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Elsafi Mabrouk MH, Zeevaert K, Henneke AC, Maaßen C, Wagner W. Substrate elasticity does not impact DNA methylation changes during differentiation of pluripotent stem cells. Cytotherapy 2024; 26:1046-1051. [PMID: 38583169 DOI: 10.1016/j.jcyt.2024.03.485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND AIMS Substrate elasticity may direct cell-fate decisions of stem cells. However, it is largely unclear how matrix stiffness affects the differentiation of induced pluripotent stem cells (iPSCs) and whether this is also reflected by epigenetic modifications. METHODS We cultured iPSCs on tissue culture plastic (TCP) and polydimethylsiloxane (PDMS) with different Young's modulus (0.2 kPa, 16 kPa or 64 kPa) to investigate the sequel on growth and differentiation toward endoderm, mesoderm and ectoderm. RESULTS Immunofluorescence and gene expression of canonical differentiation markers were hardly affected by the substrates. Notably, when we analyzed DNA methylation profiles of undifferentiated iPSCs or after three-lineage differentiation, we did not see any significant differences on the three different PDMS elasticities. Only when we compared DNA methylation profiles on PDMS-substrates versus TCP we did observe epigenetic differences, particularly on mesodermal differentiation. CONCLUSIONS Stiffness of PDMS substrates did not affect directed differentiation of iPSCs, whereas the moderate epigenetic differences on TCP might also be attributed to other chemical parameters.
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Affiliation(s)
- Mohamed H Elsafi Mabrouk
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Kira Zeevaert
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Ann-Christine Henneke
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Catharina Maaßen
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany; Institute for Stem Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany.
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Babu HWS, Kumar SM, Kaur H, Iyer M, Vellingiri B. Midbrain organoids for Parkinson's disease (PD) - A powerful tool to understand the disease pathogenesis. Life Sci 2024; 345:122610. [PMID: 38580194 DOI: 10.1016/j.lfs.2024.122610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
Brain Organiods (BOs) are a promising technique for researching disease progression in the human brain. These organoids, which are produced from human induced pluripotent stem cells (HiPSCs), can construct themselves into structured frameworks. In the context of Parkinson's disease (PD), recent advancements have been made in the development of Midbrain organoids (MBOs) models that consider key pathophysiological mechanisms such as alpha-synuclein (α-Syn), Lewy bodies, dopamine loss, and microglia activation. However, there are limitations to the current use of BOs in disease modelling and drug discovery, such as the lack of vascularization, long-term differentiation, and absence of glial cells. To address these limitations, researchers have proposed the use of spinning bioreactors to improve oxygen and nutrient perfusion. Modelling PD utilising modern experimental in vitro models is a valuable tool for studying disease mechanisms and elucidating previously unknown features of PD. In this paper, we exclusively review the unique methods available for cultivating MBOs using a pumping system that mimics the circulatory system. This mechanism may aid in delivering the required amount of oxygen and nutrients to all areas of the organoids, preventing cell death, and allowing for long-term culture and using co-culturing techniques for developing glial cell in BOs. Furthermore, we emphasise some of the significant discoveries about the BOs and the potential challenges of using BOs will be discussed.
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Affiliation(s)
- Harysh Winster Suresh Babu
- Human Cytogenetics and Stem Cell Laboratory, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda 151401, Punjab, India
| | - Sindduja Muthu Kumar
- Human Cytogenetics and Stem Cell Laboratory, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda 151401, Punjab, India
| | - Harsimrat Kaur
- Human Cytogenetics and Stem Cell Laboratory, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda 151401, Punjab, India
| | - Mahalaxmi Iyer
- Centre for Neuroscience, Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore-641021, Tamil Nadu, India; Department of Microbiology, School of Basic Sciences, Central University of Punjab, Bathinda 151401, Punjab, India
| | - Balachandar Vellingiri
- Human Cytogenetics and Stem Cell Laboratory, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda 151401, Punjab, India.
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Virdi JK, Pethe P. Assessment of human embryonic stem cells differentiation into definitive endoderm lineage on the soft substrates. Cell Biol Int 2024. [PMID: 38419492 DOI: 10.1002/cbin.12151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024]
Abstract
Pluripotent stem cells (PSCs) hold enormous potential for treating multiple diseases owing to their ability to self-renew and differentiate into any cell type. Albeit possessing such promising potential, controlling their differentiation into a desired cell type continues to be a challenge. Recent studies suggest that PSCs respond to different substrate stiffness and, therefore, can differentiate towards some lineages via Hippo pathway. Human PSCs can also differentiate and self-organize into functional cells, such as organoids. Traditionally, human PSCs are differentiated on stiff plastic or glass plates towards definitive endoderm and then into functional pancreatic progenitor cells in the presence of soluble growth factors. Thus, whether stiffness plays any role in differentiation towards definitive endoderm from human pluripotent stem cells (hPSCs) remains unclear. Our study found that the directed differentiation of human embryonic stem cells towards endodermal lineage on the varying stiffness did not differ from the differentiation on stiff plastic dishes. We also observed no statistical difference between the expression of yes-associated protein (YAP) and phosphorylated YAP. Furthermore, we demonstrate that lysophosphatidic acid, a YAP activator, enhanced definitive endoderm formation, whereas verteporfin, a YAP inhibitor, did not have the significant effect on the differentiation. In summary, our results suggest that human embryonic stem cells may not differentiate in response to changes in stiffness, and that such cues may not have as significant impact on the level of YAP. Our findings indicate that more research is needed to understand the direct relationship between biophysical forces and hPSCs differentiation.
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Affiliation(s)
- Jasmeet Kaur Virdi
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be) University, Mumbai, Maharashtra, India
| | - Prasad Pethe
- Symbiosis Centre for Stem Cell Research, Symbiosis School of Biological Sciences, Symbiosis International (Deemed) University, Pune, Maharashtra, India
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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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