1
|
Lv T, Jiang S, Wang X, Hou Y. Profiling A-to-I RNA editing during mouse somatic reprogramming at the single-cell level. Heliyon 2023; 9:e18133. [PMID: 37519753 PMCID: PMC10375800 DOI: 10.1016/j.heliyon.2023.e18133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
Mouse somatic cells can be reprogrammed into induced pluripotent stem cells through a highly heterogeneous process regulated by numerous biological factors, including adenosine-to-inosine (A-to-I) RNA editing. In this study, we analyzed A-to-I RNA editing sites using a single-cell RNA sequencing (scRNA-seq) dataset with high-depth and full-length coverage. Our method revealed that A-to-I RNA editing frequency varied widely at the single-cell level and underwent dynamic changes. We also found that A-to-I RNA editing level was correlated with the expression of the RNA editing enzyme ADAR1. The analysis combined with gene ontology (GO) enrichment revealed that ADAR1-dependent A-to-I editing may downregulate the expression levels of Igtp, Irgm2, Mndal, Ifi202b, and Tapbp in the early stage, to inhibit the pathways of cellular response to interferon-beta and regulation of protein complex stability to promote mesenchymal-epithelial transition (MET). Notably, we identified a negative correlation between A-to-I RNA editing frequency and the expression of certain genes, such as Nras, Ube2l6, Zfp987, and Adsl.
Collapse
Affiliation(s)
- Tianhang Lv
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Siyuan Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Yong Hou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| |
Collapse
|
2
|
Hassanpour M, Aghamohamadzade N, Cheraghi O, Heidarzadeh M, Nouri M. Current status of cardiac regenerative medicine; An update on point of view to cell therapy application. J Cardiovasc Thorac Res 2021; 12:256-268. [PMID: 33510874 PMCID: PMC7828760 DOI: 10.34172/jcvtr.2020.44] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 09/19/2020] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death globally. Because of the economic and social burden of acute myocardial infarction and its chronic consequences in surviving patients, understanding the pathophysiology of myocardial infarction injury is a major priority for cardiovascular research. MI is defined as cardiomyocytes death caused by an ischemic that resulted from the apoptosis, necrosis, necroptosis, and autophagy. The phases of normal repair following MI including inflammatory, proliferation, and maturation. Normal repair is slow and inefficient generally so that other treatments are required. Because of difficulties, outcomes, and backwashes of traditional therapies including coronary artery bypass grafting, balloon angioplasty, heart transplantation, and artificial heart operations, the novel strategy in the treatment of MI, cell therapy, was newly emerged. In cell therapy, a new population of cells has created that substitute with damaged cells. Different types of stem cell and progenitor cells have been shown to improve cardiac function through various mechanisms, including the formation of new myocytes, endothelial cells, and vascular smooth muscle cells. Bone marrow- and/or adipose tissue-derived mesenchymal stem cells, embryonic stem cells, autologous skeletal myoblasts, induced pluripotent stem cells, endothelial progenitor cells, cardiac progenitor cells and cardiac pericytes considered as a source for cell therapy. In this study, we focused on the point of view of the cell sources.
Collapse
Affiliation(s)
- Mehdi Hassanpour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Clinical Biochemistry and Laboratory Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Omid Cheraghi
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | | | - Mohammad Nouri
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Clinical Biochemistry and Laboratory Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
3
|
Vidal SE, Polyzos A, Chatterjee K, Ee LS, Swanzey E, Morales-Valencia J, Wang H, Parikh CN, Amlani B, Tu S, Gong Y, Snetkova V, Skok JA, Tsirigos A, Kim S, Apostolou E, Stadtfeld M. Context-Dependent Requirement of Euchromatic Histone Methyltransferase Activity during Reprogramming to Pluripotency. Stem Cell Reports 2020; 15:1233-1245. [PMID: 32976761 PMCID: PMC7724475 DOI: 10.1016/j.stemcr.2020.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 12/19/2022] Open
Abstract
Methylation of histone 3 at lysine 9 (H3K9) constitutes a roadblock for cellular reprogramming. Interference with methyltransferases or activation of demethylases by the cofactor ascorbic acid (AA) facilitates the derivation of induced pluripotent stem cells (iPSCs), but possible interactions between specific methyltransferases and AA treatment remain insufficiently explored. We show that chemical inhibition of the methyltransferases EHMT1 and EHMT2 counteracts iPSC formation in an enhanced reprogramming system in the presence of AA, an effect that is dependent on EHMT1. EHMT inhibition during enhanced reprogramming is associated with rapid loss of H3K9 dimethylation, inefficient downregulation of somatic genes, and failed mesenchymal-to-epithelial transition. Furthermore, transient EHMT inhibition during reprogramming yields iPSCs that fail to efficiently give rise to viable mice upon blastocyst injection. Our observations establish novel functions of H3K9 methyltransferases and suggest that a functional balance between AA-stimulated enzymes and EHMTs supports efficient and less error-prone iPSC reprogramming to pluripotency. EHMT function during mouse cell reprogramming is modulated by ascorbic acid (AA) EHMT inhibition counteracts reprogramming in the presence of AA EHMT inhibition in the presence of AA results in global erasure of H3K9 dimethylation Cells reprogrammed in the presence of EHMT inhibitor are functionally impaired
Collapse
Affiliation(s)
- Simon E Vidal
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016, USA; Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU Langone Medical Center, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA; Pharma Technical Development, Genentech, South San Francisco, CA 94080, USA
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kaushiki Chatterjee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ly-Sha Ee
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016, USA; Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU Langone Medical Center, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Emily Swanzey
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016, USA; Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU Langone Medical Center, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA; The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Jorge Morales-Valencia
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Hongsu Wang
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016, USA; Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU Langone Medical Center, New York, NY 10016, USA
| | - Chaitanya N Parikh
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Bhishma Amlani
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016, USA; Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU Langone Medical Center, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA
| | - Shengjiang Tu
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Langone Medical Center, New York, NY 10016, USA
| | - Yixiao Gong
- Department of Pathology, NYU Langone Medical Center, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA
| | - Valentina Snetkova
- Department of Pathology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Jane A Skok
- Department of Pathology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Langone Medical Center, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU Langone Medical Center, New York, NY 10016, USA
| | - Sangyong Kim
- Department of Pathology, NYU Langone Medical Center, New York, NY 10016, USA; Office for Collaborative Science, NYU Langone Medical Center, New York, NY 10016, USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Matthias Stadtfeld
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016, USA; Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU Langone Medical Center, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.
| |
Collapse
|
4
|
Yousefi N, Abdollahii S, Kouhbanani MAJ, Hassanzadeh A. Induced pluripotent stem cells (iPSCs) as game-changing tools in the treatment of neurodegenerative disease: Mirage or reality? J Cell Physiol 2020; 235:9166-9184. [PMID: 32437029 DOI: 10.1002/jcp.29800] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/02/2020] [Accepted: 05/02/2020] [Indexed: 12/14/2022]
Abstract
Based on investigations, there exist tight correlations between neurodegenerative diseases' incidence and progression and aberrant protein aggregreferates in nervous tissue. However, the pathology of these diseases is not well known, leading to an inability to find an appropriate therapeutic approach to delay occurrence or slow many neurodegenerative diseases' development. The accessibility of induced pluripotent stem cells (iPSCs) in mimicking the phenotypes of various late-onset neurodegenerative diseases presents a novel strategy for in vitro disease modeling. The iPSCs provide a valuable and well-identified resource to clarify neurodegenerative disease mechanisms, as well as prepare a promising human stem cell platform for drug screening. Undoubtedly, neurodegenerative disease modeling using iPSCs has established innovative opportunities for both mechanistic types of research and recognition of novel disease treatments. Most important, the iPSCs have been considered as a novel autologous cell origin for cell-based therapy of neurodegenerative diseases following differentiation to varied types of neural lineage cells (e.g. GABAergic neurons, dopamine neurons, cortical neurons, and motor neurons). In this review, we summarize iPSC-based disease modeling in neurodegenerative diseases including Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease, and Huntington's disease. Moreover, we discuss the efficacy of cell-replacement therapies for neurodegenerative disease.
Collapse
Affiliation(s)
- Niloufar Yousefi
- Department of Physiology and Pharmacology, Pasteur Instittableute of Iran, Tehran, Iran.,Stem Cell and Regenerative Medicine Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahla Abdollahii
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Mohammad Amin Jadidi Kouhbanani
- Stem Cell and Regenerative Medicine Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Hassanzadeh
- Stem Cell and Regenerative Medicine Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
5
|
|
6
|
Mayer D, Stadler MB, Rittirsch M, Hess D, Lukonin I, Winzi M, Smith A, Buchholz F, Betschinger J. Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2. EMBO J 2019; 39:e102591. [PMID: 31782544 DOI: 10.15252/embj.2019102591] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022] Open
Abstract
Developmental cell fate specification is a unidirectional process that can be reverted in response to injury or experimental reprogramming. Whether differentiation and de-differentiation trajectories intersect mechanistically is unclear. Here, we performed comparative screening in lineage-related mouse naïve embryonic stem cells (ESCs) and primed epiblast stem cells (EpiSCs), and identified the constitutively expressed zinc finger transcription factor (TF) Zfp281 as a bidirectional regulator of cell state interconversion. We showed that subtle chromatin binding changes in differentiated cells translate into activation of the histone H3 lysine 9 (H3K9) methyltransferase Ehmt1 and stabilization of the zinc finger TF Zic2 at enhancers and promoters. Genetic gain-of-function and loss-of-function experiments confirmed a critical role of Ehmt1 and Zic2 downstream of Zfp281 both in driving exit from the ESC state and in restricting reprogramming of EpiSCs. Our study reveals that cell type-invariant chromatin association of Zfp281 provides an interaction platform for remodeling the cis-regulatory network underlying cellular plasticity.
Collapse
Affiliation(s)
- Daniela Mayer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Melanie Rittirsch
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ilya Lukonin
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Maria Winzi
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Austin Smith
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| |
Collapse
|
7
|
Velychko S, Adachi K, Kim KP, Hou Y, MacCarthy CM, Wu G, Schöler HR. Excluding Oct4 from Yamanaka Cocktail Unleashes the Developmental Potential of iPSCs. Cell Stem Cell 2019; 25:737-753.e4. [PMID: 31708402 PMCID: PMC6900749 DOI: 10.1016/j.stem.2019.10.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/23/2019] [Accepted: 10/04/2019] [Indexed: 02/01/2023]
Abstract
Oct4 is widely considered the most important among the four Yamanaka reprogramming factors. Here, we show that the combination of Sox2, Klf4, and cMyc (SKM) suffices for reprogramming mouse somatic cells to induced pluripotent stem cells (iPSCs). Simultaneous induction of Sox2 and cMyc in fibroblasts triggers immediate retroviral silencing, which explains the discrepancy with previous studies that attempted but failed to generate iPSCs without Oct4 using retroviral vectors. SKM induction could partially activate the pluripotency network, even in Oct4-knockout fibroblasts. Importantly, reprogramming in the absence of exogenous Oct4 results in greatly improved developmental potential of iPSCs, determined by their ability to give rise to all-iPSC mice in the tetraploid complementation assay. Our data suggest that overexpression of Oct4 during reprogramming leads to off-target gene activation during reprogramming and epigenetic aberrations in resulting iPSCs and thereby bear major implications for further development and application of iPSC technology. SKM can induce pluripotency in somatic cells in the absence of exogenous Oct4 SM coexpression activates the retroviral silencing machinery in somatic cells Oct4 overexpression drives massive off-target gene activation during reprogramming OSKM, but not SKM, iPSCs show abnormal imprinting and differentiation patterns
Collapse
Affiliation(s)
- Sergiy Velychko
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Kenjiro Adachi
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Kee-Pyo Kim
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Yanlin Hou
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Caitlin M MacCarthy
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Guangming Wu
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, 6 Luoxuan Avenue, Haizhu District, 510320 Guangzhou, PRC.
| | - Hans R Schöler
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany; Medical Faculty, University of Münster, Domagkstrasse 3, 48449 Münster, Germany.
| |
Collapse
|
8
|
Francesconi M, Di Stefano B, Berenguer C, de Andrés-Aguayo L, Plana-Carmona M, Mendez-Lago M, Guillaumet-Adkins A, Rodriguez-Esteban G, Gut M, Gut IG, Heyn H, Lehner B, Graf T. Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming. eLife 2019; 8:41627. [PMID: 30860479 PMCID: PMC6435319 DOI: 10.7554/elife.41627] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 03/11/2019] [Indexed: 12/31/2022] Open
Abstract
Forced transcription factor expression can transdifferentiate somatic cells into other specialised cell types or reprogram them into induced pluripotent stem cells (iPSCs) with variable efficiency. To better understand the heterogeneity of these processes, we used single-cell RNA sequencing to follow the transdifferentation of murine pre-B cells into macrophages as well as their reprogramming into iPSCs. Even in these highly efficient systems, there was substantial variation in the speed and path of fate conversion. We predicted and validated that these differences are inversely coupled and arise in the starting cell population, with Mychigh large pre-BII cells transdifferentiating slowly but reprogramming efficiently and Myclow small pre-BII cells transdifferentiating rapidly but failing to reprogram. Strikingly, differences in Myc activity predict the efficiency of reprogramming across a wide range of somatic cell types. These results illustrate how single cell expression and computational analyses can identify the origins of heterogeneity in cell fate conversion processes.
Collapse
Affiliation(s)
- Mirko Francesconi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Bruno Di Stefano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
| | - Clara Berenguer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Luisa de Andrés-Aguayo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marcos Plana-Carmona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Maria Mendez-Lago
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Amy Guillaumet-Adkins
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Gustavo Rodriguez-Esteban
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ivo G Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|