151
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Comparison of Magnetic Resonance Imaging and Serum Biomarkers for Detection of Human Pluripotent Stem Cell-Derived Teratomas. Stem Cell Reports 2016; 6:176-87. [PMID: 26777057 PMCID: PMC4750097 DOI: 10.1016/j.stemcr.2015.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 12/14/2022] Open
Abstract
The use of cells derived from pluripotent stem cells (PSCs) for regenerative therapies confers a considerable risk for neoplastic growth and teratoma formation. Preclinical and clinical assessment of such therapies will require suitable monitoring strategies to understand and mitigate these risks. Here we generated human-induced pluripotent stem cells (iPSCs), selected clones that continued to express reprogramming factors after differentiation into cardiomyocytes, and transplanted these cardiomyocytes into immunocompromised rat hearts post-myocardial infarction. We compared magnetic resonance imaging (MRI), cardiac ultrasound, and serum biomarkers for their ability to delineate teratoma formation and growth. MRI enabled the detection of teratomas with a volume >8 mm3. A combination of three plasma biomarkers (CEA, AFP, and HCG) was able to detect teratomas with a volume >17 mm3 and with a sensitivity of more than 87%. Based on our findings, a combination of serum biomarkers with MRI screening may offer the highest sensitivity for teratoma detection and tracking. A combination of three serum biomarkers can detect teratomas >17 mm3 MRI can detect teratomas >8 mm3 Immature teratomas not detectable by serum biomarkers can be detected with MRI Combining MRI and serum biomarkers enables sensitive detection of neoplastic growth
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152
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Zhang G, Zhang Y. "Mouse Clone Model" for evaluating the immunogenicity and tumorigenicity of pluripotent stem cells. Stem Cell Res Ther 2015; 6:255. [PMID: 26687081 PMCID: PMC4684929 DOI: 10.1186/s13287-015-0262-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
To investigate the immune-rejection and tumor-formation potentials of induced pluripotent stem cells and other stem cells, we devised a model—designated the “Mouse Clone Model”—which combined the theory of somatic animal cloning, tetraploid complementation, and induced pluripotent stem cells to demonstrate the applicability of stem cells for transplantation therapy.
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Affiliation(s)
- Gang Zhang
- Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, M5S 3G5, Canada. .,Department of Medicine, Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Krembil Discovery Tower, 60 Leonard Avenue, 4th Floor - 4KD481, Toronto, Ontario, M5T 2S8, Canada. .,Division of Nephrology, Massachusetts General Hospital, Harvard Medical School, Harvard University, 149 13th Street, Charlestown, MA, 02129, USA.
| | - Yi Zhang
- Program in Life Science, New College, University of Toronto, 40 Willcocks Street, Toronto, Ontario, M5S 1C6, Canada.
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153
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Hoff AM, Alagaratnam S, Zhao S, Bruun J, Andrews PW, Lothe RA, Skotheim RI. Identification of Novel Fusion Genes in Testicular Germ Cell Tumors. Cancer Res 2015; 76:108-16. [PMID: 26659575 DOI: 10.1158/0008-5472.can-15-1790] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/01/2015] [Indexed: 11/16/2022]
Abstract
Testicular germ cell tumors (TGCT) are the most frequently diagnosed solid tumors in young men ages 15 to 44 years. Embryonal carcinomas (EC) comprise a subset of TGCTs that exhibit pluripotent characteristics similar to embryonic stem (ES) cells, but the genetic drivers underlying malignant transformation of ECs are unknown. To elucidate the abnormal genetic events potentially contributing to TGCT malignancy, such as the existence of fusion genes or aberrant fusion transcript expression, we performed RNA sequencing of EC cell lines and their nonmalignant ES cell line counterparts. We identified eight novel fusion transcripts and one gene with alternative promoter usage, ETV6. Four out of nine transcripts were found recurrently expressed in an extended panel of primary TGCTs and additional EC cell lines, but not in normal parenchyma of the testis, implying tumor-specific expression. Two of the recurrent transcripts involved an intrachromosomal fusion between RCC1 and HENMT1 located 80 Mbp apart and an interchromosomal fusion between RCC1 and ABHD12B. RCC1-ABHD12B and the ETV6 transcript variant were found to be preferentially expressed in the more undifferentiated TGCT subtypes. In vitro differentiation of the NTERA2 EC cell line resulted in significantly reduced expression of both fusion transcripts involving RCC1 and the ETV6 transcript variant, indicating that they are markers of pluripotency in a malignant setting. In conclusion, we identified eight novel fusion transcripts that, to our knowledge, are the first fusion genes described in TGCT and may therefore potentially serve as genomic biomarkers of malignant progression.
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Affiliation(s)
- Andreas M Hoff
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Sharmini Alagaratnam
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Sen Zhao
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Peter W Andrews
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, United Kingdom. Centre for Stem Cell Biology, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, Oslo, Norway. Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway.
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154
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Genomic Instability in Human Pluripotent Stem Cells Arises from Replicative Stress and Chromosome Condensation Defects. Cell Stem Cell 2015; 18:253-61. [PMID: 26669899 DOI: 10.1016/j.stem.2015.11.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 08/31/2015] [Accepted: 11/05/2015] [Indexed: 12/27/2022]
Abstract
Human pluripotent stem cells (hPSCs) frequently acquire chromosomal aberrations such as aneuploidy in culture. These aberrations progressively increase over time and may compromise the properties and clinical utility of the cells. The underlying mechanisms that drive initial genomic instability and its continued progression are largely unknown. Here, we show that aneuploid hPSCs undergo DNA replication stress, resulting in defective chromosome condensation and segregation. Aneuploid hPSCs show altered levels of actin cytoskeletal genes controlled by the transcription factor SRF, and overexpression of SRF rescues impaired chromosome condensation and segregation defects in aneuploid hPSCs. Furthermore, SRF downregulation in diploid hPSCs induces replication stress and perturbed condensation similar to that seen in aneuploid cells. Together, these results suggest that decreased SRF expression induces replicative stress and chromosomal condensation defects that underlie the ongoing chromosomal instability seen in aneuploid hPSCs. A similar mechanism may also operate during initiation of instability in diploid cells.
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155
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Function and significance of MicroRNAs in benign and malignant human stem cells. Semin Cancer Biol 2015; 35:200-11. [DOI: 10.1016/j.semcancer.2015.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 12/16/2022]
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156
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Canham MA, Van Deusen A, Brison DR, De Sousa PA, Downie J, Devito L, Hewitt ZA, Ilic D, Kimber SJ, Moore HD, Murray H, Kunath T. The Molecular Karyotype of 25 Clinical-Grade Human Embryonic Stem Cell Lines. Sci Rep 2015; 5:17258. [PMID: 26607962 PMCID: PMC4660465 DOI: 10.1038/srep17258] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/27/2015] [Indexed: 12/22/2022] Open
Abstract
The application of human embryonic stem cell (hESC) derivatives to regenerative medicine is now becoming a reality. Although the vast majority of hESC lines have been derived for research purposes only, about 50 lines have been established under Good Manufacturing Practice (GMP) conditions. Cell types differentiated from these designated lines may be used as a cell therapy to treat macular degeneration, Parkinson’s, Huntington’s, diabetes, osteoarthritis and other degenerative conditions. It is essential to know the genetic stability of the hESC lines before progressing to clinical trials. We evaluated the molecular karyotype of 25 clinical-grade hESC lines by whole-genome single nucleotide polymorphism (SNP) array analysis. A total of 15 unique copy number variations (CNVs) greater than 100 kb were detected, most of which were found to be naturally occurring in the human population and none were associated with culture adaptation. In addition, three copy-neutral loss of heterozygosity (CN-LOH) regions greater than 1 Mb were observed and all were relatively small and interstitial suggesting they did not arise in culture. The large number of available clinical-grade hESC lines with defined molecular karyotypes provides a substantial starting platform from which the development of pre-clinical and clinical trials in regenerative medicine can be realised.
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Affiliation(s)
- Maurice A Canham
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, UK
| | - Amy Van Deusen
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, UK
| | - Daniel R Brison
- Department of Reproductive Medicine, St. Mary's Hospital, Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Paul A De Sousa
- Roslin Cells Limited, Nine Edinburgh BioQuarter, Edinburgh, UK.,Centre for Clinical Brain Sciences and MRC Centre for Regenerative Medicine, The University of Edinburgh, UK
| | - Janet Downie
- Roslin Cells Limited, Nine Edinburgh BioQuarter, Edinburgh, UK
| | - Liani Devito
- Stem Cell Laboratories, Guy's Assisted Conception Unit, Division of Women's Health, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Zoe A Hewitt
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, UK
| | - Dusko Ilic
- Stem Cell Laboratories, Guy's Assisted Conception Unit, Division of Women's Health, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Susan J Kimber
- Faculty of Life Sciences, The University of Manchester, Manchester, UK
| | - Harry D Moore
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, UK
| | - Helen Murray
- Roslin Cells Limited, Nine Edinburgh BioQuarter, Edinburgh, UK
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, UK
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157
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Rebuzzini P, Zuccotti M, Redi CA, Garagna S. Chromosomal Abnormalities in Embryonic and Somatic Stem Cells. Cytogenet Genome Res 2015; 147:1-9. [PMID: 26583376 DOI: 10.1159/000441645] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2015] [Indexed: 12/20/2022] Open
Abstract
The potential use of stem cells (SCs) for tissue engineering, regenerative medicine, disease modeling, toxicological studies, drug delivery, and as in vitro model for the study of basic developmental processes implies large-scale in vitro culture. Here, after a brief description of the main techniques used for karyotype analysis, we will give a detailed overview of the chromosome abnormalities described in pluripotent (embryonic and induced pluripotent SCs) and somatic SCs, and the possible causes of their origin during culture.
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Affiliation(s)
- Paola Rebuzzini
- Laboratorio di Biologia dello Sviluppo, Dipartimento di Biologia e Biotecnologie, Universitx00E0; degli Studi di Pavia, Pavia, Italy
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158
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Reinius B, Sandberg R. Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation. Nat Rev Genet 2015; 16:653-64. [PMID: 26442639 DOI: 10.1038/nrg3888] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Random monoallelic expression (RME) of genes represents a striking example of how stochastic molecular processes can result in cellular heterogeneity. Recent transcriptome-wide studies have revealed both mitotically stable and cell-to-cell dynamic forms of autosomal RME, with the latter presumably resulting from burst-like stochastic transcription. Here, we discuss the distinguishing features of these two forms of RME and revisit literature on their nature, pervasiveness and regulation. Finally, we explore how RME may contribute to phenotypic variation, including the incomplete penetrance and variable expressivity often seen in genetic disease.
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Affiliation(s)
- Björn Reinius
- Ludwig Institute for Cancer Research, Box 240, and the Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rickard Sandberg
- Ludwig Institute for Cancer Research, Box 240, and the Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
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159
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Uniparental disomy of the entire X chromosome in Turner syndrome patient-specific induced pluripotent stem cells. Cell Discov 2015; 1:15022. [PMID: 27462421 PMCID: PMC4860828 DOI: 10.1038/celldisc.2015.22] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/30/2015] [Indexed: 12/21/2022] Open
Abstract
The human induced pluripotent stem cell (iPSC) technique promises to provide an unlimited, reliable source of genetically matched pluripotent cells for personalized therapy and disease modeling. Recently, it is observed that cells with ring chromosomes 13 or 17 autonomously correct the defects via compensatory uniparental disomy during cellular reprogramming to iPSCs. This breakthrough finding suggests a potential therapeutic approach to repair large-scale chromosomal aberrations. However, due to the scarceness of ring chromosome samples, the reproducibility of this approach in different individuals is not carefully evaluated yet. Moreover, the underlying mechanism and the applicability to other types of chromosomal aberrations remain unknown. Here we generated iPSCs from four 45,X chorionic villous fibroblast lines and found that only one reprogrammed line acquired 46,XX karyotype via uniparental disomy of the entire X chromosome. The karyotype correction was reproducible in the same cell line by either retroviral or episomal reprogramming. The karyotype-corrected iPSCs were subject to X chromosome inactivation and obtained better colony morphology and higher proliferation rate than other uncorrected ones. Further transcriptomic comparison among the fibroblast lines identified a distinct expression pattern of cell cycle regulators in the uncorrectable ones. These findings demonstrate that the iPSC technique holds the potential to correct X monosomy, but the correction rate is very low, probably due to differential regulation of cell cycle genes between individuals. Our data strongly suggest that more systematic investigations are needed before defining the iPSC technique as a novel means of chromosome therapy.
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160
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Vapniarsky N, Arzi B, Hu JC, Nolta JA, Athanasiou KA. Concise Review: Human Dermis as an Autologous Source of Stem Cells for Tissue Engineering and Regenerative Medicine. Stem Cells Transl Med 2015; 4:1187-98. [PMID: 26253713 DOI: 10.5966/sctm.2015-0084] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/08/2015] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED The exciting potential for regenerating organs from autologous stem cells is on the near horizon, and adult dermis stem cells (DSCs) are particularly appealing because of the ease and relative minimal invasiveness of skin collection. A substantial number of reports have described DSCs and their potential for regenerating tissues from mesenchymal, ectodermal, and endodermal lineages; however, the exact niches of these stem cells in various skin types and their antigenic surface makeup are not yet clearly defined. The multilineage potential of DSCs appears to be similar, despite great variability in isolation and in vitro propagation methods. Despite this great potential, only limited amounts of tissues and clinical applications for organ regeneration have been developed from DSCs. This review summarizes the literature on DSCs regarding their niches and the specific markers they express. The concept of the niches and the differentiation capacity of cells residing in them along particular lineages is discussed. Furthermore, the advantages and disadvantages of widely used methods to demonstrate lineage differentiation are considered. In addition, safety considerations and the most recent advancements in the field of tissue engineering and regeneration using DSCs are discussed. This review concludes with thoughts on how to prospectively approach engineering of tissues and organ regeneration using DSCs. Our expectation is that implementation of the major points highlighted in this review will lead to major advancements in the fields of regenerative medicine and tissue engineering. SIGNIFICANCE Autologous dermis-derived stem cells are generating great excitement and efforts in the field of regenerative medicine and tissue engineering. The substantial impact of this review lies in its critical coverage of the available literature and in providing insight regarding niches, characteristics, and isolation methods of stem cells derived from the human dermis. Furthermore, it provides analysis of the current state-of-the-art regenerative approaches using human-derived dermal stem cells, with consideration of current guidelines, to assist translation toward therapeutic use.
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Affiliation(s)
- Natalia Vapniarsky
- Department of Biomedical Engineering, Department of Surgical and Radiological Sciences, School of Veterinary Medicine, Institute for Regenerative Cures and Department of Internal Medicine, School of Medicine, and Department of Orthopaedic Surgery, University of California, Davis, Davis, California, USA
| | - Boaz Arzi
- Department of Biomedical Engineering, Department of Surgical and Radiological Sciences, School of Veterinary Medicine, Institute for Regenerative Cures and Department of Internal Medicine, School of Medicine, and Department of Orthopaedic Surgery, University of California, Davis, Davis, California, USA
| | - Jerry C Hu
- Department of Biomedical Engineering, Department of Surgical and Radiological Sciences, School of Veterinary Medicine, Institute for Regenerative Cures and Department of Internal Medicine, School of Medicine, and Department of Orthopaedic Surgery, University of California, Davis, Davis, California, USA
| | - Jan A Nolta
- Department of Biomedical Engineering, Department of Surgical and Radiological Sciences, School of Veterinary Medicine, Institute for Regenerative Cures and Department of Internal Medicine, School of Medicine, and Department of Orthopaedic Surgery, University of California, Davis, Davis, California, USA
| | - Kyriacos A Athanasiou
- Department of Biomedical Engineering, Department of Surgical and Radiological Sciences, School of Veterinary Medicine, Institute for Regenerative Cures and Department of Internal Medicine, School of Medicine, and Department of Orthopaedic Surgery, University of California, Davis, Davis, California, USA
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161
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Chen Y, Cao J, Xiong M, Petersen AJ, Dong Y, Tao Y, Huang CTL, Du Z, Zhang SC. Engineering Human Stem Cell Lines with Inducible Gene Knockout using CRISPR/Cas9. Cell Stem Cell 2015; 17:233-44. [PMID: 26145478 PMCID: PMC4530040 DOI: 10.1016/j.stem.2015.06.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/27/2015] [Accepted: 06/04/2015] [Indexed: 12/26/2022]
Abstract
Precise temporal control of gene expression or deletion is critical for elucidating gene function in biological systems. However, the establishment of human pluripotent stem cell (hPSC) lines with inducible gene knockout (iKO) remains challenging. We explored building iKO hPSC lines by combining CRISPR/Cas9-mediated genome editing with the Flp/FRT and Cre/LoxP system. We found that "dual-sgRNA targeting" is essential for biallelic knockin of FRT sequences to flank the exon. We further developed a strategy to simultaneously insert an activity-controllable recombinase-expressing cassette and remove the drug-resistance gene, thus speeding up the generation of iKO hPSC lines. This two-step strategy was used to establish human embryonic stem cell (hESC) and induced pluripotent stem cell (iPSC) lines with iKO of SOX2, PAX6, OTX2, and AGO2, genes that exhibit diverse structural layout and temporal expression patterns. The availability of iKO hPSC lines will substantially transform the way we examine gene function in human cells.
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Affiliation(s)
- Yuejun Chen
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA.
| | - Jingyuan Cao
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA
| | - Man Xiong
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA; Institute of Pediatrics, Children's Hospital, Fudan University, 399 Wanyuan Road, Shanghai 201102, China
| | | | - Yi Dong
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA
| | - Yunlong Tao
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA
| | | | - Zhongwei Du
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA
| | - Su-Chun Zhang
- Waisman Center, University of Wisconsin, Madison, WI 53705, USA; Neuroscience Training Program, University of Wisconsin, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA; Department of Neurology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA.
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162
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Liu WQ, Li JL, Wang J, He WY, Va L, Sheng XM, Wu BL, Sun XF. Genetic Evaluation of Copy Number Variations, Loss of Heterozygosity, and Single-Nucleotide Variant Levels in Human Embryonic Stem Cells With or Without Skewed X Chromosome Inactivation. Stem Cells Dev 2015; 24:1779-92. [DOI: 10.1089/scd.2014.0463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Wei-Qiang Liu
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Jie-Liang Li
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jian Wang
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Wen-Yin He
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Lip Va
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Xiao-Ming Sheng
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Bai-Lin Wu
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Xiao-Fang Sun
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
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163
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Shum C, Macedo SC, Warre-Cornish K, Cocks G, Price J, Srivastava DP. Utilizing induced pluripotent stem cells (iPSCs) to understand the actions of estrogens in human neurons. Horm Behav 2015; 74:228-42. [PMID: 26143621 PMCID: PMC4579404 DOI: 10.1016/j.yhbeh.2015.06.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/11/2015] [Accepted: 06/25/2015] [Indexed: 01/05/2023]
Abstract
This article is part of a Special Issue "Estradiol and Cognition". Over recent years tremendous progress has been made towards understanding the molecular and cellular mechanism by which estrogens exert enhancing effects on cognition, and how they act as a neuroprotective or neurotrophic agent in disease. Currently, much of this work has been carried out in animal models with only a limited number of studies using native human tissue or cells. Recent advances in stem cell technology now make it possible to reprogram somatic cells from humans into induced pluripotent stem cells (iPSCs), which can subsequently be differentiated into neurons of specific lineages. Importantly, the reprogramming of cells allows for the generation of iPSCs that retain the genetic "makeup" of the donor. Therefore, it is possible to generate iPSC-derived neurons from patients diagnosed with specific diseases, that harbor the complex genetic background associated with the disorder. Here, we review the iPSC technology and how it's currently being used to model neural development and neurological diseases. Furthermore, we explore whether this cellular system could be used to understand the role of estrogens in human neurons, and present preliminary data in support of this. We further suggest that the use of iPSC technology offers a novel system to not only further understand estrogens' effects in human cells, but also to investigate the mechanism by which estrogens are beneficial in disease. Developing a greater understanding of these mechanisms in native human cells will also aid in the development of safer and more effective estrogen-based therapeutics.
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Affiliation(s)
- Carole Shum
- Department of Basic and Clinical Neuroscience, Cell and Behaviour Unit, The James Black Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - Sara C Macedo
- Department of Basic and Clinical Neuroscience, Cell and Behaviour Unit, The James Black Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK; Faculty of Engineering, Universidade do Porto, 4200-465 Porto, Portugal
| | - Katherine Warre-Cornish
- Department of Basic and Clinical Neuroscience, Cell and Behaviour Unit, The James Black Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - Graham Cocks
- Department of Basic and Clinical Neuroscience, Cell and Behaviour Unit, The James Black Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - Jack Price
- Department of Basic and Clinical Neuroscience, Cell and Behaviour Unit, The James Black Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Cell and Behaviour Unit, The James Black Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK.
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164
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Sikorski DJ, Caron NJ, VanInsberghe M, Zahn H, Eaves CJ, Piret JM, Hansen CL. Clonal analysis of individual human embryonic stem cell differentiation patterns in microfluidic cultures. Biotechnol J 2015; 10:1546-54. [PMID: 26059045 DOI: 10.1002/biot.201500035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/04/2015] [Accepted: 06/05/2015] [Indexed: 01/23/2023]
Abstract
Heterogeneity in the clonal outputs of individual human embryonic stem cells (hESCs) confounds analysis of their properties in studies of bulk populations and how to manipulate them for clinical applications. To circumvent this problem we developed a microfluidic device that supports the robust generation of colonies derived from single ESCs. This microfluidic system contains 160 individually addressable chambers equipped for perfusion culture of individual hESCs that could be shown to match the growth rates, marker expression and colony morphologies obtained in conventional cultures. Use of this microfluidic device to analyze the clonal growth kinetics of multiple individual hESCs induced to differentiation revealed variable shifts in the growth rate, area per cell and expression of OCT4 in the progeny of individual hESCs. Interestingly, low OCT4 expression, a slower growth rate and low nuclear to cytoplasmic ratios were found to be correlated responses. This study demonstrates how microfluidic systems can be used to enable large scale live-cell imaging of isolated hESCs exposed to changing culture conditions, to examine how different aspects of their variable responses are correlated.
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Affiliation(s)
- Darek J Sikorski
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada.,Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Nicolas J Caron
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Michael VanInsberghe
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Hans Zahn
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - James M Piret
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Carl L Hansen
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada. .,Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada.
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165
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Pells S, Koutsouraki E, Morfopoulou S, Valencia-Cadavid S, Tomlinson SR, Kalathur R, Futschik ME, De Sousa PA. Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State. PLoS One 2015; 10:e0131102. [PMID: 26151932 PMCID: PMC4495055 DOI: 10.1371/journal.pone.0131102] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/27/2015] [Indexed: 12/21/2022] Open
Abstract
Human embryonic stem cells (hESCs) undergo epigenetic changes in vitro which may compromise function, so an epigenetic pluripotency “signature” would be invaluable for line validation. We assessed Cytosine-phosphate-Guanine Island (CGI) methylation in hESCs by genomic DNA hybridisation to a CGI array, and saw substantial variation in CGI methylation between lines. Comparison of hESC CGI methylation profiles to corresponding somatic tissue data and hESC mRNA expression profiles identified a conserved hESC-specific methylation pattern associated with expressed genes. Transcriptional repressors and activators were over-represented amongst genes whose associated CGIs were methylated or unmethylated specifically in hESCs, respectively. Knockdown of candidate transcriptional regulators (HMGA1, GLIS2, PFDN5) induced differentiation in hESCs, whereas ectopic expression in fibroblasts modulated iPSC colony formation. Chromatin immunoprecipitation confirmed interaction between the candidates and the core pluripotency transcription factor network. We thus identify novel pluripotency genes on the basis of a conserved and distinct epigenetic configuration in human stem cells.
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Affiliation(s)
- Steve Pells
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- * E-mail: (PDS); (SP)
| | - Eirini Koutsouraki
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Sofia Morfopoulou
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Sara Valencia-Cadavid
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Simon R. Tomlinson
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Ravi Kalathur
- Centre for Molecular and Structural Biomedicine, University of Algarve, 8005–139, Faro, Portugal
| | - Matthias E. Futschik
- Centre for Molecular and Structural Biomedicine, University of Algarve, 8005–139, Faro, Portugal
| | - Paul A. De Sousa
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- * E-mail: (PDS); (SP)
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166
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Salci KR, Lee JB, Mitchell RR, Orlando L, Fiebig-Comyn A, Shapovalova Z, Bhatia M. Derivation of human induced pluripotent stem cells through continued exposure of OCT4-induced plastic human fibroblasts to reprogramming media. Stem Cell Res 2015; 15:240-2. [PMID: 26141785 DOI: 10.1016/j.scr.2015.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 06/12/2015] [Indexed: 11/26/2022] Open
Abstract
The combination of OCT4 expression and short-term exposure to reprogramming media induces a state of transcriptional plasticity in human fibroblasts, capable of responding to changes in the extracellular environment. Here we provide characterization of iPSCs established through continued culture of OCT4-induced plastic human fibroblasts in pluripotent-supportive reprogramming media. Human iPSC(OCT4) are morphologically indistinguishable from conventionally derived iPSCs and express core proteins involved in maintenance of pluripotency. iPSC(OCT4) display bona fide functional pluripotency as measured by in vivo teratoma formation consisting of the three germ layers.
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Affiliation(s)
- Kyle R Salci
- McMaster Stem Cell and Cancer Research Institute, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4L8, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Jung Bok Lee
- McMaster Stem Cell and Cancer Research Institute, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Ryan R Mitchell
- McMaster Stem Cell and Cancer Research Institute, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4L8, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Luca Orlando
- McMaster Stem Cell and Cancer Research Institute, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Aline Fiebig-Comyn
- McMaster Stem Cell and Cancer Research Institute, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Zoya Shapovalova
- McMaster Stem Cell and Cancer Research Institute, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Mickie Bhatia
- McMaster Stem Cell and Cancer Research Institute, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4L8, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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167
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Salci KR, Lee JB, Mitchell RR, Orlando L, Fiebig-Comyn A, Shapovalova Z, Bhatia M. Acquisition of pluripotency through continued environmental influence on OCT4-induced plastic human fibroblasts. Stem Cell Res 2015; 15:221-30. [DOI: 10.1016/j.scr.2015.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 05/29/2015] [Accepted: 06/11/2015] [Indexed: 01/02/2023] Open
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168
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Lin YC, Murayama Y, Hashimoto K, Nakamura Y, Lin CS, Yokoyama KK, Saito S. Role of tumor suppressor genes in the cancer-associated reprogramming of human induced pluripotent stem cells. Stem Cell Res Ther 2015; 5:58. [PMID: 25157408 PMCID: PMC4056745 DOI: 10.1186/scrt447] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Because of their pluripotent characteristics, human induced pluripotent stem cells (iPSCs) possess great potential for therapeutic application and for the study of degenerative disorders. These cells are generated from normal somatic cells, multipotent stem cells, or cancer cells. They express embryonic stem cell markers, such as OCT4, SOX2, NANOG, SSEA-3, SSEA-4, and REX1, and can differentiate into all adult tissue types, both in vitro and in vivo. However, some of the pluripotency-promoting factors have been implicated in tumorigenesis. Here, we describe the merits of tumor suppresser genes as reprogramming factors for the generation of iPSCs without tumorigenic activity. The initial step of reprogramming is induction of the exogenous pluripotent factors to generate the oxidative stress that leads to senescence by DNA damage and metabolic stresses, thus inducing the expression of tumor suppressor genes such as p21CIP1 and p16INK4a through the activation of p53 to be the pre-induced pluripotent stem cells (pre-iPSCs). The later stage includes overcoming the barrier of reprogramming-induced senescence or cell-cycle arrest by shutting off the function of these tumor suppressor genes, followed by the induction of endogenous stemness genes for the full commitment of iPSCs (full-iPSCs). Thus, the reactive oxygen species (ROS) produced by oxidative stress might be critical for the induction of endogenous reprogramming-factor genes via epigenetic changes or antioxidant reactions. We also discuss the critical role of tumor suppressor genes in the evaluation of the tumorigenicity of human cancer cell-derived pluripotent stem cells, and describe how to overcome their tumorigenic properties for application in stem cell therapy in the field of regenerative medicine.
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169
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Liu P, Kaplan A, Yuan B, Hanna JH, Lupski JR, Reiner O. Passage number is a major contributor to genomic structural variations in mouse iPSCs. Stem Cells 2015; 32:2657-67. [PMID: 24965231 DOI: 10.1002/stem.1779] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/11/2014] [Accepted: 05/23/2014] [Indexed: 12/24/2022]
Abstract
Emergence of genomic instability is a practical issue in preparing neural stem cells (NSCs) and induced pluripotent stem cells (iPSCs). However, it is still not fully understood what the origins and mechanisms for formation are for the genomic alternations observed. Here, we studied the extent of genomic variation on the scale of individual cells originating from the same animal. We used mouse NSCs grown from embryonic cells and iPSCs generated from embryonic brain cells, B cells or fibroblasts, and performed comparative analysis with cultures of fibroblasts from the same mouse. In the first passage of these cell lines, aneuploidies were only observed for chromosomes 6, 11, 12, 19, and Y, which is overall at a rate lower than previously reported; de novo copy number variations (CNVs) were observed in 4.3% of neural iPSCs, 29% of B cell iPSCs, 10% of fibroblast iPSCs, and 1.3% of neurospheres. In contrast, propagation of these first passage cells to a later passage induced additional aneuploidies and CNVs. Breakpoint sequencing analysis suggested that the majority of the detected CNVs arose by replicative mechanisms. Interestingly, we detected identical de novo CNVs in different single cell colonies that appeared to have arisen independently from each other, which suggests a novel CNV formation mechanism in these cells. Our findings provide insights into mechanisms of CNV formation during reprogramming and suggest that replicative mechanisms for CNV formation accompany mitotic divisions.
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Affiliation(s)
- Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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170
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Sobol M, Raykova D, Cavelier L, Khalfallah A, Schuster J, Dahl N. Methods of Reprogramming to Induced Pluripotent Stem Cell Associated with Chromosomal Integrity and Delineation of a Chromosome 5q Candidate Region for Growth Advantage. Stem Cells Dev 2015; 24:2032-40. [PMID: 25867454 DOI: 10.1089/scd.2015.0061] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) have brought great promises for disease modeling and cell-based therapies. One concern related to the use of reprogrammed somatic cells is the loss of genomic integrity and chromosome stability, a hallmark for cancer and many other human disorders. We investigated 16 human iPSC lines reprogrammed by nonintegrative Sendai virus (SeV) and another 16 iPSC lines generated by integrative lentivirus for genetic changes. At early passages we detected cytogenetic rearrangements in 44% (7/16) of iPSC lines generated by lentiviral integration whereas the corresponding figure was 6% (1/16) using SeV-based delivery. The rearrangements were numerical and/or structural with chromosomes 5 and 12 as the most frequently involved chromosomes. Three iPSC lines with chromosome 5 aberrations were derived from one and the same donor. We present in this study the aberrant karyotypes including a duplication of chromosome 5q13q33 that restricts a candidate region for growth advantage. Our results suggest that the use of integrative lentivirus confers a higher risk for cytogenetic abnormalities at early passages when compared to SeV-based reprogramming. In combination, our findings expand the knowledge on acquired cytogenetic aberrations in iPSC after reprogramming and during culture.
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Affiliation(s)
- Maria Sobol
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University , Uppsala, Sweden
| | - Doroteya Raykova
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University , Uppsala, Sweden
| | - Lucia Cavelier
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University , Uppsala, Sweden
| | - Ayda Khalfallah
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University , Uppsala, Sweden
| | - Jens Schuster
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University , Uppsala, Sweden
| | - Niklas Dahl
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Biomedical Centre, Uppsala University , Uppsala, Sweden
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171
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Yvon C, Ramsden CM, Lane A, Powner MB, da Cruz L, Coffey PJ, Carr AJF. Using Stem Cells to Model Diseases of the Outer Retina. Comput Struct Biotechnol J 2015; 13:382-9. [PMID: 26106463 PMCID: PMC4477013 DOI: 10.1016/j.csbj.2015.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/30/2015] [Accepted: 05/01/2015] [Indexed: 12/13/2022] Open
Abstract
Retinal degeneration arises from the loss of photoreceptors or retinal pigment epithelium (RPE). It is one of the leading causes of irreversible blindness worldwide with limited effective treatment options. Generation of induced pluripotent stem cell (IPSC)-derived retinal cells and tissues from individuals with retinal degeneration is a rapidly evolving technology that holds a great potential for its use in disease modelling. IPSCs provide an ideal platform to investigate normal and pathological retinogenesis, but also deliver a valuable source of retinal cell types for drug screening and cell therapy. In this review, we will provide some examples of the ways in which IPSCs have been used to model diseases of the outer retina including retinitis pigmentosa (RP), Usher syndrome (USH), Leber congenital amaurosis (LCA), gyrate atrophy (GA), juvenile neuronal ceroid lipofuscinosis (NCL), Best vitelliform macular dystrophy (BVMD) and age related macular degeneration (AMD).
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Affiliation(s)
- Camille Yvon
- The London Project to Cure Blindness, Division of ORBIT, Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Conor M. Ramsden
- The London Project to Cure Blindness, Division of ORBIT, Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust, UCL Institute of Ophthalmology, London, EC1V 2PD, UK
| | - Amelia Lane
- The London Project to Cure Blindness, Division of ORBIT, Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Michael B. Powner
- The London Project to Cure Blindness, Division of ORBIT, Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Lyndon da Cruz
- The London Project to Cure Blindness, Division of ORBIT, Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust, UCL Institute of Ophthalmology, London, EC1V 2PD, UK
| | - Peter J. Coffey
- The London Project to Cure Blindness, Division of ORBIT, Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
- Center for Stem Cell Biology and Engineering, NRI, UC, Santa Barbara, USA
| | - Amanda-Jayne F. Carr
- The London Project to Cure Blindness, Division of ORBIT, Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
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172
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Tosca L, Feraud O, Magniez A, Bas C, Griscelli F, Bennaceur-Griscelli A, Tachdjian G. Genomic instability of human embryonic stem cell lines using different passaging culture methods. Mol Cytogenet 2015; 8:30. [PMID: 26052346 PMCID: PMC4456787 DOI: 10.1186/s13039-015-0133-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/07/2015] [Indexed: 12/22/2022] Open
Abstract
Background Human embryonic stem cells exhibit genomic instability that can be related to culture duration or to the passaging methods used for cell dissociation. In order to study the impact of cell dissociation techniques on human embryonic stem cells genomic instability, we cultured H1 and H9 human embryonic stem cells lines using mechanical/manual or enzymatic/collagenase-IV dissociation methods. Genomic instability was evaluated at early (<p60) and late (>p60) passages by using oligonucleotide based array-comparative genomic hybridization 105 K with a mean resolution of 50 Kb. Results DNA variations were mainly located on subtelomeric and pericentromeric regions with sizes <100 Kb. In this study, 9 recurrent genomic variations were acquired during culture including the well known duplication 20q11.21. When comparing cell dissociation methods, we found no significant differences between DNA variations number and size, DNA gain or DNA loss frequencies, homozygous loss frequencies and no significant difference on the content of genes involved in development, cell cycle tumorigenesis and syndrome disease. In addition, we have never found any malignant tissue in 4 different teratoma representative of the two independent stem cell lines. Conclusions These results show that the occurrence of genomic instability in human embryonic stem cells is similar using mechanical or collagenase IV-based enzymatic cell culture dissociation methods. All the observed genomic variations have no impact on the development of malignancy. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0133-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lucie Tosca
- AP-HP, Histologie-Embryologie-Cytogénétique, Hôpitaux Universitaires Paris Sud, Clamart, F-92141 France ; Université Paris Sud, Le Kremlin-Bicêtre, F-94275 France ; Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France
| | - Olivier Feraud
- Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France
| | - Aurélie Magniez
- Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France
| | - Cécile Bas
- AP-HP, Histologie-Embryologie-Cytogénétique, Hôpitaux Universitaires Paris Sud, Clamart, F-92141 France ; Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France
| | - Frank Griscelli
- Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France ; Université Paris Descartes, Sorbonne Paris Cité, F-75006 France
| | - Annelise Bennaceur-Griscelli
- Université Paris Sud, Le Kremlin-Bicêtre, F-94275 France ; Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France ; AP-HP, Hématologie, Hôpitaux Universitaires Paris Sud, Villejuif, F-94801 France
| | - Gérard Tachdjian
- AP-HP, Histologie-Embryologie-Cytogénétique, Hôpitaux Universitaires Paris Sud, Clamart, F-92141 France ; Université Paris Sud, Le Kremlin-Bicêtre, F-94275 France ; Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France
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174
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Concise Review: Methods and Cell Types Used to Generate Down Syndrome Induced Pluripotent Stem Cells. J Clin Med 2015; 4:696-714. [PMID: 26239351 PMCID: PMC4470162 DOI: 10.3390/jcm4040696] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/23/2015] [Accepted: 03/31/2015] [Indexed: 01/29/2023] Open
Abstract
Down syndrome (DS, trisomy 21), is the most common viable chromosomal disorder, with an incidence of 1 in 800 live births. Its phenotypic characteristics include intellectual impairment and several other developmental abnormalities, for the majority of which the pathogenetic mechanisms remain unknown. Several models have been used to investigate the mechanisms by which the extra copy of chromosome 21 leads to the DS phenotype. In the last five years, several laboratories have been successful in reprogramming patient cells carrying the trisomy 21 anomaly into induced pluripotent stem cells, i.e., T21-iPSCs. In this review, we summarize the different T21-iPSCs that have been generated with a particular interest in the technical procedures and the somatic cell types used for the reprogramming.
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175
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Gokhale PJ, Au-Young JK, Dadi S, Keys DN, Harrison NJ, Jones M, Soneji S, Enver T, Sherlock JK, Andrews PW. Culture adaptation alters transcriptional hierarchies among single human embryonic stem cells reflecting altered patterns of differentiation. PLoS One 2015; 10:e0123467. [PMID: 25875838 PMCID: PMC4397016 DOI: 10.1371/journal.pone.0123467] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 03/03/2015] [Indexed: 01/17/2023] Open
Abstract
We have used single cell transcriptome analysis to re-examine the substates of early passage, karyotypically Normal, and late passage, karyotypically Abnormal (‘Culture Adapted’) human embryonic stem cells characterized by differential expression of the cell surface marker antigen, SSEA3. The results confirmed that culture adaptation is associated with alterations to the dynamics of the SSEA3(+) and SSEA3(-) substates of these cells, with SSEA3(-) Adapted cells remaining within the stem cell compartment whereas the SSEA3(-) Normal cells appear to have differentiated. However, the single cell data reveal that these substates are characterized by further heterogeneity that changes on culture adaptation. Notably the Adapted population includes cells with a transcriptome substate suggestive of a shift to a more naïve-like phenotype in contrast to the cells of the Normal population. Further, a subset of the Normal SSEA3(+) cells expresses genes typical of endoderm differentiation, despite also expressing the undifferentiated stem cell genes, POU5F1 (OCT4) and NANOG, whereas such apparently lineage-primed cells are absent from the Adapted population. These results suggest that the selective growth advantage gained by genetically variant, culture adapted human embryonic stem cells may derive in part from a changed substate structure that influences their propensity for differentiation.
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Affiliation(s)
- Paul J. Gokhale
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | | | - SriVidya Dadi
- ThermoFisher, Foster City, California, United States of America
| | - David N. Keys
- ThermoFisher, Foster City, California, United States of America
| | - Neil J. Harrison
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Mark Jones
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Shamit Soneji
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Tariq Enver
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Jon K. Sherlock
- ThermoFisher, Foster City, California, United States of America
| | - Peter W. Andrews
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
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176
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Abstract
Stem cells have generated great interest for their potential therapeutic use because of their capacity to self-renew indefinitely and to generate all cell lineages (pluripotency). Many diseases such as neurodegenerative disorders or diabetes are caused by loss of functionality or deficiency of a particular cell type. Stem cells differentiated into a specific cell type such as pancreatic β-cells or neurons, for example, thus hold great promise for regenerative medicine. However, many challenges have to be overcome before stem cell therapy can become a viable clinical approach.
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Affiliation(s)
- Satyakam Bhagavati
- Department of Neurology, State University of New York, Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY, 11203, USA,
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177
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Lee CT, Bendriem RM, Kindberg AA, Worden LT, Williams MP, Drgon T, Mallon BS, Harvey BK, Richie CT, Hamilton RS, Chen J, Errico SL, Tsai SYA, Uhl GR, Freed WJ. Functional consequences of 17q21.31/WNT3-WNT9B amplification in hPSCs with respect to neural differentiation. Cell Rep 2015; 10:616-32. [PMID: 25640183 DOI: 10.1016/j.celrep.2014.12.050] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 11/18/2014] [Accepted: 12/22/2014] [Indexed: 10/24/2022] Open
Abstract
Human pluripotent stem cell (hPSC) lines exhibit repeated patterns of genetic variation, which can alter in vitro properties as well as suitability for clinical use. We examined associations between copy-number variations (CNVs) on chromosome 17 and hPSC mesodiencephalic dopaminergic (mDA) differentiation. Among 24 hPSC lines, two karyotypically normal lines, BG03 and CT3, and BG01V2, with trisomy 17, exhibited amplification of the WNT3/WNT9B region and rapid mDA differentiation. In hPSC lines with amplified WNT3/WNT9B, basic fibroblast growth factor (bFGF) signaling through mitogen-activated protein kinase (MAPK)/ERK amplifies canonical WNT signaling by phosphorylating LRP6, resulting in enhanced undifferentiated proliferation. When bFGF is absent, noncanonical WNT signaling becomes dominant due to upregulation of SIAH2, enhancing JNK signaling and promoting loss of pluripotency. When bFGF is present during mDA differentiation, stabilization of canonical WNT signaling causes upregulation of LMX1A and mDA induction. Therefore, CNVs in 17q21.31, a "hot spot" for genetic variation, have multiple and complex effects on hPSC cellular phenotype.
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Affiliation(s)
- Chun-Ting Lee
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA.
| | - Raphael M Bendriem
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
| | - Abigail A Kindberg
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
| | - Lila T Worden
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
| | - Melanie P Williams
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
| | - Tomas Drgon
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
| | - Barbara S Mallon
- NIH Stem Cell Unit, Intramural Research Program, National Institute of Neurological Disorders and Stroke, Department of Health and Human Services, NIH, Bethesda, MD 20892, USA
| | - Brandon K Harvey
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
| | - Christopher T Richie
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
| | - Rebecca S Hamilton
- NIH Stem Cell Unit, Intramural Research Program, National Institute of Neurological Disorders and Stroke, Department of Health and Human Services, NIH, Bethesda, MD 20892, USA
| | - Jia Chen
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
| | - Stacie L Errico
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
| | - Shang-Yi A Tsai
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
| | - George R Uhl
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
| | - William J Freed
- Intramural Research Program, National Institute on Drug Abuse, Department of Health and Human Services, NIH, Baltimore, MD 21224, USA
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Aldahmash A, Atteya M, Elsafadi M, Al-Nbaheen M, Al-Mubarak HA, Vishnubalaji R, Al-Roalle A, Al-Harbi S, Manikandan M, Matthaei KI, Mahmood A. Teratoma formation in immunocompetent mice after syngeneic and allogeneic implantation of germline capable mouse embryonic stem cells. Asian Pac J Cancer Prev 2015; 14:5705-11. [PMID: 24289566 DOI: 10.7314/apjcp.2013.14.10.5705] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Embryonic stem cells (ESCs) have the potential to form teratomas when implanted into immunodeficient mice, but data in immunocompetent mice are limited. We therefore investigated teratoma formation after implantation of three different mouse ESC (mESC) lines into immunocompetent mice. MATERIALS AND METHODS BALB/c mice were injected with three highly germline competent mESCs (129Sv, BALB/c and C57BL/6) subcutaneously or under the kidney capsule. After 4 weeks, mice were euthanized and examined histologically for teratoma development. The incidence, size and composition of teratomas were compared using Pearson Chi-square, t-test for dependent variables, one-way analysis of variance and the nonparametric Kruskal- Wallis analysis of variance and median test. RESULTS Teratomas developed from all three cell lines. The incidence of formation was significantly higher under the kidney capsule compared to subcutaneous site and occurred in both allogeneic and syngeneic mice. Overall, the size of teratoma was largest with the 129Sv cell line and under the kidney capsule. Diverse embryonic stem cell-derived tissues, belonging to the three embryonic germ layers, were encountered, reflecting the pluripotency of embryonic stem cells. Most commonly represented tissues were nervous tissue, keratinizing stratified squamous epithelium (ectoderm), smooth muscle, striated muscle, cartilage, bone (mesoderm), and glandular tissue in the form of gut- and respiratory-like epithelia (endoderm). CONCLUSIONS ESCs can form teratomas in immunocompetent mice and, therefore, removal of undifferentiated ESC is a pre-requisite for a safe use of ESC in cell-based therapies. In addition the genetic relationship of the origin of the cell lines to the ability to transplant plays a major role.
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Affiliation(s)
- Abdullah Aldahmash
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University and King Khalid University Hospital, Riyadh, Kingdom of Saudi Arabia E-mail : ,
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179
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Huch M, Gehart H, van Boxtel R, Hamer K, Blokzijl F, Verstegen MMA, Ellis E, van Wenum M, Fuchs SA, de Ligt J, van de Wetering M, Sasaki N, Boers SJ, Kemperman H, de Jonge J, Ijzermans JNM, Nieuwenhuis EES, Hoekstra R, Strom S, Vries RRG, van der Laan LJW, Cuppen E, Clevers H. Long-term culture of genome-stable bipotent stem cells from adult human liver. Cell 2015; 160:299-312. [PMID: 25533785 PMCID: PMC4313365 DOI: 10.1016/j.cell.2014.11.050] [Citation(s) in RCA: 1020] [Impact Index Per Article: 113.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/21/2014] [Accepted: 11/21/2014] [Indexed: 02/08/2023]
Abstract
Despite the enormous replication potential of the human liver, there are currently no culture systems available that sustain hepatocyte replication and/or function in vitro. We have shown previously that single mouse Lgr5+ liver stem cells can be expanded as epithelial organoids in vitro and can be differentiated into functional hepatocytes in vitro and in vivo. We now describe conditions allowing long-term expansion of adult bile duct-derived bipotent progenitor cells from human liver. The expanded cells are highly stable at the chromosome and structural level, while single base changes occur at very low rates. The cells can readily be converted into functional hepatocytes in vitro and upon transplantation in vivo. Organoids from α1-antitrypsin deficiency and Alagille syndrome patients mirror the in vivo pathology. Clonal long-term expansion of primary adult liver stem cells opens up experimental avenues for disease modeling, toxicology studies, regenerative medicine, and gene therapy.
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Affiliation(s)
- Meritxell Huch
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, CancerGenomics.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Helmuth Gehart
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, CancerGenomics.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ruben van Boxtel
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, CancerGenomics.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Karien Hamer
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, CancerGenomics.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Francis Blokzijl
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, CancerGenomics.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Monique M A Verstegen
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, the Netherlands
| | - Ewa Ellis
- Unit for Transplantation Surgery, Department of CLINTEC, Karolinska Institute, Karolinska University Hospital Huddinge, Hälsovägen, Flemingsberg, SE-141 86 Stockholm, Sweden
| | - Martien van Wenum
- Surgical Laboratory, Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Sabine A Fuchs
- Division of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Joep de Ligt
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, CancerGenomics.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Marc van de Wetering
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, CancerGenomics.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Hubrecht Organoid Technology (HUB), Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Nobuo Sasaki
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, CancerGenomics.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Susanne J Boers
- Division of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Hans Kemperman
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Jeroen de Jonge
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, the Netherlands
| | - Jan N M Ijzermans
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, the Netherlands
| | - Edward E S Nieuwenhuis
- Division of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Ruurdtje Hoekstra
- Surgical Laboratory, Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Stephen Strom
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Alle 8, F 56 141-86 Stockholm, Sweden
| | - Robert R G Vries
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, CancerGenomics.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Hubrecht Organoid Technology (HUB), Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, the Netherlands
| | - Edwin Cuppen
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, CancerGenomics.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, CancerGenomics.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
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180
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Li P, Ma X, Adams IR, Yuan P. A tight control of Rif1 by Oct4 and Smad3 is critical for mouse embryonic stem cell stability. Cell Death Dis 2015; 6:e1588. [PMID: 25569105 PMCID: PMC4669749 DOI: 10.1038/cddis.2014.551] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 11/03/2014] [Accepted: 11/17/2014] [Indexed: 12/20/2022]
Abstract
Prolonged culture of embryonic stem cells (ESCs) leads them to adopt embryonal carcinoma cell features, creating enormous dangers for their further application. The mechanism involved in ESC stability has not, however, been extensively studied. We previously reported that SMAD family member 3 (Smad3) has an important role in maintaining mouse ESC stability, as depletion of Smad3 results in cancer cell-like properties in ESCs and Smad3-/- ESCs are prone to grow large, malignant teratomas. To understand how Smad3 contributes to ESC stability, we performed microarray analysis to compare the transcriptome of wild-type and Smad3-/- ESCs. We found that Rif1 (RAP1-associated protein 1), a factor important for genomic stability, is significantly upregulated in Smad3-/- ESCs. The expression level of Rif1 needs to be tightly controlled in ESCs, as a low level of Rif1 is associated with ESC differentiation, but a high level of Rif1 is linked to ESC transformation. In ESCs, Oct4 activates Rif1, whereas Smad3 represses its expression. Oct4 recruits Smad3 to bind to Rif1 promoter, but Smad3 joining facilitates the loading of a polycomb complex that generates a repressive epigenetic modification on Rif1 promoter, and thus maintains the expression of Rif1 at a proper level in ESCs. Interestingly, Rif1 short hairpin RNA (shRNA)-transduced Smad3-/- ESCs showed less malignant properties than the control shRNA-transduced Smad3-/- ESCs, suggesting a critical role of Rif1 in maintaining the stability of ESCs during proliferation.
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Affiliation(s)
- P Li
- 1] Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [2] Department of Chemical Pathology, Stem Cell and Functional Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [3] The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - X Ma
- 1] Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [2] Department of Chemical Pathology, Stem Cell and Functional Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - I R Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - P Yuan
- 1] Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [2] Department of Chemical Pathology, Stem Cell and Functional Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [3] The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China [4] School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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181
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Kim JS, Hwang ST, Lee SH. Porous membrane culture method for expansion of human pluripotent stem cells. Methods Mol Biol 2015; 1212:65-72. [PMID: 25556655 DOI: 10.1007/7651_2014_174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
For the clinical application of human pluripotent stem cells (hPSCs), it is critical to develop novel culture techniques that completely exclude the use of animal feeder cells and enzyme treatments used in conventional hPSC culture systems. Here, we describe a novel culture method using a porous membrane that allows to maintain stable attachment and expansion of hPSCs, obviates the need for enzyme treatment, and also reduces feeder layer contamination.
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Affiliation(s)
- Jin-Su Kim
- Department of Biomedical Science, CHA University, CHA Bio Complex, 335 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea
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182
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Bai Q, Ramirez JM, Becker F, Pantesco V, Lavabre-Bertrand T, Hovatta O, Lemaître JM, Pellestor F, De Vos J. Temporal analysis of genome alterations induced by single-cell passaging in human embryonic stem cells. Stem Cells Dev 2014; 24:653-62. [PMID: 25254421 DOI: 10.1089/scd.2014.0292] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Simplified culture conditions are essential for large-scale drug screening and medical applications of human pluripotent stem cells (hPSCs). However, hPSCs [ie, human embryonic stem cells (hESCs), and human induced pluripotent stem cells (iPSCs) are prone to genomic instability, a phenomenon that is highly influenced by the culture conditions. Enzymatic dissociation, a cornerstone of large-scale hPSC culture systems, has been reported to be deleterious, but the extent and the timeline of the genomic alterations induced by this passaging technique are still unclear. We prospectively monitored three hESC lines that were initially derived and cultured on human feeders and passaged mechanically before switching to enzymatic single-cell passaging. We show that karyotype abnormalities and copy number variations are not restricted to long-term culture, but can occur very rapidly, within five passages after switching hESCs to enzymatic dissociation. Subchromosomal abnormalities preceded or accompanied karyotype abnormalities and were associated with increased occurrence of DNA double-strand breaks. Our results indicate that enzymatic single-cell passaging can be highly deleterious to the hPSC genome, even when used only for a limited period of time. Moreover, hPSC culture techniques should be reappraised by complementing the routine karyotype analysis with more sensitive techniques, such as microarrays, to detect subchromosomal abnormalities.
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Affiliation(s)
- Qiang Bai
- 1 INSERM , U1040, Montpellier, France
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183
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Mournetas V, Nunes QM, Murray PA, Sanderson CM, Fernig DG. Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells. PeerJ 2014; 2:e618. [PMID: 25374775 PMCID: PMC4217173 DOI: 10.7717/peerj.618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/22/2014] [Indexed: 12/19/2022] Open
Abstract
Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell-cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and Results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein-protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.
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Affiliation(s)
- Virginie Mournetas
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool , Liverpool , United Kingdom ; Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
| | - Quentin M Nunes
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom ; NIHR Liverpool Pancreas Biomedical Research Unit, Institute of Translational Medicine, University of Liverpool , Liverpool , United Kingdom
| | - Patricia A Murray
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool , Liverpool , United Kingdom
| | - Christopher M Sanderson
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool , Liverpool , United Kingdom
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
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184
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Oliveira PH, da Silva CL, Cabral JM. Concise Review: Genomic Instability in Human Stem Cells: Current Status and Future Challenges. Stem Cells 2014; 32:2824-32. [DOI: 10.1002/stem.1796] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/03/2014] [Accepted: 06/09/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Pedro H. Oliveira
- Institut Pasteur; Microbial Evolutionary Genomics, Département Génomes et Génétique; Paris France
- CNRS; UMR3525 Paris France
| | - Cláudia Lobato da Silva
- Institute for Biotechnology and Bioengineering, Department of Bioengineering; Instituto Superior Técnico, Universidade de Lisboa; Lisboa Portugal
| | - Joaquim M.S. Cabral
- Institute for Biotechnology and Bioengineering, Department of Bioengineering; Instituto Superior Técnico, Universidade de Lisboa; Lisboa Portugal
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185
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Villa-Diaz LG, Kim JK, Lahann J, Krebsbach PH. Derivation and long-term culture of transgene-free human induced pluripotent stem cells on synthetic substrates. Stem Cells Transl Med 2014; 3:1410-7. [PMID: 25313201 DOI: 10.5966/sctm.2014-0087] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We describe a platform to derive, culture, and differentiate genomically stable, transgene-free human induced pluripotent stem cells (iPSCs) on a fully synthetic polymer substrate made of a grafted zwitterionic hydrogel: poly2-(methacryloyloxy)ethyl dimethyl-(3-sulfopropyl) ammonium hydroxide (PMEDSAH). Three independent transgene-free iPSC lines derived in these conditions demonstrated continuous self-renewal, genomic stability, and pluripotency in vitro and in vivo after up to 9 months of continuous in vitro culture on PMEDSAH-grafted plates. Together, these data demonstrate the strength this alternative platform offers to generate and maintain human iPSCs for regenerative medicine.
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Affiliation(s)
- Luis Gerardo Villa-Diaz
- Department of Biologic and Materials Sciences, Biointerfaces Institute, and Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Jin Koo Kim
- Department of Biologic and Materials Sciences, Biointerfaces Institute, and Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Joerg Lahann
- Department of Biologic and Materials Sciences, Biointerfaces Institute, and Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Paul H Krebsbach
- Department of Biologic and Materials Sciences, Biointerfaces Institute, and Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
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186
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Sinha A, Cherba D, Bartlam H, Lenkiewicz E, Evers L, Barrett MT, Haab BB. Mesenchymal-like pancreatic cancer cells harbor specific genomic alterations more frequently than their epithelial-like counterparts. Mol Oncol 2014; 8:1253-65. [PMID: 24837184 PMCID: PMC4198499 DOI: 10.1016/j.molonc.2014.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 04/24/2014] [Accepted: 04/25/2014] [Indexed: 01/06/2023] Open
Abstract
The aggressiveness of pancreatic cancer is associated with the acquisition of mesenchymal characteristics by a subset of pancreatic cancer cells. The factors driving the development of this subset are not well understood. In this study, we tested the hypothesis that acquisition of a mesenchymal phenotype occurs selectively in tumor cells that harbor specific enabling genetic alterations. We obtained whole-genome comparative genomic hybridization (CGH) measurements on pancreatic cancer cell lines that have either an epithelial-like (17 cell lines) or a mesenchymal-like (9 cell lines) phenotype in vitro. The total amounts of amplifications and deletions were equivalent between the epithelial and mesenchymal groups, but 20 genes showed a major difference between the groups in prevalence of alterations. All 20 alterations (18 deletions and 2 amplifications) were more prevalent in the mesenchymal group, confirming the advanced nature of this cellular subtype. CDKN2A was altered in more than 50% of both groups, but co-deletions in neighboring genes, and concomitant loss of gene expression, were more prevalent in the mesenchymal group, suggesting that the size of the loss around CDKN2A affects cell phenotype. Whole-genome CGH on 11 primary cancer tissues revealed that the 20 genes were altered at a higher prevalence (up to 55% of the cases for certain genes) than randomly selected sets of 20 genes, with the same direction of alteration as in the cell lines. These findings support the concept that specific genetic alterations enable phenotype plasticity and provide promising candidate genes for further research.
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Affiliation(s)
- Arkadeep Sinha
- Van Andel Research Institute, 333 Bostwick NE, Grand Rapids, MI 49503, USA; Genetics Program, Michigan State University, East Lansing, MI, USA
| | - David Cherba
- Van Andel Research Institute, 333 Bostwick NE, Grand Rapids, MI 49503, USA
| | - Heather Bartlam
- Van Andel Research Institute, 333 Bostwick NE, Grand Rapids, MI 49503, USA
| | - Elizabeth Lenkiewicz
- Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, AZ, USA
| | - Lisa Evers
- Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, AZ, USA
| | - Michael T Barrett
- Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, AZ, USA
| | - Brian B Haab
- Van Andel Research Institute, 333 Bostwick NE, Grand Rapids, MI 49503, USA; Genetics Program, Michigan State University, East Lansing, MI, USA.
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187
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Lane A, Philip LR, Ruban L, Fynes K, Smart M, Carr A, Mason C, Coffey P. Engineering efficient retinal pigment epithelium differentiation from human pluripotent stem cells. Stem Cells Transl Med 2014; 3:1295-304. [PMID: 25273541 DOI: 10.5966/sctm.2014-0094] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Human embryonic stem cells (hESCs) are a promising source of retinal pigment epithelium (RPE) cells: cells that can be used for the treatment of common and incurable forms of blindness, such as age-related macular degeneration. Although most hESC lines will produce a number of clusters of pigmented RPE cells within 30-50 days when allowed to spontaneously differentiate, the timing and efficiency of differentiation is highly variable. This could prove problematic in the design of robust processes for the large scale production of RPE cells for cell therapy. In this study we sought to identify, quantify, and reduce the sources of variability in hESC-RPE differentiation. By monitoring the emergence of pigmented cells over time, we show how the cell line, passaging method, passage number, and seeding density have a significant and reproducible effect on the RPE yield. To counter this variability, we describe the production of RPE cells from two cell lines in feeder-free, density controlled conditions using single cell dissociation and seeding that is more amenable to scaled up production. The efficacy of small molecules in directing differentiation toward the RPE lineage was tested in two hESC lines with divergent RPE differentiation capacities. Neural induction by treatment with a bone morphogenetic protein inhibitor, dorsomorphin, significantly enhanced the RPE yield in one cell line but significantly reduce it in another, generating instead a Chx10 positive neural progenitor phenotype. This result underlines the necessity to tailor differentiation protocols to suit the innate properties of different cell lines.
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Affiliation(s)
- Amelia Lane
- Institute of Ophthalmology and Advanced Centre for Biochemical Engineering, University College London, London, United Kingdom
| | - Lissa Rachel Philip
- Institute of Ophthalmology and Advanced Centre for Biochemical Engineering, University College London, London, United Kingdom
| | - Ludmila Ruban
- Institute of Ophthalmology and Advanced Centre for Biochemical Engineering, University College London, London, United Kingdom
| | - Kate Fynes
- Institute of Ophthalmology and Advanced Centre for Biochemical Engineering, University College London, London, United Kingdom
| | - Matthew Smart
- Institute of Ophthalmology and Advanced Centre for Biochemical Engineering, University College London, London, United Kingdom
| | - Amanda Carr
- Institute of Ophthalmology and Advanced Centre for Biochemical Engineering, University College London, London, United Kingdom
| | - Chris Mason
- Institute of Ophthalmology and Advanced Centre for Biochemical Engineering, University College London, London, United Kingdom
| | - Pete Coffey
- Institute of Ophthalmology and Advanced Centre for Biochemical Engineering, University College London, London, United Kingdom
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188
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Xie P, Sun Y, Ouyang Q, Hu L, Tan Y, Zhou X, Xiong B, Zhang Q, Yuan D, Pan Y, Liu T, Liang P, Lu G, Lin G. Physiological oxygen prevents frequent silencing of the DLK1-DIO3 cluster during human embryonic stem cells culture. Stem Cells 2014; 32:391-401. [PMID: 24123616 DOI: 10.1002/stem.1558] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 07/28/2013] [Accepted: 08/25/2013] [Indexed: 12/18/2022]
Abstract
Genetic and epigenetic alterations are observed in long-term culture (>30 passages) of human embryonic stem cells (hESCs); however, little information is available in early cultures. Through a large-scale gene expression analysis between initial-passage hESCs (ihESCs, <10 passages) and early-passage hESCs (ehESCs, 20-30 passages) of 12 hESC lines, we found that the DLK1-DIO3 gene cluster was normally expressed and showed normal methylation pattern in ihESC, but was frequently silenced after 20 passages. Both the DLK1-DIO3 active status in ihESCs and the inactive status in ehESCs were inheritable during differentiation. Silencing of the DLK1-DIO3 cluster did not seem to compromise the multilineage differentiation ability of hESCs, but was associated with reduced DNA damage-induced apoptosis in ehESCs and their differentiated hepatocyte-like cell derivatives, possibly through attenuation of the expression and phosphorylation of p53. Furthermore, we demonstrated that 5% oxygen, instead of the commonly used 20% oxygen, is required for preserving the expression of the DLK1-DIO3 cluster. Overall, the data suggest that active expression of the DLK1-DIO3 cluster represents a new biomarker for epigenetic stability of hESCs and indicates the importance of using a proper physiological oxygen level during the derivation and culture of hESCs.
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Affiliation(s)
- Pingyuan Xie
- Institute of Reproductive & Stem Cell Engineering, Central South University, Changsha, China; Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Changsha, China
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189
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Aneuploidy induces profound changes in gene expression, proliferation and tumorigenicity of human pluripotent stem cells. Nat Commun 2014; 5:4825. [PMID: 25198699 DOI: 10.1038/ncomms5825] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 07/25/2014] [Indexed: 12/24/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) tend to acquire genomic aberrations in culture, the most common of which is trisomy of chromosome 12. Here we dissect the cellular and molecular implications of this trisomy in hPSCs. Global gene expression analyses reveal that trisomy 12 profoundly affects the gene expression profile of hPSCs, inducing a transcriptional programme similar to that of germ cell tumours. Comparison of proliferation, differentiation and apoptosis between diploid and aneuploid hPSCs shows that trisomy 12 significantly increases the proliferation rate of hPSCs, mainly as a consequence of increased replication. Furthermore, trisomy 12 increases the tumorigenicity of hPSCs in vivo, inducing transcriptionally distinct teratomas from which pluripotent cells can be recovered. Last, a chemical screen of 89 anticancer drugs discovers that trisomy 12 raises the sensitivity of hPSCs to several replication inhibitors. Together, these findings demonstrate the extensive effect of trisomy 12 and highlight its perils for successful hPSC applications.
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190
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Qian X, Villa-Diaz LG, Kumar R, Lahann J, Krebsbach PH. Enhancement of the propagation of human embryonic stem cells by modifications in the gel architecture of PMEDSAH polymer coatings. Biomaterials 2014; 35:9581-90. [PMID: 25189518 DOI: 10.1016/j.biomaterials.2014.08.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 08/08/2014] [Indexed: 01/08/2023]
Abstract
Well-defined culture conditions are essential for realizing the full potential of human embryonic stem cells (hESCs) in regenerative medicine where large numbers of cells are required. Synthetic polymers such as poly[2-(methacryloyloxy) ethyl dimethyl-(3-sulfopropyl) ammonium hydroxide] (PMEDSAH), offer multiple advantages over mouse embryonic fibroblasts (MEFs) and Matrigel™ for hESC culture and expansion. However, there is limited understanding of the mechanisms by which hESCs are propagated on synthetic polymers coatings. Here, the effects of PMEDSAH gel architecture on hESC self-renewal were determined. By increasing the atom transfer radical polymerization (ATRP) reaction time, the thickness of PMEDSAH was increased and its internal hydrogel architecture was modified, while maintaining its overall chemical structure. A 105 nm thick ATRP PMEDSAH coating showed a significant increase in the expansion rate of hESCs. Theoretical calculations suggested that 20,000 hESCs cultured on this substrate could be expanded up to 4.7 × 10(9) undifferentiated cells in five weeks. In addition, hESCs grown on ATRP PMEDSAH coatings retained pluripotency and displayed a normal karyotype after long-term culture. These data demonstrate the importance of polymer physical properties in hESC expansion. This modification of PMEDSAH coatings may be used to obtain large populations of hESCs required for many applications in regenerative medicine.
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Affiliation(s)
- Xu Qian
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Luis G Villa-Diaz
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Ramya Kumar
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Joerg Lahann
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Paul H Krebsbach
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, MI, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
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191
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Koh S, Piedrahita JA. From "ES-like" cells to induced pluripotent stem cells: a historical perspective in domestic animals. Theriogenology 2014; 81:103-11. [PMID: 24274415 DOI: 10.1016/j.theriogenology.2013.09.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/05/2013] [Accepted: 09/05/2013] [Indexed: 01/10/2023]
Abstract
Pluripotent stem cells such as embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) provide great potential as cell sources for gene editing to generate genetically modified animals, as well as in the field of regenerative medicine. Stable, long-term ESCs have been established in laboratory mouse and rat; however, isolation of true pluripotent ESCs in domesticated animals such as pigs and dogs have been less successful. Initially, domesticated animal pluripotent cell lines were referred to as "embryonic stem-like" cells owing to their similar morphologic characteristics to mouse ESCs, but accompanied by a limited ability to proliferate in vitro in an undifferentiated state. That is, they shared some but not all the characteristics of true ESCs. More recently, advances in reprogramming using exogenous transcription factors, combined with the utilization of small chemical inhibitors of key biochemical pathways, have led to the isolation of iPSCs. In this review, we provide a historical perspective of the isolation of various types of pluripotent stem cells in domesticated animals. In addition, we summarize the latest progress and limitations in the derivation and application of iPSCs.
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Affiliation(s)
- Sehwon Koh
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA; Genomics Program, North Carolina State University, Raleigh, North Carolina, USA
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192
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Yoon SW, Kim DK, Kim KP, Park KS. Rad51 regulates cell cycle progression by preserving G2/M transition in mouse embryonic stem cells. Stem Cells Dev 2014; 23:2700-11. [PMID: 24991985 DOI: 10.1089/scd.2014.0129] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Homologous recombination (HR) maintains genomic integrity against DNA replication stress and deleterious lesions, such as double-strand breaks (DSBs). Rad51 recombinase is critical for HR events that mediate the exchange of genetic information between parental chromosomes in eukaryotes. Additionally, Rad51 and HR accessory factors may facilitate replication fork progression by preventing replication fork collapse and repair DSBs that spontaneously arise during the normal cell cycle. In this study, we demonstrated a novel role for Rad51 during the cell cycle in mouse embryonic stem cells (mESCs). In mESCs, Rad51 was constitutively expressed throughout the cell cycle, and the formation of Rad51 foci increased as the cells entered S phase. Suppression of Rad51 expression caused cells to accumulate at G2/M phase and activated the DNA damage checkpoint, but it did not affect the self-renewal or differentiation capacity of mESCs. Even though Rad51 suppression significantly inhibited the proliferation rate of mESCs, Rad51 suppression did not affect the replication fork progression and speed, indicating that Rad51 repaired DNA damage and promoted DNA replication in S phase through an independent mechanism. In conclusion, Rad51 may contribute to G2/M transition in mESCs, while preserving genomic integrity in global organization of DNA replication fork.
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Affiliation(s)
- Sang-Wook Yoon
- 1 Department of Life Science, Chung-Ang University , Seoul, Korea
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193
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Ben-David U. Genomic instability, driver genes and cell selection: Projections from cancer to stem cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:427-35. [PMID: 25132386 DOI: 10.1016/j.bbagrm.2014.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/03/2014] [Accepted: 08/02/2014] [Indexed: 12/13/2022]
Abstract
Cancer cells and stem cells share many traits, including a tendency towards genomic instability. Human cancers exhibit tumor-specific genomic aberrations, which often affect their malignancy and drug response. During their culture propagation, human pluripotent stem cells (hPSCs) also acquire characteristic genomic aberrations, which may have significant impact on their molecular and cellular phenotypes. These aberrations vary in size from single nucleotide alterations to copy number alterations to whole chromosome gains. A prominent challenge in both cancer and stem cell research is to identify "driver aberrations" that confer a selection advantage, and "driver genes" that underlie the recurrence of these aberrations. Following principles that are already well-established in cancer research, candidate driver genes have also been suggested in hPSCs. Experimental validation of the functional role of such candidates can uncover whether these are bona fide driver genes. The identification of driver genes may bring us closer to a mechanistic understanding of the genomic instability of stem cells. Guided by terminologies and methodologies commonly applied in cancer research, such understanding may have important ramifications for both stem cell and cancer biology. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
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Affiliation(s)
- Uri Ben-David
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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194
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Amatori S, Ballarini M, Faversani A, Belloni E, Fusar F, Bosari S, Pelicci PG, Minucci S, Fanelli M. PAT-ChIP coupled with laser microdissection allows the study of chromatin in selected cell populations from paraffin-embedded patient samples. Epigenetics Chromatin 2014; 7:18. [PMID: 25104973 PMCID: PMC4124777 DOI: 10.1186/1756-8935-7-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 07/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The recent introduction of pathology tissue-chromatin immunoprecipitation (PAT-ChIP), a technique allowing chromatin immunoprecipitation from formalin-fixed and paraffin-embedded (FFPE) tissues, has expanded the application potential of epigenetic studies in tissue samples. However, FFPE tissue section analysis is strongly limited by tissue heterogeneity, which hinders linking the observed epigenetic events to the corresponding cellular population. Thus, ideally, to take full advantage of PAT-ChIP approaches, procedures able to increase the purity and homogeneity of cell populations from FFPE tissues are required. RESULTS In this study, we tested the use of both core needle biopsies (CNBs) and laser microdissection (LMD), evaluating the compatibility of these methods with the PAT-ChIP procedure. Modifications of the original protocols were introduced in order to increase reproducibility and reduce experimental time. We first demonstrated that chromatin can be prepared and effectively immunoprecipitated starting from 0.6-mm-diameter CNBs. Subsequently, in order to assess the applicability of PAT-ChIP to LMD samples, we tested the effects of hematoxylin or eosin staining on chromatin extraction and immunoprecipitation, as well as the reproducibility of our technique when using particularly low quantities of starting material. Finally, we carried out the PAT-ChIP using chromatin extracted from either normal tissue or neoplastic lesions, the latter obtained by LMD from FFPE lung sections derived from mutant K-ras(v12) transgenic mice or from human adeno- or squamous lung carcinoma samples. Well characterized histone post-translational modifications (HPTMs), such as H3K4me3, H3K27me3, H3K27Ac, and H3K9me3, were specifically immunoselected, as well as the CTCF transcription factor and RNA polymerase II (Pol II). CONCLUSIONS Epigenetic profiling can be performed on enriched cell populations obtained from FFPE tissue sections. The improved PAT-ChIP protocol will be used for the discovery and/or validation of novel epigenetic biomarkers in FFPE human samples.
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Affiliation(s)
- Stefano Amatori
- Department of Biomolecular Sciences, University of Urbino 'Carlo Bo', Molecular Pathology Lab. 'PaoLa', Via Arco d'Augusto, 2, Fano 61032, Italy ; Department of Experimental Oncology, European Institute of Oncology, Via Adamello, 16, Milan 20139, Italy
| | - Marco Ballarini
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello, 16, Milan 20139, Italy
| | - Alice Faversani
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 33, Milan 20122, Italy
| | - Elena Belloni
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello, 16, Milan 20139, Italy
| | - Fulvia Fusar
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello, 16, Milan 20139, Italy
| | - Silvano Bosari
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 33, Milan 20122, Italy ; Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 35, Milan 20122, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello, 16, Milan 20139, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello, 16, Milan 20139, Italy ; Department of Biosciences, University of Milan, Via Giovanni Celoria, 26, Milan 20133, Italy
| | - Mirco Fanelli
- Department of Biomolecular Sciences, University of Urbino 'Carlo Bo', Molecular Pathology Lab. 'PaoLa', Via Arco d'Augusto, 2, Fano 61032, Italy
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195
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Nguyen HT, Markouli C, Geens M, Barbe L, Sermon K, Spits C. Human embryonic stem cells show low-grade microsatellite instability. Mol Hum Reprod 2014; 20:981-9. [DOI: 10.1093/molehr/gau059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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196
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Sutiwisesak R, Kitiyanant N, Kotchabhakdi N, Felsenfeld G, Andrews PW, Wongtrakoongate P. Induced pluripotency enables differentiation of human nullipotent embryonal carcinoma cells N2102Ep. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2611-9. [PMID: 25086345 DOI: 10.1016/j.bbamcr.2014.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/18/2014] [Accepted: 07/22/2014] [Indexed: 12/21/2022]
Abstract
Embryonal carcinoma (EC) cells, which are considered to be malignant counterparts of embryonic stem cells, comprise the pluripotent stem cell component of teratocarcinomas, a form of testicular germ cell tumors (GCTs). Nevertheless, many established human EC cell lines are nullipotent with limited or no capacity to differentiate under normal circumstances. In this study, we tested whether an over-expression of Yamanaka's reprogramming factors OCT4, SOX2, c-MYC and KLF4 might enable differentiation of the human nullipotent EC cells N2102Ep. Using OCT4 knockdown differentiated N2102Ep cells, we are able to derive reprogrammed N2102Ep cell lines. The induced pluripotency of N2102Ep allows the cells to differentiate toward neural lineage by retinoic acid; the expression of SSEA3 and SSEA4 is down-regulated, whereas that of neural surface markers is up-regulated. Consistent with the up-regulation of neural surface markers, the expression of the master neuroectodermal transcription factor PAX6 is also induced in reprogrammed N2102Ep. We next investigated whether PAX6 might induce spontaneous differentiation of nullipotent stem cells N2102Ep. However, while an ectopic expression of PAX6 promotes differentiation of NTERA2, it induces cell death in N2102Ep. We nevertheless find that upon induction of retinoic acid, the reprogrammed N2102Ep cells form mature neuronal morphology similar to differentiated pluripotent stem cells NTERA2 as determined by TUJ1 expression, which is absent in N2102Ep parental cells. Altogether, we conclude that the nullipotent state of human EC cells can be reprogrammed to acquire a more relaxed state of differentiation potential by Yamanaka's factors.
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Affiliation(s)
- Rujapope Sutiwisesak
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhonpathom 73170, Thailand; Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Narisorn Kitiyanant
- Stem Cell Research Group, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhonpathom, 73170, Thailand
| | - Naiphinich Kotchabhakdi
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhonpathom 73170, Thailand
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter W Andrews
- Centre for Stem Cell Biology, University of Sheffield, S10 2TN, UK
| | - Patompon Wongtrakoongate
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Centre for Stem Cell Biology, University of Sheffield, S10 2TN, UK.
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197
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Krutá M, Šeneklová M, Raška J, Salykin A, Zerzánková L, Pešl M, Bártová E, Franek M, Baumeisterová A, Košková S, Neelsen KJ, Hampl A, Dvořák P, Rotrekl V. Mutation frequency dynamics in HPRT locus in culture-adapted human embryonic stem cells and induced pluripotent stem cells correspond to their differentiated counterparts. Stem Cells Dev 2014; 23:2443-54. [PMID: 24836366 DOI: 10.1089/scd.2013.0611] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The genomic destabilization associated with the adaptation of human embryonic stem cells (hESCs) to culture conditions or the reprogramming of induced pluripotent stem cells (iPSCs) increases the risk of tumorigenesis upon the clinical use of these cells and decreases their value as a model for cell biology studies. Base excision repair (BER), a major genomic integrity maintenance mechanism, has been shown to fail during hESC adaptation. Here, we show that the increase in the mutation frequency (MF) caused by the inhibition of BER was similar to that caused by the hESC adaptation process. The increase in MF reflected the failure of DNA maintenance mechanisms and the subsequent increase in MF rather than being due solely to the accumulation of mutants over a prolonged period, as was previously suggested. The increase in the ionizing-radiation-induced MF in adapted hESCs exceeded the induced MF in nonadapted hESCs and differentiated cells. Unlike hESCs, the overall DNA maintenance in iPSCs, which was reflected by the MF, was similar to that in differentiated cells regardless of the time spent in culture and despite the upregulation of several genes responsible for genome maintenance during the reprogramming process. Taken together, our results suggest that the changes in BER activity during the long-term cultivation of hESCs increase the mutagenic burden, whereas neither reprogramming nor long-term propagation in culture changes the MF in iPSCs.
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Affiliation(s)
- Miriama Krutá
- 1 Department of Biology, Faculty of Medicine, Masaryk University , Brno, Czech Republic
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198
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Chen KG, Hamilton RS, Robey PG, Mallon BS. Alternative cultures for human pluripotent stem cell production, maintenance, and genetic analysis. J Vis Exp 2014. [PMID: 25077932 DOI: 10.3791/51519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) hold great promise for regenerative medicine and biopharmaceutical applications. Currently, optimal culture and efficient expansion of large amounts of clinical-grade hPSCs are critical issues in hPSC-based therapies. Conventionally, hPSCs are propagated as colonies on both feeder and feeder-free culture systems. However, these methods have several major limitations, including low cell yields and generation of heterogeneously differentiated cells. To improve current hPSC culture methods, we have recently developed a new method, which is based on non-colony type monolayer (NCM) culture of dissociated single cells. Here, we present detailed NCM protocols based on the Rho-associated kinase (ROCK) inhibitor Y-27632. We also provide new information regarding NCM culture with different small molecules such as Y-39983 (ROCK I inhibitor), phenylbenzodioxane (ROCK II inhibitor), and thiazovivin (a novel ROCK inhibitor). We further extend our basic protocol to cultivate hPSCs on defined extracellular proteins such as the laminin isoform 521 (LN-521) without the use of ROCK inhibitors. Moreover, based on NCM, we have demonstrated efficient transfection or transduction of plasmid DNAs, lentiviral particles, and oligonucleotide-based microRNAs into hPSCs in order to genetically modify these cells for molecular analyses and drug discovery. The NCM-based methods overcome the major shortcomings of colony-type culture, and thus may be suitable for producing large amounts of homogeneous hPSCs for future clinical therapies, stem cell research, and drug discovery.
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Affiliation(s)
- Kevin G Chen
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health;
| | - Rebecca S Hamilton
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health
| | - Pamela G Robey
- Craniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health
| | - Barbara S Mallon
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health
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199
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Gaztelumendi N, Nogués C. Chromosome instability in mouse embryonic stem cells. Sci Rep 2014; 4:5324. [PMID: 24937170 PMCID: PMC4060510 DOI: 10.1038/srep05324] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/28/2014] [Indexed: 02/06/2023] Open
Abstract
Embryonic Stem Cells (ESCs) are expected to show a stable euploid karyotype, but in the last decade (sub)chromosomal aberrations have been systematically described in these cell lines when maintained in vitro. Culture conditions and long-term culture have been traditionally proposed as possible factors involved in the acquisition of chromosomal abnormalities. Thus, we analyzed the chromosome constitution, the undifferentiated state and the functional pluripotency of three different mouse ESCs grown under the same culture conditions. Two cell lines were unstable from early passages, whereas the third one retained its chromosome integrity after long-term culture despite using enzymatic methods for cell disaggregation. Trisomy 8 and 11 were clonally selected in both unstable cell lines, which also showed a higher growth rate than our normal cell line and suffered morphological changes in colony shape with increasing passage number. Regardless of the length of culture or the chromosome instability, all cell lines preserved their differentiation potential. These results confirm that double trisomy 8 and 11 confers a growth advantage to the abnormal cells, but not at the expense of cell differentiation. The presence of chromosome instability, widely related to tumor development and cancer disease, highlights the risk of using pluripotent cells in regenerative medicine.
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Affiliation(s)
| | - Carme Nogués
- Universitat Autònoma de Barcelona (UAB). Bellaterra, Catalonia, Spain
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200
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Time-lapse analysis of human embryonic stem cells reveals multiple bottlenecks restricting colony formation and their relief upon culture adaptation. Stem Cell Reports 2014; 3:142-55. [PMID: 25068128 PMCID: PMC4110749 DOI: 10.1016/j.stemcr.2014.05.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 12/26/2022] Open
Abstract
Using time-lapse imaging, we have identified a series of bottlenecks that restrict growth of early-passage human embryonic stem cells (hESCs) and that are relieved by karyotypically abnormal variants that are selected by prolonged culture. Only a minority of karyotypically normal cells divided after plating, and these were mainly cells in the later stages of cell cycle at the time of plating. Furthermore, the daughter cells showed a continued pattern of cell death after division, so that few formed long-term proliferating colonies. These colony-forming cells showed distinct patterns of cell movement. Increasing cell density enhanced cell movement facilitating cell:cell contact, which resulted in increased proportion of dividing cells and improved survival postplating of normal hESCs. In contrast, most of the karyotypically abnormal cells reentered the cell cycle on plating and gave rise to healthy progeny, without the need for cell:cell contacts and independent of their motility patterns. The growth of karyotypically normal hESCs is limited by multiple bottlenecks Bottlenecks include initial survival, entry into mitosis, and death following mitosis A privileged clonogenic state in normal hESCs is characterized by distinct motility Variant adapted cells and ROCK inhibition alleviate identified bottlenecks
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