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Sinenko SA, Tomilin AN. Metabolic control of induced pluripotency. Front Cell Dev Biol 2024; 11:1328522. [PMID: 38274274 PMCID: PMC10808704 DOI: 10.3389/fcell.2023.1328522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Pluripotent stem cells of the mammalian epiblast and their cultured counterparts-embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs)-have the capacity to differentiate in all cell types of adult organisms. An artificial process of reactivation of the pluripotency program in terminally differentiated cells was established in 2006, which allowed for the generation of induced pluripotent stem cells (iPSCs). This iPSC technology has become an invaluable tool in investigating the molecular mechanisms of human diseases and therapeutic drug development, and it also holds tremendous promise for iPSC applications in regenerative medicine. Since the process of induced reprogramming of differentiated cells to a pluripotent state was discovered, many questions about the molecular mechanisms involved in this process have been clarified. Studies conducted over the past 2 decades have established that metabolic pathways and retrograde mitochondrial signals are involved in the regulation of various aspects of stem cell biology, including differentiation, pluripotency acquisition, and maintenance. During the reprogramming process, cells undergo major transformations, progressing through three distinct stages that are regulated by different signaling pathways, transcription factor networks, and inputs from metabolic pathways. Among the main metabolic features of this process, representing a switch from the dominance of oxidative phosphorylation to aerobic glycolysis and anabolic processes, are many critical stage-specific metabolic signals that control the path of differentiated cells toward a pluripotent state. In this review, we discuss the achievements in the current understanding of the molecular mechanisms of processes controlled by metabolic pathways, and vice versa, during the reprogramming process.
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Affiliation(s)
- Sergey A. Sinenko
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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Golic M, Stojanovska V, Bendix I, Wehner A, Herse F, Haase N, Kräker K, Fischer C, Alenina N, Bader M, Schütte T, Schuchardt M, van der Giet M, Henrich W, Muller DN, Felderhoff-Müser U, Scherjon S, Plösch T, Dechend R. Diabetes Mellitus in Pregnancy Leads to Growth Restriction and Epigenetic Modification of the
Srebf2
Gene in Rat Fetuses. Hypertension 2018; 71:911-920. [DOI: 10.1161/hypertensionaha.117.10782] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/08/2018] [Accepted: 02/06/2018] [Indexed: 11/16/2022]
Abstract
Diabetic pregnancy is correlated with increased risk of metabolic and neurological disorders in the offspring putatively mediated epigenetically. Little is known about epigenetic changes already present in fetuses of diabetic pregnancies. We aimed at characterizing the perinatal environment after preexisting maternal diabetes mellitus and at identifying relevant epigenetic changes in the fetus. We focused on the transcription factor
Srebf2
(sterol regulatory element binding transcription factor 2), a master gene in regulation of cholesterol metabolism. We tested whether diabetic pregnancy induces epigenetic changes in the
Srebf2
promoter and if they become manifest in altered
Srebf2
gene expression. We worked with a transgenic rat model of type 2 diabetes mellitus (Tet29) in which the insulin receptor is knocked down by doxycycline-induced RNA interference. Doxycycline was administered preconceptionally to Tet29 and wild-type control rats. Only Tet29 doxycycline dams were hyperglycemic, hyperinsulinemic, and hyperlipidemic. Gene expression was analyzed with quantitative real-time reverse transcriptase polymerase chain reaction and CpG promoter methylation with pyrosequencing. Immunohistochemistry was performed on fetal brains. Fetuses from diabetic Tet29 dams were hyperglycemic and growth restricted at the end of pregnancy. They further displayed decreased liver and brain weight with concomitant decreased microglial activation in the hippocampus in comparison to fetuses of normoglycemic mothers. Importantly, diabetic pregnancy induced CpG hypermethylation of the
Srebf2
promoter in the fetal liver and brain, which was associated with decreased
Srebf2
gene expression. In conclusion, diabetic and hyperlipidemic pregnancy induces neurological, metabolic, and epigenetic alterations in the rat fetus.
Srebf2
is a potential candidate mediating intrauterine environment-driven epigenetic changes and later diabetic offspring health.
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Affiliation(s)
- Michaela Golic
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Violeta Stojanovska
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Ivo Bendix
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Anika Wehner
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Florian Herse
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Nadine Haase
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Kristin Kräker
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Caroline Fischer
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Natalia Alenina
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Michael Bader
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Till Schütte
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Mirjam Schuchardt
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Markus van der Giet
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Wolfgang Henrich
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Dominik N. Muller
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Ursula Felderhoff-Müser
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Sicco Scherjon
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Torsten Plösch
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
| | - Ralf Dechend
- From the Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Obstetrics, Germany (M.G., W.H.); Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gynecology with Breast Center, Campus Charité Mitte, Germany (M.G.); Experimental and Clinical Research Center, a cooperation between the
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Pasque V, Karnik R, Chronis C, Petrella P, Langerman J, Bonora G, Song J, Vanheer L, Sadhu Dimashkie A, Meissner A, Plath K. X Chromosome Dosage Influences DNA Methylation Dynamics during Reprogramming to Mouse iPSCs. Stem Cell Reports 2018; 10:1537-1550. [PMID: 29681539 PMCID: PMC5995367 DOI: 10.1016/j.stemcr.2018.03.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 11/03/2022] Open
Abstract
A dramatic difference in global DNA methylation between male and female cells characterizes mouse embryonic stem cells (ESCs), unlike somatic cells. We analyzed DNA methylation changes during reprogramming of male and female somatic cells and in resulting induced pluripotent stem cells (iPSCs). At an intermediate reprogramming stage, somatic and pluripotency enhancers are targeted for partial methylation and demethylation. Demethylation within pluripotency enhancers often occurs at ESC binding sites of pluripotency transcription factors. Late in reprogramming, global hypomethylation is induced in a female-specific manner. Genome-wide hypomethylation in female cells affects many genomic landmarks, including enhancers and imprint control regions, and accompanies the reactivation of the inactive X chromosome. The loss of one of the two X chromosomes in propagating female iPSCs is associated with genome-wide methylation gain. Collectively, our findings highlight the dynamic regulation of DNA methylation at enhancers during reprogramming and reveal that X chromosome dosage dictates global DNA methylation levels in iPSCs.
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Affiliation(s)
- Vincent Pasque
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, CA 90095, USA; KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Cancer Institute, Herestraat 49, 3000 Leuven, Belgium.
| | - Rahul Karnik
- Department of Stem Cell and Regenerative Biology, Harvard University, Harvard Stem Cell Institute, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Constantinos Chronis
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, CA 90095, USA
| | - Paula Petrella
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, CA 90095, USA
| | - Justin Langerman
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, CA 90095, USA
| | - Giancarlo Bonora
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, CA 90095, USA
| | - Juan Song
- KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Cancer Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Lotte Vanheer
- KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Cancer Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Anupama Sadhu Dimashkie
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, CA 90095, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Harvard Stem Cell Institute, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Kathrin Plath
- Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, 615 Charles E. Young Drive South, BSRB 390D, Los Angeles, CA 90095, USA.
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Abstract
Pregnancy is known to induce rapid, progressive, and substantial changes to the cardiovascular system, ultimately facilitating successful pregnancy outcomes. Women who develop hypertensive disorders during pregnancy are considered to have "failed" the cardiovascular stress test of pregnancy and likely represent a subpopulation with inadequate cardiovascular accommodation. Preeclampsia is a serious complication with a myriad of manifestations in both mother and offspring. This pregnancy syndrome is a polygenic disease and has now been linked to a greater incidence of cardiovascular disease. Moreover, offsprings born to preeclamptic mothers exhibit an elevated risk of cardiovascular disease, stroke, and mental disorders during adulthood. This suggests that preeclampsia not only exposes the mother and the fetus to complications during pregnancy but also programs chronic diseases during adulthood in the offspring. The etiology of preeclampsia remains unknown, with various theories being suggested to explain its origin. It is primarily thought to be associated with poor placentation and entails excessive maternal inflammation and endothelial dysfunction. It is well established now that the maternal immune system and the placenta are involved in a highly choreographed cross talk that underlies adequate spiral artery remodeling required for uteroplacental perfusion and free flow of nutrients to the fetus. Although it is not clear whether immunological alterations occur early during pregnancy, studies have proposed that dysregulated systemic and placental immunity contribute to impaired angiogenesis and the onset of preeclampsia. Recently emerged strong evidence suggests a potential link among epigenetics, microRNAs (miRNAs), and pregnancy complications. This chapter will focus on important aspects of epigenetics, immunological aspects, and cardiovascular and vascular remodeling of preeclampsia.
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Wianny F, Blachère T, Godet M, Guillermas R, Cortay V, Bourillot PY, Lefèvre A, Savatier P, Dehay C. Epigenetic status of H19/IGF2 and SNRPN imprinted genes in aborted and successfully derived embryonic stem cell lines in non-human primates. Stem Cell Res 2016; 16:557-67. [DOI: 10.1016/j.scr.2016.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 03/04/2016] [Accepted: 03/07/2016] [Indexed: 12/20/2022] Open
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Stojanovska V, Scherjon SA, Plösch T. Preeclampsia As Modulator of Offspring Health. Biol Reprod 2016; 94:53. [PMID: 26792940 DOI: 10.1095/biolreprod.115.135780] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 01/15/2016] [Indexed: 02/01/2023] Open
Abstract
A balanced intrauterine homeostasis during pregnancy is crucial for optimal growth and development of the fetus. The intrauterine environment is extremely vulnerable to multisystem pregnancy disorders such as preeclampsia, which can be triggered by various pathophysiological factors, such as angiogenic imbalance, immune responses, and inflammation. The fetus adapts to these conditions by a mechanism known as developmental programming that can lead to increased risk of chronic noncommunicable diseases in later life. This is shown in a substantial number of epidemiological studies that associate preeclampsia with increased onset of cardiovascular and metabolic diseases in the later life of the offspring. Furthermore, animal models based predominantly on one of the pathophysiological mechanism of preeclampsia, for example, angiogenic imbalance, immune response, or inflammation, do address the susceptibility of the preeclamptic offspring to increased maternal blood pressure and disrupted metabolic homeostasis. Accordingly, we extensively reviewed the latest research on the role of preeclampsia on the offspring's metabolism and cardiovascular phenotype. We conclude that future research on the pathophysiological changes during preeclampsia and methods to intervene in the harsh intrauterine environment will be essential for effective therapies.
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Affiliation(s)
- Violeta Stojanovska
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Sicco A Scherjon
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Torsten Plösch
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, The Netherlands
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The Epigenetic Reprogramming Roadmap in Generation of iPSCs from Somatic Cells. J Genet Genomics 2015; 42:661-70. [PMID: 26743984 DOI: 10.1016/j.jgg.2015.10.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 10/09/2015] [Accepted: 10/15/2015] [Indexed: 12/30/2022]
Abstract
Reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) is a comprehensive epigenetic process involving genome-wide modifications of histones and DNA methylation. This process is often incomplete, which subsequently affects iPSC reprogramming, pluripotency, and differentiation capacity. Here, we review the epigenetic changes with a focus on histone modification (methylation and acetylation) and DNA modification (methylation) during iPSC induction. We look at changes in specific epigenetic signatures, aberrations and epigenetic memory during reprogramming and small molecules influencing the epigenetic reprogramming of somatic cells. Finally, we discuss how to improve iPSC generation and pluripotency through epigenetic manipulations.
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Baronchelli S, La Spada A, Conforti P, Redaelli S, Dalprà L, De Blasio P, Cattaneo E, Biunno I. Investigating DNA Methylation Dynamics and Safety of Human Embryonic Stem Cell Differentiation Toward Striatal Neurons. Stem Cells Dev 2015; 24:2366-77. [DOI: 10.1089/scd.2015.0057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Simona Baronchelli
- Institute of Genetic and Biomedical Research, National Research Council (UOS IRGB-CNR), Milan, Italy
| | - Alberto La Spada
- Institute of Genetic and Biomedical Research, National Research Council (UOS IRGB-CNR), Milan, Italy
| | - Paola Conforti
- Department of Biosciences, Center for Stem Cell Research, University of Milan, Milan, Italy
| | - Serena Redaelli
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | - Leda Dalprà
- Department of Surgery and Translational Medicine, University of Milan-Bicocca, Monza, Italy
| | | | - Elena Cattaneo
- Department of Biosciences, Center for Stem Cell Research, University of Milan, Milan, Italy
| | - Ida Biunno
- Institute of Genetic and Biomedical Research, National Research Council (UOS IRGB-CNR), Milan, Italy
- IRCCS Multimedica, Milan, Italy
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Epigenetic modifications and long noncoding RNAs influence pancreas development and function. Trends Genet 2015; 31:290-9. [PMID: 25812926 DOI: 10.1016/j.tig.2015.02.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 01/29/2023]
Abstract
Insulin-producing β cells within the pancreatic islet of Langerhans are responsible for maintaining glucose homeostasis; the loss or malfunction of β cells results in diabetes mellitus. Recent advances in cell purification strategies and sequencing technologies as well as novel molecular tools have revealed that epigenetic modifications and long noncoding RNAs (lncRNAs) represent an integral part of the transcriptional mechanisms regulating pancreas development and β cell function. Importantly, these findings have uncovered a new layer of gene regulation in the pancreas that can be exploited to enhance the restoration and/or repair of β cells to treat diabetes.
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10
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Barrett R, Ornelas L, Yeager N, Mandefro B, Sahabian A, Lenaeus L, Targan SR, Svendsen CN, Sareen D. Reliable generation of induced pluripotent stem cells from human lymphoblastoid cell lines. Stem Cells Transl Med 2014; 3:1429-34. [PMID: 25298370 DOI: 10.5966/sctm.2014-0121] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Patient-specific induced pluripotent stem cells (iPSCs) hold great promise for many applications, including disease modeling to elucidate mechanisms involved in disease pathogenesis, drug screening, and ultimately regenerative medicine therapies. A frequently used starting source of cells for reprogramming has been dermal fibroblasts isolated from skin biopsies. However, numerous repositories containing lymphoblastoid cell lines (LCLs) generated from a wide array of patients also exist in abundance. To date, this rich bioresource has been severely underused for iPSC generation. We first attempted to create iPSCs from LCLs using two existing methods but were unsuccessful. Here we report a new and more reliable method for LCL reprogramming using episomal plasmids expressing pluripotency factors and p53 shRNA in combination with small molecules. The LCL-derived iPSCs (LCL-iPSCs) exhibited identical characteristics to fibroblast-derived iPSCs (fib-iPSCs), wherein they retained their genotype, exhibited a normal pluripotency profile, and readily differentiated into all three germ-layer cell types. As expected, they also maintained rearrangement of the heavy chain immunoglobulin locus. Importantly, we also show efficient iPSC generation from LCLs of patients with spinal muscular atrophy and inflammatory bowel disease. These LCL-iPSCs retained the disease mutation and could differentiate into neurons, spinal motor neurons, and intestinal organoids, all of which were virtually indistinguishable from differentiated cells derived from fib-iPSCs. This method for reliably deriving iPSCs from patient LCLs paves the way for using invaluable worldwide LCL repositories to generate new human iPSC lines, thus providing an enormous bioresource for disease modeling, drug discovery, and regenerative medicine applications.
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Affiliation(s)
- Robert Barrett
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Loren Ornelas
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nicole Yeager
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Berhan Mandefro
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Anais Sahabian
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lindsay Lenaeus
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Stephan R Targan
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Clive N Svendsen
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dhruv Sareen
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
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11
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He W, Kang X, Du H, Song B, Lu Z, Huang Y, Wang D, Sun X, Yu Y, Fan Y. Defining differentially methylated regions specific for the acquisition of pluripotency and maintenance in human pluripotent stem cells via microarray. PLoS One 2014; 9:e108350. [PMID: 25250679 PMCID: PMC4177110 DOI: 10.1371/journal.pone.0108350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/18/2014] [Indexed: 02/08/2023] Open
Abstract
Background Epigenetic regulation is critical for the maintenance of human pluripotent stem cells. It has been shown that pluripotent stem cells, such as embryonic stem cells and induced pluripotent stem cells, appear to have a hypermethylated status compared with differentiated cells. However, the epigenetic differences in genes that maintain stemness and regulate reprogramming between embryonic stem cells and induced pluripotent stem cells remain unclear. Additionally, differential methylation patterns of induced pluripotent stem cells generated using diverse methods require further study. Methodology Here, we determined the DNA methylation profiles of 10 human cell lines, including 2 ESC lines, 4 virally derived iPSC lines, 2 episomally derived iPSC lines, and the 2 parental cell lines from which the iPSCs were derived using Illumina's Infinium HumanMethylation450 BeadChip. The iPSCs exhibited a hypermethylation status similar to that of ESCs but with distinct differences from the parental cells. Genes with a common methylation pattern between iPSCs and ESCs were classified as critical factors for stemness, whereas differences between iPSCs and ESCs suggested that iPSCs partly retained the parental characteristics and gained de novo methylation aberrances during cellular reprogramming. No significant differences were identified between virally and episomally derived iPSCs. This study determined in detail the de novo differential methylation signatures of particular stem cell lines. Conclusions This study describes the DNA methylation profiles of human iPSCs generated using both viral and episomal methods, the corresponding somatic cells, and hESCs. Series of ss-DMRs and ES-iPS-DMRs were defined with high resolution. Knowledge of this type of epigenetic information could be used as a signature for stemness and self-renewal and provides a potential method for selecting optimal pluripotent stem cells for human regenerative medicine.
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Affiliation(s)
- WenYin He
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - XiangJin Kang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - HongZi Du
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bing Song
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - ZhenYu Lu
- Union Stem Cell & Gene Engineering Co., Ltd., Tianjin, China
| | - Yuling Huang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ding Wang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaofang Sun
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- * E-mail: (YY); (YF); (XFS)
| | - Yang Yu
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- * E-mail: (YY); (YF); (XFS)
| | - Yong Fan
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- * E-mail: (YY); (YF); (XFS)
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