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Papandreou A, Singh N, Gianfrancesco L, Budinger D, Barwick K, Agrotis A, Luft C, Shao Y, Lenaerts AS, Gregory A, Jeong SY, Hogarth P, Hayflick S, Barral S, Kriston-Vizi J, Gissen P, Kurian MA, Ketteler R. Cardiac glycosides restore autophagy flux in an iPSC-derived neuronal model of WDR45 deficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.13.556416. [PMID: 37745522 PMCID: PMC10515824 DOI: 10.1101/2023.09.13.556416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Beta-Propeller Protein-Associated Neurodegeneration (BPAN) is one of the commonest forms of Neurodegeneration with Brain Iron Accumulation, caused by mutations in the gene encoding the autophagy-related protein, WDR45. The mechanisms linking autophagy, iron overload and neurodegeneration in BPAN are poorly understood and, as a result, there are currently no disease-modifying treatments for this progressive disorder. We have developed a patient-derived, induced pluripotent stem cell (iPSC)-based midbrain dopaminergic neuronal cell model of BPAN (3 patient, 2 age-matched controls and 2 isogenic control lines) which shows defective autophagy and aberrant gene expression in key neurodegenerative, neurodevelopmental and collagen pathways. A high content imaging-based medium-throughput blinded drug screen using the FDA-approved Prestwick library identified 5 cardiac glycosides that both corrected disease-related defective autophagosome formation and restored BPAN-specific gene expression profiles. Our findings have clear translational potential and emphasise the utility of iPSC-based modelling in elucidating disease pathophysiology and identifying targeted therapeutics for early-onset monogenic disorders.
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Affiliation(s)
- Apostolos Papandreou
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, University College London Great Ormond Street Institute of Child Health, London, UK
- Laboratory for Molecular Cell Biology, University College London, London, UK
- Department of Neurology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Nivedita Singh
- Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Lorita Gianfrancesco
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Dimitri Budinger
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Katy Barwick
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Alexander Agrotis
- Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Christin Luft
- Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Ying Shao
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | | | | | | | | | | | - Serena Barral
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Janos Kriston-Vizi
- Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Paul Gissen
- Inborn Errors of Metabolism, Genetics & Genomic Medicine Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Metabolic Medicine, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Manju A Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, University College London Great Ormond Street Institute of Child Health, London, UK
- Department of Neurology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- These authors contributed equally
| | - Robin Ketteler
- Laboratory for Molecular Cell Biology, University College London, London, UK
- Department of Human Medicine, Medical School Berlin, Berlin, Germany
- These authors contributed equally
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Puri D, Maaßen C, Varona Baranda M, Zeevaert K, Hahnfeld L, Hauser A, Fornero G, Elsafi Mabrouk MH, Wagner W. CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs. Front Cell Dev Biol 2023; 11:1302448. [PMID: 38099298 PMCID: PMC10720430 DOI: 10.3389/fcell.2023.1302448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Pluripotent stem cells are characterized by their differentiation potential toward endoderm, mesoderm, and ectoderm. However, it is still largely unclear how these cell-fate decisions are mediated by epigenetic mechanisms. In this study, we explored the relevance of CCCTC-binding factor (CTCF), a zinc finger-containing DNA-binding protein, which mediates long-range chromatin organization, for directed cell-fate determination. We generated human induced pluripotent stem cell (iPSC) lines with deletions in the protein-coding region in exon 3 of CTCF, resulting in shorter transcripts and overall reduced protein expression. Chromatin immunoprecipitation showed a considerable loss of CTCF binding to target sites. The CTCF deletions resulted in slower growth and modest global changes in gene expression, with downregulation of a subset of pluripotency-associated genes and neuroectodermal genes. CTCF deletion also evoked DNA methylation changes, which were moderately associated with differential gene expression. Notably, CTCF-deletions lead to upregulation of endo-mesodermal associated marker genes and epigenetic signatures, whereas ectodermal differentiation was defective. These results indicate that CTCF plays an important role in the maintenance of pluripotency and differentiation, especially towards ectodermal lineages.
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Affiliation(s)
- Deepika Puri
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Catharina Maaßen
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Monica Varona Baranda
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Kira Zeevaert
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Lena Hahnfeld
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Annika Hauser
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Giulia Fornero
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Mohamed H. Elsafi Mabrouk
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Wolfgang Wagner
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
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Zeevaert K, Goetzke R, Elsafi Mabrouk MH, Schmidt M, Maaßen C, Henneke AC, He C, Gillner A, Zenke M, Wagner W. YAP1 is essential for self-organized differentiation of pluripotent stem cells. BIOMATERIALS ADVANCES 2023; 146:213308. [PMID: 36774716 DOI: 10.1016/j.bioadv.2023.213308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023]
Abstract
Induced pluripotent stem cells (iPSCs) form aggregates that recapitulate aspects of the self-organization in early embryogenesis. Within few days, cells undergo a transition from epithelial-like structures to organized three-dimensional embryoid bodies (EBs) with upregulation of germ layer-specific genes. However, it is largely unclear, which signaling cascades regulate self-organized differentiation. The Yes-associated protein 1 (YAP1) is a downstream effector of the Hippo pathway and essential mechanotransducer. YAP1 has been suggested to play a crucial role for early embryo development, but the relevance for early germ layer commitment of human iPSCs remains to be elucidated. To gain insights into the function of YAP1 in early cell-fate decisions, we generated YAP1 knockout (YAP-/-) iPSC lines with CRISPR/Cas9 technology and analyzed transcriptomic and epigenetic modifications. YAP-/- iPSCs showed increased expression of several YAP1 targets and of NODAL, an important regulator of cell differentiation. Furthermore, YAP1 deficiency evoked global DNA methylation changes. Directed differentiation of adherent iPSC colonies towards endoderm, mesoderm, and ectoderm could be induced, albeit endodermal and ectodermal differentiation showed transcriptomic and epigenetic changes in YAP-/- lines. Notably, in undirected self-organized YAP-/- EBs germ layer specification was clearly impaired. This phenotype was rescued via lentiviral overexpression of YAP1 and also by NODAL inhibitors. Our results demonstrate that YAP1 plays an important role during early germ layer specification of iPSCs, particularly for the undirected self-organization of EBs, and this is at least partly attributed to activation of the NODAL signaling.
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Affiliation(s)
- Kira Zeevaert
- Helmholtz-Institute for Biomedical Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, 52074 Aachen, Germany.
| | - Roman Goetzke
- Helmholtz-Institute for Biomedical Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, 52074 Aachen, Germany; PL BioScience, Technology Centre Aachen, 52068 Aachen, Germany
| | - Mohamed H Elsafi Mabrouk
- Helmholtz-Institute for Biomedical Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, 52074 Aachen, Germany
| | - Marco Schmidt
- Helmholtz-Institute for Biomedical Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, 52074 Aachen, Germany
| | - Catharina Maaßen
- Helmholtz-Institute for Biomedical Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, 52074 Aachen, Germany
| | - Ann-Christine Henneke
- Helmholtz-Institute for Biomedical Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, 52074 Aachen, Germany
| | - Chao He
- Chair for Laser Technology LLT, RWTH Aachen University, 52074 Aachen, Germany
| | - Arnold Gillner
- Chair for Laser Technology LLT, RWTH Aachen University, 52074 Aachen, Germany
| | - Martin Zenke
- Helmholtz-Institute for Biomedical Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, 52074 Aachen, Germany; Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Medical Faculty of RWTH Aachen University, 52074 Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany.
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Papandreou A, Luft C, Barral S, Kriston-Vizi J, Kurian MA, Ketteler R. Automated high-content imaging in iPSC-derived neuronal progenitors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:42-51. [PMID: 36610640 PMCID: PMC10602900 DOI: 10.1016/j.slasd.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/18/2022] [Accepted: 12/31/2022] [Indexed: 01/07/2023]
Abstract
Induced pluripotent stem cells (iPSCs) have great potential as physiological disease models for human disorders where access to primary cells is difficult, such as neurons. In recent years, many protocols have been developed for the generation of iPSCs and the differentiation into specialised cell subtypes of interest. More recently, these models have been modified to allow large-scale phenotyping and high-content screening of small molecule compounds in iPSC-derived neuronal cells. Here, we describe the automated seeding of day 11 ventral midbrain progenitor cells into 96-well plates, administration of compounds, automated staining for immunofluorescence, the acquisition of images on a high-content screening platform and workflows for image analysis.
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Affiliation(s)
- Apostolos Papandreou
- University College London MRC Laboratory for Molecular Cell Biology, London, UK; Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Christin Luft
- University College London MRC Laboratory for Molecular Cell Biology, London, UK
| | - Serena Barral
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Janos Kriston-Vizi
- University College London MRC Laboratory for Molecular Cell Biology, London, UK
| | - Manju A Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Robin Ketteler
- University College London MRC Laboratory for Molecular Cell Biology, London, UK
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Variation of DNA methylation on the IRX1/2 genes is responsible for the neural differentiation propensity in human induced pluripotent stem cells. Regen Ther 2022; 21:620-630. [PMID: 36514370 PMCID: PMC9719094 DOI: 10.1016/j.reth.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/05/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Introduction Human induced pluripotent stem cells (hiPSCs) are useful tools for reproducing neural development in vitro. However, each hiPSC line has a different ability to differentiate into specific lineages, known as differentiation propensity, resulting in reduced reproducibility and increased time and funding requirements for research. To overcome this issue, we searched for predictive signatures of neural differentiation propensity of hiPSCs focusing on DNA methylation, which is the main modulator of cellular properties. Methods We obtained 32 hiPSC lines and their comprehensive DNA methylation data using the Infinium MethylationEPIC BeadChip. To assess the neural differentiation efficiency of these hiPSCs, we measured the percentage of neural stem cells on day 7 of induction. Using the DNA methylation data of undifferentiated hiPSCs and their measured differentiation efficiency into neural stem cells as the set of data, and HSIC Lasso, a machine learning-based nonlinear feature selection method, we attempted to identify neural differentiation-associated differentially methylated sites. Results Epigenome-wide unsupervised clustering cannot distinguish hiPSCs with varying differentiation efficiencies. In contrast, HSIC Lasso identified 62 CpG sites that could explain the neural differentiation efficiency of hiPSCs. Features selected by HSIC Lasso were particularly enriched within 3 Mbp of chromosome 5, harboring IRX1, IRX2, and C5orf38 genes. Within this region, DNA methylation rates were correlated with neural differentiation efficiency and were negatively correlated with gene expression of the IRX1/2 genes, particularly in female hiPSCs. In addition, forced expression of the IRX1/2 impaired the neural differentiation ability of hiPSCs in both sexes. Conclusion We for the first time showed that the DNA methylation state of the IRX1/2 genes of hiPSCs is a predictive biomarker of their potential for neural differentiation. The predictive markers for neural differentiation efficiency identified in this study may be useful for the selection of suitable undifferentiated hiPSCs prior to differentiation induction.
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Schmidt M, Zeevaert K, Elsafi Mabrouk MH, Goetzke R, Wagner W. Epigenetic biomarkers to track differentiation of pluripotent stem cells. Stem Cell Reports 2022; 18:145-158. [PMID: 36460001 PMCID: PMC9860076 DOI: 10.1016/j.stemcr.2022.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 12/03/2022] Open
Abstract
Quality control of induced pluripotent stem cells remains a challenge. For validation of the pluripotent state, it is crucial to determine trilineage differentiation potential toward endoderm, mesoderm, and ectoderm. Here, we report GermLayerTracker, a combination of site-specific DNA methylation (DNAm) assays that serve as biomarker for early germ layer specification. CG dinucleotides (CpGs) were identified with characteristic DNAm at pluripotent state and after differentiation into endoderm, mesoderm, and ectoderm. Based on this, a pluripotency score was derived that tracks reprogramming and may indicate differentiation capacity, as well as lineage-specific scores to monitor either directed differentiation or self-organized multilineage differentiation in embryoid bodies. Furthermore, we established pyrosequencing assays for fast and cost-effective analysis. In the future, the GermLayerTracker could be used for quality control of pluripotent cells and to estimate lineage-specific commitment during initial differentiation events.
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Affiliation(s)
- Marco Schmidt
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Kira Zeevaert
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Mohamed H. Elsafi Mabrouk
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Roman Goetzke
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Wolfgang Wagner
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany; Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany.
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Ávila-González D, Portillo W, Barragán-Álvarez CP, Hernandez-Montes G, Flores-Garza E, Molina-Hernández A, Diaz-Martinez NE, Diaz NF. The human amniotic epithelium confers a bias to differentiate toward the neuroectoderm lineage in human embryonic stem cells. eLife 2022; 11:68035. [PMID: 35815953 PMCID: PMC9313526 DOI: 10.7554/elife.68035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
Human embryonic stem cells (hESCs) derive from the epiblast and have pluripotent potential. To maintain the conventional conditions of the pluripotent potential in an undifferentiated state, inactivated mouse embryonic fibroblast (iMEF) is used as a feeder layer. However, it has been suggested that hESC under this conventional condition (hESC-iMEF) is an artifact that does not correspond to the in vitro counterpart of the human epiblast. Our previous studies demonstrated the use of an alternative feeder layer of human amniotic epithelial cells (hAECs) to derive and maintain hESC. We wondered if the hESC-hAEC culture could represent a different pluripotent stage than that of naïve or primed conventional conditions, simulating the stage in which the amniotic epithelium derives from the epiblast during peri-implantation. Like the conventional primed hESC-iMEF, hESC-hAEC has the same levels of expression as the ‘pluripotency core’ and does not express markers of naïve pluripotency. However, it presents a downregulation of HOX genes and genes associated with the endoderm and mesoderm, and it exhibits an increase in the expression of ectoderm lineage genes, specifically in the anterior neuroectoderm. Transcriptome analysis showed in hESC-hAEC an upregulated signature of genes coding for transcription factors involved in neural induction and forebrain development, and the ability to differentiate into a neural lineage was superior in comparison with conventional hESC-iMEF. We propose that the interaction of hESC with hAEC confers hESC a biased potential that resembles the anteriorized epiblast, which is predisposed to form the neural ectoderm.
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Affiliation(s)
- Daniela Ávila-González
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
| | - Wendy Portillo
- Behavioral and Cognitive Neurobiology, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Carla P Barragán-Álvarez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
| | | | - Eliezer Flores-Garza
- Departamento de Biología Molecular y Biotecnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Anayansi Molina-Hernández
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
| | | | - Nestor F Diaz
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
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Cypris O, Franzen J, Frobel J, Glück P, Kuo CC, Schmitz S, Nüchtern S, Zenke M, Wagner W. Hematopoietic differentiation persists in human iPSCs defective in de novo DNA methylation. BMC Biol 2022; 20:141. [PMID: 35705990 PMCID: PMC9202186 DOI: 10.1186/s12915-022-01343-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is involved in the epigenetic regulation of gene expression during developmental processes and is primarily established by the DNA methyltransferase 3A (DNMT3A) and 3B (DNMT3B). DNMT3A is one of the most frequently mutated genes in clonal hematopoiesis and leukemia, indicating that it plays a crucial role for hematopoietic differentiation. However, the functional relevance of Dnmt3a for hematopoietic differentiation and hematological malignancies has mostly been analyzed in mice, with the specific role for human hematopoiesis remaining elusive. In this study, we therefore investigated if DNMT3A is essential for hematopoietic differentiation of human induced pluripotent stem cells (iPSCs). RESULTS We generated iPSC lines with knockout of either exon 2, 19, or 23 and analyzed the impact of different DNMT3A exon knockouts on directed differentiation toward mesenchymal and hematopoietic lineages. Exon 19-/- and 23-/- lines displayed an almost entire absence of de novo DNA methylation during mesenchymal and hematopoietic differentiation. Yet, differentiation efficiency was only slightly reduced in exon 19-/- and rather increased in exon 23-/- lines, while there was no significant impact on gene expression in hematopoietic progenitors (iHPCs). Notably, DNMT3A-/- iHPCs recapitulate some DNA methylation patterns of acute myeloid leukemia (AML) with DNMT3A mutations. Furthermore, multicolor genetic barcoding revealed growth advantage of exon 23-/- iHPCs in a syngeneic competitive differentiation assay. CONCLUSIONS Our results demonstrate that iPSCs with homozygous knockout of different exons of DNMT3A remain capable of mesenchymal and hematopoietic differentiation-and exon 23-/- iHPCs even gained growth advantage-despite loss of almost the entire de novo DNA methylation. Partial recapitulation of DNA methylation patterns of AML with DNMT3A mutations by our DNMT3A knockout iHPCs indicates that our model system can help to elucidate mechanisms of clonal hematopoiesis.
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Affiliation(s)
- Olivia Cypris
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Joana Frobel
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Philipp Glück
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Chao-Chung Kuo
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Stephani Schmitz
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Selina Nüchtern
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Martin Zenke
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany. .,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany. .,Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), 52074, Aachen, North-Rhine Westphalia, Germany.
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9
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The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates. Biomaterials 2022; 282:121389. [PMID: 35121357 DOI: 10.1016/j.biomaterials.2022.121389] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/13/2021] [Accepted: 01/23/2022] [Indexed: 12/13/2022]
Abstract
Colonies of induced pluripotent stem cells (iPSCs) reveal aspects of self-organization even under culture conditions that maintain pluripotency. To investigate the dynamics of this process under spatial confinement, we used either polydimethylsiloxane (PDMS) pillars or micro-contact printing of vitronectin. There was a progressive upregulation of OCT4, E-cadherin, and NANOG within 70 μm from the outer rim of iPSC colonies. Single-cell RNA-sequencing and spatial reconstruction of gene expression demonstrated that OCT4high subsets, residing at the edge of the colony, have pronounced up-regulation of the TGF-β pathway, particularly of NODAL and its inhibitor LEFTY. Interestingly, after 5-7 days, iPSC colonies detached spontaneously from micro-contact printed substrates to form 3D aggregates. This new method allowed generation of embryoid bodies (EBs) of controlled size without enzymatic or mechanical treatment. Within the early 3D aggregates, radial organization and differential gene expression continued in analogy to the changes observed during self-organization of iPSC colonies. Early self-detached aggregates revealed up-regulated germline-specific gene expression patterns as compared to conventional EBs. However, there were no marked differences after further directed differentiation toward hematopoietic, mesenchymal, and neuronal lineages. Our results provide further insight into the gradual self-organization within iPSC colonies and at their transition into EBs.
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10
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Ng J, Barral S, De La Fuente Barrigon C, Lignani G, Erdem FA, Wallings R, Privolizzi R, Rossignoli G, Alrashidi H, Heasman S, Meyer E, Ngoh A, Pope S, Karda R, Perocheau D, Baruteau J, Suff N, Antinao Diaz J, Schorge S, Vowles J, Marshall LR, Cowley SA, Sucic S, Freissmuth M, Counsell JR, Wade-Martins R, Heales SJR, Rahim AA, Bencze M, Waddington SN, Kurian MA. Gene therapy restores dopamine transporter expression and ameliorates pathology in iPSC and mouse models of infantile parkinsonism. Sci Transl Med 2021; 13:eaaw1564. [PMID: 34011628 PMCID: PMC7612279 DOI: 10.1126/scitranslmed.aaw1564] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 08/20/2020] [Accepted: 02/20/2021] [Indexed: 12/11/2022]
Abstract
Most inherited neurodegenerative disorders are incurable, and often only palliative treatment is available. Precision medicine has great potential to address this unmet clinical need. We explored this paradigm in dopamine transporter deficiency syndrome (DTDS), caused by biallelic loss-of-function mutations in SLC6A3, encoding the dopamine transporter (DAT). Patients present with early infantile hyperkinesia, severe progressive childhood parkinsonism, and raised cerebrospinal fluid dopamine metabolites. The absence of effective treatments and relentless disease course frequently leads to death in childhood. Using patient-derived induced pluripotent stem cells (iPSCs), we generated a midbrain dopaminergic (mDA) neuron model of DTDS that exhibited marked impairment of DAT activity, apoptotic neurodegeneration associated with TNFα-mediated inflammation, and dopamine toxicity. Partial restoration of DAT activity by the pharmacochaperone pifithrin-μ was mutation-specific. In contrast, lentiviral gene transfer of wild-type human SLC6A3 complementary DNA restored DAT activity and prevented neurodegeneration in all patient-derived mDA lines. To progress toward clinical translation, we used the knockout mouse model of DTDS that recapitulates human disease, exhibiting parkinsonism features, including tremor, bradykinesia, and premature death. Neonatal intracerebroventricular injection of human SLC6A3 using an adeno-associated virus (AAV) vector provided neuronal expression of human DAT, which ameliorated motor phenotype, life span, and neuronal survival in the substantia nigra and striatum, although off-target neurotoxic effects were seen at higher dosage. These were avoided with stereotactic delivery of AAV2.SLC6A3 gene therapy targeted to the midbrain of adult knockout mice, which rescued both motor phenotype and neurodegeneration, suggesting that targeted AAV gene therapy might be effective for patients with DTDS.
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Affiliation(s)
- Joanne Ng
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, WC1E 6HX, UK
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, GOS-Institute of Child Health, University College London, London, WC1N 1DZ, UK
| | - Serena Barral
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, GOS-Institute of Child Health, University College London, London, WC1N 1DZ, UK.
| | | | - Gabriele Lignani
- Clinical and Experimental Epilepsy, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Fatma A Erdem
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, GOS-Institute of Child Health, University College London, London, WC1N 1DZ, UK
- Institute of Pharmacology and Gaston H. Glock Laboratories for Exploratory Drug Research, Centre of Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Rebecca Wallings
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Riccardo Privolizzi
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, WC1E 6HX, UK
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, GOS-Institute of Child Health, University College London, London, WC1N 1DZ, UK
| | - Giada Rossignoli
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, GOS-Institute of Child Health, University College London, London, WC1N 1DZ, UK
| | - Haya Alrashidi
- Genetics and Genomic Medicine, GOS-Institute of Child Health, University College London, London, WC1N 1EH, UK
| | - Sonja Heasman
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, GOS-Institute of Child Health, University College London, London, WC1N 1DZ, UK
| | - Esther Meyer
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, GOS-Institute of Child Health, University College London, London, WC1N 1DZ, UK
| | - Adeline Ngoh
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, GOS-Institute of Child Health, University College London, London, WC1N 1DZ, UK
| | - Simon Pope
- Neurometabolic Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Rajvinder Karda
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, WC1E 6HX, UK
| | - Dany Perocheau
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, WC1E 6HX, UK
| | - Julien Baruteau
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, WC1E 6HX, UK
- Genetics and Genomic Medicine, GOS-Institute of Child Health, University College London, London, WC1N 1EH, UK
| | - Natalie Suff
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, WC1E 6HX, UK
- Department of Women and Children's Health, King's College London, London, WC2R 2LS, UK
| | - Juan Antinao Diaz
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, WC1E 6HX, UK
| | - Stephanie Schorge
- Clinical and Experimental Epilepsy, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- Pharmacology, School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Jane Vowles
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Lucy R Marshall
- Infection, Immunity, Inflammation, GOS-Institute of Child Health, University College London, London, WC1N 1EH, UK
| | - Sally A Cowley
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Sonja Sucic
- Institute of Pharmacology and Gaston H. Glock Laboratories for Exploratory Drug Research, Centre of Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Michael Freissmuth
- Institute of Pharmacology and Gaston H. Glock Laboratories for Exploratory Drug Research, Centre of Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - John R Counsell
- Developmental Neurosciences, GOS-Institute of Child Health, University College London, London, WC1N 1EH, UK
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Simon J R Heales
- Genetics and Genomic Medicine, GOS-Institute of Child Health, University College London, London, WC1N 1EH, UK
- Neurometabolic Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Ahad A Rahim
- Pharmacology, School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Maximilien Bencze
- Developmental Neurosciences, GOS-Institute of Child Health, University College London, London, WC1N 1EH, UK
- University Paris Est Creteil, INSERM, IMRB, 94000 Creteil, France
| | - Simon N Waddington
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, WC1E 6HX, UK.
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, 2193 Johannesburg, South Africa
| | - Manju A Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, GOS-Institute of Child Health, University College London, London, WC1N 1DZ, UK
- Department of Neurology, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK
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11
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Nintedanib targets KIT D816V neoplastic cells derived from induced pluripotent stem cells of systemic mastocytosis. Blood 2021; 137:2070-2084. [PMID: 33512435 DOI: 10.1182/blood.2019004509] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 12/08/2020] [Indexed: 01/10/2023] Open
Abstract
The KIT D816V mutation is found in >80% of patients with systemic mastocytosis (SM) and is key to neoplastic mast cell (MC) expansion and accumulation in affected organs. Therefore, KIT D816V represents a prime therapeutic target for SM. Here, we generated a panel of patient-specific KIT D816V induced pluripotent stem cells (iPSCs) from patients with aggressive SM and mast cell leukemia to develop a patient-specific SM disease model for mechanistic and drug-discovery studies. KIT D816V iPSCs differentiated into neoplastic hematopoietic progenitor cells and MCs with patient-specific phenotypic features, thereby reflecting the heterogeneity of the disease. CRISPR/Cas9n-engineered KIT D816V human embryonic stem cells (ESCs), when differentiated into hematopoietic cells, recapitulated the phenotype observed for KIT D816V iPSC hematopoiesis. KIT D816V causes constitutive activation of the KIT tyrosine kinase receptor, and we exploited our iPSCs and ESCs to investigate new tyrosine kinase inhibitors targeting KIT D816V. Our study identified nintedanib, a US Food and Drug Administration-approved angiokinase inhibitor that targets vascular endothelial growth factor receptor, platelet-derived growth factor receptor, and fibroblast growth factor receptor, as a novel KIT D816V inhibitor. Nintedanib selectively reduced the viability of iPSC-derived KIT D816V hematopoietic progenitor cells and MCs in the nanomolar range. Nintedanib was also active on primary samples of KIT D816V SM patients. Molecular docking studies show that nintedanib binds to the adenosine triphosphate binding pocket of inactive KIT D816V. Our results suggest nintedanib as a new drug candidate for KIT D816V-targeted therapy of advanced SM.
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Elanzew A, Nießing B, Langendoerfer D, Rippel O, Piotrowski T, Schenk F, Kulik M, Peitz M, Breitkreuz Y, Jung S, Wanek P, Stappert L, Schmitt RH, Haupt S, Zenke M, König N, Brüstle O. The StemCellFactory: A Modular System Integration for Automated Generation and Expansion of Human Induced Pluripotent Stem Cells. Front Bioeng Biotechnol 2020; 8:580352. [PMID: 33240865 PMCID: PMC7680974 DOI: 10.3389/fbioe.2020.580352] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
While human induced pluripotent stem cells (hiPSCs) provide novel prospects for disease-modeling, the high phenotypic variability seen across different lines demands usage of large hiPSC cohorts to decipher the impact of individual genetic variants. Thus, a much higher grade of parallelization, and throughput in the production of hiPSCs is needed, which can only be achieved by implementing automated solutions for cell reprogramming, and hiPSC expansion. Here, we describe the StemCellFactory, an automated, modular platform covering the entire process of hiPSC production, ranging from adult human fibroblast expansion, Sendai virus-based reprogramming to automated isolation, and parallel expansion of hiPSC clones. We have developed a feeder-free, Sendai virus-mediated reprogramming protocol suitable for cell culture processing via a robotic liquid handling unit that delivers footprint-free hiPSCs within 3 weeks with state-of-the-art efficiencies. Evolving hiPSC colonies are automatically detected, harvested, and clonally propagated in 24-well plates. In order to ensure high fidelity performance, we have implemented a high-speed microscope for in-process quality control, and image-based confluence measurements for automated dilution ratio calculation. This confluence-based splitting approach enables parallel, and individual expansion of hiPSCs in 24-well plates or scale-up in 6-well plates across at least 10 passages. Automatically expanded hiPSCs exhibit normal growth characteristics, and show sustained expression of the pluripotency associated stem cell marker TRA-1-60 over at least 5 weeks (10 passages). Our set-up enables automated, user-independent expansion of hiPSCs under fully defined conditions, and could be exploited to generate a large number of hiPSC lines for disease modeling, and drug screening at industrial scale, and quality.
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Affiliation(s)
- Andreas Elanzew
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, Germany.,LIFE&BRAIN GmbH, Cellomics Unit, Bonn, Germany
| | - Bastian Nießing
- Fraunhofer Institute for Production Technology, Aachen, Germany
| | | | - Oliver Rippel
- LIFE&BRAIN GmbH, Cellomics Unit, Bonn, Germany.,Fraunhofer Institute for Production Technology, Aachen, Germany
| | | | | | - Michael Kulik
- Fraunhofer Institute for Production Technology, Aachen, Germany
| | - Michael Peitz
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, Germany.,Cell Programming Core Facility, University of Bonn Medical Faculty, Bonn, Germany
| | - Yannik Breitkreuz
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, Germany.,LIFE&BRAIN GmbH, Cellomics Unit, Bonn, Germany
| | - Sven Jung
- Fraunhofer Institute for Production Technology, Aachen, Germany
| | - Paul Wanek
- Institute for Biomedical Engineering, Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany.,Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | | | - Robert H Schmitt
- Fraunhofer Institute for Production Technology, Aachen, Germany.,Laboratory for Machine Tools and Production, RWTH Aachen University, Aachen, Germany
| | - Simone Haupt
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, Germany.,LIFE&BRAIN GmbH, Cellomics Unit, Bonn, Germany
| | - Martin Zenke
- Institute for Biomedical Engineering, Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany.,Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Niels König
- Fraunhofer Institute for Production Technology, Aachen, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, Germany.,LIFE&BRAIN GmbH, Cellomics Unit, Bonn, Germany
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13
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Panina Y, Karagiannis P, Kurtz A, Stacey GN, Fujibuchi W. Human Cell Atlas and cell-type authentication for regenerative medicine. Exp Mol Med 2020; 52:1443-1451. [PMID: 32929224 PMCID: PMC8080834 DOI: 10.1038/s12276-020-0421-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 12/22/2022] Open
Abstract
In modern biology, the correct identification of cell types is required for the developmental study of tissues and organs and the production of functional cells for cell therapies and disease modeling. For decades, cell types have been defined on the basis of morphological and physiological markers and, more recently, immunological markers and molecular properties. Recent advances in single-cell RNA sequencing have opened new doors for the characterization of cells at the individual and spatiotemporal levels on the basis of their RNA profiles, vastly transforming our understanding of cell types. The objective of this review is to survey the current progress in the field of cell-type identification, starting with the Human Cell Atlas project, which aims to sequence every cell in the human body, to molecular marker databases for individual cell types and other sources that address cell-type identification for regenerative medicine based on cell data guidelines.
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Affiliation(s)
- Yulia Panina
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Peter Karagiannis
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Andreas Kurtz
- BIH Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Glyn N Stacey
- International Stem Cell Banking Initiative, 2 High Street, Barley, Herts, SG88HZ, UK
- National Stem Cell Resource Centre, Institute of Zoology, Chinese Academy of Sciences, 100190, Beijing, China
- Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Wataru Fujibuchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
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14
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Cypris O, Eipel M, Franzen J, Rösseler C, Tharmapalan V, Kuo CC, Vieri M, Nikolić M, Kirschner M, Brümmendorf TH, Zenke M, Lampert A, Beier F, Wagner W. PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation. Clin Epigenetics 2020; 12:125. [PMID: 32819411 PMCID: PMC7439574 DOI: 10.1186/s13148-020-00914-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Dyskeratosis congenita (DKC) and idiopathic aplastic anemia (AA) are bone marrow failure syndromes that share characteristics of premature aging with severe telomere attrition. Aging is also reflected by DNA methylation changes, which can be utilized to predict donor age. There is evidence that such epigenetic age predictions are accelerated in premature aging syndromes, but it is yet unclear how this is related to telomere length. DNA methylation analysis may support diagnosis of DKC and AA, which still remains a challenge for these rare diseases. RESULTS In this study, we analyzed blood samples of 70 AA and 18 DKC patients to demonstrate that their epigenetic age predictions are overall increased, albeit not directly correlated with telomere length. Aberrant DNA methylation was observed in the gene PRDM8 in DKC and AA as well as in other diseases with premature aging phenotype, such as Down syndrome and Hutchinson-Gilford-Progeria syndrome. Aberrant DNA methylation patterns were particularly found within subsets of cell populations in DKC and AA samples as measured with barcoded bisulfite amplicon sequencing (BBA-seq). To gain insight into the functional relevance of PRDM8, we used CRISPR/Cas9 technology to generate induced pluripotent stem cells (iPSCs) with heterozygous and homozygous knockout. Loss of PRDM8 impaired hematopoietic and neuronal differentiation of iPSCs, even in the heterozygous knockout clone, but it did not impact on epigenetic age. CONCLUSION Taken together, our results demonstrate that epigenetic aging is accelerated in DKC and AA, independent from telomere attrition. Furthermore, aberrant DNA methylation in PRDM8 provides another biomarker for bone marrow failure syndromes and modulation of this gene in cellular subsets may be related to the hematopoietic and neuronal phenotypes observed in premature aging syndromes.
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Affiliation(s)
- Olivia Cypris
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Monika Eipel
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Corinna Rösseler
- Institute of Physiology, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Vithurithra Tharmapalan
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Chao-Chung Kuo
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Margherita Vieri
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Miloš Nikolić
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Tim H. Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Martin Zenke
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Angelika Lampert
- Institute of Physiology, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
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15
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The role of Nav1.7 in human nociceptors: insights from human induced pluripotent stem cell-derived sensory neurons of erythromelalgia patients. Pain 2020; 160:1327-1341. [PMID: 30720580 PMCID: PMC6554007 DOI: 10.1097/j.pain.0000000000001511] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Supplemental Digital Content is Available in the Text. Human sodium channel NaV1.7 in induced pluripotent stem cell–derived sensory neurons sets the action potential threshold but does not support subthreshold depolarizations. The chronic pain syndrome inherited erythromelalgia (IEM) is attributed to mutations in the voltage-gated sodium channel (NaV) 1.7. Still, recent studies targeting NaV1.7 in clinical trials have provided conflicting results. Here, we differentiated induced pluripotent stem cells from IEM patients with the NaV1.7/I848T mutation into sensory nociceptors. Action potentials in these IEM nociceptors displayed a decreased firing threshold, an enhanced upstroke, and afterhyperpolarization, all of which may explain the increased pain experienced by patients. Subsequently, we investigated the voltage dependence of the tetrodotoxin-sensitive NaV activation in these human sensory neurons using a specific prepulse voltage protocol. The IEM mutation induced a hyperpolarizing shift of NaV activation, which leads to activation of NaV1.7 at more negative potentials. Our results indicate that NaV1.7 is not active during subthreshold depolarizations, but that its activity defines the action potential threshold and contributes significantly to the action potential upstroke. Thus, our model system with induced pluripotent stem cell–derived sensory neurons provides a new rationale for NaV1.7 function and promises to be valuable as a translational tool to profile and develop more efficacious clinical analgesics.
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16
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Joe S, Nam H. Prediction model construction of mouse stem cell pluripotency using CpG and non-CpG DNA methylation markers. BMC Bioinformatics 2020; 21:175. [PMID: 32366211 PMCID: PMC7199378 DOI: 10.1186/s12859-020-3448-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/06/2020] [Indexed: 01/06/2023] Open
Abstract
Background Genome-wide studies of DNA methylation across the epigenetic landscape provide insights into the heterogeneity of pluripotent embryonic stem cells (ESCs). Differentiating into embryonic somatic and germ cells, ESCs exhibit varying degrees of pluripotency, and epigenetic changes occurring in this process have emerged as important factors explaining stem cell pluripotency. Results Here, using paired scBS-seq and scRNA-seq data of mice, we constructed a machine learning model that predicts degrees of pluripotency for mouse ESCs. Since the biological activities of non-CpG markers have yet to be clarified, we tested the predictive power of CpG and non-CpG markers, as well as a combination thereof, in the model. Through rigorous performance evaluation with both internal and external validation, we discovered that a model using both CpG and non-CpG markers predicted the pluripotency of ESCs with the highest prediction performance (0.956 AUC, external test). The prediction model consisted of 16 CpG and 33 non-CpG markers. The CpG and most of the non-CpG markers targeted depletions of methylation and were indicative of cell pluripotency, whereas only a few non-CpG markers reflected accumulations of methylation. Additionally, we confirmed that there exists the differing pluripotency between individual developmental stages, such as E3.5 and E6.5, as well as between induced mouse pluripotent stem cell (iPSC) and somatic cell. Conclusions In this study, we investigated CpG and non-CpG methylation in relation to mouse stem cell pluripotency and developed a model thereon that successfully predicts the pluripotency of mouse ESCs.
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Affiliation(s)
- Soobok Joe
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Buk-gu, Gwangju, 61005, Republic of Korea
| | - Hojung Nam
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Buk-gu, Gwangju, 61005, Republic of Korea.
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17
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Genetic barcoding reveals clonal dominance in iPSC-derived mesenchymal stromal cells. Stem Cell Res Ther 2020; 11:105. [PMID: 32138773 PMCID: PMC7059393 DOI: 10.1186/s13287-020-01619-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/10/2020] [Accepted: 02/24/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The use of mesenchymal stromal cells (MSCs) for research and clinical application is hampered by cellular heterogeneity and replicative senescence. Generation of MSC-like cells from induced pluripotent stem cells (iPSCs) may circumvent these limitations, and such iPSC-derived MSCs (iMSCs) are already tested in clinical trials. So far, a comparison of MSCs and iMSCs was particularly addressed in bulk culture. Despite the high hopes in cellular therapy, only little is known how the composition of different subclones changes in these cell preparations during culture expansion. METHODS In this study, we used multicolor lentiviral genetic barcoding for the marking of individual cells within cell preparations. Based on this, we could track the clonal composition of syngenic MSCs, iPSCs, and iMSCs during culture expansion. Furthermore, we analyzed DNA methylation patterns at senescence-associated genomic regions by barcoded bisulfite amplicon sequencing. The proliferation and differentiation capacities of individual subclones within MSCs and iMSCs were investigated with limiting dilution assays. RESULTS Overall, the clonal composition of primary MSCs and iPSCs gradually declined during expansion. In contrast, iMSCs became oligoclonal early during differentiation, indicating that they were derived from few individual iPSCs. This dominant clonal outgrowth of iMSCs was not associated with changes in chromosomal copy number variation. Furthermore, clonal dynamics were not clearly reflected by stochastically acquired DNA methylation patterns. Limiting dilution assays revealed that iMSCs are heterogeneous in colony formation and in vitro differentiation potential, while this was even more pronounced in primary MSCs. CONCLUSIONS Our results indicate that the subclonal diversity of MSCs and iPSCs declines gradually during in vitro culture, whereas derivation of iMSCs may stem from few individual iPSCs. Differentiation regimen needs to be further optimized to achieve homogeneous differentiation of iPSCs towards iMSCs.
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18
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Fernandez-Rebollo E, Franzen J, Goetzke R, Hollmann J, Ostrowska A, Oliverio M, Sieben T, Rath B, Kornfeld JW, Wagner W. Senescence-Associated Metabolomic Phenotype in Primary and iPSC-Derived Mesenchymal Stromal Cells. Stem Cell Reports 2020; 14:201-209. [PMID: 31983656 PMCID: PMC7013233 DOI: 10.1016/j.stemcr.2019.12.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 01/09/2023] Open
Abstract
Long-term culture of primary cells is characterized by functional and secretory changes, which ultimately result in replicative senescence. It is largely unclear how the metabolome of cells changes during replicative senescence and if such changes are consistent across different cell types. We have directly compared culture expansion of primary mesenchymal stromal cells (MSCs) and induced pluripotent stem cell-derived MSCs (iMSCs) until they reached growth arrest. Both cell types acquired similar changes in morphology, in vitro differentiation potential, senescence-associated β-galactosidase, and DNA methylation. Furthermore, MSCs and iMSCs revealed overlapping gene expression changes, particularly in functional categories related to metabolic processes. We subsequently compared the metabolomes of MSCs and iMSCs and observed overlapping senescence-associated changes in both cell types, including downregulation of nicotinamide ribonucleotide and upregulation of orotic acid. Taken together, replicative senescence is associated with a highly reproducible senescence-associated metabolomics phenotype, which may be used to monitor the state of cellular aging.
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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; University of Southern Denmark, Functional Genomics and Metabolism Unit, Department for Biochemistry and Molecular Biology, Campusvej 55, Odense 5230, Denmark.
| | - 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
| | - Roman Goetzke
- 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
| | - Jonathan Hollmann
- 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
| | - Matteo Oliverio
- Max Planck Institute for Metabolism Research (MPI-MR), Noncoding RNAs and Energy Homeostasis, Gleueler Strasse 50, Cologne 50931, Germany; Cologne Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, 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
| | - Björn Rath
- Department for Orthopedics, RWTH Aachen University Medical School, Aachen 52074, Germany
| | - Jan-Wilhelm Kornfeld
- Max Planck Institute for Metabolism Research (MPI-MR), Noncoding RNAs and Energy Homeostasis, Gleueler Strasse 50, Cologne 50931, Germany; Cologne Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany; University of Southern Denmark, Functional Genomics and Metabolism Unit, Department for Biochemistry and Molecular Biology, Campusvej 55, Odense 5230, Denmark
| | - 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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19
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Goetzke R, Keijdener H, Franzen J, Ostrowska A, Nüchtern S, Mela P, Wagner W. Differentiation of Induced Pluripotent Stem Cells towards Mesenchymal Stromal Cells is Hampered by Culture in 3D Hydrogels. Sci Rep 2019; 9:15578. [PMID: 31666572 PMCID: PMC6821810 DOI: 10.1038/s41598-019-51911-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 10/10/2019] [Indexed: 01/08/2023] Open
Abstract
Directed differentiation of induced pluripotent stem cells (iPSCs) towards specific lineages remains a major challenge in regenerative medicine, while there is a growing perception that this process can be influenced by the three-dimensional environment. In this study, we investigated whether iPSCs can differentiate towards mesenchymal stromal cells (MSCs) when embedded into fibrin hydrogels to enable a one-step differentiation procedure within a scaffold. Differentiation of iPSCs on tissue culture plastic or on top of fibrin hydrogels resulted in a typical MSC-like phenotype. In contrast, iPSCs embedded into fibrin gel gave rise to much smaller cells with heterogeneous growth patterns, absence of fibronectin, faint expression of CD73 and CD105, and reduced differentiation potential towards osteogenic and adipogenic lineage. Transcriptomic analysis demonstrated that characteristic genes for MSCs and extracellular matrix were upregulated on flat substrates, whereas genes of neural development were upregulated in 3D culture. Furthermore, the 3D culture had major effects on DNA methylation profiles, particularly within genes for neuronal and cardiovascular development, while there was no evidence for epigenetic maturation towards MSCs. Taken together, iPSCs could be differentiated towards MSCs on tissue culture plastic or on a flat fibrin hydrogel. In contrast, the differentiation process was heterogeneous and not directed towards MSCs when iPSCs were embedded into the hydrogel.
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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
| | - Hans Keijdener
- Department of Biohybrid & Medical Textiles (BioTex), AME-Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, 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
| | - Selina Nüchtern
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Petra Mela
- Department of Biohybrid & Medical Textiles (BioTex), AME-Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany. .,Medical Materials and Implants, Department of Mechanical Engineering and Munich School of BioEngineering, Technical University of Munich, Garching, 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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20
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Cypris O, Frobel J, Rai S, Franzen J, Sontag S, Goetzke R, Szymanski de Toledo MA, Zenke M, Wagner W. Tracking of epigenetic changes during hematopoietic differentiation of induced pluripotent stem cells. Clin Epigenetics 2019; 11:19. [PMID: 30717806 PMCID: PMC6360658 DOI: 10.1186/s13148-019-0617-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/17/2019] [Indexed: 01/09/2023] Open
Abstract
Background Differentiation of induced pluripotent stem cells (iPSCs) toward hematopoietic progenitor cells (HPCs) raises high hopes for disease modeling, drug screening, and cellular therapy. Various differentiation protocols have been established to generate iPSC-derived HPCs (iHPCs) that resemble their primary counterparts in morphology and immunophenotype, whereas a systematic epigenetic comparison was yet elusive. Results In this study, we compared genome-wide DNA methylation (DNAm) patterns of iHPCs with various different hematopoietic subsets. After 20 days of in vitro differentiation, cells revealed typical hematopoietic morphology, CD45 expression, and colony-forming unit (CFU) potential. DNAm changes were particularly observed in genes that are associated with hematopoietic differentiation. On the other hand, the epigenetic profiles of iHPCs remained overall distinct from natural HPCs. Furthermore, we analyzed if additional co-culture for 2 weeks with syngenic primary mesenchymal stromal cells (MSCs) or iPSC-derived MSCs (iMSCs) further supports epigenetic maturation toward the hematopoietic lineage. Proliferation of iHPCs and maintenance of CFU potential was enhanced upon co-culture. However, DNAm profiles support the notion that additional culture expansion with stromal support did not increase epigenetic maturation of iHPCs toward natural HPCs. Conclusion Differentiation of iPSCs toward the hematopoietic lineage remains epigenetically incomplete. These results substantiate the need to elaborate advanced differentiation regimen while DNAm profiles provide a suitable measure to track this process. Electronic supplementary material The online version of this article (10.1186/s13148-019-0617-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Olivia Cypris
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany
| | - Joana Frobel
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany
| | - Shivam Rai
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany
| | - Stephanie Sontag
- Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Roman Goetzke
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany
| | - Marcelo A Szymanski de Toledo
- Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Martin Zenke
- Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany. .,Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.
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21
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Schöndorf DC, Elschami M, Schieck M, Ercan-Herbst E, Weber C, Riesinger Y, Kalman S, Steinemann D, Ehrnhoefer DE. Generation of an induced pluripotent stem cell cohort suitable to investigate sporadic Alzheimer's Disease. Stem Cell Res 2018; 34:101351. [PMID: 30611016 DOI: 10.1016/j.scr.2018.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/20/2018] [Indexed: 11/25/2022] Open
Abstract
Alzheimer's Disease (AD) is the major cause of dementia in the elderly, and cortical neurons differentiated from patient-derived induced pluripotent stem cells (iPSCs) can recapitulate disease phenotypes such as tau phosphorylation or amyloid beta (Aß) deposition. Here we describe the generation of an iPSC cohort consisting of 2 sporadic AD cases and 3 controls, derived from dermal fibroblasts. All lines were karyotypically normal, showed expression of stem cell markers and efficiently differentiated into cells of all three germ layers.
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Affiliation(s)
| | | | | | | | | | | | - Sara Kalman
- BioMedX Innovation Center, Heidelberg, Germany
| | - Doris Steinemann
- Institut für Humangenetik, Medizinische Hochschule Hannover, Germany
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22
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Erdlenbruch F, Rohwedel J, Ralfs P, Thomitzek A, Kramer J, Cakiroglu F. Generation of induced pluripotent stem cells (iPSCs) from human foreskin fibroblasts. Stem Cell Res 2018; 33:79-82. [PMID: 30321832 DOI: 10.1016/j.scr.2018.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/27/2018] [Accepted: 10/04/2018] [Indexed: 12/26/2022] Open
Abstract
The human iPS cell line VUZUZLi001-A (hVH-1) was generated from human foreskin fibroblasts to be used as a control line. Reprogramming was performed by retroviral transduction of reprogramming factors OCT4, SOX2, KLF4 and c-MYC. Resource table.
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Affiliation(s)
| | - Jürgen Rohwedel
- Institute for Virology and Cell Biology, University of Lübeck, Germany.
| | - Philipp Ralfs
- Institute for Virology and Cell Biology, University of Lübeck, Germany
| | - Antonia Thomitzek
- Institute for Virology and Cell Biology, University of Lübeck, Germany
| | - Jan Kramer
- Institute for Virology and Cell Biology, University of Lübeck, Germany
| | - Figen Cakiroglu
- Institute for Virology and Cell Biology, University of Lübeck, Germany
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23
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Interrupted reprogramming into induced pluripotent stem cells does not rejuvenate human mesenchymal stromal cells. Sci Rep 2018; 8:11676. [PMID: 30076334 PMCID: PMC6076311 DOI: 10.1038/s41598-018-30069-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 07/24/2018] [Indexed: 12/22/2022] Open
Abstract
Replicative senescence hampers application of mesenchymal stromal cells (MSCs) because it limits culture expansion, impairs differentiation potential, and hinders reliable standardization of cell products. MSCs can be rejuvenated by reprogramming into induced pluripotent stem cells (iPSCs), which is associated with complete erasure of age- and senescence-associated DNA methylation (DNAm) patterns. However, this process is also associated with erasure of cell-type and tissue-specific epigenetic characteristics that are not recapitulated upon re-differentiation towards MSCs. In this study, we therefore followed the hypothesis that overexpression of pluripotency factors under culture conditions that do not allow full reprogramming might reset senescence-associated changes without entering a pluripotent state. MSCs were transfected with episomal plasmids and either successfully reprogrammed into iPSCs or cultured in different media with continuous passaging every week. Overexpression of pluripotency factors without reprogramming did neither prolong culture expansion nor ameliorate molecular and epigenetic hallmarks of senescence. Notably, transfection resulted in immortalization of one cell preparation with gain of large parts of the long arm of chromosome 1. Taken together, premature termination of reprogramming does not result in rejuvenation of MSCs and harbours the risk of transformation. This approach is therefore not suitable to rejuvenate cells for cellular therapy.
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24
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Defining essential genes for human pluripotent stem cells by CRISPR-Cas9 screening in haploid cells. Nat Cell Biol 2018; 20:610-619. [PMID: 29662178 DOI: 10.1038/s41556-018-0088-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 03/20/2018] [Indexed: 12/20/2022]
Abstract
The maintenance of pluripotency requires coordinated expression of a set of essential genes. Using our recently established haploid human pluripotent stem cells (hPSCs), we generated a genome-wide loss-of-function library targeting 18,166 protein-coding genes to define the essential genes in hPSCs. With this we could allude to an intrinsic bias of essentiality across cellular compartments, uncover two opposing roles for tumour suppressor genes and link autosomal-recessive disorders with growth-retardation phenotypes to early embryogenesis. hPSC-enriched essential genes mainly encode transcription factors and proteins related to cell-cycle and DNA-repair, revealing that a quarter of the nuclear factors are essential for normal growth. Our screen also led to the identification of growth-restricting genes whose loss of function provides a growth advantage to hPSCs, highlighting the role of the P53-mTOR pathway in this context. Overall, we have constructed an atlas of essential and growth-restricting genes in hPSCs, revealing key aspects of cellular essentiality and providing a reference for future studies on human pluripotency.
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25
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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: 22] [Impact Index Per Article: 3.1] [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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26
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Epigenetic age predictions based on buccal swabs are more precise in combination with cell type-specific DNA methylation signatures. Aging (Albany NY) 2017; 8:1034-48. [PMID: 27249102 PMCID: PMC4931852 DOI: 10.18632/aging.100972] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/18/2016] [Indexed: 12/11/2022]
Abstract
Aging is reflected by highly reproducible DNA methylation (DNAm) changes that open new perspectives for estimation of chronological age in legal medicine. DNA can be harvested non-invasively from cells at the inside of a person's cheek using buccal swabs - but these specimens resemble heterogeneous mixtures of buccal epithelial cells and leukocytes with different epigenetic makeup. In this study, we have trained an age predictor based on three age-associated CpG sites (associated with the genesPDE4C, ASPA, and ITGA2B) for swab samples to reach a mean absolute deviation (MAD) between predicted and chronological age of 4.3 years in a training set and of 7.03 years in a validation set. Subsequently, the composition of buccal epithelial cells versus leukocytes was estimated by two additional CpGs (associated with the genes CD6 and SERPINB5). Results of this "Buccal-Cell-Signature" correlated with cell counts in cytological stains (R2 = 0.94). Combination of cell type-specific and age-associated CpGs into one multivariate model enabled age predictions with MADs of 5.09 years and 5.12 years in two independent validation sets. Our results demonstrate that the cellular composition in buccal swab samples can be determined by DNAm at two cell type-specific CpGs to improve epigenetic age predictions.
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27
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Ntai A, Baronchelli S, La Spada A, Moles A, Guffanti A, De Blasio P, Biunno I. A Review of Research-Grade Human Induced Pluripotent Stem Cells Qualification and Biobanking Processes. Biopreserv Biobank 2017; 15:384-392. [DOI: 10.1089/bio.2016.0097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Aikaterini Ntai
- Integrated Systems Engineering S.r.l. (ISENET), Milan, Italy
| | - Simona Baronchelli
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), Department of Biomedicine, Milan, Italy
| | - Alberto La Spada
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), Department of Biomedicine, Milan, Italy
| | | | | | | | - Ida Biunno
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), Department of Biomedicine, Milan, Italy
- IRCCS MultiMedica, Department of Stem Cell Research, Milan, Italy
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28
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Abagnale G, Sechi A, Steger M, Zhou Q, Kuo CC, Aydin G, Schalla C, Müller-Newen G, Zenke M, Costa IG, van Rijn P, Gillner A, Wagner W. Surface Topography Guides Morphology and Spatial Patterning of Induced Pluripotent Stem Cell Colonies. Stem Cell Reports 2017; 9:654-666. [PMID: 28757164 PMCID: PMC5550028 DOI: 10.1016/j.stemcr.2017.06.016] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 12/31/2022] Open
Abstract
The relevance of topographic cues for commitment of induced pluripotent stem cells (iPSCs) is largely unknown. In this study, we demonstrate that groove-ridge structures with a periodicity in the submicrometer range induce elongation of iPSC colonies, guide the orientation of apical actin fibers, and direct the polarity of cell division. Elongation of iPSC colonies impacts also on their intrinsic molecular patterning, which seems to be orchestrated from the rim of the colonies. BMP4-induced differentiation is enhanced in elongated colonies, and the submicron grooves impact on the spatial modulation of YAP activity upon induction with this morphogen. Interestingly, TAZ, a YAP paralog, shows distinct cytoskeletal localization in iPSCs. These findings demonstrate that topography can guide orientation and organization of iPSC colonies, which may affect the interaction between mechanosensors and mechanotransducers in iPSCs.
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Affiliation(s)
- Giulio Abagnale
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, 52074 Aachen, Germany
| | - Antonio Sechi
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany
| | - Michael Steger
- Laser Technology (ILT), RWTH Aachen University, 52074 Aachen, Germany
| | - Qihui Zhou
- University of Groningen, University Medical Center Groningen, Biomedical Engineering Department-FB40, Groningen, the Netherlands
| | - Chao-Chung Kuo
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany; IZKF Bioinformatics Research Group, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Gülcan Aydin
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany
| | - Carmen Schalla
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany
| | - Gerhard Müller-Newen
- Department of Biochemistry and Molecular Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Martin Zenke
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074 Aachen, Germany
| | - Ivan G Costa
- Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany; IZKF Bioinformatics Research Group, RWTH Aachen University Medical School, 52074 Aachen, Germany; Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, 52074 Aachen, Germany
| | - Patrick van Rijn
- University of Groningen, University Medical Center Groningen, Biomedical Engineering Department-FB40, Groningen, the Netherlands
| | - Arnold Gillner
- Laser Technology (ILT), RWTH Aachen University, 52074 Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, 52074 Aachen, Germany; Institute of Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany.
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29
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Baud A, Wessely F, Mazzacuva F, McCormick J, Camuzeaux S, Heywood WE, Little D, Vowles J, Tuefferd M, Mosaku O, Lako M, Armstrong L, Webber C, Cader MZ, Peeters P, Gissen P, Cowley SA, Mills K. Multiplex High-Throughput Targeted Proteomic Assay To Identify Induced Pluripotent Stem Cells. Anal Chem 2017; 89:2440-2448. [PMID: 28192931 DOI: 10.1021/acs.analchem.6b04368] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Induced pluripotent stem cells have great potential as a human model system in regenerative medicine, disease modeling, and drug screening. However, their use in medical research is hampered by laborious reprogramming procedures that yield low numbers of induced pluripotent stem cells. For further applications in research, only the best, competent clones should be used. The standard assays for pluripotency are based on genomic approaches, which take up to 1 week to perform and incur significant cost. Therefore, there is a need for a rapid and cost-effective assay able to distinguish between pluripotent and nonpluripotent cells. Here, we describe a novel multiplexed, high-throughput, and sensitive peptide-based multiple reaction monitoring mass spectrometry assay, allowing for the identification and absolute quantitation of multiple core transcription factors and pluripotency markers. This assay provides simpler and high-throughput classification into either pluripotent or nonpluripotent cells in 7 min analysis while being more cost-effective than conventional genomic tests.
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Affiliation(s)
- Anna Baud
- Centre for Translational Omics, UCL Great Ormond Street Institute of Child Health , London, WC1N 1EH, United Kingdom
| | - Frank Wessely
- Department of Physiology, Anatomy & Genetics, Oxford University , Oxford, OX1 3PT, United Kingdom
| | - Francesca Mazzacuva
- Centre for Translational Omics, UCL Great Ormond Street Institute of Child Health , London, WC1N 1EH, United Kingdom
| | - James McCormick
- Centre for Translational Omics, UCL Great Ormond Street Institute of Child Health , London, WC1N 1EH, United Kingdom
| | - Stephane Camuzeaux
- Centre for Translational Omics, UCL Great Ormond Street Institute of Child Health , London, WC1N 1EH, United Kingdom
| | - Wendy E Heywood
- Centre for Translational Omics, UCL Great Ormond Street Institute of Child Health , London, WC1N 1EH, United Kingdom
| | - Daniel Little
- MRC Laboratory for Molecular Cell Biology, University College London , London, WC1E 6BT, United Kingdom
| | - Jane Vowles
- Oxford Parkinson's Disease Centre, University of Oxford , Oxford, OX1 3QX, United Kingdom
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford , Oxford, OX1 3RE, United Kingdom
| | | | - Olukunbi Mosaku
- MRC Laboratory for Molecular Cell Biology, University College London , London, WC1E 6BT, United Kingdom
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University , Newcastle, NE1 3BZ, United Kingdom
| | - Lyle Armstrong
- Institute of Genetic Medicine, Newcastle University , Newcastle, NE1 3BZ, United Kingdom
| | - Caleb Webber
- Department of Physiology, Anatomy & Genetics, Oxford University , Oxford, OX1 3PT, United Kingdom
| | - M Zameel Cader
- The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital , Oxford, OX3 9DS, United Kingdom
| | - Pieter Peeters
- Janssen Research and Development , Beerse, 2340, Belgium
| | - Paul Gissen
- MRC Laboratory for Molecular Cell Biology, University College London , London, WC1E 6BT, United Kingdom
| | - Sally A Cowley
- Oxford Parkinson's Disease Centre, University of Oxford , Oxford, OX1 3QX, United Kingdom
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford , Oxford, OX1 3RE, United Kingdom
| | - Kevin Mills
- Centre for Translational Omics, UCL Great Ormond Street Institute of Child Health , London, WC1N 1EH, United Kingdom
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30
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Sontag S, Förster M, Qin J, Wanek P, Mitzka S, Schüler HM, Koschmieder S, Rose-John S, Seré K, Zenke M. Modelling IRF8 Deficient Human Hematopoiesis and Dendritic Cell Development with Engineered iPS Cells. Stem Cells 2017; 35:898-908. [DOI: 10.1002/stem.2565] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/20/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Stephanie Sontag
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Malrun Förster
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Jie Qin
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Paul Wanek
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Saskia Mitzka
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Herdit M. Schüler
- Department of Human Genetics, 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
| | - Stefan Rose-John
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University; Kiel Germany
| | - Kristin Seré
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
| | - Martin Zenke
- Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University Medical School; Aachen Germany
- Helmholtz Institute for Biomedical Engineering; RWTH Aachen University; Aachen Germany
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31
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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: 5.4] [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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32
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Utilizing Regulatory Networks for Pluripotency Assessment in Stem Cells. CURRENT STEM CELL REPORTS 2016. [DOI: 10.1007/s40778-016-0054-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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33
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Stanurova J, Neureiter A, Hiber M, de Oliveira Kessler H, Stolp K, Goetzke R, Klein D, Bankfalvi A, Klump H, Steenpass L. Angelman syndrome-derived neurons display late onset of paternal UBE3A silencing. Sci Rep 2016; 6:30792. [PMID: 27484051 PMCID: PMC4971516 DOI: 10.1038/srep30792] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/02/2016] [Indexed: 01/21/2023] Open
Abstract
Genomic imprinting is an epigenetic phenomenon resulting in parent-of-origin-specific gene expression that is regulated by a differentially methylated region. Gene mutations or failures in the imprinting process lead to the development of imprinting disorders, such as Angelman syndrome. The symptoms of Angelman syndrome are caused by the absence of functional UBE3A protein in neurons of the brain. To create a human neuronal model for Angelman syndrome, we reprogrammed dermal fibroblasts of a patient carrying a defined three-base pair deletion in UBE3A into induced pluripotent stem cells (iPSCs). In these iPSCs, both parental alleles are present, distinguishable by the mutation, and express UBE3A. Detailed characterization of these iPSCs demonstrated their pluripotency and exceptional stability of the differentially methylated region regulating imprinted UBE3A expression. We observed strong induction of SNHG14 and silencing of paternal UBE3A expression only late during neuronal differentiation, in vitro. This new Angelman syndrome iPSC line allows to study imprinted gene regulation on both parental alleles and to dissect molecular pathways affected by the absence of UBE3A protein.
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Affiliation(s)
- Jana Stanurova
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Anika Neureiter
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Michaela Hiber
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Hannah de Oliveira Kessler
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Kristin Stolp
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Roman Goetzke
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstr. 20, 52074 Aachen, Germany
| | - Diana Klein
- Institute for Cell Biology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Agnes Bankfalvi
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Hannes Klump
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
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