in mammalian embryos), which systematically organizes the genes from development-related pathways, and which we have already established and continue to update it. The current version of EmExplorer incorporates over 26 000 genes obtained from 306 functional pathways in five species. The function annotations of development-related genes were also integrated into EmExplorer. To facilitate data extraction, the database also contains the following information. (i) The dynamic expression values for each development stage are matched to the corresponding genes. (ii) A two-layer search tool which supports multi-option searching, such as by official symbol, pathway name and function annotation. The returned entries can directly link to the analysis results for the corresponding gene or pathway in the analysis module. (iii) The analysis module provides different gene comparisons at the multi-species level and functional pathway level, which shows the species specificity and stage specificity at the gene or pathway level. (iv) The analysis based on the hypergeometric distribution test reveals the enrichment of gene functions at a particular stage of one organism's pathway. (v) The browser is designed for users with ambiguous searching goals and greatly helps new users to get a general idea of the contents of the database. (vi) The experimentally validated pathways are manually curated and shown on the home page. EmExplorer will be helpful for elucidating early developmental mechanisms and exploring time activation genes. EmExplorer is freely available at http://bioinfor.imu.edu.cn/emexplorer.
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Affiliation(s)
- Bosu Hu
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Lei Zheng
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Chunshen Long
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Mingmin Song
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Tao Li
- 2 College of Life Sciences, Inner Mongolia Agricultural University , Hohhot 010018 , People's Republic of China
| | - Lei Yang
- 3 College of Bioinformatics Science and Technology, Harbin Medical University , Harbin 150081 , People's Republic of China
| | - Yongchun Zuo
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
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10
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The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells. Nat Commun 2019; 10:1109. [PMID: 30846691 PMCID: PMC6406003 DOI: 10.1038/s41467-019-09041-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 02/13/2019] [Indexed: 12/20/2022] Open
Abstract
Transcription factor networks, together with histone modifications and signalling pathways, underlie the establishment and maintenance of gene regulatory architectures associated with the molecular identity of each cell type. However, how master transcription factors individually impact the epigenomic landscape and orchestrate the behaviour of regulatory networks under different environmental constraints is only partially understood. Here, we show that the transcription factor Nanog deploys multiple distinct mechanisms to enhance embryonic stem cell self-renewal. In the presence of LIF, which fosters self-renewal, Nanog rewires the pluripotency network by promoting chromatin accessibility and binding of other pluripotency factors to thousands of enhancers. In the absence of LIF, Nanog blocks differentiation by sustaining H3K27me3, a repressive histone mark, at developmental regulators. Among those, we show that the repression of Otx2 plays a preponderant role. Our results underscore the versatility of master transcription factors, such as Nanog, to globally influence gene regulation during developmental processes.
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11
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Kanitz A, Syed AP, Kaji K, Zavolan M. Conserved regulation of RNA processing in somatic cell reprogramming. BMC Genomics 2019; 20:100. [PMID: 30704403 PMCID: PMC6357513 DOI: 10.1186/s12864-019-5438-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at the level of RNA processing. These include the expression of specific transcript isoforms and 3' untranslated regions. A number of studies have uncovered RNA processing factors that modulate the efficiency of the reprogramming process. However, a comprehensive evaluation of the involvement of RNA processing factors in the reprogramming of somatic mammalian cells is lacking. RESULTS Here, we used data from a large number of studies carried out in three mammalian species, mouse, chimpanzee and human, to uncover consistent changes in gene expression upon reprogramming of somatic cells. We found that a core set of nine splicing factors have consistent changes across the majority of data sets in all three species. Most striking among these are ESRP1 and ESRP2, which accelerate and enhance the efficiency of somatic cell reprogramming by promoting isoform expression changes associated with mesenchymal-to-epithelial transition. We further identify genes and processes in which splicing changes are observed in both human and mouse. CONCLUSIONS Our results provide a general resource for gene expression and splicing changes that take place during somatic cell reprogramming. Furthermore, they support the concept that splicing factors with evolutionarily conserved, cell type-specific expression can modulate the efficiency of the process by reinforcing intermediate states resembling the cell types in which these factors are normally expressed.
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Affiliation(s)
- Alexander Kanitz
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Afzal Pasha Syed
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Keisuke Kaji
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
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12
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Feng Y, Ning Y, Lin X, Zhang D, Liao S, Zheng C, Chen J, Wang Y, Ma L, Xie D, Han C. Reprogramming p53-Deficient Germline Stem Cells Into Pluripotent State by Nanog. Stem Cells Dev 2018; 27:692-703. [PMID: 29631477 DOI: 10.1089/scd.2018.0047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cultured mouse spermatogonial stem cells (SSCs), also known as germline stem cells (GSCs), revert back to pluripotent state either spontaneously or upon being modified genetically. However, the reprogramming efficiencies are low, and the underlying mechanism remains poorly understood. In the present study, we conducted transcriptomic analysis and found that many transcription factors and epigenetic modifiers were differentially expressed between GSCs and embryonic stem cells. We failed in reprogramming GSCs to pluripotent state using the Yamanaka 4 Factors, but succeeded when Nanog and Tet1 were included. More importantly, reprogramming was also achieved with Nanog alone in a p53-deficient GSC line with an efficiency of 0.02‰. These GSC-derived-induced pluripotent stem cells possessed in vitro and in vivo differentiation abilities despite the low rate of chimera formation, which might be caused by abnormal methylation in certain paternally imprinted genes. Together, these results show that GSCs can be reprogrammed to pluripotent state via multiple avenues and contribute to our understanding of the mechanisms of GSC reprogramming.
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Affiliation(s)
- Yanmin Feng
- 1 State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, China .,2 University of Chinese Academy of Sciences , Beijing, China
| | - Yan Ning
- 1 State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, China .,2 University of Chinese Academy of Sciences , Beijing, China
| | - Xiwen Lin
- 1 State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, China
| | - Daoqin Zhang
- 1 State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, China .,2 University of Chinese Academy of Sciences , Beijing, China
| | - Shangying Liao
- 1 State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, China
| | - Chunwei Zheng
- 1 State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, China .,2 University of Chinese Academy of Sciences , Beijing, China
| | - Jian Chen
- 1 State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, China .,2 University of Chinese Academy of Sciences , Beijing, China
| | - Yang Wang
- 1 State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, China .,2 University of Chinese Academy of Sciences , Beijing, China
| | - Longfei Ma
- 1 State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, China .,2 University of Chinese Academy of Sciences , Beijing, China
| | - Dan Xie
- 1 State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, China .,2 University of Chinese Academy of Sciences , Beijing, China
| | - Chunsheng Han
- 1 State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology , Chinese Academy of Sciences, Beijing, China
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13
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Gagnon JA, Obbad K, Schier AF. The primary role of zebrafish nanog is in extra-embryonic tissue. Development 2018; 145:dev.147793. [PMID: 29180571 DOI: 10.1242/dev.147793] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 11/07/2017] [Indexed: 12/17/2022]
Abstract
The role of the zebrafish transcription factor Nanog has been controversial. It has been suggested that Nanog is primarily required for the proper formation of the extra-embryonic yolk syncytial layer (YSL) and only indirectly regulates gene expression in embryonic cells. In an alternative scenario, Nanog has been proposed to directly regulate transcription in embryonic cells during zygotic genome activation. To clarify the roles of Nanog, we performed a detailed analysis of zebrafish nanog mutants. Whereas zygotic nanog mutants survive to adulthood, maternal-zygotic (MZnanog) and maternal mutants exhibit developmental arrest at the blastula stage. In the absence of Nanog, YSL formation and epiboly are abnormal, embryonic tissue detaches from the yolk, and the expression of dozens of YSL and embryonic genes is reduced. Epiboly defects can be rescued by generating chimeric embryos of MZnanog embryonic tissue with wild-type vegetal tissue that includes the YSL and yolk cell. Notably, cells lacking Nanog readily respond to Nodal signals and when transplanted into wild-type hosts proliferate and contribute to embryonic tissues and adult organs from all germ layers. These results indicate that zebrafish Nanog is necessary for proper YSL development but is not directly required for embryonic cell differentiation.
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Affiliation(s)
- James A Gagnon
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kamal Obbad
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA .,Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.,The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
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14
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Festuccia N, Owens N, Navarro P. Esrrb, an estrogen-related receptor involved in early development, pluripotency, and reprogramming. FEBS Lett 2017; 592:852-877. [DOI: 10.1002/1873-3468.12826] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/11/2017] [Accepted: 08/19/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
| | - Nick Owens
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
| | - Pablo Navarro
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
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15
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Davis TL, Rebay I. Master regulators in development: Views from the Drosophila retinal determination and mammalian pluripotency gene networks. Dev Biol 2016; 421:93-107. [PMID: 27979656 DOI: 10.1016/j.ydbio.2016.12.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/03/2016] [Accepted: 12/03/2016] [Indexed: 02/07/2023]
Abstract
Among the mechanisms that steer cells to their correct fate during development, master regulatory networks are unique in their sufficiency to trigger a developmental program outside of its normal context. In this review we discuss the key features that underlie master regulatory potency during normal and ectopic development, focusing on two examples, the retinal determination gene network (RDGN) that directs eye development in the fruit fly and the pluripotency gene network (PGN) that maintains cell fate competency in the early mammalian embryo. In addition to the hierarchical transcriptional activation, extensive positive transcriptional feedback, and cooperative protein-protein interactions that enable master regulators to override competing cellular programs, recent evidence suggests that network topology must also be dynamic, with extensive rewiring of the interactions and feedback loops required to navigate the correct sequence of developmental transitions to reach a final fate. By synthesizing the in vivo evidence provided by the RDGN with the extensive mechanistic insight gleaned from the PGN, we highlight the unique regulatory capabilities that continual reorganization into new hierarchies confers on master control networks. We suggest that deeper understanding of such dynamics should be a priority, as accurate spatiotemporal remodeling of network topology will undoubtedly be essential for successful stem cell based therapeutic efforts.
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Affiliation(s)
- Trevor L Davis
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Ilaria Rebay
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA; Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA.
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16
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Jin J, Liu J, Chen C, Liu Z, Jiang C, Chu H, Pan W, Wang X, Zhang L, Li B, Jiang C, Ge X, Xie X, Wang P. The deubiquitinase USP21 maintains the stemness of mouse embryonic stem cells via stabilization of Nanog. Nat Commun 2016; 7:13594. [PMID: 27886188 PMCID: PMC5133637 DOI: 10.1038/ncomms13594] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 10/18/2016] [Indexed: 12/11/2022] Open
Abstract
Nanog is a master pluripotency factor of embryonic stem cells (ESCs). Stable expression of Nanog is essential to maintain the stemness of ESCs. However, Nanog is a short-lived protein and quickly degraded by the ubiquitin-dependent proteasome system. Here we report that the deubiquitinase USP21 interacts with, deubiquitinates and stabilizes Nanog, and therefore maintains the protein level of Nanog in mouse ESCs (mESCs). Loss of USP21 results in Nanog degradation, mESCs differentiation and reduces somatic cell reprogramming efficiency. USP21 is a transcriptional target of the LIF/STAT3 pathway and is downregulated upon differentiation. Moreover, differentiation cues promote ERK-mediated phosphorylation and dissociation of USP21 from Nanog, thus leading to Nanog degradation. In addition, USP21 is recruited to gene promoters by Nanog to deubiquitinate histone H2A at K119 and thus facilitates Nanog-mediated gene expression. Together, our findings provide a regulatory mechanism by which extrinsic signals regulate mESC fate via deubiquitinating Nanog. Nanog regulates embryonic stem cell (ESC) pluripotency but what controls Nanog protein stability is unclear. Here, the authors show that in mouse ESCs, Nanog protein is ubiquitinated and stabilized by the deubiquitinase USP21, which in turn is regulated by extrinsic signals, STAT3 and ERK.
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Affiliation(s)
- Jiali Jin
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Jian Liu
- Chinese Academy of Sciences Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences No. 19A Yuquan Road, Beijing 100049, China
| | - Cong Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zhenping Liu
- Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Cong Jiang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hongshang Chu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Weijuan Pan
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xinbo Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing 100850, China
| | - Bin Li
- Key Laboratory of Molecular Virology and Immunology, Unit of Molecular Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cizhong Jiang
- Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Xin Ge
- Department of Clinical Medicine, Shanghai Tenth People's Hospital of Tongji University, Tongji University, Shanghai 200072, China
| | - Xin Xie
- Chinese Academy of Sciences Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences No. 19A Yuquan Road, Beijing 100049, China
| | - Ping Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.,Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, School of Life Science and Technology, Tongji University, Shanghai 200072, China
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17
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Xiao X, Li N, Zhang D, Yang B, Guo H, Li Y. Generation of Induced Pluripotent Stem Cells with Substitutes for Yamanaka's Four Transcription Factors. Cell Reprogram 2016; 18:281-297. [PMID: 27696909 DOI: 10.1089/cell.2016.0020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) share many characteristics with embryonic stem cells, but lack ethical controversy. They provide vast opportunities for disease modeling, pathogenesis understanding, therapeutic drug development, toxicology, organ synthesis, and treatment of degenerative disease. However, this procedure also has many potential challenges, including a slow generation time, low efficiency, partially reprogrammed colonies, as well as somatic coding mutations in the genome. Pioneered by Shinya Yamanaka's team in 2006, iPSCs were first generated by introducing four transcription factors: Oct 4, Sox 2, Klf 4, and c-Myc (OSKM). Of those factors, Klf 4 and c-Myc are oncogenes, which are potentially a tumor risk. Therefore, to avoid problems such as tumorigenesis and low throughput, one of the key strategies has been to use other methods, including members of the same subgroup of transcription factors, activators or inhibitors of signaling pathways, microRNAs, epigenetic modifiers, or even differentiation-associated factors, to functionally replace the reprogramming transcription factors. In this study, we will mainly focus on the advances in the generation of iPSCs with substitutes for OSKM. The identification and combination of novel proteins or chemicals, particularly small molecules, to induce pluripotency will provide useful tools to discover the molecular mechanisms governing reprogramming and ultimately lead to the development of new iPSC-based therapeutics for future clinical applications.
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Affiliation(s)
- Xiong Xiao
- 1 College of Animal Science and Technology, Southwest University , Chongqing, China .,2 Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California , Los Angeles, California
| | - Nan Li
- 1 College of Animal Science and Technology, Southwest University , Chongqing, China
| | - Dapeng Zhang
- 1 College of Animal Science and Technology, Southwest University , Chongqing, China
| | - Bo Yang
- 1 College of Animal Science and Technology, Southwest University , Chongqing, China
| | - Hongmei Guo
- 1 College of Animal Science and Technology, Southwest University , Chongqing, China
| | - Yuemin Li
- 1 College of Animal Science and Technology, Southwest University , Chongqing, China
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18
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Olariu V, Lövkvist C, Sneppen K. Nanog, Oct4 and Tet1 interplay in establishing pluripotency. Sci Rep 2016; 6:25438. [PMID: 27146218 PMCID: PMC4857071 DOI: 10.1038/srep25438] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 04/18/2016] [Indexed: 01/12/2023] Open
Abstract
A few central transcription factors inside mouse embryonic stem (ES) cells and induced pluripotent stem (iPS) cells are believed to control the cells’ pluripotency. Characterizations of pluripotent state were put forward on both transcription factor and epigenetic levels. Whereas core players have been identified, it is desirable to map out gene regulatory networks which govern the reprogramming of somatic cells as well as the early developmental decisions. Here we propose a multiple level model where the regulatory network of Oct4, Nanog and Tet1 includes positive feedback loops involving DNA-demethylation around the promoters of Oct4 and Tet1. We put forward a mechanistic understanding of the regulatory dynamics which account for i) Oct4 overexpression is sufficient to induce pluripotency in somatic cell types expressing the other Yamanaka reprogramming factors endogenously; ii) Tet1 can replace Oct4 in reprogramming cocktail; iii) Nanog is not necessary for reprogramming however its over-expression leads to enhanced self-renewal; iv) DNA methylation is the key to the regulation of pluripotency genes; v) Lif withdrawal leads to loss of pluripotency. Overall, our paper proposes a novel framework combining transcription regulation with DNA methylation modifications which, takes into account the multi-layer nature of regulatory mechanisms governing pluripotency acquisition through reprogramming.
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Affiliation(s)
- Victor Olariu
- Centre for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.,Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Cecilia Lövkvist
- Centre for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kim Sneppen
- Centre for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.,Centre for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
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19
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Novo CL, Tang C, Ahmed K, Djuric U, Fussner E, Mullin NP, Morgan NP, Hayre J, Sienerth AR, Elderkin S, Nishinakamura R, Chambers I, Ellis J, Bazett-Jones DP, Rugg-Gunn PJ. The pluripotency factor Nanog regulates pericentromeric heterochromatin organization in mouse embryonic stem cells. Genes Dev 2016; 30:1101-15. [PMID: 27125671 PMCID: PMC4863740 DOI: 10.1101/gad.275685.115] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 03/23/2016] [Indexed: 12/31/2022]
Abstract
Here, Novo et al. identify a new critical role for the transcription factor Nanog in maintaining an open heterochromatin state in pluripotent mouse embryonic stem cells and demonstrate that forced expression of Nanog is sufficient to remodel and decondense chromatin in more developmentally advanced mammalian cell types. This study delineates a direct connection between the pluripotency network and chromatin organization and shows that maintainence of an open heterochromatin architecture is highly regulated in embryonic stem cells. An open and decondensed chromatin organization is a defining property of pluripotency. Several epigenetic regulators have been implicated in maintaining an open chromatin organization, but how these processes are connected to the pluripotency network is unknown. Here, we identified a new role for the transcription factor NANOG as a key regulator connecting the pluripotency network with constitutive heterochromatin organization in mouse embryonic stem cells. Deletion of Nanog leads to chromatin compaction and the remodeling of heterochromatin domains. Forced expression of NANOG in epiblast stem cells is sufficient to decompact chromatin. NANOG associates with satellite repeats within heterochromatin domains, contributing to an architecture characterized by highly dispersed chromatin fibers, low levels of H3K9me3, and high major satellite transcription, and the strong transactivation domain of NANOG is required for this organization. The heterochromatin-associated protein SALL1 is a direct cofactor for NANOG, and loss of Sall1 recapitulates the Nanog-null phenotype, but the loss of Sall1 can be circumvented through direct recruitment of the NANOG transactivation domain to major satellites. These results establish a direct connection between the pluripotency network and chromatin organization and emphasize that maintaining an open heterochromatin architecture is a highly regulated process in embryonic stem cells.
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Affiliation(s)
- Clara Lopes Novo
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Calvin Tang
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario MSG 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Kashif Ahmed
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario MSG 1L7, Canada
| | - Ugljesa Djuric
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Eden Fussner
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario MSG 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nicholas P Mullin
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
| | - Natasha P Morgan
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Jasvinder Hayre
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Arnold R Sienerth
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Sarah Elderkin
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, United Kingdom
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
| | - James Ellis
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David P Bazett-Jones
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario MSG 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, United Kingdom
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20
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Dynamic stem cell states: naive to primed pluripotency in rodents and humans. Nat Rev Mol Cell Biol 2016; 17:155-69. [PMID: 26860365 DOI: 10.1038/nrm.2015.28] [Citation(s) in RCA: 410] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The molecular mechanisms and signalling pathways that regulate the in vitro preservation of distinct pluripotent stem cell configurations, and their induction in somatic cells by direct reprogramming, constitute a highly exciting area of research. In this Review, we integrate recent discoveries related to isolating unique naive and primed pluripotent stem cell states with altered functional and molecular characteristics, and from different species. We provide an overview of the pathways underlying pluripotent state transitions and interconversion in vitro and in vivo. We conclude by highlighting unresolved key questions, future directions and potential novel applications of such dynamic pluripotent cell states.
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21
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Marthaler AG, Adachi K, Tiemann U, Wu G, Sabour D, Velychko S, Kleiter I, Schöler HR, Tapia N. Enhanced OCT4 transcriptional activity substitutes for exogenous SOX2 in cellular reprogramming. Sci Rep 2016; 6:19415. [PMID: 26762895 PMCID: PMC4725906 DOI: 10.1038/srep19415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/11/2015] [Indexed: 01/12/2023] Open
Abstract
Adenoviral early region 1A (E1A) is a viral gene that can promote cellular proliferation and de-differentiation in mammalian cells, features required for the reprogramming of somatic cells to a pluripotent state. E1A has been shown to interact with OCT4, and as a consequence, to increase OCT4 transcriptional activity. Indeed, E1A and OCT4 are sufficient to revert neuroepithelial hybrids to pluripotency, as demonstrated in previous cell fusion experiments. However, the role that E1A might play in the generation of induced pluripotent stem cells (iPSCs) has not been investigated yet. In this report, we show that E1A can generate iPSCs in combination with OCT4 and KLF4, thus replacing exogenous SOX2. The generated iPSCs are bona fide pluripotent cells as shown by in vitro and in vivo tests. Overall, our study suggests that E1A might replace SOX2 through enhancing OCT4 transcriptional activity at the early stages of reprogramming.
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Affiliation(s)
- Adele G Marthaler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Kenjiro Adachi
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Ulf Tiemann
- Medical Faculty, Heinrich Heine University, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Davood Sabour
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Sergiy Velychko
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Ingo Kleiter
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, Gudrunstraße 56, 44791 Bochum, Germany
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany.,Medical Faculty, University of Münster, Domagkstraße 3, 48149 Münster, Germany
| | - Natalia Tapia
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany.,Medical Faculty, Heinrich Heine University, Moorenstraße 5, 40225 Düsseldorf, Germany
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22
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Murakami K, Günesdogan U, Zylicz JJ, Tang WWC, Sengupta R, Kobayashi T, Kim S, Butler R, Dietmann S, Surani MA. NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers. Nature 2016; 529:403-407. [PMID: 26751055 DOI: 10.1038/nature16480] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/23/2015] [Indexed: 12/18/2022]
Abstract
Nanog, a core pluripotency factor in the inner cell mass of blastocysts, is also expressed in unipotent primordial germ cells (PGCs) in mice, where its precise role is yet unclear. We investigated this in an in vitro model, in which naive pluripotent embryonic stem (ES) cells cultured in basic fibroblast growth factor (bFGF) and activin A develop as epiblast-like cells (EpiLCs) and gain competence for a PGC-like fate. Consequently, bone morphogenetic protein 4 (BMP4), or ectopic expression of key germline transcription factors Prdm1, Prdm14 and Tfap2c, directly induce PGC-like cells (PGCLCs) in EpiLCs, but not in ES cells. Here we report an unexpected discovery that Nanog alone can induce PGCLCs in EpiLCs, independently of BMP4. We propose that after the dissolution of the naive ES-cell pluripotency network during establishment of EpiLCs, the epigenome is reset for cell fate determination. Indeed, we found genome-wide changes in NANOG-binding patterns between ES cells and EpiLCs, indicating epigenetic resetting of regulatory elements. Accordingly, we show that NANOG can bind and activate enhancers of Prdm1 and Prdm14 in EpiLCs in vitro; BLIMP1 (encoded by Prdm1) then directly induces Tfap2c. Furthermore, while SOX2 and NANOG promote the pluripotent state in ES cells, they show contrasting roles in EpiLCs, as Sox2 specifically represses PGCLC induction by Nanog. This study demonstrates a broadly applicable mechanistic principle for how cells acquire competence for cell fate determination, resulting in the context-dependent roles of key transcription factors during development.
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Affiliation(s)
- Kazuhiro Murakami
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.,Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Laboratory for Pluripotent Cell Studies, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Laboratory for Molecular and Cellular Biology, Faculty of Advanced Life Science, Hokkaido University, Kita21 Nishi11, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Ufuk Günesdogan
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.,Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jan J Zylicz
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.,Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Walfred W C Tang
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.,Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Roopsha Sengupta
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.,Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Toshihiro Kobayashi
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.,Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Shinseog Kim
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.,Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Richard Butler
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Sabine Dietmann
- Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.,Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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23
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Sebban S, Buganim Y. Nuclear Reprogramming by Defined Factors: Quantity Versus Quality. Trends Cell Biol 2015; 26:65-75. [PMID: 26437595 DOI: 10.1016/j.tcb.2015.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/04/2015] [Accepted: 08/21/2015] [Indexed: 01/29/2023]
Abstract
The generation of induced pluripotent stem cells (iPSCs) and directly converted cells holds great promise in regenerative medicine. However, after in-depth studies of the murine system, we know that the current methodologies to produce these cells are not ideal and mostly yield cells of poor quality that might hold a risk in therapeutic applications. In this review we address the duality found in the literature regarding the use of 'quality' as a criterion for the clinic. We discuss the elements that influence reprogramming quality, and provide evidence that safety and functionality are directly linked to cell quality. Finally, because most of the available data come from murine systems, we speculate about what aspects can be applied to human cells.
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Affiliation(s)
- Shulamit Sebban
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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24
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Reprogramming Roadblocks Are System Dependent. Stem Cell Reports 2015; 5:350-64. [PMID: 26278041 PMCID: PMC4618455 DOI: 10.1016/j.stemcr.2015.07.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 07/20/2015] [Accepted: 07/20/2015] [Indexed: 12/20/2022] Open
Abstract
Since the first generation of induced pluripotent stem cells (iPSCs), several reprogramming systems have been used to study its molecular mechanisms. However, the system of choice largely affects the reprogramming efficiency, influencing our view on the mechanisms. Here, we demonstrate that reprogramming triggered by less efficient polycistronic reprogramming cassettes not only highlights mesenchymal-to-epithelial transition (MET) as a roadblock but also faces more severe difficulties to attain a pluripotent state even post-MET. In contrast, more efficient cassettes can reprogram both wild-type and Nanog−/− fibroblasts with comparable efficiencies, routes, and kinetics, unlike the less efficient reprogramming systems. Moreover, we attribute a previously reported variation in the N terminus of KLF4 as a dominant factor underlying these critical differences. Our data establish that some reprogramming roadblocks are system dependent, highlighting the need to pursue mechanistic studies with close attention to the systems to better understand reprogramming. Distinct reprogramming cassettes yield different reprogramming intermediates MET is not a major rate-limiting step in reprogramming with high KLF4 expression A lack of endogenous Nanog becomes trivial in efficient reprogramming systems Roadblocks toward iPSCs depend on the reprogramming systems
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25
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Maza I, Caspi I, Zviran A, Chomsky E, Rais Y, Viukov S, Geula S, Buenrostro JD, Weinberger L, Krupalnik V, Hanna S, Zerbib M, Dutton JR, Greenleaf WJ, Massarwa R, Novershtern N, Hanna JH. Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors. Nat Biotechnol 2015; 33:769-74. [PMID: 26098448 PMCID: PMC4500825 DOI: 10.1038/nbt.3270] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 06/01/2015] [Indexed: 01/20/2023]
Abstract
Somatic cells can be transdifferentiated to other cell types without passing through a pluripotent state by ectopic expression of appropriate transcription factors1,2. Recent reports have proposed an alternative transdifferentiation method in which fibroblasts are directly converted to various mature somatic cell types by brief expression of the induced pluripotent stem cell (iPSC) reprogramming factors Oct4, Sox2, Klf4 and c-Myc (OSKM) followed by cell expansion in media that promote lineage differentiation3–6. Here we test this method using genetic lineage tracing for expression of endogenous Nanog and Oct4 and for X chromosome reactivation, as these events mark acquisition of pluripotency. We show that the vast majority of reprogrammed cardiomyocytes or neural stem cells obtained from mouse fibroblasts by OSKM-induced transdifferentiation pass through a transient pluripotent state, and that their derivation is molecularly coupled to iPSC formation mechanisms. Our findings underscore the importance of defining trajectories during cell reprogramming by different methods.
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Affiliation(s)
- Itay Maza
- 1] The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. [2] The Department of Gastroenterology, Rambam Health Care Campus &Bruce Rappaport School of Medicine, Technion Institute of Technology, Haifa, Israel
| | - Inbal Caspi
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Asaf Zviran
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Elad Chomsky
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yoach Rais
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Viukov
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shay Geula
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jason D Buenrostro
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Leehee Weinberger
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Vladislav Krupalnik
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Suhair Hanna
- 1] The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. [2] The Department of Pediatrics and the Pediatric Immunology Unit, Rambam Health Care Campus &Bruce Rappaport School of Medicine, Technion Institute of Technology, Haifa, Israel
| | - Mirie Zerbib
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - James R Dutton
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - William J Greenleaf
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rada Massarwa
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Novershtern
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob H Hanna
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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26
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Abstract
Pluripotency is the remarkable capacity of a single cell to engender all the specialized cell types of an adult organism. This property can be captured indefinitely through derivation of self-renewing embryonic stem cells (ESCs), which represent an invaluable platform to investigate cell fate decisions and disease. Recent advances have revealed that manipulation of distinct signaling cues can render ESCs in a uniform "ground state" of pluripotency, which more closely recapitulates the pluripotent naive epiblast. Here we discuss the extrinsic and intrinsic regulatory principles that underpin the nature of pluripotency and consider the emerging spectrum of pluripotent states.
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Affiliation(s)
- Jamie A Hackett
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1QN, UK
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1QN, UK.
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27
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Abstract
Deciphering the mechanisms of epigenetic reprogramming provides fundamental insights into cell fate decisions, which in turn reveal strategies to make the reprogramming process increasingly efficient. Here we review recent advances in epigenetic reprogramming to pluripotency with a focus on the principal molecular regulators. We examine the trajectories connecting somatic and pluripotent cells, genetic and chemical methodologies for inducing pluripotency, the role of endogenous master transcription factors in establishing the pluripotent state, and functional interactions between reprogramming factors and epigenetic regulators. Defining the crosstalk among the diverse molecular actors implicated in cellular reprogramming presents a major challenge for future inquiry.
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Affiliation(s)
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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28
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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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29
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Kranc KR, Oliveira DV, Armesilla-Diaz A, Pacheco-Leyva I, Catarina Matias A, Luisa Escapa A, Subramani C, Wheadon H, Trindade M, Nichols J, Kaji K, Enver T, Bragança J. Acute Loss of Cited2 Impairs Nanog Expression and Decreases Self-Renewal of Mouse Embryonic Stem Cells. Stem Cells 2015; 33:699-712. [DOI: https:/doi.org/10.1002/stem.1889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Abstract
Identifying novel players of the pluripotency gene regulatory network centered on Oct4, Sox2, and Nanog as well as delineating the interactions within the complex network is key to understanding self-renewal and early cell fate commitment of embryonic stem cells (ESC). While overexpression of the transcriptional regulator Cited2 sustains ESC pluripotency, its role in ESC functions remains unclear. Here, we show that Cited2 is important for proliferation, survival, and self-renewal of mouse ESC. We position Cited2 within the pluripotency gene regulatory network by defining Nanog, Tbx3, and Klf4 as its direct targets. We also demonstrate that the defects caused by Cited2 depletion are, at least in part, rescued by Nanog constitutive expression. Finally, we demonstrate that Cited2 is required for and enhances reprogramming of mouse embryonic fibroblasts to induced pluripotent stem cells. Stem Cells 2015;33:699–712
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Affiliation(s)
- Kamil R. Kranc
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel V. Oliveira
- Departamento de Ciências Biomédicas e Medicina Universidade do Algarve, Faro, Portugal
| | | | - Ivette Pacheco-Leyva
- Departamento de Ciências Biomédicas e Medicina Universidade do Algarve, Faro, Portugal
| | - Ana Catarina Matias
- Departamento de Ciências Biomédicas e Medicina Universidade do Algarve, Faro, Portugal
| | - Ana Luisa Escapa
- Departamento de Ciências Biomédicas e Medicina Universidade do Algarve, Faro, Portugal
| | - Chithra Subramani
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Helen Wheadon
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Gartnavel General Hospital, Glasgow, United Kingdom
| | - Marlene Trindade
- Departamento de Ciências Biomédicas e Medicina Universidade do Algarve, Faro, Portugal
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
| | - Keisuke Kaji
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Tariq Enver
- Stem Cell Laboratory UCL Cancer Institute, University College London, Paul O'Gorman Building, London, United Kingdom
| | - José Bragança
- Departamento de Ciências Biomédicas e Medicina Universidade do Algarve, Faro, Portugal
- IBB-Centro de Biomedicina Molecular e Estrutural, Universidade do Algarve, Campus de Gambelas, Faro, Portugal
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30
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Kranc KR, Oliveira DV, Armesilla-Diaz A, Pacheco-Leyva I, Catarina Matias A, Luisa Escapa A, Subramani C, Wheadon H, Trindade M, Nichols J, Kaji K, Enver T, Bragança J. Acute loss of Cited2 impairs Nanog expression and decreases self-renewal of mouse embryonic stem cells. Stem Cells 2015; 33:699-712. [PMID: 25377420 PMCID: PMC4583779 DOI: 10.1002/stem.1889] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/16/2014] [Accepted: 10/11/2014] [Indexed: 12/23/2022]
Abstract
Identifying novel players of the pluripotency gene regulatory network centered on Oct4, Sox2, and Nanog as well as delineating the interactions within the complex network is key to understanding self-renewal and early cell fate commitment of embryonic stem cells (ESC). While overexpression of the transcriptional regulator Cited2 sustains ESC pluripotency, its role in ESC functions remains unclear. Here, we show that Cited2 is important for proliferation, survival, and self-renewal of mouse ESC. We position Cited2 within the pluripotency gene regulatory network by defining Nanog, Tbx3, and Klf4 as its direct targets. We also demonstrate that the defects caused by Cited2 depletion are, at least in part, rescued by Nanog constitutive expression. Finally, we demonstrate that Cited2 is required for and enhances reprogramming of mouse embryonic fibroblasts to induced pluripotent stem cells.
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Affiliation(s)
- Kamil R Kranc
- MRC Centre for Regenerative Medicine, University of EdinburghEdinburgh, United Kingdom
| | - Daniel V Oliveira
- Departamento de Ciências Biomédicas e Medicina, Universidade do AlgarveFaro, Portugal
| | | | - Ivette Pacheco-Leyva
- Departamento de Ciências Biomédicas e Medicina, Universidade do AlgarveFaro, Portugal
| | - Ana Catarina Matias
- Departamento de Ciências Biomédicas e Medicina, Universidade do AlgarveFaro, Portugal
| | - Ana Luisa Escapa
- Departamento de Ciências Biomédicas e Medicina, Universidade do AlgarveFaro, Portugal
| | - Chithra Subramani
- MRC Centre for Regenerative Medicine, University of EdinburghEdinburgh, United Kingdom
| | - Helen Wheadon
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Gartnavel General HospitalGlasgow, United Kingdom
| | - Marlene Trindade
- Departamento de Ciências Biomédicas e Medicina, Universidade do AlgarveFaro, Portugal
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of CambridgeTennis Court Road, Cambridge, United Kingdom
| | - Keisuke Kaji
- MRC Centre for Regenerative Medicine, University of EdinburghEdinburgh, United Kingdom
| | - Tariq Enver
- Stem Cell Laboratory, UCL Cancer Institute, University College LondonPaul O'Gorman Building, London, United Kingdom
| | - José Bragança
- Departamento de Ciências Biomédicas e Medicina, Universidade do AlgarveFaro, Portugal
- IBB-Centro de Biomedicina Molecular e Estrutural, Universidade do Algarve, Campus de GambelasFaro, Portugal
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31
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Pasque V, Tchieu J, Karnik R, Uyeda M, Sadhu Dimashkie A, Case D, Papp B, Bonora G, Patel S, Ho R, Schmidt R, McKee R, Sado T, Tada T, Meissner A, Plath K. X chromosome reactivation dynamics reveal stages of reprogramming to pluripotency. Cell 2015; 159:1681-97. [PMID: 25525883 DOI: 10.1016/j.cell.2014.11.040] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 09/30/2014] [Accepted: 11/12/2014] [Indexed: 12/16/2022]
Abstract
Reprogramming to iPSCs resets the epigenome of somatic cells, including the reversal of X chromosome inactivation. We sought to gain insight into the steps underlying the reprogramming process by examining the means by which reprogramming leads to X chromosome reactivation (XCR). Analyzing single cells in situ, we found that hallmarks of the inactive X (Xi) change sequentially, providing a direct readout of reprogramming progression. Several epigenetic changes on the Xi occur in the inverse order of developmental X inactivation, whereas others are uncoupled from this sequence. Among the latter, DNA methylation has an extraordinary long persistence on the Xi during reprogramming, and, like Xist expression, is erased only after pluripotency genes are activated. Mechanistically, XCR requires both DNA demethylation and Xist silencing, ensuring that only cells undergoing faithful reprogramming initiate XCR. Our study defines the epigenetic state of multiple sequential reprogramming intermediates and establishes a paradigm for studying cell fate transitions during reprogramming.
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Affiliation(s)
- Vincent Pasque
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jason Tchieu
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Rahul Karnik
- Department of Stem Cell and Regenerative Biology, Harvard University, Harvard Stem Cell Institute, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Molly Uyeda
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Anupama Sadhu Dimashkie
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Dana Case
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bernadett Papp
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Giancarlo Bonora
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sanjeet Patel
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ritchie Ho
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ryan Schmidt
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Robin McKee
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kinki University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Takashi Tada
- Department of Stem Cell Engineering, Stem Cell Research Center, Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Harvard Stem Cell Institute, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Kathrin Plath
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
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32
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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: 101] [Impact Index Per Article: 11.2] [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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33
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Peter Y, Weingarten M, Akhavan N, Hanau J. A Place to Call Home: Bioengineering Pluripotential Stem Cell Cultures. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.2.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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German SD, Campbell KHS, Thornton E, McLachlan G, Sweetman D, Alberio R. Ovine induced pluripotent stem cells are resistant to reprogramming after nuclear transfer. Cell Reprogram 2014; 17:19-27. [PMID: 25513856 DOI: 10.1089/cell.2014.0071] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) share similar characteristics of indefinite in vitro growth with embryonic stem cells (ESCs) and may therefore serve as a useful tool for the targeted genetic modification of farm animals via nuclear transfer (NT). Derivation of stable ESC lines from farm animals has not been possible, therefore, it is important to determine whether iPSCs can be used as substitutes for ESCs in generating genetically modified cloned farm animals. We generated ovine iPSCs by conventional retroviral transduction using the four Yamanaka factors. These cells were basic fibroblast growth factor (bFGF)- and activin A-dependent, showed persistent expression of the transgenes, acquired chromosomal abnormalities, and failed to activate endogenous NANOG. Nonetheless, iPSCs could differentiate into the three somatic germ layers in vitro. Because cloning of farm animals is best achieved with diploid cells (G1/G0), we synchronized the iPSCs in G1 prior to NT. Despite the cell cycle synchronization, preimplantation development of iPSC-NT embryos was lower than with somatic cells (2% vs. 10% blastocysts, p<0.01). Furthermore, analysis of the blastocysts produced demonstrated persistent expression of the transgenes, aberrant expression of endogenous SOX2, and a failure to activate NANOG consistently. In contrast, gene expression in blastocysts produced with the parental fetal fibroblasts was similar to those generated by in vitro fertilization. Taken together, our data suggest that the persistent expression of the exogenous factors and the acquisition of chromosomal abnormalities are incompatible with normal development of NT embryos produced with iPSCs.
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Affiliation(s)
- Sergio D German
- 1 Division of Animal Sciences, School of Biosciences, University of Nottingham , Loughborough, LE12 5RD, United Kingdom
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35
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Park SJ, Shirahige K, Ohsugi M, Nakai K. DBTMEE: a database of transcriptome in mouse early embryos. Nucleic Acids Res 2014; 43:D771-6. [PMID: 25336621 PMCID: PMC4383872 DOI: 10.1093/nar/gku1001] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DBTMEE (http://dbtmee.hgc.jp/) is a searchable and browsable database designed to manipulate gene expression information from our ultralarge-scale whole-transcriptome analysis of mouse early embryos. Since integrative approaches with multiple public analytical data have become indispensable for studying embryogenesis due to technical challenges such as biological sample collection, we intend DBTMEE to be an integrated gateway for the research community. To do so, we combined the gene expression profile with various public resources. Thereby, users can extensively investigate molecular characteristics among totipotent, pluripotent and differentiated cells while taking genetic and epigenetic characteristics into consideration. We have also designed user friendly web interfaces that enable users to access the data quickly and easily. DBTMEE will help to promote our understanding of the enigmatic fertilization dynamics.
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Affiliation(s)
- Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure & Function, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Miho Ohsugi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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36
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Gingold JA, Fidalgo M, Guallar D, Lau Z, Sun Z, Zhou H, Faiola F, Huang X, Lee DF, Waghray A, Schaniel C, Felsenfeld DP, Lemischka IR, Wang J. A genome-wide RNAi screen identifies opposing functions of Snai1 and Snai2 on the Nanog dependency in reprogramming. Mol Cell 2014; 56:140-52. [PMID: 25240402 PMCID: PMC4184964 DOI: 10.1016/j.molcel.2014.08.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/21/2014] [Accepted: 08/08/2014] [Indexed: 12/30/2022]
Abstract
Nanog facilitates embryonic stem cell self-renewal and induced pluripotent stem cell generation during the final stage of reprogramming. From a genome-wide small interfering RNA screen using a Nanog-GFP reporter line, we discovered opposing effects of Snai1 and Snai2 depletion on Nanog promoter activity. We further discovered mutually repressive expression profiles and opposing functions of Snai1 and Snai2 during Nanog-driven reprogramming. We found that Snai1, but not Snai2, is both a transcriptional target and protein partner of Nanog in reprogramming. Ectopic expression of Snai1 or depletion of Snai2 greatly facilitates Nanog-driven reprogramming. Snai1 (but not Snai2) and Nanog cobind to and transcriptionally activate pluripotency-associated genes including Lin28 and miR-290-295. Ectopic expression of miR-290-295 cluster genes partially rescues reprogramming inefficiency caused by Snai1 depletion. Our study thus uncovers the interplay between Nanog and mesenchymal factors Snai1 and Snai2 in the transcriptional regulation of pluripotency-associated genes and miRNAs during the Nanog-driven reprogramming process.
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Affiliation(s)
- Julian A Gingold
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miguel Fidalgo
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Diana Guallar
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zerlina Lau
- Integrated Screening Core, Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhen Sun
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hongwei Zhou
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesco Faiola
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xin Huang
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dung-Fang Lee
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avinash Waghray
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christoph Schaniel
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan P Felsenfeld
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Integrated Screening Core, Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ihor R Lemischka
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Jianlong Wang
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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37
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Kuijk E, Geijsen N, Cuppen E. Pluripotency in the light of the developmental hourglass. Biol Rev Camb Philos Soc 2014; 90:428-43. [DOI: 10.1111/brv.12117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 04/10/2014] [Accepted: 04/28/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Ewart Kuijk
- Hubrecht Institute, KNAW and University Medical Center Utrecht; Utrecht 3584 CT The Netherlands
| | - Niels Geijsen
- Hubrecht Institute, KNAW and University Medical Center Utrecht; Utrecht 3584 CT The Netherlands
- Department of Companion Animals; School of Veterinary Medicine, Utrecht University; Utrecht 3584 CM The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute, KNAW and University Medical Center Utrecht; Utrecht 3584 CT The Netherlands
- Center for Molecular Medicine; UMC Utrecht; Universiteitsweg 100 Utrecht 3584 GG The Netherlands
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