51
|
Samudyata, Amaral PP, Engström PG, Robson SC, Nielsen ML, Kouzarides T, Castelo-Branco G. Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells. Exp Cell Res 2019; 381:129-138. [PMID: 31077711 PMCID: PMC6994247 DOI: 10.1016/j.yexcr.2019.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/03/2019] [Accepted: 05/04/2019] [Indexed: 01/08/2023]
Abstract
Sox2 is a master transcriptional regulator of embryonic development. In this study, we determined the protein interactome of Sox2 in the chromatin and nucleoplasm of mouse embryonic stem (mES) cells. Apart from canonical interactions with pluripotency-regulating transcription factors, we identified interactions with several chromatin modulators, including members of the heterochromatin protein 1 (HP1) family, suggesting a role for Sox2 in chromatin-mediated transcriptional repression. Sox2 was also found to interact with RNA binding proteins (RBPs), including proteins involved in RNA processing. RNA immunoprecipitation followed by sequencing revealed that Sox2 associates with different messenger RNAs, as well as small nucleolar RNA Snord34 and the non-coding RNA 7SK. 7SK has been shown to regulate transcription at gene regulatory regions, which could suggest a functional interaction with Sox2 for chromatin recruitment. Nevertheless, we found no evidence of Sox2 modulating recruitment of 7SK to chromatin when examining 7SK chromatin occupancy by Chromatin Isolation by RNA Purification (ChIRP) in Sox2 depleted mES cells. In addition, knockdown of 7SK in mES cells did not lead to any change in Sox2 occupancy at 7SK-regulated genes. Thus, our results show that Sox2 extensively interacts with RBPs, and suggest that Sox2 and 7SK co-exist in a ribonucleoprotein complex whose function is not to regulate chromatin recruitment, but could rather regulate other processes in the nucleoplasm.
Collapse
Affiliation(s)
- Samudyata
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Paulo P Amaral
- The Gurdon Institute, University of Cambridge, United Kingdom
| | - Pär G Engström
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Samuel C Robson
- School of Pharmacy and Biomedical Science, University of Portsmouth, United Kingdom
| | - Michael L Nielsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, United Kingdom
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
52
|
Gatinois V, Desprat R, Becker F, Pichard L, Bernex F, Corsini C, Pellestor F, Lemaitre JM. Reprogramming of Human Peripheral Blood Mononuclear Cell (PBMC) from a patient suffering of a Werner syndrome resulting in iPSC line (REGUi003-A) maintaining a short telomere length. Stem Cell Res 2019; 39:101515. [PMID: 31404747 DOI: 10.1016/j.scr.2019.101515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 10/26/2022] Open
Abstract
Werner syndrome (WS) is a rare human autosomal recessive disorder characterized by early onset of aging-associated diseases, chromosomal instability, and cancer predisposition, without therapeutic treatment solution. Major clinical symptoms of WS include common age-associated diseases, such as insulin-resistant diabetes mellitus, and atherosclerosis. WRN, the gene responsible for the disease, encodes a RECQL-type DNA helicase with a role in telomere metabolism. We derived a stable iPSC line from 53 years old patient's PBMC, with a normal karyotype, but exhibiting a short telomere length, as a major aspect of the cellular phenotype involved in the pathology.
Collapse
Affiliation(s)
- Vincent Gatinois
- Laboratory of Genome and Stem Cell Plasticity in Development and Aging, Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France; Laboratory of Cytogenetics, ChromoStem Facility, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Romain Desprat
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Fabienne Becker
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Lydiane Pichard
- Laboratory of Genome and Stem Cell Plasticity in Development and Aging, Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France; SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Florence Bernex
- Institut de Recherche en Cancérologie de Montpellier, Univ Montpellier, INSERM, U1194, Montpellier, France; Network of Experimental Histology, Univ Montpellier, BioCampus, CNRS, UMS3426, Montpellier, France
| | - Carole Corsini
- Medical Genetics Department, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Franck Pellestor
- Laboratory of Genome and Stem Cell Plasticity in Development and Aging, Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France; Laboratory of Cytogenetics, ChromoStem Facility, Univ Montpellier, CHU de Montpellier, Montpellier, France; SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France.
| | - Jean-Marc Lemaitre
- Laboratory of Genome and Stem Cell Plasticity in Development and Aging, Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France; SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France.
| |
Collapse
|
53
|
Lee Chong T, Ahearn EL, Cimmino L. Reprogramming the Epigenome With Vitamin C. Front Cell Dev Biol 2019; 7:128. [PMID: 31380368 PMCID: PMC6646595 DOI: 10.3389/fcell.2019.00128] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/02/2019] [Indexed: 12/19/2022] Open
Abstract
The erasure of epigenetic modifications across the genome of somatic cells is an essential requirement during their reprogramming into induced pluripotent stem cells (iPSCs). Vitamin C plays a pivotal role in remodeling the epigenome by enhancing the activity of Jumonji-C domain-containing histone demethylases (JHDMs) and the ten-eleven translocation (TET) proteins. By maintaining differentiation plasticity in culture, vitamin C also improves the quality of tissue specific stem cells derived from iPSCs that are highly sought after for use in regenerative medicine. The ability of vitamin C to potentiate the activity of histone and DNA demethylating enzymes also has clinical application in the treatment of cancer. Vitamin C deficiency has been widely reported in cancer patients and has recently been shown to accelerate cancer progression in disease models. Therapies involving high-dose vitamin C administration are currently gaining traction in the treatment of epigenetic dysregulation, by targeting aberrant histone and DNA methylation patterns associated with cancer progression.
Collapse
Affiliation(s)
- Taylor Lee Chong
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Emily L Ahearn
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Luisa Cimmino
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, United States.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States
| |
Collapse
|
54
|
Stem cell therapy in heart failure: Where do we stand today? Biochim Biophys Acta Mol Basis Dis 2019; 1866:165489. [PMID: 31199998 DOI: 10.1016/j.bbadis.2019.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/30/2019] [Accepted: 06/01/2019] [Indexed: 02/06/2023]
Abstract
Heart failure is a global epidemic that drastically cuts short longevity and compromises quality of life. Approximately 6 million Americans ≥20 years of age carry a diagnosis of heart failure. Worldwide, about 40 million adults are affected. The treatment of HF depends on the etiology. If left untreated it rapidly progresses and compromises quality of life. One of the newer technologies still in its infancy is stem cell therapy for heart failure. This review attempts to highlight the clinical studies done in ischemic cardiomyopathy, dilated cardiomyopathy and restrictive cardiomyopathy. A combined approach of simultaneous revascularization and stem cell therapy appears to produce maximum benefit in ischemic cardiomyopathy. Treatment of dilated cardiomyopathy with stem cells also holds promise but needs more definition with regards to timing, route of cell delivery and type of cell used to achieve reproducible results. The variability noted in response to stem cell therapy in patients could also be secondary to their co-morbidities. Abnormalities of glucose metabolism and diabetes in particular impair stem cell and angiogenic cell mobilization. This opens up a whole new area of investigation into exploring the biochemical microenvironment which could influence the efficacy of stem cell therapy. This article is part of a Special Issue entitled: Stem Cells and Their Applications to Human Diseases edited by Hemachandra Reddy.
Collapse
|
55
|
Chen X, Ye Y, Gu L, Sun J, Du Y, Liu WJ, Li W, Zhang X, Jiang C. H3K27me3 Signal in the Cis Regulatory Elements Reveals the Differentiation Potential of Progenitors During Drosophila Neuroglial Development. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:297-304. [PMID: 31195140 PMCID: PMC6818177 DOI: 10.1016/j.gpb.2018.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/14/2018] [Accepted: 12/14/2018] [Indexed: 01/24/2023]
Abstract
Drosophila neural development undergoes extensive chromatin remodeling and precise epigenetic regulation. However, the roles of chromatin remodeling in establishment and maintenance of cell identity during cell fate transition remain enigmatic. Here, we compared the changes in gene expression, as well as the dynamics of nucleosome positioning and key histone modifications between the four major neural cell types during Drosophila neural development. We find that the neural progenitors can be separated from the terminally differentiated cells based on their gene expression profiles, whereas nucleosome distribution in the flanking regions of transcription start sites fails to identify the relationships between the progenitors and the differentiated cells. H3K27me3 signal in promoters and enhancers can not only distinguish the progenitors from the differentiated cells but also identify the differentiation path of the neural stem cells (NSCs) to the intermediate progenitor cells to the glial cells. In contrast, H3K9ac signal fails to identify the differentiation path, although it activates distinct sets of genes with neuron-specific and glia-related functions during the differentiation of the NSCs into neurons and glia, respectively. Together, our study provides novel insights into the crucial roles of chromatin remodeling in determining cell type during Drosophila neural development.
Collapse
Affiliation(s)
- Xiaolong Chen
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Youqiong Ye
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Liang Gu
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Jin Sun
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Yanhua Du
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Wen-Ju Liu
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Wei Li
- Tongji University Library, Tongji University, Shanghai 200092, China
| | - Xiaobai Zhang
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China; Research Center of Stem Cells and Ageing, Tsingtao Advanced Research Institute, Tongji University, Tsingtao 266071, China.
| |
Collapse
|
56
|
Bar S, Benvenisty N. Epigenetic aberrations in human pluripotent stem cells. EMBO J 2019; 38:embj.2018101033. [PMID: 31088843 DOI: 10.15252/embj.2018101033] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are being increasingly utilized worldwide in investigating human development, and modeling and discovering therapies for a wide range of diseases as well as a source for cellular therapy. Yet, since the first isolation of human embryonic stem cells (hESCs) 20 years ago, followed by the successful reprogramming of human-induced pluripotent stem cells (hiPSCs) 10 years later, various studies shed light on abnormalities that sometimes accumulate in these cells in vitro Whereas genetic aberrations are well documented, epigenetic alterations are not as thoroughly discussed. In this review, we highlight frequent epigenetic aberrations found in hPSCs, including alterations in DNA methylation patterns, parental imprinting, and X chromosome inactivation. We discuss the potential origins of these abnormalities in hESCs and hiPSCs, survey the different methods for detecting them, and elaborate on their potential consequences for the different utilities of hPSCs.
Collapse
Affiliation(s)
- Shiran Bar
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Nissim Benvenisty
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| |
Collapse
|
57
|
Kumar R, Evans T. Activation-Induced Cytidine Deaminase Regulates Fibroblast Growth Factor/Extracellular Signal-Regulated Kinases Signaling to Achieve the Naïve Pluripotent State During Reprogramming. Stem Cells 2019; 37:1003-1017. [PMID: 31021461 PMCID: PMC6766926 DOI: 10.1002/stem.3023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 03/20/2019] [Accepted: 03/31/2019] [Indexed: 11/12/2022]
Abstract
Induced pluripotent stem cells (iPSCs) derived by in vitro reprogramming of somatic cells retain the capacity to self-renew and to differentiate into many cell types. Pluripotency encompasses multiple states, with naïve iPSCs considered as ground state, possessing high levels of self-renewal capacity and maximum potential without lineage restriction. We showed previously that activation-induced cytidine deaminase (AICDA) facilitates stabilization of pluripotency during reprogramming. Here, we report that Acida-/- iPSCs, even when successfully reprogrammed, fail to achieve the naïve pluripotent state and remain primed for differentiation because of a failure to suppress fibroblast growth factor (FGF)/extracellular signal-regulated kinases (ERK) signaling. Although the mutant cells display marked genomic hypermethylation, suppression of FGF/ERK signaling by AICDA is independent of deaminase activity. Thus, our study identifies AICDA as a novel regulator of naïve pluripotency through its activity on FGF/ERK signaling. Stem Cells 2019;37:1003-1017.
Collapse
Affiliation(s)
- Ritu Kumar
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
| |
Collapse
|
58
|
Shuzui E, Kim MH, Kino-oka M. Anomalous cell migration triggers a switch to deviation from the undifferentiated state in colonies of human induced pluripotent stems on feeder layers. J Biosci Bioeng 2019; 127:246-255. [DOI: 10.1016/j.jbiosc.2018.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/02/2018] [Accepted: 07/24/2018] [Indexed: 01/07/2023]
|
59
|
Henry MP, Hawkins JR, Boyle J, Bridger JM. The Genomic Health of Human Pluripotent Stem Cells: Genomic Instability and the Consequences on Nuclear Organization. Front Genet 2019; 9:623. [PMID: 30719030 PMCID: PMC6348275 DOI: 10.3389/fgene.2018.00623] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are increasingly used for cell-based regenerative therapies worldwide, with embryonic and induced pluripotent stem cells as potential treatments for debilitating and chronic conditions, such as age-related macular degeneration, Parkinson's disease, spinal cord injuries, and type 1 diabetes. However, with the level of genomic anomalies stem cells generate in culture, their safety may be in question. Specifically, hPSCs frequently acquire chromosomal abnormalities, often with gains or losses of whole chromosomes. This review discusses how important it is to efficiently and sensitively detect hPSC aneuploidies, to understand how these aneuploidies arise, consider the consequences for the cell, and indeed the individual to whom aneuploid cells may be administered.
Collapse
Affiliation(s)
- Marianne P Henry
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom.,Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
| | - J Ross Hawkins
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Jennifer Boyle
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Joanna M Bridger
- Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
| |
Collapse
|
60
|
Liu J, An L, Wang J, Liu Z, Dai Y, Liu Y, Yang L, Du F. Dynamic patterns of H3K4me3, H3K27me3, and Nanog during rabbit embryo development. Am J Transl Res 2019; 11:430-441. [PMID: 30787999 PMCID: PMC6357316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/14/2018] [Indexed: 06/09/2023]
Abstract
Epigenetic modification and expression of key pluripotent factors are critical for development, cell fate determination, and differentiation in early embryos. In this study, we systematically examined the dynamic patterns of histone modifications (H3K4me3 and H3K27me3) and Nanog expression during the development of preimplantation rabbit embryos. Rabbit oocytes, 1-, 2-, 4-, 8-, and 16-cell embryos, morulae, and blastocysts were collected at specific time points following superovulation and assessed for nuclear H3K4me3, H3K27me3, and Nanog expression by immunofluorescence microscopy. The frequency of H3K4me3-positive nuclear staining was highest in oocytes through 4-cell embryos (100%), decreased in 8-cell (97.2%) and 16-cell (94.4%) embryos (P > 0.05), declined dramatically in morulae (86.7%) (1- through 8-cell embryos vs morulae, P < 0.05), and was the lowest in blastocysts (76.2%) (P < 0.05). Nuclear staining of H3K27me3 was negative in oocytes and embryos through the 16-cell stage but was positive in 25.9% of morulae and 34.2% of blastocyst (P < 0.05). Similarly, rabbit oocytes and embryos through the 16-cell stage did not express Nanog, but Nanog was expressed in 24.9% of morulae and 36.5% of blastocysts (P < 0.05). The observed decrease in H3K4me3 and increase in H3K27me3 as development progressed in preimplantation rabbit embryos, together with late Nanog expression, indicates a correlation of these factors with early embryonic cell fate determination and differentiation. Our study provides a specific and dynamic profile of histone modifications and gene expression that will be important for the derivation of rabbit embryonic stem cells and improving rabbit cloning by somatic cell nuclear transfer.
Collapse
Affiliation(s)
- Jiao Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Liyou An
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Jiqiang Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Zhihui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Yujian Dai
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Yanhong Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
| | - Lan Yang
- Lannuo Biotechnologies Wuxi Inc.Wuxi 214000, PR China
| | - Fuliang Du
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, PR China
- Lannuo Biotechnologies Wuxi Inc.Wuxi 214000, PR China
| |
Collapse
|
61
|
Fang B, Wang D, Zheng J, Wei Q, Zhan D, Liu Y, Yang X, Wang H, Li G, He W, Xu L. Involvement of tumor necrosis factor alpha in steroid-associated osteonecrosis of the femoral head: friend or foe? Stem Cell Res Ther 2019; 10:5. [PMID: 30606261 PMCID: PMC6318982 DOI: 10.1186/s13287-018-1112-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/05/2018] [Accepted: 12/17/2018] [Indexed: 02/07/2023] Open
Abstract
Background The etiology and pathology osteonecrosis of the femoral head (ONFH) are not completely clarified. As a cytokine participating in systemic inflammation, tumor necrosis factor alpha (TNFα) has been shown to be involved in the pathogenesis of ONFH. However, the role of TNFα in ONFH is not clearly clarified. In the present study, we investigated the effects of TNFα on proliferation, angiogenesis, and osteogenic differentiation of rat bone mesenchymal stem cells (rMSCs) and the underlying mechanisms. Methods All femoral bone tissues were separated in surgeries. After extracting total RNA and protein, we evaluated TNFα content by ELISA and the relative expression levels of genes by quantitative real-time PCR and western blot. Also, immunohistochemistry staining was performed to observe the expression of Runx2 in the bone samples. Chick embryo chorioallantoic membrane (CAM) assay was performed to observe the effect of TNFα on angiogenesis. The genomic DNAs were treated by bisulfite modification, and methylation status of CpG sites in the CpG islands of human and rat Runx2 gene promoter was determined by DNA sequencing. The binding of H3K4me3 and H3K27me3 in Runx2 promoter was checked by ChIP assay. RNA-seq analysis was used to find out the genes and pathways changed by TNFα in rMSCs. Results The results demonstrate TNFα promotes cell proliferation and angiogenesis whereas inhibits osteogenesis. Epigenetic regulations including DNA methylation and histone modifications play important roles in mediating the effect of TNFα on osteogenic differentiation. We find an increased rate of CpG methylation in rat Runx2 promoter in TNFα-treated rMSCs, as well as significantly increased occupancy of H3K27me3 in Runx2 gene promoter. The content of TNFα in necrotic tissue is much lower than that of normal tissue. And relevantly, human Runx2 promoter is demethylated in necrotic tissue using bone samples from patient with ONFH. In addition, we have observed that Wnt signaling pathway is inhibited by TNFα as multiple Wnts are markedly decreased in TNFα-treated rMSCs by RNA-seq analysis. Conclusion Taken together, our study shows that TNFα plays complicated roles in the pathogenesis of ONFH, including proliferation, angiogenesis, and osteogenesis. Targeting TNFα should not be considered as an applicable strategy to inhibit the progression of ONFH. Electronic supplementary material The online version of this article (10.1186/s13287-018-1112-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Bin Fang
- Key laboratory of Orthopaedics and Traumatology of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, People's Republic of China.,Department of Orthopaedics Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Baiyun District, Guangzhou, 510405, Guangdong, People's Republic of China
| | - Ding Wang
- Key laboratory of Orthopaedics and Traumatology of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, People's Republic of China
| | - Jiaqian Zheng
- Key laboratory of Orthopaedics and Traumatology of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, People's Republic of China
| | - Qiushi Wei
- Department of Orthopaedics Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Baiyun District, Guangzhou, 510405, Guangdong, People's Republic of China
| | - Dongxiang Zhan
- Key laboratory of Orthopaedics and Traumatology of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, People's Republic of China
| | - Yamei Liu
- Departments of Diagnostics of Traditional Chinese Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, People's Republic of China
| | - Xuesong Yang
- Division of Histology and Embryology, Key Laboratory for Regenerative Medicine of the Ministry of Education, Medical College, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Haibin Wang
- Key laboratory of Orthopaedics and Traumatology of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, People's Republic of China.,Department of Orthopaedics Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Baiyun District, Guangzhou, 510405, Guangdong, People's Republic of China
| | - Gang Li
- Department of Orthopaedics and Traumatology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong, Special Administrative Region of China.
| | - Wei He
- Key laboratory of Orthopaedics and Traumatology of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, People's Republic of China. .,Department of Orthopaedics Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Baiyun District, Guangzhou, 510405, Guangdong, People's Republic of China. .,Laboratory of Orthopaedics and Traumatology, Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, People's Republic of China.
| | - Liangliang Xu
- Key laboratory of Orthopaedics and Traumatology of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, People's Republic of China. .,Department of Orthopaedics Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Baiyun District, Guangzhou, 510405, Guangdong, People's Republic of China. .,Laboratory of Orthopaedics and Traumatology, Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, People's Republic of China.
| |
Collapse
|
62
|
Abstract
The development of the reprogramming technology led to generation of induced Pluripotent Stem Cells (iPSC) from a variety of somatic cells. Ever since, fast growing knowledge of different efficient protocols enabled the differentiation of these iPSCs into different cells types utilized for disease modeling. Indeed, iPSC-derived cells have been increasingly used for investigating molecular and cellular pathophysiological mechanisms underlying inherited diseases. However, a major barrier in the field of iPSC-based disease modeling relies on discriminating between the effects of the causative mutation and the genetic background of these cells. In the past decade, researchers have made great improvement in genome editing techniques, with one of the latest being CRISPR/Cas9. Using a single non-sequence specific protein combined with a small guiding RNA molecule, this state-of-the-art approach enables modifications of genes with high efficiency and accuracy. By so doing, this technique enables the generation of isogenic controls or isogenic mutated cell lines in order to focus on the pathologies caused by a specific mutation. In this article, we review the latest studies combining iPSC and CRISPR/Cas9 technologies for the investigation of the molecular and cellular mechanisms underlying inherited diseases including immunological, metabolic, hematological, neurodegenerative and cardiac diseases.
Collapse
|
63
|
Saetersmoen ML, Hammer Q, Valamehr B, Kaufman DS, Malmberg KJ. Off-the-shelf cell therapy with induced pluripotent stem cell-derived natural killer cells. Semin Immunopathol 2018; 41:59-68. [PMID: 30361801 DOI: 10.1007/s00281-018-0721-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 09/28/2018] [Indexed: 12/15/2022]
Abstract
Cell therapy is emerging as a very promising therapeutic modality against cancer, spearheaded by the clinical success of chimeric antigen receptor (CAR) modified T cells for B cell malignancies. Currently, FDA-approved CAR-T cell products are based on engineering of autologous T cells harvested from the patient, typically using a central manufacturing facility for gene editing before the product can be delivered to the clinic and infused to the patients. For a broader implementation of advanced cell therapy and to reduce costs, it would be advantageous to use allogeneic "universal" cell therapy products that can be stored in cell banks and provided upon request, in a manner analogous to biopharmaceutical drug products. In this review, we outline a roadmap for development of off-the-shelf cell therapy based on natural killer (NK) cells derived from induced pluripotent stem cells (iPSCs). We discuss strategies to engineer iPSC-derived NK (iPSC-NK) cells for enhanced functional potential, persistence, and homing.
Collapse
Affiliation(s)
| | - Quirin Hammer
- Department of Medicine, Huddinge, Karolinska Institute, Solna, Sweden
| | | | - Dan S Kaufman
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Karl-Johan Malmberg
- The KG Jebsen Center for Cancer Immunotherapy, University of Oslo, Oslo, Norway. .,Department of Medicine, Huddinge, Karolinska Institute, Solna, Sweden. .,Institute for Cancer research, Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
64
|
Hu S, Zhao MT, Jahanbani F, Shao NY, Lee WH, Chen H, Snyder MP, Wu JC. Effects of cellular origin on differentiation of human induced pluripotent stem cell-derived endothelial cells. JCI Insight 2018; 1:85558. [PMID: 27398408 DOI: 10.1172/jci.insight.85558] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Human induced pluripotent stem cells (iPSCs) can be derived from various types of somatic cells by transient overexpression of 4 Yamanaka factors (OCT4, SOX2, C-MYC, and KLF4). Patient-specific iPSC derivatives (e.g., neuronal, cardiac, hepatic, muscular, and endothelial cells [ECs]) hold great promise in drug discovery and regenerative medicine. In this study, we aimed to evaluate whether the cellular origin can affect the differentiation, in vivo behavior, and single-cell gene expression signatures of human iPSC-derived ECs. We derived human iPSCs from 3 types of somatic cells of the same individuals: fibroblasts (FB-iPSCs), ECs (EC-iPSCs), and cardiac progenitor cells (CPC-iPSCs). We then differentiated them into ECs by sequential administration of Activin, BMP4, bFGF, and VEGF. EC-iPSCs at early passage (10 < P < 20) showed higher EC differentiation propensity and gene expression of EC-specific markers (PECAM1 and NOS3) than FB-iPSCs and CPC-iPSCs. In vivo transplanted EC-iPSC-ECs were recovered with a higher percentage of CD31+ population and expressed higher EC-specific gene expression markers (PECAM1, KDR, and ICAM) as revealed by microfluidic single-cell quantitative PCR (qPCR). In vitro EC-iPSC-ECs maintained a higher CD31+ population than FB-iPSC-ECs and CPC-iPSC-ECs with long-term culturing and passaging. These results indicate that cellular origin may influence lineage differentiation propensity of human iPSCs; hence, the somatic memory carried by early passage iPSCs should be carefully considered before clinical translation.
Collapse
Affiliation(s)
- Shijun Hu
- Stanford Cardiovascular Institute.,Department of Medicine, Division of Cardiology, and.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA.,Institute for Cardiovascular Science, Soochow University & Department of Cardiovascular Surgery of the First Affiliated Hospital, Suzhou, Jiangsu, China
| | - Ming-Tao Zhao
- Stanford Cardiovascular Institute.,Department of Medicine, Division of Cardiology, and.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Fereshteh Jahanbani
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ning-Yi Shao
- Stanford Cardiovascular Institute.,Department of Medicine, Division of Cardiology, and.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Won Hee Lee
- Stanford Cardiovascular Institute.,Department of Medicine, Division of Cardiology, and.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Haodong Chen
- Stanford Cardiovascular Institute.,Department of Medicine, Division of Cardiology, and.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute.,Department of Medicine, Division of Cardiology, and.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| |
Collapse
|
65
|
Schlaeger TM. Nonintegrating Human Somatic Cell Reprogramming Methods. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 163:1-21. [PMID: 29075799 DOI: 10.1007/10_2017_29] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Traditional biomedical research and preclinical studies frequently rely on animal models and repeatedly draw on a relatively small set of human cell lines, such as HeLa, HEK293, HepG2, HL60, and PANC1 cells. However, animal models often fail to reproduce important clinical phenotypes and conventional cell lines only represent a small number of cell types or diseases, have very limited ethnic/genetic diversity, and either senesce quickly or carry potentially confounding immortalizing mutations. In recent years, human pluripotent stem cells have attracted a lot of attention, in part because these cells promise more precise modeling of human diseases. Expectations are also high that pluripotent stem cell technologies can deliver cell-based therapeutics for the cure of a wide range of degenerative and other diseases. This review focuses on episomal and Sendai viral reprogramming modalities, which are the most popular methods for generating transgene-free human induced pluripotent stem cells (hiPSCs) from easily accessible cell sources. Graphical Abstract.
Collapse
Affiliation(s)
- Thorsten M Schlaeger
- Stem Cell Program, Boston Children's Hospital, Karp RB09213, 1 Blackfan Circle, Boston, MA, 02446, USA.
| |
Collapse
|
66
|
Wang F, Kong J, Cui YY, Liu P, Wen JY. Is Human-induced Pluripotent Stem Cell the Best Optimal? Chin Med J (Engl) 2018; 131:852-856. [PMID: 29578130 PMCID: PMC5887745 DOI: 10.4103/0366-6999.228231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Objective: Since the advent of induced pluripotent stem cell (iPSC) technology a decade ago, enormous progress has been made in stem cell biology and regenerative medicine. Human iPSCs have been widely used for disease modeling, drug discovery, and cell therapy development. In this review, we discuss the progress in applications of iPSC technology that are particularly relevant to drug discovery and regenerative medicine, and consider the remaining challenges and the emerging opportunities in the field. Data Sources: Articles in this review were searched from PubMed database from January 2014 to December 2017. Study Selection: Original articles about iPSCs and cardiovascular diseases were included and analyzed. Results: iPSC holds great promises for human disease modeling, drug discovery, and stem cell-based therapy, and this potential is only beginning to be realized. However, several important issues remain to be addressed. Conclusions: The recent availability of human cardiomyocytes derived from iPSCs opens new opportunities to build in vitro models of cardiac disease, screening for new drugs and patient-specific cardiac therapy.
Collapse
Affiliation(s)
- Feng Wang
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029; Department of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing 100029, China
| | - Jie Kong
- Department of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yi-Yao Cui
- Department of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing 100029, China
| | - Peng Liu
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029; Department of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing 100029, China
| | - Jian-Yan Wen
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029; Department of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing 100029, China
| |
Collapse
|
67
|
Omole AE, Fakoya AOJ. Ten years of progress and promise of induced pluripotent stem cells: historical origins, characteristics, mechanisms, limitations, and potential applications. PeerJ 2018; 6:e4370. [PMID: 29770269 PMCID: PMC5951134 DOI: 10.7717/peerj.4370] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/24/2018] [Indexed: 12/11/2022] Open
Abstract
The discovery of induced pluripotent stem cells (iPSCs) by Shinya Yamanaka in 2006 was heralded as a major breakthrough of the decade in stem cell research. The ability to reprogram human somatic cells to a pluripotent embryonic stem cell-like state through the ectopic expression of a combination of embryonic transcription factors was greeted with great excitement by scientists and bioethicists. The reprogramming technology offers the opportunity to generate patient-specific stem cells for modeling human diseases, drug development and screening, and individualized regenerative cell therapy. However, fundamental questions have been raised regarding the molecular mechanism of iPSCs generation, a process still poorly understood by scientists. The efficiency of reprogramming of iPSCs remains low due to the effect of various barriers to reprogramming. There is also the risk of chromosomal instability and oncogenic transformation associated with the use of viral vectors, such as retrovirus and lentivirus, which deliver the reprogramming transcription factors by integration in the host cell genome. These challenges can hinder the therapeutic prospects and promise of iPSCs and their clinical applications. Consequently, extensive studies have been done to elucidate the molecular mechanism of reprogramming and novel strategies have been identified which help to improve the efficiency of reprogramming methods and overcome the safety concerns linked with iPSC generation. Distinct barriers and enhancers of reprogramming have been elucidated, and non-integrating reprogramming methods have been reported. Here, we summarize the progress and the recent advances that have been made over the last 10 years in the iPSC field, with emphasis on the molecular mechanism of reprogramming, strategies to improve the efficiency of reprogramming, characteristics and limitations of iPSCs, and the progress made in the applications of iPSCs in the field of disease modelling, drug discovery and regenerative medicine. Additionally, this study appraises the role of genomic editing technology in the generation of healthy iPSCs.
Collapse
Affiliation(s)
- Adekunle Ebenezer Omole
- Department of Basic Sciences, American University of Antigua College of Medicine, St. John's, Antigua
| | | |
Collapse
|
68
|
Papatsenko D, Waghray A, Lemischka IR. Feedback control of pluripotency in embryonic stem cells: Signaling, transcription and epigenetics. Stem Cell Res 2018; 29:180-188. [DOI: 10.1016/j.scr.2018.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 02/06/2018] [Accepted: 02/16/2018] [Indexed: 12/19/2022] Open
|
69
|
Gao F, Li J, Zhang H, Yang X, An T. Identifying Candidate Reprogramming Genes in Mouse Induced Pluripotent Stem Cells. Stem Cell Rev Rep 2018; 13:532-541. [PMID: 28063063 DOI: 10.1007/s12015-016-9704-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Factor-based induced reprogramming approaches have tremendous potential for human regenerative medicine, but the efficiencies of these approaches are still low. In this study, we analyzed the global transcriptional profiles of mouse induced pluripotent stem cells (miPSCs) and mouse embryonic stem cells (mESCs) from seven different labs and present here the first successful clustering according to cell type, not by lab of origin. We identified 2131 different expression genes (DEs) as candidate pluripotency-associated genes by comparing mESCs/miPSCs with somatic cells and 720 DEs between miPSCs and mESCs. Interestingly, there was a significant overlap between the two DE sets. Therefore, we defined the overlap DEs as "consensus DEs" including 313 miPSC-specific genes expressed at a higher level in miPSCs versus mESCs and 184 mESC-specific genes in total and reasoned that these may contribute to the differences in pluripotency between mESCs and miPSCs. A classification of "consensus DEs" according to their different expression levels between somatic cells and mESCs/miPSCs shows that 86% of the miPSC-specific genes are more highly expressed in somatic cells, while 73% of mESC-specific genes are highly expressed in mESCs/miPSCs, indicating that the miPSCs have not efficiently silenced the expression pattern of the somatic cells from which they are derived and failed to completely induce the genes with high expression levels in mESCs. We further revealed a strong correlation between oocyte-enriched factors and insufficiently induced mESC-specific genes and identified 11 hub genes via network analysis. In light of these findings, we postulated that these key hub genes might not only drive somatic cell nuclear transfer (SCNT) reprogramming but also augment the efficiency and quality of miPSC reprogramming.
Collapse
Affiliation(s)
- Fang Gao
- College of Life Science, Northeast Forestry University, Harbin, China, 150040
- College of Life Science, Northeast Agricultural University, Harbin, China, 150030
| | - Jingyu Li
- College of Life Science, Northeast Agricultural University, Harbin, China, 150030
- Chong Qing Reproductive and Genetics Institute, Chongqing Obstetrics and Gynecology Hospital, 64 Jing Tang ST, Yu Zhong District , Chongqing, China, 400013
| | - Heng Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China, 150030
| | - Xu Yang
- College of Life Science, Northeast Agricultural University, Harbin, China, 150030
| | - Tiezhu An
- College of Life Science, Northeast Forestry University, Harbin, China, 150040.
| |
Collapse
|
70
|
de Boni L, Gasparoni G, Haubenreich C, Tierling S, Schmitt I, Peitz M, Koch P, Walter J, Wüllner U, Brüstle O. DNA methylation alterations in iPSC- and hESC-derived neurons: potential implications for neurological disease modeling. Clin Epigenetics 2018; 10:13. [PMID: 29422978 PMCID: PMC5789607 DOI: 10.1186/s13148-018-0440-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/04/2018] [Indexed: 12/21/2022] Open
Abstract
Background Genetic predisposition and epigenetic alterations are both considered to contribute to sporadic neurodegenerative diseases (NDDs) such as Parkinson's disease (PD). Since cell reprogramming and the generation of induced pluripotent stem cells (iPSCs) are themselves associated with major epigenetic remodeling, it remains unclear to what extent iPSC-derived neurons lend themselves to model epigenetic disease-associated changes. A key question to be addressed in this context is whether iPSC-derived neurons exhibit epigenetic signatures typically observed in neurons derived from non-reprogrammed human embryonic stem cells (hESCs). Results Here, we compare mature neurons derived from hESC and isogenic human iPSC generated from hESC-derived neural stem cells. Genome-wide 450 K-based DNA methylation and HT12v4 gene array expression analyses were complemented by a deep analysis of selected genes known to be involved in NDD. Our studies show that DNA methylation and gene expression patterns of isogenic hESC- and iPSC-derived neurons are markedly preserved on a genome-wide and single gene level. Conclusions Overall, iPSC-derived neurons exhibit similar DNA methylation patterns compared to isogenic hESC-derived neurons. Further studies will be required to explore whether the epigenetic patterns observed in iPSC-derived neurons correspond to those detectable in native brain neurons.
Collapse
Affiliation(s)
- Laura de Boni
- Department of Neurology, University Hospital of Bonn, Bonn, Germany
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Gilles Gasparoni
- Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Carolin Haubenreich
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Sascha Tierling
- Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Ina Schmitt
- Department of Neurology, University Hospital of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Michael Peitz
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Philipp Koch
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Jörn Walter
- Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Ullrich Wüllner
- Department of Neurology, University Hospital of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| |
Collapse
|
71
|
Induced Pluripotent Stem Cells and Induced Pluripotent Cancer Cells in Cancer Disease Modeling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1119:169-183. [PMID: 30069853 DOI: 10.1007/5584_2018_257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In 2006, Noble Prize laureate Shinya Yamanaka discovered that a set of transcription factors can reprogram terminally differentiated somatic cells to a pluripotent stem cell state. Since then, induced pluripotent stem cells (iPSCs) have come into the public spotlight. Amidst a growing field of promising clinical uses of iPSCs in recent years, cancer disease modeling has emerged as a particularly promising and rapidly translatable application of iPSCs. Technological advances in genome editing over the past few years have facilitated increasingly rapid progress in generation of iPSCs with clearly defined genetic backgrounds to complement existing patient-derived models. Improved protocols for differentiation of iPSCs, engineered iPSCs and embryonic stem cells (ESCs) now permit the study of disease biology in the majority of somatic cell types. Here, we highlight current efforts to create patient-derived iPSC disease models to study various cancer types. We review the advantages and current challenges of using iPSCs in cancer disease modeling.
Collapse
|
72
|
Kim MH, Kino-oka M. Bioprocessing Strategies for Pluripotent Stem Cells Based on Waddington’s Epigenetic Landscape. Trends Biotechnol 2018; 36:89-104. [DOI: 10.1016/j.tibtech.2017.10.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 10/02/2017] [Accepted: 10/10/2017] [Indexed: 12/12/2022]
|
73
|
Genetically unmatched human iPSC and ESC exhibit equivalent gene expression and neuronal differentiation potential. Sci Rep 2017; 7:17504. [PMID: 29235536 PMCID: PMC5727499 DOI: 10.1038/s41598-017-17882-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 12/02/2017] [Indexed: 11/08/2022] Open
Abstract
The potential uniformity between differentiation and therapeutic potential of human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) remains debatable. We studied the gene expression profiles, pathways analysis and the ability to differentiated into neural progenitor cells (NPCs) and motor neurons (MNs) of genetically unmatched integration-free hiPSC versus hESC to highlight possible differences/similarities between them at the molecular level. We also provided the functional information of the neurons derived from the different hESCs and hiPSCs lines using the Neural Muscular Junction (NMJ) Assay. The hiPSC line was generated by transfecting human epidermal fibroblasts (HEF) with episomal DNAs expressing Oct4, Sox2, Klf4, Nanog, L-Myc and shRNA against p53. For the hESCs line, we used the NIH-approved H9 cell line. Using unsupervised clustering both hESCs and hiPSCs were clustered together implying homogeneous genetic states. The genetic profiles of hiPSCs and hESCs were clearly similar but not identical. Collectively, our data indicate close molecular similarities between genetically unmatched hESCs and hiPS in term of gene expression, and signaling pathways. Moreover, both cell types exhibited similar cholinergic motor neurons differentiation potential with marked ability of the differentiated hESCs and hiPSCs-derived MNs to induce contraction of myotubes after 4 days of co-culture.
Collapse
|
74
|
|
75
|
Baghbaderani BA, Syama A, Sivapatham R, Pei Y, Mukherjee O, Fellner T, Zeng X, Rao MS. Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications. Stem Cell Rev Rep 2017; 12:394-420. [PMID: 27283945 PMCID: PMC4919381 DOI: 10.1007/s12015-016-9662-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We have recently described manufacturing of human induced pluripotent stem cells (iPSC) master cell banks (MCB) generated by a clinically compliant process using cord blood as a starting material (Baghbaderani et al. in Stem Cell Reports, 5(4), 647-659, 2015). In this manuscript, we describe the detailed characterization of the two iPSC clones generated using this process, including whole genome sequencing (WGS), microarray, and comparative genomic hybridization (aCGH) single nucleotide polymorphism (SNP) analysis. We compare their profiles with a proposed calibration material and with a reporter subclone and lines made by a similar process from different donors. We believe that iPSCs are likely to be used to make multiple clinical products. We further believe that the lines used as input material will be used at different sites and, given their immortal status, will be used for many years or even decades. Therefore, it will be important to develop assays to monitor the state of the cells and their drift in culture. We suggest that a detailed characterization of the initial status of the cells, a comparison with some calibration material and the development of reporter sublcones will help determine which set of tests will be most useful in monitoring the cells and establishing criteria for discarding a line.
Collapse
Affiliation(s)
| | - Adhikarla Syama
- Centre for Brain development and Repair, Institute of Stem Cells and Regenerative Medicine (InSTEM), Bangalore, India
| | | | | | - Odity Mukherjee
- Centre for Brain development and Repair, Institute of Stem Cells and Regenerative Medicine (InSTEM), Bangalore, India
| | | | - Xianmin Zeng
- Buck Institute for Researching on Aging, Novato, CA, USA.,XCell Science, Novato, CA, USA
| | - Mahendra S Rao
- NxCell Inc, Novato, CA, USA. .,Q therapeutics, Salt Lake City, UT, USA.
| |
Collapse
|
76
|
OCT4 impedes cell fate redirection by the melanocyte lineage master regulator MITF in mouse ESCs. Nat Commun 2017; 8:1022. [PMID: 29044103 PMCID: PMC5647326 DOI: 10.1038/s41467-017-01122-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 08/19/2017] [Indexed: 11/09/2022] Open
Abstract
Ectopic expression of lineage master regulators induces transdifferentiation. Whether cell fate transitions can be induced during various developmental stages has not been systemically examined. Here we discover that amongst different developmental stages, mouse embryonic stem cells (mESCs) are resistant to cell fate conversion induced by the melanocyte lineage master regulator MITF. By generating a transgenic system we exhibit that in mESCs, the pluripotency master regulator Oct4, counteracts pro-differentiation induced by Mitf by physical interference with MITF transcriptional activity. We further demonstrate that mESCs must be released from Oct4-maintained pluripotency prior to ectopically induced differentiation. Moreover, Oct4 induction in various differentiated cells represses their lineage identity in vivo. Alongside, chromatin architecture combined with ChIP-seq analysis suggest that Oct4 competes with various lineage master regulators for binding promoters and enhancers. Our analysis reveals pluripotency and transdifferentiation regulatory principles and could open new opportunities in the field of regenerative medicine.
Collapse
|
77
|
Lin Y, Gil CH, Yoder MC. Differentiation, Evaluation, and Application of Human Induced Pluripotent Stem Cell-Derived Endothelial Cells. Arterioscler Thromb Vasc Biol 2017; 37:2014-2025. [PMID: 29025705 DOI: 10.1161/atvbaha.117.309962] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/26/2017] [Indexed: 12/13/2022]
Abstract
The emergence of induced pluripotent stem cell (iPSC) technology paves the way to generate large numbers of patient-specific endothelial cells (ECs) that can be potentially delivered for regenerative medicine in patients with cardiovascular disease. In the last decade, numerous protocols that differentiate EC from iPSC have been developed by many groups. In this review, we will discuss several common strategies that have been optimized for human iPSC-EC differentiation and subsequent studies that have evaluated the potential of human iPSC-EC as a cell therapy or as a tool in disease modeling. In addition, we will emphasize the importance of using in vivo vessel-forming ability and in vitro clonogenic colony-forming potential as a gold standard with which to evaluate the quality of human iPSC-EC derived from various protocols.
Collapse
Affiliation(s)
- Yang Lin
- From the Department of Pediatrics, Herman B. Wells Center for Pediatric Research (Y.L., C.-H.G., M.C.Y.) and Department of Biochemistry and Molecular Biology (Y.L., M.C.Y.), Indiana University School of Medicine, Indianapolis
| | - Chang-Hyun Gil
- From the Department of Pediatrics, Herman B. Wells Center for Pediatric Research (Y.L., C.-H.G., M.C.Y.) and Department of Biochemistry and Molecular Biology (Y.L., M.C.Y.), Indiana University School of Medicine, Indianapolis
| | - Mervin C Yoder
- From the Department of Pediatrics, Herman B. Wells Center for Pediatric Research (Y.L., C.-H.G., M.C.Y.) and Department of Biochemistry and Molecular Biology (Y.L., M.C.Y.), Indiana University School of Medicine, Indianapolis.
| |
Collapse
|
78
|
Transcriptomic and epigenomic differences in human induced pluripotent stem cells generated from six reprogramming methods. Nat Biomed Eng 2017; 1:826-837. [PMID: 30263871 DOI: 10.1038/s41551-017-0141-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Many reprogramming methods can generate human induced pluripotent stem cells (hiPSCs) that closely resemble human embryonic stem cells (hESCs). This has led to assessments of how similar hiPSCs are to hESCs, by evaluating differences in gene expression, epigenetic marks and differentiation potential. However, all previous studies were performed using hiPSCs acquired from different laboratories, passage numbers, culturing conditions, genetic backgrounds and reprogramming methods, all of which may contribute to the reported differences. Here, by using high-throughput sequencing under standardized cell culturing conditions and passage number, we compare the epigenetic signatures (H3K4me3, H3K27me3 and HDAC2 ChIP-seq profiles) and transcriptome differences (by RNA-seq) of hiPSCs generated from the same primary fibroblast population by using six different reprogramming methods. We found that the reprogramming method impacts the resulting transcriptome and that all hiPSC lines could terminally differentiate, regardless of the reprogramming method. Moreover, by comparing the differences between the hiPSC and hESC lines, we observed a significant proportion of differentially expressed genes that could be attributed to polycomb repressive complex targets.
Collapse
|
79
|
Ortmann D, Vallier L. Variability of human pluripotent stem cell lines. Curr Opin Genet Dev 2017; 46:179-185. [DOI: 10.1016/j.gde.2017.07.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/07/2017] [Accepted: 07/14/2017] [Indexed: 12/23/2022]
|
80
|
Sharma V, Malgulwar PB, Purkait S, Patil V, Pathak P, Agrawal R, Kulshreshtha R, Mallick S, Julka PK, Suri A, Sharma BS, Suri V, Sharma MC, Sarkar C. Genome-wide ChIP-seq analysis of EZH2-mediated H3K27me3 target gene profile highlights differences between low- and high-grade astrocytic tumors. Carcinogenesis 2017; 38:152-161. [PMID: 27993893 DOI: 10.1093/carcin/bgw126] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/30/2016] [Indexed: 01/19/2023] Open
Abstract
Enhancer of zeste homolog-2(EZH2) is a key epigenetic regulator that functions as oncogene and also known for inducing altered trimethylation of histone at lysine-27 (H3K27me3) mark in various tumors. However, H3K27me3 targets and their precise relationship with gene expression are largely unknown in astrocytic tumors. In this study, we checked EZH2 messenger RNA and protein expression in 90 astrocytic tumors of different grades using quantitative PCR and immunohistochemistry, respectively. Further, genome-wide ChIP-seq analysis for H3K27me3 modification was also performed on 11 glioblastomas (GBMs) and 2 diffuse astrocytoma (DA) samples. Our results showed EZH2 to be highly overexpressed in astrocytic tumors with a significant positive correlation with grade. Interestingly, ChIP-seq mapping revealed distinct differences in genes and pathways targeted by these H3K27me3 modifications between GBM versus DA. Neuroactive ligand receptor pathway was found most enriched in GBM (P = 9.4 × 10-25), whereas DA were found to be enriched in metabolic pathways. Also, GBM showed a higher enrichment of H3K27me3 targets reported in embryonic stem cells and glioma stem cells as compared with DAs. Our results show majority of these H3K27me3 target genes were downregulated, not only due to H3K27me3 modification but also due to concomitant DNA methylation. Further, H3K27me3 modification-associated gene silencing was not restricted to promoter but also present in gene body and transcription start site regions. To the best of our knowledge, this is the first high-resolution genome-wide mapping of H3K27me3 modification in adult astrocytic primary tissue samples of human, highlighting the differences between grades. Interestingly, we identified SLC25A23 as important target of H3K27me3 modification, which was downregulated in GBM and its low expression was associated with poor prognosis in GBMs.
Collapse
Affiliation(s)
- Vikas Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Suvendu Purkait
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Vikas Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rahul Agrawal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | | | | | - Ashish Suri
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Bhawani Shankar Sharma
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| |
Collapse
|
81
|
Abstract
It is extremely rare for a single experiment to be so impactful and timely that it shapes and forecasts the experiments of the next decade. Here, we review how two such experiments-the generation of human induced pluripotent stem cells (iPSCs) and the development of CRISPR/Cas9 technology-have fundamentally reshaped our approach to biomedical research, stem cell biology, and human genetics. We will also highlight the previous knowledge that iPSC and CRISPR/Cas9 technologies were built on as this groundwork demonstrated the need for solutions and the benefits that these technologies provided and set the stage for their success.
Collapse
Affiliation(s)
- Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Rudolf Jaenisch
- The Whitehead Institute for Biomedical Research and Department of Biology, MIT, Cambridge, MA 02142, USA
| |
Collapse
|
82
|
Papapetrou EP. Patient-derived induced pluripotent stem cells in cancer research and precision oncology. Nat Med 2017; 22:1392-1401. [PMID: 27923030 DOI: 10.1038/nm.4238] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/21/2016] [Indexed: 12/13/2022]
Abstract
Together with recent advances in the processing and culture of human tissue, bioengineering, xenotransplantation and genome editing, Induced pluripotent stem cells (iPSCs) present a range of new opportunities for the study of human cancer. Here we discuss the main advantages and limitations of iPSC modeling, and how the method intersects with other patient-derived models of cancer, such as organoids, organs-on-chips and patient-derived xenografts (PDXs). We highlight the opportunities that iPSC models can provide beyond those offered by existing systems and animal models and present current challenges and crucial areas for future improvements toward wider adoption of this technology.
Collapse
Affiliation(s)
- Eirini P Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
83
|
Mullen AC, Wrana JL. TGF-β Family Signaling in Embryonic and Somatic Stem-Cell Renewal and Differentiation. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a022186. [PMID: 28108485 DOI: 10.1101/cshperspect.a022186] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Soon after the discovery of transforming growth factor-β (TGF-β), seminal work in vertebrate and invertebrate models revealed the TGF-β family to be central regulators of tissue morphogenesis. Members of the TGF-β family direct some of the earliest cell-fate decisions in animal development, coordinate complex organogenesis, and contribute to tissue homeostasis in the adult. Here, we focus on the role of the TGF-β family in mammalian stem-cell biology and discuss its wide and varied activities both in the regulation of pluripotency and in cell-fate commitment.
Collapse
Affiliation(s)
- Alan C Mullen
- Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbam Research Institute, Mount Sinai Hospital and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1X5, Canada
| |
Collapse
|
84
|
Sayed N, Liu C, Wu JC. Translation of Human-Induced Pluripotent Stem Cells: From Clinical Trial in a Dish to Precision Medicine. J Am Coll Cardiol 2017; 67:2161-2176. [PMID: 27151349 DOI: 10.1016/j.jacc.2016.01.083] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/26/2016] [Accepted: 01/26/2016] [Indexed: 12/14/2022]
Abstract
The prospect of changing the plasticity of terminally differentiated cells toward pluripotency has completely altered the outlook for biomedical research. Human-induced pluripotent stem cells (iPSCs) provide a new source of therapeutic cells free from the ethical issues or immune barriers of human embryonic stem cells. iPSCs also confer considerable advantages over conventional methods of studying human diseases. Since its advent, iPSC technology has expanded with 3 major applications: disease modeling, regenerative therapy, and drug discovery. Here we discuss, in a comprehensive manner, the recent advances in iPSC technology in relation to basic, clinical, and population health.
Collapse
Affiliation(s)
- Nazish Sayed
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California.
| | - Chun Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California.
| |
Collapse
|
85
|
Nucleosome eviction along with H3K9ac deposition enhances Sox2 binding during human neuroectodermal commitment. Cell Death Differ 2017; 24:1121-1131. [PMID: 28475175 PMCID: PMC5442478 DOI: 10.1038/cdd.2017.62] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 02/06/2023] Open
Abstract
Neuroectoderm is an important neural precursor. However, chromatin remodeling and its epigenetic regulatory roles during the differentiation of human neuroectodermal cells (hNECs) from human embryonic stem cells (hESCs) remain largely unexplored. Here, we obtained hNECs through directed differentiation from hESCs, and determined chromatin states in the two cell types. Upon differentiation, H2A.Z-mediated nucleosome depletion leads to an open chromatin structure in promoters and upregulates expression of neuroectodermal genes. Increase in H3K9ac signals and decrease in H3K27me3 signals in promoters result in an active chromatin state and activate neuroectodermal genes. Conversely, decrease in H3K9ac signals and increase in H3K27me3 signals in promoters repress pluripotency genes. Moreover, H3K9ac signals facilitate the pluripotency factor Sox2 binding to target sites unique to hNECs. Knockdown of the acetyltransferase Kat2b erases H3K9ac signals, disrupts Sox2 binding, and fails the differentiation. Our results demonstrate a hierarchy of epigenetic regulation of gene expression during the differentiation of hNECs from hESCs through chromatin remodeling.
Collapse
|
86
|
The potential of induced pluripotent stem cells as a tool to study skeletal dysplasias and cartilage-related pathologic conditions. Osteoarthritis Cartilage 2017; 25:616-624. [PMID: 27919783 DOI: 10.1016/j.joca.2016.11.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 11/10/2016] [Accepted: 11/28/2016] [Indexed: 02/07/2023]
Abstract
The development of induced pluripotent stem cells (iPSCs) technology has opened up new horizons for development of new research tools especially for skeletal dysplasias, which often lack human disease models. Regenerative medicine and tissue engineering could be the next areas to benefit from refinement of iPSC methods to repair focal cartilage defects, while applications for osteoarthritis (OA) and drug screening have evolved rather slowly. Although the advances in iPSC research of skeletal dysplasias and repair of focal cartilage lesions are not directly relevant to OA, they can be considered to pave the way to future prospects and solutions to OA research, too. The same problems which face the present cell-based treatments of cartilage injuries concern also the iPSC-based ones. However, established iPSC lines, which have no genomic aberrations and which efficiently differentiate into extracellular matrix secreting chondrocytes, could be an invaluable cell source for cell transplantations in the future. The safety issues concerning the recipient risks of teratoma formation and immune response still have to be solved before the potential use of iPSCs in cartilage repair of focal cartilage defects and OA.
Collapse
|
87
|
Ardhanareeswaran K, Mariani J, Coppola G, Abyzov A, Vaccarino FM. Human induced pluripotent stem cells for modelling neurodevelopmental disorders. Nat Rev Neurol 2017; 13:265-278. [PMID: 28418023 DOI: 10.1038/nrneurol.2017.45] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We currently have a poor understanding of the pathogenesis of neurodevelopmental disorders, owing to the fact that postmortem and imaging studies can only measure the postnatal status quo and offer little insight into the processes that give rise to the observed outcomes. Human induced pluripotent stem cells (hiPSCs) should, in principle, prove powerful for elucidating the pathways that give rise to neurodevelopmental disorders. hiPSCs are embryonic-stem-cell-like cells that can be derived from somatic cells. They retain the unique genetic signature of the individual from whom they were derived, and thus enable researchers to recapitulate that individual's idiosyncratic neural development in a dish. In the case of individuals with disease, we can re-enact the disease-altered trajectory of brain development and examine how and why phenotypic and molecular abnormalities arise in these diseased brains. Here, we review hiPSC biology and possible experimental designs when using hiPSCs to model disease. We then discuss existing hiPSC models of neurodevelopmental disorders. Our hope is that, as some studies have already shown, hiPSCs will illuminate the pathophysiology of developmental disorders of the CNS and lead to therapeutic options for the millions that are affected by these conditions.
Collapse
Affiliation(s)
- Karthikeyan Ardhanareeswaran
- Child Study Center, Yale University School of Medicine, 230 South Frontage Road, New Haven, Connecticut 06520, USA
| | - Jessica Mariani
- Child Study Center, Yale University School of Medicine, 230 South Frontage Road, New Haven, Connecticut 06520, USA
| | - Gianfilippo Coppola
- Child Study Center, Yale University School of Medicine, 230 South Frontage Road, New Haven, Connecticut 06520, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - Flora M Vaccarino
- Child Study Center, Yale University School of Medicine, 230 South Frontage Road, New Haven, Connecticut 06520, USA.,Department of Neuroscience, Yale Kavli Institute for Neuroscience, Yale University School of Medicine, 200 South Frontage Road, New Haven, Connecticut 06510, USA
| |
Collapse
|
88
|
Natalwala A, Kunath T. Preparation, characterization, and banking of clinical-grade cells for neural transplantation: Scale up, fingerprinting, and genomic stability of stem cell lines. PROGRESS IN BRAIN RESEARCH 2017; 230:133-150. [PMID: 28552226 DOI: 10.1016/bs.pbr.2017.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Parkinson's disease is a complex and progressive neurodegenerative condition that is characterized by the severe loss of midbrain dopaminergic (mDA) neurons, which innervate the striatum. Cell transplantation therapies to rebuild this dopaminergic network have been attempted for over 30 years. The most promising outcomes were observed when human fetal mesencephalic tissue was used as the source of cells for transplantation. However, reliance on terminations for a Parkinson's therapy presents significant logistical and ethical hurdles. An alternative source of transplantable mDA neurons is urgently needed, and the solution may come from human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs). Protocols to differentiate hESCs/iPSCs toward mDA neurons are now robust and efficient, and upon grafting the cells rescue preclinical animal models of Parkinson's disease. The challenge now is to apply Good Manufacturing Practice (GMP) to the academic discoveries and protocols to produce clinical-grade transplantable mDA cells. Major technical and logistical considerations include (i) source of hESC or iPSC line, (ii) GMP compliance of the differentiation protocol and all reagents, (iii) characterization of the cell product in terms of identity, safety, and efficacy, (iv) characterization of genomic state and stability, and (v) banking of a transplantation-ready cell product. Approaches and solutions to these challenges are reviewed here.
Collapse
Affiliation(s)
- Ammar Natalwala
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom; Translational Neurosurgery Group, Western General Hospital, Crewe Road South, Edinburgh, United Kingdom
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
| |
Collapse
|
89
|
C9ORF135 encodes a membrane protein whose expression is related to pluripotency in human embryonic stem cells. Sci Rep 2017; 7:45311. [PMID: 28345668 PMCID: PMC5366912 DOI: 10.1038/srep45311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/23/2017] [Indexed: 12/14/2022] Open
Abstract
Human embryonic stem cells (hESCs) are a unique population of cells defined by their capacity for self-renewal and pluripotency. Here, we identified a previously uncharacterized gene in hESCs, C9ORF135, which is sharply downregulated during gastrulation and gametogenesis, along with the pluripotency factors OCT4, SOX2, and NANOG. Human ESCs express two C9ORF135 isoforms, the longer of which encodes a membrane-associated protein, as determined by immunostaining and western blotting of fractionated cell lysates. Moreover, the results of chromatin immunoprecipitation (ChIP), mass spectrometry (MS), and co-immunoprecipitation (co-IP) analyses demonstrated that C9ORF135 expression is regulated by OCT4 and SOX2 and that C9ORF135 interacts with non-muscle myosin IIA and myosin IIB. Collectively, these data indicated that C9ORF135 encodes a membrane-associated protein that may serve as a surface marker for undifferentiated hESCs.
Collapse
|
90
|
Rohart F, Eslami A, Matigian N, Bougeard S, Lê Cao KA. MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. BMC Bioinformatics 2017; 18:128. [PMID: 28241739 PMCID: PMC5327533 DOI: 10.1186/s12859-017-1553-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/16/2017] [Indexed: 12/12/2022] Open
Abstract
Background Molecular signatures identified from high-throughput transcriptomic studies often have poor reliability and fail to reproduce across studies. One solution is to combine independent studies into a single integrative analysis, additionally increasing sample size. However, the different protocols and technological platforms across transcriptomic studies produce unwanted systematic variation that strongly confounds the integrative analysis results. When studies aim to discriminate an outcome of interest, the common approach is a sequential two-step procedure; unwanted systematic variation removal techniques are applied prior to classification methods. Results To limit the risk of overfitting and over-optimistic results of a two-step procedure, we developed a novel multivariate integration method, MINT, that simultaneously accounts for unwanted systematic variation and identifies predictive gene signatures with greater reproducibility and accuracy. In two biological examples on the classification of three human cell types and four subtypes of breast cancer, we combined high-dimensional microarray and RNA-seq data sets and MINT identified highly reproducible and relevant gene signatures predictive of a given phenotype. MINT led to superior classification and prediction accuracy compared to the existing sequential two-step procedures. Conclusions MINT is a powerful approach and the first of its kind to solve the integrative classification framework in a single step by combining multiple independent studies. MINT is computationally fast as part of the mixOmics R CRAN package, available at http://www.mixOmics.org/mixMINT/and http://cran.r-project.org/web/packages/mixOmics/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1553-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Florian Rohart
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, 4102, QLD, Australia
| | - Aida Eslami
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC V6Z 1Y6, Canada
| | - Nicholas Matigian
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, 4102, QLD, Australia
| | - Stéphanie Bougeard
- French agency for food, environmental and occupational health safety (Anses), Department of Epidemiology, Ploufragan, 22440, France
| | - Kim-Anh Lê Cao
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, 4102, QLD, Australia.
| |
Collapse
|
91
|
Synergetic effects of DNA methylation and histone modification during mouse induced pluripotent stem cell generation. Sci Rep 2017; 7:39527. [PMID: 28155862 PMCID: PMC5290738 DOI: 10.1038/srep39527] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/23/2016] [Indexed: 12/14/2022] Open
Abstract
DNA methylation and histone methylation (H3K27me3) have been reported as major barriers to induced pluripotent stem cell (iPSC) generation using four core transcription factors (Oct4, Sox2, Klf4, and c-Myc, termed OSKM). Here, to illustrate the possibility of deriving iPSCs via demethylation, as well as the exact effects of DNA methylation and histone modification on gene expression regulation, we performed RNA sequencing to characterize the transcriptomes of ES cells and iPSCs derived by demethylation with miR-29b or shDnmt3a, and carried out integrated analyses. Results showed that OSKM + miR-29b-iPSC was more close to ES cells than the others, and up-regulated genes typically presented with methylated CpG-dense promoters and H3K27me3-enriched regions. The differentially expressed genes caused by introduction of DNA demethylation during somatic cell reprogramming mainly focus on stem cell associated GO terms and KEGG signaling pathways, which may decrease the tumorigenesis risk of iPSCs. These findings indicated that DNA methylation and histone methylation have synergetic effects on regulating gene expression during iPSC generation, and demethylation by miR-29b is better than shDnmt3a for iPSC quality. Furthermore, integrated analyses are superior for exploration of slight differences as missed by individual analysis.
Collapse
|
92
|
Park J, Kwon YW, Ham S, Hong CP, Seo S, Choe MK, Shin SI, Lee CS, Kim HS, Roh TY. Identification of the early and late responder genes during the generation of induced pluripotent stem cells from mouse fibroblasts. PLoS One 2017; 12:e0171300. [PMID: 28152015 PMCID: PMC5289558 DOI: 10.1371/journal.pone.0171300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/19/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The generation of induced pluripotent stem cell (iPSC), a substitute for embryonic stem cell (ESC), requires the proper orchestration of a transcription program at the chromatin level. Our recent approach for the induction of pluripotent stem cells from fibroblasts using protein extracts from mouse ESCs could overcome the potential tumorigenicity risks associated with random retroviral integration. Here, we examine the epigenetic modifications and the transcriptome of two types of iPSC and of partially reprogrammed iPSCs (iPSCp) generated independently from adult cardiac and skin fibroblasts to assess any perturbations of the transcription program during reprogramming. RESULTS The comparative dissection of the transcription profiles and histone modification patterns at lysines 4 and 27 of histone H3 of the iPSC, iPSCp, ESC, and somatic cells revealed that the iPSC was almost completely comparable to the ESC, regardless of their origins, whereas the genes of the iPSCp were dysregulated to a larger extent. Regardless of the origins of the somatic cells, the fibroblasts induced using the ESC protein extracts appear to be completely reprogrammed into pluripotent cells, although they show unshared marginal differences in their gene expression programs, which may not affect the maintenance of stemness. A comparative investigation of the iPSCp generated by unwanted reprogramming showed that the two groups of genes on the pathway from somatic cells to iPSC might function as sequential reprogramming-competent early and late responders to the induction stimulus. Moreover, some of the divergent genes expressed only in the iPSCp were associated with many tumor-related pathways. CONCLUSIONS Faithful transcriptional reprogramming should follow epigenetic alterations to generate induced pluripotent stem cells from somatic cells. This genome-wide comparison enabled us to define the early and late responder genes during the cell reprogramming process to iPSC. Our results indicate that the cellular responsiveness to external stimuli should be pre-determined and sequentially orchestrated through the tight modulation of the chromatin environment during cell reprogramming to prevent unexpected reprogramming.
Collapse
Affiliation(s)
- Jihwan Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Yoo-Wook Kwon
- National Research Laboratory for Stem Cell Niche, Seoul National University College of Medicine, Seoul, Republic of Korea
- Innovative Research Institute for Cell Therapy and Cardiovascular Center & Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seokjin Ham
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Chang-Pyo Hong
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Seonghye Seo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Moon Kyung Choe
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - So-I Shin
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Choon-Soo Lee
- National Research Laboratory for Stem Cell Niche, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyo-Soo Kim
- National Research Laboratory for Stem Cell Niche, Seoul National University College of Medicine, Seoul, Republic of Korea
- Innovative Research Institute for Cell Therapy and Cardiovascular Center & Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- * E-mail:
| |
Collapse
|
93
|
Fossati V, Jain T, Sevilla A. The silver lining of induced pluripotent stem cell variation. Stem Cell Investig 2016; 3:86. [PMID: 28066788 DOI: 10.21037/sci.2016.11.16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 11/23/2016] [Indexed: 11/06/2022]
Abstract
Induced pluripotent stem cells (iPSCs) are being generated using various reprogramming methods and from different cell sources. Hence, a lot of effort has been devoted to evaluating the differences among iPSC lines, in particular with respect to their differentiation capacity. While line-to-line variability should mainly reflect the genetic diversity within the human population, here we review some studies that have brought attention to additional variation caused by genomic and epigenomic alterations. We discuss strategies to evaluate aberrant changes and to minimize technical and culture-induced noise, in order to generate safe cells for clinical applications. We focus on the findings from a recent study, which compared the differentiation capacity of several iPSC lines committed to the hematopoietic lineage and correlated the differential maturation capacity with aberrant DNA methylations. Although iPSC variation represents a challenge for the field, we embrace the authors' perspective that iPSC variations should be used to our advantage for predicting and selecting the best performing iPSC lines, depending on the desired application.
Collapse
Affiliation(s)
- Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, NY 10023, USA
| | - Tanya Jain
- The New York Stem Cell Foundation Research Institute, New York, NY 10023, USA
| | - Ana Sevilla
- The New York Stem Cell Foundation Research Institute, New York, NY 10023, USA
| |
Collapse
|
94
|
Abstract
Pluripotent stem cells (PSCs) can differentiate into virtually any cell type in the body, making them attractive for both regenerative medicine and drug discovery. Over the past 10 years, technological advances and innovative platforms have yielded first-in-man PSC-based clinical trials and opened up new approaches for disease modeling and drug development. Induced PSCs have become the foremost alternative to embryonic stem cells and accelerated the development of disease-in-a-dish models. Over the years and with each new discovery, PSCs have proven to be extremely versatile. This review article highlights key advancements in PSC research, from 2006 to 2016, and how they will guide the direction of the field over the next decade.
Collapse
Affiliation(s)
- Erin A Kimbrel
- Astellas Institute for Regenerative Medicine, 33 Locke Drive, Marlborough, MA 01752, USA
| | - Robert Lanza
- Astellas Institute for Regenerative Medicine, 33 Locke Drive, Marlborough, MA 01752, USA
| |
Collapse
|
95
|
Grzybek M, Golonko A, Walczak M, Lisowski P. Epigenetics of cell fate reprogramming and its implications for neurological disorders modelling. Neurobiol Dis 2016; 99:84-120. [PMID: 27890672 DOI: 10.1016/j.nbd.2016.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 11/03/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
The reprogramming of human induced pluripotent stem cells (hiPSCs) proceeds in a stepwise manner with reprogramming factors binding and epigenetic composition changes during transition to maintain the epigenetic landscape, important for pluripotency. There arises a question as to whether the aberrant epigenetic state after reprogramming leads to epigenetic defects in induced stem cells causing unpredictable long term effects in differentiated cells. In this review, we present a comprehensive view of epigenetic alterations accompanying reprogramming, cell maintenance and differentiation as factors that influence applications of hiPSCs in stem cell based technologies. We conclude that sample heterogeneity masks DNA methylation signatures in subpopulations of cells and thus believe that beside a genetic evaluation, extensive epigenomic screening should become a standard procedure to ensure hiPSCs state before they are used for genome editing and differentiation into neurons of interest. In particular, we suggest that exploitation of the single-cell composition of the epigenome will provide important insights into heterogeneity within hiPSCs subpopulations to fast forward development of reliable hiPSC-based analytical platforms in neurological disorders modelling and before completed hiPSC technology will be implemented in clinical approaches.
Collapse
Affiliation(s)
- Maciej Grzybek
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-950 Lublin, Poland; Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Aleksandra Golonko
- Department of Biotechnology, Faculty of Civil and Environmental Engineering, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland.
| | - Marta Walczak
- Department of Animal Behavior, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Pawel Lisowski
- Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland; iPS Cell-Based Disease Modelling Group, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany.
| |
Collapse
|
96
|
Gomez NC, Hepperla AJ, Dumitru R, Simon JM, Fang F, Davis IJ. Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer. Cell Rep 2016; 17:1607-1620. [PMID: 27806299 PMCID: PMC5267842 DOI: 10.1016/j.celrep.2016.10.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 06/02/2016] [Accepted: 10/02/2016] [Indexed: 11/15/2022] Open
Abstract
Chromatin regulation is critical for differentiation and disease. However, features linking the chromatin environment of stem cells with disease remain largely unknown. We explored chromatin accessibility in embryonic and multipotent stem cells and unexpectedly identified widespread chromatin accessibility at repetitive elements. Integrating genomic and biochemical approaches, we demonstrate that these sites of increased accessibility are associated with well-positioned nucleosomes marked by distinct histone modifications. Differentiation is accompanied by chromatin remodeling at repetitive elements associated with altered expression of genes in relevant developmental pathways. Remarkably, we found that the chromatin environment of Ewing sarcoma, a mesenchymally derived tumor, is shared with primary mesenchymal stem cells (MSCs). Accessibility at repetitive elements in MSCs offers a permissive environment that is exploited by the critical oncogene responsible for this cancer. Our data demonstrate that stem cells harbor a unique chromatin landscape characterized by accessibility at repetitive elements, a feature associated with differentiation and oncogenesis.
Collapse
Affiliation(s)
- Nicholas C Gomez
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Austin J Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Raluca Dumitru
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Human Pluripotent Stem Cell Core Facility, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Fang Fang
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|
97
|
Hirsch CL, Wrana JL, Dent SYR. KATapulting toward Pluripotency and Cancer. J Mol Biol 2016; 429:1958-1977. [PMID: 27720985 DOI: 10.1016/j.jmb.2016.09.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/30/2016] [Indexed: 12/20/2022]
Abstract
Development is generally regarded as a unidirectional process that results in the acquisition of specialized cell fates. During this process, cellular identity is precisely defined by signaling cues that tailor the chromatin landscape for cell-specific gene expression programs. Once established, these pathways and cell states are typically resistant to disruption. However, loss of cell identity occurs during tumor initiation and upon injury response. Moreover, terminally differentiated cells can be experimentally provoked to become pluripotent. Chromatin reorganization is key to the establishment of new gene expression signatures and thus new cell identity. Here, we explore an emerging concept that lysine acetyltransferase (KAT) enzymes drive cellular plasticity in the context of somatic cell reprogramming and tumorigenesis.
Collapse
Affiliation(s)
- Calley L Hirsch
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada.
| | - Jeffrey L Wrana
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Sharon Y R Dent
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA.
| |
Collapse
|
98
|
Ahmadian Baghbaderani B, Tian X, Scotty Cadet J, Shah K, Walde A, Tran H, Kovarcik DP, Clarke D, Fellner T. A Newly Defined and Xeno-Free Culture Medium Supports Every-Other-Day Medium Replacement in the Generation and Long-Term Cultivation of Human Pluripotent Stem Cells. PLoS One 2016; 11:e0161229. [PMID: 27606941 PMCID: PMC5016087 DOI: 10.1371/journal.pone.0161229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 08/02/2016] [Indexed: 12/12/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) present an unprecedented opportunity to advance human health by offering an alternative and renewable cell resource for cellular therapeutics and regenerative medicine. The present demand for high quality hPSCs for use in both research and clinical studies underscores the need to develop technologies that will simplify the cultivation process and control variability. Here we describe the development of a robust, defined and xeno-free hPSC medium that supports reliable propagation of hPSCs and generation of human induced pluripotent stem cells (hiPSCs) from multiple somatic cell types; long-term serial subculturing of hPSCs with every-other-day (EOD) medium replacement; and banking fully characterized hPSCs. The hPSCs cultured in this medium for over 40 passages are genetically stable, retain high expression levels of the pluripotency markers TRA-1-60, TRA-1-81, Oct-3/4 and SSEA-4, and readily differentiate into ectoderm, mesoderm and endoderm. Importantly, the medium plays an integral role in establishing a cGMP-compliant process for the manufacturing of hiPSCs that can be used for generation of clinically relevant cell types for cell replacement therapy applications.
Collapse
Affiliation(s)
| | - Xinghui Tian
- Lonza Walkersville, Inc., Walkersville, MD, United States of America
| | - Jean Scotty Cadet
- Lonza Walkersville, Inc., Walkersville, MD, United States of America
| | - Kevan Shah
- Lonza Walkersville, Inc., Walkersville, MD, United States of America
| | - Amy Walde
- Lonza Walkersville, Inc., Walkersville, MD, United States of America
| | - Huan Tran
- Lonza Walkersville, Inc., Walkersville, MD, United States of America
| | - Don Paul Kovarcik
- Lonza Walkersville, Inc., Walkersville, MD, United States of America
| | - Diana Clarke
- Lonza Walkersville, Inc., Walkersville, MD, United States of America
| | - Thomas Fellner
- Lonza Walkersville, Inc., Walkersville, MD, United States of America
| |
Collapse
|
99
|
Chamberlain SJ. Disease modelling using human iPSCs. Hum Mol Genet 2016; 25:R173-R181. [PMID: 27493026 DOI: 10.1093/hmg/ddw209] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 12/17/2022] Open
Affiliation(s)
- Stormy J Chamberlain
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| |
Collapse
|
100
|
Abstract
The ability to reprogram somatic cells into induced pluripotent stem cells (iPSCs) using defined factors provides new tools for biomedical research. However, some iPSC clones display tumorigenic and immunogenic potential, thus raising concerns about their utility and safety in the clinical setting. Furthermore, variability in iPSC differentiation potential has also been described. Here we discuss whether these therapeutic obstacles are specific to transcription-factor-mediated reprogramming or inherent to every cellular reprogramming method. Finally, we address whether a better understanding of the mechanism underlying the reprogramming process might improve the fidelity of reprogramming and, therefore, the iPSC quality.
Collapse
Affiliation(s)
- Natalia Tapia
- Institute of Biomedicine of Valencia, Spanish National Research Council, Jaime Roig 11, 46010 Valencia, Spain.
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany; Medical Faculty, University of Münster, Domagkstraße 3, 48149 Münster, Germany.
| |
Collapse
|