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Yamagata Y, Parietti V, Stockholm D, Corre G, Poinsignon C, Touleimat N, Delafoy D, Besse C, Tost J, Galy A, Paldi A. Lentiviral transduction of CD34(+) cells induces genome-wide epigenetic modifications. PLoS One 2012; 7:e48943. [PMID: 23145033 PMCID: PMC3492239 DOI: 10.1371/journal.pone.0048943] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/02/2012] [Indexed: 02/01/2023] Open
Abstract
Epigenetic modifications may occur during in vitro manipulations of stem cells but these effects have remained unexplored in the context of cell and gene therapy protocols. In an experimental model of ex vivo gene modification for hematopoietic gene therapy, human CD34+ cells were cultured shortly in the presence of cytokines then with a gene transfer lentiviral vector (LV) expected to transduce cells but to have otherwise limited biological effects on the cells. At the end of the culture, the population of cells remained largely similar at the phenotypic level but some epigenetic changes were evident. Exposure of CD34+ cells to cytokines increased nuclear expression of epigenetic regulators SIRT1 or DNMT1 and caused genome-wide DNA methylation changes. Surprisingly, the LV caused additional and distinct effects. Large-scale genomic DNA methylation analysis showed that balanced methylation changes occurred in about 200 genes following culture of CD34+ cells in the presence of cytokines but 900 genes were modified following addition of the LV, predominantly increasing CpG methylation. Epigenetic effects resulting from ex vivo culture and from the use of LV may constitute previously unsuspected sources of biological effects in stem cells and may provide new biomarkers to rationally optimize gene and cell therapy protocols.
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Affiliation(s)
- Yoshiaki Yamagata
- Inserm, U951, Genethon, Evry, France
- Ecole Pratique des Hautes Etudes, UMRS_951, Genethon, Evry, France
- Department of Obstetrics and Gynaecology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Véronique Parietti
- Inserm, U951, Genethon, Evry, France
- Ecole Pratique des Hautes Etudes, UMRS_951, Genethon, Evry, France
| | - Daniel Stockholm
- Inserm, U951, Genethon, Evry, France
- Ecole Pratique des Hautes Etudes, UMRS_951, Genethon, Evry, France
| | - Guillaume Corre
- Inserm, U951, Genethon, Evry, France
- Ecole Pratique des Hautes Etudes, UMRS_951, Genethon, Evry, France
| | - Catherine Poinsignon
- Inserm, U951, Genethon, Evry, France
- Université Evry Val d’Essonne, UMRS_951, Genethon, Evry, France
| | - Nizar Touleimat
- Centre National de Génotypage, CEA – Institut de Génomique, Evry, France
| | - Damien Delafoy
- Centre National de Génotypage, CEA – Institut de Génomique, Evry, France
| | - Céline Besse
- Centre National de Génotypage, CEA – Institut de Génomique, Evry, France
| | - Jörg Tost
- Centre National de Génotypage, CEA – Institut de Génomique, Evry, France
- Fondation Jean Dausset- CEPH, Paris, France
| | - Anne Galy
- Inserm, U951, Genethon, Evry, France
- Ecole Pratique des Hautes Etudes, UMRS_951, Genethon, Evry, France
- Université Evry Val d’Essonne, UMRS_951, Genethon, Evry, France
- * E-mail: (AP); (AG)
| | - András Paldi
- Inserm, U951, Genethon, Evry, France
- Ecole Pratique des Hautes Etudes, UMRS_951, Genethon, Evry, France
- * E-mail: (AP); (AG)
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Stockholm D, Edom-Vovard F, Coutant S, Sanatine P, Yamagata Y, Corre G, Le Guillou L, Neildez-Nguyen TMA, Pàldi A. Bistable cell fate specification as a result of stochastic fluctuations and collective spatial cell behaviour. PLoS One 2010; 5:e14441. [PMID: 21203432 PMCID: PMC3010982 DOI: 10.1371/journal.pone.0014441] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Accepted: 11/30/2010] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND In culture, isogenic mammalian cells typically display enduring phenotypic heterogeneity that arises from fluctuations of gene expression and other intracellular processes. This diversity is not just simple noise but has biological relevance by generating plasticity. Noise driven plasticity was suggested to be a stem cell-specific feature. RESULTS Here we show that the phenotypes of proliferating tissue progenitor cells such as primary mononuclear muscle cells can also spontaneously fluctuate between different states characterized by the either high or low expression of the muscle-specific cell surface molecule CD56 and by the corresponding high or low capacity to form myotubes. Although this capacity is a cell-intrinsic property, the cells switch their phenotype under the constraints imposed by the highly heterogeneous microenvironment created by their own collective movement. The resulting heterogeneous cell population is characterized by a dynamic equilibrium between "high CD56" and "low CD56" phenotype cells with distinct spatial distribution. Computer simulations reveal that this complex dynamic is consistent with a context-dependent noise driven bistable model where local microenvironment acts on the cellular state by encouraging the cell to fluctuate between the phenotypes until the low noise state is found. CONCLUSIONS These observations suggest that phenotypic fluctuations may be a general feature of any non-terminally differentiated cell. The cellular microenvironment created by the cells themselves contributes actively and continuously to the generation of fluctuations depending on their phenotype. As a result, the cell phenotype is determined by the joint action of the cell-intrinsic fluctuations and by collective cell-to-cell interactions.
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Affiliation(s)
| | | | - Sophie Coutant
- Généthon, Evry, France
- INSERM U951, Université Evry Val d'Essonne, Evry, France
- UMR951, Ecole Pratique des Hautes Etudes, Evry, France
| | | | - Yoshiaki Yamagata
- Généthon, Evry, France
- INSERM U951, Université Evry Val d'Essonne, Evry, France
- UMR951, Ecole Pratique des Hautes Etudes, Evry, France
| | - Guillaume Corre
- Généthon, Evry, France
- INSERM U951, Université Evry Val d'Essonne, Evry, France
- UMR951, Ecole Pratique des Hautes Etudes, Evry, France
| | - Laurent Le Guillou
- LPNHE - Université Paris 6, Bureau 412 - Tour 43 RdC, Campus de Jussieu, Paris, France
| | - Thi My Anh Neildez-Nguyen
- Généthon, Evry, France
- INSERM U951, Université Evry Val d'Essonne, Evry, France
- UMR951, Ecole Pratique des Hautes Etudes, Evry, France
| | - Andràs Pàldi
- Généthon, Evry, France
- INSERM U951, Université Evry Val d'Essonne, Evry, France
- UMR951, Ecole Pratique des Hautes Etudes, Evry, France
- * E-mail:
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Smith PJ, Furon E, Wiltshire M, Campbell L, Feeney GP, Snyder RD, Errington RJ. ABCG2-associated resistance to Hoechst 33342 and topotecan in a murine cell model with constitutive expression of side population characteristics. Cytometry A 2010; 75:924-33. [PMID: 19802874 DOI: 10.1002/cyto.a.20800] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Drug resistant tumor "side-populations," enriched in cancer stem cells and identified by reduced accumulation of Hoechst 33342 under ABCG2-mediated efflux, may compromise therapeutic outcome. Side-population cells have predicted resistance to minor groove ligands, including the DNA topoisomerase I poison topotecan. We have used a stable Hoechst 33342-resistant murine L cell system (HoeR415) to study resistance patterns, removing the need for SP isolation before microarray analysis of gene expression and the tracking of cell cycle dynamics and cytotoxicity. The majority of HoeR415 cells displayed a side-population phenotype comparable with that of the side-population resident in the ABCG2 over-expressing A549 lung cancer cell line. Photo-crosslinking showed direct protection against minor groove ligand residence on DNA, driven by ABCG2-mediated efflux and not arising from any binding competition with endogenous polyamines. The covalent minor-groove binding properties of the drug FCE24517 (tallimustine) prevented resistance suggesting a mechanism for overcoming SP-related drug resistance. Hoechst 33342-resistant murine cells showed lower but significant crossresistance to topotecan, again attributable to enhanced ABCG2 expression, enabling cells to evade S-phase arrest. Hoechst 33342/TPT-resistant cells showed limited ancillary gene expression changes that could modify cellular capacity to cope with chronic stress including over-expression of Aldh1a1 and Mgst1, but under-expression of Plk2 and Nnt. There was no evidence to link the putative stem cell marker ALDH1A1 with any augmentation of the TPT resistance phenotype. The study has implications for the patterns of drug resistance arising during tumor repopulation and the basal resistance to minor groove-binding drugs of tumor side-populations.
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Affiliation(s)
- Paul J Smith
- Department of Pathology, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom.
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Khodabukus A, Baar K. Regulating fibrinolysis to engineer skeletal muscle from the C2C12 cell line. Tissue Eng Part C Methods 2009; 15:501-11. [PMID: 19191517 DOI: 10.1089/ten.tec.2008.0286] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Muscles engineered from transformed cells would be a powerful model for the study of muscle physiology by allowing long-term in vitro studies of muscle adaptation. However, previously described methods either take >5 weeks to produce a tissue or use collagen as a scaffold, which decreases the specific force of the muscle, making it hard to measure the function of the constructs. The aim of this study was to rapidly engineer muscle using the C2C12 cell line in fibrin, which has a stiffness similar to muscle tissue, allowing accurate functional testing. Both the protease inhibitor aprotinin and the natural cross-linker genipin increased the length of time that muscle could be cultured, with genipin increasing the time in culture to 10 weeks. The function of the tissues was significantly affected by the batch of serum (64-78%) or thrombin (41%), the differentiation medium (78%), and the seeding protocol (38%), but was unaffected by initial cell number. Strikingly, different C2C12 clones produced up to a 3.6-fold variation in force production. Under optimal conditions, the tissues form in 10.4+/-0.3 days and remain fully functional for 5 weeks over which time they continue to mature. The optimized model described here provides rapid, reliable, and functional tissues that will be useful in the study of skeletal muscle physiology.
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Affiliation(s)
- Alastair Khodabukus
- Functional Molecular Biology Lab, Division of Molecular Physiology, University of Dundee, Dundee DD1 5EH, United Kingdom
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Preffer F, Dombkowski D. Advances in complex multiparameter flow cytometry technology: Applications in stem cell research. CYTOMETRY PART B-CLINICAL CYTOMETRY 2009; 76:295-314. [PMID: 19492350 DOI: 10.1002/cyto.b.20480] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Flow cytometry and cell sorting are critical tools in stem cell research. Recent advances in flow cytometric hardware, reagents, and software have synergized to permit the stem cell biologist to more fully identify and isolate rare cells based on their immunofluorescent and light scatter characteristics. Some of these improvements include physically smaller air-cooled lasers, new designs in optics, new fluorescent conjugate-excitation pairs, and improved software to visualize data, all which combine to open up new horizons in the study of stem cells, by enhancing the resolution and specificity of inquiry. In this review, these recent improvements in technology will be outlined and important cell surface and functional antigenic markers useful for the study of stem cells described.
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Affiliation(s)
- Frederic Preffer
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.
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Gilbert DF, Meinhof T, Pepperkok R, Runz H. DetecTiff: a novel image analysis routine for high-content screening microscopy. ACTA ACUST UNITED AC 2009; 14:944-55. [PMID: 19641223 DOI: 10.1177/1087057109339523] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this article, the authors describe the image analysis software DetecTiff, which allows fully automated object recognition and quantification from digital images. The core module of the LabView-based routine is an algorithm for structure recognition that employs intensity thresholding and size-dependent particle filtering from microscopic images in an iterative manner. Detected structures are converted into templates, which are used for quantitative image analysis. DetecTiff enables processing of multiple detection channels and provides functions for template organization and fast interpretation of acquired data. The authors demonstrate the applicability of DetecTiff for automated analysis of cellular uptake of fluorescence-labeled low-density lipoproteins as well as diverse other image data sets from a variety of biomedical applications. Moreover, the performance of DetecTiff is compared with preexisting image analysis tools. The results show that DetecTiff can be applied with high consistency for automated quantitative analysis of image data (e.g., from large-scale functional RNAi screening projects).
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Takács L, Tóth E, Berta A, Vereb G. Stem cells of the adult cornea: from cytometric markers to therapeutic applications. Cytometry A 2009; 75:54-66. [PMID: 19051301 DOI: 10.1002/cyto.a.20671] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cornea is a major protective shield of the interior of the eye and represents two thirds of its refractive power. It is made up of three tissue layers that have different developmental origins: the outer, epithelial layer develops from the ectoderm overlying the lens vesicle, whereas the stroma and the endothelium have mesenchymal origin. In the adult organism, the outermost corneal epithelium is the most exposed to environmental damage, and its constant renewal is assured by the epithelial stem cells that reside in the limbus, the circular border of the cornea. Cell turnover in the stromal layer is very slow and the endothelial cells probably do not reproduce in the adult organism. However, recent experimental evidence indicates that stem cells may be found in these layers. Damage to any of the corneal layers leads to loss of transparency and low vision. Corneal limbal stem cell deficiency results in severe ocular surface disease and its treatment by transplantating ex vivo expanded limbal epithelial cells is becoming widely accepted today. Stromal and endothelial stem cells are potential tools of tissue engineering and regenerative therapies of corneal ulcers and endothelial cell loss. In the past few years, intensive research has focused on corneal stem cells aiming to improve the outcomes of the current corneal stem cell transplantation techniques. This review summarizes the current state of knowledge on corneal epithelial, stromal and endothelial stem cells. Special emphasis is placed on the molecular markers that may help to identify these cells, and the recently revealed mechanisms that could maintain their "stemness" or drive their differentiation. The techniques for isolating and culturing/expanding these cells are also described.
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Affiliation(s)
- Lili Takács
- Department of Ophthalmology, Medical and Health Science Center, University of Debrecen, Hungary
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Fábián A, Barok M, Vereb G, Szöllosi J. Die hard: are cancer stem cells the Bruce Willises of tumor biology? Cytometry A 2009; 75:67-74. [PMID: 19051297 DOI: 10.1002/cyto.a.20690] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In recent years, an exponentially growing number of studies have focused on identifying cancer stem cells (CSC) in human malignancies. The rare CSCs could be crucial in controlling and curing cancer: through asymmetric division CSCs supposedly drive tumor growth and evade therapy with the help of traits shared with normal stem cells such as quiescence, self-renewal ability, and multidrug resistance pump activity. Here, we give a brief overview of techniques used to confirm the stem cell-like behavior of putative CSCs and discuss markers and methods for identifying, isolating, and culturing them. We touch on the limitations of each marker and why the combined use of CSC markers, in vitro and in vivo assays may still fail to identify all relevant CSC populations. Finally, the various experimental findings supporting and contradicting the CSC hypothesis are summarized. The large number of tumor types thus far with a subpopulation of uniquely tumorigenic and therapy resistant cells suggests that despite the unanswered questions and inconsistencies, the CSC hypothesis has a legitimate role to play in tumor biology. At the same time, experimental evidence supporting the established alternative theory of clonal evolution can be found as well. Therefore, a model that describes cancer initiation and progression should combine elements of clonal evolution and CSC theory.
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Affiliation(s)
- Akos Fábián
- Department of Biophysics and Cell Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Hungary
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Shan SW, Tang MK, Chow PH, Maroto M, Cai DQ, Lee KKH. Induction of growth arrest and polycomb gene expression by reversine allows C2C12 cells to be reprogrammed to various differentiated cell types. Proteomics 2008; 7:4303-16. [PMID: 17973295 DOI: 10.1002/pmic.200700636] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Reversine is a small, cell permeable synthetic chemical that has the ability to reprogram C2C12 myogenic cells to become various differentiated cell types. However, we still do not know how reversine works or the genes and proteins involved. Hence, we have used comparative proteomic techniques to address this issue. We have identified several proteins that were associated with cell cycle progression which were downregulated by reversine. Simultaneously, there were proteins associated with the induction of growth arrest that were upregulated. Consequently, we investigated the effects of reversine on C2C12 cell growth and established that it inhibited cell growth. Reversine had little affects on cell survival. We also investigated whether expressions of the polycomb genes, polycomb repressive complex 1 (PHC1) and Ezh2, were affected by reversine. Polycomb group genes are normally involved in chromatin based gene silencing. We found that PHC1 and Ezh2 expressions were enhanced by reversine and that it correlated with the inhibition of muscle specific transcriptional factor genes, myogenin, MyoD, and Myf5. Therefore, we believe that reversine is able to reprogram C2C12 cells to various differentiated cell types by inducing cell growth arrest, and promoting PHC1 and Ezh2 expressions.
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Affiliation(s)
- Sze Wan Shan
- Department of Anatomy, Basic Medical Science Building, Chinese University of Hong Kong, Shatin, Hong Kong
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Stockholm D, Benchaouir R, Picot J, Rameau P, Neildez TMA, Landini G, Laplace-Builhé C, Paldi A. The origin of phenotypic heterogeneity in a clonal cell population in vitro. PLoS One 2007; 2:e394. [PMID: 17460761 PMCID: PMC1851097 DOI: 10.1371/journal.pone.0000394] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Accepted: 04/02/2007] [Indexed: 11/18/2022] Open
Abstract
Background The spontaneous emergence of phenotypic heterogeneity in clonal populations of mammalian cells in vitro is a rule rather than an exception. We consider two simple, mutually non-exclusive models that explain the generation of diverse cell types in a homogeneous population. In the first model, the phenotypic switch is the consequence of extrinsic factors. Initially identical cells may become different because they encounter different local environments that induce adaptive responses. According to the second model, the phenotypic switch is intrinsic to the cells that may occur even in homogeneous environments. Principal Findings We have investigated the “extrinsic” and the “intrinsic” mechanisms using computer simulations and experimentation. First, we simulated in silico the emergence of two cell types in a clonal cell population using a multiagent model. Both mechanisms produced stable phenotypic heterogeneity, but the distribution of the cell types was different. The “intrinsic” model predicted an even distribution of the rare phenotype cells, while in the “extrinsic” model these cells formed small clusters. The key predictions of the two models were confronted with the results obtained experimentally using a myogenic cell line. Conclusions The observations emphasize the importance of the “ecological” context and suggest that, consistently with the “extrinsic” model, local stochastic interactions between phenotypically identical cells play a key role in the initiation of phenotypic switch. Nevertheless, the “intrinsic” model also shows some other aspects of reality: The phenotypic switch is not triggered exclusively by the local environmental variations, but also depends to some extent on the phenotypic intrinsic robustness of the cells.
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Affiliation(s)
- Daniel Stockholm
- GENETHON–Centre National de la Recherche Scientifique (CNRS), UMR 8115, Evry, France
| | - Rachid Benchaouir
- GENETHON–Centre National de la Recherche Scientifique (CNRS), UMR 8115, Evry, France
| | - Julien Picot
- GENETHON–Centre National de la Recherche Scientifique (CNRS), UMR 8115, Evry, France
| | - Philippe Rameau
- GENETHON–Centre National de la Recherche Scientifique (CNRS), UMR 8115, Evry, France
| | - Thi My Anh Neildez
- GENETHON–Centre National de la Recherche Scientifique (CNRS), UMR 8115, Evry, France
- Ecole Pratique des Hautes Etudes, Paris, France
| | - Gabriel Landini
- Oral Pathology Unit, School of Dentistry, The University of Birmingham, Birmingham, England
| | | | - Andras Paldi
- GENETHON–Centre National de la Recherche Scientifique (CNRS), UMR 8115, Evry, France
- Ecole Pratique des Hautes Etudes, Paris, France
- * To whom correspondence should be addressed. E-mail:
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