51
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Fernandez-Rebollo E, Eipel M, Seefried L, Hoffmann P, Strathmann K, Jakob F, Wagner W. Primary Osteoporosis Is Not Reflected by Disease-Specific DNA Methylation or Accelerated Epigenetic Age in Blood. J Bone Miner Res 2018; 33:356-361. [PMID: 28926142 DOI: 10.1002/jbmr.3298] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 12/12/2022]
Abstract
Osteoporosis is an age-related metabolic bone disease. Hence, osteoporotic patients might suffer from molecular features of accelerated aging, which is generally reflected by specific age-associated DNA methylation (DNAm) changes. In this study, we analyzed genomewide DNAm profiles of peripheral blood from patients with manifest primary osteoporosis and non-osteoporotic controls. Statistical analysis did not reveal any individual CG dinucleotides (CpG sites) with significant aberrant DNAm in osteoporosis. Subsequently, we analyzed if age-associated DNAm patterns are increased in primary osteoporosis (OP). Using three independent age-predictors we did not find any evidence for accelerated epigenetic age in blood of osteoporotic patients. Taken together, osteoporosis is not reflected by characteristic DNAm patterns of peripheral blood that might be used as biomarker for the disease. The prevalence of osteoporosis is age-associated-but it is not associated with premature epigenetic aging in peripheral blood. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Eduardo Fernandez-Rebollo
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Technology-Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Monika Eipel
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Technology-Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Lothar Seefried
- Orthopedic Center for Musculoskeletal Research, Orthopedic Department, University of Würzburg, Würzburg, Germany
| | - Per Hoffmann
- Department of Genomics, Institute of Human Genetics, University of Bonn, Bonn, Germany.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Switzerland
| | - Klaus Strathmann
- Institute for Transfusion Medicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Franz Jakob
- Orthopedic Center for Musculoskeletal Research, Orthopedic Department, University of Würzburg, Würzburg, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Technology-Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
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52
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Ubiquitin C decrement plays a pivotal role in replicative senescence of bone marrow mesenchymal stromal cells. Cell Death Dis 2018; 9:139. [PMID: 29382826 PMCID: PMC5833785 DOI: 10.1038/s41419-017-0032-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/27/2017] [Accepted: 10/04/2017] [Indexed: 12/18/2022]
Abstract
Human bone marrow-mesenchymal stromal cells (hBM-MSCs) undergo cellular senescence during in vitro culture. In this study, we defined this replicative senescence as impaired proliferation, deterioration in representative cell characteristics, accumulated DNA damage, and decreased telomere length and telomerase activity with or without genomic abnormalities. The UBC gene expression gradually decreased during passaging along with the reduction in series of molecules including hub genes; CDK1, CCNA2, MCM10, E2F1, BRCA1, HIST1H1A and HIST1H3B. UBC knockdown in hBM-MSCs induced impaired proliferation in dose-dependent manner and showed replicative senescence-like phenomenon. Gene expression changes after UBC knockdown were similar to late passage hBM-MSCs. Additionally, UBC overexpession improved the proliferation activity of hBM-MSCs accompanied by increased expression of the hub genes. Consequently, UBC worked in higher-order through regulation of the hub genes controlling cell cycle and proliferation. These results indicate that the decrement of UBC expression plays a pivotal role in replicative senescence of hBM-MSCs.
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53
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Strässler ET, Aalto-Setälä K, Kiamehr M, Landmesser U, Kränkel N. Age Is Relative-Impact of Donor Age on Induced Pluripotent Stem Cell-Derived Cell Functionality. Front Cardiovasc Med 2018; 5:4. [PMID: 29423397 PMCID: PMC5790033 DOI: 10.3389/fcvm.2018.00004] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/09/2018] [Indexed: 01/20/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) avoid many of the restrictions that hamper the application of human embryonic stem cells: limited availability of source material due to legal restrictions in some countries, immunogenic rejection and ethical concerns. Also, the donor’s clinical phenotype is often known when working with iPSCs. Therefore, iPSCs seem ideal to tackle the two biggest tasks of regenerative medicine: degenerative diseases with genetic cause (e.g., Duchenne’s muscular dystrophy) and organ replacement in age-related diseases (e.g., end-stage heart or renal failure), especially in combination with recently developed gene-editing tools. In the setting of autologous transplantation in elderly patients, donor age becomes a potentially relevant factor that needs to be assessed. Here, we review and critically discuss available data pertinent to the questions: How does donor age influence the reprogramming process and iPSC functionality? Would it even be possible to reprogram senescent somatic cells? How does donor age affect iPSC differentiation into specialised cells and their functionality? We also identify research needs, which might help resolve current unknowns. Until recently, most hallmarks of ageing were attributed to an accumulation of DNA damage over time, and it was thus expected that DNA damage from a somatic cell would accumulate in iPSCs and the cells derived from them. In line with this, a decreased lifespan of cloned organisms compared with the donor was also observed in early cloning experiments. Therefore, it was questioned for a time whether iPSC derived from an old individual’s somatic cells would suffer from early senescence and, thus, may not be a viable option either for disease modelling nor future clinical applications. Instead, typical signs of cellular ageing are reverted in the process of iPSC reprogramming, and iPSCs from older donors do not show diminished differentiation potential nor do iPSC-derived cells from older donors suffer early senescence or show functional impairments when compared with those from younger donors. Thus, the data would suggest that donor age does not limit iPSC application for modelling genetic diseases nor regenerative therapies. However, open questions remain, e.g., regarding the potential tumourigenicity of iPSC-derived cells and the impact of epigenetic pattern retention.
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Affiliation(s)
- Elisabeth Tamara Strässler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Partner Site Berlin, German Centre for Cardiovascular Research (DZHK), Berlin, Germany
| | - Katriina Aalto-Setälä
- University of Tampere, Department of Medicine and Life Sciences, Tampere, Finland.,Heart Center, Tampere University Hospital, Tampere, Finland
| | - Mostafa Kiamehr
- University of Tampere, Department of Medicine and Life Sciences, Tampere, Finland.,Heart Center, Tampere University Hospital, Tampere, Finland
| | - Ulf Landmesser
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Partner Site Berlin, German Centre for Cardiovascular Research (DZHK), Berlin, Germany
| | - Nicolle Kränkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Partner Site Berlin, German Centre for Cardiovascular Research (DZHK), Berlin, Germany
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54
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Gao C, Xing X, He Z, Chen S, Wang S, Li Q, Guo P, Zhang H, Li H, Chen L, Wang Q, Zhao J, Xiao Y, Chen W, Li D. Hypermethylation of PGCP gene is associated with human bronchial epithelial cells immortalization. Gene 2017; 642:505-512. [PMID: 29196255 DOI: 10.1016/j.gene.2017.11.063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/30/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023]
Abstract
Cell immortalization is the initial step for cancer development. To identify the differentially expressed genes regulated by DNA methylation over the course of human primary bronchial epithelial cell (HPBECs) immortalization, an immortalized HBE cell line (HBETT) was generated via introduction of an SV40 LT and a catalytic subunit of human telomerase reverse transcriptase (hTERT) into the HPBECs. Microarrays of mRNA and DNA methylation were performed to compare the transcriptomes and DNA methylomes between these two types of cells. The results from the mRNA microarray revealed many genes whose expression changed upon cell immortalization. We identified signatures including global hypomethylation, perturbation of ECM-receptor interaction, focal adhesion, and PI3K-Akt pathways associated with cell immortalization. Moreover, we revealed 155 differentiated methylation regions (DMRs) within the CpG islands (CGIs) of 42 genes and the perturbation of several key pathways that might be involved in HBE cell immortalization. Among these genes, the hypermethylation of the plasma glutamate carboxypeptidase (PGCP) gene appeared specifically in lung cancer tissues. The inhibition of PGCP expression by promoter hypermethylation was observed in both immortal HBETT cells and benzo[a]pyrene (Bap)-transformed HBE cells. In conclusion, these findings provide new insight into the epigenetic modifications that are critical in the transition and maintenance of cell immortalization.
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Affiliation(s)
- Chen Gao
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiumei Xing
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zhini He
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Shen Chen
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Shan Wang
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qingye Li
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ping Guo
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Haiyan Zhang
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Huiyao Li
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Liping Chen
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qing Wang
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jian Zhao
- Department of Chest Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Yongmei Xiao
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wen Chen
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China.
| | - Daochuan Li
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China.
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55
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Goetzke R, Franzen J, Ostrowska A, Vogt M, Blaeser A, Klein G, Rath B, Fischer H, Zenke M, Wagner W. Does soft really matter? Differentiation of induced pluripotent stem cells into mesenchymal stromal cells is not influenced by soft hydrogels. Biomaterials 2017; 156:147-158. [PMID: 29197223 DOI: 10.1016/j.biomaterials.2017.11.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 11/21/2017] [Indexed: 01/22/2023]
Abstract
Induced pluripotent stem cells (iPSCs) can be differentiated toward mesenchymal stromal cells (MSCs), but this transition remains incomplete. It has been suggested that matrix elasticity directs cell-fate decisions. Therefore, we followed the hypothesis that differentiation of primary MSCs and generation of iPSC-derived MSCs (iMSCs) is supported by a soft matrix of human platelet lysate (hPL-gel). We demonstrate that this fibrin-based hydrogel supports growth of primary MSCs with pronounced deposition of extracellular matrix, albeit it hardly impacts on gene expression profiles or in vitro differentiation of MSCs. Furthermore, iPSCs can be effectively differentiated toward MSC-like cells on the hydrogel. Unexpectedly, this complex differentiation process is not affected by the substrate: iMSCs generated on tissue culture plastic (TCP) or hPL-gel have the same morphology, immunophenotype, differentiation potential, and gene expression profiles. Moreover, global DNA methylation patterns are essentially identical in iMSCs generated on TCP or hPL-gel, indicating that they are epigenetically alike. Taken together, hPL-gel provides a powerful matrix that supports growth and differentiation of primary MSCs and iMSCs - but this soft hydrogel does not impact on lineage-specific differentiation.
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Affiliation(s)
- Roman Goetzke
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Julia Franzen
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Alina Ostrowska
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Michael Vogt
- Interdisciplinary Center for Clinical Research IZKF Aachen, RWTH Aachen, University Medical School, Aachen, Germany
| | - Andreas Blaeser
- Department of Dental Materials and Biomaterials Research, RWTH Aachen University Hospital, Aachen, Germany
| | - Gerd Klein
- Center for Medical Research, Department of Medicine II, University of Tübingen, Tübingen, Germany
| | - Björn Rath
- Department of Orthopedics, RWTH Aachen University Medical School, Aachen, Germany
| | - Horst Fischer
- Department of Dental Materials and Biomaterials Research, RWTH Aachen University Hospital, Aachen, Germany
| | - Martin Zenke
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany; Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany; Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.
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56
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Epigenetic regulation in cell senescence. J Mol Med (Berl) 2017; 95:1257-1268. [DOI: 10.1007/s00109-017-1581-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/26/2022]
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57
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Pasumarthy KK, Doni Jayavelu N, Kilpinen L, Andrus C, Battle SL, Korhonen M, Lehenkari P, Lund R, Laitinen S, Hawkins RD. Methylome Analysis of Human Bone Marrow MSCs Reveals Extensive Age- and Culture-Induced Changes at Distal Regulatory Elements. Stem Cell Reports 2017; 9:999-1015. [PMID: 28844656 PMCID: PMC5599244 DOI: 10.1016/j.stemcr.2017.07.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 12/26/2022] Open
Abstract
Human bone marrow stromal cells, or mesenchymal stem cells (BM-MSCs), need expansion prior to use as cell-based therapies in immunological and tissue repair applications. Aging and expansion of BM-MSCs induce epigenetic changes that can impact therapeutic outcomes. By applying sequencing-based methods, we reveal that the breadth of DNA methylation dynamics associated with aging and expansion is greater than previously reported. Methylation changes are enriched at known distal transcription factor binding sites such as enhancer elements, instead of CpG-rich regions, and are associated with changes in gene expression. From this, we constructed hypo- and hypermethylation-specific regulatory networks, including a sub-network of BM-MSC master regulators and their predicted target genes, and identified putatively disrupted signaling pathways. Our genome-wide analyses provide a broader overview of age- and expansion-induced DNA methylation changes and a better understanding of the extent to which these changes alter gene expression and functionality of human BM-MSCs.
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Affiliation(s)
| | - Naresh Doni Jayavelu
- Turku Centre for Biotechnology, University of Turku, Turku 20520, Finland; Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Lotta Kilpinen
- Research and Development, Medical Services, Finnish Red Cross Blood Service, Helsinki 00310, Finland
| | - Colin Andrus
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stephanie L Battle
- Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Matti Korhonen
- Cell Therapy Services, Medical Services, Finnish Red Cross Blood Service, Helsinki 00310, Finland
| | - Petri Lehenkari
- Institute of Clinical Medicine, Division of Surgery and Institute of Biomedicine, Department of Anatomy and Cell Biology, University of Oulu, Oulu 90014, Finland; Clinical Research Center, Department of Surgery and Intensive Care, Oulu University Hospital, Oulu 90014, Finland
| | - Riikka Lund
- Turku Centre for Biotechnology, University of Turku, Turku 20520, Finland; Åbo Akademi University, Turku 20520, Finland
| | - Saara Laitinen
- Research and Development, Medical Services, Finnish Red Cross Blood Service, Helsinki 00310, Finland
| | - R David Hawkins
- Turku Centre for Biotechnology, University of Turku, Turku 20520, Finland; Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.
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58
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Fernandez-Rebollo E, Mentrup B, Ebert R, Franzen J, Abagnale G, Sieben T, Ostrowska A, Hoffmann P, Roux PF, Rath B, Goodhardt M, Lemaitre JM, Bischof O, Jakob F, Wagner W. Human Platelet Lysate versus Fetal Calf Serum: These Supplements Do Not Select for Different Mesenchymal Stromal Cells. Sci Rep 2017; 7:5132. [PMID: 28698620 PMCID: PMC5506010 DOI: 10.1038/s41598-017-05207-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/25/2017] [Indexed: 01/23/2023] Open
Abstract
Culture medium of mesenchymal stromal cells (MSCs) is usually supplemented with either human platelet lysate (HPL) or fetal calf serum (FCS). Many studies have demonstrated that proliferation and cellular morphology are affected by these supplements – it is therefore important to determine if they favor outgrowth of different subpopulations and thereby impact on the heterogeneous composition of MSCs. We have isolated and expanded human bone marrow-derived MSCs in parallel with HPL or FCS and demonstrated that HPL significantly increases proliferation and leads to dramatic differences in cellular morphology. Remarkably, global DNA-methylation profiles did not reveal any significant differences. Even at the transcriptomic level, there were only moderate changes in pairwise comparison. Furthermore, the effects on proliferation, cytoskeletal organization, and focal adhesions were reversible by interchanging to opposite culture conditions. These results indicate that cultivation of MSCs with HPL or FCS has no systematic bias for specific cell types.
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Affiliation(s)
- Eduardo Fernandez-Rebollo
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, 52074, Germany. .,Institute for Biomedical Technology - Cell Biology, RWTH Aachen University Medical School, Aachen, 52074, Germany.
| | - Birgit Mentrup
- Orthopedic Center for Musculoskeletal Research, Orthopedic Department, University of Würzburg, Würzburg, 97074, Germany
| | - Regina Ebert
- Orthopedic Center for Musculoskeletal Research, Orthopedic Department, University of Würzburg, Würzburg, 97074, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH Aachen University Medical School, Aachen, 52074, Germany
| | - Giulio Abagnale
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH Aachen University Medical School, Aachen, 52074, Germany
| | - Torsten Sieben
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH Aachen University Medical School, Aachen, 52074, Germany
| | - Alina Ostrowska
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH Aachen University Medical School, Aachen, 52074, Germany
| | - Per Hoffmann
- Department of Genomics, Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, 4031, Switzerland
| | - Pierre-François Roux
- Laboratory of Nuclear Organization and Oncogenesis, Department of Cell Biology and Infection, INSERM U.993, Institute Pasteur, 75015, Paris, France
| | - Björn Rath
- Department for Orthopedics, RWTH Aachen University Medical School, Aachen, 52074, Germany
| | - Michele Goodhardt
- Institut Universitaire d'Hématologie, INSERM UMRS-1126, University Paris Diderot, 75010, Paris, France
| | - Jean-Marc Lemaitre
- Institute of Regenerative Medicine and Biotherapies (IRMB), INSERM U1183, University of Montpellier, Montpellier, Cedex 05, 34295, France
| | - Oliver Bischof
- Laboratory of Nuclear Organization and Oncogenesis, Department of Cell Biology and Infection, INSERM U.993, Institute Pasteur, 75015, Paris, France
| | - Franz Jakob
- Orthopedic Center for Musculoskeletal Research, Orthopedic Department, University of Würzburg, Würzburg, 97074, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, 52074, Germany. .,Institute for Biomedical Technology - Cell Biology, RWTH Aachen University Medical School, Aachen, 52074, Germany.
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59
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Franzen J, Zirkel A, Blake J, Rath B, Benes V, Papantonis A, Wagner W. Senescence-associated DNA methylation is stochastically acquired in subpopulations of mesenchymal stem cells. Aging Cell 2017; 16:183-191. [PMID: 27785870 PMCID: PMC5242294 DOI: 10.1111/acel.12544] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2016] [Indexed: 01/01/2023] Open
Abstract
Replicative senescence has a major impact on function and integrity of cell preparations. This process is reflected by continuous DNA methylation (DNAm) changes at specific CpG dinucleotides in the course of in vitro culture, and such modifications can be used to estimate the state of cellular senescence for quality control of cell preparations. Still, it is unclear how senescence‐associated DNAm changes are regulated and whether they occur simultaneously across a cell population. In this study, we analyzed global DNAm profiles of human mesenchymal stem cells (MSCs) and human umbilical vein endothelial cells (HUVECs) to demonstrate that senescence‐associated DNAm changes are overall similar in these different cell types. Subsequently, an Epigenetic‐Senescence‐Signature, based on six CpGs, was either analyzed by pyrosequencing or by bar‐coded bisulfite amplicon sequencing. There was a good correlation between predicted and real passage numbers in bulk populations of MSCs (R2 = 0.67) and HUVECs (R2 = 0.97). However, when we analyzed the Epigenetic‐Senescence‐Signature in subclones of MSCs, the predictions revealed high variation and they were not related to the adipogenic or osteogenic differentiation potential of the subclones. Notably, in clonally derived subpopulations, the DNAm levels of neighboring CpGs differed extensively, indicating that these genomic regions are not synchronously modified during senescence. Taken together, senescence‐associated DNAm changes occur in a highly reproducible manner, but they are not synchronously co‐regulated. They rather appear to be acquired stochastically—potentially evoked by other epigenetic modifications.
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Affiliation(s)
- Julia Franzen
- Helmholtz-Institute for Biomedical Engineering; RWTH Aachen University Medical School; 52074 Aachen Germany
| | - Anne Zirkel
- Center for Molecular Medicine (CMMC); University of Cologne; 50931 Cologne Germany
| | - Jonathon Blake
- Genomics Core Facility; European Molecular Biology Laboratory (EMBL); 69117 Heidelberg Germany
| | - Björn Rath
- Department for Orthopedics; RWTH Aachen University Medical School; 52074 Aachen Germany
| | - Vladimir Benes
- Genomics Core Facility; European Molecular Biology Laboratory (EMBL); 69117 Heidelberg Germany
| | - Argyris Papantonis
- Center for Molecular Medicine (CMMC); University of Cologne; 50931 Cologne Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering; RWTH Aachen University Medical School; 52074 Aachen Germany
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60
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Characteristics, applications and prospects of mesenchymal stem cells in cell therapy. Med Clin (Barc) 2017; 148:408-414. [PMID: 28126234 DOI: 10.1016/j.medcli.2016.11.033] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 11/24/2016] [Indexed: 02/08/2023]
Abstract
Recent advances in the field of cell therapy and regenerative medicine describe mesenchymal stem cells (MSCs) as potential biological products due to their ability to self-renew and differentiate. MSCs are multipotent adult cells with immunomodulatory and regenerative properties, and, given their therapeutic potential, they are being widely studied in order to evaluate their viability, safety and efficacy. In this review, we describe the main characteristics and cellular sources of MSCs, in addition to providing an overview of their properties and current clinical applications, as well offering updated information on the regulatory aspects that define them as somatic cell therapy products. Cell therapy based on MSCs is offered nowadays as a pharmacological alternative, although there are still challenges to be addressed in this regard.
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61
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Abstract
A confounding aspect of biological ageing is the nature and role of senescent cells. It is unclear whether the three major types of cellular senescence, namely replicative senescence, oncogene-induced senescence and DNA damage-induced senescence are descriptions of the same phenomenon instigated by different sources, or if each of these is distinct, and how they are associated with ageing. Recently, we devised an epigenetic clock with unprecedented accuracy and precision based on very specific DNA methylation changes that occur in function of age. Using primary cells, telomerase-expressing cells and oncogene-expressing cells of the same genetic background, we show that induction of replicative senescence (RS) and oncogene-induced senescence (OIS) are accompanied by ageing of the cell. However, senescence induced by DNA damage is not, even though RS and OIS activate the cellular DNA damage response pathway, highlighting the independence of senescence from cellular ageing. Consistent with this, we observed that telomerase-immortalised cells aged in culture without having been treated with any senescence inducers or DNA-damaging agents, re-affirming the independence of the process of ageing from telomeres and senescence. Collectively, our results reveal that cellular ageing is distinct from cellular senescence and independent of DNA damage response and telomere length.
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62
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Dhasarathy A, Roemmich JN, Claycombe KJ. Influence of maternal obesity, diet and exercise on epigenetic regulation of adipocytes. Mol Aspects Med 2016; 54:37-49. [PMID: 27825817 DOI: 10.1016/j.mam.2016.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 10/25/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Archana Dhasarathy
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - James N Roemmich
- USDA-ARS-PA, Grand Forks Human Nutrition Research Center, 2420 2nd Avenue North, Grand Forks, ND 58203, USA
| | - Kate J Claycombe
- USDA-ARS-PA, Grand Forks Human Nutrition Research Center, 2420 2nd Avenue North, Grand Forks, ND 58203, USA.
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63
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de Almeida DC, Ferreira MRP, Franzen J, Weidner CI, Frobel J, Zenke M, Costa IG, Wagner W. Epigenetic Classification of Human Mesenchymal Stromal Cells. Stem Cell Reports 2016; 6:168-75. [PMID: 26862701 PMCID: PMC4750140 DOI: 10.1016/j.stemcr.2016.01.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/04/2016] [Accepted: 01/07/2016] [Indexed: 01/05/2023] Open
Abstract
Standardization of mesenchymal stromal cells (MSCs) is hampered by the lack of a precise definition for these cell preparations; for example, there are no molecular markers to discern MSCs and fibroblasts. In this study, we followed the hypothesis that specific DNA methylation (DNAm) patterns can assist classification of MSCs. We utilized 190 DNAm profiles to address the impact of tissue of origin, donor age, replicative senescence, and serum supplements on the epigenetic makeup. Based on this, we elaborated a simple epigenetic signature based on two CpG sites to classify MSCs and fibroblasts, referred to as the Epi-MSC-Score. Another two-CpG signature can distinguish between MSCs from bone marrow and adipose tissue, referred to as the Epi-Tissue-Score. These assays were validated by site-specific pyrosequencing analysis in 34 primary cell preparations. Furthermore, even individual subclones of MSCs were correctly classified by our epigenetic signatures. In summary, we propose an alternative concept to use DNAm patterns for molecular definition of cell preparations, and our epigenetic scores facilitate robust and cost-effective quality control of MSC cultures.
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Affiliation(s)
- Danilo Candido de Almeida
- Division of Stem Cell Biology and Cellular Engineering, Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074 Aachen, Germany; Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany; Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Marcelo R P Ferreira
- Department of Cell Biology, IZKF Research Group Bioinformatics, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany; Department of Statistics, Centre for Natural and Exact Sciences, Federal University of Paraiba, João Pessoa 58051-900, Brazil
| | - Julia Franzen
- Division of Stem Cell Biology and Cellular Engineering, Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074 Aachen, Germany; Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Carola I Weidner
- Division of Stem Cell Biology and Cellular Engineering, Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074 Aachen, Germany; Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Joana Frobel
- Division of Stem Cell Biology and Cellular Engineering, Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074 Aachen, Germany; Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Martin Zenke
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany
| | - Ivan G Costa
- Department of Cell Biology, IZKF Research Group Bioinformatics, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Wolfgang Wagner
- Division of Stem Cell Biology and Cellular Engineering, Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074 Aachen, Germany; Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany.
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64
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Kalwa M, Hänzelmann S, Otto S, Kuo CC, Franzen J, Joussen S, Fernandez-Rebollo E, Rath B, Koch C, Hofmann A, Lee SH, Teschendorff AE, Denecke B, Lin Q, Widschwendter M, Weinhold E, Costa IG, Wagner W. The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation. Nucleic Acids Res 2016; 44:10631-10643. [PMID: 27634931 PMCID: PMC5159544 DOI: 10.1093/nar/gkw802] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 02/06/2023] Open
Abstract
There is a growing perception that long non-coding RNAs (lncRNAs) modulate cellular function. In this study, we analyzed the role of the lncRNA HOTAIR in mesenchymal stem cells (MSCs) with particular focus on senescence-associated changes in gene expression and DNA-methylation (DNAm). HOTAIR binding sites were enriched at genomic regions that become hypermethylated with increasing cell culture passage. Overexpression and knockdown of HOTAIR inhibited or stimulated adipogenic differentiation of MSCs, respectively. Modification of HOTAIR expression evoked only very moderate effects on gene expression, particularly of polycomb group target genes. Furthermore, overexpression and knockdown of HOTAIR resulted in DNAm changes at HOTAIR binding sites. Five potential triple helix forming domains were predicted within the HOTAIR sequence based on reverse Hoogsteen hydrogen bonds. Notably, the predicted triple helix target sites for these HOTAIR domains were also enriched in differentially expressed genes and close to DNAm changes upon modulation of HOTAIR Electrophoretic mobility shift assays provided further evidence that HOTAIR domains form RNA-DNA-DNA triplexes with predicted target sites. Our results demonstrate that HOTAIR impacts on differentiation of MSCs and that it is associated with senescence-associated DNAm. Targeting of epigenetic modifiers to relevant loci in the genome may involve triple helix formation with HOTAIR.
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Affiliation(s)
- Marie Kalwa
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
| | - Sonja Hänzelmann
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany.,Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH University Medical School, Aachen 52074, Germany
| | - Sabrina Otto
- Institute of Organic Chemistry, RWTH Aachen University, Aachen 52056, Germany
| | - Chao-Chung Kuo
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany.,Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH University Medical School, Aachen 52074, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
| | - Sylvia Joussen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH University Medical School, Aachen 52074, Germany
| | - Eduardo Fernandez-Rebollo
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
| | - Björn Rath
- Department for Orthopedics, RWTH Aachen University Medical School, Aachen 52074, Germany
| | - Carmen Koch
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, Department of Genomics, Life & Brain Center, University of Bonn, Bonn 53127, Germany
| | - Shih-Han Lee
- Department of Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, University College London, London WC1E 6AU, UK.,Statistical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew E Teschendorff
- Department of Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, University College London, London WC1E 6AU, UK.,Statistical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK.,CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bernd Denecke
- Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH University Medical School, Aachen 52074, Germany
| | - Qiong Lin
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
| | - Martin Widschwendter
- Department of Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, University College London, London WC1E 6AU, UK.,Statistical Genomics Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Aachen 52056, Germany
| | - Ivan G Costa
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany .,Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH University Medical School, Aachen 52074, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen 52074, Germany .,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen 52074, Germany
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65
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Wagner W, Frobel J, Goetzke R. Epigenetic quality check - how good are your mesenchymal stromal cells? Epigenomics 2016; 8:889-94. [PMID: 27366986 DOI: 10.2217/epi-2016-0054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology & Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Joana Frobel
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology & Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Roman Goetzke
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology & Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
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66
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67
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In Vitro Expansion of Bone Marrow Derived Mesenchymal Stem Cells Alters DNA Double Strand Break Repair of Etoposide Induced DNA Damage. Stem Cells Int 2016; 2016:8270464. [PMID: 26880992 PMCID: PMC4736568 DOI: 10.1155/2016/8270464] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/22/2015] [Accepted: 11/25/2015] [Indexed: 12/12/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are of interest for use in diverse cellular therapies. Ex vivo expansion of MSCs intended for transplantation must result in generation of cells that maintain fidelity of critical functions. Previous investigations have identified genetic and phenotypic alterations of MSCs with in vitro passage, but little is known regarding how culturing influences the ability of MSCs to repair double strand DNA breaks (DSBs), the most severe of DNA lesions. To investigate the response to DSB stress with passage in vitro, primary human MSCs were exposed to etoposide (VP16) at various passages with subsequent evaluation of cellular damage responses and DNA repair. Passage number did not affect susceptibility to VP16 or the incidence and repair kinetics of DSBs. Nonhomologous end joining (NHEJ) transcripts showed little alteration with VP16 exposure or passage; however, homologous recombination (HR) transcripts were reduced following VP16 exposure with this decrease amplified as MSCs were passaged in vitro. Functional evaluations of NHEJ and HR showed that MSCs were unable to activate NHEJ repair following VP16 stress in cells after successive passage. These results indicate that ex vivo expansion of MSCs alters their ability to perform DSB repair, a necessary function for cells intended for transplantation.
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68
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Wagner W, Fernandez-Rebollo E, Frobel J. DNA-methylation changes in replicative senescence and aging: two sides of the same coin? Epigenomics 2016; 8:1-3. [DOI: 10.2217/epi.15.100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, 52074 Aachen, Germany
| | - Eduardo Fernandez-Rebollo
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, 52074 Aachen, Germany
| | - Joana Frobel
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, 52074 Aachen, Germany
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69
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Teschendorff AE, Lee SH, Jones A, Fiegl H, Kalwa M, Wagner W, Chindera K, Evans I, Dubeau L, Orjalo A, Horlings HM, Niederreiter L, Kaser A, Yang W, Goode EL, Fridley BL, Jenner RG, Berns EMJJ, Wik E, Salvesen HB, Wisman GBA, van der Zee AGJ, Davidson B, Trope CG, Lambrechts S, Vergote I, Calvert H, Jacobs IJ, Widschwendter M. HOTAIR and its surrogate DNA methylation signature indicate carboplatin resistance in ovarian cancer. Genome Med 2015; 7:108. [PMID: 26497652 PMCID: PMC4619324 DOI: 10.1186/s13073-015-0233-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/12/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Understanding carboplatin resistance in ovarian cancer is critical for the improvement of patients' lives. Multipotent mesenchymal stem cells or an aggravated epithelial to mesenchymal transition phenotype of a cancer are integrally involved in pathways conferring chemo-resistance. Long non-coding RNA HOTAIR (HOX transcript antisense intergenic RNA) is involved in mesenchymal stem cell fate and cancer biology. METHODS We analyzed HOTAIR expression and associated surrogate DNA methylation (DNAme) in 134 primary ovarian cancer cases (63 received carboplatin, 55 received cisplatin and 16 no chemotherapy). We validated our findings by HOTAIR expression and DNAme analysis in a multicentre setting of five additional sets, encompassing 946 ovarian cancers. Chemo-sensitivity has been assessed in cell culture experiments. RESULTS HOTAIR expression was significantly associated with poor survival in carboplatin-treated patients with adjusted hazard ratios for death of 3.64 (95 % confidence interval [CI] 1.78-7.42; P < 0.001) in the discovery and 1.63 (95 % CI 1.04-2.56; P = 0.032) in the validation set. This effect was not seen in patients who did not receive carboplatin (0.97 [95 % CI 0.52-1.80; P = 0.932]). HOTAIR expression or its surrogate DNAme signature predicted poor outcome in all additional sets of carboplatin-treated ovarian cancer patients while HOTAIR expressors responded preferentially to cisplatin (multivariate interaction P = 0.008). CONCLUSIONS Non-coding RNA HOTAIR or its more stable DNAme surrogate may indicate the presence of a subset of cells which confer resistance to carboplatin and can serve as (1) a marker to personalise treatment and (2) a novel target to overcome carboplatin resistance.
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Affiliation(s)
- Andrew E Teschendorff
- Statistical Genomics Group, UCL Cancer Institute, University College London, London, UK.
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Shih-Han Lee
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK.
- Sloan Kettering Institute, Cancer Biology & Genetics Program, New York, NY, USA.
| | - Allison Jones
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK.
| | - Heidi Fiegl
- Department of Gynaecology and Obstetrics, Innsbruck Medical University, Innsbruck, Austria.
| | - Marie Kalwa
- Helmholtz-Institute for Biomedical Technology, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Technology, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.
| | - Kantaraja Chindera
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK.
| | - Iona Evans
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK.
| | - Louis Dubeau
- Department of Pathology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA.
| | | | - Hugo M Horlings
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Lukas Niederreiter
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.
| | - Arthur Kaser
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.
| | - Winnie Yang
- Department of Molecular Oncology, British Columbia Cancer Agency Research Centre, Vancouver, Canada.
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA.
| | - Brooke L Fridley
- Biostatistics and Informatics Shared Resource, The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA.
| | - Richard G Jenner
- UCL Division of Infection and Immunity, University College London, London, UK.
| | - Els M J J Berns
- Department of Medical Oncology, Erasmus MC-Cancer Center, Rotterdam, The Netherlands.
| | - Elisabeth Wik
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Pathology, Haukeland University Hospital, Bergen, Norway.
| | - Helga B Salvesen
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway.
| | - G Bea A Wisman
- Department of Gynaecological Oncology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.
| | - Ate G J van der Zee
- Department of Gynaecological Oncology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.
| | - Ben Davidson
- Division of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway.
| | - Claes G Trope
- Department of Gynaecological Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway.
| | - Sandrina Lambrechts
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology and Leuven Cancer Institute, University Hospitals Leuven, Katholieke Universiteit Leuven, Leuven, Belgium.
| | - Ignace Vergote
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology and Leuven Cancer Institute, University Hospitals Leuven, Katholieke Universiteit Leuven, Leuven, Belgium.
| | - Hilary Calvert
- Drug Development Group, UCL Cancer Institute, University College London, London, UK.
| | - Ian J Jacobs
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK.
- University of Manchester, Manchester, UK.
- University of New South Wales, Sydney, Australia.
| | - Martin Widschwendter
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK.
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70
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Nätt D, Johansson I, Faresjö T, Ludvigsson J, Thorsell A. High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases. Clin Epigenetics 2015; 7:91. [PMID: 26339299 PMCID: PMC4559301 DOI: 10.1186/s13148-015-0123-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/07/2015] [Indexed: 12/21/2022] Open
Abstract
Background Childhood stress leads to increased risk of many adult diseases, such as major depression and cardiovascular disease. Studies show that adults with experienced childhood stress have specific epigenetic changes, but to understand the pathways that lead to disease, we also need to study the epigenetic link prospectively in children. Results Here, we studied a homogenous group of 48 5-year-old children. By combining hair cortisol measurements (a well-documented biomarker for chronic stress), with whole-genome DNA-methylation sequencing, we show that high cortisol associates with a genome-wide decrease in DNA methylation and targets short interspersed nuclear elements (SINEs; a type of retrotransposon) and genes important for calcium transport: phenomena commonly affected in stress-related diseases and in biological aging. More importantly, we identify a zinc-finger transcription factor, ZNF263, whose binding sites where highly overrepresented in regions experiencing methylation loss. This type of zinc-finger protein has previously shown to be involved in the defense against retrotransposons. Conclusions Our results show that stress in preschool children leads to changes in DNA methylation similar to those seen in biological aging. We suggest that this may affect future disease susceptibility by alterations in the epigenetic mechanisms that keep retrotransposons dormant. Future treatments for stress- and age-related diseases may therefore seek to target zinc-finger proteins that epigenetically control retrotransposon reactivation, such as ZNF263. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0123-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Nätt
- Department of Clinical and Experimental Medicine, Division of Cell Biology, Linkoping University, Linkoping, 58183 Sweden
| | - Ingela Johansson
- Department of Clinical and Experimental Medicine, Division of Pediatrics, Linkoping University, Linkoping, 58183 Sweden
| | - Tomas Faresjö
- Department of Medicine and Health Sciences, Community Medicine/General Practice, Linkoping University, Linkoping, 58183 Sweden
| | - Johnny Ludvigsson
- Department of Clinical and Experimental Medicine, Division of Pediatrics, Linkoping University, Linkoping, 58183 Sweden
| | - Annika Thorsell
- Department of Clinical and Experimental Medicine, Division of Cell Biology, Linkoping University, Linkoping, 58183 Sweden
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71
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Gonzalez LC, Ghadaouia S, Martinez A, Rodier F. Premature aging/senescence in cancer cells facing therapy: good or bad? Biogerontology 2015; 17:71-87. [DOI: 10.1007/s10522-015-9593-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 07/22/2015] [Indexed: 01/07/2023]
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72
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Nicolay NH, Perez RL, Saffrich R, Huber PE. Radio-resistant mesenchymal stem cells: mechanisms of resistance and potential implications for the clinic. Oncotarget 2015; 6:19366-80. [PMID: 26203772 PMCID: PMC4637291 DOI: 10.18632/oncotarget.4358] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 05/30/2015] [Indexed: 12/12/2022] Open
Abstract
Mesenchymal stem cells (MSCs) comprise a heterogeneous population of multipotent stromal cells and can be isolated from various tissues and organs. Due to their regenerative potential, they have been subject to intense research efforts, and they may provide an efficient means for treating radiation-induced tissue damage. MSCs are relatively resistant to ionizing radiation and retain their stem cell characteristics even after high radiation doses. The underlying mechanisms for the observed MSC radioresistance have been extensively studied and may involve efficient DNA damage recognition, double strand break repair and evasion of apoptosis. Here, we present a concise review of the published scientific data on the radiobiological features of MSCs. The involvement of different DNA damage recognition and repair pathways in the creation of a radioresistant MSC phenotype is outlined, and the roles of apoptosis, senescence and autophagy regarding the reported radioresistance are summarized. Finally, potential influences of the radioresistant MSCs for the clinic are discussed with respect to the repair and radioprotection of irradiated tissues.
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Affiliation(s)
- Nils H. Nicolay
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology, Heidelberg, Germany
- Department of Molecular and Radiation Oncology, German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Ramon Lopez Perez
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology, Heidelberg, Germany
- Department of Molecular and Radiation Oncology, German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Rainer Saffrich
- Department of Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter E. Huber
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology, Heidelberg, Germany
- Department of Molecular and Radiation Oncology, German Cancer Research Center (dkfz), Heidelberg, Germany
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73
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Lin Q, Wagner W. Epigenetic Aging Signatures Are Coherently Modified in Cancer. PLoS Genet 2015; 11:e1005334. [PMID: 26110659 PMCID: PMC4482318 DOI: 10.1371/journal.pgen.1005334] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 06/03/2015] [Indexed: 12/31/2022] Open
Abstract
Aging is associated with highly reproducible DNA methylation (DNAm) changes, which may contribute to higher prevalence of malignant diseases in the elderly. In this study, we analyzed epigenetic aging signatures in 5,621 DNAm profiles of 25 cancer types from The Cancer Genome Atlas (TCGA). Overall, age-associated DNAm patterns hardly reflect chronological age of cancer patients, but they are coherently modified in a non-stochastic manner, particularly at CpGs that become hypermethylated upon aging in non-malignant tissues. This coordinated regulation in epigenetic aging signatures can therefore be used for aberrant epigenetic age-predictions, which facilitate disease stratification. For example, in acute myeloid leukemia (AML) higher epigenetic age-predictions are associated with increased incidence of mutations in RUNX1, WT1, and IDH2, whereas mutations in TET2, TP53, and PML-PARA translocation are more frequent in younger age-predictions. Furthermore, epigenetic aging signatures correlate with overall survival in several types of cancer (such as lower grade glioma, glioblastoma multiforme, esophageal carcinoma, chromophobe renal cell carcinoma, cutaneous melanoma, lung squamous cell carcinoma, and neuroendocrine neoplasms). In conclusion, age-associated DNAm patterns in cancer are not related to chronological age of the patient, but they are coordinately regulated, particularly at CpGs that become hypermethylated in normal aging. Furthermore, the apparent epigenetic age-predictions correlate with clinical parameters and overall survival in several types of cancer, indicating that regulation of DNAm patterns in age-associated CpGs is relevant for cancer development. Our genome harbors epigenetic marks, such as DNA methylation (DNAm) at cytosine residues, which govern cellular differentiation. Some epigenetic modifications accumulate throughout life in a highly reproducible manner–they may contribute to the aging process and facilitate reliable age-predictions. So far, little is known how these “epigenetic aging signatures” are modified in cancer tissue and whether or not they are accelerated as compared to normal tissue. In this study, we systematically analyzed age-associated DNAm patterns in many types of cancer. In contrast to non-malignant tissue the epigenetic aging signatures hardly reflect chronological age of cancer patients. This may at least partially be attributed to the fact that cancer is a clonal disease capturing only the epigenetic make-up of the tumor-initiating cell. Notably, the aberrant DNAm patterns are not randomly distributed but reveal co-regulation at regions that become methylated upon aging in non-malignant tissue. Furthermore, we demonstrate that deviations of epigenetic age-predictions correlate with clinical parameters. In fact, they are clearly associated with overall survival in many types of cancer. These findings are particularly important, as they indicate relevance of age-associated DNA methylation patterns for malignant transformation, cancer development and prognosis.
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Affiliation(s)
- Qiong Lin
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
- * E-mail:
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74
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Weidner CI, Wagner W. The epigenetic tracks of aging. Biol Chem 2015; 395:1307-14. [PMID: 25205717 DOI: 10.1515/hsz-2014-0180] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/18/2014] [Indexed: 11/15/2022]
Abstract
Abstract Aging is associated with the deterioration of biological functions, which is either caused by accumulation of random defects or mediated by a controlled process. This article provides an overview of age-associated epigenetic alterations in the histone code, DNA-methylation (DNAm) pattern, and chromatin structure. In particular, age-related DNAm changes are highly reproducible at specific sites in the genome. The DNAm level at few CpGs facilitates estimation of chronological age and there is evidence that such predictions are indicative for biological age. Overall, aging appears to be associated with a tightly regulated epigenetic process, but the underlying mechanism remains to be elucidated.
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75
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Affiliation(s)
- James W. Larrick
- Panorama Research Institute and Regenerative Sciences Institute, Sunnyvale, California
| | - Andrew R. Mendelsohn
- Panorama Research Institute and Regenerative Sciences Institute, Sunnyvale, California
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76
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Lenz M, Goetzke R, Schenk A, Schubert C, Veeck J, Hemeda H, Koschmieder S, Zenke M, Schuppert A, Wagner W. Epigenetic biomarker to support classification into pluripotent and non-pluripotent cells. Sci Rep 2015; 5:8973. [PMID: 25754700 PMCID: PMC4354028 DOI: 10.1038/srep08973] [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: 10/08/2014] [Accepted: 02/11/2015] [Indexed: 12/12/2022] Open
Abstract
Quality control of human induced pluripotent stem cells (iPSCs) can be performed by several methods. These methods are usually relatively labor-intensive, difficult to standardize, or they do not facilitate reliable quantification. Here, we describe a biomarker to distinguish between pluripotent and non-pluripotent cells based on DNA methylation (DNAm) levels at only three specific CpG sites. Two of these CpG sites were selected by their discriminatory power in 258 DNAm profiles – they were either methylated in pluripotent or non-pluripotent cells. The difference between these two β-values provides an Epi-Pluri-Score that was validated on independent DNAm-datasets (264 pluripotent and 1,951 non-pluripotent samples) with 99.9% specificity and 98.9% sensitivity. This score was complemented by a third CpG within the gene POU5F1 (OCT4), which better demarcates early differentiation events. We established pyrosequencing assays for the three relevant CpG sites and thereby correctly classified DNA of 12 pluripotent cell lines and 31 non-pluripotent cell lines. Furthermore, DNAm changes at these three CpGs were tracked in the course of differentiation of iPSCs towards mesenchymal stromal cells. The Epi-Pluri-Score does not give information on lineage-specific differentiation potential, but it provides a simple, reliable, and robust biomarker to support high-throughput classification into either pluripotent or non-pluripotent cells.
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Affiliation(s)
- Michael Lenz
- 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany [3] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Roman Goetzke
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Arne Schenk
- 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Bayer Technology Services GmbH, Leverkusen, Germany
| | - Claudia Schubert
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - Jürgen Veeck
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Hatim Hemeda
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - Martin Zenke
- 1] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany [2] Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Andreas Schuppert
- 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany [3] Bayer Technology Services GmbH, Leverkusen, Germany
| | - Wolfgang Wagner
- 1] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany [2] Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
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77
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Hänzelmann S, Beier F, Gusmao EG, Koch CM, Hummel S, Charapitsa I, Joussen S, Benes V, Brümmendorf TH, Reid G, Costa IG, Wagner W. Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites. Clin Epigenetics 2015; 7:19. [PMID: 25763115 PMCID: PMC4356053 DOI: 10.1186/s13148-015-0057-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/10/2015] [Indexed: 02/08/2023] Open
Abstract
Background Primary cells enter replicative senescence after a limited number of cell divisions. This process needs to be considered in cell culture experiments, and it is particularly important for regenerative medicine. Replicative senescence is associated with reproducible changes in DNA methylation (DNAm) at specific sites in the genome. The mechanism that drives senescence-associated DNAm changes remains unknown - it may involve stochastic DNAm drift due to imperfect maintenance of epigenetic marks or it is directly regulated at specific sites in the genome. Results In this study, we analyzed the reorganization of nuclear architecture and DNAm changes during long-term culture of human fibroblasts and mesenchymal stromal cells (MSCs). We demonstrate that telomeres shorten and shift towards the nuclear center at later passages. In addition, DNAm profiles, either analyzed by MethylCap-seq or by 450k IlluminaBeadChip technology, revealed consistent senescence-associated hypermethylation in regions associated with H3K27me3, H3K4me3, and H3K4me1 histone marks, whereas hypomethylation was associated with chromatin containing H3K9me3 and lamina-associated domains (LADs). DNA hypermethylation was significantly enriched in the vicinity of genes that are either up- or downregulated at later passages. Furthermore, specific transcription factor binding motifs (e.g. EGR1, TFAP2A, and ETS1) were significantly enriched in differentially methylated regions and in the promoters of differentially expressed genes. Conclusions Senescence-associated DNA hypermethylation occurs at specific sites in the genome and reflects functional changes in the course of replicative senescence. These results indicate that tightly regulated epigenetic modifications during long-term culture contribute to changes in nuclear organization and gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0057-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonja Hänzelmann
- Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany ; Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - Eduardo G Gusmao
- Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany ; Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Carmen M Koch
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany ; Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany
| | - Sebastian Hummel
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | | | - Sylvia Joussen
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany ; Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - George Reid
- Institute for Molecular Biology, Mainz, Germany
| | - Ivan G Costa
- Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany ; Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Wolfgang Wagner
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany ; Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany
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78
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Wagner W, Weidner CI, Lin Q. Do age-associated DNA methylation changes increase the risk of malignant transformation? Bioessays 2014; 37:20-4. [DOI: 10.1002/bies.201400063] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering; Stem Cell Biology and Cellular Engineering; RWTH University Medical School; Aachen Germany
| | - Carola I. Weidner
- Helmholtz-Institute for Biomedical Engineering; Stem Cell Biology and Cellular Engineering; RWTH University Medical School; Aachen Germany
| | - Qiong Lin
- Helmholtz-Institute for Biomedical Engineering; Stem Cell Biology and Cellular Engineering; RWTH University Medical School; Aachen Germany
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79
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Polycomb Protein EED is Required for Silencing of Pluripotency Genes upon ESC Differentiation. Stem Cell Rev Rep 2014; 11:50-61. [DOI: 10.1007/s12015-014-9550-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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80
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Frobel J, Hemeda H, Lenz M, Abagnale G, Joussen S, Denecke B, Sarić T, Zenke M, Wagner W. Epigenetic rejuvenation of mesenchymal stromal cells derived from induced pluripotent stem cells. Stem Cell Reports 2014; 3:414-22. [PMID: 25241740 PMCID: PMC4266008 DOI: 10.1016/j.stemcr.2014.07.003] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 07/07/2014] [Accepted: 07/09/2014] [Indexed: 02/07/2023] Open
Abstract
Standardization of mesenchymal stromal cells (MSCs) remains a major obstacle in regenerative medicine. Starting material and culture expansion affect cell preparations and render comparison between studies difficult. In contrast, induced pluripotent stem cells (iPSCs) assimilate toward a ground state and may therefore give rise to more standardized cell preparations. We reprogrammed MSCs into iPSCs, which were subsequently redifferentiated toward MSCs. These iPS-MSCs revealed similar morphology, immunophenotype, in vitro differentiation potential, and gene expression profiles as primary MSCs. However, iPS-MSCs were impaired in suppressing T cell proliferation. DNA methylation (DNAm) profiles of iPSCs maintained donor-specific characteristics, whereas tissue-specific, senescence-associated, and age-related DNAm patterns were erased during reprogramming. iPS-MSCs reacquired senescence-associated DNAm during culture expansion, but they remained rejuvenated with regard to age-related DNAm. Overall, iPS-MSCs are similar to MSCs, but they reveal incomplete reacquisition of immunomodulatory function and MSC-specific DNAm patterns—particularly of DNAm patterns associated with tissue type and aging. MSC-derived iPSCs are redifferentiated toward MSCs in a one-step protocol Gene expression profiles of iPS-MSCs closely resemble those of primary MSCs DNA methylation (DNAm) profiles of iPS-MSCs lag behind those of MSCs Age-related and tissue-specific DNAm patterns remain erased in iPS-MSCs
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Affiliation(s)
- Joana Frobel
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Hatim Hemeda
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Michael Lenz
- Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, 52074 Aachen, Germany
| | - Giulio Abagnale
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Sylvia Joussen
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Bernd Denecke
- Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Tomo Sarić
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Martin Zenke
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany; Institute for Biomedical Engineering, Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany.
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81
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Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias. Neoplasia 2014; 16:606-15. [PMID: 25065939 PMCID: PMC4198827 DOI: 10.1016/j.neo.2014.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/01/2014] [Accepted: 07/03/2014] [Indexed: 01/10/2023] Open
Abstract
We have previously described gene expression changes during spontaneous immortalization of T-cells, thereby identifying cellular processes important for cell growth crisis escape and unlimited proliferation. Here, we analyze the same model to investigate the role of genome-wide methylation in the immortalization process at different time points pre-crisis and post-crisis using high-resolution arrays. We show that over time in culture there is an overall accumulation of methylation alterations, with preferential increased methylation close to transcription start sites (TSSs), islands, and shore regions. Methylation and gene expression alterations did not correlate for the majority of genes, but for the fraction that correlated, gain of methylation close to TSS was associated with decreased gene expression. Interestingly, the pattern of CpG site methylation observed in immortal T-cell cultures was similar to clinical T-cell acute lymphoblastic leukemia (T-ALL) samples classified as CpG island methylator phenotype positive. These sites were highly overrepresented by polycomb target genes and involved in developmental, cell adhesion, and cell signaling processes. The presence of non-random methylation events in in vitro immortalized T-cell cultures and diagnostic T-ALL samples indicates altered methylation of CpG sites with a possible role in malignant hematopoiesis.
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82
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Wuchter P, Bieback K, Schrezenmeier H, Bornhäuser M, Müller LP, Bönig H, Wagner W, Meisel R, Pavel P, Tonn T, Lang P, Müller I, Renner M, Malcherek G, Saffrich R, Buss EC, Horn P, Rojewski M, Schmitt A, Ho AD, Sanzenbacher R, Schmitt M. Standardization of Good Manufacturing Practice-compliant production of bone marrow-derived human mesenchymal stromal cells for immunotherapeutic applications. Cytotherapy 2014; 17:128-39. [PMID: 24856898 DOI: 10.1016/j.jcyt.2014.04.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 03/26/2014] [Accepted: 04/05/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND AIMS Human mesenchymal stem or stromal cells (MSCs) represent a potential resource not only for regenerative medicine but also for immunomodulatory cell therapies. The application of different MSC culture protocols has significantly hampered the comparability of experimental and clinical data from different laboratories and has posed a major obstacle for multicenter clinical trials. Manufacturing of cell products for clinical application in the European Community must be conducted in compliance with Good Manufacturing Practice and requires a manufacturing license. In Germany, the Paul-Ehrlich-Institut as the Federal Authority for Vaccines and Biomedicines is critically involved in the approval process. METHODS This report summarizes a consensus meeting between researchers, clinicians and regulatory experts on standard quality requirements for MSC production. RESULTS The strategy for quality control testing depends on the product's cell composition, the manufacturing process and the indication and target patient population. Important quality criteria in this sense are, among others, the immunophenotype of the cells, composition of the culture medium and the risk for malignant transformation, as well as aging and the immunosuppressive potential of the manufactured MSCs. CONCLUSIONS This position paper intends to provide relevant information to interested parties regarding these criteria to foster the development of scientifically valid and harmonized quality standards and to support approval of MSC-based investigational medicinal products.
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Affiliation(s)
- Patrick Wuchter
- Department of Medicine V, Heidelberg University, Heidelberg, Germany.
| | - Karen Bieback
- Institute of Transfusion Medicine and Immunology Mannheim, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Donor Service Baden-Württemberg-Hessen, Mannheim, Germany
| | - Hubert Schrezenmeier
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, Red Cross Blood Transfusion Service Baden-Württemberg-Hessen and University of Ulm, Ulm, Germany
| | - Martin Bornhäuser
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Lutz P Müller
- Department of Medicine IV, University Hospital Halle (Saale), Halle (Saale), Germany
| | - Halvard Bönig
- Institute for Transfusion Medicine and Immunohematology, Goethe University, Frankfurt/Main and German Red Cross Blood Service Baden-Württemberg-Hessen, Frankfurt/Main, Germany
| | - Wolfgang Wagner
- Helmholtz Institute for Biomedical Technology, Stem Cell Biology and Cellular Engineering, University of Aachen Medical School, Aachen, Germany
| | - Roland Meisel
- Division of Pediatric Stem Cell Therapy, Clinic for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Petra Pavel
- Stem Cell Laboratory, IKTZ Heidelberg GmbH, Heidelberg, Germany
| | - Torsten Tonn
- Institute of Transfusion Medicine, Red Cross Blood Transfusion Service Dresden, Dresden, Germany
| | - Peter Lang
- Department of Pediatrics, University Clinic Tübingen, Tübingen, Germany
| | - Ingo Müller
- Clinic for Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Renner
- Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Georg Malcherek
- Department of Medicine V, Heidelberg University, Heidelberg, Germany
| | - Rainer Saffrich
- Department of Medicine V, Heidelberg University, Heidelberg, Germany
| | - Eike C Buss
- Department of Medicine V, Heidelberg University, Heidelberg, Germany
| | - Patrick Horn
- Department of Medicine V, Heidelberg University, Heidelberg, Germany
| | - Markus Rojewski
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, Red Cross Blood Transfusion Service Baden-Württemberg-Hessen and University of Ulm, Ulm, Germany
| | - Anita Schmitt
- Department of Medicine V, Heidelberg University, Heidelberg, Germany
| | - Anthony D Ho
- Department of Medicine V, Heidelberg University, Heidelberg, Germany
| | - Ralf Sanzenbacher
- Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Michael Schmitt
- Department of Medicine V, Heidelberg University, Heidelberg, Germany
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83
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Abnaof K, Mallela N, Walenda G, Meurer SK, Seré K, Lin Q, Smeets B, Hoffmann K, Wagner W, Zenke M, Weiskirchen R, Fröhlich H. TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level. BMC SYSTEMS BIOLOGY 2014; 8:55. [PMID: 24886091 PMCID: PMC4049504 DOI: 10.1186/1752-0509-8-55] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/06/2014] [Indexed: 01/03/2023]
Abstract
Background The TGF-β signaling pathway is a fundamental pathway in the living cell, which plays a key role in many central cellular processes. The complex and sometimes contradicting mechanisms by which TGF-β yields phenotypic effects are not yet completely understood. In this study we investigated and compared the transcriptional response profile of TGF-β1 stimulation in different cell types. For this purpose, extensive experiments are performed and time-course microarray data are generated in human and mouse parenchymal liver cells, human mesenchymal stromal cells and mouse hematopoietic progenitor cells at different time points. We applied a panel of bioinformatics methods on our data to uncover common patterns in the dynamic gene expression response in respective cells. Results Our analysis revealed a quite variable and multifaceted transcriptional response profile of TGF-β1 stimulation, which goes far beyond the well-characterized classical TGF-β1 signaling pathway. Nonetheless, we could identify several commonly affected processes and signaling pathways across cell types and species. In addition our analysis suggested an important role of the transcription factor EGR1, which appeared to have a conserved influence across cell-types and species. Validation via an independent dataset on A549 lung adenocarcinoma cells largely confirmed our findings. Network analysis suggested explanations, how TGF-β1 stimulation could lead to the observed effects. Conclusions The analysis of dynamical transcriptional response to TGF-β treatment experiments in different human and murine cell systems revealed commonly affected biological processes and pathways, which could be linked to TGF-β1 via network analysis. This helps to gain insights about TGF-β pathway activities in these cell systems and its conserved interactions between the species and tissue types.
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Affiliation(s)
- Khalid Abnaof
- Bonn-Aachen International Center for IT, University of Bonn, Dahlmannstr, 2, 53113 Bonn, Germany.
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Schellenberg A, Joussen S, Moser K, Hampe N, Hersch N, Hemeda H, Schnitker J, Denecke B, Lin Q, Pallua N, Zenke M, Merkel R, Hoffmann B, Wagner W. Matrix elasticity, replicative senescence and DNA methylation patterns of mesenchymal stem cells. Biomaterials 2014; 35:6351-8. [PMID: 24824582 DOI: 10.1016/j.biomaterials.2014.04.079] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/22/2014] [Indexed: 12/28/2022]
Abstract
Matrix elasticity guides differentiation of mesenchymal stem cells (MSCs) but it is unclear if these effects are only transient - while the cells reside on the substrate - or if they reflect persistent lineage commitment. In this study, MSCs were continuously culture-expanded in parallel either on tissue culture plastic (TCP) or on polydimethylsiloxane (PDMS) gels of different elasticity to compare impact on replicative senescence, in vitro differentiation, gene expression, and DNA methylation (DNAm) profiles. The maximal number of cumulative population doublings was not affected by matrix elasticity. Differentiation towards adipogenic and osteogenic lineage was increased on soft and rigid biomaterials, respectively - but this propensity was no more evident if cells were transferred to TCP. Global gene expression profiles and DNAm profiles revealed relatively few differences in MSCs cultured on soft or rigid matrices. Furthermore, only moderate DNAm changes were observed upon culture on very soft hydrogels of human platelet lysate. Our results support the notion that matrix elasticity influences cellular behavior while the cells reside on the substrate, but it does not have major impact on cell-intrinsic lineage determination, replicative senescence or DNAm patterns.
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Affiliation(s)
- Anne Schellenberg
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany
| | - Sylvia Joussen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany
| | - Kristin Moser
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany; Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Nico Hampe
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Nils Hersch
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Hatim Hemeda
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany
| | - Jan Schnitker
- Institute of Complex Systems, ICS-8: Bioelectronics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Bernd Denecke
- Interdisciplinary Centre for Clinical Research (IZKF) Aachen, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Qiong Lin
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany; Institute for Biomedical Technology - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Norbert Pallua
- Department of Plastic and Reconstructive Surgery, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Martin Zenke
- Institute for Biomedical Technology - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Rudolf Merkel
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Bernd Hoffmann
- Institute of Complex Systems, ICS-7: Biomechanics, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, Aachen 52074, Germany.
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85
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Schellenberg A, Mauen S, Koch CM, Jans R, de Waele P, Wagner W. Proof of principle: quality control of therapeutic cell preparations using senescence-associated DNA-methylation changes. BMC Res Notes 2014; 7:254. [PMID: 24755407 PMCID: PMC4005405 DOI: 10.1186/1756-0500-7-254] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 04/11/2014] [Indexed: 12/31/2022] Open
Abstract
Background Tracking of replicative senescence is of fundamental relevance in cellular therapy. Cell preparations – such as mesenchymal stromal cells (MSCs) - undergo continuous changes during culture expansion, which is reflected by impaired proliferation and loss of differentiation potential. This process is associated with epigenetic modifications: during in vitro culture, cells acquire senescence-associated DNA methylation (SA-DNAm) changes at specific sites in the genome. We have recently described an Epigenetic-Senescence-Signature that facilitates prediction of the state of cellular aging by analysis of DNAm at six CpG sites (associated with the genes GRM7, CASR, PRAMEF2, SELP, CASP14 and KRTAP13-3), but this has not yet been proven over subsequent passages and with MSCs isolated under good manufacturing practice (GMP) conditions. Findings MSCs were isolated from human bone marrow and GMP-conform expanded for up to 11 passages. Cumulative population doublings (cPDs) and long-term growth curves were calculated based on cell numbers at each passage. Furthermore, 32 cryopreserved aliquots of these cell preparations were retrospectively analyzed using our Epigenetic-Senescence-Signature: DNAm-level was analyzed at six specific CpGs, and the results were used to estimate cPDs, time of culture expansion, and passage numbers. Overall, predicted and real parameters revealed a good correlation, particularly in cPDs. Based on predicted cPDs we could reconstruct long-term growth curves and demonstrated the continuous increase in replicative senescence on molecular level. Conclusion Epigenetic analysis of specific CpG sites in the genome can be used to estimate the state of cellular aging for quality control of therapeutic cell products.
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Affiliation(s)
| | | | | | | | | | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Technology, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, 52074 Aachen, Germany.
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86
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Tigges J, Krutmann J, Fritsche E, Haendeler J, Schaal H, Fischer JW, Kalfalah F, Reinke H, Reifenberger G, Stühler K, Ventura N, Gundermann S, Boukamp P, Boege F. The hallmarks of fibroblast ageing. Mech Ageing Dev 2014; 138:26-44. [PMID: 24686308 DOI: 10.1016/j.mad.2014.03.004] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 03/11/2014] [Accepted: 03/18/2014] [Indexed: 12/26/2022]
Abstract
Ageing is influenced by the intrinsic disposition delineating what is maximally possible and extrinsic factors determining how that frame is individually exploited. Intrinsic and extrinsic ageing processes act on the dermis, a post-mitotic skin compartment mainly consisting of extracellular matrix and fibroblasts. Dermal fibroblasts are long-lived cells constantly undergoing damage accumulation and (mal-)adaptation, thus constituting a powerful indicator system for human ageing. Here, we use the systematic of ubiquitous hallmarks of ageing (Lopez-Otin et al., 2013, Cell 153) to categorise the available knowledge regarding dermal fibroblast ageing. We discriminate processes inducible in culture from phenomena apparent in skin biopsies or primary cells from old donors, coming to the following conclusions: (i) Fibroblasts aged in culture exhibit most of the established, ubiquitous hallmarks of ageing. (ii) Not all of these hallmarks have been detected or investigated in fibroblasts aged in situ (in the skin). (iii) Dermal fibroblasts aged in vitro and in vivo exhibit additional features currently not considered ubiquitous hallmarks of ageing. (iv) The ageing process of dermal fibroblasts in their physiological tissue environment has only been partially elucidated, although these cells have been a preferred model of cell ageing in vitro for decades.
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Affiliation(s)
- Julia Tigges
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany
| | - Jean Krutmann
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany
| | - Ellen Fritsche
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany
| | - Judith Haendeler
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany; Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Heiner Schaal
- Center for Microbiology and Virology, Institute of Virology, Heinrich-Heine-University, Med. Faculty, D-40225 Düsseldorf, Germany
| | - Jens W Fischer
- Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Faiza Kalfalah
- Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Hans Reinke
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany; Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Kai Stühler
- Institute for Molecular Medicine, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany; Molecular Proteomics Laboratory, Centre for Biological and Medical Research (BMFZ), Heinrich-Heine-University, Düsseldorf, Germany
| | - Natascia Ventura
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany; Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | | | - Petra Boukamp
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Fritz Boege
- Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany.
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87
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Weidner CI, Lin Q, Koch CM, Eisele L, Beier F, Ziegler P, Bauerschlag DO, Jöckel KH, Erbel R, Mühleisen TW, Zenke M, Brümmendorf TH, Wagner W. Aging of blood can be tracked by DNA methylation changes at just three CpG sites. Genome Biol 2014; 15:R24. [PMID: 24490752 PMCID: PMC4053864 DOI: 10.1186/gb-2014-15-2-r24] [Citation(s) in RCA: 619] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 02/03/2014] [Indexed: 01/03/2023] Open
Abstract
Background Human aging is associated with DNA methylation changes at specific sites in the genome. These epigenetic modifications may be used to track donor age for forensic analysis or to estimate biological age. Results We perform a comprehensive analysis of methylation profiles to narrow down 102 age-related CpG sites in blood. We demonstrate that most of these age-associated methylation changes are reversed in induced pluripotent stem cells (iPSCs). Methylation levels at three age-related CpGs - located in the genes ITGA2B, ASPA and PDE4C - were subsequently analyzed by bisulfite pyrosequencing of 151 blood samples. This epigenetic aging signature facilitates age predictions with a mean absolute deviation from chronological age of less than 5 years. This precision is higher than age predictions based on telomere length. Variation of age predictions correlates moderately with clinical and lifestyle parameters supporting the notion that age-associated methylation changes are associated more with biological age than with chronological age. Furthermore, patients with acquired aplastic anemia or dyskeratosis congenita - two diseases associated with progressive bone marrow failure and severe telomere attrition - are predicted to be prematurely aged. Conclusions Our epigenetic aging signature provides a simple biomarker to estimate the state of aging in blood. Age-associated DNA methylation changes are counteracted in iPSCs. On the other hand, over-estimation of chronological age in bone marrow failure syndromes is indicative for exhaustion of the hematopoietic cell pool. Thus, epigenetic changes upon aging seem to reflect biological aging of blood.
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88
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Ding X, Wang X, Sontag S, Qin J, Wanek P, Lin Q, Zenke M. The polycomb protein Ezh2 impacts on induced pluripotent stem cell generation. Stem Cells Dev 2014; 23:931-40. [PMID: 24325319 DOI: 10.1089/scd.2013.0267] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Reprogramming of somatic cells toward pluripotency involves extensive chromatin reorganization and changes in gene expression. Polycomb group (PcG) proteins are key regulators of chromatin structure, cell identity, and development. In this study, we investigated the impact of Ezh2, a core subunit of Polycomb repressive complex 2 (PRC2), on the generation of induced pluripotent stem (iPS) cells. We found that Ezh2 expression is induced during iPS cell generation and iPS cells contain high levels of Ezh2 mRNA and protein. Importantly, shRNA knockdown of Ezh2 during reprogramming severely impairs iPS cell generation. Mechanistically, Ezh2 acts during reprogramming at least in part through repressing the Ink4a/Arf locus, which represents a major roadblock for iPS cell generation. Interestingly, knockdown of Ezh2 in established pluripotent cells leaves pluripotency and self-renewal of embryonic stem cells and iPS cells unaffected. Altogether, our results demonstrate that Ezh2 is critical for efficient iPS cell generation, whereas it is dispensable for maintaining the reprogrammed iPS cell state.
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Affiliation(s)
- Xiaolei Ding
- 1 Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School , Aachen, Germany
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89
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Lipps C, May T, Hauser H, Wirth D. Eternity and functionality – rational access to physiologically relevant cell lines. Biol Chem 2013; 394:1637-48. [DOI: 10.1515/hsz-2013-0158] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/11/2013] [Indexed: 01/08/2023]
Abstract
Abstract
In the first 50 years of cell culture, the development of new cell lines was mainly based on trial and error. Due to the understanding of the molecular networks of aging, senescence, proliferation, and adaption by mutation, the generation of new cell lines with physiologic properties has become more systematic. This endeavor has been supported by the availability of new technological achievements and increasing knowledge about the biology of cell differentiation and cell-cell communication. Here, we review some promising developments that are contributing toward this goal. These include molecular tools frequently used for the immortalization process. In addition to these broadly acting immortalization regimens, we focus on the developments of cell type-specific immortalization and on the methodologies of how to control the growth of newly established cell lines.
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90
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Hematopoietic stem and progenitor cells acquire distinct DNA-hypermethylation during in vitro culture. Sci Rep 2013; 3:3372. [PMID: 24284763 PMCID: PMC3842544 DOI: 10.1038/srep03372] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 11/11/2013] [Indexed: 01/08/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HPCs) can be maintained invitro, but the vast majority of their progeny loses stemness during culture. In this study, we compared DNA-methylation (DNAm) profiles of freshly isolated and culture-expanded HPCs. Culture conditions of CD34+ cells - either with or without mesenchymal stromal cells (MSCs) - had relatively little impact on DNAm, although proliferation is greatly increased by stromal support. However, all cultured HPCs - even those which remained CD34+ - acquired significant DNA-hypermethylation. DNA-hypermethylation occurred particularly in up-stream promoter regions, shore-regions of CpG islands, binding sites for PU.1, HOXA5 and RUNX1, and it was reflected in differential gene expression and variant transcripts of DNMT3A. Low concentrations of DNAm inhibitors slightly increased the frequency of colony-forming unit initiating cells. Our results demonstrate that HPCs acquire DNA-hypermethylation at specific sites in the genome which is relevant for the rapid loss of stemness during in vitro manipulation.
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91
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Fuellen G, Boerries M, Busch H, de Grey A, Hahn U, Hiller T, Hoeflich A, Jansen L, Janssens GE, Kaleta C, Meinema AC, Schäuble S, Simm A, Schofield PN, Smith B, Sühnel J, Vera J, Wagner W, Wönne EC, Wuttke D. In silico approaches and the role of ontologies in aging research. Rejuvenation Res 2013; 16:540-6. [PMID: 24188080 DOI: 10.1089/rej.2013.1517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, because these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focused on marker development and cellular stress as well as on diseases, in particular on diseases of kidney and skin.
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Affiliation(s)
- Georg Fuellen
- 1 Institute for Biostatistics and Informatics in Medicine and Aging Research, Department of Medicine, Rostock University , Rostock, Germany
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92
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Florath I, Butterbach K, Müller H, Bewerunge-Hudler M, Brenner H. Cross-sectional and longitudinal changes in DNA methylation with age: an epigenome-wide analysis revealing over 60 novel age-associated CpG sites. Hum Mol Genet 2013; 23:1186-201. [PMID: 24163245 DOI: 10.1093/hmg/ddt531] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Understanding the role of epigenetic modifications, e.g. DNA methylation, in the process of aging requires the characterization of methylation patterns in large cohorts. We analysed >480 000 CpG sites using Infinium HumanMethylation450 BeadChip (Illumina) in whole blood DNA of 965 participants of a population-based cohort study aged between 50 and 75 years. In an exploratory analysis in 400 individuals, 200 CpG sites with the highest Spearman correlation coefficients for the association between methylation and age were identified. Of these 200 CpGs, 162 were significantly associated with age, which was verified in an independent cohort of 498 individuals using mixed linear regression models adjusted for gender, smoking behaviour, age-related diseases and random batch effect and corrected for multiple testing by Bonferroni. In another independent cohort of 67 individuals without history of major age-related diseases and with a follow-up of 8 years, we observed a gain in methylation at 96% (52%, significant) of the positively age-associated CpGs and a loss at all (89%, significant) of the negatively age-associated CpGs in each individual while getting 8 years older. A regression model for age prediction based on 17 CpGs as predicting variables explained 71% of the variance in age with an average accuracy of 2.6 years. In comparison with cord blood samples obtained from the Ulm Birth Cohort Study, we observed a more than 2-fold change in mean methylation levels from birth to older age at 86 CpGs. We were able to identify 65 novel CpG sites with significant association of methylation with age.
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Affiliation(s)
- Ines Florath
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
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93
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Chiou YW, Lin HK, Tang MJ, Lin HH, Yeh ML. The influence of physical and physiological cues on atomic force microscopy-based cell stiffness assessment. PLoS One 2013; 8:e77384. [PMID: 24194882 PMCID: PMC3806741 DOI: 10.1371/journal.pone.0077384] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 09/04/2013] [Indexed: 01/16/2023] Open
Abstract
Atomic force microscopy provides a novel technique for differentiating the mechanical properties of various cell types. Cell elasticity is abundantly used to represent the structural strength of cells in different conditions. In this study, we are interested in whether physical or physiological cues affect cell elasticity in Atomic force microscopy (AFM)-based assessments. The physical cues include the geometry of the AFM tips, the indenting force and the operating temperature of the AFM. All of these cues show a significant influence on the cell elasticity assessment. Sharp AFM tips create a two-fold increase in the value of the effective Young's modulus (E(eff)) relative to that of the blunt tips. Higher indenting force at the same loading rate generates higher estimated cell elasticity. Increasing the operation temperature of the AFM leads to decreases in the cell stiffness because the structure of actin filaments becomes disorganized. The physiological cues include the presence of fetal bovine serum or extracellular matrix-coated surfaces, the culture passage number, and the culture density. Both fetal bovine serum and the extracellular matrix are critical for cells to maintain the integrity of actin filaments and consequently exhibit higher elasticity. Unlike primary cells, mouse kidney progenitor cells can be passaged and maintain their morphology and elasticity for a very long period without a senescence phenotype. Finally, cell elasticity increases with increasing culture density only in MDCK epithelial cells. In summary, for researchers who use AFM to assess cell elasticity, our results provide basic and significant information about the suitable selection of physical and physiological cues.
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Affiliation(s)
- Yu-Wei Chiou
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
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94
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Walenda G, Abnaof K, Joussen S, Meurer S, Smeets H, Rath B, Hoffmann K, Fröhlich H, Zenke M, Weiskirchen R, Wagner W. TGF-beta1 does not induce senescence of multipotent mesenchymal stromal cells and has similar effects in early and late passages. PLoS One 2013; 8:e77656. [PMID: 24147049 PMCID: PMC3798389 DOI: 10.1371/journal.pone.0077656] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/03/2013] [Indexed: 01/01/2023] Open
Abstract
Transforming growth factor-beta 1 (TGF-β1) stimulates a broad range of effects which are cell type dependent, and it has been suggested to induce cellular senescence. On the other hand, long-term culture of multipotent mesenchymal stromal cells (MSCs) has a major impact on their cellular physiology and therefore it is well conceivable that the molecular events triggered by TGF-β1 differ considerably in cells of early and late passages. In this study, we analyzed the effect of TGF-β1 on and during replicative senescence of MSCs. Stimulation with TGF-β1 enhanced proliferation, induced a network like growth pattern and impaired adipogenic and osteogenic differentiation. TGF-β1 did not induce premature senescence. However, due to increased proliferation rates the cells reached replicative senescence earlier than untreated controls. This was also evident, when we analyzed senescence-associated DNA-methylation changes. Gene expression profiles of MSCs differed considerably at relatively early (P 3-5) and later passages (P 10). Nonetheless, relative gene expression differences provoked by TGF-β1 at individual time points or in a time course dependent manner (stimulation for 0, 1, 4 and 12 h) were very similar in MSCs of early and late passage. These results support the notion that TGF-β1 has major impact on MSC function, but it does not induce senescence and has similar molecular effects during culture expansion.
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Affiliation(s)
- Gudrun Walenda
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Khalid Abnaof
- Algorithmic Bioinformatics, Bonn-Aachen International Center for Information Technology, University of Bonn, Bonn, Germany
- Bioanalytical Resource Centre Aachen, Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Sylvia Joussen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Steffen Meurer
- Institute of Clinical Chemistry and Pathobiochemistry, RWTH Aachen University Medical School, Aachen, Germany
| | - Hubert Smeets
- Genetics and Molecular Cell Biology, CARIM School for Cardiovascular Diseases, University of Maastricht, Maastricht, Netherlands
| | - Björn Rath
- Department for Orthopedics, RWTH Aachen University Medical School, Aachen, Germany
| | - Kurt Hoffmann
- Bioanalytical Resource Centre Aachen, Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Holger Fröhlich
- Algorithmic Bioinformatics, Bonn-Aachen International Center for Information Technology, University of Bonn, Bonn, Germany
| | - Martin Zenke
- Institute for Biomedical Technology, Department of Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Ralf Weiskirchen
- Institute of Clinical Chemistry and Pathobiochemistry, RWTH Aachen University Medical School, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
- * E-mail:
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95
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McClay JL, Aberg KA, Clark SL, Nerella S, Kumar G, Xie LY, Hudson AD, Harada A, Hultman CM, Magnusson PKE, Sullivan PF, Van Den Oord EJCG. A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects. Hum Mol Genet 2013; 23:1175-85. [PMID: 24135035 DOI: 10.1093/hmg/ddt511] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The central importance of epigenetics to the aging process is increasingly being recognized. Here we perform a methylome-wide association study (MWAS) of aging in whole blood DNA from 718 individuals, aged 25-92 years (mean = 55). We sequenced the methyl-CpG-enriched genomic DNA fraction, averaging 67.3 million reads per subject, to obtain methylation measurements for the ∼27 million autosomal CpGs in the human genome. Following extensive quality control, we adaptively combined methylation measures for neighboring, highly-correlated CpGs into 4 344 016 CpG blocks with which we performed association testing. Eleven age-associated differentially methylated regions (DMRs) passed Bonferroni correction (P-value < 1.15 × 10(-8)). Top findings replicated in an independent sample set of 558 subjects using pyrosequencing of bisulfite-converted DNA (min P-value < 10(-30)). To examine biological themes, we selected 70 DMRs with false discovery rate of <0.1. Of these, 42 showed hypomethylation and 28 showed hypermethylation with age. Hypermethylated DMRs were more likely to overlap with CpG islands and shores. Hypomethylated DMRs were more likely to be in regions associated with polycomb/regulatory proteins (e.g. EZH2) or histone modifications H3K27ac, H3K4m1, H3K4m2, H3K4m3 and H3K9ac. Among genes implicated by the top DMRs were protocadherins, homeobox genes, MAPKs and ryanodine receptors. Several of our DMRs are at genes with potential relevance for age-related disease. This study successfully demonstrates the application of next-generation sequencing to MWAS, by interrogating a large proportion of the methylome and returning potentially novel age DMRs, in addition to replicating several loci implicated in previous studies using microarrays.
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Affiliation(s)
- Joseph L McClay
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
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96
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Hemeda H, Kalz J, Walenda G, Lohmann M, Wagner W. Heparin concentration is critical for cell culture with human platelet lysate. Cytotherapy 2013; 15:1174-81. [PMID: 23845186 DOI: 10.1016/j.jcyt.2013.05.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 04/25/2013] [Accepted: 05/11/2013] [Indexed: 12/26/2022]
Abstract
BACKGROUND AIMS Culture media for mesenchymal stromal cells (MSCs) are generally supplemented with fetal bovine serum. Human platelet lysate (hPL) has been proven to be a very effective alternative without the risk of xenogeneic infections or immune reactions. In contrast to fetal bovine serum, hPL comprises plasma, and anticoagulants-usually unfractionated heparin (UFH)-need to be added to prevent gel formation. METHODS Cultures of MSCs in hPL media with various concentrations of UFH and enoxaparin, a low-molecular-weight heparin (LMWH), were systematically compared with regard to proliferation, fibroblastoid colony-forming unit frequency, immunophenotype and in vitro differentiation. RESULTS At least 0.61 IU/mL UFH or 0.024 mg/mL LMWH was necessary for reliable prevention of coagulation of hPL pools used in this study. Higher concentrations impaired cellular proliferation in a dose-dependent manner even without benzyl alcohol, which is commonly added to heparins as a bacteriostatic agent. Colony-forming unit frequency was also reduced at higher heparin concentrations, particularly with LMWH, whereas no significant effect was observed on cellular morphology or immunophenotype. High concentrations of heparins reduced the in vitro differentiation toward adipogenic and osteogenic lineages. CONCLUSIONS Heparin concentration is critical for culture of MSCs in hPL media; this is of particular relevance for cellular therapy where cell culture procedures need to be optimized and standardized.
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Affiliation(s)
- Hatim Hemeda
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
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97
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Willmann CA, Hemeda H, Pieper LA, Lenz M, Qin J, Joussen S, Sontag S, Wanek P, Denecke B, Schüler HM, Zenke M, Wagner W. To clone or not to clone? Induced pluripotent stem cells can be generated in bulk culture. PLoS One 2013; 8:e65324. [PMID: 23734247 PMCID: PMC3667031 DOI: 10.1371/journal.pone.0065324] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 04/23/2013] [Indexed: 12/31/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are usually clonally derived. The selection of fully reprogrammed cells generally involves picking of individual colonies with morphology similar to embryonic stem cells (ESCs). Given that fully reprogrammed cells are highly proliferative and escape from cellular senescence, it is conceivable that they outgrow non-pluripotent and partially reprogrammed cells during culture expansion without the need of clonal selection. In this study, we have reprogrammed human dermal fibroblasts (HDFs) with episomal plasmid vectors. Colony frequency was higher and size was larger when using murine embryonic fibroblasts (MEFs) as stromal support instead of HDFs or human mesenchymal stromal cells (MSCs). We have then compared iPSCs which were either clonally derived by manual selection of a single colony, or derived from bulk-cultures of all initial colonies. After few passages their morphology, expression of pluripotency markers, and gene expression profiles did not reveal any significant differences. Furthermore, clonally-derived and bulk-cultured iPSCs revealed similar in vitro differentiation potential towards the three germ layers. Therefore, manual selection of individual colonies does not appear to be necessary for the generation of iPSCs - this is of relevance for standardization and automation of cell culture procedures.
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Affiliation(s)
- Charlotte A. Willmann
- Helmholtz-Institute for Biomedical Technology, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Hatim Hemeda
- Helmholtz-Institute for Biomedical Technology, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Lisa A. Pieper
- Helmholtz-Institute for Biomedical Technology, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Michael Lenz
- Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany
| | - Jie Qin
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen Medical School, Aachen, Germany
| | - Sylvia Joussen
- Helmholtz-Institute for Biomedical Technology, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Stephanie Sontag
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen Medical School, Aachen, Germany
| | - Paul Wanek
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen Medical School, Aachen, Germany
| | - Bernd Denecke
- Interdisciplinary Center for Clinical Research, RWTH Aachen Medical School, Aachen, Germany
| | - Herdit M. Schüler
- Institute of Human Genetics, RWTH Aachen Medical School, Aachen, Germany
| | - Martin Zenke
- Helmholtz-Institute for Biomedical Technology, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen Medical School, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Technology, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
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Koch CM, Wagner W. Epigenetic biomarker to determine replicative senescence of cultured cells. Methods Mol Biol 2013; 1048:309-21. [PMID: 23929112 DOI: 10.1007/978-1-62703-556-9_20] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Somatic cells change continuously during culture expansion-long-term culture evokes increasing cell size, declining differentiation potential, and ultimate cell cycle arrest upon senescence. These changes are of particular relevance for cellular therapy which necessitates standardized products and reliable quality control. Recently, replicative senescence has been shown to be associated with highly reproducible epigenetic modifications. Here, we describe a simple method to track the state of senescence in mesenchymal stromal cells (MSCs) or fibroblasts by monitoring continuous DNA methylation (DNAm) changes at specific sites in the genome. Six CpG sites have been identified which reveal either linear hypermethylation or hypomethylation with respect to the number of cumulative population doublings (cPDs). Conversely, the DNAm level at these CpG sites can be analyzed-for example, by pyrosequencing of bisulfite-converted DNA-and then used for linear regression models to predict cPDs. Our method provides an epigenetic biomarker to determine the state of senescence in cell preparations.
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Affiliation(s)
- Carmen M Koch
- Stem Cell Biology and Cellular Engineering, Helmholtz-Institute for Biomedical Engineering; RWTH Aachen University Medical School, Aachen, Germany
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Wagner W. Implications of long-term culture for mesenchymal stem cells: genetic defects or epigenetic regulation? Stem Cell Res Ther 2012; 3:54. [PMID: 23257053 PMCID: PMC3580484 DOI: 10.1186/scrt145] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mesenchymal stem cells change dramatically during culture expansion. Long-term culture has been suspected to evoke oncogenic transformation: overall, the genome appears to be relatively stable throughout culture but transient clonal aneuploidies have been observed. Oncogenic transformation does not necessarily entail growth advantage in vitro and, therefore, the available methods - such as karyotypic analysis or genomic profiling - cannot exclude this risk. On the other hand, long-term culture is associated with specific senescence-associated DNA methylation (SA-DNAm) changes, particularly in developmental genes. SA-DNAm changes are highly reproducible and can be used to monitor the state of senescence for quality control. Notably, neither telomere attrition nor SA-DNAm changes occur in pluripotent stem cells, which can evade the 'Hayflick limit'. Long-term culture of mesenchymal stem cells seems to involve a tightly regulated epigenetic program. These epigenetic modifications may counteract dominant clones, which are more prone to transformation.
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