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Lenardič A, Domenig SA, Zvick J, Bundschuh N, Tarnowska-Sengül M, Furrer R, Noé F, Trautmann CL, Ghosh A, Bacchin G, Gjonlleshaj P, Qabrati X, Masschelein E, De Bock K, Handschin C, Bar-Nur O. Generation of allogeneic and xenogeneic functional muscle stem cells for intramuscular transplantation. J Clin Invest 2024; 134:e166998. [PMID: 38713532 PMCID: PMC11178549 DOI: 10.1172/jci166998] [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: 11/08/2022] [Accepted: 04/23/2024] [Indexed: 05/09/2024] Open
Abstract
Satellite cells, the stem cells of skeletal muscle tissue, hold a remarkable regeneration capacity and therapeutic potential in regenerative medicine. However, low satellite cell yield from autologous or donor-derived muscles hinders the adoption of satellite cell transplantation for the treatment of muscle diseases, including Duchenne muscular dystrophy (DMD). To address this limitation, here we investigated whether satellite cells can be derived in allogeneic or xenogeneic animal hosts. First, injection of CRISPR/Cas9-corrected Dmdmdx mouse induced pluripotent stem cells (iPSCs) into mouse blastocysts carrying an ablation system of host satellite cells gave rise to intraspecies chimeras exclusively carrying iPSC-derived satellite cells. Furthermore, injection of genetically corrected DMD iPSCs into rat blastocysts resulted in the formation of interspecies rat-mouse chimeras harboring mouse satellite cells. Notably, iPSC-derived satellite cells or derivative myoblasts produced in intraspecies or interspecies chimeras restored dystrophin expression in DMD mice following intramuscular transplantation and contributed to the satellite cell pool. Collectively, this study demonstrates the feasibility of producing therapeutically competent stem cells across divergent animal species, raising the possibility of generating human muscle stem cells in large animals for regenerative medicine purposes.
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MESH Headings
- Animals
- Mice
- Muscular Dystrophy, Duchenne/therapy
- Muscular Dystrophy, Duchenne/genetics
- Induced Pluripotent Stem Cells/transplantation
- Induced Pluripotent Stem Cells/cytology
- Induced Pluripotent Stem Cells/metabolism
- Rats
- Satellite Cells, Skeletal Muscle/transplantation
- Satellite Cells, Skeletal Muscle/metabolism
- Satellite Cells, Skeletal Muscle/cytology
- Stem Cell Transplantation
- Humans
- Dystrophin/genetics
- Dystrophin/metabolism
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/cytology
- Mice, Inbred mdx
- Heterografts
- Transplantation, Heterologous
- Injections, Intramuscular
- Transplantation, Homologous
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Affiliation(s)
- Ajda Lenardič
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Seraina A. Domenig
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Joel Zvick
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Nicola Bundschuh
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Monika Tarnowska-Sengül
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | | | - Falko Noé
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Christine L. Trautmann
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Adhideb Ghosh
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Giada Bacchin
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Pjeter Gjonlleshaj
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Xhem Qabrati
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Evi Masschelein
- Laboratory of Exercise and Health, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Katrien De Bock
- Laboratory of Exercise and Health, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | | | - Ori Bar-Nur
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
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2
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Paine PT, Rechsteiner C, Morandini F, Desdín-Micó G, Mrabti C, Parras A, Haghani A, Brooke R, Horvath S, Seluanov A, Gorbunova V, Ocampo A. Initiation phase cellular reprogramming ameliorates DNA damage in the ERCC1 mouse model of premature aging. FRONTIERS IN AGING 2024; 4:1323194. [PMID: 38322248 PMCID: PMC10844398 DOI: 10.3389/fragi.2023.1323194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024]
Abstract
Unlike aged somatic cells, which exhibit a decline in molecular fidelity and eventually reach a state of replicative senescence, pluripotent stem cells can indefinitely replenish themselves while retaining full homeostatic capacity. The conferment of beneficial-pluripotency related traits via in vivo partial cellular reprogramming in vivo partial reprogramming significantly extends lifespan and restores aging phenotypes in mouse models. Although the phases of cellular reprogramming are well characterized, details of the rejuvenation processes are poorly defined. To understand whether cellular reprogramming can ameliorate DNA damage, we created a reprogrammable accelerated aging mouse model with an ERCC1 mutation. Importantly, using enhanced partial reprogramming by combining small molecules with the Yamanaka factors, we observed potent reversion of DNA damage, significant upregulation of multiple DNA damage repair processes, and restoration of the epigenetic clock. In addition, we present evidence that pharmacological inhibition of ALK5 and ALK2 receptors in the TGFb pathway are able to phenocopy some benefits including epigenetic clock restoration suggesting a role in the mechanism of rejuvenation by partial reprogramming.
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Affiliation(s)
- Patrick Treat Paine
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Center for Virology and Vaccine Research, Harvard Medical School, Boston, MA, United States
| | | | - Francesco Morandini
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Gabriela Desdín-Micó
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Calida Mrabti
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alberto Parras
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- EPITERNA SA, Vaud, Switzerland
| | | | - Robert Brooke
- Epigenetic Clock Development Foundation, Torrance, CA, United States
| | - Steve Horvath
- Altos Labs, San Diego, CA, United States
- Epigenetic Clock Development Foundation, Torrance, CA, United States
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, United States
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, United States
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Alejandro Ocampo
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- EPITERNA SA, Vaud, Switzerland
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3
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Kondoh H. Molecular Basis of Cell Reprogramming into iPSCs with Exogenous Transcription Factors. Results Probl Cell Differ 2024; 72:193-218. [PMID: 38509259 DOI: 10.1007/978-3-031-39027-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
A striking discovery in recent decades concerning the transcription factor (TF)-dependent process was the production of induced pluripotent stem cell (iPSCs) from fibroblasts by the exogenous expression of the TF cocktail containing Oct3/4 (Pou5f1), Sox2, Klf4, and Myc, collectively called OSKM. How fibroblast cells can be remodeled into embryonic stem cell (ESC)-like iPSCs despite high epigenetic barriers has opened a new essential avenue to understanding the action of TFs in developmental regulation. Two forerunning investigations preceded the iPSC phenomenon: exogenous TF-mediated cell remodeling driven by the action of MyoD, and the "pioneer TF" action to preopen chromatin, allowing multiple TFs to access enhancer sequences. The process of remodeling somatic cells into iPSCs has been broken down into multiple subprocesses: the initial attack of OSKM on closed chromatin, sequential changes in cytosine modification, enhancer usage, and gene silencing and activation. Notably, the OSKM TFs change their genomic binding sites extensively. The analyses are still at the descriptive stage, but currently available information is discussed in this chapter.
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Affiliation(s)
- Hisato Kondoh
- Osaka University, Suita, Osaka, Japan
- Biohistory Research Hall, Takatsuki, Osaka, Japan
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4
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Hoetker MS, Yagi M, Di Stefano B, Langerman J, Cristea S, Wong LP, Huebner AJ, Charlton J, Deng W, Haggerty C, Sadreyev RI, Meissner A, Michor F, Plath K, Hochedlinger K. H3K36 methylation maintains cell identity by regulating opposing lineage programmes. Nat Cell Biol 2023; 25:1121-1134. [PMID: 37460697 PMCID: PMC10896483 DOI: 10.1038/s41556-023-01191-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/19/2023] [Indexed: 08/12/2023]
Abstract
The epigenetic mechanisms that maintain differentiated cell states remain incompletely understood. Here we employed histone mutants to uncover a crucial role for H3K36 methylation in the maintenance of cell identities across diverse developmental contexts. Focusing on the experimental induction of pluripotency, we show that H3K36M-mediated depletion of H3K36 methylation endows fibroblasts with a plastic state poised to acquire pluripotency in nearly all cells. At a cellular level, H3K36M facilitates epithelial plasticity by rendering fibroblasts insensitive to TGFβ signals. At a molecular level, H3K36M enables the decommissioning of mesenchymal enhancers and the parallel activation of epithelial/stem cell enhancers. This enhancer rewiring is Tet dependent and redirects Sox2 from promiscuous somatic to pluripotency targets. Our findings reveal a previously unappreciated dual role for H3K36 methylation in the maintenance of cell identity by integrating a crucial developmental pathway into sustained expression of cell-type-specific programmes, and by opposing the expression of alternative lineage programmes through enhancer methylation.
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Affiliation(s)
- Michael S Hoetker
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Masaki Yagi
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Justin Langerman
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lai Ping Wong
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron J Huebner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jocelyn Charlton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Genome Regulation, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Weixian Deng
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Chuck Haggerty
- Department of Genome Regulation, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Alexander Meissner
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Genome Regulation, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Franziska Michor
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- The Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA
- The Ludwig Center at Harvard, Boston, MA, USA
| | - Kathrin Plath
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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5
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Garg V, Yang Y, Nowotschin S, Setty M, Kuo YY, Sharma R, Polyzos A, Salataj E, Murphy D, Jang A, Pe’er D, Apostolou E, Hadjantonakis AK. Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534648. [PMID: 37034770 PMCID: PMC10081288 DOI: 10.1101/2023.03.28.534648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Two distinct fates, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common progenitor cells, the inner cell mass (ICM), in mammalian embryos. To study how these sister identities are forged, we leveraged embryonic (ES) and eXtraembryonic ENdoderm (XEN) stem cells - in vitro counterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses uncovered distinct rates, efficiencies and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions. While GATA4-mediated ES-to-iXEN conversion was rapid and nearly deterministic, OCT4, KLF4 and SOX2-induced XEN-to-iPS reprogramming progressed with diminished efficiency and kinetics. The dominant PrE transcriptional program, safeguarded by Gata4, and globally elevated chromatin accessibility of EPI underscored the differential plasticities of the two states. Mapping in vitro trajectories to embryos revealed reprogramming in either direction tracked along, and toggled between, EPI and PrE in vivo states without transitioning through the ICM.
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Affiliation(s)
- Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Yang Yang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Manu Setty
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ying-Yi Kuo
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Roshan Sharma
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Polyzos
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Eralda Salataj
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Dylan Murphy
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Amy Jang
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Pe’er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Effie Apostolou
- Joan & Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
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6
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Rochford AE, Carnicer-Lombarte A, Kawan M, Jin A, Hilton S, Curto VF, Rutz AL, Moreau T, Kotter MR, Malliaras GG, Barone DG. Functional neurological restoration of amputated peripheral nerve using biohybrid regenerative bioelectronics. SCIENCE ADVANCES 2023; 9:eadd8162. [PMID: 36947608 PMCID: PMC10032597 DOI: 10.1126/sciadv.add8162] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The development of neural interfaces with superior biocompatibility and improved tissue integration is vital for treating and restoring neurological functions in the nervous system. A critical factor is to increase the resolution for mapping neuronal inputs onto implants. For this purpose, we have developed a new category of neural interface comprising induced pluripotent stem cell (iPSC)-derived myocytes as biological targets for peripheral nerve inputs that are grafted onto a flexible electrode arrays. We show long-term survival and functional integration of a biohybrid device carrying human iPSC-derived cells with the forearm nerve bundle of freely moving rats, following 4 weeks of implantation. By improving the tissue-electronics interface with an intermediate cell layer, we have demonstrated enhanced resolution and electrical recording in vivo as a first step toward restorative therapies using regenerative bioelectronics.
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Affiliation(s)
- Amy E. Rochford
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, UK
| | | | - Malak Kawan
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Amy Jin
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, UK
| | - Sam Hilton
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, UK
| | - Vincenzo F. Curto
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, UK
| | - Alexandra L. Rutz
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, UK
| | | | - Mark R. N. Kotter
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Bit Bio, Cambridge, UK
| | - George G. Malliaras
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, UK
| | - Damiano G. Barone
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
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7
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Brandt G, Sedivy LJ, Mitchell M, Phiel CJ. Vitamin C and Transferrin Reduce RNA Methylation in Mouse Embryonic Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529811. [PMID: 36865322 PMCID: PMC9980082 DOI: 10.1101/2023.02.23.529811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Methylation of mRNA on adenosine bases (referred to as m 6 A) is the most common internal modification of mRNA in eukaryotic cells. Recent work has revealed a detailed view of the biological significance of m 6 A-modified mRNA, with a role in mRNA splicing, control of mRNA stability, and mRNA translation efficiency. Importantly, m 6 A is a reversible modification, and the primary enzymes responsible for methylating (Mettl3/Mettl14) and demethylating RNA (FTO/Alkbh5) have been identified. Given this reversibility, we are interested in understanding how m 6 A addition/removal is regulated. Recently, we identified glycogen synthase kinase-3 (Gsk-3) activity as a mediator of m 6 A regulation via controlling the levels of the FTO demethylase in mouse embryonic stem cells (ESCs), with Gsk-3 inhibitors and Gsk-3 knockout both leading to increased FTO protein and decreased m 6 A mRNA levels. To our knowledge, this remains one of the only mechanisms identified for the regulation of m 6 A modifications in ESCs. Several small molecules that have been shown to promote the retention of pluripotency of ESCs, and interestingly, many have connections to the regulation of FTO and m 6 A. Here we show that the combination of Vitamin C and transferrin potently reduces levels of m 6 A and promotes retention of pluripotency in mouse ESCs. Combining Vitamin C and transferrin should prove to be valuable in growing and maintaining pluripotent mouse ESCs.
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8
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Sedivy LJ, Brandt G, Martin AL, Abroe HM, Phiel CJ. Mouse Embryonic Stem Cell Pluripotency Factors Regulate RNA Methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529801. [PMID: 36865332 PMCID: PMC9980107 DOI: 10.1101/2023.02.23.529801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The pluripotency of embryonic stem cells (ESCs) is actively promoted by a diverse set of factors, including leukemia inhibitory factor (LIF), glycogen synthase kinase-3 (Gsk-3) and mitogen-activated protein kinase kinase (MEK) inhibitors, ascorbic acid, and α-ketoglutarate. Strikingly, several of these factors intersect with the post-transcriptional methylation of RNA (m 6 A), which has also been shown to play a role in ESC pluripotency. Therefore, we explored the possibility that these factors converge on this biochemical pathway to promote the retention of ESC pluripotency. Mouse ESCs were treated with various combinations of small molecules, and the relative levels of m 6 A RNA were measured, as well as the expression of genes marking naïve and primed ESCs. The most surprising result was the discovery that replacing glucose with high levels of fructose pushed ESCs to a more naïve state and reduced m 6 A RNA abundance. Our results suggest a correlation between molecules previously shown to promote the retention of ESC pluripotency and m 6 A RNA levels, strengthening a molecular connection between reduced m 6 A RNA and the pluripotent state, and provides a foundation for future mechanistic studies on the role of m 6 A and ESC pluripotency.
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9
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Xu J, Fang S, Wang N, Li B, Huang Y, Fan Q, Shi J, Liu H, Shao Z. Dual-specificity Tyrosine Phosphorylation-regulated Kinase Inhibitor ID-8 Promotes Human Somatic Cell Reprogramming by Activating PDK4 Expression. Stem Cell Rev Rep 2022; 18:2074-2087. [PMID: 35080746 DOI: 10.1007/s12015-021-10294-9] [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] [Accepted: 10/27/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Human induced pluripotent stem cells (hiPSCs) hold great potentials in disease modeling, drug screening and cell therapy. However, efficiency and costs of hiPSCs preparation still need to be improved. METHODS We screened the compounds that target signaling pathways, epigenetic modifications or metabolic-process regulation to replace the growth factors. After small molecule treatment, TRA-1-60, which is a cell surface antigen expressed by human embryonic stem cells (hESCs), staining was performed to quantify the efficiency of somatic cell reprogramming. Next, small molecule cocktail-induced ESCs or iPSCs were examined with pluripotent markers expression. Finally, Genome-wide gene expression profile was analyzed by RNA-seq to illustrate the mechanism of human somatic cell reprogramming. RESULT Here, we found that a dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) inhibitor ID-8 robustly enhanced human somatic cell reprogramming by upregulation of pyruvate dehydrogenase kinase 4 (PDK4) and activation of glycolysis. Furthermore, we identified a novel growth-factor-free hiPSC generation system using small molecules ID-8 (I) and TGFβ signal pathway agonist Kartogenin (K). Importantly, we developed IK medium combined with low-dose bFGF to support the long-term expansion of human pluripotent stem cells. IK-iPSCs showed pluripotency and normal karyotype. CONCLUSIONS Our studies may provide a novel growth-factor-free culture system to facilitate the generation of hiPSCs for multiple applications in regenerative medicine. In Brief Xu et at. found that a dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) inhibitor ID-8 robustly enhanced human somatic cell reprogramming by upregulation of PDK4 and activation of glycolysis. Furthermore, we established a novel growth-factor-free hiPSC generation system using small molecules ID-8/Kartogenin (IK). IK medium combined with Low-dose bFGF (IKB medium) supported the long-term expansion of human pluripotent stem cells. Highlights ID-8 Enhanced Reprogramming of Human Fibroblasts and Astrocytes Establishment of the Growth-factor-free Reprogramming System Using Small Molecule Compounds IK IKB Medium Maintained the Long-term Expansion of Human Pluripotent Stem Cells ID-8 Promoted Human Somatic Cell Reprogramming by Activating PDK4 Expression.
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Affiliation(s)
- Jinhong Xu
- Fujian Provincial Key Laboratory of Neurodegenerative, Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361005, Fujian, China
- Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Shi Fang
- Fujian Provincial Key Laboratory of Neurodegenerative, Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361005, Fujian, China
- Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Naweng Wang
- Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Bo Li
- Key Laboratory of Biomedical Engineering of Fujian Province, Research Center of Biomedical Engineering of Xiamen, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Yongheng Huang
- Fujian Provincial Key Laboratory of Neurodegenerative, Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361005, Fujian, China
- Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Qi Fan
- Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Jingyi Shi
- Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Huihui Liu
- Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Zhicheng Shao
- Fujian Provincial Key Laboratory of Neurodegenerative, Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361005, Fujian, China.
- Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China.
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10
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Zvick J, Tarnowska-Sengül M, Ghosh A, Bundschuh N, Gjonlleshaj P, Hinte LC, Trautmann CL, Noé F, Qabrati X, Domenig SA, Kim I, Hennek T, von Meyenn F, Bar-Nur O. Exclusive generation of rat spermatozoa in sterile mice utilizing blastocyst complementation with pluripotent stem cells. Stem Cell Reports 2022; 17:1942-1958. [PMID: 35931077 PMCID: PMC9481912 DOI: 10.1016/j.stemcr.2022.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Blastocyst complementation denotes a technique that aims to generate organs, tissues, or cell types in animal chimeras via injection of pluripotent stem cells (PSCs) into genetically compromised blastocyst-stage embryos. Here, we report on successful complementation of the male germline in adult chimeras following injection of mouse or rat PSCs into mouse blastocysts carrying a mutation in Tsc22d3, an essential gene for spermatozoa production. Injection of mouse PSCs into Tsc22d3-Knockout (KO) blastocysts gave rise to intraspecies chimeras exclusively embodying PSC-derived functional spermatozoa. In addition, injection of rat embryonic stem cells (rESCs) into Tsc22d3-KO embryos produced interspecies mouse-rat chimeras solely harboring rat spermatids and spermatozoa capable of fertilizing oocytes. Furthermore, using single-cell RNA sequencing, we deconstructed rat spermatogenesis occurring in a mouse-rat chimera testis. Collectively, this study details a method for exclusive xenogeneic germ cell production in vivo, with implications that may extend to rat transgenesis, or endangered animal species conservation efforts.
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Affiliation(s)
- Joel Zvick
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland
| | - Monika Tarnowska-Sengül
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland
| | - Adhideb Ghosh
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland; Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - Nicola Bundschuh
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland
| | - Pjeter Gjonlleshaj
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland
| | - Laura C Hinte
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland
| | - Christine L Trautmann
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland
| | - Falko Noé
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland; Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich 8057, Switzerland
| | - Xhem Qabrati
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland
| | - Seraina A Domenig
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland
| | - Inseon Kim
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland
| | - Thomas Hennek
- ETH Phenomics Center, ETH Zurich, Zurich 8049, Switzerland
| | - Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland
| | - Ori Bar-Nur
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach 8603, Switzerland.
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11
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Echegaray CV, Salvati B, Vivien SD, Francia MG, Solari CM, Cosentino MS, Guberman A, Perullini M. Design of silica nanocarriers: tuning the release to embryonic stem cells by simple strategies. J Biotechnol 2022; 353:19-27. [DOI: 10.1016/j.jbiotec.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 04/11/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022]
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12
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Wang Y, Hou Q, Wu Y, Xu Y, Liu Y, Chen J, Xu L, Guo Y, Gao S, Yuan J. Methionine deficiency and its hydroxy analogue influence chicken intestinal 3-dimensional organoid development. ANIMAL NUTRITION 2022; 8:38-51. [PMID: 34977374 PMCID: PMC8669257 DOI: 10.1016/j.aninu.2021.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/13/2022]
Abstract
Methionine and its hydroxy analogue (MHA) have been shown to benefit mouse intestinal regeneration. The intestinal organoid is a good model that directly reflects the impact of certain nutrients or chemicals on intestinal development. Here, we aimed to establish a chicken intestinal organoid culture method first and then use the model to explore the influence of methionine deficiency and MHA on intestinal organoid development. The results showed that 125-μm cell strainer exhibited the highest efficiency for chicken embryo crypt harvesting. We found that transforming growth factor-β inhibitor (A8301) supplementation promoted enterocyte differentiation at the expense of the proliferation of intestinal stem cells (ISC). The mitogen-activated protein kinase p38 inhibitor (SB202190) promoted intestinal organoid formation and enterocyte differentiation but suppressed the differentiation of enteroendocrine cells, goblet cells and Paneth cells. However, the suppression of enteroendocrine cell and Paneth cell differentiation by SB202190 was alleviated at the presence of A8301. The glycogen synthase kinase 3 inhibitor (CHIR99021), valproic acid (VPA) alone and their combination promoted chicken intestinal organoid formation and enterocyte differentiation at the expense of the expression of Paneth cells and goblet cells. Chicken serum significantly improved organoid formation, especially in the presence of A8301, SB202190, CHIR99021, and VPA, but inhibited the differentiation of Paneth cells and enteroendocrine cells. Chicken serum at a concentration of 0.25% meets the requirement of chicken intestinal organoid development, and the beneficial effect of chicken serum on chicken intestinal organoid culture could not be replaced by fetal bovine serum and insulin-like growth factor-1. Moreover, commercial mouse organoid culture medium supplemented with A8301, SB202190, CHIR99021, VPA, and chicken serum promotes chicken organoid budding. Based on the chicken intestinal organoid model, we found that methionine deficiency mimicked by cycloleucine suppressed organoid formation and organoid size, and this effect was reinforced with increased cycloleucine concentrations. Methionine hydroxy analogue promoted regeneration of ISC but decreased cell differentiation compared with the results obtained with L-methionine. In conclusion, our results provide a potentially excellent guideline for chicken intestinal organoid culture and insights into methionine function in crypt development.
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Affiliation(s)
- Youli Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qihang Hou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yuqin Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanwei Xu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yan Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jing Chen
- Sichuan New Hope Liuhe Co. Ltd, Chengdu, 610100, China
| | - Lingling Xu
- Beijing Dafa Chia Tai Co. Ltd., Beijing, 101206, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shuai Gao
- Key Laboratory of Animal Gene Breeding and Reproductivity, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Corresponding authors.
| | - Jianmin Yuan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Corresponding authors.
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13
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The Use of Trichostatin A during Pluripotent Stem Cell Generation Does Not Affect MHC Expression Level. Stem Cells Int 2022; 2022:9346767. [PMID: 35371264 PMCID: PMC8967593 DOI: 10.1155/2022/9346767] [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: 08/07/2021] [Revised: 01/02/2022] [Accepted: 01/28/2022] [Indexed: 11/17/2022] Open
Abstract
Pluripotent stem cells (PSCs) are considered as a potent tool for use in regenerative medicine. Highly efficient generation of PSCs through chromatin modulators such as trichostatin A (TSA) might change their MHC molecule expression profile. The efficiency of PSC generation and their immunogenicity is major obstacles for clinical use. Hence, we aim to investigate whether the use of TSA during PSC generation affects MHC expression level. Three PSC lines were generated by iPSCs, NT-ESCs, and IVF-ESCs' reprogramming methods from B6D2F1 mouse embryonic fibroblast cells. Established PSC lines were characterized by alkaline phosphatase assay (ALP) and immunocytochemistry. Their chromosome fidelity was checked by karyotyping. The expression level of pluripotent genes (oct4, nanog, sox2, klf4), HDACs (hdac1, hdac2, and hdac3), and immune-related genes (including Qa-1, Qa-2, H2kb, H2kd, H2db, H2db, CIITA, H2-IE-βb, H2-IE-βd) in iPSC and ESC lines were assessed by real-time PCR analysis. The presence of MHC molecules on the surface of pluripotent stem cells was also checked by flow cytometry technique. Significant increase of pluripotency markers, oct4, nanog, sox2, and klf4, was observed in 100 nM TSA-treated samples. 100 nM TSA induced significant upregulation of H2db in generated iPSCs. H2-IE-βd was remarkably downregulated in 50 and 100 nM TSA-treated iPSC lines. The expression level of other immune-related genes was not greatly affected by TSA in iPSC and NT-ESC lines. It is concluded that the use of short-term and low concentration of TSA during reprogramming in PSC generation procedure significantly increases PSC generation efficiency, but do not affect the MHC expression in established cell lines, which is in the benefit of cell transplantation in regenerative medicine.
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14
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Dissecting TET2 Regulatory Networks in Blood Differentiation and Cancer. Cancers (Basel) 2022; 14:cancers14030830. [PMID: 35159097 PMCID: PMC8834528 DOI: 10.3390/cancers14030830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Bone marrow disorders such as leukemia and myelodysplastic syndromes are characterized by abnormal healthy blood cells production and function. Uncontrolled growth and impaired differentiation of white blood cells hinder the correct development of healthy cells in the bone marrow. One of the most frequent alterations that appear to initiate this deregulation and persist in leukemia patients are mutations in epigenetic regulators such as TET2. This review summarizes the latest molecular findings regarding TET2 functions in hematopoietic cells and their potential implications in blood cancer origin and evolution. Our goal was to encompass and interlink up-to-date discoveries of the convoluted TET2 functional network to provide a more precise overview of the leukemic burden of this protein. Abstract Cytosine methylation (5mC) of CpG is the major epigenetic modification of mammalian DNA, playing essential roles during development and cancer. Although DNA methylation is generally associated with transcriptional repression, its role in gene regulation during cell fate decisions remains poorly understood. DNA demethylation can be either passive or active when initiated by TET dioxygenases. During active demethylation, transcription factors (TFs) recruit TET enzymes (TET1, 2, and 3) to specific gene regulatory regions to first catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and subsequently to higher oxidized cytosine derivatives. Only TET2 is frequently mutated in the hematopoietic system from the three TET family members. These mutations initially lead to the hematopoietic stem cells (HSCs) compartment expansion, eventually evolving to give rise to a wide range of blood malignancies. This review focuses on recent advances in characterizing the main TET2-mediated molecular mechanisms that activate aberrant transcriptional programs in blood cancer onset and development. In addition, we discuss some of the key outstanding questions in the field.
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15
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Chen L, Guttieres D, Koenigsberg A, Barone PW, Sinskey AJ, Springs SL. Large-scale cultured meat production: Trends, challenges and promising biomanufacturing technologies. Biomaterials 2021; 280:121274. [PMID: 34871881 DOI: 10.1016/j.biomaterials.2021.121274] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/17/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023]
Abstract
Food systems of the future will need to face an increasingly clear reality - that a protein-rich diet is essential for good health, but traditional meat products will not suffice to ensure safety, sustainability, and equity of food supply chains at a global scale. This paper provides an in-depth analysis of bioprocess technologies needed for cell-based meat production and challenges in reaching commercial scale. Specifically, it reviews state-of-the-art bioprocess technologies, current limitations, and opportunities for research across four domains: cell line development, cell culture media, scaffolding, and bioreactors. This also includes exploring innovations to make cultured meat a viable protein alternative across numerous key performance indicators and for specific applications where traditional livestock is not an option (e.g., local production, space exploration). The paper explores tradeoffs between production scale, product quality, production cost, and footprint over different time horizons. Finally, a discussion explores various factors that may impact the ability to successfully scale and market cultured meat products: social acceptance, environmental tradeoffs, regulatory guidance, and public health benefits. While the exact nature of the transition from traditional livestock to alternative protein products is uncertain, it has already started and will likely continue to build momentum in the next decade.
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Affiliation(s)
- Lu Chen
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States
| | - Donovan Guttieres
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States
| | - Andrea Koenigsberg
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States
| | - Paul W Barone
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States
| | - Anthony J Sinskey
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States
| | - Stacy L Springs
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States.
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16
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Kimura K, Tsukamoto M, Tanaka M, Kuwamura M, Ohtaka M, Nishimura K, Nakanishi M, Sugiura K, Hatoya S. Efficient Reprogramming of Canine Peripheral Blood Mononuclear Cells into Induced Pluripotent Stem Cells. Stem Cells Dev 2021; 30:79-90. [PMID: 33256572 DOI: 10.1089/scd.2020.0084] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Forced coexpression of the transcription factors Oct3/4, Klf4, Sox2, and c-Myc reprograms somatic cells into pluripotent stem cells (PSCs). Such induced PSCs (iPSCs) can generate any cell type of the adult body or indefinitely proliferate without losing their potential. Accordingly, iPSCs can serve as an unlimited cell source for the development of various disease models and regenerative therapies for animals and humans. Although canine peripheral blood mononuclear cells (PBMCs) can be easily obtained, they have a very low iPSC reprogramming efficiency. In this study, we determined the reprogramming efficiency of canine PBMCs under several conditions involving three types of media supplemented with small-molecule compounds. We found that canine iPSCs (ciPSCs) could be efficiently generated from PBMCs using N2B27 medium supplemented with leukemia inhibitory factor (LIF), basic fibroblast growth factor (bFGF), and a small-molecule cocktail (Y-27632, PD0325901, CHIR99021, A-83-01, Forskolin, and l-ascorbic acid). We generated five ciPSC lines that could be maintained in StemFit® medium supplemented with LIF. The SeVdp(KOSM)302L vectors were appropriately silenced in four ciPSC lines. Of the two lines characterized, both were positive for alkaline phosphatase activity and expressed pluripotency markers, including the Oct3/4, Sox2, and Nanog transcripts, as well as the octamer-binding transcription factor (OCT) 3/4 and NANOG proteins, and the SSEA-1 carbohydrate antigen. The ciPSCs could form embryoid bodies and differentiate into the three germ layers, as indicated by marker gene and protein expression. Furthermore, one ciPSC line formed teratomas comprising several tissues from every germ layer. Our ciPSC lines maintained a normal karyotype even after multiple passages. Moreover, our new reprogramming method was able to generate ciPSCs from multiple donor PBMCs. In conclusion, we developed an easy and efficient strategy for the generation of footprint-free ciPSCs from PBMCs. We believe that this strategy can be useful for disease modeling and regenerative medicine in the veterinary field.
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Affiliation(s)
- Kazuto Kimura
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Masaya Tsukamoto
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Miyuu Tanaka
- Department of Integrated Structural Biosciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Mitsuru Kuwamura
- Department of Integrated Structural Biosciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | | | - Ken Nishimura
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Mahito Nakanishi
- TOKIWA-Bio, Inc., Tsukuba, Japan
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Kikuya Sugiura
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Shingo Hatoya
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
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17
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Lu Y, Brommer B, Tian X, Krishnan A, Meer M, Wang C, Vera DL, Zeng Q, Yu D, Bonkowski MS, Yang JH, Zhou S, Hoffmann EM, Karg MM, Schultz MB, Kane AE, Davidsohn N, Korobkina E, Chwalek K, Rajman LA, Church GM, Hochedlinger K, Gladyshev VN, Horvath S, Levine ME, Gregory-Ksander MS, Ksander BR, He Z, Sinclair DA. Reprogramming to recover youthful epigenetic information and restore vision. Nature 2020; 588:124-129. [PMID: 33268865 PMCID: PMC7752134 DOI: 10.1038/s41586-020-2975-4] [Citation(s) in RCA: 372] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/22/2020] [Indexed: 02/07/2023]
Abstract
Ageing is a degenerative process that leads to tissue dysfunction and death. A proposed cause of ageing is the accumulation of epigenetic noise that disrupts gene expression patterns, leading to decreases in tissue function and regenerative capacity1-3. Changes to DNA methylation patterns over time form the basis of ageing clocks4, but whether older individuals retain the information needed to restore these patterns-and, if so, whether this could improve tissue function-is not known. Over time, the central nervous system (CNS) loses function and regenerative capacity5-7. Using the eye as a model CNS tissue, here we show that ectopic expression of Oct4 (also known as Pou5f1), Sox2 and Klf4 genes (OSK) in mouse retinal ganglion cells restores youthful DNA methylation patterns and transcriptomes, promotes axon regeneration after injury, and reverses vision loss in a mouse model of glaucoma and in aged mice. The beneficial effects of OSK-induced reprogramming in axon regeneration and vision require the DNA demethylases TET1 and TET2. These data indicate that mammalian tissues retain a record of youthful epigenetic information-encoded in part by DNA methylation-that can be accessed to improve tissue function and promote regeneration in vivo.
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Affiliation(s)
- Yuancheng Lu
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Benedikt Brommer
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Xiao Tian
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Anitha Krishnan
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Margarita Meer
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Chen Wang
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Daniel L Vera
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Qiurui Zeng
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Doudou Yu
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Michael S Bonkowski
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Jae-Hyun Yang
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Songlin Zhou
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Emma M Hoffmann
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Margarete M Karg
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Michael B Schultz
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Alice E Kane
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Noah Davidsohn
- Department of Genetics, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ekaterina Korobkina
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Karolina Chwalek
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Luis A Rajman
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - George M Church
- Department of Genetics, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Morgan E Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Meredith S Gregory-Ksander
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Bruce R Ksander
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Schepens Eye Research Institute of Mass Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Zhigang He
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - David A Sinclair
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA.
- Laboratory for Ageing Research, Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, New South Wales, Australia.
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18
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Salazar‐Roa M, Trakala M, Álvarez‐Fernández M, Valdés‐Mora F, Zhong C, Muñoz J, Yu Y, Peters TJ, Graña‐Castro O, Serrano R, Zapatero‐Solana E, Abad M, Bueno MJ, de Cedrón MG, Fernández‐Piqueras J, Serrano M, Blasco MA, Wang D, Clark SJ, Izpisua‐Belmonte JC, Ortega S, Malumbres M. Transient exposure to miR-203 enhances the differentiation capacity of established pluripotent stem cells. EMBO J 2020; 39:e104324. [PMID: 32614092 PMCID: PMC7429746 DOI: 10.15252/embj.2019104324] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 11/09/2022] Open
Abstract
Full differentiation potential along with self-renewal capacity is a major property of pluripotent stem cells (PSCs). However, the differentiation capacity frequently decreases during expansion of PSCs in vitro. We show here that transient exposure to a single microRNA, expressed at early stages during normal development, improves the differentiation capacity of already-established murine and human PSCs. Short exposure to miR-203 in PSCs (miPSCs) induces a transient expression of 2C markers that later results in expanded differentiation potency to multiple lineages, as well as improved efficiency in tetraploid complementation and human-mouse interspecies chimerism assays. Mechanistically, these effects are at least partially mediated by direct repression of de novo DNA methyltransferases Dnmt3a and Dnmt3b, leading to transient and reversible erasure of DNA methylation. These data support the use of transient exposure to miR-203 as a versatile method to reset the epigenetic memory in PSCs, and improve their effectiveness in regenerative medicine.
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Affiliation(s)
- María Salazar‐Roa
- Cell Division and Cancer GroupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | - Marianna Trakala
- Cell Division and Cancer GroupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | | | - Fátima Valdés‐Mora
- Epigenetics Research Program, Genomics and Epigenetics DivisionGarvan Institute of Medical ResearchSydneyNSWAustralia
- St. Vincent's Clinical SchoolUNSW, SydneySydneyNSWAustralia
| | - Cuiqing Zhong
- Gene Expression LaboratoryThe Salk Institute for Biological StudiesLa JollaCAUSA
| | | | - Yang Yu
- Gene Expression LaboratoryThe Salk Institute for Biological StudiesLa JollaCAUSA
| | - Timothy J Peters
- Epigenetics Research Program, Genomics and Epigenetics DivisionGarvan Institute of Medical ResearchSydneyNSWAustralia
| | | | | | | | | | - María José Bueno
- Cell Division and Cancer GroupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | - Marta Gómez de Cedrón
- Cell Division and Cancer GroupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | - José Fernández‐Piqueras
- Centro de Biología Molecular Severo Ochoa (CBMSO)Consejo Superior de Investigaciones Científicas‐Universidad Autónoma de Madrid (CSIC‐UAM)MadridSpain
- Centro de Investigación Biomédica en Red para Enfermedades Raras (CIBERER)Instituto de Salud Carlos IIIMadridSpain
- Instituto de Investigación BiosanitariaFundación Jimenez DíazMadridSpain
| | - Manuel Serrano
- Tumor Suppression GroupCNIOMadridSpain
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Catalan Institution for Research and Advanced Studies (ICREA)BarcelonaSpain
| | | | - Da‐Zhi Wang
- Cardiovascular Research DivisionBoston Children′s HospitalHarvard Medical SchoolBostonMAUSA
| | - Susan J Clark
- Epigenetics Research Program, Genomics and Epigenetics DivisionGarvan Institute of Medical ResearchSydneyNSWAustralia
- St. Vincent's Clinical SchoolUNSW, SydneySydneyNSWAustralia
| | | | | | - Marcos Malumbres
- Cell Division and Cancer GroupSpanish National Cancer Research Centre (CNIO)MadridSpain
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19
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Borgohain MP, Haridhasapavalan KK, Dey C, Adhikari P, Thummer RP. An Insight into DNA-free Reprogramming Approaches to Generate Integration-free Induced Pluripotent Stem Cells for Prospective Biomedical Applications. Stem Cell Rev Rep 2020; 15:286-313. [PMID: 30417242 DOI: 10.1007/s12015-018-9861-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
More than a decade ago, a pioneering study reported generation of induced Pluripotent Stem Cells (iPSCs) by ectopic expression of a cocktail of reprogramming factors in fibroblasts. This study has revolutionized stem cell research and has garnered immense interest from the scientific community globally. iPSCs hold tremendous potential for understanding human developmental biology, disease modeling, drug screening and discovery, and personalized cell-based therapeutic applications. The seminal study identified Oct4, Sox2, Klf4 and c-Myc as a potent combination of genes to induce reprogramming. Subsequently, various reprogramming factors were identified by numerous groups. Most of these studies have used integrating viral vectors to overexpress reprogramming factors in somatic cells to derive iPSCs. However, these techniques restrict the clinical applicability of these cells as they may alter the genome due to random viral integration resulting in insertional mutagenesis and tumorigenicity. To circumvent this issue, alternative integration-free reprogramming approaches are continuously developed that eliminate the risk of genomic modifications and improve the prospects of iPSCs from lab to clinic. These methods establish that integration of transgenes into the genome is not essential to induce pluripotency in somatic cells. This review provides a comprehensive overview of the most promising DNA-free reprogramming techniques that have the potential to derive integration-free iPSCs without genomic manipulation, such as sendai virus, recombinant proteins, microRNAs, synthetic messenger RNA and small molecules. The understanding of these approaches shall pave a way for the generation of clinical-grade iPSCs. Subsequently, these iPSCs can be differentiated into desired cell type(s) for various biomedical applications.
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Affiliation(s)
- Manash P Borgohain
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Krishna Kumar Haridhasapavalan
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Chandrima Dey
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Poulomi Adhikari
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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20
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Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency. Cell Rep 2020; 27:1726-1741.e5. [PMID: 31067459 PMCID: PMC6555151 DOI: 10.1016/j.celrep.2019.04.056] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 03/04/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022] Open
Abstract
Elucidating the mechanism of reprogramming is confounded by heterogeneity due to the low efficiency and differential kinetics of obtaining induced pluripotent stem cells (iPSCs) from somatic cells. Therefore, we increased the efficiency with a combination of epigenomic modifiers and signaling molecules and profiled the transcriptomes of individual reprogramming cells. Contrary to the established temporal order, somatic gene inactivation and upregulation of cell cycle, epithelial, and early pluripotency genes can be triggered independently such that any combination of these events can occur in single cells. Sustained co-expression of Epcam, Nanog, and Sox2 with other genes is required to progress toward iPSCs. Ehf, Phlda2, and translation initiation factor Eif4a1 play functional roles in robust iPSC generation. Using regulatory network analysis, we identify a critical role for signaling inhibition by 2i in repressing somatic expression and synergy between the epigenomic modifiers ascorbic acid and a Dot1L inhibitor for pluripotency gene activation.
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21
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Babaie A, Lumicisi J, Thissen H, Wang PY, Sumer H, Kingshott P. Binary Colloidal Crystal (BCC) Substrates for Controlling the Fate of Mouse Embryonic Stem Cells. Colloids Surf B Biointerfaces 2020; 194:111133. [PMID: 32554259 DOI: 10.1016/j.colsurfb.2020.111133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/20/2020] [Accepted: 05/11/2020] [Indexed: 11/28/2022]
Abstract
Understanding the interactions of stem cells with surface topography can give us an invaluable tool in controlling stemness and fate of stem cells for further use in biomedical applications. In this study, we have fabricated topographical features using a class of cell culture substrates called binary colloidal crystals (BCCs), that are made by self-assembly of mixtures of spherical micron sized silica (Si) and nanometer sized polystyrene (PS) or poly (methyl methacrylate) (PMMA) particles. The substrates formed are arrays of ordered, hexagonally packed large Si particles inter-dispersed with the PS particles that are stabilized by gentle heating, which melts the PS or PMMA forming substrates suitable for cell culture. BCC substrates were used for culture of mouse embryonic stem cells (mESCs). Compared to tissue culture plates, COM1 (Si5-PMMA0.4), COM2 (Si5-PS0.4) and COM4 (Si2-PSC0.22) have shown to provide a better support for mESC proliferation in the presence of the cytokine leukemia inhibitory factor (LIF). The behavior of mESCs with the BCCs in presence and absence of LIF, was further explored and it was found that interaction of mESCs with the culture substrate can be controlled by tuning surface topography and roughness, which is determined by the size and type of particles used in making BCCs. Furthermore, it was shown that limiting cell-surface interactions and controlling colony shape can promote stemness maintenance on COM1 and COM2 substrates as indicated by better proliferation and higher expression of pluripotency genes including Nanog both in presence and in absence of LIF. Together with higher expression of GATA6 gene, it can be stated that these surfaces can be used for endodermic priming of mESCs. Therefore, we believe that these surfaces, especially COM1 and COM2 surfaces can be beneficial as stem cell culture systems for further use in biomedical research.
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Affiliation(s)
- Ali Babaie
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia; CSIRO Manufacturing, Research Way, Clayton, Victoria 3168, Australia
| | - James Lumicisi
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
| | - Helmut Thissen
- CSIRO Manufacturing, Research Way, Clayton, Victoria 3168, Australia
| | - Peng-Yuan Wang
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia; Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Huseyin Sumer
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia.
| | - Peter Kingshott
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
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22
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Park TS, Zimmerlin L, Evans-Moses R, Thomas J, Huo JS, Kanherkar R, He A, Ruzgar N, Grebe R, Bhutto I, Barbato M, Koldobskiy MA, Lutty G, Zambidis ET. Vascular progenitors generated from tankyrase inhibitor-regulated naïve diabetic human iPSC potentiate efficient revascularization of ischemic retina. Nat Commun 2020; 11:1195. [PMID: 32139672 PMCID: PMC7058090 DOI: 10.1038/s41467-020-14764-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 01/28/2020] [Indexed: 01/15/2023] Open
Abstract
Here, we report that the functionality of vascular progenitors (VP) generated from normal and disease-primed conventional human induced pluripotent stem cells (hiPSC) can be significantly improved by reversion to a tankyrase inhibitor-regulated human naïve epiblast-like pluripotent state. Naïve diabetic vascular progenitors (N-DVP) differentiated from patient-specific naïve diabetic hiPSC (N-DhiPSC) possessed higher vascular functionality, maintained greater genomic stability, harbored decreased lineage-primed gene expression, and were more efficient in migrating to and re-vascularizing the deep neural layers of the ischemic retina than isogenic diabetic vascular progenitors (DVP). These findings suggest that reprogramming to a stable naïve human pluripotent stem cell state may effectively erase dysfunctional epigenetic donor cell memory or disease-associated aberrations in patient-specific hiPSC. More broadly, tankyrase inhibitor-regulated naïve hiPSC (N-hiPSC) represent a class of human stem cells with high epigenetic plasticity, improved multi-lineage functionality, and potentially high impact for regenerative medicine.
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Affiliation(s)
- Tea Soon Park
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ludovic Zimmerlin
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rebecca Evans-Moses
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Justin Thomas
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jeffrey S Huo
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Riya Kanherkar
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alice He
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nensi Ruzgar
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rhonda Grebe
- Wilmer Eye Institute, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Imran Bhutto
- Wilmer Eye Institute, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael Barbato
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael A Koldobskiy
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gerard Lutty
- Wilmer Eye Institute, The Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Elias T Zambidis
- Institute for Cell Engineering, Department of Oncology, The Johns Hopkins School of Medicine, Baltimore, MD, USA.
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23
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Brumbaugh J, Di Stefano B, Hochedlinger K. Reprogramming: identifying the mechanisms that safeguard cell identity. Development 2019; 146:146/23/dev182170. [PMID: 31792064 DOI: 10.1242/dev.182170] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Development and homeostasis rely upon concerted regulatory pathways to establish the specialized cell types needed for tissue function. Once a cell type is specified, the processes that restrict and maintain cell fate are equally important in ensuring tissue integrity. Over the past decade, several approaches to experimentally reprogram cell fate have emerged. Importantly, efforts to improve and understand these approaches have uncovered novel molecular determinants that reinforce lineage commitment and help resist cell fate changes. In this Review, we summarize recent studies that have provided insights into the various chromatin factors, post-transcriptional processes and features of genomic organization that safeguard cell identity in the context of reprogramming to pluripotency. We also highlight how these factors function in other experimental, physiological and pathological cell fate transitions, including direct lineage conversion, pluripotency-to-totipotency reversion and cancer.
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Affiliation(s)
- Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.,Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA .,Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.,Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
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24
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Edgar JA. L-ascorbic acid and the evolution of multicellular eukaryotes. J Theor Biol 2019; 476:62-73. [DOI: 10.1016/j.jtbi.2019.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/10/2019] [Accepted: 06/02/2019] [Indexed: 12/26/2022]
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25
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The interplay of chromatin and transcription factors during cell fate transitions in development and reprogramming. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194407. [DOI: 10.1016/j.bbagrm.2019.194407] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 12/17/2022]
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26
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Direct Reprogramming of Mouse Fibroblasts into Functional Skeletal Muscle Progenitors. Stem Cell Reports 2019; 10:1505-1521. [PMID: 29742392 PMCID: PMC5995754 DOI: 10.1016/j.stemcr.2018.04.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 02/06/2023] Open
Abstract
Skeletal muscle harbors quiescent stem cells termed satellite cells and proliferative progenitors termed myoblasts, which play pivotal roles during muscle regeneration. However, current technology does not allow permanent capture of these cell populations in vitro. Here, we show that ectopic expression of the myogenic transcription factor MyoD, combined with exposure to small molecules, reprograms mouse fibroblasts into expandable induced myogenic progenitor cells (iMPCs). iMPCs express key skeletal muscle stem and progenitor cell markers including Pax7 and Myf5 and give rise to dystrophin-expressing myofibers upon transplantation in vivo. Notably, a subset of transplanted iMPCs maintain Pax7 expression and sustain serial regenerative responses. Similar to satellite cells, iMPCs originate from Pax7+ cells and require Pax7 itself for maintenance. Finally, we show that myogenic progenitor cell lines can be established from muscle tissue following small-molecule exposure alone. This study thus reports on a robust approach to derive expandable myogenic stem/progenitor-like cells from multiple cell types. MyoD and small molecules reprogram fibroblasts to myogenic progenitors termed iMPCs iMPCs self-renew and express key satellite cell and myoblast markers iMPC growth is driven by Pax7+ cells and requires Pax7 gene function Transplanted iMPCs engraft and sustain muscle regeneration in vivo
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27
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Lee Chong T, Ahearn EL, Cimmino L. Reprogramming the Epigenome With Vitamin C. Front Cell Dev Biol 2019; 7:128. [PMID: 31380368 PMCID: PMC6646595 DOI: 10.3389/fcell.2019.00128] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/02/2019] [Indexed: 12/19/2022] Open
Abstract
The erasure of epigenetic modifications across the genome of somatic cells is an essential requirement during their reprogramming into induced pluripotent stem cells (iPSCs). Vitamin C plays a pivotal role in remodeling the epigenome by enhancing the activity of Jumonji-C domain-containing histone demethylases (JHDMs) and the ten-eleven translocation (TET) proteins. By maintaining differentiation plasticity in culture, vitamin C also improves the quality of tissue specific stem cells derived from iPSCs that are highly sought after for use in regenerative medicine. The ability of vitamin C to potentiate the activity of histone and DNA demethylating enzymes also has clinical application in the treatment of cancer. Vitamin C deficiency has been widely reported in cancer patients and has recently been shown to accelerate cancer progression in disease models. Therapies involving high-dose vitamin C administration are currently gaining traction in the treatment of epigenetic dysregulation, by targeting aberrant histone and DNA methylation patterns associated with cancer progression.
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Affiliation(s)
- Taylor Lee Chong
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Emily L Ahearn
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Luisa Cimmino
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States
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28
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de Leeuw S, Tackenberg C. Alzheimer's in a dish - induced pluripotent stem cell-based disease modeling. Transl Neurodegener 2019; 8:21. [PMID: 31338163 PMCID: PMC6624934 DOI: 10.1186/s40035-019-0161-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/25/2019] [Indexed: 02/06/2023] Open
Abstract
Background Since the discovery of the induced pluripotent stem cell (iPSC) technique more than a decade ago, extensive progress has been made to develop clinically relevant cell culture systems. Alzheimer’s disease (AD) is the most common neurodegenerative disease, accounting for approximately two thirds of all cases of dementia. The massively increasing number of affected individuals explains the major interest of research in this disease as well as the strong need for better understanding of disease mechanisms. Main body IPSC-derived neural cells have been widely used to recapitulating key aspects of AD. In this Review we highlight the progress made in studying AD pathophysiology and address the currently available techniques, such as specific differentiation techniques for AD-relevant cell types as well as 2D and 3D cultures. Finally, we critically discuss the key challenges and future directions of this field and how some of the major limitations of the iPSC technique may be overcome. Conclusion Stem cell-based disease models have the potential to induce a paradigm shift in biomedical research. In particular, the combination of the iPSC technology with recent advances in gene editing or 3D cell cultures represents a breakthrough for in vitro disease modeling and provides a platform for a better understanding of disease mechanisms in human cells and the discovery of novel therapeutics.
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Affiliation(s)
- Sherida de Leeuw
- 1Institute for Regenerative Medicine, University of Zurich, Schlieren, Switzerland.,2Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Christian Tackenberg
- 1Institute for Regenerative Medicine, University of Zurich, Schlieren, Switzerland.,2Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
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29
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Zhao Y. Chemically induced cell fate reprogramming and the acquisition of plasticity in somatic cells. Curr Opin Chem Biol 2019; 51:146-153. [PMID: 31153758 DOI: 10.1016/j.cbpa.2019.04.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/08/2019] [Accepted: 04/25/2019] [Indexed: 12/14/2022]
Abstract
The nature of somatic cell fate has always been considered relatively unchangeable. Only in rare cases, in response to highly specific environmental cues, do differentiated mammalian somatic cells transform into other cell types. However, the fact that cell fate reprogramming can be accomplished by utilizing chemical cocktails, in the absence of any genetic alterations, suggests that the fate determination of somatic cells is much more malleable than previously believed. The use of chemical cocktails to directly alter cell fate sheds light on an important, yet less explored approach to regenerative medicine: the use of chemicals to restore functions to injured, aging or diseased tissues. Here, we review and discuss the recent developments, inspirations, and challenges encountered when modulating cell fate reprogramming with chemicals, and investigate how chemical biology impacts the future of cell fate reprogramming and regenerative medicine.
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Affiliation(s)
- Yang Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, China.
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30
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Lee J, Lee J, Cho YS. Peroxisome Proliferator-Activated Receptor α Agonist and Its Target Nanog Cooperate to Induce Pluripotency. J Clin Med 2018; 7:jcm7120488. [PMID: 30486372 PMCID: PMC6306698 DOI: 10.3390/jcm7120488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 01/23/2023] Open
Abstract
The pharmaceutical compounds that modulate pluripotent stem cell (PSC) identity and function are increasingly adopted to generate qualified PSCs and their derivatives, which have promising potential in regenerative medicine, in pursuit of more accuracy and safety and less cost. Here, we demonstrate the peroxisome proliferator-activated receptor α (PPARα) agonist as a novel enhancer of pluripotency acquisition and induced pluripotent stem cell (iPSC) generation. We found that PPARα agonist, examined and selected Food and Drug Administration (FDA) -approved compound libraries, increase the expression of pluripotency-associated genes, such as Nanog, Nr5A2, Oct4, and Rex1, during the reprogramming process and facilitate iPSC generation by enhancing their reprogramming efficiency. A reprogramming-promoting effect of PPARα occurred via the upregulation of Nanog, which is essential for the induction and maintenance of pluripotency. Through bioinformatic analysis, we identified putative peroxisome proliferator responsive elements (PPREs) located within the promoter region of the Nanog gene. We also determined that PPARα can activate Nanog transcription by specific binding to putative PPREs. Taken together, our findings suggest that PPARα is an important regulator of PSC pluripotency and reprogramming, and PPARα agonists can be used to improve PSC technology and regenerative medicine.
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Affiliation(s)
- Jungwoon Lee
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
| | - Jinhyuk Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
- Department of Biotechnology, KRIBB School, University of Science and Technology (UST), Daejeon 34113, Korea.
| | - Yee Sook Cho
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
- Department of Bioscience, KRIBB School, University of Science and Technology (UST), Daejeon 34113, Korea.
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31
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Sardina JL, Collombet S, Tian TV, Gómez A, Di Stefano B, Berenguer C, Brumbaugh J, Stadhouders R, Segura-Morales C, Gut M, Gut IG, Heath S, Aranda S, Di Croce L, Hochedlinger K, Thieffry D, Graf T. Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate. Cell Stem Cell 2018; 23:727-741.e9. [DOI: 10.1016/j.stem.2018.08.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/07/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022]
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32
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Schwarz BA, Cetinbas M, Clement K, Walsh RM, Cheloufi S, Gu H, Langkabel J, Kamiya A, Schorle H, Meissner A, Sadreyev RI, Hochedlinger K. Prospective Isolation of Poised iPSC Intermediates Reveals Principles of Cellular Reprogramming. Cell Stem Cell 2018; 23:289-305.e5. [PMID: 30017590 DOI: 10.1016/j.stem.2018.06.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 03/29/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022]
Abstract
Cellular reprogramming converts differentiated cells into induced pluripotent stem cells (iPSCs). However, this process is typically very inefficient, complicating mechanistic studies. We identified and molecularly characterized rare, early intermediates poised to reprogram with up to 95% efficiency, without perturbing additional genes or pathways, during iPSC generation from mouse embryonic fibroblasts. Analysis of these cells uncovered transcription factors (e.g., Tfap2c and Bex2) that are important for reprogramming but dispensable for pluripotency maintenance. Additionally, we observed striking patterns of chromatin hyperaccessibility at pluripotency loci, which preceded gene expression in poised intermediates. Finally, inspection of these hyperaccessible regions revealed an early wave of DNA demethylation that is uncoupled from de novo methylation of somatic regions late in reprogramming. Our study underscores the importance of investigating rare intermediates poised to produce iPSCs, provides insights into reprogramming mechanisms, and offers a valuable resource for the dissection of transcriptional and epigenetic dynamics intrinsic to cell fate change.
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Affiliation(s)
- Benjamin A Schwarz
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Murat Cetinbas
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kendell Clement
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan M Walsh
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sihem Cheloufi
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jan Langkabel
- University of Bonn Medical School, Institute of Pathology, Department of Developmental Pathology, Bonn, Germany
| | - Akihide Kamiya
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Hubert Schorle
- University of Bonn Medical School, Institute of Pathology, Department of Developmental Pathology, Bonn, Germany
| | - Alexander Meissner
- Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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33
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Apostolou E, Stadtfeld M. Cellular trajectories and molecular mechanisms of iPSC reprogramming. Curr Opin Genet Dev 2018; 52:77-85. [PMID: 29925040 DOI: 10.1016/j.gde.2018.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/24/2018] [Accepted: 06/04/2018] [Indexed: 12/30/2022]
Abstract
The discovery of induced pluripotent stem cells (iPSCs) has solidified the concept of transcription factors as major players in controlling cell identity and provided a tractable tool to study how somatic cell identity can be dismantled and pluripotency established. A number of landmark studies have established hallmarks and roadmaps of iPSC formation by describing relative kinetics of transcriptional, protein and epigenetic changes, including alterations in DNA methylation and histone modifications. Recently, technological advancements such as single-cell analyses, high-resolution genome-wide chromatin assays and more efficient reprogramming systems have been used to challenge and refine our understanding of the reprogramming process. Here, we will outline novel insights into the molecular mechanisms underlying iPSC formation, focusing on how the core reprogramming factors OCT4, KLF4, SOX2 and MYC (OKSM) drive changes in gene expression, chromatin state and 3D genome topology. In addition, we will discuss unexpected consequences of reprogramming factor expression in in vitro and in vivo systems that may point towards new applications of iPSC technology.
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Affiliation(s)
- Effie Apostolou
- Edward and Sandra Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Matthias Stadtfeld
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology and Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, NY 10016, USA.
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34
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Faulds KJ, Egelston JN, Sedivy LJ, Mitchell MK, Garimella S, Kozlowski H, D'Alessandro A, Hansen KC, Balsbaugh JL, Phiel CJ. Glycogen synthase kinase-3 (GSK-3) activity regulates mRNA methylation in mouse embryonic stem cells. J Biol Chem 2018; 293:10731-10743. [PMID: 29777057 DOI: 10.1074/jbc.ra117.001298] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/09/2018] [Indexed: 12/22/2022] Open
Abstract
Glycogen synthase kinase-3 (GSK-3) activity regulates multiple signal transduction pathways and is also a key component of the network responsible for maintaining stem cell pluripotency. Genetic deletion of Gsk-3α and Gsk-3β or inhibition of GSK-3 activity via small molecules promotes stem cell pluripotency, yet the mechanism underlying the role for GSK-3 in this process remains ambiguous. Another cellular process that has been shown to affect stem cell pluripotency is mRNA methylation (m6A). Here, we describe an intersection between these components, the regulation of m6A by GSK-3. We find that protein levels for the RNA demethylase, FTO (fat mass and obesity-associated protein), are elevated in Gsk-3α;Gsk-3β-deficient mouse embryonic stem cells (ESCs). FTO is normally phosphorylated by GSK-3, and MS identified the sites on FTO that are phosphorylated in a GSK-3-dependent fashion. GSK-3 phosphorylation of FTO leads to polyubiquitination, but in Gsk-3 knockout ESCs, that process is impaired, resulting in elevated levels of FTO protein. As a consequence of altered FTO protein levels, mRNAs in Gsk-3 knockout ESCs have 50% less m6A than WT ESCs, and m6A-Seq analysis reveals the specific mRNAs that have reduced m6A modifications. Taken together, we provide the first evidence for how m6A demethylation is regulated in mammalian cells and identify a putative novel mechanism by which GSK-3 activity regulates stem cell pluripotency.
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Affiliation(s)
- Kelsie J Faulds
- From the Department of Integrative Biology, University of Colorado Denver, Denver, Colorado 80204
| | - Jennifer N Egelston
- From the Department of Integrative Biology, University of Colorado Denver, Denver, Colorado 80204
| | - Laura J Sedivy
- From the Department of Integrative Biology, University of Colorado Denver, Denver, Colorado 80204
| | - Matthew K Mitchell
- From the Department of Integrative Biology, University of Colorado Denver, Denver, Colorado 80204
| | - Sanjana Garimella
- From the Department of Integrative Biology, University of Colorado Denver, Denver, Colorado 80204
| | - Hanna Kozlowski
- From the Department of Integrative Biology, University of Colorado Denver, Denver, Colorado 80204
| | - Angelo D'Alessandro
- the Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, and
| | - Kirk C Hansen
- the Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, and
| | - Jeremy L Balsbaugh
- the Mass Spectrometry Core Facility, Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309
| | - Christopher J Phiel
- From the Department of Integrative Biology, University of Colorado Denver, Denver, Colorado 80204,
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35
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Lin PY, Hsu SC, Chen HC, Len WB, Hsiao FC, Liu MC, Pan PL, Lin TC, Lee YH, Meir YJJ. Optimization of reprogramming culture conditions for the generation of induced pluripotent stem cells from Col1a1 4F2A-Oct4-GFP mice with high efficiency. FEBS J 2018; 285:1667-1683. [PMID: 29575491 DOI: 10.1111/febs.14436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/25/2018] [Accepted: 03/09/2018] [Indexed: 11/30/2022]
Abstract
A reprogrammable transgenic mouse strain, called Col1a1 4F2A-Oct4-GFP, was bred for the present study. Because the somatic cells of this mouse strain contain only two copies of each Yamanaka factor, these animals are inefficient at producing induced pluripotent stem cells (iPSCs; approx. 0.005%) under traditional culture conditions. With an optimized culture condition, the iPSC production rate of mouse embryonic fibroblasts (MEFs) of Col1a1 4F2A-Oct4-GFP mice (MEFCol1a14F2A-Oct4-GFP ) was increased to approximately 8%. Further, promotion of cell proliferation by serum supplementation did not enhance iPSC production. Inhibition of transforming growth factor β (TGF-β) in the serum by SB431542 neither affected the growth rate of MEFCol1a14F2A-Oct4-GFP nor promoted iPSC production. However, the use of the gamma-irradiated STO-NEO-LIF (γSNL) cells to serve as feeders for iPSC production resulted in a 5-fold higher rate of iPSC production than the use of γMEFICR feeders. Interestingly, the use of SB431542 with the γMEFICR -adopted system could eliminate this difference. RT-PCR-based comparative analysis further demonstrated that TGF-β expression was 10-fold higher in γMEFICR than in γSNL cells. Consistent with previous reports, mesenchymal to epithelial transition was found to participate in the initial steps of reprogramming in the specific context of MEFCol1a14F2A-Oct4-GFP . Moreover, we found that the initial seeding density is one of the pivotal factors for determining a high efficiency of iPSC generation. The iPSCs efficiently generated from our MEFCol1a14F2A-Oct4-GFP resembled mouse embryonic stem cells (mESCs) in aspects of teratoma formation and germline transmission. Depending on the culture conditions, our Col1a1 4F2A-Oct4-GFP mouse system can generate bona fide iPSCs with variable efficiencies, which can serve as a tool for interrogating the route taken by cells during somatic reprogramming.
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Affiliation(s)
- Po-Ying Lin
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Linkou, Taiwan
| | - Sheng-Chieh Hsu
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Linkou, Taiwan.,Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Hung-Chi Chen
- Center for Tissue Engineering, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Wen-Bin Len
- Department of Nursing, Chang Gung University of Science and Technology, Linkou, Taiwan
| | - Fang-Chi Hsiao
- Department of Medicine, College of Medicine, Chang Gung University, Linkou, Taiwan
| | - Mei-Chun Liu
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Linkou, Taiwan
| | - Pei-Ling Pan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Linkou, Taiwan
| | - Tsai-Chen Lin
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Linkou, Taiwan
| | - Ying-Hsuan Lee
- Department of Medicine, College of Medicine, Chang Gung University, Linkou, Taiwan
| | - Yaa-Jyuhn James Meir
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Linkou, Taiwan.,Center for Tissue Engineering, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou, Taiwan
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36
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Liu D, Pavathuparambil Abdul Manaph N, Al-Hawwas M, Zhou XF, Liao H. Small Molecules for Neural Stem Cell Induction. Stem Cells Dev 2018; 27:297-312. [PMID: 29343174 DOI: 10.1089/scd.2017.0282] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Generation of induced pluripotent stem cells (iPSCs) from other somatic cells has provided great hopes for transplantation therapies. However, these cells still cannot be used for clinical application due to the low reprogramming and differentiation efficiency beside the risk of mutagenesis and tumor formation. Compared to iPSCs, induced neural stem cells (iNSCs) are easier to terminally differentiate into neural cells and safe; thus, iNSCs hold more opportunities than iPSCs to treat neural diseases. On the other hand, recent studies have showed that small molecules (SMs) can dramatically improve the efficiency of reprogramming and SMs alone can even convert one kind of somatic cells into another, which is much safer and more effective than transcription factor-based methods. In this study, we provide a review of SMs that are generally used in recent neural stem cell induction studies, and discuss the main mechanisms and pathways of each SM.
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Affiliation(s)
- Donghui Liu
- 1 Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University , Nanjing, China .,2 School of Pharmacy and Medical Sciences, Sansom Institute, University of South Austrralia , Adelaide, South Australia
| | - Nimshitha Pavathuparambil Abdul Manaph
- 2 School of Pharmacy and Medical Sciences, Sansom Institute, University of South Austrralia , Adelaide, South Australia .,3 Central Northern Adelaide Renal and Transplantation Service, Royal Adelaide Hospital , Adelaide, South Australia
| | - Mohammed Al-Hawwas
- 2 School of Pharmacy and Medical Sciences, Sansom Institute, University of South Austrralia , Adelaide, South Australia
| | - Xin-Fu Zhou
- 2 School of Pharmacy and Medical Sciences, Sansom Institute, University of South Austrralia , Adelaide, South Australia
| | - Hong Liao
- 1 Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University , Nanjing, China
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37
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High-efficiency RNA-based reprogramming of human primary fibroblasts. Nat Commun 2018; 9:745. [PMID: 29467427 PMCID: PMC5821705 DOI: 10.1038/s41467-018-03190-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 01/25/2018] [Indexed: 12/13/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) hold great promise for regenerative medicine; however, their potential clinical application is hampered by the low efficiency of somatic cell reprogramming. Here, we show that the synergistic activity of synthetic modified mRNAs encoding reprogramming factors and miRNA-367/302s delivered as mature miRNA mimics greatly enhances the reprogramming of human primary fibroblasts into iPSCs. This synergistic activity is dependent upon an optimal RNA transfection regimen and culturing conditions tailored specifically to human primary fibroblasts. As a result, we can now generate up to 4,019 iPSC colonies from only 500 starting human primary neonatal fibroblasts and reprogram up to 90.7% of individually plated cells, producing multiple sister colonies. This methodology consistently generates clinically relevant, integration-free iPSCs from a variety of human patient’s fibroblasts under feeder-free conditions and can be applicable for the clinical translation of iPSCs and studying the biology of reprogramming. Induced pluripotent stem cells (iPSCs) have potential for regenerative medicine applications, but are generated with very low efficiency. Here, the authors show highly efficient reprogramming of human primary fibroblasts to iPSCs via the synergistic activity of synthetic modified mRNAs, mature miRNA mimics, and optimized culture methods.
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38
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Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion GJ, Beato M, Marti-Renom MA, Graf T. Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming. Nat Genet 2018; 50:238-249. [PMID: 29335546 PMCID: PMC5810905 DOI: 10.1038/s41588-017-0030-7] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 12/01/2017] [Indexed: 01/28/2023]
Abstract
Chromosomal architecture is known to influence gene expression, yet its role in controlling cell fate remains poorly understood. Reprogramming of somatic cells into pluripotent stem cells (PSCs) by the transcription factors (TFs) OCT4, SOX2, KLF4 and MYC offers an opportunity to address this question but is severely limited by the low proportion of responding cells. We have recently developed a highly efficient reprogramming protocol that synchronously converts somatic into pluripotent stem cells. Here, we used this system to integrate time-resolved changes in genome topology with gene expression, TF binding and chromatin-state dynamics. The results showed that TFs drive topological genome reorganization at multiple architectural levels, often before changes in gene expression. Removal of locus-specific topological barriers can explain why pluripotency genes are activated sequentially, instead of simultaneously, during reprogramming. Together, our results implicate genome topology as an instructive force for implementing transcriptional programs and cell fate in mammals.
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Affiliation(s)
- Ralph Stadhouders
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands.
| | - Enrique Vidal
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - François Serra
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Bruno Di Stefano
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University and Harvard Medical School, Cambridge, MA, USA
| | - François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Antonio Gomez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Samuel Collombet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, Paris, France
| | - Clara Berenguer
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Yasmina Cuartero
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Jochen Hecht
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Genomics Unit, CRG, BIST, Barcelona, Spain
| | - Guillaume J Filion
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc A Marti-Renom
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Thomas Graf
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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39
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Amlani B, Liu Y, Chen T, Ee LS, Lopez P, Heguy A, Apostolou E, Kim SY, Stadtfeld M. Nascent Induced Pluripotent Stem Cells Efficiently Generate Entirely iPSC-Derived Mice while Expressing Differentiation-Associated Genes. Cell Rep 2018; 22:876-884. [PMID: 29420174 DOI: 10.1016/j.celrep.2017.12.098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/22/2017] [Accepted: 12/26/2017] [Indexed: 01/02/2023] Open
Abstract
The ability of induced pluripotent stem cells (iPSCs) to differentiate into all adult cell types makes them attractive for research and regenerative medicine; however, it remains unknown when and how this capacity is established. We characterized the acquisition of developmental pluripotency in a suitable reprogramming system to show that iPSCs prior to passaging become capable of generating all tissues upon injection into preimplantation embryos. The developmental potential of nascent iPSCs is comparable to or even surpasses that of established pluripotent cells. Further functional assays and genome-wide molecular analyses suggest that cells acquiring developmental pluripotency exhibit a unique combination of properties that distinguish them from canonical naive and primed pluripotency states. These include reduced clonal self-renewal potential and the elevated expression of differentiation-associated transcriptional regulators. Our observations close a gap in the understanding of induced pluripotency and provide an improved roadmap of cellular reprogramming with ramifications for the use of iPSCs.
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Affiliation(s)
- Bhishma Amlani
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology and Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Yiyuan Liu
- Edward and Sandra Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Taotao Chen
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology and Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Ly-Sha Ee
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology and Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Peter Lopez
- Cytometry and Cell Sorting Laboratory, NYU School of Medicine, New York, NY 10016, USA
| | - Adriana Heguy
- Department of Pathology and Office for Collaborative Science, NYU School of Medicine, New York, NY 10016, USA
| | - Effie Apostolou
- Edward and Sandra Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Sang Yong Kim
- Department of Pathology and Office for Collaborative Science, NYU School of Medicine, New York, NY 10016, USA.
| | - Matthias Stadtfeld
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology and Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, NY 10016, USA.
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40
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Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K. Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling. Cell 2018; 172:106-120.e21. [PMID: 29249356 PMCID: PMC5766360 DOI: 10.1016/j.cell.2017.11.023] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/08/2017] [Accepted: 11/10/2017] [Indexed: 10/18/2022]
Abstract
Cell fate transitions involve rapid gene expression changes and global chromatin remodeling, yet the underlying regulatory pathways remain incompletely understood. Here, we identified the RNA-processing factor Nudt21 as a novel regulator of cell fate change using transcription-factor-induced reprogramming as a screening assay. Suppression of Nudt21 enhanced the generation of induced pluripotent stem cells, facilitated transdifferentiation into trophoblast stem cells, and impaired differentiation of myeloid precursors and embryonic stem cells, suggesting a broader role for Nudt21 in cell fate change. We show that Nudt21 directs differential polyadenylation of over 1,500 transcripts in cells acquiring pluripotency, although only a fraction changed protein levels. Remarkably, these proteins were strongly enriched for chromatin regulators, and their suppression neutralized the effect of Nudt21 during reprogramming. Collectively, our data uncover Nudt21 as a novel post-transcriptional regulator of cell fate and establish a direct, previously unappreciated link between alternative polyadenylation and chromatin signaling.
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Affiliation(s)
- Justin Brumbaugh
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Xiuye Wang
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Marti Borkent
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Elmira Forouzmand
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Katie J Clowers
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin A Schwarz
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Marian Kalocsay
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Howard Hughes Medical Institute, Brigham and Women's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences, University of Minnesota, Saint Paul, MN 55018, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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41
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Atlasi Y, Stunnenberg HG. The interplay of epigenetic marks during stem cell differentiation and development. Nat Rev Genet 2017; 18:643-658. [PMID: 28804139 DOI: 10.1038/nrg.2017.57] [Citation(s) in RCA: 313] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chromatin, the template for epigenetic regulation, is a highly dynamic entity that is constantly reshaped during early development and differentiation. Epigenetic modification of chromatin provides the necessary plasticity for cells to respond to environmental and positional cues, and enables the maintenance of acquired information without changing the DNA sequence. The mechanisms involve, among others, chemical modifications of chromatin, changes in chromatin constituents and reconfiguration of chromatin interactions and 3D structure. New advances in genome-wide technologies have paved the way towards an integrative view of epigenome dynamics during cell state transitions, and recent findings in embryonic stem cells highlight how the interplay between different epigenetic layers reshapes the transcriptional landscape.
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Affiliation(s)
- Yaser Atlasi
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, The Netherlands
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42
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Driessen BJ, Logie C, Vonk LA. Cellular reprogramming for clinical cartilage repair. Cell Biol Toxicol 2017; 33:329-349. [PMID: 28144824 PMCID: PMC5493710 DOI: 10.1007/s10565-017-9382-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/17/2017] [Indexed: 01/06/2023]
Abstract
The repair of articular cartilage needs a sufficient number of chondrocytes to replace the defect tissue, and therefore, expansion of cells is generally required. Chondrocytes derived by cellular reprogramming may provide a solution to the limitations of current (stem) cell-based therapies. In this article, two distinct approaches-induced pluripotent stem cell (iPSC)-mediated reprogramming and direct lineage conversion-are analysed and compared according to criteria that encompass the qualification of the method and the derived chondrocytes for the purpose of clinical application. Progress in iPSC generation has provided insights into the replacement of reprogramming factors by small molecules and chemical compounds. As follows, multistage chondrogenic differentiation methods have shown to improve the chondrocyte yield and quality. Nevertheless, the iPSC 'detour' remains a time- and cost-consuming approach. Direct conversion of fibroblasts into chondrocytes provides a slight advantage over these aspects compared to the iPSC detour. However, the requirement of constitutive transgene expression to inhibit hypertrophic differentiation limits this approach of being translated to the clinic. It can be concluded that the quality of the derived chondrocytes highly depends on the characteristics of the reprogramming method and that this is important to keep in mind during the experimental set-up. Further research into both reprogramming approaches for clinical cartilage repair has to include proper control groups and epigenetic profiling to optimize the techniques and eventually derive functionally stable articular chondrocytes.
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Affiliation(s)
- Britta J.H. Driessen
- Department of Orthopaedics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Colin Logie
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Lucienne A. Vonk
- Department of Orthopaedics, University Medical Center Utrecht, Utrecht, The Netherlands
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Surface tuning laser desorption/ionization mass spectrometry (STLDI-MS) for the analysis of small molecules using quantum dots. Anal Bioanal Chem 2017; 409:4943-4950. [DOI: 10.1007/s00216-017-0433-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/20/2017] [Accepted: 05/25/2017] [Indexed: 12/11/2022]
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Baranek M, Belter A, Naskręt-Barciszewska MZ, Stobiecki M, Markiewicz WT, Barciszewski J. Effect of small molecules on cell reprogramming. MOLECULAR BIOSYSTEMS 2017; 13:277-313. [PMID: 27918060 DOI: 10.1039/c6mb00595k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The essential idea of regenerative medicine is to fix or replace tissues or organs with alive and patient-specific implants. Pluripotent stem cells are able to indefinitely self-renew and differentiate into all cell types of the body which makes them a potent substantial player in regenerative medicine. The easily accessible source of induced pluripotent stem cells may allow obtaining and cultivating tissues in vitro. Reprogramming refers to regression of mature cells to its initial pluripotent state. One of the approaches affecting pluripotency is the usage of low molecular mass compounds that can modulate enzymes and receptors leading to the formation of pluripotent stem cells (iPSCs). It would be great to assess the general character of such compounds and reveal their new derivatives or modifications to increase the cell reprogramming efficiency. Many improvements in the methods of pluripotency induction have been made by various groups in order to limit the immunogenicity and tumorigenesis, increase the efficiency and accelerate the kinetics. Understanding the epigenetic changes during the cellular reprogramming process will extend the comprehension of stem cell biology and lead to potential therapeutic approaches. There are compounds which have been already proven to be or for now only putative inducers of the pluripotent state that may substitute for the classic reprogramming factors (Oct3/4, Sox2, Klf4, c-Myc) in order to improve the time and efficiency of pluripotency induction. The effect of small molecules on gene expression is dosage-dependent and their application concentration needs to be strictly determined. In this review we analysed the role of small molecules in modulations leading to pluripotency induction, thereby contributing to our understanding of stem cell biology and uncovering the major mechanisms involved in that process.
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Affiliation(s)
- M Baranek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
| | - A Belter
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
| | - M Z Naskręt-Barciszewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
| | - M Stobiecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
| | - W T Markiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
| | - J Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
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Velasquez-Mao AJ, Tsao CJM, Monroe MN, Legras X, Bissig-Choisat B, Bissig KD, Ruano R, Jacot JG. Differentiation of spontaneously contracting cardiomyocytes from non-virally reprogrammed human amniotic fluid stem cells. PLoS One 2017; 12:e0177824. [PMID: 28545044 PMCID: PMC5435315 DOI: 10.1371/journal.pone.0177824] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/03/2017] [Indexed: 11/18/2022] Open
Abstract
Congenital heart defects are the most common birth defect. The limiting factor in tissue engineering repair strategies is an autologous source of functional cardiomyocytes. Amniotic fluid contains an ideal cell source for prenatal harvest and use in correction of congenital heart defects. This study aims to investigate the potential of amniotic fluid-derived stem cells (AFSC) to undergo non-viral reprogramming into induced pluripotent stem cells (iPSC) followed by growth-factor-free differentiation into functional cardiomyocytes. AFSC from human second trimester amniotic fluid were transfected by non-viral vesicle fusion with modified mRNA of OCT4, KLF4, SOX2, LIN28, cMYC and nuclear GFP over 18 days, then differentiated using inhibitors of GSK3 followed 48 hours later by inhibition of WNT. AFSC-derived iPSC had high expression of OCT4, NANOG, TRA-1-60, and TRA-1-81 after 18 days of mRNA transfection and formed teratomas containing mesodermal, ectodermal, and endodermal germ layers in immunodeficient mice. By Day 30 of cardiomyocyte differentiation, cells contracted spontaneously, expressed connexin 43 and β-myosin heavy chain organized in sarcomeric banding patterns, expressed cardiac troponin T and β-myosin heavy chain, showed upregulation of NKX2.5, ISL-1 and cardiac troponin T with downregulation of POU5F1, and displayed calcium and voltage transients similar to those in developing cardiomyocytes. These results demonstrate that cells from human amniotic fluid can be differentiated through a pluripotent state into functional cardiomyocytes.
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Affiliation(s)
| | | | - Madeline N. Monroe
- Department of Bioengineering, Rice University, Houston, TX, United States of America
| | - Xavier Legras
- Department of Molecular and Cellular Biology, Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, United States of America
| | - Beatrice Bissig-Choisat
- Department of Molecular and Cellular Biology, Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, United States of America
| | - Karl-Dimiter Bissig
- Department of Molecular and Cellular Biology, Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, United States of America
| | - Rodrigo Ruano
- Department of Obstetrics and Gynecology, Maternal Fetal Medicine Texas Children’s Hospital, Houston, TX, United States of America
| | - Jeffrey G. Jacot
- Department of Bioengineering, Rice University, Houston, TX, United States of America
- Congenital Heart Surgery Service, Texas Children’s Hospital, Houston, TX, United States of America
- University of Colorado Denver, Department of Bioengineering, Aurora, CO, United States of America
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Sone M, Morone N, Nakamura T, Tanaka A, Okita K, Woltjen K, Nakagawa M, Heuser JE, Yamada Y, Yamanaka S, Yamamoto T. Hybrid Cellular Metabolism Coordinated by Zic3 and Esrrb Synergistically Enhances Induction of Naive Pluripotency. Cell Metab 2017; 25:1103-1117.e6. [PMID: 28467928 DOI: 10.1016/j.cmet.2017.04.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/06/2017] [Accepted: 04/15/2017] [Indexed: 01/05/2023]
Abstract
Naive pluripotent stem cells (PSCs) utilize both glycolysis and oxidative phosphorylation (OXPHOS) to satisfy their metabolic demands. However, it is unclear how somatic cells acquire this hybrid energy metabolism during reprogramming toward naive pluripotency. Here, we show that when transduced with Oct4, Sox2, and Klf4 (OSK) into murine fibroblasts, Zic3 and Esrrb synergistically enhance the reprogramming efficiency by regulating cellular metabolic pathways. These two transcription factors (TFs) cooperatively activate glycolytic metabolism independently of hypoxia inducible factors (HIFs). In contrast, the regulatory modes of the TFs on OXPHOS are antagonistic: Zic3 represses OXPHOS, whereas Esrrb activates it. Therefore, when introduced with Zic3, Esrrb restores OXPHOS activity, which is essential for efficient reprogramming. In addition, Esrrb-mediated OXPHOS activation is critical for the conversion of primed PSCs into the naive state. Our study suggests that the combinatorial function of TFs achieves an appropriate balance of metabolic pathways to induce naive PSCs.
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Affiliation(s)
- Masamitsu Sone
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Nobuhiro Morone
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; MRC Toxicology Unit, University of Leicester, Leicester, LE1 9HN, UK
| | - Tomonori Nakamura
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Akito Tanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Keisuke Okita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan
| | - Masato Nakagawa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - John E Heuser
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yasuhiro Yamada
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinya Yamanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; AMED-CREST, AMED 1-7-1 Otemach, Chiyodaku, Tokyo, 100-0004, Japan.
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47
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Eberwein P, Reinhard T. [New biomaterials and alternative stem cell sources for the reconstruction of the limbal stem cell niche]. Ophthalmologe 2017; 114:318-326. [PMID: 28378048 DOI: 10.1007/s00347-017-0463-5] [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] [Indexed: 11/26/2022]
Abstract
Reconstruction of the limbal stem cell niche in patients with limbal stem cell insufficiency remains one of the most challenging tasks in the treatment of ocular surface diseases. Ex vivo expansion of limbal stem cells still has potential for optimization despite positive reports in centers worldwide. New biomaterials as well as alternative cell sources for the reconstruction of the limbal stem cell niche have been published in recent years. The aim of this review is to provide insight into new biomaterials and cell sources which may find their way into clinical routine in the upcoming decades.
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Affiliation(s)
- P Eberwein
- Klinik für Augenheilkunde, Uniklinikum Freiburg, Killianstr. 5, 79106, Freiburg, Deutschland.
| | - T Reinhard
- Klinik für Augenheilkunde, Uniklinikum Freiburg, Killianstr. 5, 79106, Freiburg, Deutschland
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48
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Yunusova AM, Fishman VS, Vasiliev GV, Battulin NR. Deterministic versus stochastic model of reprogramming: new evidence from cellular barcoding technique. Open Biol 2017; 7:160311. [PMID: 28446707 PMCID: PMC5413903 DOI: 10.1098/rsob.160311] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/16/2017] [Indexed: 12/20/2022] Open
Abstract
Factor-mediated reprogramming of somatic cells towards pluripotency is a low-efficiency process during which only small subsets of cells are successfully reprogrammed. Previous analyses of the determinants of the reprogramming potential are based on average measurements across a large population of cells or on monitoring a relatively small number of single cells with live imaging. Here, we applied lentiviral genetic barcoding, a powerful tool enabling the identification of familiar relationships in thousands of cells. High-throughput sequencing of barcodes from successfully reprogrammed cells revealed a significant number of barcodes from related cells. We developed a computer model, according to which a probability of synchronous reprogramming of sister cells equals 10-30%. We conclude that the reprogramming success is pre-established in some particular cells and, being a heritable trait, can be maintained through cell division. Thus, reprogramming progresses in a deterministic manner, at least at the level of cell lineages.
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Affiliation(s)
- Anastasia M Yunusova
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Veniamin S Fishman
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Gennady V Vasiliev
- Sector of Genomic Investigation, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Nariman R Battulin
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
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49
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Inducible and Deterministic Forward Programming of Human Pluripotent Stem Cells into Neurons, Skeletal Myocytes, and Oligodendrocytes. Stem Cell Reports 2017; 8:803-812. [PMID: 28344001 PMCID: PMC5390118 DOI: 10.1016/j.stemcr.2017.02.016] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 02/17/2017] [Accepted: 02/17/2017] [Indexed: 12/31/2022] Open
Abstract
The isolation or in vitro derivation of many human cell types remains challenging and inefficient. Direct conversion of human pluripotent stem cells (hPSCs) by forced expression of transcription factors provides a potential alternative. However, deficient inducible gene expression in hPSCs has compromised efficiencies of forward programming approaches. We have systematically optimized inducible gene expression in hPSCs using a dual genomic safe harbor gene-targeting strategy. This approach provides a powerful platform for the generation of human cell types by forward programming. We report robust and deterministic reprogramming of hPSCs into neurons and functional skeletal myocytes. Finally, we present a forward programming strategy for rapid and highly efficient generation of human oligodendrocytes. Dual genomic safe harbor targeting of the Tet-ON system Optimized inducible transgene expression in human pluripotent stem cells Deterministic forward programming into neurons, myocytes, and oligodendrocytes
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50
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Liu LL, Brumbaugh J, Bar-Nur O, Smith Z, Stadtfeld M, Meissner A, Hochedlinger K, Michor F. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell Rep 2016; 17:3395-3406. [PMID: 28009305 PMCID: PMC5467646 DOI: 10.1016/j.celrep.2016.11.080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/04/2016] [Accepted: 11/24/2016] [Indexed: 01/01/2023] Open
Abstract
Reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) is typically an inefficient and asynchronous process. A variety of technological efforts have been made to accelerate and/or synchronize this process. To define a unified framework to study and compare the dynamics of reprogramming under different conditions, we developed an in silico analysis platform based on mathematical modeling. Our approach takes into account the variability in experimental results stemming from probabilistic growth and death of cells and potentially heterogeneous reprogramming rates. We suggest that reprogramming driven by the Yamanaka factors alone is a more heterogeneous process, possibly due to cell-specific reprogramming rates, which could be homogenized by the addition of additional factors. We validated our approach using publicly available reprogramming datasets, including data on early reprogramming dynamics as well as cell count data, and thus we demonstrated the general utility and predictive power of our methodology for investigating reprogramming and other cell fate change systems.
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Affiliation(s)
- Lin L Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Justin Brumbaugh
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Cambridge, MA 02138, USA
| | - Ori Bar-Nur
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Cambridge, MA 02138, USA
| | - Zachary Smith
- Department of Stem Cell and Regenerative Biology, Cambridge, MA 02138, USA
| | - Matthias Stadtfeld
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Cambridge, MA 02138, USA
| | - Konrad Hochedlinger
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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