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Warmenhoven JW, Henthorn NT, McNamara AL, Ingram SP, Merchant MJ, Kirkby KJ, Schuemann J, Paganetti H, Prise KM, McMahon SJ. Effects of Differing Underlying Assumptions in In Silico Models on Predictions of DNA Damage and Repair. Radiat Res 2023; 200:509-522. [PMID: 38014593 DOI: 10.1667/rade-21-00147.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/05/2023] [Indexed: 11/29/2023]
Abstract
The induction and repair of DNA double-strand breaks (DSBs) are critical factors in the treatment of cancer by radiotherapy. To investigate the relationship between incident radiation and cell death through DSB induction many in silico models have been developed. These models produce and use custom formats of data, specific to the investigative aims of the researchers, and often focus on particular pairings of damage and repair models. In this work we use a standard format for reporting DNA damage to evaluate combinations of different, independently developed, models. We demonstrate the capacity of such inter-comparison to determine the sensitivity of models to both known and implicit assumptions. Specifically, we report on the impact of differences in assumptions regarding patterns of DNA damage induction on predicted initial DSB yield, and the subsequent effects this has on derived DNA repair models. The observed differences highlight the importance of considering initial DNA damage on the scale of nanometres rather than micrometres. We show that the differences in DNA damage models result in subsequent repair models assuming significantly different rates of random DSB end diffusion to compensate. This in turn leads to disagreement on the mechanisms responsible for different biological endpoints, particularly when different damage and repair models are combined, demonstrating the importance of inter-model comparisons to explore underlying model assumptions.
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Affiliation(s)
- John W Warmenhoven
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Nicholas T Henthorn
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Aimee L McNamara
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Samuel P Ingram
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Michael J Merchant
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Karen J Kirkby
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Jan Schuemann
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Harald Paganetti
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Massachusetts
| | - Kevin M Prise
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
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Durdik M, Kosik P, Jakl L, Kozackova M, Markova E, Vigasova K, Beresova K, Jakubikova J, Horvathova E, Zastko L, Fekete M, Zavacka I, Pobijakova M, Belyaev I. Imaging flow cytometry and fluorescence microscopy in assessing radiation response in lymphocytes from umbilical cord blood and cancer patients. Cytometry A 2021; 99:1198-1208. [PMID: 34089242 DOI: 10.1002/cyto.a.24468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/28/2022]
Abstract
DNA double strand breaks (DSB) induced by ionizing radiation (IR) are usually measured using γH2AX/53BP1 DNA repair foci, that is considered to be the most sensitive assay for DSB analysis. While fluorescence microscopy (FM) is the gold standard for this analysis, imaging flow cytometry (IFC) may offer number of advantages such as lack of the fluorescence background, higher number of cells analyzed, and higher sensitivity in detection of DNA damage induced by IR at low doses. Along with appearance of γH2AX foci, the variable fraction of the cells exhibits homogeneously stained γH2AX signal resulting in so-called γH2AX pan-staining, which is believed to appear at early stages of apoptosis. Here, we investigated incidence of γH2AX pan-staining at different time points after irradiation with γ-rays using IFC and compared the obtained data with the data from FM. Appearance of γH2AX pan-staining during the apoptotic process was further analyzed by fluorescence-activated cell sorting (FACS) of cells at different stages of apoptosis and subsequent immunofluorescence analysis. Our results show that IFC was able to reveal dose dependence of pan-staining, while FM failed to detect all pan-staining cells. Moreover, we found that γH2AX pan-staining could be induced by therapeutic, but not low doses of γ-rays and correlate well with percentage of apoptotic cells was analyzed using flow cytometric Annexin-V/7-AAD assay. Further investigations showed that γH2AX pan-staining is formed in the early phases of apoptosis and remains until later stages of apoptotic process. Apoptotic DNA fragmentation as detected with comet assay using FM correlated with the percentage of live and late apoptotic/necrotic cells as analyzed by flow cytometry. Lastly, we successfully tested IFC for detection of γH2AX pan-staining and γH2AX/53BP1 DNA repair foci in lymphocyte of breast cancer patients after radiotherapy, which may be useful for assessing individual radiosensitivity in a clinically relevant cohort of patients.
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Affiliation(s)
- Matus Durdik
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Pavol Kosik
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lukas Jakl
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Maria Kozackova
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Eva Markova
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Katarina Vigasova
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Katarina Beresova
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jana Jakubikova
- Department of Tumor Immunology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Eva Horvathova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lucian Zastko
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marta Fekete
- Department of Radiation Oncology, National Cancer Institute, Bratislava, Slovakia
| | - Ingrid Zavacka
- Department of Radiation Oncology, National Cancer Institute, Bratislava, Slovakia
| | - Margita Pobijakova
- Department of Radiation Oncology, National Cancer Institute, Bratislava, Slovakia
| | - Igor Belyaev
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Bratislava, Slovakia
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Evaluation of Calyculin A Effect on γH2AX/53BP1 Focus Formation and Apoptosis in Human Umbilical Cord Blood Lymphocytes. Int J Mol Sci 2021; 22:ijms22115470. [PMID: 34067339 PMCID: PMC8196852 DOI: 10.3390/ijms22115470] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Dephosphorylation inhibitor calyculin A (cal A) has been reported to inhibit the disappearance of radiation-induced γH2AX DNA repair foci in human lymphocytes. However, other studies reported no change in the kinetics of γH2AX focus induction and loss in irradiated cells. While apoptosis might interplay with the kinetics of focus formation, it was not followed in irradiated cells along with DNA repair foci. Thus, to validate plausible explanations for significant variability in outputs of these studies, we evaluated the effect of cal A (1 and 10 nM) on γH2AX/53BP1 DNA repair foci and apoptosis in irradiated (1, 5, 10, and 100 cGy) human umbilical cord blood lymphocytes (UCBL) using automated fluorescence microscopy and annexin V-FITC/propidium iodide assay/γH2AX pan-staining, respectively. No effect of cal A on γH2AX and colocalized γH2AX/53BP1 foci induced by low doses (≤10 cGy) of γ-rays was observed. Moreover, 10 nM cal A treatment decreased the number of all types of DNA repair foci induced by 100 cGy irradiation. 10 nM cal A treatment induced apoptosis already at 2 h of treatment, independently from the delivered dose. Apoptosis was also detected in UCBL treated with lower cal A concentration, 1 nM, at longer cell incubation, 20 and 44 h. Our data suggest that apoptosis triggered by cal A in UCBL may underlie the failure of cal A to maintain radiation-induced γH2AX foci. All DSB molecular markers used in this study responded linearly to low-dose irradiation. Therefore, their combination may represent a strong biodosimetry tool for estimation of radiation response to low doses. Assessment of colocalized γH2AX/53BP1 improved the threshold of low dose detection.
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Kosik P, Durdik M, Skorvaga M, Klimova D, Kochanova D, Cerna Z, Kubes M, Holop M, Belyaev I. Induction of AML Preleukemic Fusion Genes in HSPCs and DNA Damage Response in Preleukemic Fusion Gene Positive Samples. Antioxidants (Basel) 2021; 10:antiox10030481. [PMID: 33803739 PMCID: PMC8003332 DOI: 10.3390/antiox10030481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 11/27/2022] Open
Abstract
Preleukemic fusion genes (PFGs) occurring after DNA damage in hematopoietic stem progenitor cells (HSPCs) in utero often represent the initial event in the development of childhood leukemia. While the incidence of PFGs characteristic for acute lymphoblastic leukemia (ALL) was relatively well examined by several research groups and estimated to be 1–5% in umbilical cord blood (UCB) of healthy newborns, PFGs that are relevant to acute myeloid leukemia (AML) were poorly investigated. Therefore, this study is focused on the estimation of the incidence of the most frequent AML PFGs in newborns. For the first time, this study considered the inducibility of AML PFGs in different subsets of UCB HSPCs by low-dose γ-rays and also compared endogenous DNA damage, apoptosis, and reactive oxygen species (ROS) level between UCB samples containing or lacking AML PFGs. We found that: (i) the incidence of AML PFGs in UCB was 3.19% for RUNX1-RUNX1T1, 3.19% for PML-RARα, and 1.17% for KMT2A-MLLT3, (ii) 50 cGy of γ-rays did not induce RUNX1-RUNX1T1, PML-RARα, or KMT2A-MLLT3 PFGs in different subsets of sorted and expanded HSPCs, and (iii) the AML PFG+ samples accumulated the same level of endogenous DNA damage, as measured by the γH2AX/53BP1 focus formation, and also the same ROS level, and apoptosis as compared to PFG− controls. Our study provides critical insights into the prevalence of AML PFGs in UCB of newborns, without the evidence of a specific HSPC population more susceptible for PFG formation after irradiation to low-dose γ-rays or increased amount of ROS, apoptosis and DNA damage.
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Affiliation(s)
- Pavol Kosik
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (M.D.); (M.S.); (D.K.); (D.K.); (Z.C.); (I.B.)
- Correspondence: ; Tel.: +421-2-32295-118
| | - Matus Durdik
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (M.D.); (M.S.); (D.K.); (D.K.); (Z.C.); (I.B.)
| | - Milan Skorvaga
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (M.D.); (M.S.); (D.K.); (D.K.); (Z.C.); (I.B.)
| | - Daniela Klimova
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (M.D.); (M.S.); (D.K.); (D.K.); (Z.C.); (I.B.)
- Institute of Medical Biology, Genetics and Clinical Genetics, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| | - Dominika Kochanova
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (M.D.); (M.S.); (D.K.); (D.K.); (Z.C.); (I.B.)
| | - Zlatica Cerna
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (M.D.); (M.S.); (D.K.); (D.K.); (Z.C.); (I.B.)
| | - Miroslav Kubes
- Stem Cell Lab, BIOM-R, Ltd., 841 05 Bratislava, Slovakia; (M.K.); (M.H.)
| | - Marek Holop
- Stem Cell Lab, BIOM-R, Ltd., 841 05 Bratislava, Slovakia; (M.K.); (M.H.)
| | - Igor Belyaev
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (M.D.); (M.S.); (D.K.); (D.K.); (Z.C.); (I.B.)
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Zastko L, Petrovičová P, Račková A, Jakl L, Jakušová V, Marková E, Belyaev I. DNA damage response and apoptosis induced by hyperthermia in human umbilical cord blood lymphocytes. Toxicol In Vitro 2021; 73:105127. [PMID: 33652125 DOI: 10.1016/j.tiv.2021.105127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/04/2021] [Accepted: 02/25/2021] [Indexed: 01/30/2023]
Abstract
While hyperthermia (HT) is a promising modality for cancer treatment, the knowledge on mechanisms of its effect on cells is still limited. We have investigated DNA double-strand break (DSB) and apoptosis induced by HT. Umbilical cord blood lymphocytes (UCBL) were subjected to HT at 43 °C. We have treated cells for 1 h (1 h HT), 2 h (2 h HT) and by combined HT and ice treatment (both lasting 1 h). Enumeration of DSB by 53BP1/γH2AX DNA repair focus formation and early apoptosis by γH2AX pan-staining was conducted by automated fluorescent microscopy. Apoptotic stages and viability were assessed by the annexin/propidium iodide (PI) assay using flow cytometry 0, 18, and 42 h post-treatment. HT induced either immediate (2 h HT) or postponed (1 h HT) DNA damage. The levels of 53BP1 and γH2AX foci differed under the same treatment conditions, suggesting that the ratio of co-localized γH2AX/53BP1 foci to all γH2AX and also to all 53BP1 foci could be a valuable marker. The ratio of co-localized foci increased immediately after 2 h HT regardless the way of assessment. For the first time we show, by both annexin/PI and γH2AX pan-staining assay that apoptosis can be induced during or immediately after the 2 h HT treatment. Our results suggest that HT may induce DSB in dependence on treatment duration and post-treatment time due to inhibition of DNA repair pathways and that HT-induced apoptosis might be dependent or associated with DSB formation in human lymphocytes. Assessment of γH2AX pan-staining in lymphocytes affected by HT may represent a valuable marker of HT treatment side effects.
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Affiliation(s)
- Lucián Zastko
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, Slovakia; Department of Medical Biophysics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Malá Hora 4, Martin, Slovakia.
| | - Petra Petrovičová
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, Slovakia
| | - Anna Račková
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, Slovakia
| | - Lukáš Jakl
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, Slovakia
| | - Viera Jakušová
- Department of Public Health, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Malá Hora 4B, Martin, Slovakia
| | - Eva Marková
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, Slovakia
| | - Igor Belyaev
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, Slovakia
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C-Terminal Binding Protein is Involved in Promoting to the Carcinogenesis of Human Glioma. Mol Neurobiol 2016; 54:6121-6132. [PMID: 27699603 DOI: 10.1007/s12035-016-0159-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 09/22/2016] [Indexed: 12/13/2022]
Abstract
C-terminal binding protein (CtBP) is responsible for regulating the pathogenesis of a lot of cancer types. However, whether CtBP1/2 is involved in regulating the growth and development of human glioma is still obscure. In the present study presented here, our results firstly reveal that CtBP1/2 deficiency, induced by siRNA interference, disrupts the functional integrity of the MRN complex that is responsible for DNA repair in human glioma cells. The dysfunction of the MRN complex further contributes to the up-regulation of ATM and Rad3-related kinase (ATR) and Chk1 signaling pathway, which inhibits cell cycle progression mediated by CDK2, preparing for the initiation of DNA repair. Under the condition of hypoxia, hypoxia-inducible factor-1α (HIF-1α) can be directly regulated by CDK2 on protein level, playing coordinately regulatory role in the carcinogenesis of human glioma cells. Overall, our findings reveal that CtBP1/2 is essential to promote to human glioma cell growth through maintaining the DNA stability regulated by the MRN/ATR/Chk1/CDK2/HIF-1α signaling pathway.
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