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de Jaime-Soguero A, Hattemer J, Bufe A, Haas A, van den Berg J, van Batenburg V, Das B, di Marco B, Androulaki S, Böhly N, Landry JJM, Schoell B, Rosa VS, Villacorta L, Baskan Y, Trapp M, Benes V, Chabes A, Shahbazi M, Jauch A, Engel U, Patrizi A, Sotillo R, van Oudenaarden A, Bageritz J, Alfonso J, Bastians H, Acebrón SP. Developmental signals control chromosome segregation fidelity during pluripotency and neurogenesis by modulating replicative stress. Nat Commun 2024; 15:7404. [PMID: 39191776 DOI: 10.1038/s41467-024-51821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 08/09/2024] [Indexed: 08/29/2024] Open
Abstract
Human development relies on the correct replication, maintenance and segregation of our genetic blueprints. How these processes are monitored across embryonic lineages, and why genomic mosaicism varies during development remain unknown. Using pluripotent stem cells, we identify that several patterning signals-including WNT, BMP, and FGF-converge into the modulation of DNA replication stress and damage during S-phase, which in turn controls chromosome segregation fidelity in mitosis. We show that the WNT and BMP signals protect from excessive origin firing, DNA damage and chromosome missegregation derived from stalled forks in pluripotency. Cell signalling control of chromosome segregation declines during lineage specification into the three germ layers, but re-emerges in neural progenitors. In particular, we find that the neurogenic factor FGF2 induces DNA replication stress-mediated chromosome missegregation during the onset of neurogenesis, which could provide a rationale for the elevated chromosomal mosaicism of the developing brain. Our results highlight roles for morphogens and cellular identity in genome maintenance that contribute to somatic mosaicism during mammalian development.
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Affiliation(s)
| | - Janina Hattemer
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Anja Bufe
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Alexander Haas
- Department of Molecular Oncology, Section for Cellular Oncology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Jeroen van den Berg
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
- KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Vincent van Batenburg
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
- KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Biswajit Das
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Barbara di Marco
- Department of Clinical Neurobiology, University Hospital Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefania Androulaki
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Nicolas Böhly
- Department of Molecular Oncology, Section for Cellular Oncology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Jonathan J M Landry
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Brigitte Schoell
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Laura Villacorta
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Yagmur Baskan
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Marleen Trapp
- Schaller Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | | | - Anna Jauch
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ulrike Engel
- Nikon Imaging Center at the University of Heidelberg, Bioquant, Heidelberg, Germany
| | - Annarita Patrizi
- Schaller Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander van Oudenaarden
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
- KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Josephine Bageritz
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Julieta Alfonso
- Department of Clinical Neurobiology, University Hospital Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Holger Bastians
- Department of Molecular Oncology, Section for Cellular Oncology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Sergio P Acebrón
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
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2
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Fatehi A, Sadat M, Fayyad M, Tang J, Han D, Rogers IM, Taylor D. Efficient Generation of Pancreatic Progenitor Cells from Induced Pluripotent Stem Cells Derived from a Non-Invasive and Accessible Tissue Source-The Plucked Hair Follicle. Cells 2024; 13:1010. [PMID: 38920642 PMCID: PMC11202038 DOI: 10.3390/cells13121010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
The advent of induced pluripotent stem cell (iPSC) technology has brought about transformative advancements in regenerative medicine, offering novel avenues for disease modeling, drug testing, and cell-based therapies. Patient-specific iPSC-based treatments hold the promise of mitigating immune rejection risks. However, the intricacies and costs of producing autologous therapies present commercial challenges. The hair follicle is a multi-germ layered versatile cell source that can be harvested at any age. It is a rich source of keratinocytes, fibroblasts, multipotent stromal cells, and the newly defined Hair Follicle-Associated Pluripotent Stem Cells (HAP). It can also be obtained non-invasively and transported via regular mail channels, making it the ideal starting material for an autologous biobank. In this study, cryopreserved hair follicle-derived iPSC lines (HF-iPS) were established through integration-free vectors, encompassing a diverse cohort. These genetically stable lines exhibited robust expression of pluripotency markers, and showcased tri-lineage differentiation potential. The HF-iPSCs effectively differentiated into double-positive cKIT+/CXCR4+ definitive endoderm cells and NKX6.1+/PDX1+ pancreatic progenitor cells, affirming their pluripotent attributes. We anticipate that the use of plucked hair follicles as an accessible, non-invasive cell source to obtain patient cells, in conjunction with the use of episomal vectors for reprogramming, will improve the future generation of clinically applicable pancreatic progenitor cells for the treatment of Type I Diabetes.
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Affiliation(s)
- Amatullah Fatehi
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A1, Canada; (A.F.); (M.S.)
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada;
- Acorn Biolabs Inc., Toronto, ON M5G 2N2, Canada; (M.F.); (D.H.)
| | - Marwa Sadat
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A1, Canada; (A.F.); (M.S.)
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada;
| | - Muneera Fayyad
- Acorn Biolabs Inc., Toronto, ON M5G 2N2, Canada; (M.F.); (D.H.)
| | - Jean Tang
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada;
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Duhyun Han
- Acorn Biolabs Inc., Toronto, ON M5G 2N2, Canada; (M.F.); (D.H.)
| | - Ian M. Rogers
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A1, Canada; (A.F.); (M.S.)
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada;
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Drew Taylor
- Acorn Biolabs Inc., Toronto, ON M5G 2N2, Canada; (M.F.); (D.H.)
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3
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Herr LM, Schaffer ED, Fuchs KF, Datta A, Brosh RM. Replication stress as a driver of cellular senescence and aging. Commun Biol 2024; 7:616. [PMID: 38777831 PMCID: PMC11111458 DOI: 10.1038/s42003-024-06263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Replication stress refers to slowing or stalling of replication fork progression during DNA synthesis that disrupts faithful copying of the genome. While long considered a nexus for DNA damage, the role of replication stress in aging is under-appreciated. The consequential role of replication stress in promotion of organismal aging phenotypes is evidenced by an extensive list of hereditary accelerated aging disorders marked by molecular defects in factors that promote replication fork progression and operate uniquely in the replication stress response. Additionally, recent studies have revealed cellular pathways and phenotypes elicited by replication stress that align with designated hallmarks of aging. Here we review recent advances demonstrating the role of replication stress as an ultimate driver of cellular senescence and aging. We discuss clinical implications of the intriguing links between cellular senescence and aging including application of senotherapeutic approaches in the context of replication stress.
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Affiliation(s)
- Lauren M Herr
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ethan D Schaffer
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kathleen F Fuchs
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Arindam Datta
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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4
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Ubieto-Capella P, Ximénez-Embún P, Giménez-Llorente D, Losada A, Muñoz J, Méndez J. A rewiring of DNA replication mediated by MRE11 exonuclease underlies primed-to-naive cell de-differentiation. Cell Rep 2024; 43:114024. [PMID: 38581679 DOI: 10.1016/j.celrep.2024.114024] [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: 09/08/2023] [Revised: 02/01/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024] Open
Abstract
Mouse embryonic stem cells (mESCs) in the primed pluripotency state, which resembles the post-implantation epiblast, can be de-differentiated in culture to a naive state that resembles the pre-implantation inner cell mass. We report that primed-to-naive mESC transition entails a significant slowdown of DNA replication forks and the compensatory activation of dormant origins. Using isolation of proteins on nascent DNA coupled to mass spectrometry, we identify key changes in replisome composition that are responsible for these effects. Naive mESC forks are enriched in MRE11 nuclease and other DNA repair proteins. MRE11 is recruited to newly synthesized DNA in response to transcription-replication conflicts, and its inhibition or genetic downregulation in naive mESCs is sufficient to restore the fork rate of primed cells. Transcriptomic analyses indicate that MRE11 exonuclease activity is required for the complete primed-to-naive mESC transition, demonstrating a direct link between DNA replication dynamics and the mESC de-differentiation process.
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Affiliation(s)
- Patricia Ubieto-Capella
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Pilar Ximénez-Embún
- Proteomics Unit-ProteoRed-ISCIII, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Daniel Giménez-Llorente
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Javier Muñoz
- Proteomics Unit-ProteoRed-ISCIII, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.
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5
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Georgieva D, Wang N, Taglialatela A, Jerabek S, Reczek CR, Lim PX, Sung J, Du Q, Horiguchi M, Jasin M, Ciccia A, Baer R, Egli D. BRCA1 and 53BP1 regulate reprogramming efficiency by mediating DNA repair pathway choice at replication-associated double-strand breaks. Cell Rep 2024; 43:114006. [PMID: 38554279 PMCID: PMC11272184 DOI: 10.1016/j.celrep.2024.114006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 11/26/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
Reprogramming to pluripotency is associated with DNA damage and requires the functions of the BRCA1 tumor suppressor. Here, we leverage separation-of-function mutations in BRCA1/2 as well as the physical and/or genetic interactions between BRCA1 and its associated repair proteins to ascertain the relevance of homology-directed repair (HDR), stalled fork protection (SFP), and replication gap suppression (RGS) in somatic cell reprogramming. Surprisingly, loss of SFP and RGS is inconsequential for the transition to pluripotency. In contrast, cells deficient in HDR, but proficient in SFP and RGS, reprogram with reduced efficiency. Conversely, the restoration of HDR function through inactivation of 53bp1 rescues reprogramming in Brca1-deficient cells, and 53bp1 loss leads to elevated HDR and enhanced reprogramming in mouse and human cells. These results demonstrate that somatic cell reprogramming is especially dependent on repair of replication-associated double-strand breaks (DSBs) by the HDR activity of BRCA1 and BRCA2 and can be improved in the absence of 53BP1.
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Affiliation(s)
- Daniela Georgieva
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Angelo Taglialatela
- Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Stepan Jerabek
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 160 00 Praha 6, Czech Republic
| | - Colleen R Reczek
- Department of Pathology & Cell Biology, Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Pei Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julie Sung
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Qian Du
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michiko Horiguchi
- Department of Pathology & Cell Biology, Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alberto Ciccia
- Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Richard Baer
- Department of Pathology & Cell Biology, Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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6
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Huang J, Jiang T, Li J, Qie J, Cheng X, Wang Y, Zhou T, Liu J, Han H, Yao K, Yu L. Biomimetic Corneal Stroma for Scarless Corneal Wound Healing via Structural Restoration and Microenvironment Modulation. Adv Healthc Mater 2024; 13:e2302889. [PMID: 37988231 DOI: 10.1002/adhm.202302889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/31/2023] [Indexed: 11/23/2023]
Abstract
Corneal injury-induced stromal scarring causes the most common subtype of corneal blindness, and there is an unmet need to promote scarless corneal wound healing. Herein, a biomimetic corneal stroma with immunomodulatory properties is bioengineered for scarless corneal defect repair. First, a fully defined serum-free system is established to derive stromal keratocytes (hAESC-SKs) from a current Good Manufacturing Practice (cGMP)-grade human amniotic epithelial stem cells (hAESCs), and RNA-seq is used to validate the phenotypic transition. Moreover, hAESC-SKs are shown to possess robust immunomodulatory properties in addition to the keratocyte phenotype. Inspired by the corneal stromal extracellular matrix (ECM), a photocurable gelatin-based hydrogel is fabricated to serve as a scaffold for hAESC-SKs for bioengineering of a biomimetic corneal stroma. The rabbit corneal defect model is used to confirm that this biomimetic corneal stroma rapidly restores the corneal structure, and effectively reshapes the tissue microenvironment via proteoglycan secretion to promote transparency and inhibition of the inflammatory cascade to alleviate fibrosis, which synergistically reduces scar formation by ≈75% in addition to promoting wound healing. Overall, the strategy proposed here provides a promising solution for scarless corneal defect repair.
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Affiliation(s)
- Jianan Huang
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou, 310009, P. R. China
- MOE Laboratory of Biosystems Homeostasis & Protection & College of Life Sciences-iCell Biotechnology Regenerative Biomedicine Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Tuoying Jiang
- MOE Laboratory of Biosystems Homeostasis & Protection & College of Life Sciences-iCell Biotechnology Regenerative Biomedicine Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Jinying Li
- MOE Laboratory of Biosystems Homeostasis & Protection & College of Life Sciences-iCell Biotechnology Regenerative Biomedicine Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- College of Traditional Chinese Medicine and Health Industry, Lishui University, Lishui, 323000, P. R. China
| | - Jiqiao Qie
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou, 310009, P. R. China
| | - Xiaoyu Cheng
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou, 310009, P. R. China
| | - Yiyao Wang
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou, 310009, P. R. China
| | - Tinglian Zhou
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou, 310009, P. R. China
| | - Jia Liu
- MOE Laboratory of Biosystems Homeostasis & Protection & College of Life Sciences-iCell Biotechnology Regenerative Biomedicine Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Haijie Han
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou, 310009, P. R. China
- State Key Laboratory of Trauma, Burn and Combined Injury, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Ke Yao
- Eye Center, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou, 310009, P. R. China
| | - Luyang Yu
- MOE Laboratory of Biosystems Homeostasis & Protection & College of Life Sciences-iCell Biotechnology Regenerative Biomedicine Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
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7
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Edwards MM, Wang N, Massey DJ, Bhatele S, Egli D, Koren A. Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells. Cell Rep 2024; 43:113664. [PMID: 38194345 PMCID: PMC11231959 DOI: 10.1016/j.celrep.2023.113664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024] Open
Abstract
Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.
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Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sakshi Bhatele
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA.
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
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8
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Schmit MM, Baxley RM, Wang L, Hinderlie P, Kaufman M, Simon E, Raju A, Miller JS, Bielinsky AK. A critical threshold of MCM10 is required to maintain genome stability during differentiation of induced pluripotent stem cells into natural killer cells. Open Biol 2024; 14:230407. [PMID: 38262603 PMCID: PMC10805602 DOI: 10.1098/rsob.230407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/23/2023] [Indexed: 01/25/2024] Open
Abstract
Natural killer (NK) cell deficiency (NKD) is a rare disease in which NK cell function is reduced, leaving affected individuals susceptible to repeated viral infections and cancer. Recently, a patient with NKD was identified carrying compound heterozygous variants of MCM10 (minichromosome maintenance protein 10), an essential gene required for DNA replication, that caused a significant decrease in the amount of functional MCM10. NKD in this patient presented as loss of functionally mature late-stage NK cells. To understand how MCM10 deficiency affects NK cell development, we generated MCM10 heterozygous (MCM10+/-) induced pluripotent stem cell (iPSC) lines. Analyses of these cell lines demonstrated that MCM10 was haploinsufficient, similar to results in other human cell lines. Reduced levels of MCM10 in mutant iPSCs was associated with impaired clonogenic survival and increased genomic instability, including micronuclei formation and telomere erosion. The severity of these phenotypes correlated with the extent of MCM10 depletion. Significantly, MCM10+/- iPSCs displayed defects in NK cell differentiation, exhibiting reduced yields of hematopoietic stem cells (HSCs). Although MCM10+/- HSCs were able to give rise to lymphoid progenitors, these did not generate mature NK cells. The lack of mature NK cells coincided with telomere erosion, suggesting that NKD caused by these MCM10 variants arose from the accumulation of genomic instability including degradation of chromosome ends.
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Affiliation(s)
- Megan M. Schmit
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ryan M. Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Liangjun Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Peter Hinderlie
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Marissa Kaufman
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Emily Simon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Anjali Raju
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jeffrey S. Miller
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
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9
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Wang N, Xu S, Egli D. Replication stress in mammalian embryo development, differentiation, and reprogramming. Trends Cell Biol 2023; 33:872-886. [PMID: 37202286 PMCID: PMC11214770 DOI: 10.1016/j.tcb.2023.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 05/20/2023]
Abstract
Duplicating a genome of 3 billion nucleotides is challenged by a variety of obstacles that can cause replication stress and affect the integrity of the genome. Recent studies show that replication fork slowing and stalling is prevalent in early mammalian development, resulting in genome instability and aneuploidy, and constituting a barrier to development in human reproduction. Genome instability resulting from DNA replication stress is a barrier to the cloning of animals and to the reprogramming of differentiated cells to induced pluripotent stem cells, as well as a barrier to cell transformation. Remarkably, the regions most impacted by replication stress are shared in these different cellular contexts, affecting long genes and flanking intergenic areas. In this review we integrate our knowledge of DNA replication stress in mammalian embryos, in programming, and in reprogramming, and we discuss a potential role for fragile sites in sensing replication stress and restricting cell cycle progression in health and disease.
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Affiliation(s)
- Ning Wang
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shuangyi Xu
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dieter Egli
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA.
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10
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Kislova AV, Zheglo D, Pozhitnova VO, Sviridov PS, Gadzhieva EP, Voronina ES. Replication stress causes delayed mitotic entry and chromosome 12 fragility at the ANKS1B large neuronal gene in human induced pluripotent stem cells. Chromosome Res 2023; 31:23. [PMID: 37597021 DOI: 10.1007/s10577-023-09729-5] [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: 04/05/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/21/2023]
Abstract
Substantial background level of replication stress is a feature of embryonic and induced pluripotent stem cells (iPSCs), which can predispose to numerical and structural chromosomal instability, including recurrent aberrations of chromosome 12. In differentiated cells, replication stress-sensitive genomic regions, including common fragile sites, are widely mapped through mitotic chromosome break induction by mild aphidicolin treatment, an inhibitor of replicative polymerases. IPSCs exhibit lower apoptotic threshold and higher repair capacity hindering fragile site mapping. Caffeine potentiates genotoxic effects and abrogates G2/M checkpoint delay induced by chemical and physical mutagens. Using 5-ethynyl-2'-deoxyuridine (EdU) for replication labeling, we characterized the mitotic entry dynamics of asynchronous iPSCs exposed to aphidicolin and/or caffeine. Under the adjusted timing of replication stress exposure accounting revealed cell cycle delay, higher metaphase chromosome breakage rate was observed in iPSCs compared to primary lymphocytes. Using differential chromosome staining and subsequent locus-specific fluorescent in situ hybridization, we mapped the FRA12L fragile site spanning the large neuronal ANKS1B gene at 12q23.1, which may contribute to recurrent chromosome 12 missegregation and rearrangements in iPSCs. Publicly available data on the ANKS1B genetic alterations and their possible functional impact are reviewed. Our study provides the first evidence of common fragile site induction in iPSCs and reveals potential somatic instability of a clinically relevant gene during early human development and in vitro cell expansion.
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Affiliation(s)
| | - Diana Zheglo
- Laboratory of Mutagenesis, Research Centre for Medical Genetics, Moscow, Russia.
| | | | - Philipp S Sviridov
- Laboratory of Mutagenesis, Research Centre for Medical Genetics, Moscow, Russia
| | - Elmira P Gadzhieva
- Laboratory of Mutagenesis, Research Centre for Medical Genetics, Moscow, Russia
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11
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Milagre I, Pereira C, Oliveira RA. Compromised Mitotic Fidelity in Human Pluripotent Stem Cells. Int J Mol Sci 2023; 24:11933. [PMID: 37569309 PMCID: PMC10418648 DOI: 10.3390/ijms241511933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Human pluripotent stem cells (PSCs), which include both embryonic and induced pluripotent stem cells, are widely used in fundamental and applied biomedical research. They have been instrumental for better understanding development and cell differentiation processes, disease origin and progression and can aid in the discovery of new drugs. PSCs also hold great potential in regenerative medicine to treat or diminish the effects of certain debilitating diseases, such as degenerative disorders. However, some concerns have recently been raised over their safety for use in regenerative medicine. One of the major concerns is the fact that PSCs are prone to errors in passing the correct number of chromosomes to daughter cells, resulting in aneuploid cells. Aneuploidy, characterised by an imbalance in chromosome number, elicits the upregulation of different stress pathways that are deleterious to cell homeostasis, impair proper embryo development and potentiate cancer development. In this review, we will summarize known molecular mechanisms recently revealed to impair mitotic fidelity in human PSCs and the consequences of the decreased mitotic fidelity of these cells. We will finish with speculative views on how the physiological characteristics of PSCs can affect the mitotic machinery and how their suboptimal mitotic fidelity may be circumvented.
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Affiliation(s)
- Inês Milagre
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa, 1649-023 Lisbon, Portugal
| | | | - Raquel A. Oliveira
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa, 1649-023 Lisbon, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
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12
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Shimada M, Tokumiya T, Miyake T, Tsukada K, Kanzaki N, Yanagihara H, Kobayashi J, Matsumoto Y. Implication of E3 ligase RAD18 in UV-induced mutagenesis in human induced pluripotent stem cells and neuronal progenitor cells. JOURNAL OF RADIATION RESEARCH 2023; 64:345-351. [PMID: 36634340 PMCID: PMC10036092 DOI: 10.1093/jrr/rrac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/24/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Pluripotent stem cells (PSCs) have the potential to differentiate to any of the other organs. The genome DNA integrity of PSCs is maintained by a high level of transcription for a number of genes involved in DNA repair, cell cycle and apoptosis. However, it remains unclear how high the frequency of genetic mutation is and how these DNA repair factors function in PSCs. In this study, we employed Sup F assay for the measurement of mutation frequency after UV-C irradiation in induced pluripotent stem cells (iPSCs) as PSC models and neural progenitor cells (NPCs) were derived from iPSCs as differentiated cells. iPSCs and NPCs exhibited a lower mutation frequency compared with the original skin fibroblasts. In RNA-seq analysis, iPSCs and NPCs showed a high expression of RAD18, which is involved in trans-lesion synthesis (TLS) for the emergency tolerance system during the replication process of DNA. Although RAD18 is involved in both error free and error prone TLS in somatic cells, it still remains unknown the function of RAD18 in PSCs. In this study we depleted of the RAD18 by siRNA knockdown resulted in decreased frequency of mutation in iPSCs and NPCs. Our results will provide information on the genome maintenance machinery in PSCs.
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Affiliation(s)
- Mikio Shimada
- Corresponding author. Mikio Shimada, Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Oookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Takumi Tokumiya
- Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550 Japan
| | - Tomoko Miyake
- Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550 Japan
| | - Kaima Tsukada
- Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550 Japan
| | - Norie Kanzaki
- Ningyo-toge Environmental Engineering Center, Japan Atomic Energy Agency, 1550 Kamisaibara, Kagamino-cho, Tomata-gun, Okayama 708-0698, Japan
| | - Hiromi Yanagihara
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Junya Kobayashi
- Department of Radiological Sciences, School of Health Science at Narita, International University of Health and Welfare, Kozunomori 4-3, Narita 286-8686, Japan
| | - Yoshihisa Matsumoto
- Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550 Japan
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13
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Hossain ME, Cevallos RR, Zhang R, Hu K. Attenuating iPSC reprogramming stress with dominant-negative BET peptides. iScience 2023; 26:105889. [PMID: 36691621 PMCID: PMC9860338 DOI: 10.1016/j.isci.2022.105889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/06/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
Generation of induced pluripotent stem cells (iPSCs) is inefficient and stochastic. The underlying causes for these deficiencies are elusive. Here, we showed that the reprogramming factors (OCT4, SOX2, and KLF4, collectively OSK) elicit dramatic reprogramming stress even without the pro-oncogene MYC including massive transcriptional turbulence, massive and random deregulation of stress-response genes, cell cycle impairment, downregulation of mitotic genes, illegitimate reprogramming, and cytotoxicity. The conserved dominant-negative (DN) peptides of the three ubiquitous human bromodomain and extraterminal (BET) proteins enhanced iPSC reprogramming and mitigated all the reprogramming stresses mentioned above. The concept of reprogramming stress developed here affords an alternative avenue to understanding and improving iPSC reprogramming. These DN BET fragments target a similar set of the genes as the BET chemical inhibitors do, indicating a distinct approach to targeting BET proteins.
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Affiliation(s)
- Md Emon Hossain
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ricardo Raul Cevallos
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ruowen Zhang
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kejin Hu
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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14
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Franca MM, Condezo YB, Elzaiat M, Felipe-Medina N, Sánchez-Sáez F, Muñoz S, Sainz-Urruela R, Martín-Hervás MR, García-Valiente R, Sánchez-Martín MA, Astudillo A, Mendez J, Llano E, Veitia RA, Mendonca BB, Pendás AM. A truncating variant of RAD51B associated with primary ovarian insufficiency provides insights into its meiotic and somatic functions. Cell Death Differ 2022; 29:2347-2361. [PMID: 35624308 PMCID: PMC9751091 DOI: 10.1038/s41418-022-01021-z] [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: 10/28/2021] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/31/2023] Open
Abstract
Primary ovarian insufficiency (POI) causes female infertility by abolishing normal ovarian function. Although its genetic etiology has been extensively investigated, most POI cases remain unexplained. Using whole-exome sequencing, we identified a homozygous variant in RAD51B -(c.92delT) in two sisters with POI. In vitro studies revealed that this variant leads to translation reinitiation at methionine 64. Here, we show that this is a pathogenic hypomorphic variant in a mouse model. Rad51bc.92delT/c.92delT mice exhibited meiotic DNA repair defects due to RAD51 and HSF2BP/BMRE1 accumulation in the chromosome axes leading to a reduction in the number of crossovers. Interestingly, the interaction of RAD51B-c.92delT with RAD51C and with its newly identified interactors RAD51 and HELQ was abrogated or diminished. Repair of mitomycin-C-induced chromosomal aberrations was impaired in RAD51B/Rad51b-c.92delT human and mouse somatic cells in vitro and in explanted mouse bone marrow cells. Accordingly, Rad51b-c.92delT variant reduced replication fork progression of patient-derived lymphoblastoid cell lines and pluripotent reprogramming efficiency of primary mouse embryonic fibroblasts. Finally, Rad51bc.92delT/c.92delT mice displayed increased incidence of pituitary gland hyperplasia. These results provide new mechanistic insights into the role of RAD51B not only in meiosis but in the maintenance of somatic genome stability.
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Affiliation(s)
- Monica M Franca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42 and SELA, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brasil
- Section of Endocrinology Diabetes and Metabolism, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Yazmine B Condezo
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Maëva Elzaiat
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Natalia Felipe-Medina
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Fernando Sánchez-Sáez
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Sergio Muñoz
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Raquel Sainz-Urruela
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - M Rosario Martín-Hervás
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Rodrigo García-Valiente
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Manuel A Sánchez-Martín
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
- Transgenic Facility, Nucleus platform, Universidad de Salamanca, Salamanca, Spain
| | | | - Juan Mendez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Elena Llano
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
- Departamento de Fisiología y Farmacología, Universidad de Salamanca, Salamanca, Spain
| | - Reiner A Veitia
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France.
- Université Paris-Saclay and Institut François Jacob, Comissariat à l'Energie Atomique, Gif-sur-Yvette, France.
| | - Berenice B Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42 and SELA, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brasil.
| | - Alberto M Pendás
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain.
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15
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Shaikh N, Mazzagatti A, De Angelis S, Johnson SC, Bakker B, Spierings DCJ, Wardenaar R, Maniati E, Wang J, Boemo MA, Foijer F, McClelland SE. Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses. Genome Biol 2022; 23:223. [PMID: 36266663 PMCID: PMC9583511 DOI: 10.1186/s13059-022-02781-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 10/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A major driver of cancer chromosomal instability is replication stress, the slowing or stalling of DNA replication. How replication stress and genomic instability are connected is not known. Aphidicolin-induced replication stress induces breakages at common fragile sites, but the exact causes of fragility are debated, and acute genomic consequences of replication stress are not fully explored. RESULTS We characterize DNA copy number alterations (CNAs) in single, diploid non-transformed cells, caused by one cell cycle in the presence of either aphidicolin or hydroxyurea. Multiple types of CNAs are generated, associated with different genomic regions and features, and observed copy number landscapes are distinct between aphidicolin and hydroxyurea-induced replication stress. Coupling cell type-specific analysis of CNAs to gene expression and single-cell replication timing analyses pinpointed the causative large genes of the most recurrent chromosome-scale CNAs in aphidicolin. These are clustered on chromosome 7 in RPE1 epithelial cells but chromosome 1 in BJ fibroblasts. Chromosome arm level CNAs also generate acentric lagging chromatin and micronuclei containing these chromosomes. CONCLUSIONS Chromosomal instability driven by replication stress occurs via focal CNAs and chromosome arm scale changes, with the latter confined to a very small subset of chromosome regions, potentially heavily skewing cancer genome evolution. Different inducers of replication stress lead to distinctive CNA landscapes providing the opportunity to derive copy number signatures of specific replication stress mechanisms. Single-cell CNA analysis thus reveals the impact of replication stress on the genome, providing insights into the molecular mechanisms which fuel chromosomal instability in cancer.
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Affiliation(s)
- Nadeem Shaikh
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Alice Mazzagatti
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Simone De Angelis
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sarah C Johnson
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
- Current address: The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Eleni Maniati
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Michael A Boemo
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Sarah E McClelland
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
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16
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Michel N, Young HMR, Atkin ND, Arshad U, Al-Humadi R, Singh S, Manukyan A, Gore L, Burbulis IE, Wang YH, McConnell MJ. Transcription-associated DNA DSBs activate p53 during hiPSC-based neurogenesis. Sci Rep 2022; 12:12156. [PMID: 35840793 PMCID: PMC9287420 DOI: 10.1038/s41598-022-16516-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Neurons are overproduced during cerebral cortical development. Neural progenitor cells (NPCs) divide rapidly and incur frequent DNA double-strand breaks (DSBs) throughout cortical neurogenesis. Although half of the neurons born during neurodevelopment die, many neurons with inaccurate DNA repair survive leading to brain somatic mosaicism. Recurrent DNA DSBs during neurodevelopment are associated with both gene expression level and gene length. We used imaging flow cytometry and a genome-wide DNA DSB capture approach to quantify and map DNA DSBs during human induced pluripotent stem cell (hiPSC)-based neurogenesis. Reduced p53 signaling was brought about by knockdown (p53KD); p53KD led to elevated DNA DSB burden in neurons that was associated with gene expression level but not gene length in neural progenitor cells (NPCs). Furthermore, DNA DSBs incurred from transcriptional, but not replicative, stress lead to p53 activation in neurotypical NPCs. In p53KD NPCs, DNA DSBs accumulate at transcription start sites of genes that are associated with neurological and psychiatric disorders. These findings add to a growing understanding of how neuronal genome dynamics are engaged by high transcriptional or replicative burden during neurodevelopment.
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Affiliation(s)
- Nadine Michel
- Neuroscience Graduate Program, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Heather M Raimer Young
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Umar Arshad
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Reem Al-Humadi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Sandeep Singh
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Arkadi Manukyan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Lana Gore
- Lieber Institute for Brain Development, 855 N. Wolfe St., Ste. 300, Baltimore, MD, 21205, USA
| | - Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
- Sede de la Patagonia, Facultad de Medicina y Ciencias, Universidad San Sebastián, Puerto Montt, Chile
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Michael J McConnell
- Lieber Institute for Brain Development, 855 N. Wolfe St., Ste. 300, Baltimore, MD, 21205, USA.
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17
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Zhao K, Sun X, Zheng C, Wang M, Xu Z, Wang M, Chen J, Guo M, Le R, Wu L, Wang Y, Kou X, Zhao Y, Yin J, Wang H, Mao Z, Gao S, Gao S. Enhancement of Xrcc1-mediated base excision repair improves the genetic stability and pluripotency of iPSCs. Sci Bull (Beijing) 2022; 67:1126-1130. [PMID: 36545978 DOI: 10.1016/j.scib.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/03/2022] [Accepted: 03/25/2022] [Indexed: 01/07/2023]
Affiliation(s)
- Kun Zhao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Xiaoxiang Sun
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Caihong Zheng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
| | - Mengting Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Zhu Xu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Mingzhu Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Jiayu Chen
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Mingyue Guo
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Rongrong Le
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Li Wu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yibin Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Xiaochen Kou
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Yanhong Zhao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Jiqing Yin
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Hong Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Zhiyong Mao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Shaorong Gao
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Shuai Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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18
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Poetsch MS, Strano A, Guan K. Human induced pluripotent stem cells: From cell origin, genomic stability and epigenetic memory to translational medicine. Stem Cells 2022; 40:546-555. [PMID: 35291013 PMCID: PMC9216482 DOI: 10.1093/stmcls/sxac020] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/06/2022] [Indexed: 11/14/2022]
Abstract
The potential of human induced pluripotent stem cells (iPSCs) to self-renew indefinitely and to differentiate virtually into any cell type in unlimited quantities makes them attractive for in-vitro disease modeling, drug screening, personalized medicine, and regenerative therapies. As the genome of iPSCs thoroughly reproduces that of the somatic cells from which they are derived, they may possess genetic abnormalities, which would seriously compromise their utility and safety. Genetic aberrations could be present in donor somatic cells and then transferred during iPSC generation, or they could occur as de novo mutations during reprogramming or prolonged cell culture. Therefore, to warrant safety of human iPSCs for clinical applications, analysis of genetic integrity, particularly during iPSC generation and differentiation, should be carried out on a regular basis. On the other hand, reprogramming of somatic cells to iPSCs requires profound modifications in the epigenetic landscape. Changes in chromatin structure by DNA methylations and histone tail modifications aim to reset the gene expression pattern of somatic cells to facilitate and establish self-renewal and pluripotency. However, residual epigenetic memory influences the iPSC phenotype, which may affect their application in disease therapeutics. The present review discusses the somatic cell origin, genetic stability, and epigenetic memory of iPSCs and their impact on basic and translational research.
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Affiliation(s)
- Mareike S Poetsch
- Institute of Pharmacology and Toxicology, Technische Universität Dresden, Dresden, Germany
| | - Anna Strano
- Institute of Pharmacology and Toxicology, Technische Universität Dresden, Dresden, Germany
| | - Kaomei Guan
- Institute of Pharmacology and Toxicology, Technische Universität Dresden, Dresden, Germany
- Corresponding author: Kaomei Guan, Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany. Tel: +49 351 458 6246; Fax: +49 351 458 6315;
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19
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Bialic M, Al Ahmad Nachar B, Koźlak M, Coulon V, Schwob E. Measuring S-Phase Duration from Asynchronous Cells Using Dual EdU-BrdU Pulse-Chase Labeling Flow Cytometry. Genes (Basel) 2022; 13:genes13030408. [PMID: 35327961 PMCID: PMC8951228 DOI: 10.3390/genes13030408] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/17/2022] [Accepted: 02/20/2022] [Indexed: 02/07/2023] Open
Abstract
Eukaryotes duplicate their chromosomes during the cell cycle S phase using thousands of initiation sites, tunable fork speed and megabase-long spatio-temporal replication programs. The duration of S phase is fairly constant within a given cell type, but remarkably plastic during development, cell differentiation or various stresses. Characterizing the dynamics of S phase is important as replication defects are associated with genome instability, cancer and ageing. Methods to measure S-phase duration are so far indirect, and rely on mathematical modelling or require cell synchronization. We describe here a simple and robust method to measure S-phase duration in cell cultures using a dual EdU-BrdU pulse-labeling regimen with incremental thymidine chases, and quantification by flow cytometry of cells entering and exiting S phase. Importantly, the method requires neither cell synchronization nor genome engineering, thus avoiding possible artifacts. It measures the duration of unperturbed S phases, but also the effect of drugs or mutations on it. We show that this method can be used for both adherent and suspension cells, cell lines and primary cells of different types from human, mouse and Drosophila. Interestingly, the method revealed that several commonly-used cancer cell lines have a longer S phase compared to untransformed cells.
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Affiliation(s)
- Marta Bialic
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
- Institut de Médecine Régénératrice et Biothérapie, INSERM, CHU, 34295 Montpellier, France
| | - Baraah Al Ahmad Nachar
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
| | - Maria Koźlak
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
| | - Vincent Coulon
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
- Correspondence: ; Tel.: +33-43435-9679
| | - Etienne Schwob
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, 34293 Montpellier, France; (M.B.); (B.A.A.N.); (M.K.); (E.S.)
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20
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Song C, Wang L, Li Q, Liao B, Qiao W, Li Q, Dong N, Li L. Generation of individualized immunocompatible endothelial cells from HLA-I-matched human pluripotent stem cells. Stem Cell Res Ther 2022; 13:48. [PMID: 35109922 PMCID: PMC8812039 DOI: 10.1186/s13287-022-02720-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/16/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Endothelial cells (ECs) derived from human-induced pluripotent stem cell (iPSC) are a valuable cell resource for cardiovascular regeneration. To avoid time-consuming preparation from primary autologous cells, the allogeneic iPSC-ECs are being expected to become "off-the-shelf" cell products. However, allorejection caused by HLA mismatching is a major barrier for this strategy. Although the "hypoimmunogenic" iPSCs could be simply generated by inhibition of HLA-I expression via β-2 microglobulin knockout (B2M KO), the deletion of HLA-I expression will activate natural killer (NK) cells, which kill the HLA-I negative cells. To inhibit NK activation, we proposed to generate HLA-matched iPSCs based on patient's HLA genotyping by HLA exchanging approach to express the required HLA allele. METHODS To establish a prototype of HLA exchanging system, the expression of HLA-I molecules of iPSCs was inhibited by CRISPR/Cas9-mediated B2M KO, and then HLA-A*11:01 allele, as a model molecule, was introduced into B2M KO iPSCs by lentiviral gene transfer. HLA-I-modified iPSCs were tested for their pluripotency and ability to differentiate into ECs. The stimulation of iPSC-EC to allogeneic T and NK cells was detected by respective co-culture of PBMC-EC and NK-EC. Finally, the iPSC-ECs were used as the seeding cells to re-endothelialize the decellularized valves. RESULTS We generated the iPSCs only expressed one HLA-A allele (HLA-A *11:01) by B2M KO plus HLA gene transfer. These HLA-I-modified iPSCs maintained pluripotency and furthermore were successfully differentiated into functional ECs assessed by tube formation assay. Single HLA-A*11:01-matched iPSC-ECs significantly less induced the allogeneic response of CD8+ T cell and NK cells expressing matched HLA-A*11:01 and other HLA-A,-B and -C alleles. These cells were successfully used to re-endothelialize the decellularized valves. CONCLUSIONS In summary, a simple HLA-I exchanging system has been created by efficient HLA engineering of iPSCs to evade both of the alloresponse of CD8+ T cells and the activation of NK cells. This technology has been applied to generate iPSC-ECs for the engineering of cellular heart valves. Our strategy should be extremely useful if the "off-the-shelf" and "non-immunogenic" allogeneic iPSCs were created for the common HLA alleles.
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Affiliation(s)
- Chanchan Song
- Institute of Clinical Oncology, Research Center of Cancer Diagnosis and Therapy, and Department of Clinical Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Linlin Wang
- Guangzhou Future Homo Sapiens Institute of Biomedicine and Health (GFBH), Guangzhou, China.,Guangzhou Regenerative Medicine Research Center, Future Homo Sapiens Institute of Regenerative Medicine Co., Ltd (FHIR), Guangzhou, China
| | - Qingyang Li
- Institute of Clinical Oncology, Research Center of Cancer Diagnosis and Therapy, and Department of Clinical Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Baoyi Liao
- Institute of Clinical Oncology, Research Center of Cancer Diagnosis and Therapy, and Department of Clinical Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Weihua Qiao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiang Li
- Guangzhou Future Homo Sapiens Institute of Biomedicine and Health (GFBH), Guangzhou, China.,Guangzhou Regenerative Medicine Research Center, Future Homo Sapiens Institute of Regenerative Medicine Co., Ltd (FHIR), Guangzhou, China
| | - Nianguo Dong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Liangping Li
- Institute of Clinical Oncology, Research Center of Cancer Diagnosis and Therapy, and Department of Clinical Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China.
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21
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Chen CXQ, Abdian N, Maussion G, Thomas RA, Demirova I, Cai E, Tabatabaei M, Beitel LK, Karamchandani J, Fon EA, Durcan TM. A Multistep Workflow to Evaluate Newly Generated iPSCs and Their Ability to Generate Different Cell Types. Methods Protoc 2021; 4:mps4030050. [PMID: 34287353 PMCID: PMC8293472 DOI: 10.3390/mps4030050] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/10/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) derived from human somatic cells have created new opportunities to generate disease-relevant cells. Thus, as the use of patient-derived stem cells has become more widespread, having a workflow to monitor each line is critical. This ensures iPSCs pass a suite of quality-control measures, promoting reproducibility across experiments and between labs. With this in mind, we established a multistep workflow to assess our newly generated iPSCs. Our workflow tests four benchmarks: cell growth, genomic stability, pluripotency, and the ability to form the three germline layers. We also outline a simple test for assessing cell growth and highlight the need to compare different growth media. Genomic integrity in the human iPSCs is analyzed by G-band karyotyping and a qPCR-based test for the detection of common karyotypic abnormalities. Finally, we confirm that the iPSC lines can differentiate into a given cell type, using a trilineage assay, and later confirm that each iPSC can be differentiated into one cell type of interest, with a focus on the generation of cortical neurons. Taken together, we present a multistep quality-control workflow to evaluate newly generated iPSCs and detail the findings on these lines as they are tested within the workflow.
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Affiliation(s)
- Carol X.-Q. Chen
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada; (C.X.-Q.C.); (N.A.); (G.M.); (R.A.T.); (I.D.); (E.C.); (L.K.B.); (E.A.F.)
| | - Narges Abdian
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada; (C.X.-Q.C.); (N.A.); (G.M.); (R.A.T.); (I.D.); (E.C.); (L.K.B.); (E.A.F.)
| | - Gilles Maussion
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada; (C.X.-Q.C.); (N.A.); (G.M.); (R.A.T.); (I.D.); (E.C.); (L.K.B.); (E.A.F.)
| | - Rhalena A. Thomas
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada; (C.X.-Q.C.); (N.A.); (G.M.); (R.A.T.); (I.D.); (E.C.); (L.K.B.); (E.A.F.)
| | - Iveta Demirova
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada; (C.X.-Q.C.); (N.A.); (G.M.); (R.A.T.); (I.D.); (E.C.); (L.K.B.); (E.A.F.)
| | - Eddie Cai
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada; (C.X.-Q.C.); (N.A.); (G.M.); (R.A.T.); (I.D.); (E.C.); (L.K.B.); (E.A.F.)
| | - Mahdieh Tabatabaei
- The Neuro’s Clinical Biological Imaging and Genetic Repository (C-BIG), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada; (M.T.); (J.K.)
| | - Lenore K. Beitel
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada; (C.X.-Q.C.); (N.A.); (G.M.); (R.A.T.); (I.D.); (E.C.); (L.K.B.); (E.A.F.)
| | - Jason Karamchandani
- The Neuro’s Clinical Biological Imaging and Genetic Repository (C-BIG), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada; (M.T.); (J.K.)
| | - Edward A. Fon
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada; (C.X.-Q.C.); (N.A.); (G.M.); (R.A.T.); (I.D.); (E.C.); (L.K.B.); (E.A.F.)
| | - Thomas M. Durcan
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada; (C.X.-Q.C.); (N.A.); (G.M.); (R.A.T.); (I.D.); (E.C.); (L.K.B.); (E.A.F.)
- Correspondence: ; Tel.: +1-514-398-6933
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22
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Chen S, Sato Y, Tada Y, Suzuki Y, Takahashi R, Okanojo M, Nakashima K. Facile bead-to-bead cell-transfer method for serial subculture and large-scale expansion of human mesenchymal stem cells in bioreactors. Stem Cells Transl Med 2021; 10:1329-1342. [PMID: 34008349 PMCID: PMC8380445 DOI: 10.1002/sctm.20-0501] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/29/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
The conventional planar culture of adherent cells is inefficient for large‐scale manufacturing of cell and gene therapy products. We developed a facile and efficient bead‐to‐bead cell‐transfer method for serial subculture and large‐scale expansion of human mesenchymal stem cells (hMSCs) with microcarriers in bioreactors. We first compared culture medium with and without nucleosides and found the former maintained the expression of surface markers of hMSCs during their prolonged culture and enabled faster cell proliferation. Subsequently, we developed our bead‐to‐bead cell transfer method to subculture hMSCs and found that intermittent agitation after adding fresh microcarriers to cell‐populated microcarriers could promote spontaneous cell migration to fresh microcarriers, reduce microcarrier aggregation, and improve cell yield. This method enabled serial subculture of hMSCs in spinner flasks from passage 4 to passage 9 without using proteolytic enzymes, which showed faster cell proliferation than the serial planar cultures undergoing multiple enzyme treatment. Finally, we used the medium containing nucleosides and our bead‐to‐bead cell transfer method for cell culture scale‐up from 4‐ to 50‐L cultures in single‐use bioreactors. We achieved a 242‐fold increase in the number of cells to 1.45 × 1010 after 27‐day culture and found that the cells harvested from the bioreactors maintained proliferation ability, expression of their surface markers, tri‐lineage differentiation potential and immunomodulatory property. This study shows the promotive effect of nucleosides on hMSC expansion and the potential of using our bead‐to‐bead transfer method for larger‐scale manufacturing of hMSCs for cell therapy.
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Affiliation(s)
- Shangwu Chen
- Regenerative Medicine Business Sector, Showa Denko Materials Co, Ltd, Yokohama-shi, Kanagawa, Japan
| | - Yushi Sato
- Regenerative Medicine Business Sector, Showa Denko Materials Co, Ltd, Yokohama-shi, Kanagawa, Japan
| | - Yasuhiko Tada
- Regenerative Medicine Business Sector, Showa Denko Materials Co, Ltd, Yokohama-shi, Kanagawa, Japan
| | - Yuma Suzuki
- Regenerative Medicine Business Sector, Showa Denko Materials Co, Ltd, Yokohama-shi, Kanagawa, Japan
| | - Ryosuke Takahashi
- Regenerative Medicine Business Sector, Showa Denko Materials Co, Ltd, Yokohama-shi, Kanagawa, Japan
| | - Masahiro Okanojo
- Regenerative Medicine Business Sector, Showa Denko Materials Co, Ltd, Yokohama-shi, Kanagawa, Japan
| | - Katsuhiko Nakashima
- Regenerative Medicine Business Sector, Showa Denko Materials Co, Ltd, Yokohama-shi, Kanagawa, Japan
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23
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Luke Krishnan CS, Brasch HD, Patel J, Bockett N, Paterson E, Davis PF, Tan ST. Stemness-Associated Markers Are Expressed in Extracranial Arteriovenous Malformation. Front Surg 2021; 8:621089. [PMID: 33816543 PMCID: PMC8017302 DOI: 10.3389/fsurg.2021.621089] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/02/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives: Arteriovenous malformation (AVM) consists of a nidus with poorly formed low-resistance vessels in place of a functional capillary network. The role of somatic mutations in embryonic stem cells (ESCs) and vascular anomalies and the presence of primitive populations in vascular anomalies led us to investigate the presence of a primitive population in extracranial AVM. Methods: Extracranial AVM tissue samples from 12 patients were stained for stemness-associated markers OCT4, SOX2, NANOG, KLF4, and c-MYC using immunohistochemical staining. In situ hybridization (ISH) was performed on six tissue samples to determine transcript expression. Western blotting and RT-qPCR were performed on two AVM-derived primary cell lines to determine protein and transcript expression of these markers, respectively. Immunofluorescence staining was performed on two tissue samples to investigate marker co-localization. Results: Immunohistochemical staining demonstrated the expression of OCT4, SOX2, KLF4, and c-MYC on the endothelium and media of lesional vessels and cells within the stroma of the nidus in all 12 AVM tissue samples. ISH and RT-qPCR confirmed transcript expression of all five markers. Western blotting showed protein expression of all markers except NANOG. Immunofluorescence staining demonstrated an OCT4+/SOX2+/KLF4+/c-MYC+ population within the endothelium and media of the lesional vessels and cells within the stroma of the AVM nidus. Conclusions: Our findings may suggest the presence of a primitive population within the AVM nidus. Further investigation may lead to novel therapeutic targeting of this population.
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Affiliation(s)
| | - Helen D Brasch
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Josie Patel
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | | | - Erin Paterson
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Paul F Davis
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Swee T Tan
- Gillies McIndoe Research Institute, Wellington, New Zealand.,Centre for the Study & Treatment of Vascular Birthmarks, Wellington Regional Plastic, Maxillofacial and Burns Unit, Hutt Hospital, Wellington, New Zealand.,Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
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24
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Giallongo S, Rehakova D, Raffaele M, Lo Re O, Koutna I, Vinciguerra M. Redox and Epigenetics in Human Pluripotent Stem Cells Differentiation. Antioxid Redox Signal 2021; 34:335-349. [PMID: 32567336 DOI: 10.1089/ars.2019.7983] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Significance: Since their discovery, induced pluripotent stem cells (iPSCs) had generated considerable interest in the scientific community for their great potential in regenerative medicine, disease modeling, and cell-based therapeutic approach, due to their unique characteristics of self-renewal and pluripotency. Recent Advances: Technological advances in iPSC genome-wide epigenetic profiling led to the elucidation of the epigenetic control of cellular identity during nuclear reprogramming. Moreover, iPSC physiology and metabolism are tightly regulated by oxidation-reduction events that mainly occur during the respiratory chain. In theory, iPSC-derived differentiated cells would be ideal for stem cell transplantation as autologous cells from donors, as the risks of rejection are minimal. Critical Issues: However, iPSCs experience high oxidative stress that, in turn, confers a high risk of increased genomic instability, which is most often linked to DNA repair deficiencies. Genomic instability has to be assessed before iPSCs can be used in therapeutic designs. Future Directions: This review will particularly focus on the links between redox balance and epigenetic modifications-in particular based on the histone variant macroH2A1-that determine DNA damage response in iPSCs and derived differentiated cells, and that might be exploited to decrease the teratogenic potential on iPSC transplantation. Antioxid. Redox Signal. 34, 335-349.
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Affiliation(s)
- Sebastiano Giallongo
- International Clinical Research Center, St' Anne's University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Daniela Rehakova
- International Clinical Research Center, St' Anne's University Hospital, Brno, Czech Republic.,Faculty of Informatics, Centre for Biomedical Image Analysis, Masaryk University, Brno, Czech Republic
| | - Marco Raffaele
- International Clinical Research Center, St' Anne's University Hospital, Brno, Czech Republic
| | - Oriana Lo Re
- International Clinical Research Center, St' Anne's University Hospital, Brno, Czech Republic
| | - Irena Koutna
- International Clinical Research Center, St' Anne's University Hospital, Brno, Czech Republic.,Faculty of Informatics, Centre for Biomedical Image Analysis, Masaryk University, Brno, Czech Republic
| | - Manlio Vinciguerra
- International Clinical Research Center, St' Anne's University Hospital, Brno, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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25
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Calzetta NL, González Besteiro MA, Gottifredi V. Mus81-Eme1-dependent aberrant processing of DNA replication intermediates in mitosis impairs genome integrity. SCIENCE ADVANCES 2020; 6:6/50/eabc8257. [PMID: 33298441 PMCID: PMC7725468 DOI: 10.1126/sciadv.abc8257] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/21/2020] [Indexed: 06/12/2023]
Abstract
Chromosome instability (CIN) underpins cancer evolution and is associated with drug resistance and poor prognosis. Understanding the mechanistic basis of CIN is thus a priority. The structure-specific endonuclease Mus81-Eme1 is known to prevent CIN. Intriguingly, however, here we show that the aberrant processing of late replication intermediates by Mus81-Eme1 is a source of CIN. Upon depletion of checkpoint kinase 1 (Chk1), Mus81-Eme1 cleaves under-replicated DNA engaged in mitotic DNA synthesis, leading to chromosome segregation defects. Supplementing cells with nucleosides allows the completion of mitotic DNA synthesis, restraining Mus81-Eme1-dependent DNA damage in mitosis and the ensuing CIN. We found no correlation between CIN arising from nucleotide shortage in mitosis and cell death, which were selectively linked to DNA damage load in mitosis and S phase, respectively. Our findings imply the possibility of optimizing Chk1-directed therapies by inducing cell death while curtailing CIN, a common side effect of chemotherapy.
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Affiliation(s)
- Nicolás Luis Calzetta
- Fundación Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - Marina Alejandra González Besteiro
- Fundación Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina.
| | - Vanesa Gottifredi
- Fundación Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina.
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26
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Tamura N, Shaikh N, Muliaditan D, Soliman TN, McGuinness JR, Maniati E, Moralli D, Durin MA, Green CM, Balkwill FR, Wang J, Curtius K, McClelland SE. Specific Mechanisms of Chromosomal Instability Indicate Therapeutic Sensitivities in High-Grade Serous Ovarian Carcinoma. Cancer Res 2020; 80:4946-4959. [PMID: 32998996 DOI: 10.1158/0008-5472.can-19-0852] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/23/2020] [Accepted: 09/25/2020] [Indexed: 11/16/2022]
Abstract
Chromosomal instability (CIN) comprises continual gain and loss of chromosomes or parts of chromosomes and occurs in the majority of cancers, often conferring poor prognosis. Because of a scarcity of functional studies and poor understanding of how genetic or gene expression landscapes connect to specific CIN mechanisms, causes of CIN in most cancer types remain unknown. High-grade serous ovarian carcinoma (HGSC), the most common subtype of ovarian cancer, is the major cause of death due to gynecologic malignancy in the Western world, with chemotherapy resistance developing in almost all patients. HGSC exhibits high rates of chromosomal aberrations and knowledge of causative mechanisms would represent an important step toward combating this disease. Here we perform the first in-depth functional characterization of mechanisms driving CIN in HGSC in seven cell lines that accurately recapitulate HGSC genetics. Multiple mechanisms coexisted to drive CIN in HGSC, including elevated microtubule dynamics and DNA replication stress that can be partially rescued to reduce CIN by low doses of paclitaxel and nucleoside supplementation, respectively. Distinct CIN mechanisms indicated relationships with HGSC-relevant therapy including PARP inhibition and microtubule-targeting agents. Comprehensive genomic and transcriptomic profiling revealed deregulation of various genes involved in genome stability but were not directly predictive of specific CIN mechanisms, underscoring the importance of functional characterization to identify causes of CIN. Overall, we show that HGSC CIN is complex and suggest that specific CIN mechanisms could be used as functional biomarkers to indicate appropriate therapy. SIGNIFICANCE: These findings characterize multiple deregulated mechanisms of genome stability that lead to CIN in ovarian cancer and demonstrate the benefit of integrating analysis of said mechanisms into predictions of therapy response.
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Affiliation(s)
- Naoka Tamura
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Nadeem Shaikh
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Daniel Muliaditan
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Tanya N Soliman
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | | | - Eleni Maniati
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Daniela Moralli
- Chromosome Dynamics, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Mary-Anne Durin
- Chromosome Dynamics, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Catherine M Green
- Chromosome Dynamics, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Frances R Balkwill
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Kit Curtius
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Sarah E McClelland
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.
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Sharma S, Bhonde R. Genetic and epigenetic stability of stem cells: Epigenetic modifiers modulate the fate of mesenchymal stem cells. Genomics 2020; 112:3615-3623. [DOI: 10.1016/j.ygeno.2020.04.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/08/2020] [Accepted: 04/24/2020] [Indexed: 12/11/2022]
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Albers E, Avram A, Sbroggio M, Fernandez-Capetillo O, Lopez-Contreras AJ. Supraphysiological protection from replication stress does not extend mammalian lifespan. Aging (Albany NY) 2020; 12:5612-5624. [PMID: 32253367 PMCID: PMC7185120 DOI: 10.18632/aging.103039] [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: 01/08/2020] [Accepted: 03/10/2020] [Indexed: 12/05/2022]
Abstract
Replication Stress (RS) is a type of DNA damage generated at the replication fork, characterized by single-stranded DNA (ssDNA) accumulation, and which can be caused by a variety of factors. Previous studies have reported elevated RS levels in aged cells. In addition, mouse models with a deficient RS response show accelerated aging. However, the relevance of endogenous or physiological RS, compared to other sources of genomic instability, for the normal onset of aging is unknown. We have performed long term survival studies of transgenic mice with extra copies of the Chk1 and/or Rrm2 genes, which we previously showed extend the lifespan of a progeroid ATR-hypomorphic model suffering from high levels of RS. In contrast to their effect in the context of progeria, the lifespan of Chk1, Rrm2 and Chk1/Rrm2 transgenic mice was similar to WT littermates in physiological settings. Most mice studied died due to tumors -mainly lymphomas- irrespective of their genetic background. Interestingly, a higher but not statistically significant percentage of transgenic mice developed tumors compared to WT mice. Our results indicate that supraphysiological protection from RS does not extend lifespan, indicating that RS may not be a relevant source of genomic instability on the onset of normal aging.
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Affiliation(s)
- Eliene Albers
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra Avram
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | - Mauro Sbroggio
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | | | - Andres J Lopez-Contreras
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
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29
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Yoshihara M, Oguchi A, Murakawa Y. Genomic Instability of iPSCs and Challenges in Their Clinical Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1201:23-47. [PMID: 31898780 DOI: 10.1007/978-3-030-31206-0_2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Generation of human-induced pluripotent stem cells (iPSCs) from somatic cells has opened the possibility to design novel therapeutic approaches. In 2014, the first-in-human clinical trial of iPSC-based therapy was conducted. However, the transplantation for the second patient was discontinued at least in part due to genetic aberrations detected in iPSCs. Moreover, many studies have reported genetic aberrations in iPSCs with the rapid progress in genomic technologies. The presence of genomic instability raises serious safety concerns and can hamper the advancement of iPSC-based therapies. Here, we summarize our current knowledge on genomic instability of iPSCs and challenges in their clinical applications. In view of the recent expansion of stem cell therapies, it is crucial to gain deeper mechanistic insights into the genetic aberrations, ranging from chromosomal aberrations, copy number variations to point mutations. On the basis of their origin, these genetic aberrations in iPSCs can be classified as (i) preexisting mutations in parental somatic cells, (ii) reprogramming-induced mutations, and (iii) mutations that arise during in vitro culture. However, it is still unknown whether these genetic aberrations in iPSCs can be an actual risk factor for adverse effects. Intersection of the genomic data on iPSCs with the patients' clinical follow-up data will help to produce evidence-based criteria for clinical application. Furthermore, we discuss novel approaches to generate iPSCs with fewer genetic aberrations. Better understanding of iPSCs from both basic and clinical aspects will pave the way for iPSC-based therapies.
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Affiliation(s)
- Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Akiko Oguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy.
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30
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Zhu Q, Lu P. Stem Cell Transplantation for Amyotrophic Lateral Sclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1266:71-97. [PMID: 33105496 DOI: 10.1007/978-981-15-4370-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a motor neuronal degeneration disease, in which the death of motor neurons causes lost control of voluntary muscles. The consequence is weakness of muscles with a wide range of disabilities and eventually death. Most patients died within 5 years after diagnosis, and there is no cure for this devastating neurodegenerative disease up to date. Stem cells, including non-neural stem cells and neural stem cells (NSCs) or neural progenitor cells (NPCs), are very attractive cell sources for potential neuroprotection and motor neuron replacement therapy which bases on the idea that transplant-derived and newly differentiated motor neurons can replace lost motor neurons to re-establish voluntary motor control of muscles in ALS. Our recent studies show that transplanted NSCs or NPCs not only survive well in injured spinal cord, but also function as neuronal relays to receive regenerated host axonal connection and extend their own axons to host for connectivity, including motor axons in ventral root. This reciprocal connection between host neurons and transplanted neurons provides a strong rationale for neuronal replacement therapy for ALS to re-establish voluntary motor control of muscles. In addition, a variety of new stem cell resources and the new methodologies to generate NSCs or motor neuron-specific progenitor cells have been discovered and developed. Together, it provides the basis for motor neuron replacement therapy with NSCs or NPCs in ALS.
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Affiliation(s)
- Qiang Zhu
- Ludwig Institute, University of California - San Diego, La Jolla, CA, USA
| | - Paul Lu
- Veterans Administration San Diego Healthcare System, San Diego, CA, USA. .,Department of Neurosciences, University of California - San Diego, La Jolla, CA, USA.
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31
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Shimada M, Tsukada K, Kagawa N, Matsumoto Y. Reprogramming and differentiation-dependent transcriptional alteration of DNA damage response and apoptosis genes in human induced pluripotent stem cells. JOURNAL OF RADIATION RESEARCH 2019; 60:719-728. [PMID: 31665364 PMCID: PMC7357234 DOI: 10.1093/jrr/rrz057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 05/22/2023]
Abstract
Pluripotent stem cells (PSCs), such as embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), have a dual capability to self-renew and differentiate into all cell types necessary to develop an entire organism. Differentiation is associated with dynamic epigenetic alteration and transcriptional change, while self-renewal depends on maintaining the genome DNA accurately. Genome stability of PSCs is strictly regulated to maintain pluripotency. However, the DNA damage response (DDR) mechanism in PSCs is still unclear. There is accumulating evidence that genome stability and pluripotency are regulated by a transcriptional change in undifferentiated and differentiated states. iPSCs are ideal for analyzing transcriptional regulation during reprogramming and differentiation. This study aimed to elucidate the transcriptional alteration surrounding genome stability maintenance, including DNA repair, cell cycle checkpoints and apoptosis in fibroblasts, iPSCs and neural progenitor cells (NPCs) derived from iPSCs as differentiated cells. After ionizing radiation exposure, foci for the DNA double-stranded break marker γ-H2AX increased, peaking at 0.5 h in all cells (>90%), decreasing after 4 h in fibroblasts (32.3%) and NPCs (22.3%), but still remaining at 52.5% (NB1RGB C2 clone) and 54.7% (201B7 cells) in iPSCs. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL)-positive cells were detected, indicating that iPSCs' apoptosis increases. In addition, RNA sequencing (RNA-Seq) analysis showed high expression of apoptosis genes (TP53, CASP3 and BID) in iPSCs. Results suggested that increased apoptosis activity maintains accurate, undifferentiated genome DNA in the cell population.
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Affiliation(s)
- Mikio Shimada
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Oookayaka, Meguro-ku, 152-8550, Tokyo, Japan
- Corresponding author: Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Oookayaka, Meguro-ku, 152-8550, Tokyo, Japan. Tel: +81-3-5734-3703; Fax: +81-3-5734-3703.
| | - Kaima Tsukada
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Oookayaka, Meguro-ku, 152-8550, Tokyo, Japan
| | - Nozomi Kagawa
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Oookayaka, Meguro-ku, 152-8550, Tokyo, Japan
| | - Yoshihisa Matsumoto
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Oookayaka, Meguro-ku, 152-8550, Tokyo, Japan
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32
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Steichen C, Hannoun Z, Luce E, Hauet T, Dubart-Kupperschmitt A. Genomic integrity of human induced pluripotent stem cells: Reprogramming, differentiation and applications. World J Stem Cells 2019; 11:729-747. [PMID: 31692979 PMCID: PMC6828592 DOI: 10.4252/wjsc.v11.i10.729] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/13/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023] Open
Abstract
Ten years after the initial generation of induced pluripotent stem cells (hiPSCs) from human tissues, their potential is no longer questioned, with over 15000 publications listed on PubMed, covering various fields of research; including disease modeling, cell therapy strategies, pharmacology/toxicology screening and 3D organoid systems. However, despite evidences that the presence of mutations in hiPSCs should be a concern, publications addressing genomic integrity of these cells represent less than 1% of the literature. After a first overview of the mutation types currently reported in hiPSCs, including karyotype abnormalities, copy number variations, single point mutation as well as uniparental disomy, this review will discuss the impact of reprogramming parameters such as starting cell type and reprogramming method on the maintenance of the cellular genomic integrity. Then, a specific focus will be placed on culture conditions and subsequent differentiation protocols and how their may also trigger genomic aberrations within the cell population of interest. Finally, in a last section, the impact of genomic alterations on the possible usages of hiPSCs and their derivatives will also be exemplified and discussed. We will also discuss which techniques or combination of techniques should be used to screen for genomic abnormalities with a particular focus on the necessary quality controls and the potential alternatives.
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Affiliation(s)
- Clara Steichen
- INSERM U1082 IRTOMIT, CHU de Poitiers, Poitiers F-86021, France
- Université de Poitiers, Faculté de Médecine et Pharmacie, Bâtiment D1, 6 rue de la milétrie, TSA 51115, 86073 Poitiers Cedex 9, France
| | - Zara Hannoun
- INSERM U1193, Hôpital Paul Brousse, Villejuif F-94800, France
- UMR_S1193, Université Paris-Saclay, Hôpital Paul Brousse, Villejuif F-94800, France
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Eléanor Luce
- INSERM U1193, Hôpital Paul Brousse, Villejuif F-94800, France
- UMR_S1193, Université Paris-Saclay, Hôpital Paul Brousse, Villejuif F-94800, France
- Département Hospitalo-Universitaire Hepatinov, Hôpital Paul Brousse, Villejuif F-94807, France
| | - Thierry Hauet
- INSERM U1082 IRTOMIT, CHU de Poitiers, Poitiers F-86021, France
- Université de Poitiers, Faculté de Médecine et Pharmacie, Bâtiment D1, 6 rue de la milétrie, TSA 51115, 86073 Poitiers Cedex 9, France
- Service de Biochimie, Pôle Biospharm, CHU de Poitiers, Poitiers F-86021, France
- Fédération Hospitalo-Universitaire SUPORT, CHU de Poitiers, Poitiers F-86021, France
| | - Anne Dubart-Kupperschmitt
- INSERM U1193, Hôpital Paul Brousse, Villejuif F-94800, France
- UMR_S1193, Université Paris-Saclay, Hôpital Paul Brousse, Villejuif F-94800, France
- Département Hospitalo-Universitaire Hepatinov, Hôpital Paul Brousse, Villejuif F-94807, France
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Nikitina TV, Kashevarova AA, Lebedev IN. Chromosomal Instability and Karyotype Correction in Human Induced Pluripotent Stem Cells. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419100090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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A Cell-Intrinsic Interferon-like Response Links Replication Stress to Cellular Aging Caused by Progerin. Cell Rep 2019; 22:2006-2015. [PMID: 29466729 PMCID: PMC5848491 DOI: 10.1016/j.celrep.2018.01.090] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/22/2017] [Accepted: 01/30/2018] [Indexed: 12/05/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disease caused by a truncated lamin A protein (progerin) that drives cellular and organismal decline. HGPS patient-derived fibroblasts accumulate genomic instability, but its underlying mechanisms and contribution to disease remain poorly understood. Here, we show that progerin-induced replication stress (RS) drives genomic instability by eliciting replication fork (RF) stalling and nuclease-mediated degradation. Rampant RS is accompanied by upregulation of the cGAS/STING cytosolic DNA sensing pathway and activation of a robust STAT1-regulated interferon (IFN)-like response. Reducing RS and the IFN-like response, especially with calcitriol, improves the fitness of progeria cells and increases the efficiency of cellular reprogramming. Importantly, other compounds that improve HGPS phenotypes reduce RS and the IFN-like response. Our study reveals mechanisms underlying progerin toxicity, including RS-induced genomic instability and activation of IFN-like responses, and their relevance for cellular decline in HGPS.
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35
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Placental imprinted gene expression mediates the effects of maternal psychosocial stress during pregnancy on fetal growth. J Dev Orig Health Dis 2019; 10:196-205. [PMID: 30968809 DOI: 10.1017/s2040174418000545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Imprinted genes uniquely drive and support fetoplacental growth by controlling the allocation of maternal resources to the fetus and affecting the newborn's growth. We previously showed that alterations of the placental imprinted gene expression are associated with suboptimal perinatal growth and respond to environmental stimuli including socio-economic determinants. At the same time, maternal psychosocial stress during pregnancy (MPSP) has been shown to affect fetal growth. Here, we set out to test the hypothesis that placental imprinted gene expression mediates the effects of MPSP on fetal growth in a well-characterized birth cohort, the Stress in Pregnancy (SIP) Study. We observed that mothers experiencing high MPSP deliver infants with lower birthweight (P=0.047). Among the 109 imprinted genes tested, we detected panels of placental imprinted gene expression of 23 imprinted genes associated with MPSP and 26 with birthweight. Among these genes, five imprinted genes (CPXM2, glucosidase alpha acid (GAA), GPR1, SH3 and multiple ankyrin repeat domains 2 (SHANK2) and THSD7A) were common to the two panels. In multivariate analyses, controlling for maternal age and education and gestational age at birth and infant gender, two genes, GAA and SHANK2, each showed a 22% mediation of MPSP on fetal growth. These data provide new insights into the role that imprinted genes play in translating the maternal stress message into a fetoplacental growth pattern.
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36
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Tarnawski L, Eugster E, DeCamp L, Jovinge S. The Efficacy and Safety ofSendaiViral Reprograming of Mouse Primary Cells Using Human Vectors. Cell Reprogram 2019; 21:78-88. [DOI: 10.1089/cell.2018.0048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Laura Tarnawski
- Department of Medicine, Center for Bioelectronic Medicine, Bioclinicum, Solna, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Stefan Jovinge
- Van Andel Institute, Grand Rapids, Michigan
- DeVos Cardiovascular Research Program of Spectrum Health, Grand Rapids, Michigan
- Cardiovascular Institute, Stanford University, Palo Alto, California
- Spectrum Health Frederik Meijer Heart and Vascular Institute, Grand Rapids, Michigan
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37
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Abstract
Cell reprogramming has been considered a powerful technique in the regenerative medicine field. In addition to diverse its strengths, cell reprogramming technology also has several drawbacks generated during the process of reprogramming. Telomere shortening caused by the cell reprogramming process impedes the efficiency of cell reprogramming. Transcription factors used for reprogramming alter genomic contents and result in genetic mutations. Additionally, defective mitochondria functioning such as excessive mitochondrial fission leads to the limitation of pluripotency and ultimately reduces the efficiency of reprogramming. These problems including genomic instability and impaired mitochondrial dynamics should be resolved to apply cell reprograming in clinical research and to address efficiency and safety concerns. Sirtuin (NAD+-dependent histone deacetylase) has been known to control the chromatin state of the telomere and influence mitochondria function in cells. Recently, several studies reported that Sirtuins could control for genomic instability in cell reprogramming. Here, we review recent findings regarding the role of Sirtuins in cell reprogramming. And we propose that the manipulation of Sirtuins may improve defects that result from the steps of cell reprogramming.
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Affiliation(s)
- Jaein Shin
- Laboratory of Stem Cells and Cell Reprogramming, Department of Biomedical Engineering (BKplus21 team), Dongguk University, Seoul 04620, Korea
| | - Junyeop Kim
- Laboratory of Stem Cells and Cell Reprogramming, Department of Biomedical Engineering (BKplus21 team), Dongguk University, Seoul 04620, Korea
| | - Hanseul Park
- Laboratory of Stem Cells and Cell Reprogramming, Department of Biomedical Engineering (BKplus21 team), Dongguk University, Seoul 04620, Korea
| | - Jongpil Kim
- Laboratory of Stem Cells and Cell Reprogramming, Department of Biomedical Engineering (BKplus21 team), Dongguk University, Seoul 04620, and Department of Chemistry, Dongguk University, Seoul 04620, Korea
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38
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Pollard BS, Pollard HB. Induced pluripotent stem cells for treating cystic fibrosis: State of the science. Pediatr Pulmonol 2018; 53:S12-S29. [PMID: 30062693 DOI: 10.1002/ppul.24118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/31/2018] [Indexed: 12/20/2022]
Abstract
Induced pluripotent stem cells (iPSCs) are a recently developed technology in which fully differentiated cells such as fibroblasts from individual CF patients can be repaired with [wildtype] CFTR, and reprogrammed to differentiate into fully differentiated cells characteristic of the proximal and distal airways. Here, we review properties of different epithelial cells in the airway, and the in vitro genetic roadmap which iPSCs follow as they are step-wise differentiated into either basal stem cells, for the proximal airway, or into Type II Alveolar cells for the distal airways. The central theme is that iPSC-derived basal stem cells, are penultimately dependent on NOTCH signaling for differentiation into club cells, goblet cells, ciliated cells, and neuroendocrine cells. Furthermore, given the proper matrix, these cellular progenies are also able to self-assemble into a fully functional pseudostratified squamous proximal airway epithelium. By contrast, club cells are reserve stem cells which are able to either differentiate into goblet or ciliated cells, but also to de-differentiate into basal stem cells. Variant club cells, located at the transition between airway and alveoli, may also be responsible for differentiation into Type II Alveolar cells, which then differentiate into Type I Alveolar cells for gas exchange in the distal airway. Using gene editing, the mutant CFTR gene in iPSCs from CF patients can be repaired, and fully functional epithelial cells can thus be generated through directed differentiation. However, there is a limitation in that the lung has other CFTR-dependent cells besides epithelial cells. Another limitation is that there are CFTR-dependent cells in other organs which would continue to contribute to CF disease. Furthermore, there are also bystander or modifier genes which affect disease outcome, not only in the lung, but specifically in other CF-affected organs. Finally, we discuss future personalized applications of the iPSC technology, many of which have already survived the "proof-of-principle" test. These include (i) patient-derived iPSCs used as a "lung-on-a-chip" tool for personalized drug discovery; (ii) replacement of mutant lung cells by wildtype lung cells in the living lung; and (iii) development of bio-artificial lungs. It is hoped that this review will give the reader a roadmap through the most complicated of the obstacles, and foster a guardedly optimistic view of how some of the remaining obstacles might one day be overcome.
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Affiliation(s)
| | - Harvey B Pollard
- Department of Cell Biology and Genetics, Uniformed Services University School of Medicine-America's Medical School, Uniformed Services University of the Health Sciences, Bethesda, Maryland
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39
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Rohani L, Johnson AA, Naghsh P, Rancourt DE, Ulrich H, Holland H. Concise Review: Molecular Cytogenetics and Quality Control: Clinical Guardians for Pluripotent Stem Cells. Stem Cells Transl Med 2018; 7:867-875. [PMID: 30218497 PMCID: PMC6265634 DOI: 10.1002/sctm.18-0087] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/07/2018] [Indexed: 12/13/2022] Open
Abstract
Now that induced pluripotent stem cell (iPSC)‐based transplants have been performed in humans and organizations have begun producing clinical‐grade iPSCs, it is imperative that strict quality control standards are agreed upon. This is essential as both ESCs and iPSCs have been shown to accumulate genomic aberrations during long‐term culturing. These aberrations can include copy number variations, trisomy, amplifications of chromosomal regions, deletions of chromosomal regions, loss of heterozygosity, and epigenetic abnormalities. Moreover, although the differences between iPSCs and ESCs appear largely negligible when a high enough n number is used for comparison, the reprogramming process can generate further aberrations in iPSCs, including copy number variations and deletions in tumor‐suppressor genes. If mutations or epigenetic signatures are present in parental cells, these can also be carried over into iPSCs. To maximize patient safety, we recommend a set of standards to be utilized when preparing iPSCs for clinical use. Reprogramming methods that do not involve genomic integration should be used. Cultured cells should be grown using feeder‐free and serum‐free systems to avoid animal contamination. Karyotyping, whole‐genome sequencing, gene expression analyses, and standard sterility tests should all become routine quality control tests. Analysis of mitochondrial DNA integrity, whole‐epigenome analyses, as well as single‐cell genome sequencing of large cell populations may also prove beneficial. Furthermore, clinical‐grade stem cells need to be produced under accepted regulatory good manufacturing process standards. The creation of haplobanks that provide major histocompatibility complex matching is also recommended to improve allogeneic stem cell engraftment. Stem Cells Translational Medicine2018;7:867–875
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Affiliation(s)
- Leili Rohani
- Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Adiv A Johnson
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Pooyan Naghsh
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Derrick E Rancourt
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Heidrun Holland
- Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
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40
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Abstract
The chemical treatment of cancer started with the realization that DNA damaging agents such as mustard gas present notable antitumoural properties. Consequently, early drug development focused on genotoxic chemicals, some of which are still widely used in the clinic. However, the efficacy of such therapies is often limited by the side effects of these drugs on healthy cells. A refinement to this approach is to use compounds that can exploit the presence of DNA damage in cancer cells. Given that replication stress (RS) is a major source of genomic instability in cancer, targeting the RS-response kinase ataxia telangiectasia and Rad3-related protein (ATR) has emerged as a promising alternative. With ATR inhibitors now entering clinical trials, we here revisit the biology behind this strategy and discuss potential biomarkers that could be used for a better selection of patients who respond to therapy.
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Affiliation(s)
- Emilio Lecona
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
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41
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Abstract
Flaws in the DNA replication process have emerged as a leading driver of genome instability in human diseases. Alteration to replication fork progression is a defining feature of replication stress and the consequent failure to maintain fork integrity and complete genome duplication within a single round of S-phase compromises genetic integrity. This includes increased mutation rates, small and large scale genomic rearrangement and deleterious consequences for the subsequent mitosis that result in the transmission of additional DNA damage to the daughter cells. Therefore, preserving fork integrity and replication competence is an important aspect of how cells respond to replication stress and avoid genetic change. Homologous recombination is a pivotal pathway in the maintenance of genome integrity in the face of replication stress. Here we review our recent understanding of the mechanisms by which homologous recombination acts to protect, restart and repair replication forks. We discuss the dynamics of these genetically distinct functions and their contribution to faithful mitoticsegregation.
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42
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The potential of human induced pluripotent stem cells for modelling diabetic wound healing in vitro. Clin Sci (Lond) 2018; 132:1629-1643. [PMID: 30108152 DOI: 10.1042/cs20171483] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/28/2018] [Accepted: 07/23/2018] [Indexed: 12/11/2022]
Abstract
Impaired wound healing and ulceration caused by diabetes mellitus, is a significant healthcare burden, markedly impairs quality of life for patients, and is the major cause of amputation worldwide. Current experimental approaches used to investigate the complex wound healing process often involve cultures of fibroblasts and/or keratinocytes in vitro, which can be limited in terms of complexity and capacity, or utilisation of rodent models in which the mechanisms of wound repair differ substantively from that in humans. However, advances in tissue engineering, and the discovery of strategies to reprogramme adult somatic cells to pluripotency, has led to the possibility of developing models of human skin on a large scale. Generation of induced pluripotent stem cells (iPSCs) from tissues donated by diabetic patients allows the (epi)genetic background of this disease to be studied, and the ability to differentiate iPSCs to multiple cell types found within skin may facilitate the development of more complex skin models; these advances offer key opportunities for improving modelling of wound healing in diabetes, and the development of effective therapeutics for treatment of chronic wounds.
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Vallabhaneni H, Lynch PJ, Chen G, Park K, Liu Y, Goehe R, Mallon BS, Boehm M, Hursh DA. High Basal Levels of γH2AX in Human Induced Pluripotent Stem Cells Are Linked to Replication-Associated DNA Damage and Repair. Stem Cells 2018; 36:1501-1513. [PMID: 29873142 DOI: 10.1002/stem.2861] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 05/02/2018] [Accepted: 05/19/2018] [Indexed: 01/07/2023]
Abstract
Human induced pluripotent stem cells (iPSCs) have great potential as source cells for therapeutic uses. However, reports indicate that iPSCs carry genetic abnormalities, which may impede their medical use. Little is known about mechanisms contributing to intrinsic DNA damage in iPSCs that could lead to genomic instability. In this report, we investigated the level of DNA damage in human iPSC lines compared with their founder fibroblast line and derived mesenchymal stromal cell (MSC) lines using the phosphorylated histone variant, γH2AX, as a marker of DNA damage. We show that human iPSCs have elevated basal levels of γH2AX, which correlate with markers of DNA replication: 5-ethynyl-2'-deoxyuridine and the single-stranded binding protein, replication protein A. γH2AX foci in iPSCs also colocalize to BRCA1 and RAD51, proteins in the homologous repair pathway, implying γH2AX in iPSCs marks sites of double strand breaks. Our study demonstrates an association between increased basal levels of γH2AX and the rapid replication of iPSCs. Stem Cells 2018;36:1501-1513.
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Affiliation(s)
- Haritha Vallabhaneni
- Division of Cellular and Gene Therapy, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Patrick J Lynch
- Division of Biotechnology Review and Research II, Office of Pharmaceutical Quality, Center for Drugs Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Guibin Chen
- Laboratory of Cardiovascular Regenerative Medicine, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Kyeyoon Park
- Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Yangtengyu Liu
- Laboratory of Cardiovascular Regenerative Medicine, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Rachel Goehe
- Division of Cellular and Gene Therapy, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Barbara S Mallon
- Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Manfred Boehm
- Laboratory of Cardiovascular Regenerative Medicine, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
| | - Deborah A Hursh
- Division of Cellular and Gene Therapy, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
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Ohmine S, Salisbury JL, Ingle J, Pettinato G, Haddox CL, Haddad T, Galanis E, Ikeda Y, D'Assoro AB. Aurora-A overexpression is linked to development of aggressive teratomas derived from human iPS cells. Oncol Rep 2018; 39:1725-1730. [PMID: 29393405 PMCID: PMC5868406 DOI: 10.3892/or.2018.6239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 12/07/2017] [Indexed: 01/02/2023] Open
Abstract
The discovery of human induced pluripotent stem cells (hiPSCs) is a promising advancement in the field of regenerative and personalized medicine. Expression of SOX2, KLF4, OCT4 and MYC transcription factors induces the nuclear reprogramming of somatic cells into hiPSCs that share striking similarities with human embryonic stem cells (hESCs). However, several studies have demonstrated that hESCs and hiPSCs could lead to teratoma formation in vivo, thus limiting their current clinical applications. Aberrant cell cycle regulation of hESCs is linked to centrosome amplification, which may account, for their enhanced chromosomal instability (CIN), and thus increase their tumorigenicity. Significantly, the tumor suppressor p53 plays a key role as a 'guardian of reprogramming', safeguarding genomic integrity during hiPSC reprogramming. Nevertheless, the molecular mechanisms leading to development of CIN during reprogramming and increased tumorigenic potential of hiPSCs remains to be fully elucidated. In the present study, we analyzed CIN in hiPSCs derived from keratinocytes and established that chromosomal and mitotic aberrations were linked to centrosome amplification, Aurora-A overexpression, abrogation of p53-mediated G1/S cell cycle checkpoint and loss of Rb tumor-suppressor function. When hiPSCs were transplanted into the kidney capsules of immunocompromised mice, they developed high-grade teratomas characterized by the presence of cells that exhibited non-uniform shapes and sizes, high nuclear pleomorphism and centrosome amplification. Significantly, ex vivo cells derived from teratomas exhibited high self-renewal capacity that was linked to Aurora-A kinase activity and gave rise to lung metastasis when injected into the tail vein of immunocompromised mice. Collectively, these findings demonstrated a high risk for malignancy of hiPSCs that exhibit Aurora-A overexpression, loss of Rb function, centrosome amplification and CIN. Based on these findings, we proposed that Aurora-A-targeted therapy could represent a promising prophylactic therapeutic strategy to decrease the likelihood of CIN and development of aggressive teratomas derived from hiPSCs.
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Affiliation(s)
- Seiga Ohmine
- Department of Molecular Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Jeffrey L. Salisbury
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - James Ingle
- Department of Medical Oncology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Giuseppe Pettinato
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Candace L. Haddox
- Department of Medical Oncology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Tufia Haddad
- Department of Medical Oncology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Evanthia Galanis
- Department of Molecular Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
- Department of Medical Oncology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Yasuhiro Ikeda
- Department of Molecular Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Antonino B. D'Assoro
- Department of Medical Oncology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
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Assou S, Bouckenheimer J, De Vos J. Concise Review: Assessing the Genome Integrity of Human Induced Pluripotent Stem Cells: What Quality Control Metrics? Stem Cells 2018; 36:814-821. [PMID: 29441649 DOI: 10.1002/stem.2797] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 01/19/2018] [Accepted: 01/24/2018] [Indexed: 12/20/2022]
Abstract
Human induced pluripotent stem cells (hiPSCs) have the potential to differentiate virtually into any cell type in unlimited quantities. Therefore, they are ideal for in vitro tissue modeling or to produce cells for clinical use. Importantly, and differently from immortalized and cancer cell lines, the hiPSC genome scrupulously reproduces that of the cell from which they were derived. However, hiPSCs can develop genetic abnormalities during reprogramming or prolonged cell culture, such as aneuploidies or oncogenic mutations (e.g., in TP53). Therefore, hiPSC genome integrity must be routinely monitored because serious genome alterations would greatly compromise their usefulness or safety of use. Here, we reviewed hiPSC genome quality control monitoring methods and laboratory practice. Indeed, due to their frequency and functional consequences, recurrent genetic defects found in cultured hiPSCs are inacceptable and their appearance should be monitored by routine screening. Hence, for research purposes, we propose that the genome of hiPSC lines should be systematically screened at derivation, at least by karyotyping, and then regularly (every 12 weeks) during experiments, for instance with polymerase chain reaction-based techniques. For some specific applications, such as research on aging, cell cycle, apoptosis or cancer, other tests (e.g., TP53 mutation detection) should also be included. For clinical use, in addition to karyotyping, we advise exome sequencing. Stem Cells 2018;36:814-821.
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Affiliation(s)
- Said Assou
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | | | - John De Vos
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France.,CHU Montpellier, Department of Cell and Tissue Engineering, Hospital Saint-Eloi, Montpellier, France
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46
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Wangsa D, Quintanilla I, Torabi K, Vila-Casadesús M, Ercilla A, Klus G, Yuce Z, Galofré C, Cuatrecasas M, Lozano JJ, Agell N, Cimini D, Castells A, Ried T, Camps J. Near-tetraploid cancer cells show chromosome instability triggered by replication stress and exhibit enhanced invasiveness. FASEB J 2018; 32:3502-3517. [PMID: 29452566 DOI: 10.1096/fj.201700247rr] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A considerable proportion of tumors exhibit aneuploid karyotypes, likely resulting from the progressive loss of chromosomes after whole-genome duplication. Here, by using isogenic diploid and near-tetraploid (4N) single-cell-derived clones from the same parental cell lines, we aimed at exploring how polyploidization affects cellular functions and how tetraploidy generates chromosome instability. Gene expression profiling in 4N clones revealed a significant enrichment of transcripts involved in cell cycle and DNA replication. Increased levels of replication stress in 4N cells resulted in DNA damage, impaired proliferation caused by a cell cycle delay during S phase, and higher sensitivity to S phase checkpoint inhibitors. In fact, increased levels of replication stress were also observed in nontransformed, proliferative posttetraploid RPE1 cells. Additionally, replication stress promoted higher levels of intercellular genomic heterogeneity and ongoing genomic instability, which could be explained by high rates of mitotic defects, and was alleviated by the supplementation of exogenous nucleosides. Finally, our data found that 4N cancer cells displayed increased migratory and invasive capacity, both in vitro and in primary colorectal tumors, indicating that tetraploidy can promote aggressive cancer cell behavior.-Wangsa, D., Quintanilla, I., Torabi, K., Vila-Casadesús, M., Ercilla, A., Klus, G., Yuce, Z., Galofré, C., Cuatrecasas, M., Lozano, J. J., Agell, N., Cimini, D., Castells, A., Ried, T., Camps, J. Near-tetraploid cancer cells show chromosome instability triggered by replication stress and exhibit enhanced invasiveness.
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Affiliation(s)
- Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Isabel Quintanilla
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Keyvan Torabi
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain.,Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Maria Vila-Casadesús
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain.,Bioinformatics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Amaia Ercilla
- Departament de Biologia Cel·lular, Immunologia i Neurociències, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Gregory Klus
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zeynep Yuce
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Department of Medical Biology and Genetics, School of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Claudia Galofré
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Miriam Cuatrecasas
- Department of Pathology-Centro de Diagnóstico Biomédico (CDB), Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Juan José Lozano
- Bioinformatics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Neus Agell
- Departament de Biologia Cel·lular, Immunologia i Neurociències, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Daniela Cimini
- Department of Biological Sciences, Biocomplexity Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Antoni Castells
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain.,Unitat de Biologia Cel·lular i Genètica Mèdica, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
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47
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Sirt6 Promotes DNA End Joining in iPSCs Derived from Old Mice. Cell Rep 2017; 18:2880-2892. [PMID: 28329681 DOI: 10.1016/j.celrep.2017.02.082] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/22/2017] [Accepted: 02/28/2017] [Indexed: 12/11/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) have great potential for treating age-related diseases, but the genome integrity of iPSCs is critically important. Here, we demonstrate that non-homologous end joining (NHEJ), rather than homologous recombination (HR), is less efficient in iPSCs from old mice than young mice. We further find that Sirt6 is downregulated in iPSCs from old mice. Sirt6 directly binds to Ku80 and facilitates the Ku80/DNA-PKcs interaction, thus promoting DNA-PKcs phosphorylation at residue S2056, leading to efficient NHEJ. Rescue experiments show that introducing a combination of Sirt6 and the Yamanaka factors during reprogramming significantly promotes DNA double-strand break (DSB) repair by activating NHEJ in iPSCs derived from old mice. Thus, our study suggests a strategy to improve the quality of iPSCs derived from old donors by activating NHEJ and stabilizing the genome.
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48
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Yoshihara M, Hayashizaki Y, Murakawa Y. Genomic Instability of iPSCs: Challenges Towards Their Clinical Applications. Stem Cell Rev Rep 2017; 13:7-16. [PMID: 27592701 PMCID: PMC5346115 DOI: 10.1007/s12015-016-9680-6] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Induced pluripotent stem cells (iPSCs) are a type of pluripotent stem cells generated directly from mature cells through the introduction of key transcription factors. iPSCs can be propagated and differentiated into many cell types in the human body, holding enormous potential in the field of regenerative medicine. However, genomic instability of iPSCs has been reported with the advent of high-throughput technologies such as next-generation sequencing. The presence of genetic variations in iPSCs has raised serious safety concerns, hampering the advancement of iPSC-based novel therapies. Here we summarize our current knowledge on genomic instability of iPSCs, with a particular focus on types of genetic variations and their origins. Importantly, it remains elusive whether genetic variations in iPSCs can be an actual risk factor for adverse effects including malignant outgrowth. Furthermore, we discuss novel approaches to generate iPSCs with fewer genetic variations. Lastly, we outline the safety issues and monitoring strategies of iPSCs in clinical settings.
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Affiliation(s)
- Masahito Yoshihara
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan.,Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | | | - Yasuhiro Murakawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan. .,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan.
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49
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Tousley A, Kegel-Gleason KB. Induced Pluripotent Stem Cells in Huntington's Disease Research: Progress and Opportunity. J Huntingtons Dis 2017; 5:99-131. [PMID: 27372054 PMCID: PMC4942721 DOI: 10.3233/jhd-160199] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Induced pluripotent stem cells (iPSCs) derived from controls and patients can act as a starting point for in vitro differentiation into human brain cells for discovery of novel targets and treatments for human disease without the same ethical limitations posed by embryonic stem cells. Numerous groups have successfully produced and characterized Huntington’s disease (HD) iPSCs with different CAG repeat lengths, including cells from patients with one or two HD alleles. HD iPSCs and the neural cell types derived from them recapitulate some disease phenotypes found in both human patients and animal models. Although these discoveries are encouraging, the use of iPSCs for cutting edge and reproducible research has been limited due to some of the inherent problems with cell lines and the technological differences in the way laboratories use them. The goal of this review is to summarize the current state of the HD iPSC field, and to highlight some of the issues that need to be addressed to maximize their potential as research tools.
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Affiliation(s)
| | - Kimberly B. Kegel-Gleason
- Correspondence to: Kimberly Kegel-Gleason, Assistant Professor in Neurology, Massachusetts General Hospital and Harvard Medical School, 114 16th Street, Room 2001, Charlestown, MA 02129, USA. Tel.: +1 617 724 8754; E-mail:
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50
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Lin K, Xiao AZ. Quality control towards the application of induced pluripotent stem cells. Curr Opin Genet Dev 2017; 46:164-169. [PMID: 28823985 DOI: 10.1016/j.gde.2017.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 07/06/2017] [Accepted: 07/14/2017] [Indexed: 01/27/2023]
Abstract
The advance of iPS technology holds great promise for regenerative medicine. Despite their global similarity to ES cells, fully reprogrammed iPS cells generated by current procedures still display clone-to-clone variations in molecular properties and developmental potentials, which calls for the development of reliable quality control assays. The differences in developmental potentials in iPS cells may be caused by epigenetic variations, such as histone variant H2A.X deposition. In this review, we discuss the current understanding of molecular variations of iPS cells and their implication on quality assessments.
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Affiliation(s)
- Kaixuan Lin
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Andrew Z Xiao
- Department of Genetics and Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA.
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