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Toprani SM, Scheibler C, Mordukhovich I, McNeely E, Nagel ZD. Cosmic Ionizing Radiation: A DNA Damaging Agent That May Underly Excess Cancer in Flight Crews. Int J Mol Sci 2024; 25:7670. [PMID: 39062911 PMCID: PMC11277465 DOI: 10.3390/ijms25147670] [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: 06/04/2024] [Revised: 06/20/2024] [Accepted: 06/30/2024] [Indexed: 07/28/2024] Open
Abstract
In the United States, the Federal Aviation Administration has officially classified flight crews (FC) consisting of commercial pilots, cabin crew, or flight attendants as "radiation workers" since 1994 due to the potential for cosmic ionizing radiation (CIR) exposure at cruising altitudes originating from solar activity and galactic sources. Several epidemiological studies have documented elevated incidence and mortality for several cancers in FC, but it has not yet been possible to establish whether this is attributable to CIR. CIR and its constituents are known to cause a myriad of DNA lesions, which can lead to carcinogenesis unless DNA repair mechanisms remove them. But critical knowledge gaps exist with regard to the dosimetry of CIR, the role of other genotoxic exposures among FC, and whether possible biological mechanisms underlying higher cancer rates observed in FC exist. This review summarizes our understanding of the role of DNA damage and repair responses relevant to exposure to CIR in FC. We aimed to stimulate new research directions and provide information that will be useful for guiding regulatory, public health, and medical decision-making to protect and mitigate the risks for those who travel by air.
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Affiliation(s)
- Sneh M. Toprani
- John B. Little Center for Radiation Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; (C.S.); (I.M.); (E.M.)
| | - Christopher Scheibler
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; (C.S.); (I.M.); (E.M.)
| | - Irina Mordukhovich
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; (C.S.); (I.M.); (E.M.)
- Sustainability and Health Initiative (SHINE), Department of Environmental Health, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Eileen McNeely
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; (C.S.); (I.M.); (E.M.)
- Sustainability and Health Initiative (SHINE), Department of Environmental Health, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Zachary D. Nagel
- John B. Little Center for Radiation Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; (C.S.); (I.M.); (E.M.)
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2
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Sito H, Tan SC. Genetic polymorphisms as potential pharmacogenetic biomarkers for platinum-based chemotherapy in non-small cell lung cancer. Mol Biol Rep 2024; 51:102. [PMID: 38217759 DOI: 10.1007/s11033-023-08915-2] [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: 09/04/2023] [Accepted: 11/08/2023] [Indexed: 01/15/2024]
Abstract
Platinum-based chemotherapy (PBC) is a widely used treatment for various solid tumors, including non-small cell lung cancer (NSCLC). However, its efficacy is often compromised by the emergence of drug resistance in patients. There is growing evidence that genetic variations may influence the susceptibility of NSCLC patients to develop resistance to PBC. Here, we provide a comprehensive overview of the mechanisms underlying platinum drug resistance and highlight the important role that genetic polymorphisms play in this process. This paper discussed the genetic variants that regulate DNA repair, cellular movement, drug transport, metabolic processing, and immune response, with a focus on their effects on response to PBC. The potential applications of these genetic polymorphisms as predictive indicators in clinical practice are explored, as are the challenges associated with their implementation.
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Affiliation(s)
- Hilary Sito
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Shing Cheng Tan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
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3
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Tuesuwan B, Vongsutilers V. Current Threat of Nitrosamines in Pharmaceuticals and Scientific Strategies for Risk Mitigation. J Pharm Sci 2023; 112:1192-1209. [PMID: 36739905 DOI: 10.1016/j.xphs.2023.01.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
The current global situation of nitrosamine contamination has expanded from angiotensin-II receptor blockers (ARBs) to wide range of medicines as the risk of contamination via the drug substances, formulation, manufacturing process, and packaging is possible for many drug products. The understanding of chemistry, toxicology, and root causes of nitrosamines are mandatory to effectively evaluate and mitigate the risks associated with the contaminated mutagen. Lessons learnt and scientific findings from previously identified root causes are good examples on how to perform effective risk assessments and establish control strategies. Addressing the risk of nitrosamine contamination in pharmaceuticals requires significant knowledge and considerable resources to collect the necessary information for risk evaluation. Examples of the resources required include a reliable laboratory facility, reference material, highly specific and sensitive instrumentation able handle trace levels of contamination, data management, and the most limited resource - time. Therefore, the supporting tools to assist with risk assessment e.g., shared databases for drug and excipients in concern, screening models for the determination of nitrosamine formation potential, and an in silico model to help with toxicity estimation, have proven to be beneficial to tackle the risk and concern of nitrosamine contamination in pharmaceuticals.
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Affiliation(s)
- Bodin Tuesuwan
- Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorasit Vongsutilers
- Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand.
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4
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Styk J, Pös Z, Pös O, Radvanszky J, Turnova EH, Buglyó G, Klimova D, Budis J, Repiska V, Nagy B, Szemes T. Microsatellite instability assessment is instrumental for Predictive, Preventive and Personalised Medicine: status quo and outlook. EPMA J 2023; 14:143-165. [PMID: 36866160 PMCID: PMC9971410 DOI: 10.1007/s13167-023-00312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023]
Abstract
A form of genomic alteration called microsatellite instability (MSI) occurs in a class of tandem repeats (TRs) called microsatellites (MSs) or short tandem repeats (STRs) due to the failure of a post-replicative DNA mismatch repair (MMR) system. Traditionally, the strategies for determining MSI events have been low-throughput procedures that typically require assessment of tumours as well as healthy samples. On the other hand, recent large-scale pan-tumour studies have consistently highlighted the potential of massively parallel sequencing (MPS) on the MSI scale. As a result of recent innovations, minimally invasive methods show a high potential to be integrated into the clinical routine and delivery of adapted medical care to all patients. Along with advances in sequencing technologies and their ever-increasing cost-effectiveness, they may bring about a new era of Predictive, Preventive and Personalised Medicine (3PM). In this paper, we offered a comprehensive analysis of high-throughput strategies and computational tools for the calling and assessment of MSI events, including whole-genome, whole-exome and targeted sequencing approaches. We also discussed in detail the detection of MSI status by current MPS blood-based methods and we hypothesised how they may contribute to the shift from conventional medicine to predictive diagnosis, targeted prevention and personalised medical services. Increasing the efficacy of patient stratification based on MSI status is crucial for tailored decision-making. Contextually, this paper highlights drawbacks both at the technical level and those embedded deeper in cellular/molecular processes and future applications in routine clinical testing.
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Affiliation(s)
- Jakub Styk
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia ,Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia
| | - Zuzana Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Institute of Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Ondrej Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia
| | - Jan Radvanszky
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Institute of Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia ,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
| | - Evelina Hrckova Turnova
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Slovgen Ltd, 841 04 Bratislava, Slovakia
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Daniela Klimova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia ,Medirex Group Academy, NPO, 949 05 Nitra, Slovakia
| | - Bálint Nagy
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
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5
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Vodicka P, Vodenkova S, Horak J, Opattova A, Tomasova K, Vymetalkova V, Stetina R, Hemminki K, Vodickova L. An investigation of DNA damage and DNA repair in chemical carcinogenesis triggered by small-molecule xenobiotics and in cancer: Thirty years with the comet assay. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 885:503564. [PMID: 36669813 DOI: 10.1016/j.mrgentox.2022.503564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/04/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
In the present review we addressed the determination of DNA damage induced by small-molecule carcinogens, considered their persistence in DNA and mutagenicity in in vitro and in vivo systems over a period of 30 years. The review spans from the investigation of the role of DNA damage in the cascade of chemical carcinogenesis. In the nineties, this concept evolved into the biomonitoring studies comprising multiple biomarkers that not only reflected DNA/chromosomal damage, but also the potential of the organism for biotransformation/elimination of various xenobiotics. Since first years of the new millennium, dynamic system of DNA repair and host susceptibility factors started to appear in studies and a considerable knowledge has been accumulated on carcinogens and their role in carcinogenesis. It was understood that the final biological links bridging the arising DNA damage and cancer onset remain to be elucidated. In further years the community of scientists learnt that cancer is a multifactorial disease evolving over several decades of individual´s life. Moreover, DNA damage and DNA repair are inseparable players also in treatment of malignant diseases, but affect substantially other processes, such as degeneration. Functional monitoring of DNA repair pathways and DNA damage response may cast some light on above aspects. Very little is currently known about the relationship between telomere homeostasis and DNA damage formation and repair. DNA damage/repair in genomic and mitochondrial DNA and crosstalk between these two entities emerge as a new interesting topic.
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Affiliation(s)
- Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Josef Horak
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Alena Opattova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Kristyna Tomasova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
| | - Rudolf Stetina
- Department of Research and Development, University Hospital Hradec Kralove, 500 03 Hradec Kralove, Czech Republic
| | - Kari Hemminki
- Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic; Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), 691 20 Heidelberg, Germany
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Centre in Pilsen, Charles University, 306 05 Pilsen, Czech Republic.
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6
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Cheong A, Nagel ZD. Human Variation in DNA Repair, Immune Function, and Cancer Risk. Front Immunol 2022; 13:899574. [PMID: 35935942 PMCID: PMC9354717 DOI: 10.3389/fimmu.2022.899574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
DNA damage constantly threatens genome integrity, and DNA repair deficiency is associated with increased cancer risk. An intuitive and widely accepted explanation for this relationship is that unrepaired DNA damage leads to carcinogenesis due to the accumulation of mutations in somatic cells. But DNA repair also plays key roles in the function of immune cells, and immunodeficiency is an important risk factor for many cancers. Thus, it is possible that emerging links between inter-individual variation in DNA repair capacity and cancer risk are driven, at least in part, by variation in immune function, but this idea is underexplored. In this review we present an overview of the current understanding of the links between cancer risk and both inter-individual variation in DNA repair capacity and inter-individual variation in immune function. We discuss factors that play a role in both types of variability, including age, lifestyle, and environmental exposures. In conclusion, we propose a research paradigm that incorporates functional studies of both genome integrity and the immune system to predict cancer risk and lay the groundwork for personalized prevention.
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7
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O'Neill E, Cornelissen B. Know thy tumour: Biomarkers to improve treatment of molecular radionuclide therapy. Nucl Med Biol 2022; 108-109:44-53. [PMID: 35276447 DOI: 10.1016/j.nucmedbio.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 10/18/2022]
Abstract
Molecular radionuclide therapy (MRT) is an effective treatment for both localised and disseminated tumours. Biomarkers can be used to identify potential subtypes of tumours that are known to respond better to standard MRT protocols. These enrolment-based biomarkers can further be used to develop dose-response relationships using image-based dosimetry within these defined subtypes. However, the biological identity of the cancers treated with MRT are commonly not well-defined, particularly for neuroendocrine neoplasms. The biological heterogeneity of such cancers has hindered the establishment of dose-responses and minimum tumour dose thresholds. Biomarkers could also be used to determine normal tissue MRT dose limits and permit greater injected doses of MRT in patients. An alternative approach is to understand the repair capacity limits of tumours using radiobiology-based biomarkers within and outside patient cohorts currently treated with MRT. It is hoped that by knowing more about tumours and how they respond to MRT, biomarkers can provide needed dimensionality to image-based biodosimetry to improve MRT with optimized protocols and personalised therapies.
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Affiliation(s)
- Edward O'Neill
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK.
| | - Bart Cornelissen
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK; Department of Nuclear Medicine and Molecular Imaging, University Medical Center Groningen, Groningen, the Netherlands.
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8
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Huang Z, Sun S, Lee M, Maslov AY, Shi M, Waldman S, Marsh A, Siddiqui T, Dong X, Peter Y, Sadoughi A, Shah C, Ye K, Spivack SD, Vijg J. Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking. Nat Genet 2022; 54:492-498. [PMID: 35410377 PMCID: PMC9844147 DOI: 10.1038/s41588-022-01035-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 02/16/2022] [Indexed: 01/19/2023]
Abstract
Although lung cancer risk among smokers is dependent on smoking dose, it remains unknown if this increased risk reflects an increased rate of somatic mutation accumulation in normal lung cells. Here, we applied single-cell whole-genome sequencing of proximal bronchial basal cells from 33 participants aged between 11 and 86 years with smoking histories varying from never-smoking to 116 pack-years. We found an increase in the frequency of single-nucleotide variants and small insertions and deletions with chronological age in never-smokers, with mutation frequencies significantly elevated among smokers. When plotted against smoking pack-years, mutations followed the linear increase in cancer risk until about 23 pack-years, after which no further increase in mutation frequency was observed, pointing toward individual selection for mutation avoidance. Known lung cancer-defined mutation signatures tracked with both age and smoking. No significant enrichment for somatic mutations in lung cancer driver genes was observed.
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Affiliation(s)
- Zhenqiu Huang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Shixiang Sun
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Laboratory of Applied Genomic Technologies, Voronezh State University of Engineering Technologies, Voronezh, Russia
| | - Miao Shi
- Department of Pulmonary Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Spencer Waldman
- Department of Pulmonary Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ava Marsh
- Department of Pulmonary Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Taha Siddiqui
- Department of Pulmonary Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Yakov Peter
- Department of Biology, Touro College, Queens, NY, USA
- Department of Pulmonary Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ali Sadoughi
- Department of Pulmonary Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Chirag Shah
- Department of Pulmonary Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Simon D Spivack
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Pulmonary Medicine, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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9
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Wu HC, Kehm R, Santella RM, Brenner DJ, Terry MB. DNA repair phenotype and cancer risk: a systematic review and meta-analysis of 55 case-control studies. Sci Rep 2022; 12:3405. [PMID: 35233009 PMCID: PMC8888613 DOI: 10.1038/s41598-022-07256-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 02/15/2022] [Indexed: 01/01/2023] Open
Abstract
DNA repair phenotype can be measured in blood and may be a potential biomarker of cancer risk. We conducted a systematic review and meta-analysis of epidemiological studies of DNA repair phenotype and cancer through March 2021. We used random-effects models to calculate pooled odds ratios (ORs) of cancer risk for those with the lowest DNA repair capacity compared with those with the highest capacity. We included 55 case–control studies that evaluated 12 different cancers using 10 different DNA repair assays. The pooled OR of cancer risk (all cancer types combined) was 2.92 (95% Confidence Interval (CI) 2.49, 3.43) for the lowest DNA repair. Lower DNA repair was associated with all studied cancer types, and pooled ORs (95% CI) ranged from 2.02 (1.43, 2.85) for skin cancer to 7.60 (3.26, 17.72) for liver cancer. All assays, except the homologous recombination repair assay, showed statistically significant associations with cancer. The effect size ranged from 1.90 (1.00, 3.60) for the etoposide-induced double-strand break assay to 5.06 (3.67, 6.99) for the γ-H2AX assay. The consistency and strength of the associations support the use of these phenotypic biomarkers; however large-scale prospective studies will be important for understanding their use related to age and screening initiation.
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Affiliation(s)
- Hui-Chen Wu
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, 630 West 168th St., Room P&S 16-421E, New York, NY, 10032, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.
| | - Rebecca Kehm
- Department of Epidemiology, Mailman School of Public Health of Columbia University, New York, NY, USA
| | - Regina M Santella
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, 630 West 168th St., Room P&S 16-421E, New York, NY, 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - David J Brenner
- Center for Radiological Research, Columbia University Irving Medical Center, 630W 168th Street, New York, NY, 10032, USA
| | - Mary Beth Terry
- Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, 630 West 168th St., Room P&S 16-421E, New York, NY, 10032, USA.,Department of Epidemiology, Mailman School of Public Health of Columbia University, New York, NY, USA
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10
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Hrdina AI, Kohale IN, Kaushal S, Kelly J, Selin NE, Engelward BP, Kroll JH. The Parallel Transformations of Polycyclic Aromatic Hydrocarbons in the Body and in the Atmosphere. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:25004. [PMID: 35225689 PMCID: PMC8884122 DOI: 10.1289/ehp9984] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/29/2021] [Accepted: 01/10/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Polycyclic aromatic hydrocarbons (PAHs) emitted from combustion sources are known to be mutagenic, with more potent species also being carcinogenic. Previous studies show that PAHs can undergo complex transformations both in the body and in the atmosphere, yet these transformation processes are generally investigated separately. OBJECTIVES Drawing from the literature in atmospheric chemistry and toxicology, we highlight the parallel transformations of PAHs that occur in the atmosphere and the body and discuss implications for public health. We also examine key uncertainties related to the toxicity of atmospheric oxidation products of PAHs and explore critical areas for future research. DISCUSSION We focus on a key mode of toxicity for PAHs, in which metabolic processes (driven by cytochrome P450 enzymes), leads to the formation of oxidized PAHs that can damage DNA. Such species can also be formed abiotically in the atmosphere from natural oxidation processes, potentially augmenting PAH toxicity by skipping the necessary metabolic steps that activate their mutagenicity. Despite the large body of literature related to these two general pathways, the extent to which atmospheric oxidation affects a PAH's overall toxicity remains highly uncertain. Combining knowledge and promoting collaboration across both fields can help identify key oxidation pathways and the resulting products that impact public health. CONCLUSIONS Cross-disciplinary research, in which toxicology studies evaluate atmospheric oxidation products and their mixtures, and atmospheric measurements examine the formation of compounds that are known to be most toxic. Close collaboration between research communities can help narrow down which PAHs, and which PAH degradation products, should be targeted when assessing public health risks. https://doi.org/10.1289/EHP9984.
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Affiliation(s)
- Amy I.H. Hrdina
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - Ishwar N. Kohale
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
| | - Simran Kaushal
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jamie Kelly
- Department of Geography, University College London, London, UK
| | - Noelle E. Selin
- Institute for Data, Systems, and Society, MIT, Cambridge, Massachusetts, USA
- Department of Earth, Atmospheric, and Planetary Sciences, MIT, Cambridge, Massachusetts, USA
| | - Bevin P. Engelward
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
| | - Jesse H. Kroll
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
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11
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Feiveson AH, Krieger SS, von Scheven G, Crucian BE, Bürkle A, Stahn AC, Wu H, Moreno-Villanueva M. DNA Damage and Radiosensitivity in Blood Cells from Subjects Undergoing 45 Days of Isolation and Confinement: An Explorative Study. Curr Issues Mol Biol 2022; 44:654-669. [PMID: 35723331 PMCID: PMC8929106 DOI: 10.3390/cimb44020046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/02/2022] [Accepted: 01/16/2022] [Indexed: 11/16/2022] Open
Abstract
The effect of confined and isolated experience on astronauts’ health is an important factor to consider for future space exploration missions. The more confined and isolated humans are, the more likely they are to develop negative behavioral or cognitive conditions such as a mood decline, sleep disorder, depression, fatigue and/or physiological problems associated with chronic stress. Molecular mediators of chronic stress, such as cytokines, stress hormones or reactive oxygen species (ROS) are known to induce cellular damage including damage to the DNA. In view of the growing evidence of chronic stress-induced DNA damage, we conducted an explorative study and measured DNA strand breaks in 20 healthy adults. The participants were grouped into five teams (missions). Each team was composed of four participants, who spent 45 days in isolation and confinement in NASA’s Human Exploration Research Analog (HERA). Endogenous DNA integrity, ex-vivo radiation-induced DNA damage and the rates of DNA repair were assessed every week. Our results show a high inter-individual variability as well as differences between the missions, which cannot be explained by inter-individual variability alone. The ages and sex of the participants did not appear to influence the results.
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Affiliation(s)
- Alan H. Feiveson
- NASA Johnson Space Center, Houston, TX 77058, USA; (A.H.F.); (B.E.C.); (H.W.)
| | | | - Gudrun von Scheven
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany; (G.v.S.); (A.B.)
| | - Brian E. Crucian
- NASA Johnson Space Center, Houston, TX 77058, USA; (A.H.F.); (B.E.C.); (H.W.)
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany; (G.v.S.); (A.B.)
| | - Alexander C. Stahn
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, 1019 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA;
- Center for Space Medicine and Extreme Environments, Institute of Physiology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Honglu Wu
- NASA Johnson Space Center, Houston, TX 77058, USA; (A.H.F.); (B.E.C.); (H.W.)
| | - María Moreno-Villanueva
- NASA Johnson Space Center, Houston, TX 77058, USA; (A.H.F.); (B.E.C.); (H.W.)
- Human Performance Research Centre, Department of Sport Science, University of Konstanz, 78457 Konstanz, Germany
- Correspondence: ; Tel.: +49-753-188-3599
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12
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Noren Hooten N, Pacheco NL, Smith JT, Evans MK. The accelerated aging phenotype: The role of race and social determinants of health on aging. Ageing Res Rev 2022; 73:101536. [PMID: 34883202 PMCID: PMC10862389 DOI: 10.1016/j.arr.2021.101536] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 02/06/2023]
Abstract
The pursuit to discover the fundamental biology and mechanisms of aging within the context of the physical and social environment is critical to designing interventions to prevent and treat its complex phenotypes. Aging research is critically linked to understanding health disparities because these inequities shape minority aging, which may proceed on a different trajectory than the overall population. Health disparities are characteristically seen in commonly occurring age-associated diseases such as cardiovascular and cerebrovascular disease as well as diabetes mellitus and cancer. The early appearance and increased severity of age-associated disease among African American and low socioeconomic status (SES) individuals suggests that the factors contributing to the emergence of health disparities may also induce a phenotype of 'premature aging' or 'accelerated aging' or 'weathering'. In marginalized and low SES populations with high rates of early onset age-associated disease the interaction of biologic, psychosocial, socioeconomic and environmental factors may result in a phenotype of accelerated aging biologically similar to premature aging syndromes with increased susceptibility to oxidative stress, premature accumulation of oxidative DNA damage, defects in DNA repair and higher levels of biomarkers of oxidative stress and inflammation. Health disparities, therefore, may be the end product of this complex interaction in populations at high risk. This review will examine the factors that drive both health disparities and the accelerated aging phenotype that ultimately contributes to premature mortality.
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Affiliation(s)
- Nicole Noren Hooten
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Natasha L Pacheco
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Jessica T Smith
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA.
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13
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Bitounis D, Huang Q, Toprani SM, Setyawati MI, Oliveira N, Wu Z, Tay CY, Ng KW, Nagel ZD, Demokritou P. Printer center nanoparticles alter the DNA repair capacity of human bronchial airway epithelial cells. NANOIMPACT 2022; 25:100379. [PMID: 35559885 PMCID: PMC9661631 DOI: 10.1016/j.impact.2022.100379] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/08/2021] [Accepted: 01/05/2022] [Indexed: 05/26/2023]
Abstract
Nano-enabled, toner-based printing equipment emit nanoparticles during operation. The bioactivity of these nanoparticles as documented in a plethora of published toxicological studies raises concerns about their potential health effects. These include pro-inflammatory effects that can lead to adverse epigenetic alterations and cardiovascular disorders in rats. At the same time, their potential to alter DNA repair pathways at realistic doses remains unclear. In this study, size-fractionated, airborne particles from a printer center in Singapore were sampled and characterized. The PM0.1 size fraction (particles with an aerodynamic diameter less than 100 nm) of printer center particles (PCP) were then administered to human lung adenocarcinoma (Calu-3) or lymphoblastoid (TK6) cells. We evaluated plasma membrane integrity, mitochondrial activity, and intracellular reactive oxygen species (ROS) generation. Moreover, we quantified DNA damage and alterations in the cells' capacity to repair 6 distinct types of DNA lesions. Results show that PCP altered the ability of Calu-3 cells to repair 8oxoG:C lesions and perform nucleotide excision repair, in the absence of acute cytotoxicity or DNA damage. Alterations in DNA repair capacity have been correlated with the risk of various diseases, including cancer, therefore further genotoxicity studies are needed to assess the potential risks of PCP exposure, at both occupational settings and at the end-consumer level.
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Affiliation(s)
- Dimitrios Bitounis
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA 02115, USA
| | - Qiansheng Huang
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA 02115, USA; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Sneh M Toprani
- John B. Little Center of Radiation Sciences, Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA 02115, USA
| | - Magdiel I Setyawati
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Nathalia Oliveira
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA 02115, USA
| | - Zhuoran Wu
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Chor Yong Tay
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; Environmental Chemistry and Materials Centre, Nanyang Environment and Water Research Institution, 1 Cleantech Loop, CleanTech One, Singapore 637141, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Kee Woei Ng
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA 02115, USA; School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; Environmental Chemistry and Materials Centre, Nanyang Environment and Water Research Institution, 1 Cleantech Loop, CleanTech One, Singapore 637141, Singapore
| | - Zachary D Nagel
- John B. Little Center of Radiation Sciences, Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA 02115, USA.
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave, Boston, MA 02115, USA.
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14
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Atkin ND, Raimer HM, Wang Z, Zang C, Wang YH. Assessing acute myeloid leukemia susceptibility in rearrangement-driven patients by DNA breakage at topoisomerase II and CCCTC-binding factor/cohesin binding sites. Genes Chromosomes Cancer 2021; 60:808-821. [PMID: 34405474 PMCID: PMC8511143 DOI: 10.1002/gcc.22993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 12/29/2022] Open
Abstract
An initiating DNA double strand break (DSB) event precedes the formation of cancer-driven chromosomal abnormalities, such as gene rearrangements. Therefore, measuring DNA breaks at rearrangement-participating regions can provide a unique tool to identify and characterize susceptible individuals. Here, we developed a highly sensitive and low-input DNA break mapping method, the first of its kind for patient samples. We then measured genome-wide DNA breakage in normal cells of acute myeloid leukemia (AML) patients with KMT2A (previously MLL) rearrangements, compared to that of nonfusion AML individuals, as a means to evaluate individual susceptibility to gene rearrangements. DNA breakage at the KMT2A gene region was significantly greater in fusion-driven remission individuals, as compared to nonfusion individuals. Moreover, we identified select topoisomerase II (TOP2)-sensitive and CCCTC-binding factor (CTCF)/cohesin-binding sites with preferential DNA breakage in fusion-driven patients. Importantly, measuring DSBs at these sites, in addition to the KMT2A gene region, provided greater predictive power when assessing individual break susceptibility. We also demonstrated that low-dose etoposide exposure further elevated DNA breakage at these regions in fusion-driven AML patients, but not in nonfusion patients, indicating that these sites are preferentially sensitive to TOP2 activity in fusion-driven AML patients. These results support that mapping of DSBs in patients enables discovery of novel break-prone regions and monitoring of individuals susceptible to chromosomal abnormalities, and thus cancer. This will build the foundation for early detection of cancer-susceptible individuals, as well as those preferentially susceptible to therapy-related malignancies caused by treatment with TOP2 poisons.
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MESH Headings
- Binding Sites/genetics
- CCCTC-Binding Factor/blood
- CCCTC-Binding Factor/genetics
- Cell Cycle Proteins/blood
- Cell Cycle Proteins/genetics
- Chondroitin Sulfate Proteoglycans/blood
- Chondroitin Sulfate Proteoglycans/genetics
- Chromosomal Proteins, Non-Histone/blood
- Chromosomal Proteins, Non-Histone/genetics
- Chromosome Aberrations
- DNA Breaks, Double-Stranded/drug effects
- DNA Repair/genetics
- DNA Topoisomerases, Type II/blood
- DNA Topoisomerases, Type II/genetics
- DNA-Binding Proteins/blood
- DNA-Binding Proteins/genetics
- Etoposide/pharmacology
- Female
- Gene Rearrangement/genetics
- Genome, Human/genetics
- HeLa Cells
- Histone-Lysine N-Methyltransferase/blood
- Histone-Lysine N-Methyltransferase/genetics
- Humans
- Leukemia, Myeloid, Acute/blood
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Male
- Myeloid-Lymphoid Leukemia Protein/blood
- Myeloid-Lymphoid Leukemia Protein/genetics
- Oncogene Proteins, Fusion/genetics
- Poly-ADP-Ribose Binding Proteins/blood
- Poly-ADP-Ribose Binding Proteins/genetics
- Cohesins
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Affiliation(s)
- Naomi D. Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, 22908-0733, USA
| | - Heather M. Raimer
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, 22908-0733, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, 22908-0733, USA
| | - Chongzhi Zang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, 22908-0733, USA
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, 22908-0733, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, 22908-0733, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, 22908-0733, USA
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15
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Moschetta-Pinheiro MG, Colombo J, de Souza Tuckumantel M, Rebolho GK, de Campos Zuccari DAP. Treatment of Triple Negative Cell Lines with Olaparib to Block DNA Repair. Anticancer Agents Med Chem 2021; 22:2036-2045. [PMID: 34629045 DOI: 10.2174/1871520621666211008104543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/29/2021] [Accepted: 07/12/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The most aggressive breast cancer is the triple negative histological type and the gold standard for its treatment is platinum salts, such as carboplatin. Due to high recurrence, there is a need to test new drugs, such as PARP inhibitors (PARPi) that induce lethality in cells with DNA damage. Olaparib is a PARPi, already used in some tumors, but not tested in canine species. Thus, the aim of this study was demonstrating the efficacy of olaparib in inhibiting DNA repair and controlling disease progression by decreasing the migration capacity of mammary tumor cells. METHODS The cell lines, CF41.Mg and MDA-MB-468, were cultured and was performed the MTT to define the best dose of carboplatin. Next, the cells were treated with 10 µM carboplatin, olaparib and with combination of both for 24 hours. PARP-1 protein and gene expression was evaluated by immunofluorescence, western blotting and qRT-PCR, respectively. The analysis of cell migration was performed in transwell chambers. RESULTS For CF41.Mg and MDA-MB-468 cell lines, there was decrease in PARP-1 protein and gene expression after treatment with carboplatin, olaparib and both in combination compared to the group without treatment (control) (p<0.05). Moreover, in both lines, reduction in invasion rate was observed after treatment with carboplatin, olaparib and when combined, compared to the control group (p<0.05). CONCLUSION Our data suggests that carboplatin and olaparib were able to block DNA repair and control the cancer invasion, especially when used in combination. The results with olaparib in the canine line are unpublished. The olaparib should be a possible agent against human breast cancer and canine mammary tumors.
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Affiliation(s)
- Marina Gobbe Moschetta-Pinheiro
- PostGraduate Program in Health Sciences, Faculdade de Medicina de São José do Rio Preto, FAMERP, Av. Brigadeiro Faria Lima, 5416, 15090-000 - São José do Rio Preto, SP. Brazil
| | - Jucimara Colombo
- Laboratório de Investigação Molecular no Câncer (LIMC), Faculdade de Medicina de São José do Rio Preto/FAMERP, Av. Brigadeiro Faria Lima, 5416, 15090-000 - São José do Rio Preto, SP. Brazil
| | - Murilo de Souza Tuckumantel
- Laboratório de Investigação Molecular no Câncer (LIMC), Faculdade de Medicina de São José do Rio Preto/FAMERP, Av. Brigadeiro Faria Lima, 5416, 15090-000 - São José do Rio Preto, SP. Brazil
| | - Gabriela Karam Rebolho
- Laboratório de Investigação Molecular no Câncer (LIMC), Faculdade de Medicina de São José do Rio Preto/FAMERP, Av. Brigadeiro Faria Lima, 5416, 15090-000 - São José do Rio Preto, SP. Brazil
| | - Debora Aparecida Pires de Campos Zuccari
- Laboratório de Investigação Molecular no Câncer (LIMC), Faculdade de Medicina de São José do Rio Preto/FAMERP, Av. Brigadeiro Faria Lima, 5416, 15090-000 - São José do Rio Preto, SP. Brazil
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16
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Ge J, Ngo LP, Kaushal S, Tay IJ, Thadhani E, Kay JE, Mazzucato P, Chow DN, Fessler JL, Weingeist DM, Sobol RW, Samson LD, Floyd SR, Engelward BP. CometChip enables parallel analysis of multiple DNA repair activities. DNA Repair (Amst) 2021; 106:103176. [PMID: 34365116 PMCID: PMC8439179 DOI: 10.1016/j.dnarep.2021.103176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/09/2021] [Accepted: 07/08/2021] [Indexed: 12/28/2022]
Abstract
DNA damage can be cytotoxic and mutagenic, and it is directly linked to aging, cancer, and other diseases. To counteract the deleterious effects of DNA damage, cells have evolved highly conserved DNA repair pathways. Many commonly used DNA repair assays are relatively low throughput and are limited to analysis of one protein or one pathway. Here, we have explored the capacity of the CometChip platform for parallel analysis of multiple DNA repair activities. Taking advantage of the versatility of the traditional comet assay and leveraging micropatterning techniques, the CometChip platform offers increased throughput and sensitivity compared to the traditional comet assay. By exposing cells to DNA damaging agents that create substrates of Base Excision Repair, Nucleotide Excision Repair, and Non-Homologous End Joining, we show that the CometChip is an effective method for assessing repair deficiencies in all three pathways. With these applications of the CometChip platform, we expand the utility of the comet assay for precise, high-throughput, parallel analysis of multiple DNA repair activities.
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Affiliation(s)
- Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Simran Kaushal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, United States
| | - Ian J Tay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Elina Thadhani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jennifer E Kay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Patrizia Mazzucato
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Danielle N Chow
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jessica L Fessler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - David M Weingeist
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Robert W Sobol
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, United States; University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, United States
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Scott R Floyd
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27514, United States
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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17
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Li Y, Mao P, Basenko EY, Lewis Z, Smerdon MJ, Czaja W. Versatile cell-based assay for measuring DNA alkylation damage and its repair. Sci Rep 2021; 11:18393. [PMID: 34526526 PMCID: PMC8443546 DOI: 10.1038/s41598-021-97523-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
DNA alkylation damage induced by environmental carcinogens, chemotherapy drugs, or endogenous metabolites plays a central role in mutagenesis, carcinogenesis, and cancer therapy. Base excision repair (BER) is a conserved, front line DNA repair pathway that removes alkylation damage from DNA. The capacity of BER to repair DNA alkylation varies markedly between different cell types and tissues, which correlates with cancer risk and cellular responses to alkylation chemotherapy. The ability to measure cellular rates of alkylation damage repair by the BER pathway is critically important for better understanding of the fundamental processes involved in carcinogenesis, and also to advance development of new therapeutic strategies. Methods for assessing the rates of alkylation damage and repair, especially in human cells, are limited, prone to significant variability due to the unstable nature of some of the alkyl adducts, and often rely on indirect measurements of BER activity. Here, we report a highly reproducible and quantitative, cell-based assay, named alk-BER (alkylation Base Excision Repair) for measuring rates of BER following alkylation DNA damage. The alk-BER assay involves specific detection of methyl DNA adducts (7-methyl guanine and 3-methyl adenine) directly in genomic DNA. The assay has been developed and adapted to measure the activity of BER in fungal model systems and human cell lines. Considering the specificity and conserved nature of BER enzymes, the assay can be adapted to virtually any type of cultured cells. Alk-BER offers a cost efficient and reliable method that can effectively complement existing approaches to advance integrative research on mechanisms of alkylation DNA damage and repair.
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Affiliation(s)
- Yong Li
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55905, USA.,The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Peng Mao
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA.,Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Evelina Y Basenko
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.,Department of Biochemistry and Systems Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Zachary Lewis
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.,Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.,Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Michael J Smerdon
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Wioletta Czaja
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA. .,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA. .,The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.
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18
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Tatin X, Muggiolu G, Sauvaigo S, Breton J. Evaluation of DNA double-strand break repair capacity in human cells: Critical overview of current functional methods. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108388. [PMID: 34893153 DOI: 10.1016/j.mrrev.2021.108388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 02/05/2023]
Abstract
DNA double-strand breaks (DSBs) are highly deleterious lesions, responsible for mutagenesis, chromosomal translocation or cell death. DSB repair (DSBR) is therefore a critical part of the DNA damage response (DDR) to restore molecular and genomic integrity. In humans, this process is achieved through different pathways with various outcomes. The balance between DSB repair activities varies depending on cell types, tissues or individuals. Over the years, several methods have been developed to study variations in DSBR capacity. Here, we mainly focus on functional techniques, which provide dynamic information regarding global DSB repair proficiency or the activity of specific pathways. These methods rely on two kinds of approaches. Indirect techniques, such as pulse field gel electrophoresis (PFGE), the comet assay and immunofluorescence (IF), measure DSB repair capacity by quantifying the time-dependent decrease in DSB levels after exposure to a DNA-damaging agent. On the other hand, cell-free assays and reporter-based methods directly track the repair of an artificial DNA substrate. Each approach has intrinsic advantages and limitations and despite considerable efforts, there is currently no ideal method to quantify DSBR capacity. All techniques provide different information and can be regarded as complementary, but some studies report conflicting results. Parameters such as the type of biological material, the required equipment or the cost of analysis may also limit available options. Improving currently available methods measuring DSBR capacity would be a major step forward and we present direct applications in mechanistic studies, drug development, human biomonitoring and personalized medicine, where DSBR analysis may improve the identification of patients eligible for chemo- and radiotherapy.
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Affiliation(s)
- Xavier Tatin
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France; LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | | | - Sylvie Sauvaigo
- LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | - Jean Breton
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France.
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19
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Toprani SM, Bitounis D, Qiansheng H, Oliveira N, Ng KW, Tay CY, Nagel ZD, Demokritou P. High-Throughput Screening Platform for Nanoparticle-Mediated Alterations of DNA Repair Capacity. ACS NANO 2021; 15:4728-4746. [PMID: 33710878 PMCID: PMC8111687 DOI: 10.1021/acsnano.0c09254] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The potential genotoxic effects of engineered nanomaterials (ENMs) may occur through the induction of DNA damage or the disruption of DNA repair processes. Inefficient DNA repair may lead to the accumulation of DNA lesions and has been linked to various diseases, including cancer. Most studies so far have focused on understanding the nanogenotoxicity of ENM-induced damages to DNA, whereas the effects on DNA repair have been widely overlooked. The recently developed fluorescence multiplex-host-cell reactivation (FM-HCR) assay allows for the direct quantification of multiple DNA repair pathways in living cells and offers a great opportunity to address this methodological gap. Herein an FM-HCR-based method is developed to screen the impact of ENMs on six major DNA repair pathways using suspended or adherent cells. The sensitivity and efficiency of this DNA repair screening method were demonstrated in case studies using primary human small airway epithelial cells and TK6 cells exposed to various model ENMs (CuO, ZnO, and Ga2O3) at subcytotoxic doses. It was shown that ENMs may inhibit nucleotide-excision repair, base-excision repair, and the repair of oxidative damage by DNA glycosylases in TK6 cells, even in the absence of significant genomic DNA damage. It is of note that the DNA repair capacity was increased by some ENMs, whereas it was suppressed by others. Overall, this method can be part of a multitier, in vitro hazard assessment of ENMs as a functional, high-throughput platform that provides insights into the interplay of the properties of ENMs, the DNA repair efficiency, and the genomic stability.
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Affiliation(s)
- Sneh M Toprani
- John B Little Center of Radiation Sciences, Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Dimitrios Bitounis
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
| | - Huang Qiansheng
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Nathalia Oliveira
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
| | - Kee Woei Ng
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Environmental Chemistry and Materials Centre, Nanyang Environment and Water Research Institution, 1 Cleantech Loop, CleanTech One, Singapore 637141, Singapore
| | - Chor Yong Tay
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Zachary D Nagel
- John B Little Center of Radiation Sciences, Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
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20
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Shelke S, Das B. Radio-adaptive response and correlation of non-homologous end joining repair gene polymorphisms [XRRC5 (3R/2R/1R/0R), XRCC6(C/G) and XRCC7 (G/T)] in human peripheral blood mononuclear cells exposed to gamma radiation. Genes Environ 2021; 43:9. [PMID: 33685509 PMCID: PMC7938547 DOI: 10.1186/s41021-021-00176-4] [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: 09/13/2020] [Accepted: 02/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Radio-adaptive response (RAR) is transient phenomena, where cells conditioned with a small dose (priming) of ionizing radiation shows significantly reduced DNA damage with a subsequent high challenging dose. The role of DNA double strand break repair gene polymorphism in RAR is not known. In the present study attempt was made to find out the influence of NHEJ repair gene polymorphisms [a VNTR; XRCC5 (3R/2R/1R/0R); two single nucleotide polymorphisms (SNPs); XRCC6 (C/G) and XRCC7 (G/T)] with DNA damage, repair and mRNA expression in human PBMCs in dose and adaptive response studies. Genomic DNA extracted from venous blood samples of 20 random healthy donors (16 adaptive and 4 non-adaptive) and genotyping of NHEJ repair genes was carried out using PCR amplified length polymorphism. RESULTS The dose response study revealed significant positive correlation of genotypes at XRRC5 (3R/2R/1R/0R), XRCC6(C/G) and XRCC7 (G/T) with DNA damage. Donors having genotypes with 2R allele at XRCC5 showed significant positive correlation with mRNA expression level (0R/2R: r = 0.846, P = 0.034; 1R/2R: r = 0.698, P = 0.0001 and 2R/2R: r = 0.831, P = 0.0001) for dose response. Genotypes C/C and C/G of XRCC6 showed a significant positive correlation (P = 0.0001), whereas, genotype T/T of XRCC7 showed significant negative correlation (r = - 0.376, P = 0.041) with mRNA expression. CONCLUSION Interestingly, adaptive donors having C/G genotype of XRCC6 showed significantly higher (P < 0.05) mRNA expression level in primed cells suggesting their role in RAR. In addition, NHEJ repair gene polymorphisms play crucial role with radio-sensitivity and RAR in human PBMCs.
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Affiliation(s)
- Shridevi Shelke
- Low Level Radiation Research Section, Radiation Biology & Health Sciences Division, Bio-Sciences Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - Birajalaxmi Das
- Low Level Radiation Research Section, Radiation Biology & Health Sciences Division, Bio-Sciences Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India.
- Homi Bhabha National Institute (HBNI), Anushaktinagar, Mumbai, 400094, India.
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21
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The Interactions of DNA Repair, Telomere Homeostasis, and p53 Mutational Status in Solid Cancers: Risk, Prognosis, and Prediction. Cancers (Basel) 2021; 13:cancers13030479. [PMID: 33513745 PMCID: PMC7865496 DOI: 10.3390/cancers13030479] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 12/12/2022] Open
Abstract
The disruption of genomic integrity due to the accumulation of various kinds of DNA damage, deficient DNA repair capacity, and telomere shortening constitute the hallmarks of malignant diseases. DNA damage response (DDR) is a signaling network to process DNA damage with importance for both cancer development and chemotherapy outcome. DDR represents the complex events that detect DNA lesions and activate signaling networks (cell cycle checkpoint induction, DNA repair, and induction of cell death). TP53, the guardian of the genome, governs the cell response, resulting in cell cycle arrest, DNA damage repair, apoptosis, and senescence. The mutational status of TP53 has an impact on DDR, and somatic mutations in this gene represent one of the critical events in human carcinogenesis. Telomere dysfunction in cells that lack p53-mediated surveillance of genomic integrity along with the involvement of DNA repair in telomeric DNA regions leads to genomic instability. While the role of individual players (DDR, telomere homeostasis, and TP53) in human cancers has attracted attention for some time, there is insufficient understanding of the interactions between these pathways. Since solid cancer is a complex and multifactorial disease with considerable inter- and intra-tumor heterogeneity, we mainly dedicated this review to the interactions of DNA repair, telomere homeostasis, and TP53 mutational status, in relation to (a) cancer risk, (b) cancer progression, and (c) cancer therapy.
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22
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Nouws J, Wan F, Finnemore E, Roque W, Kim SJ, Bazan I, Li CX, Skold CM, Dai Q, Yan X, Chioccioli M, Neumeister V, Britto CJ, Sweasy J, Bindra R, Wheelock ÅM, Gomez JL, Kaminski N, Lee PJ, Sauler M. MicroRNA miR-24-3p reduces DNA damage responses, apoptosis, and susceptibility to chronic obstructive pulmonary disease. JCI Insight 2021; 6:134218. [PMID: 33290275 PMCID: PMC7934877 DOI: 10.1172/jci.insight.134218] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/02/2020] [Indexed: 12/27/2022] Open
Abstract
The pathogenesis of chronic obstructive pulmonary disease (COPD) involves aberrant responses to cellular stress caused by chronic cigarette smoke (CS) exposure. However, not all smokers develop COPD and the critical mechanisms that regulate cellular stress responses to increase COPD susceptibility are not understood. Because microRNAs are well-known regulators of cellular stress responses, we evaluated microRNA expression arrays performed on distal parenchymal lung tissue samples from 172 subjects with and without COPD. We identified miR-24-3p as the microRNA that best correlated with radiographic emphysema and validated this finding in multiple cohorts. In a CS exposure mouse model, inhibition of miR-24-3p increased susceptibility to apoptosis, including alveolar type II epithelial cell apoptosis, and emphysema severity. In lung epithelial cells, miR-24-3p suppressed apoptosis through the BH3-only protein BIM and suppressed homology-directed DNA repair and the DNA repair protein BRCA1. Finally, we found BIM and BRCA1 were increased in COPD lung tissue, and BIM and BRCA1 expression inversely correlated with miR-24-3p. We concluded that miR-24-3p, a regulator of the cellular response to DNA damage, is decreased in COPD, and decreased miR-24-3p increases susceptibility to emphysema through increased BIM and apoptosis.
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Affiliation(s)
- Jessica Nouws
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Feng Wan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Anatomy, Beijing University of Chinese Medicine, Beijing, China
| | - Eric Finnemore
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Willy Roque
- Department of Internal Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - So-Jin Kim
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Isabel Bazan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Chuan-Xing Li
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - C Magnus Skold
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Qile Dai
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Xiting Yan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Maurizio Chioccioli
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Veronique Neumeister
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Clemente J Britto
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joann Sweasy
- Department of Radiation Oncology, University of Arizona College of Medicine, Tucson, Arizona, USA.,Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ranjit Bindra
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Åsa M Wheelock
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jose L Gomez
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Patty J Lee
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Section of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Maor Sauler
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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23
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Toprani SM, Scheibler C, Nagel ZD. Interplay Between Air Travel, Genome Integrity, and COVID-19 Risk vis-a-vis Flight Crew. Front Public Health 2020; 8:590412. [PMID: 33392133 PMCID: PMC7775589 DOI: 10.3389/fpubh.2020.590412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/16/2020] [Indexed: 01/04/2023] Open
Abstract
During air travel, flight crew (flight attendants, pilots) can be exposed to numerous flight-related environmental DNA damaging agents that may be at the root of an excess risk of cancer and other diseases. This already complex mix of exposures is now joined by SARS-CoV-2, the virus that causes COVID-19. The complex exposures experienced during air travel present a challenge to public health research, but also provide an opportunity to consider new strategies for understanding and countering their health effects. In this article, we focus on threats to genomic integrity that occur during air travel and discuss how these threats and our ability to respond to them may influence the risk of SARS-CoV-2 infection and the development of range of severity of the symptoms. We also discuss how the virus itself may lead to compromised genome integrity. We argue that dauntingly complex public health problems, such as the challenge of protecting flight crews from COVID-19, must be met with interdisciplinary research teams that include epidemiologists, engineers, and mechanistic biologists.
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Affiliation(s)
- Sneh M. Toprani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Christopher Scheibler
- Environmental and Occupational Medicine and Epidemiology Program, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Zachary D. Nagel
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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24
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Owiti NA, Nagel ZD, Engelward BP. Fluorescence Sheds Light on DNA Damage, DNA Repair, and Mutations. Trends Cancer 2020; 7:240-248. [PMID: 33203608 DOI: 10.1016/j.trecan.2020.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/09/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
DNA damage can lead to carcinogenic mutations and toxicity that promotes diseases. Therefore, having rapid assays to quantify DNA damage, DNA repair, mutations, and cytotoxicity is broadly relevant to health. For example, DNA damage assays can be used to screen chemicals for genotoxicity, and knowledge about DNA repair capacity has applications in precision prevention and in personalized medicine. Furthermore, knowledge of mutation frequency has predictive power for downstream cancer, and assays for cytotoxicity can predict deleterious health effects. Tests for all of these purposes have been rendered faster and more effective via adoption of fluorescent readouts. Here, we provide an overview of established and emerging cell-based assays that exploit fluorescence for studies of DNA damage and its consequences.
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Affiliation(s)
- Norah A Owiti
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zachary D Nagel
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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25
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Non-muscle invasive bladder cancer tissues have increased base excision repair capacity. Sci Rep 2020; 10:16371. [PMID: 33004944 PMCID: PMC7529820 DOI: 10.1038/s41598-020-73370-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 09/15/2020] [Indexed: 12/26/2022] Open
Abstract
The molecular mechanisms underlying the development and progression of bladder cancer (BC) are complex and have not been fully elucidated. Alterations in base excision repair (BER) capacity, one of several DNA repair mechanisms assigned to preserving genome integrity, have been reported to influence cancer susceptibility, recurrence, and progression, as well as responses to chemotherapy and radiotherapy. We report herein that non-muscle invasive BC (NMIBC) tissues exhibit increased uracil incision, abasic endonuclease and gap-filling activities, as well as total BER capacity in comparison to normal bladder tissue from the same patient (p < 0.05). No significant difference was detected in 8-oxoG incision activity between cancer and normal tissues. NMIBC tissues have elevated protein levels of uracil DNA glycosylase, 8-oxoguanine DNA glycosylase, AP endonuclease 1 and DNA polymerase β protein. Moreover, the fold increase in total BER and the individual BER enzyme activities were greater in high-grade tissues than in low-grade NMIBC tissues. These findings suggest that enhanced BER activity may play a role in the etiology of NMIBC and that BER proteins could serve as biomarkers in disease prognosis, progression or response to genotoxic therapeutics, such as Bacillus Calmette–Guérin.
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26
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Li W, Sancar A. Methodologies for detecting environmentally induced DNA damage and repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:664-679. [PMID: 32083352 PMCID: PMC7442611 DOI: 10.1002/em.22365] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/08/2020] [Accepted: 02/16/2020] [Indexed: 05/07/2023]
Abstract
Environmental DNA damaging agents continuously challenge the integrity of the genome by introducing a variety of DNA lesions. The DNA damage caused by environmental factors will lead to mutagenesis and subsequent carcinogenesis if they are not removed efficiently by repair pathways. Methods for detection of DNA damage and repair can be applied to identify, visualize, and quantify the DNA damage formation and repair events, and they enable us to illustrate the molecular mechanisms of DNA damage formation, DNA repair pathways, mutagenesis, and carcinogenesis. Ever since the discovery of the double helical structure of DNA in 1953, a great number of methods have been developed to detect various types of DNA damage and repair. Rapid advances in sequencing technologies have facilitated the emergence of a variety of novel methods for detecting environmentally induced DNA damage and repair at the genome-wide scale during the last decade. In this review, we provide a historical overview of the development of various damage detection methods. We also highlight the current methodologies to detect DNA damage and repair, especially some next generation sequencing-based methods.
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Affiliation(s)
- Wentao Li
- Correspondence to: Wentao Li and Aziz Sancar, Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599. and
| | - Aziz Sancar
- Correspondence to: Wentao Li and Aziz Sancar, Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599. and
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27
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DNA Repair and Ovarian Carcinogenesis: Impact on Risk, Prognosis and Therapy Outcome. Cancers (Basel) 2020; 12:cancers12071713. [PMID: 32605254 PMCID: PMC7408288 DOI: 10.3390/cancers12071713] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
There is ample evidence for the essential involvement of DNA repair and DNA damage response in the onset of solid malignancies, including ovarian cancer. Indeed, high-penetrance germline mutations in DNA repair genes are important players in familial cancers: BRCA1, BRCA2 mutations or mismatch repair, and polymerase deficiency in colorectal, breast, and ovarian cancers. Recently, some molecular hallmarks (e.g., TP53, KRAS, BRAF, RAD51C/D or PTEN mutations) of ovarian carcinomas were identified. The manuscript overviews the role of DNA repair machinery in ovarian cancer, its risk, prognosis, and therapy outcome. We have attempted to expose molecular hallmarks of ovarian cancer with a focus on DNA repair system and scrutinized genetic, epigenetic, functional, and protein alterations in individual DNA repair pathways (homologous recombination, non-homologous end-joining, DNA mismatch repair, base- and nucleotide-excision repair, and direct repair). We suggest that lack of knowledge particularly in non-homologous end joining repair pathway and the interplay between DNA repair pathways needs to be confronted. The most important genes of the DNA repair system are emphasized and their targeting in ovarian cancer will deserve further attention. The function of those genes, as well as the functional status of the entire DNA repair pathways, should be investigated in detail in the near future.
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28
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Ghanshela R, Banerjee BD, Siddarth M, Gupta S. DNA repair gene polymorphism (XPA and XPG) and risk of urinary bladder cancer in North-Indian population. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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29
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Ngo LP, Owiti NA, Swartz C, Winters J, Su Y, Ge J, Xiong A, Han J, Recio L, Samson LD, Engelward B. Sensitive CometChip assay for screening potentially carcinogenic DNA adducts by trapping DNA repair intermediates. Nucleic Acids Res 2020; 48:e13. [PMID: 31822921 PMCID: PMC7026589 DOI: 10.1093/nar/gkz1077] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 10/08/2019] [Accepted: 11/19/2019] [Indexed: 12/27/2022] Open
Abstract
Genotoxicity testing is critical for predicting adverse effects of pharmaceutical, industrial, and environmental chemicals. The alkaline comet assay is an established method for detecting DNA strand breaks, however, the assay does not detect potentially carcinogenic bulky adducts that can arise when metabolic enzymes convert pro-carcinogens into a highly DNA reactive products. To overcome this, we use DNA synthesis inhibitors (hydroxyurea and 1-β-d-arabinofuranosyl cytosine) to trap single strand breaks that are formed during nucleotide excision repair, which primarily removes bulky lesions. In this way, comet-undetectable bulky lesions are converted into comet-detectable single strand breaks. Moreover, we use HepaRG™ cells to recapitulate in vivo metabolic capacity, and leverage the CometChip platform (a higher throughput more sensitive comet assay) to create the 'HepaCometChip', enabling the detection of bulky genotoxic lesions that are missed by current genotoxicity screens. The HepaCometChip thus provides a broadly effective approach for detection of bulky DNA adducts.
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Affiliation(s)
- Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Norah A Owiti
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carol Swartz
- Toxicology Program, Integrated Laboratory Systems, Inc., Research Triangle Park, NC 27560, USA
| | - John Winters
- Toxicology Program, Integrated Laboratory Systems, Inc., Research Triangle Park, NC 27560, USA
| | - Yang Su
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aoli Xiong
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
| | - Jongyoon Han
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
- Department of Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leslie Recio
- Toxicology Program, Integrated Laboratory Systems, Inc., Research Triangle Park, NC 27560, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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30
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Finding relationships among biological entities. LOGIC AND CRITICAL THINKING IN THE BIOMEDICAL SCIENCES 2020. [PMCID: PMC7499094 DOI: 10.1016/b978-0-12-821364-3.00005-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Confusion over the concepts of “relationships” and “similarities” lies at the heart of many battles over the direction and intent of research projects. Here is a short story that demonstrates the difference between the two concepts: You look up at the clouds, and you begin to see the shape of a lion. The cloud has a tail, like a lion’s tale, and a fluffy head, like a lion’s mane. With a little imagination the mouth of the lion seems to roar down from the sky. You have succeeded in finding similarities between the cloud and a lion. If you look at a cloud and you imagine a tea kettle producing a head of steam and you recognize that the physical forces that create a cloud and the physical forces that produced steam from a heated kettle are the same, then you have found a relationship. Most popular classification algorithms operate by grouping together data objects that have similar properties or values. In so doing, they may miss finding the true relationships among objects. Traditionally, relationships among data objects are discovered by an intellectual process. In this chapter, we will discuss the scientific gains that come when we classify biological entities by relationships, not by their similarities.
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31
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Choi JH, Han S, Kemp MG. Detection of the small oligonucleotide products of nucleotide excision repair in UVB-irradiated human skin. DNA Repair (Amst) 2019; 86:102766. [PMID: 31838380 DOI: 10.1016/j.dnarep.2019.102766] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/26/2019] [Accepted: 12/04/2019] [Indexed: 11/29/2022]
Abstract
UVB radiation results in the formation of potentially mutagenic photoproducts in the DNA of epidermal skin cells. In vitro approaches have demonstrated that the nucleotide excision repair (NER) machinery removes UV photoproducts from DNA in the form of small (∼30-nt-long), excised, damage-containing DNA oligonucleotides (sedDNAs). Though this process presumably takes place in human skin exposed to UVB radiation, sedDNAs have not previously been detected in human skin. Using surgically discarded human skin, we have optimized the detection of the sedDNA products of NER from small amounts of human epidermal tissue ex vivo within minutes of UVB exposure and after UVB doses that normally lead to minimal erythema. Moreover, sedDNA generation was inhibited by treatment of skin explants with spironolactone, which depletes the epidermis of the essential NER protein XPB to mimic the skin of xeroderma pigmentosum patients. Time course experiments revealed that a partially degraded form of the sedDNAs could be readily detected even 12 hours following UVB exposure, which indicates that these repair products are relatively stable in human skin epidermis. Together, these data suggest that sedDNA detection may be a useful assay for determining how genetic, environmental, and other factors influence NER activity in human skin epidermis and whether abnormal sedDNA processing contributes to photosensitive skin disorders.
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Affiliation(s)
- Jun-Hyuk Choi
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Republic of Korea; Department of Bio-Analytical Science, University of Science & Technology, Republic of Korea
| | - Sueji Han
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Republic of Korea; Department of Bio-Analytical Science, University of Science & Technology, Republic of Korea
| | - Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, OH 45435, United States.
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32
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Healing E, Charlier CF, Meira LB, Elliott RM. A panel of colorimetric assays to measure enzymatic activity in the base excision DNA repair pathway. Nucleic Acids Res 2019; 47:e61. [PMID: 30869144 PMCID: PMC6582407 DOI: 10.1093/nar/gkz171] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/13/2019] [Accepted: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
DNA repair is essential for the maintenance of genomic integrity, and evidence suggest that inter-individual variation in DNA repair efficiency may contribute to disease risk. However, robust assays suitable for quantitative determination of DNA repair capacity in large cohort and clinical trials are needed to evaluate these apparent associations fully. We describe here a set of microplate-based oligonucleotide assays for high-throughput, non-radioactive and quantitative determination of repair enzyme activity at individual steps and over multiple steps of the DNA base excision repair pathway. The assays are highly sensitive: using HepG2 nuclear extract, enzyme activities were quantifiable at concentrations of 0.0002 to 0.181 μg per reaction, depending on the enzyme being measured. Assay coefficients of variation are comparable with other microplate-based assays. The assay format requires no specialist equipment and has the potential to be extended for analysis of a wide range of DNA repair enzyme activities. As such, these assays hold considerable promise for gaining new mechanistic insights into how DNA repair is related to individual genetics, disease status or progression and other environmental factors and investigating whether DNA repair activities can be used a biomarker of disease risk.
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Affiliation(s)
- Eleanor Healing
- Department of Nutritional Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - Clara F Charlier
- Department of Clinical and Experimental Medicine, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - Lisiane B Meira
- Department of Clinical and Experimental Medicine, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - Ruan M Elliott
- Department of Nutritional Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
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33
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Vodicka P, Vodenkova S, Buchler T, Vodickova L. DNA repair capacity and response to treatment of colon cancer. Pharmacogenomics 2019; 20:1225-1233. [PMID: 31691643 DOI: 10.2217/pgs-2019-0070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
DNA repair, a complex biological process, ensures genomic integrity. Alterations in DNA repair, occurring in many cancers, contribute to the accumulation of mutations in the genome, resulting in genomic instability and cancer progression. DNA repair also plays a substantial role in response to chemotherapeutics: rapidly dividing colon cancer cells, vulnerable to DNA-damaging agents and overcoming DNA repair, undergo cell death. DNA repair capacity represents a complex biomarker, integrating gene variants, gene expressions, the stability of gene products, the effect of inhibitors/stimulators, lifestyle and environmental factors. Here, we discuss DNA repair capacity in sporadic colon cancer, a frequent malignancy worldwide, in relation to tumor heterogeneity, prognosis and prediction, measurements in surrogate and target tissues and suggest important tasks to be addressed.
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Affiliation(s)
- Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology & Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Laboratory of Cancer Treatment and Tissue Regeneration, Faculty of Medicine & Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology & Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruska 2411/87, 100 00 Prague, Czech Republic
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University & Thomayer Hospital, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, The Czech Academy of Sciences, Prague, Czech Republic.,Institute of Biology & Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Laboratory of Cancer Treatment and Tissue Regeneration, Faculty of Medicine & Biomedical Center in Pilsen, Charles University, Pilsen, Czech Republic
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DNA damage and repair measured by comet assay in cancer patients. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2019; 843:95-110. [DOI: 10.1016/j.mrgentox.2019.05.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 05/14/2019] [Accepted: 05/18/2019] [Indexed: 02/08/2023]
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Odongo GA, Skatchkov I, Herz C, Lamy E. Optimization of the alkaline comet assay for easy repair capacity quantification of oxidative DNA damage in PBMC from human volunteers using aphidicolin block. DNA Repair (Amst) 2019; 77:58-64. [DOI: 10.1016/j.dnarep.2019.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/18/2019] [Indexed: 01/13/2023]
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36
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Obesity, DNA Damage, and Development of Obesity-Related Diseases. Int J Mol Sci 2019; 20:ijms20051146. [PMID: 30845725 PMCID: PMC6429223 DOI: 10.3390/ijms20051146] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/28/2019] [Accepted: 03/02/2019] [Indexed: 12/13/2022] Open
Abstract
Obesity has been recognized to increase the risk of such diseases as cardiovascular diseases, diabetes, and cancer. It indicates that obesity can impact genome stability. Oxidative stress and inflammation, commonly occurring in obesity, can induce DNA damage and inhibit DNA repair mechanisms. Accumulation of DNA damage can lead to an enhanced mutation rate and can alter gene expression resulting in disturbances in cell metabolism. Obesity-associated DNA damage can promote cancer growth by favoring cancer cell proliferation and migration, and resistance to apoptosis. Estimation of the DNA damage and/or disturbances in DNA repair could be potentially useful in the risk assessment and prevention of obesity-associated metabolic disorders as well as cancers. DNA damage in people with obesity appears to be reversible and both weight loss and improvement of dietary habits and diet composition can affect genome stability.
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Cabezas M, García-Quevedo L, Alonso C, Manubens M, Álvarez Y, Barquinero JF, Ramón Y Cajal S, Ortega M, Blanco A, Caballín MR, Armengol G. Polymorphisms in MDM2 and TP53 Genes and Risk of Developing Therapy-Related Myeloid Neoplasms. Sci Rep 2019; 9:150. [PMID: 30655613 PMCID: PMC6336808 DOI: 10.1038/s41598-018-36931-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 11/22/2018] [Indexed: 12/28/2022] Open
Abstract
One of the most severe complications after successful cancer therapy is the development of therapy-related myeloid neoplasms (t-MN). Constitutional genetic variation is likely to impact on t-MN risk. We aimed to evaluate if polymorphisms in the p53 pathway can be useful for predicting t-MN susceptibility. First, an association study revealed that the Pro variant of the TP53 Arg72Pro polymorphism and the G allele of the MDM2 SNP309 were associated with t-MN risk. The Arg variant of TP53 is more efficient at inducing apoptosis, whereas the Pro variant is a more potent inductor of cell cycle arrest and DNA repair. As regards MDM2 SNP309, the G allele is associated with attenuation of the p53 apoptotic response. Second, to evaluate the biological effect of the TP53 polymorphism, we established Jurkat isogenic cell lines expressing p53Arg or p53Pro. Jurkat p53Arg cells presented higher DNA damage and higher apoptotic potential than p53Pro cells, after treatment with chemotherapy agents. Only p53Pro cells presented t(15;17) translocation and del(5q). We suggest that failure to repair DNA lesions in p53Arg cells would lead them to apoptosis, whereas some p53Pro cells, prone to cell cycle arrest and DNA repair, could undergo misrepair, generating chromosomal abnormalities typical of t-MN.
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Affiliation(s)
- Maria Cabezas
- Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Lydia García-Quevedo
- Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Cintia Alonso
- Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Marta Manubens
- Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Yolanda Álvarez
- Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Joan Francesc Barquinero
- Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Santiago Ramón Y Cajal
- Department of Pathology, Vall d'Hebron University Hospital, 08035, Barcelona, Catalonia, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Catalonia, Spain
| | - Margarita Ortega
- Department of Hematology, Vall d'Hebron University Hospital, 08035, Barcelona, Catalonia, Spain
| | - Adoración Blanco
- Department of Hematology, Vall d'Hebron University Hospital, 08035, Barcelona, Catalonia, Spain
| | - María Rosa Caballín
- Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Gemma Armengol
- Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain.
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Moore S, Berger ND, Luijsterburg MS, Piett CG, Stanley FKT, Schräder CU, Fang S, Chan JA, Schriemer DC, Nagel ZD, van Attikum H, Goodarzi AA. The CHD6 chromatin remodeler is an oxidative DNA damage response factor. Nat Commun 2019; 10:241. [PMID: 30651562 PMCID: PMC6335469 DOI: 10.1038/s41467-018-08111-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 12/14/2018] [Indexed: 02/07/2023] Open
Abstract
Cell survival after oxidative DNA damage requires signaling, repair and transcriptional events often enabled by nucleosome displacement, exchange or removal by chromatin remodeling enzymes. Here, we show that Chromodomain Helicase DNA-binding protein 6 (CHD6), distinct to other CHD enzymes, is stabilized during oxidative stress via reduced degradation. CHD6 relocates rapidly to DNA damage in a manner dependent upon oxidative lesions and a conserved N-terminal poly(ADP-ribose)-dependent recruitment motif, with later retention requiring the double chromodomain and central core. CHD6 ablation increases reactive oxygen species persistence and impairs anti-oxidant transcriptional responses, leading to elevated DNA breakage and poly(ADP-ribose) induction that cannot be rescued by catalytic or double chromodomain mutants. Despite no overt epigenetic or DNA repair abnormalities, CHD6 loss leads to impaired cell survival after chronic oxidative stress, abnormal chromatin relaxation, amplified DNA damage signaling and checkpoint hypersensitivity. We suggest that CHD6 is a key regulator of the oxidative DNA damage response. Oxidative DNA damage is associated with nucleosome respacing and transcriptional changes requiring chromatin remodeling enzymes. Here, the authors reveal that the CHD6 remodeler is a DNA damage response factor that relocates to damaged sites and promotes cell survival following oxidative damage.
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Affiliation(s)
- Shaun Moore
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - N Daniel Berger
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Cortt G Piett
- Harvard University, School of Public Health, Boston, MA, 02115, USA
| | - Fintan K T Stanley
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Christoph U Schräder
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Shujuan Fang
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Jennifer A Chan
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - David C Schriemer
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Zachary D Nagel
- Harvard University, School of Public Health, Boston, MA, 02115, USA
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Aaron A Goodarzi
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and/or Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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Vodenkova S, Jiraskova K, Urbanova M, Kroupa M, Slyskova J, Schneiderova M, Levy M, Buchler T, Liska V, Vodickova L, Vymetalkova V, Collins A, Opattova A, Vodicka P. Base excision repair capacity as a determinant of prognosis and therapy response in colon cancer patients. DNA Repair (Amst) 2018; 72:77-85. [PMID: 30314738 DOI: 10.1016/j.dnarep.2018.09.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/27/2018] [Accepted: 09/14/2018] [Indexed: 12/12/2022]
Abstract
The DNA-damaging agent 5-fluorouracil represents the most commonly used chemotherapeutic drug for colorectal cancer patients. DNA lesions associated with 5-fluorouracil therapy are primarily repaired by base excision repair (BER) and mismatch repair (MMR) pathways. Published evidence suggests that the individual DNA repair capacity (DRC) may affect a patient's prognosis and response to chemotherapy. With this in mind, we designed a prospective study of which the main aim was to investigate BER-DRC in relation to 5-fluorouracil response as potential predictive and/or prognostic biomarker. BER-DRC was supplemented by a microsatellite instability (MSI) analysis which represents an indirect marker of MMR activity in the tumor. All parameters were measured in paired samples of tumor tissue and non-malignant adjacent mucosa of 123 incident colon cancer patients. Our results indicate that BER-DRC in non-malignant adjacent mucosa was positively associated with overall survival (P = 0.007) and relapse-free survival (P = 0.04). Additionally, in multivariate analysis, good therapy responders in TNM stage II and III with an elevated BER-DRC in mucosa exhibited better overall survival. Moreover, the overall survival of these patients was even better in the presence of a decreased BER-DRC in tumor tissue. The ratio of BER-DRC in tumor tissue over BER-DRC in mucosa positively correlated with advanced tumor stage (P = 0.003). With respect to MSI, we observed that MSI-high tumors were mostly localized in proximal colon; however, in our cohort, the MSI status affected neither patients' prognosis nor survival. In summary, the results of the present study suggest that the level of BER-DRC is associated with patients' survival. BER-DRC represents a potential prognostic biomarker, applicable for prediction of therapy response and useful for individual approach to patients.
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Affiliation(s)
- Sona Vodenkova
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruska 2411/87, 100 00, Prague, Czech Republic; Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Katerina Jiraskova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Marketa Urbanova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00, Pilsen, Czech Republic
| | - Jana Slyskova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Michaela Schneiderova
- Department of Surgery, General University Hospital in Prague, U Nemocnice 499/2, 128 08, Prague, Czech Republic
| | - Miroslav Levy
- Department of Surgery, First Faculty of Medicine, Charles University and Thomayer Hospital, Thomayerova 815/5, 140 00, Prague, Czech Republic
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Videnska 800, 140 59, Prague, Czech Republic
| | - Vaclav Liska
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00, Pilsen, Czech Republic; Department of Surgery, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 80, 304 60, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00, Pilsen, Czech Republic
| | - Andrew Collins
- Department of Nutrition, Institute for Basic Medical Sciences, University of Oslo, Sognsvannsveien 9, 0372, Oslo, Norway
| | - Alena Opattova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00, Pilsen, Czech Republic
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic; Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00, Pilsen, Czech Republic.
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Parrish MC, Chaim IA, Nagel ZD, Tannenbaum SR, Samson LD, Engelward BP. Nitric oxide induced S-nitrosation causes base excision repair imbalance. DNA Repair (Amst) 2018; 68:25-33. [PMID: 29929044 DOI: 10.1016/j.dnarep.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/20/2018] [Accepted: 04/30/2018] [Indexed: 02/05/2023]
Abstract
It is well established that inflammation leads to the creation of potent DNA damaging chemicals, including reactive oxygen and nitrogen species. Nitric oxide can react with glutathione to create S-nitrosoglutathione (GSNO), which can in turn lead to S-nitrosated proteins. Of particular interest is the impact of GSNO on the function of DNA repair enzymes. The base excision repair (BER) pathway can be initiated by the alkyl-adenine DNA glycosylase (AAG), a monofunctional glycosylase that removes methylated bases. After base removal, an abasic site is formed, which then gets cleaved by AP endonuclease and processed by downstream BER enzymes. Interestingly, using the Fluorescence-based Multiplexed Host Cell Reactivation Assay (FM-HCR), we show that GSNO actually enhances AAG activity, which is consistent with the literature. This raised the possibility that there might be imbalanced BER when cells are challenged with a methylating agent. To further explore this possibility, we confirmed that GSNO can cause AP endonuclease to translocate from the nucleus to the cytoplasm, which might further exacerbate imbalanced BER by increasing the levels of AP sites. Analysis of abasic sites indeed shows GSNO induces an increase in the level of AP sites. Furthermore, analysis of DNA damage using the CometChip (a higher throughput version of the comet assay) shows an increase in the levels of BER intermediates. Finally, we found that GSNO exposure is associated with an increase in methylation-induced cytotoxicity. Taken together, these studies support a model wherein GSNO increases BER initiation while processing of AP sites is decreased, leading to a toxic increase in BER intermediates. This model is also supported by additional studies performed in our laboratory showing that inflammation in vivo leads to increased large-scale sequence rearrangements. Taken together, this work provides new evidence that inflammatory chemicals can drive cytotoxicity and mutagenesis via BER imbalance.
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Affiliation(s)
- Marcus C Parrish
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Zachary D Nagel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Steven R Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Combined effect of ERCC1 and ERCC2 polymorphisms on overall survival in non-squamous non-small-cell lung cancer patients treated with first-line pemetrexed/platinum. Lung Cancer 2018; 118:90-96. [PMID: 29572009 DOI: 10.1016/j.lungcan.2018.01.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 12/03/2017] [Accepted: 01/17/2018] [Indexed: 11/23/2022]
Abstract
OBJECTIVES Polymorphisms of DNA repair genes may affect DNA repair capacity and the sensitivity of platinum doublets chemotherapy in non-small-cell lung cancer (NSCLC). We prospectively evaluated whether single nucleotide polymorphisms (SNPs) of ERCC1, ERCC2, XRCC1, and XRCC3 were associated with treatment outcome in advanced non-squamous NSCLC patients receiving pemetrexed/platinum as their first-line chemotherapy. MATERIALS AND METHODS Genotyping of six SNPs in four DNA repair genes in 58 patients treated with first-line pemetrexed/platinum was performed using TaqMan SNP Genotyping Assays. RESULTS The wild-type ERCC1 8092 (C/C) was significantly associated with a better objective response compared to the variant genotypes (C/A + A/A) (48% vs 10%, P = .005). In the multivariate Cox proportional hazards model, we found that individuals with a wild-type genotype of ERCC1 Asn118Asn, ERCC1 C8092A and ERCC2 Asp312Asn had significantly better overall survival (OS) than those with a heterozygous or homozygous variant genotype. On the other hand, the heterozygous variant genotype of ERCC2 Lys751Gln was associated with better OS than that of the wild-type genotype. We further explored the combined effect of SNPs on OS, and found a significant allele/dose-dependent trend toward decreasing OS in patients with an increasing number of unfavorable alleles among four SNPs in ERCC1 and ERCC2. The median OS of patients with two or three unfavorable alleles (30.1 and 30.5 months, respectively) was significantly longer than that of patients with 4 unfavorable alleles (11.8 months, log-rank test for trend, P = .001). CONCLUSION A combination of ERCC1 and ERCC2 polymorphisms may predict OS among pemetrexed/platinum treated advanced non-squamous NSCLC patients.
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In vivo measurements of interindividual differences in DNA glycosylases and APE1 activities. Proc Natl Acad Sci U S A 2017; 114:E10379-E10388. [PMID: 29122935 DOI: 10.1073/pnas.1712032114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The integrity of our DNA is challenged with at least 100,000 lesions per cell on a daily basis. Failure to repair DNA damage efficiently can lead to cancer, immunodeficiency, and neurodegenerative disease. Base excision repair (BER) recognizes and repairs minimally helix-distorting DNA base lesions induced by both endogenous and exogenous DNA damaging agents. Levels of BER-initiating DNA glycosylases can vary between individuals, suggesting that quantitating and understanding interindividual differences in DNA repair capacity (DRC) may enable us to predict and prevent disease in a personalized manner. However, population studies of BER capacity have been limited because most methods used to measure BER activity are cumbersome, time consuming and, for the most part, only allow for the analysis of one DNA glycosylase at a time. We have developed a fluorescence-based multiplex flow-cytometric host cell reactivation assay wherein the activity of several enzymes [four BER-initiating DNA glycosylases and the downstream processing apurinic/apyrimidinic endonuclease 1 (APE1)] can be tested simultaneously, at single-cell resolution, in vivo. Taking advantage of the transcriptional properties of several DNA lesions, we have engineered specific fluorescent reporter plasmids for quantitative measurements of 8-oxoguanine DNA glycosylase, alkyl-adenine DNA glycosylase, MutY DNA glycosylase, uracil DNA glycosylase, and APE1 activity. We have used these reporters to measure differences in BER capacity across a panel of cell lines collected from healthy individuals, and to generate mathematical models that predict cellular sensitivity to methylmethane sulfonate, H2O2, and 5-FU from DRC. Moreover, we demonstrate the suitability of these reporters to measure differences in DRC in multiple pathways using primary lymphocytes from two individuals.
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Thakkar DN, Kodidela S, Sandhiya S, Dubashi B, Dkhar SA. A Polymorphism Located Near PMAIP1/Noxa Gene Influences Susceptibility to Hodgkin Lymphoma Development in South India. Asian Pac J Cancer Prev 2017; 18:2477-2483. [PMID: 28952280 PMCID: PMC5720654 DOI: 10.22034/apjcp.2017.18.9.2477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background: Single nucleotide polymorphisms (SNPs) in DNA repair and Toll-like receptor (TLR) genes have been reported to be associated with Hodgkin Lymphoma (HL) risk. Since such associations may be ethnicity dependent, polymorphisms in TLR4 rs1554973, Xeroderma pigmentosum C (XPC) rs2228000, rs2228001 and a variant near PMAIP1/Noxa gene rs8093763 were here investigated with regard to HL susceptibility in a south Indian population. Normative frequencies of SNPs were established and compared with data for 1000 genome populations. Methods: We conducted a case control study consisting of 200 healthy volunteers and 101 cases with HL. DNA samples were genotyped using real-time PCR. Linkage disequilibrium (LD) analysis between rs2228000 and rs2228001 was performed using HaploView (version 4.2). Results: Among the studied variants, we observed that a variant rs8093763 located near PMAIP1/Noxa gene was associated with HL risk (OR=1.72 and 95% CI=1.004-2.93). The major allele frequencies of XPC (rs2228000 and rs2228001), TLR4 (rs1554973) and PMAIP1/NOXA (rs8093763) variants were 79%, 66%, 67% and 59% respectively. The studied frequencies were significantly different from 1000 genome populations. Conclusion: The results suggest that a variant rs8093763 located near the PMAIP1/Noxa gene may modify risk of HL. We found variation in distribution of polymorphic frequencies between the study population and 1000 genome populations. The results may help identify individual risk of development of HL in our south Indian population.
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Affiliation(s)
- Dimpal N Thakkar
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Gorimedu, Puducherry, India.
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Towards precision prevention: Technologies for identifying healthy individuals with high risk of disease. Mutat Res 2017; 800-802:14-28. [PMID: 28458064 DOI: 10.1016/j.mrfmmm.2017.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/06/2017] [Indexed: 12/20/2022]
Abstract
The rise of advanced technologies for characterizing human populations at the molecular level, from sequence to function, is shifting disease prevention paradigms toward personalized strategies. Because minimization of adverse outcomes is a key driver for treatment decisions for diseased populations, developing personalized therapy strategies represent an important dimension of both precision medicine and personalized prevention. In this commentary, we highlight recently developed enabling technologies in the field of DNA damage, DNA repair, and mutagenesis. We propose that omics approaches and functional assays can be integrated into population studies that fuse basic, translational and clinical research with commercial expertise in order to accelerate personalized prevention and treatment of cancer and other diseases linked to aberrant responses to DNA damage. This collaborative approach is generally applicable to efforts to develop data-driven, individualized prevention and treatment strategies for other diseases. We also recommend strategies for maximizing the use of biological samples for epidemiological studies, and for applying emerging technologies to clinical applications.
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Lacoste S, Bhatia S, Chen Y, Bhatia R, O’Connor TR. Autologous hematopoietic stem cell transplantation in lymphoma patients is associated with a decrease in the double strand break repair capacity of peripheral blood lymphocytes. PLoS One 2017; 12:e0171473. [PMID: 28207808 PMCID: PMC5313139 DOI: 10.1371/journal.pone.0171473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/11/2017] [Indexed: 02/06/2023] Open
Abstract
Patients who undergo autologous hematopoietic stem cell transplantation (aHCT) for treatment of a relapsed or refractory lymphoma are at risk of developing therapy related- myelodysplasia/acute myeloid leukemia (t-MDS/AML). Part of the risk likely resides in inherent interindividual differences in their DNA repair capacity (DRC), which is thought to influence the effect chemotherapeutic treatments have on the patient's stem cells prior to aHCT. Measuring DRC involves identifying small differences in repair proficiency among individuals. Initially, we investigated the cell model in healthy individuals (primary lymphocytes and/or lymphoblastoid cell lines) that would be appropriate to measure genetically determined DRC using host-cell reactivation assays. We present evidence that interindividual differences in DRC double-strand break repair (by non-homologous end-joining [NHEJ] or single-strand annealing [SSA]) are better preserved in non-induced primary lymphocytes. In contrast, lymphocytes induced to proliferate are required to assay base excision (BER) or nucleotide excision repair (NER). We established that both NHEJ and SSA DRCs in lymphocytes of healthy individuals were inversely correlated with the age of the donor, indicating that DSB repair in lymphocytes is likely not a constant feature but rather something that decreases with age (~0.37% NHEJ DRC/year). To investigate the predictive value of pre-aHCT DRC on outcome in patients, we then applied the optimized assays to the analysis of primary lymphocytes from lymphoma patients and found that individuals who later developed t-MDS/AML (cases) were indistinguishable in their DRC from controls who never developed t-MDS/AML. However, when DRC was investigated shortly after aHCT in the same individuals (21.6 months later on average), aHCT patients (both cases and controls) showed a significant decrease in DSB repair measurements. The average decrease of 6.9% in NHEJ DRC observed among aHCT patients was much higher than the 0.65% predicted for such a short time frame, based on ageing results for healthy individuals.
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Affiliation(s)
- Sandrine Lacoste
- Department of Cancer Biology, Beckman Research Institute, Duarte, California, United States of America
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Yanjun Chen
- Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ravi Bhatia
- Division of Hematology and Oncology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy R. O’Connor
- Department of Cancer Biology, Beckman Research Institute, Duarte, California, United States of America
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Hall J, Jeggo PA, West C, Gomolka M, Quintens R, Badie C, Laurent O, Aerts A, Anastasov N, Azimzadeh O, Azizova T, Baatout S, Baselet B, Benotmane MA, Blanchardon E, Guéguen Y, Haghdoost S, Harms-Ringhdahl M, Hess J, Kreuzer M, Laurier D, Macaeva E, Manning G, Pernot E, Ravanat JL, Sabatier L, Tack K, Tapio S, Zitzelsberger H, Cardis E. Ionizing radiation biomarkers in epidemiological studies - An update. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2017; 771:59-84. [PMID: 28342453 DOI: 10.1016/j.mrrev.2017.01.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/09/2017] [Indexed: 01/13/2023]
Abstract
Recent epidemiology studies highlighted the detrimental health effects of exposure to low dose and low dose rate ionizing radiation (IR): nuclear industry workers studies have shown increased leukaemia and solid tumour risks following cumulative doses of <100mSv and dose rates of <10mGy per year; paediatric patients studies have reported increased leukaemia and brain tumours risks after doses of 30-60mGy from computed tomography scans. Questions arise, however, about the impact of even lower doses and dose rates where classical epidemiological studies have limited power but where subsets within the large cohorts are expected to have an increased risk. Further progress requires integration of biomarkers or bioassays of individual exposure, effects and susceptibility to IR. The European DoReMi (Low Dose Research towards Multidisciplinary Integration) consortium previously reviewed biomarkers for potential use in IR epidemiological studies. Given the increased mechanistic understanding of responses to low dose radiation the current review provides an update covering technical advances and recent studies. A key issue identified is deciding which biomarkers to progress. A roadmap is provided for biomarker development from discovery to implementation and used to summarise the current status of proposed biomarkers for epidemiological studies. Most potential biomarkers remain at the discovery stage and for some there is sufficient evidence that further development is not warranted. One biomarker identified in the final stages of development and as a priority for further research is radiation specific mRNA transcript profiles.
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Affiliation(s)
- Janet Hall
- Centre de Recherche en Cancérologie de Lyon, INSERM 1052, CNRS 5286, Univ Lyon, Université Claude Bernard, Lyon 1, Lyon, F-69424, France.
| | - Penny A Jeggo
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, United Kingdom
| | - Catharine West
- Translational Radiobiology Group, Institute of Cancer Sciences, The University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, M20 4BX, United Kingdom
| | - Maria Gomolka
- Federal Office for Radiation Protection, Department of Radiation Protection and Health, D-85764 Neuherberg, Germany
| | - Roel Quintens
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium
| | - Christophe Badie
- Cancer Mechanisms and Biomarkers group, Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, United Kingdom
| | - Olivier Laurent
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - An Aerts
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium
| | - Nataša Anastasov
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Omid Azimzadeh
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Tamara Azizova
- Southern Urals Biophysics Institute, Clinical Department, Ozyorsk, Russia
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium; Cell Systems and Imaging Research Group, Department of Molecular Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - Bjorn Baselet
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium; Pole of Pharmacology, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, B-1200 Brussels, Belgium
| | - Mohammed A Benotmane
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium
| | - Eric Blanchardon
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Yann Guéguen
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Siamak Haghdoost
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Mats Harms-Ringhdahl
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Julia Hess
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Michaela Kreuzer
- Federal Office for Radiation Protection, Department of Radiation Protection and Health, D-85764 Neuherberg, Germany
| | - Dominique Laurier
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Ellina Macaeva
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium; Cell Systems and Imaging Research Group, Department of Molecular Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - Grainne Manning
- Cancer Mechanisms and Biomarkers group, Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, United Kingdom
| | - Eileen Pernot
- INSERM U897, Université de Bordeaux, F-33076 Bordeaux cedex, France
| | - Jean-Luc Ravanat
- Laboratoire des Lésions des Acides Nucléiques, Univ. Grenoble Alpes, INAC-SCIB, F-38000 Grenoble, France; Commissariat à l'Énergie Atomique, INAC-SyMMES, F-38000 Grenoble, France
| | - Laure Sabatier
- Commissariat à l'Énergie Atomique, BP6, F-92265 Fontenay-aux-Roses, France
| | - Karine Tack
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Soile Tapio
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Horst Zitzelsberger
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Elisabeth Cardis
- Barcelona Institute of Global Health (ISGlobal), Centre for Research in Environmental Epidemiology, Radiation Programme, Barcelona Biomedical Research Park, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF) (MTD formerly), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
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Nagel ZD, Kitange GJ, Gupta SK, Joughin BA, Chaim IA, Mazzucato P, Lauffenburger DA, Sarkaria JN, Samson LD. DNA Repair Capacity in Multiple Pathways Predicts Chemoresistance in Glioblastoma Multiforme. Cancer Res 2016; 77:198-206. [PMID: 27793847 DOI: 10.1158/0008-5472.can-16-1151] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/28/2016] [Accepted: 10/20/2016] [Indexed: 12/21/2022]
Abstract
Cancer cells can resist the effects of DNA-damaging therapeutic agents via utilization of DNA repair pathways, suggesting that DNA repair capacity (DRC) measurements in cancer cells could be used to identify patients most likely to respond to treatment. However, the limitations of available technologies have so far precluded adoption of this approach in the clinic. We recently developed fluorescence-based multiplexed host cell reactivation (FM-HCR) assays to measure DRC in multiple pathways. Here we apply a mathematical model that uses DRC in multiple pathways to predict cellular resistance to killing by DNA-damaging agents. This model, developed using FM-HCR and drug sensitivity measurements in 24 human lymphoblastoid cell lines, was applied to a panel of 12 patient-derived xenograft (PDX) models of glioblastoma to predict glioblastoma response to treatment with the chemotherapeutic DNA-damaging agent temozolomide. This work showed that, in addition to changes in O6-methylguanine DNA methyltransferase (MGMT) activity, small changes in mismatch repair (MMR), nucleotide excision repair (NER), and homologous recombination (HR) capacity contributed to acquired temozolomide resistance in PDX models and led to reduced relative survival prolongation following temozolomide treatment of orthotopic mouse models in vivo Our data indicate that measuring the combined status of MMR, HR, NER, and MGMT provided a more robust prediction of temozolomide resistance than assessments of MGMT activity alone. Cancer Res; 77(1); 198-206. ©2016 AACR.
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Affiliation(s)
- Zachary D Nagel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Gaspar J Kitange
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Shiv K Gupta
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Brian A Joughin
- David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts
| | - Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Patrizia Mazzucato
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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Friedman J. It's high time to follow DNA repair in Routine Labs. DNA Repair (Amst) 2016; 47:49. [PMID: 27777098 DOI: 10.1016/j.dnarep.2016.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
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49
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Ferrucci L. Commentary: Life course epidemiology embraces geroscience. Int J Epidemiol 2016; 45:1015-1019. [PMID: 27880694 PMCID: PMC5841629 DOI: 10.1093/ije/dyw104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2016] [Indexed: 12/13/2022] Open
Affiliation(s)
- Luigi Ferrucci
- Intramural Research Program, National Institute on Aging - NIH, 251 Bayview Boulevard, Baltimore, MD, 21224 USA. E-mail:
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50
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Li F, Wang J, Chen M. Single nucleotide polymorphisms in DNA repair genes and the risk of laryngeal cancer: A meta-analysis. Biomed Pharmacother 2016; 78:92-100. [DOI: 10.1016/j.biopha.2015.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/14/2015] [Indexed: 12/19/2022] Open
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