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Parker LL, Bonner CM, Sobol RW, Arrieta MI. Co-creation and engagement in a DNA integrity cohort study. J Clin Transl Sci 2023; 7:e122. [PMID: 37313377 PMCID: PMC10260344 DOI: 10.1017/cts.2023.556] [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: 03/01/2023] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
Introduction The partnership between a research community engagement team (CE Team) and a community advisory board (CAB) formed the basis for bidirectional communication in developing resources for participant recruitment in a DNA integrity study. Engaging with a minoritized community, this partnership focused on respect, accessibility, and expanded engagement. Methods A ten-member CAB, working in two groups defined by meeting time convenience, provided insight and feedback to the CE Team in the creation of recruitment and consent materials, via an iterative design process in which one CAB group reviewed and enhanced materials, and the second group tested and refined them further. The continuous analysis of CE Team notes from CAB meetings captured information needed both for materials refinement and implementation of CAB-suggested activities. Results The partnership resulted in the co-creation of recruitment and consent materials that facilitated the enrollment of 191 individuals into the study. The CAB encouraged and assisted in expanded engagement inclusive of community leaders. This broader engagement provided information about the DNA integrity study to community decision-makers as well as responded to questions and concerns about the research. The bidirectional communication between the CAB and the CE Team encouraged the researchers to consider topics and research interests related to the current study but also responsive to community concerns. Conclusions The CAB helped the CE Team develop a better understanding of the language of partnership and respect. In this way, the partnership opened doors for expanded community engagement and effective communication with potential study participants.
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Affiliation(s)
- L. Lynette Parker
- Center for Healthy Communities, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Chantel M. Bonner
- Center for Healthy Communities, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI, USA
| | - Martha I. Arrieta
- Center for Healthy Communities, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, USA
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Roy R. Simultaneous Short- and Long-Patch Base Excision Repair (BER) Assay in Live Mammalian Cells. Methods Mol Biol 2023; 2701:3-19. [PMID: 37574472 DOI: 10.1007/978-1-0716-3373-1_1] [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] [Indexed: 08/15/2023]
Abstract
The base excision repair (BER) pathway repairs small, non-bulky DNA lesions, including oxidized, alkylated, and deaminated bases, and is responsible for the removal of at least 20,000 DNA lesions per cell per day. BER is initiated by DNA damage-specific DNA glycosylases that excise the damaged base and generates an abasic (AP) site or single-strand breaks, which are subsequently repaired in mammalian cells either by single-nucleotide (SN) or multiple-nucleotide incorporation via the SN-BER or long-patch BER (LP-BER) pathway, respectively. This chapter describes a plaque-based host cell reactivation (PL-HCR) assay system for measuring BER mechanisms in live mammalian cells using a plasmid-based assay. After transfection of a phagemid (M13mp18) containing a single modified base (representative BER DNA substrates) within a restriction site into human cells, restriction digestions detect the presence or absence (complete repair) of the adduct by the transformation of the digestion products into E. coli and counting the transformants as plaques. To monitor the patch size, different plasmids are constructed containing C:A mismatches within different restriction sites (inhibiting digestion) at various distances on both sides (5' or 3') of the modified base-containing restriction sites. Using this assay, the percentage of repair events that occur via 5' and 3' patch formation can be quantified.
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Affiliation(s)
- Rabindra Roy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
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3
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Sarhadi VK, Armengol G. Molecular Biomarkers in Cancer. Biomolecules 2022; 12:1021. [PMID: 35892331 PMCID: PMC9331210 DOI: 10.3390/biom12081021] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Molecular cancer biomarkers are any measurable molecular indicator of risk of cancer, occurrence of cancer, or patient outcome. They may include germline or somatic genetic variants, epigenetic signatures, transcriptional changes, and proteomic signatures. These indicators are based on biomolecules, such as nucleic acids and proteins, that can be detected in samples obtained from tissues through tumor biopsy or, more easily and non-invasively, from blood (or serum or plasma), saliva, buccal swabs, stool, urine, etc. Detection technologies have advanced tremendously over the last decades, including techniques such as next-generation sequencing, nanotechnology, or methods to study circulating tumor DNA/RNA or exosomes. Clinical applications of biomarkers are extensive. They can be used as tools for cancer risk assessment, screening and early detection of cancer, accurate diagnosis, patient prognosis, prediction of response to therapy, and cancer surveillance and monitoring response. Therefore, they can help to optimize making decisions in clinical practice. Moreover, precision oncology is needed for newly developed targeted therapies, as they are functional only in patients with specific cancer genetic mutations, and biomarkers are the tools used for the identification of these subsets of patients. Improvement in the field of cancer biomarkers is, however, needed to overcome the scientific challenge of developing new biomarkers with greater sensitivity, specificity, and positive predictive value.
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Affiliation(s)
- Virinder Kaur Sarhadi
- Department of Oral and Maxillofacial Diseases, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland;
| | - Gemma Armengol
- Department of Animal Biology, Plant Biology, and Ecology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Barcelona, Catalonia, Spain
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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: 0] [Impact Index Per Article: 0] [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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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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6
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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: 52] [Impact Index Per Article: 26.0] [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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7
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Capaccio C, Perrier JR, Cunha L, Mahnke RC, Lörch T, Porter M, Smith CL, Damer K, Bourland JD, Frizzell B, Torelli J, Vasquez M, Brower JB, Doyle-Eisele M, Taveras M, Turner H, Brenner DJ, Kowalski R. CytoRADx: A High-Throughput, Standardized Biodosimetry Diagnostic System Based on the Cytokinesis-Block Micronucleus Assay. Radiat Res 2021; 196:523-534. [PMID: 34515768 DOI: 10.1667/rade-20-00030.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 08/26/2021] [Indexed: 11/03/2022]
Abstract
In a large-scale catastrophe, such as a nuclear detonation in a major city, it will be crucial to accurately diagnose large numbers of people to direct scarce medical resources to those in greatest need. Currently no FDA-cleared tests are available to diagnose radiation exposures, which can lead to complex, life-threatening injuries. To address this gap, we have achieved substantial advancements in radiation biodosimetry through refinement and adaptation of the cytokinesis-block micronucleus (CBMN) assay as a high throughput, quantitative diagnostic test. The classical CBMN approach, which quantifies micronuclei (MN) resulting from DNA damage, suffers from considerable time and expert labor requirements, in addition to a lack of universal methodology across laboratories. We have developed the CytoRADx™ System to address these drawbacks by implementing a standardized reagent kit, optimized assay protocol, fully automated microscopy and image analysis, and integrated dose prediction. These enhancements allow the CytoRADx System to obtain high-throughput, standardized results without specialized labor or laboratory-specific calibration curves. The CytoRADx System has been optimized for use with both humans and non-human primates (NHP) to quantify radiation dose-dependent formation of micronuclei in lymphocytes, observed using whole blood samples. Cell nuclei and resulting MN are fluorescently stained and preserved on durable microscope slides using materials provided in the kit. Up to 1,000 slides per day are subsequently scanned using the commercially based RADxScan™ Imager with customized software, which automatically quantifies the cellular features and calculates the radiation dose. Using less than 1 mL of blood, irradiated ex vivo, our system has demonstrated accurate and precise measurement of exposures from 0 to 8 Gy (90% of results within 1 Gy of delivered dose). These results were obtained from 636 human samples (24 distinct donors) and 445 NHP samples (30 distinct subjects). The system demonstrated comparable results during in vivo studies, including an investigation of 43 NHPs receiving single-dose total-body irradiation. System performance is repeatable across laboratories, operators, and instruments. Results are also statistically similar across diverse populations, considering various demographics, common medications, medical conditions, and acute injuries associated with radiological disasters. Dose calculations are stable over time as well, providing reproducible results for at least 28 days postirradiation, and for blood specimens collected and stored at room temperature for at least 72 h. The CytoRADx System provides significant advancements in the field of biodosimetry that will enable accurate diagnoses across diverse populations in large-scale emergency scenarios. In addition, our technological enhancements to the well-established CBMN assay provide a pathway for future diagnostic applications, such as toxicology and oncology.
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Affiliation(s)
| | - Jay R Perrier
- ASELL, LLC, Owings Mills, Maryland.,Columbia University, Center for Radiological Research, New York, New York
| | - Lídia Cunha
- Columbia University, Center for Radiological Research, New York, New York
| | | | | | | | | | | | - J Daniel Bourland
- Wake Forest School of Medicine, Departments of Radiation Oncology, Physics, and Biomedical Engineering, Winston-Salem, North Carolina
| | - Bart Frizzell
- Wake Forest School of Medicine, Departments of Radiation Oncology, Physics, and Biomedical Engineering, Winston-Salem, North Carolina
| | | | | | - Jeremy B Brower
- Lovelace Biomedical Research Institute, Albuquerque, New Mexico
| | | | - Maria Taveras
- Columbia University, Center for Radiological Research, New York, New York
| | - Helen Turner
- Columbia University, Center for Radiological Research, New York, New York
| | - David J Brenner
- Columbia University, Center for Radiological Research, New York, New York
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8
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Ngo LP, Kaushal S, Chaim IA, Mazzucato P, Ricciardi C, Samson LD, Nagel ZD, Engelward BP. CometChip analysis of human primary lymphocytes enables quantification of inter-individual differences in the kinetics of repair of oxidative DNA damage. Free Radic Biol Med 2021; 174:89-99. [PMID: 34324980 PMCID: PMC8477454 DOI: 10.1016/j.freeradbiomed.2021.07.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 01/15/2023]
Abstract
Although DNA repair is known to impact susceptibility to cancer and other diseases, relatively few population studies have been performed to evaluate DNA repair kinetics in people due to the difficulty of assessing DNA repair in a high-throughput manner. Here we use the CometChip, a high-throughput comet assay, to explore inter-individual variation in repair of oxidative damage to DNA, a known risk factor for aging, cancer and other diseases. DNA repair capacity after H2O2-induced DNA oxidation damage was quantified in peripheral blood mononuclear cells (PBMCs). For 10 individuals, blood was drawn at several times over the course of 4-6 weeks. In addition, blood was drawn once from each of 56 individuals. DNA damage levels were quantified prior to exposure to H2O2 and at 0, 15, 30, 60, and 120-min post exposure. We found that there is significant variability in DNA repair efficiency among individuals. When subdivided into quartiles by DNA repair efficiency, we found that the average t1/2 is 81 min for the slowest group and 24 min for the fastest group. This work shows that the CometChip can be used to uncover significant differences in repair kinetics among people, pointing to its utility in future epidemiological and clinical studies.
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Affiliation(s)
- Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Simran Kaushal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Patrizia Mazzucato
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Catherine Ricciardi
- MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Clinical Research Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Zachary D Nagel
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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9
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Qu M, Xu H, Li W, Chen J, Zhang Y, Xu B, Li Z, Liu T, Guo L, Xie J. Dynamically monitoring cellular γ-H2AX reveals the potential of carcinogenicity evaluation for genotoxic compounds. Arch Toxicol 2021; 95:3559-3573. [PMID: 34510228 DOI: 10.1007/s00204-021-03156-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/02/2021] [Indexed: 02/07/2023]
Abstract
Amongst all toxicological endpoints, carcinogenicity might pose the greatest concern. Genetic damage has been considered an important underlying mechanism for the carcinogenicity of chemical substances. The demand for in vitro genotoxic tests as alternative approaches is growing rapidly with the implementation of new regulations for compounds. However, currently available in vitro genotoxicity tests are often limited by relatively high false positive rates. Moreover, few studies have explored carcinogenicity potential by in vitro genotoxicity testing due to the shortage of suitable toxicological biomarkers to link gene damage with cancer risk. γ-H2AX is a recently acknowledged attractive endpoint (biomarker) for evaluating DNA damage and can simultaneously reflect the DNA damage response and repair of cells. We previously reported an ultrasensitive and reliable method, namely stable-isotope dilution-liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS), for detecting cellular γ-H2AX and evaluating genotoxic chemicals. More importantly, our method can dynamically monitor the specific processes of genotoxic compounds affecting DNA damage and repair reflected by the amount of γ-H2AX. To clarify the possibility of using this method to assess the potential carcinogenicity of genotoxic chemicals, we applied it to a set of 69 model compounds recommended by the European Center for the Validation of Alternative Methods (ECVAM), with already-characterized genotoxic potential. Compared to conventional in vitro genotoxicity assays, including the Ames test, the γ-H2AX assay by MS has high accuracy (94-96%) due to high sensitivity and specificity (88% and 100%, respectively). The dynamic profiles of model compounds after exposure in HepG2 cells were explored, and a mathematical approach was employed to simulate and quantitatively model the DNA repair kinetics of genotoxic carcinogens (GCs) based on γ-H2AX time-effect curves up to 8 h. Two crucial parameters, i.e., k (rate of γ-H2AX decay) and t50 (time required for γ-H2AX from maximum decrease to half) estimated by the least squares method, were achieved. An open web server to help researchers calculate these two key parameters and profile simulated curves of the tested compound is available online ( http://ccb1.bmi.ac.cn:81/shiny-server/sample-apps/prediction1/ ). We detected a positive association between carcinogenic levels and k and t50 values of γ-H2AX in tested GCs, validating the potential of using this MS-based γ-H2AX in vitro assay to help preliminarily evaluate carcinogenicity and assess genotoxicity. This approach may be used alone or integrated into an existing battery of in vitro genetic toxicity tests.
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Affiliation(s)
- Minmin Qu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Hua Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China.
| | - Wuju Li
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Jia Chen
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Yajiao Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Bin Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Zhi Li
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Tao Liu
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Lei Guo
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Jianwei Xie
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China.
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10
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Piett CG, Pecen TJ, Laverty DJ, Nagel ZD. Large-scale preparation of fluorescence multiplex host cell reactivation (FM-HCR) reporters. Nat Protoc 2021; 16:4265-4298. [PMID: 34363069 DOI: 10.1038/s41596-021-00577-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/28/2021] [Indexed: 01/14/2023]
Abstract
Repair of DNA damage is a critical survival mechanism that affects susceptibility to various human diseases and represents a key target for cancer therapy. A major barrier to applying this knowledge in research and clinical translation has been the lack of efficient, quantitative functional assays for measuring DNA repair capacity in living primary cells. To overcome this barrier, we recently developed a technology termed 'fluorescence multiplex host cell reactivation' (FM-HCR). We describe a method for using standard molecular biology techniques to generate large quantities of FM-HCR reporter plasmids containing site-specific DNA lesions and using these reporters to assess DNA repair capacity in at least six major DNA repair pathways in live cells. We improve upon previous methodologies by (i) providing a universal workflow for generating reporter plasmids, (ii) improving yield and purity to enable large-scale studies that demand milligram quantities and (iii) reducing preparation time >ten-fold.
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Affiliation(s)
- C G Piett
- Department of Environmental Health, JBL Center for Radiation Sciences, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - T J Pecen
- Department of Environmental Health, JBL Center for Radiation Sciences, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - D J Laverty
- Department of Environmental Health, JBL Center for Radiation Sciences, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Z D Nagel
- Department of Environmental Health, JBL Center for Radiation Sciences, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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11
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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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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: 8] [Impact Index Per Article: 2.7] [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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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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Abstract
Environmental exposures have long been known to impact public health and safety. For example, exposures to airborne particulates, heavy metals in water, or certain industrial chemicals can contribute to aging and to risk of developing cancer and other diseases. Environmental factors can impact health in a variety of ways, but a key concern is DNA damage, which can lead to mutations that cause cancer. Cancer can take years to develop following chemical exposure; however, one way to predict carcinogenicity in a more practical time frame is by studying the chemical's ability to induce DNA damage. The comet assay (or single-cell gel electrophoresis assay) has been used successfully for genotoxicity testing. The comet assay allows for the detection of DNA strand breaks via analysis of DNA migration during electrophoresis. Previously, the Engelward laboratory, in collaboration with the Bhatia laboratory, developed the CometChip for measurements of DNA damage and repair. The CometChip is a high-throughput comet assay that improves user reproducibility and significantly shortens total assay time. Here, we describe how the high-throughput CometChip platform can be used to measure DNA damage in established cell lines, animal models, and human samples. We also discuss technical challenges associated with these studies and provide recommendations on how to achieve optimal results for researchers interested in adopting this assay.
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Affiliation(s)
- Christy Chao
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, Massachusetts, United States
| | - Bevin P. Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, Massachusetts, United States
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Lee Y, Wang Q, Shuryak I, Brenner DJ, Turner HC. Development of a high-throughput γ-H2AX assay based on imaging flow cytometry. Radiat Oncol 2019; 14:150. [PMID: 31438980 PMCID: PMC6704696 DOI: 10.1186/s13014-019-1344-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/23/2019] [Indexed: 11/30/2022] Open
Abstract
Background Measurement of γ-H2AX foci levels in cells provides a sensitive and reliable method for quantitation of the radiation-induced DNA damage response. The objective of the present study was to develop a rapid, high-throughput γ-H2AX assay based on imaging flow cytometry (IFC) using the ImageStream®X Mk II (ISX) platform to evaluate DNA double strand break (DSB) repair kinetics in human peripheral blood cells after exposure to ionizing irradiation. Methods The γ-H2AX protocol was developed and optimized for small volumes (100 μL) of human blood in Matrix™ 96-tube format. Blood cell lymphocytes were identified and captured by ISX INSPIRE™ software and analyzed by Data Exploration and Analysis Software. Results Dose- and time-dependent γ-H2AX levels corresponding to radiation exposure were measured at various time points over 24 h using the IFC system. γ-H2AX fluorescence intensity at 1 h after exposure, increased linearly with increasing radiation dose (R2 = 0.98) for the four human donors tested, whereas the dose response for the mean number of γ-H2AX foci/cell was not as robust (R2 = 0.81). Radiation-induced γ-H2AX levels rapidly increased within 30 min and reached a maximum by ~ 1 h, after which time there was fast decline by 6 h, followed by a much slower rate of disappearance up to 24 h. A mathematical approach for quantifying DNA repair kinetics using the rate of γ-H2AX decay (decay constant, Kdec), and yield of residual unrepaired breaks (Fres) demonstrated differences in individual repair capacity between the healthy donors. Conclusions The results indicate that the IFC-based γ-H2AX protocol may provide a practical and high-throughput platform for measurements of individual global DNA DSB repair capacity which can facilitate precision medicine by predicting individual radiosensitivity and risk of developing adverse effects related to radiotherapy treatment. Electronic supplementary material The online version of this article (10.1186/s13014-019-1344-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Younghyun Lee
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168th St, New York, NY, 10032, USA. .,Present Address: Laboratory of Biological Dosimetry, National Radiation Emergency Medical Center, Korea Institute of Radiological and Medical Sciences, 75 Nowon-ro, Nowon-gu, Seoul, 01812, Republic of Korea.
| | - Qi Wang
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168th St, New York, NY, 10032, USA
| | - Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168th St, New York, NY, 10032, USA
| | - David J Brenner
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168th St, New York, NY, 10032, USA
| | - Helen C Turner
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168th St, New York, NY, 10032, USA
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Li J, Svilar D, McClellan S, Kim JH, Ahn EYE, Vens C, Wilson DM, Sobol RW. DNA Repair Molecular Beacon assay: a platform for real-time functional analysis of cellular DNA repair capacity. Oncotarget 2018; 9:31719-31743. [PMID: 30167090 PMCID: PMC6114979 DOI: 10.18632/oncotarget.25859] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/12/2018] [Indexed: 12/15/2022] Open
Abstract
Numerous studies have shown that select DNA repair enzyme activities impact response and/or toxicity of genotoxins, suggesting a requirement for enzyme functional analyses to bolster precision medicine or prevention. To address this need, we developed a DNA Repair Molecular Beacon (DRMB) platform that rapidly measures DNA repair enzyme activity in real-time. The DRMB assay is applicable for discovery of DNA repair enzyme inhibitors, for the quantification of enzyme rates and is sufficiently sensitive to differentiate cellular enzymatic activity that stems from variation in expression or effects of amino acid substitutions. We show activity measures of several different base excision repair (BER) enzymes, including proteins with tumor-identified point mutations, revealing lesion-, lesion-context- and cell-type-specific repair dependence; suggesting application for DNA repair capacity analysis of tumors. DRMB measurements using lysates from isogenic control and APE1-deficient human cells suggests the major mechanism of base lesion removal by most DNA glycosylases may be mono-functional base hydrolysis. In addition, development of a microbead-conjugated DRMB assay amenable to flow cytometric analysis further advances its application. Our studies establish an analytical platform capable of evaluating the enzyme activity of select DNA repair proteins in an effort to design and guide inhibitor development and precision cancer therapy options.
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Affiliation(s)
- Jianfeng Li
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - David Svilar
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA, USA
| | - Steven McClellan
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Jung-Hyun Kim
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | | | - Conchita Vens
- The Netherlands Cancer Institute, Division of Cell Biology, Amsterdam, The Netherlands
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, IRP, NIH Baltimore, MD, USA
| | - Robert W Sobol
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA.,Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA, USA
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Sloan DB, Broz AK, Sharbrough J, Wu Z. Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods. Trends Biotechnol 2018; 36:729-740. [PMID: 29550161 PMCID: PMC6004327 DOI: 10.1016/j.tibtech.2018.02.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/16/2018] [Accepted: 02/20/2018] [Indexed: 12/18/2022]
Abstract
There is a great need in biomedical and genetic research to detect DNA damage and de novo mutations, but doing so is inherently challenging because of the rarity of these events. The enormous capacity of current DNA sequencing technologies has opened the door for quantifying sequence variants present at low frequencies in vivo, such as within cancerous tissues. However, these sequencing technologies are error prone, resulting in high noise thresholds. Most DNA sequencing methods are also generally incapable of identifying chemically modified bases arising from DNA damage. In recent years, numerous specialized modifications to sequencing methods have been developed to address these shortcomings. Here, we review this landscape of emerging techniques, highlighting their respective strengths, weaknesses, and target applications.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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Cristinelli S, Ciuffi A. The use of single-cell RNA-Seq to understand virus-host interactions. Curr Opin Virol 2018; 29:39-50. [PMID: 29558678 DOI: 10.1016/j.coviro.2018.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/01/2018] [Indexed: 12/14/2022]
Abstract
Single-cell analyses allow uncovering cellular heterogeneity, not only per se, but also in response to viral infection. Similarly, single cell transcriptome analyses (scRNA-Seq) can highlight specific signatures, identifying cell subsets with particular phenotypes, which are relevant in the understanding of virus-host interactions.
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Affiliation(s)
- Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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