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Zhao K, Wang M, Gao S, Chen J. Chromatin architecture reorganization during somatic cell reprogramming. Curr Opin Genet Dev 2021; 70:104-114. [PMID: 34530248 DOI: 10.1016/j.gde.2021.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/25/2021] [Accepted: 07/08/2021] [Indexed: 01/14/2023]
Abstract
It has been nearly 60 years since Dr John Gurdon achieved the first cloning of Xenopus by somatic cell nuclear transfer (SCNT). Later, in 2006, Takahashi and Yamanaka published their landmark study demonstrating the application of four transcription factors to induce pluripotency. These two amazing discoveries both clearly established that cell identity can be reprogrammed and that mature cells still contain the information required for lineage specification. Considering that different cell types possess identical genomes, what orchestrates reprogramming has attracted wide interest. Epigenetics, including high-level chromatin structure, might provide some answers. Benefitting from the tremendous progress in high-throughput and multi-omics techniques, we here address the roles and interactions of genome architecture, chromatin modifications, and transcription regulation during somatic cell reprogramming that were previously beyond reach. In addition, we provide perspectives on recent technical advances that might help to overcome certain barriers in the field.
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Affiliation(s)
- Kun Zhao
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Mingzhu Wang
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Jiayu Chen
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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2
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Ray A, Joshi JM, Sundaravadivelu PK, Raina K, Lenka N, Kaveeshwar V, Thummer RP. An Overview on Promising Somatic Cell Sources Utilized for the Efficient Generation of Induced Pluripotent Stem Cells. Stem Cell Rev Rep 2021; 17:1954-1974. [PMID: 34100193 DOI: 10.1007/s12015-021-10200-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2021] [Indexed: 01/19/2023]
Abstract
Human induced Pluripotent Stem Cells (iPSCs) have enormous potential in understanding developmental biology, disease modeling, drug discovery, and regenerative medicine. The initial human iPSC studies used fibroblasts as a starting cell source to reprogram them; however, it has been identified to be a less appealing somatic cell source by numerous studies due to various reasons. One of the important criteria to achieve efficient reprogramming is determining an appropriate starting somatic cell type to induce pluripotency since the cellular source has a major influence on the reprogramming efficiency, kinetics, and quality of iPSCs. Therefore, numerous groups have explored various somatic cell sources to identify the promising sources for reprogramming into iPSCs with different reprogramming factor combinations. This review provides an overview of promising easily accessible somatic cell sources isolated in non-invasive or minimally invasive manner such as keratinocytes, urine cells, and peripheral blood mononuclear cells used for the generation of human iPSCs derived from healthy and diseased subjects. Notably, iPSCs generated from one of these cell types derived from the patient will offer ethical and clinical advantages. In addition, these promising somatic cell sources have the potential to efficiently generate bona fide iPSCs with improved reprogramming efficiency and faster kinetics. This knowledge will help in establishing strategies for safe and efficient reprogramming and the generation of patient-specific iPSCs from these cell types.
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Affiliation(s)
- Arnab Ray
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Jahnavy Madhukar Joshi
- Central Research Laboratory, SDM College of Medical Sciences and Hospital, Shri Dharmasthala Manjunatheshwara University, Dharwad, 580009, Karnataka, India
| | - Pradeep Kumar Sundaravadivelu
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Khyati Raina
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Nibedita Lenka
- National Centre for Cell Science, S. P. Pune University Campus, Pune - 411007, Ganeshkhind, Maharashtra, India
| | - Vishwas Kaveeshwar
- Central Research Laboratory, SDM College of Medical Sciences and Hospital, Shri Dharmasthala Manjunatheshwara University, Dharwad, 580009, Karnataka, India.
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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3
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Tobias IC, Kao MMC, Parmentier T, Hunter H, LaMarre J, Betts DH. Targeted expression profiling reveals distinct stages of early canine fibroblast reprogramming are regulated by 2-oxoglutarate hydroxylases. Stem Cell Res Ther 2020; 11:528. [PMID: 33298190 PMCID: PMC7725121 DOI: 10.1186/s13287-020-02047-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Background Ectopic expression of a defined set of transcription factors allows the reprogramming of mammalian somatic cells to pluripotency. Despite continuous progress in primate and rodent reprogramming, limited attention has been paid to cell reprogramming in domestic and companion species. Previous studies attempting to reprogram canine cells have mostly assessed a small number of presumptive canine induced pluripotent stem cell (iPSC) lines for generic pluripotency attributes. However, why canine cell reprogramming remains extremely inefficient is poorly understood. Methods To better characterize the initial steps of pluripotency induction in canine somatic cells, we optimized an experimental system where canine fetal fibroblasts (cFFs) are transduced with the Yamanaka reprogramming factors by Sendai virus vectors. We use quantitative PCR arrays to measure the expression of 80 target genes at various stages of canine cell reprogramming. We ask how cFF reprogramming is influenced by small molecules affecting the epigenomic modification 5-hydroxymethylcytosine, specifically L-ascorbic acid and retinoic acid (AA/RA). Results We found that the expression and catalytic output of a class of 2-oxoglutarate-dependent (2-OG) hydroxylases, known as ten-eleven translocation (TET) enzymes, can be modulated in canine cells treated with AA/RA. We further show that AA/RA treatment induces TET1 expression and facilitates early canine reprogramming, evidenced by upregulation of epithelial and pluripotency markers. Using a chemical inhibitor of 2-OG hydroxylases, we demonstrate that 2-OG hydroxylase activity regulates the expression of a subset of genes involved in mesenchymal-to-epithelial transition (MET) and pluripotency in early canine reprogramming. We identify a set of transcription factors depleted in maturing reprogramming intermediates compared to pluripotent canine embryonic stem cells. Conclusions Our findings highlight 2-OG hydroxylases have evolutionarily conserved and divergent functions regulating the early reprogramming of canine somatic cells and show reprogramming conditions can be rationally optimized for the generation of maturing canine iPSC.
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Affiliation(s)
- Ian C Tobias
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada.,Present Affiliation: Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Mian-Mian C Kao
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada
| | - Thomas Parmentier
- Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Hailey Hunter
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada
| | - Jonathan LaMarre
- Department of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Dean H Betts
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Western University, Dental Sciences Building, Room DSB 2022, London, Ontario, N6A 5C1, Canada. .,Children's Health Research Institute, Lawson Health Research Institute, London, Ontario, Canada.
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4
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Klingenstein S, Klingenstein M, Kleger A, Liebau S. From Hair to iPSCs-A Guide on How to Reprogram Keratinocytes and Why. ACTA ACUST UNITED AC 2020; 55:e121. [PMID: 32956569 DOI: 10.1002/cpsc.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Keratinocytes, as a primary somatic cell source, offer exceptional advantages compared to fibroblasts, which are commonly used for reprogramming. Keratinocytes can beat fibroblasts in reprogramming efficiency and reprogramming time and, in addition, can be easily and non-invasively harvested from human hair roots. However, there is still much to know about acquiring keratinocytes and maintaining them in cell culture. In this article, we want to offer readers the profound knowledge that we have gained since our initial use of keratinocytes for reprogramming more than 10 years ago. Here, all hints and tricks, from plucking the hair roots to growing and maintaining keratinocytes, are described in detail. Additionally, an overview of the currently used reprogramming methods, viral and non-viral, is included, with a special focus on their applicability to keratinocytes. This overview is intended to provide a brief but comprehensive insight into the field of keratinocytes and their use for reprogramming into induced pluripotent stem cells (iPSCs). © 2020 The Authors.
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Affiliation(s)
- Stefanie Klingenstein
- Institute of Neuroanatomy & Developmental Biology, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Moritz Klingenstein
- Institute of Neuroanatomy & Developmental Biology, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Alexander Kleger
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Stefan Liebau
- Institute of Neuroanatomy & Developmental Biology, Eberhard-Karls University Tübingen, Tübingen, Germany
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5
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Zhang Y, Hu W, Ma K, Zhang C, Fu X. Reprogramming of Keratinocytes as Donor or Target Cells Holds Great Promise for Cell Therapy and Regenerative Medicine. Stem Cell Rev Rep 2020; 15:680-689. [PMID: 31197578 DOI: 10.1007/s12015-019-09900-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
One of the most crucial branches of regenerative medicine is cell therapy, in which cellular material is injected into the patient to initiate the regenerative process. Cells obtained by reprogramming of the patient's own cells offer ethical and clinical advantages could provide a new source of material for therapeutic applications. Studies to date have shown that only a subset of differentiated cell types can be reprogrammed. Among these, keratinocytes, which are the most abundant proliferating cell type in the epidermis, have gained increasing attention as both donor and target cells for reprogramming and have become a new focus of regenerative medicine. As target cells for the treatment of skin defects, keratinocytes can be differentiated or reprogrammed from embryonic stem cells, induced pluripotent stem cells, fibroblasts, adipose tissue stem cells, and mesenchymal cells. As donor cells, keratinocytes can be reprogrammed or direct reprogrammed into a number of cell types, including induced pluripotent stem cells, neural cells, and Schwann cells. In this review, we discuss recent advances in keratinocyte reprogramming, focusing on the induction methods, potential molecular mechanisms, conversion efficiency, and safety for clinical applications. Graphical Abstract KCs as target cells can be reprogrammed or differentiated from fibroblasts, iPSCs, ATSCs, and mesenchymal cells. And as donor cells, KCs can be reprogrammed or directly reprogrammded into iPSCs, neural cells, Schwann cells, and epidermal stem cells.
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Affiliation(s)
- Yuehou Zhang
- School of Medicine, NanKai University, 94 Wei Jin Road, NanKai District, Tianjin, 300071, People's Republic of China.,Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China
| | - Wenzhi Hu
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China
| | - Kui Ma
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China
| | - Cuiping Zhang
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China.
| | - Xiaobing Fu
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center of General Hospital of PLA, 51 Fu Cheng Road, HaiDian District, Beijing, 100048, People's Republic of China.
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6
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Martín B, Pappa S, Díez-Villanueva A, Mallona I, Custodio J, Barrero MJ, Peinado MA, Jordà M. Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. Epigenetics 2020; 15:765-779. [PMID: 32041475 DOI: 10.1080/15592294.2020.1722398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Alu repeats constitute a major fraction of human genome and for a small subset of them a role in gene regulation has been described. The number of studies focused on the functional characterization of particular Alu elements is very limited. Most Alu elements are DNA methylated and then assumed to lie in repressed chromatin domains. We hypothesize that Alu elements with low or variable DNA methylation are candidates for a functional role. In a genome-wide study in normal and cancer tissues, we pinpointed an Alu repeat (AluSq2) with differential methylation located upstream of the promoter region of the DIEXF gene. DIEXF encodes a highly conserved factor essential for the development of zebrafish digestive tract. To characterize the contribution of the Alu element to the regulation of DIEXF we analysed the epigenetic landscapes of the gene promoter and flanking regions in different cell types and cancers. Alternate epigenetic profiles (DNA methylation and histone modifications) of the AluSq2 element were associated with DIEXF transcript diversity as well as protein levels, while the epigenetic profile of the CpG island associated with the DIEXF promoter remained unchanged. These results suggest that AluSq2 might directly contribute to the regulation of DIEXF transcription and protein expression. Moreover, AluSq2 was DNA hypomethylated in different cancer types, pointing out its putative contribution to DIEXF alteration in cancer and its potential as tumoural biomarker.
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Affiliation(s)
- Berta Martín
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Stella Pappa
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Anna Díez-Villanueva
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Izaskun Mallona
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Joaquín Custodio
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - María José Barrero
- Center for Regenerative Medicine in Barcelona (CMRB), Avinguda de la Granvia de l'Hospitalet , Barcelona, Spain
| | - Miguel A Peinado
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Mireia Jordà
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
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7
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Andrejew R, Glaser T, Oliveira-Giacomelli Á, Ribeiro D, Godoy M, Granato A, Ulrich H. Targeting Purinergic Signaling and Cell Therapy in Cardiovascular and Neurodegenerative Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1201:275-353. [PMID: 31898792 DOI: 10.1007/978-3-030-31206-0_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Extracellular purines exert several functions in physiological and pathophysiological mechanisms. ATP acts through P2 receptors as a neurotransmitter and neuromodulator and modulates heart contractility, while adenosine participates in neurotransmission, blood pressure, and many other mechanisms. Because of their capability to differentiate into mature cell types, they provide a unique therapeutic strategy for regenerating damaged tissue, such as in cardiovascular and neurodegenerative diseases. Purinergic signaling is pivotal for controlling stem cell differentiation and phenotype determination. Proliferation, differentiation, and apoptosis of stem cells of various origins are regulated by purinergic receptors. In this chapter, we selected neurodegenerative and cardiovascular diseases with clinical trials using cell therapy and purinergic receptor targeting. We discuss these approaches as therapeutic alternatives to neurodegenerative and cardiovascular diseases. For instance, promising results were demonstrated in the utilization of mesenchymal stem cells and bone marrow mononuclear cells in vascular regeneration. Regarding neurodegenerative diseases, in general, P2X7 and A2A receptors mostly worsen the degenerative state. Stem cell-based therapy, mainly through mesenchymal and hematopoietic stem cells, showed promising results in improving symptoms caused by neurodegeneration. We propose that purinergic receptor activity regulation combined with stem cells could enhance proliferative and differentiation rates as well as cell engraftment.
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Affiliation(s)
- Roberta Andrejew
- Neuroscience Laboratory, Institute of Chemistry, Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - Talita Glaser
- Neuroscience Laboratory, Institute of Chemistry, Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - Ágatha Oliveira-Giacomelli
- Neuroscience Laboratory, Institute of Chemistry, Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - Deidiane Ribeiro
- Neuroscience Laboratory, Institute of Chemistry, Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - Mariana Godoy
- Neuroscience Laboratory, Institute of Chemistry, Department of Biochemistry, University of São Paulo, São Paulo, Brazil.,Laboratory of Neurodegenerative Diseases, Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alessandro Granato
- Neuroscience Laboratory, Institute of Chemistry, Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - Henning Ulrich
- Neuroscience Laboratory, Institute of Chemistry, Department of Biochemistry, University of São Paulo, São Paulo, Brazil.
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8
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Suelves M, Carrió E, Núñez-Álvarez Y, Peinado MA. DNA methylation dynamics in cellular commitment and differentiation. Brief Funct Genomics 2016; 15:443-453. [PMID: 27416614 DOI: 10.1093/bfgp/elw017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is an essential epigenetic modification for mammalian development and is crucial for the establishment and maintenance of cellular identity. Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of genome-wide approaches has allowed the analysis of DNA methylation in different genomic contexts, revealing a more dynamic regulation than originally thought, as active DNA methylation and demethylation occur during cell fate commitment and terminal differentiation. Recent data provide insights into the contribution of different epigenetic factors, and DNA methylation in particular, to the establishment of cellular memory during embryonic development and the modulation of cell type-specific gene regulation programs to ensure proper differentiation. This review summarizes published data regarding DNA methylation changes along lineage specification and differentiation programs. We also discuss the current knowledge about DNA methylation alterations occurring in physiological and pathological conditions such as aging and cancer.
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9
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Ben M’Barek K, Regent F, Monville C. Use of human pluripotent stem cells to study and treat retinopathies. World J Stem Cells 2015; 7:596-604. [PMID: 25914766 PMCID: PMC4404394 DOI: 10.4252/wjsc.v7.i3.596] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/13/2014] [Accepted: 12/31/2014] [Indexed: 02/06/2023] Open
Abstract
Human cell types affected by retinal diseases (such as age-related macular degeneration or retinitis pimentosa) are limited in cell number and of reduced accessibility. As a consequence, their isolation for in vitro studies of disease mechanisms or for drug screening efforts is fastidious. Human pluripotent stem cells (hPSCs), either of embryonic origin or through reprogramming of adult somatic cells, represent a new promising way to generate models of human retinopathies, explore the physiopathological mechanisms and develop novel therapeutic strategies. Disease-specific human embryonic stem cells were the first source of material to be used to study certain disease states. The recent demonstration that human somatic cells, such as fibroblasts or blood cells, can be genetically converted to induce pluripotent stem cells together with the continuous improvement of methods to differentiate these cells into disease-affected cellular subtypes opens new perspectives to model and understand a large number of human pathologies, including retinopathies. This review focuses on the added value of hPSCs for the disease modeling of human retinopathies and the study of their molecular pathological mechanisms. We also discuss the recent use of these cells for establishing the validation studies for therapeutic intervention and for the screening of large compound libraries to identify candidate drugs.
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10
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Nissenbaum J, Bar-Nur O, Ben-David E, Benvenisty N. Global indiscriminate methylation in cell-specific gene promoters following reprogramming into human induced pluripotent stem cells. Stem Cell Reports 2013; 1:509-17. [PMID: 24371806 PMCID: PMC3871396 DOI: 10.1016/j.stemcr.2013.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/31/2013] [Accepted: 11/13/2013] [Indexed: 01/05/2023] Open
Abstract
Molecular reprogramming of somatic cells into human induced pluripotent stem cells (iPSCs) is accompanied by extensive changes in gene expression patterns and epigenetic marks. To better understand the link between gene expression and DNA methylation, we have profiled human somatic cells from different embryonic cell types (endoderm, mesoderm, and parthenogenetic germ cells) and the iPSCs generated from them. We show that reprogramming is accompanied by extensive DNA methylation in CpG-poor promoters, sparing CpG-rich promoters. Intriguingly, methylation in CpG-poor promoters occurred not only in downregulated genes, but also in genes that are not expressed in the parental somatic cells or their respective iPSCs. These genes are predominantly tissue-specific genes of other cell types from different lineages. Our results suggest a role of DNA methylation in the silencing of the somatic cell identity by global nonspecific methylation of tissue-specific genes from all lineages, regardless of their expression in the parental somatic cells. Gene expression and DNA methylation profiles were compared for various human iPSCs Reprogramming is accompanied by extensive DNA methylation in CpG-poor promoters Hypermethylation occurs in cell-specific genes regardless of expression status Methylation regulates silencing of CpG-poor promoters in a nonspecific manner
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Affiliation(s)
- Jonathan Nissenbaum
- Stem Cell Unit, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel ; Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Ori Bar-Nur
- Stem Cell Unit, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel ; Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel ; Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, 185 Cambridge Street, Boston, MA 02114, USA
| | - Eyal Ben-David
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Nissim Benvenisty
- Stem Cell Unit, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel ; Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
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11
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Tucker BA, Mullins RF, Streb LM, Anfinson K, Eyestone ME, Kaalberg E, Riker MJ, Drack AV, Braun TA, Stone EM. Patient-specific iPSC-derived photoreceptor precursor cells as a means to investigate retinitis pigmentosa. eLife 2013; 2:e00824. [PMID: 23991284 PMCID: PMC3755341 DOI: 10.7554/elife.00824] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/24/2013] [Indexed: 12/11/2022] Open
Abstract
Next-generation and Sanger sequencing were combined to identify disease-causing USH2A mutations in an adult patient with autosomal recessive RP. Induced pluripotent stem cells (iPSCs), generated from the patient's keratinocytes, were differentiated into multi-layer eyecup-like structures with features of human retinal precursor cells. The inner layer of the eyecups contained photoreceptor precursor cells that expressed photoreceptor markers and exhibited axonemes and basal bodies characteristic of outer segments. Analysis of the USH2A transcripts of these cells revealed that one of the patient's mutations causes exonification of intron 40, a translation frameshift and a premature stop codon. Western blotting revealed upregulation of GRP78 and GRP94, suggesting that the patient's other USH2A variant (Arg4192His) causes disease through protein misfolding and ER stress. Transplantation into 4-day-old immunodeficient Crb1 (-/-) mice resulted in the formation of morphologically and immunohistochemically recognizable photoreceptor cells, suggesting that the mutations in this patient act via post-developmental photoreceptor degeneration. DOI:http://dx.doi.org/10.7554/eLife.00824.001.
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Affiliation(s)
- Budd A Tucker
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Luan M Streb
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Kristin Anfinson
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Mari E Eyestone
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Emily Kaalberg
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Megan J Riker
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Arlene V Drack
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Terry A Braun
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, United States
- Department of Biomedical Engineering, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences, University of Iowa Carver College of Medicine, Iowa City, United States
- Howard Hughes Medical Institute, University of Iowa, Iowa City, United States
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12
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Abstract
Skin cells from a patient with a form of inherited blindness have been reprogrammed into retinal cells and successfully transplanted into mice.
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Affiliation(s)
- Jeannette L Bennicelli
- is at the F.M. Kirby Center for Molecular Ophthalmology , University of Pennsylvania School of Medicine , Philadelphia , United States
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13
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Gutierrez SE, Romero-Oliva FA. Epigenetic changes: a common theme in acute myelogenous leukemogenesis. J Hematol Oncol 2013; 6:57. [PMID: 23938080 PMCID: PMC3751780 DOI: 10.1186/1756-8722-6-57] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/05/2013] [Indexed: 01/08/2023] Open
Abstract
Acute myeloid leukemia (AML) is a rather common disease, characterized by the presence of a clonal population of hematopoietic progenitor cells with impaired differentiation. Although traditionally AML has been considered the result of genetic alterations, more recently experimental evidence have demonstrated that epigenetic modifications are important in development and maintenance of leukemia cells. In this review we summarize current scientific knowledge of epigenetic alterations involved in leukemogenesis. We also highlight the developing of new technological strategies that are based on epigenetic processes and have been registered as Patents of Inventions in the United Nations dependent World Intellectual Property Office (WIPO) and the main Patent offices worldwide.
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Affiliation(s)
- Soraya E Gutierrez
- Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, Universidad de Concepcion, Casilla 160 C, 4089100, Concepcion, Chile.
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Chupeau MC, Granier F, Pichon O, Renou JP, Gaudin V, Chupeau Y. Characterization of the early events leading to totipotency in an Arabidopsis protoplast liquid culture by temporal transcript profiling. THE PLANT CELL 2013; 25:2444-63. [PMID: 23903317 PMCID: PMC3753376 DOI: 10.1105/tpc.113.109538] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 05/31/2013] [Accepted: 07/03/2013] [Indexed: 05/19/2023]
Abstract
The molecular mechanisms underlying plant cell totipotency are largely unknown. Here, we present a protocol for the efficient regeneration of plants from Arabidopsis thaliana protoplasts. The specific liquid medium used in our study leads to a high rate of reentry into the cell cycle of most cell types, providing a powerful system to study dedifferentiation/regeneration processes in independent somatic cells. To identify the early events in the establishment of totipotency, we monitored the genome-wide transcript profiles of plantlets and protoplast-derived cells (PdCs) during the first week of culture. Plant cells rapidly dedifferentiated. Then, we observed the reinitiation and reorientation of protein synthesis, accompanied by the reinitiation of cell division and de novo cell wall synthesis. Marked changes in the expression of chromatin-associated genes, especially of those in the histone variant family, were observed during protoplast culture. Surprisingly, the epigenetic status of PdCs and well-established cell cultures differed, with PdCs exhibiting rare reactivated transposons and epigenetic changes. The differentially expressed genes identified in this study are interesting candidates for investigating the molecular mechanisms underlying plant cell plasticity and totipotency. One of these genes, the plant-specific transcription factor ABERRANT LATERAL ROOT FORMATION4, is required for the initiation of protoplast division.
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Affiliation(s)
- Marie-Christine Chupeau
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
| | - Fabienne Granier
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
| | - Olivier Pichon
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165, Unité Mixte de Recherche en Génomique Végétale, F-91057 Évry cedex 2, France
| | - Jean-Pierre Renou
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165, Unité Mixte de Recherche en Génomique Végétale, F-91057 Évry cedex 2, France
| | - Valérie Gaudin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
| | - Yves Chupeau
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
- Address correspondence to
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Macrohistone Variants Preserve Cell Identity by Preventing the Gain of H3K4me2 during Reprogramming to Pluripotency. Cell Rep 2013; 3:1005-11. [DOI: 10.1016/j.celrep.2013.02.029] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/22/2013] [Accepted: 02/28/2013] [Indexed: 01/08/2023] Open
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16
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Berdasco M, Melguizo C, Prados J, Gómez A, Alaminos M, Pujana MA, Lopez M, Setien F, Ortiz R, Zafra I, Aranega A, Esteller M. DNA methylation plasticity of human adipose-derived stem cells in lineage commitment. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 181:2079-93. [PMID: 23031258 DOI: 10.1016/j.ajpath.2012.08.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 08/17/2012] [Accepted: 08/23/2012] [Indexed: 01/28/2023]
Abstract
Adult stem cells have an enormous potential for clinical use in regenerative medicine that avoids many of the drawbacks characteristic of embryonic stem cells and induced pluripotent stem cells. In this context, easily obtainable human adipose-derived stem cells offer an interesting option for future strategies in regenerative medicine. However, little is known about their repertoire of differentiation capacities, how closely they resemble the target primary tissues, and the potential safety issues associated with their use. DNA methylation is one of the most widely recognized epigenetic factors involved in cellular identity, prompting us to consider how the analyses of 27,578 CpG sites in the genome of these cells under different conditions reflect their different natural history. We show that human adipose-derived stem cells generate myogenic and osteogenic lineages that share much of the DNA methylation landscape characteristic of primary myocytes and osteocytes. Most important, adult stem cells and in vitro-generated myocytes and osteocytes display a significantly different DNA methylome from that observed in transformed cells from these tissue types, such as rhabdomyosarcoma and osteosarcoma. These results suggest that the plasticity of the DNA methylation patterns plays an important role in lineage commitment of adult stem cells and that it could be used for clinical purposes as a biomarker of efficient and safely differentiated cells.
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Affiliation(s)
- María Berdasco
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Biomedical Research Institute, Barcelona, Spain
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