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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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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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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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Dannenmann B, Lehle S, Lorscheid S, Huber SM, Essmann F, Schulze-Osthoff K. Simultaneous quantification of DNA damage and mitochondrial copy number by long-run DNA-damage quantification (LORD-Q). Oncotarget 2017; 8:112417-112425. [PMID: 29348835 PMCID: PMC5762520 DOI: 10.18632/oncotarget.20112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 07/26/2017] [Indexed: 11/29/2022] Open
Abstract
DNA damage and changes in the mitochondrial DNA content have been implicated in ageing and cancer development. To prevent genomic instability and tumorigenesis, cells must maintain the integrity of their nuclear and mitochondrial DNA. Advances in the research of DNA damage protection and genomic stability, however, also depend on the availability of techniques that can reliably quantify alterations of mitochondrial DNA copy numbers and DNA lesions in an accurate high-throughput manner. Unfortunately, no such method has been established yet. Here, we describe the high-sensitivity long-run real-time PCR technique for DNA-damage quantification (LORD-Q) and its suitability to simultaneously measure DNA damage rates and mitochondrial DNA copy numbers in cultured cells and tissue samples. Using the LORD-Q multiplex assay, we exemplarily show that the mitochondrial DNA content does not directly affect DNA damage susceptibility, but influences the efficacy of certain anticancer drugs. Hence, LORD-Q provides a fast and precise method to assess DNA lesions, DNA repair and mtDNA replication as well as their role in a variety of pathological settings.
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Affiliation(s)
- Benjamin Dannenmann
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Simon Lehle
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Sebastian Lorscheid
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Stephan M Huber
- Department of Radiation Oncology, University of Tübingen, 72076 Tübingen, Germany
| | - Frank Essmann
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Klaus Schulze-Osthoff
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Effects of Antioxidant Supplements on the Survival and Differentiation of Stem Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:5032102. [PMID: 28770021 PMCID: PMC5523230 DOI: 10.1155/2017/5032102] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 05/31/2017] [Indexed: 12/13/2022]
Abstract
Although physiological levels of reactive oxygen species (ROS) are required to maintain the self-renewal capacity of stem cells, elevated ROS levels can induce chromosomal aberrations, mitochondrial DNA damage, and defective stem cell differentiation. Over the past decade, several studies have shown that antioxidants can not only mitigate oxidative stress and improve stem cell survival but also affect the potency and differentiation of these cells. Further beneficial effects of antioxidants include increasing genomic stability, improving the adhesion of stem cells to culture media, and enabling researchers to manipulate stem cell proliferation by using different doses of antioxidants. These findings can have several clinical implications, such as improving neurogenesis in patients with stroke and neurodegenerative diseases, as well as improving the regeneration of infarcted myocardial tissue and the banking of spermatogonial stem cells. This article reviews the cellular and molecular effects of antioxidant supplementation to cultured or transplanted stem cells and draws up recommendations for further research in this area.
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Lyublinskaya OG, Ivanova JS, Pugovkina NA, Kozhukharova IV, Kovaleva ZV, Shatrova AN, Aksenov ND, Zenin VV, Kaulin YA, Gamaley IA, Nikolsky NN. Redox environment in stem and differentiated cells: A quantitative approach. Redox Biol 2017; 12:758-769. [PMID: 28426982 PMCID: PMC5393314 DOI: 10.1016/j.redox.2017.04.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/06/2017] [Accepted: 04/08/2017] [Indexed: 01/07/2023] Open
Abstract
Stem cells are believed to maintain a specific intracellular redox status through a combination of enhanced removal capacity and limited production of ROS. In the present study, we challenge this assumption by developing a quantitative approach for the analysis of the pro- and antioxidant ability of human embryonic stem cells in comparison with their differentiated descendants, as well as adult stem and non-stem cells. Our measurements showed that embryonic stem cells are characterized by low ROS level, low rate of extracellular hydrogen peroxide removal and low threshold for peroxide-induced cytotoxicity. However, biochemical normalization of these parameters to cell volume/protein leads to matching of normalized values in stem and differentiated cells and shows that tested in the present study cells (human embryonic stem cells and their fibroblast-like progenies, adult mesenchymal stem cells, lymphocytes, HeLa) maintain similar intracellular redox status. Based on these observations, we propose to use ROS concentration averaged over the cell volume instead of ROS level as a measure of intracellular redox balance. We show that attempts to use ROS level for comparative analysis of redox status of morphologically different cells could lead to false conclusions. Methods for the assessment of ROS concentration based on flow cytometry analysis with the use of H2DCFDA dye and HyPer, genetically encoded probe for hydrogen peroxide, are discussed. Intracellular ROS level depends on the cell size. We propose to use the concept of ROS concentration instead of the ROS level. Quantification of basic redox parameters challenges the hypothesis about the highly specific redox environment in stem cells.
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Affiliation(s)
- O G Lyublinskaya
- Department of Intracellular Signaling and Transport, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia.
| | - Ju S Ivanova
- Department of Intracellular Signaling and Transport, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia; Department of Medical Physics, Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya st. 29, St. Petersburg 195251, Russia
| | - N A Pugovkina
- Department of Intracellular Signaling and Transport, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia
| | - I V Kozhukharova
- Department of Intracellular Signaling and Transport, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia
| | - Z V Kovaleva
- Department of Intracellular Signaling and Transport, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia
| | - A N Shatrova
- Department of Intracellular Signaling and Transport, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia
| | - N D Aksenov
- Department of Intracellular Signaling and Transport, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia
| | - V V Zenin
- Department of Intracellular Signaling and Transport, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia
| | - Yu A Kaulin
- Department of Intracellular Signaling and Transport, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia
| | - I A Gamaley
- Department of Intracellular Signaling and Transport, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia
| | - N N Nikolsky
- Department of Intracellular Signaling and Transport, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg 194064, Russia
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