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Parsons BL, Beal MA, Dearfield KL, Douglas GR, Gi M, Gollapudi BB, Heflich RH, Horibata K, Kenyon M, Long AS, Lovell DP, Lynch AM, Myers MB, Pfuhler S, Vespa A, Zeller A, Johnson GE, White PA. Severity of effect considerations regarding the use of mutation as a toxicological endpoint for risk assessment: A report from the 8th International Workshop on Genotoxicity Testing (IWGT). ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 38828778 DOI: 10.1002/em.22599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/13/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Exposure levels without appreciable human health risk may be determined by dividing a point of departure on a dose-response curve (e.g., benchmark dose) by a composite adjustment factor (AF). An "effect severity" AF (ESAF) is employed in some regulatory contexts. An ESAF of 10 may be incorporated in the derivation of a health-based guidance value (HBGV) when a "severe" toxicological endpoint, such as teratogenicity, irreversible reproductive effects, neurotoxicity, or cancer was observed in the reference study. Although mutation data have been used historically for hazard identification, this endpoint is suitable for quantitative dose-response modeling and risk assessment. As part of the 8th International Workshops on Genotoxicity Testing, a sub-group of the Quantitative Analysis Work Group (WG) explored how the concept of effect severity could be applied to mutation. To approach this question, the WG reviewed the prevailing regulatory guidance on how an ESAF is incorporated into risk assessments, evaluated current knowledge of associations between germline or somatic mutation and severe disease risk, and mined available data on the fraction of human germline mutations expected to cause severe disease. Based on this review and given that mutations are irreversible and some cause severe human disease, in regulatory settings where an ESAF is used, a majority of the WG recommends applying an ESAF value between 2 and 10 when deriving a HBGV from mutation data. This recommendation may need to be revisited in the future if direct measurement of disease-causing mutations by error-corrected next generation sequencing clarifies selection of ESAF values.
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Affiliation(s)
- Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Kerry L Dearfield
- U.S. Environmental Protection Agency and U.S. Department of Agriculture, Washington, DC, USA
| | - George R Douglas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Min Gi
- Department of Environmental Risk Assessment, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | | | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Michelle Kenyon
- Portfolio and Regulatory Strategy, Drug Safety Research and Development, Pfizer, Groton, Connecticut, USA
| | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - David P Lovell
- Population Health Research Institute, St George's Medical School, University of London, London, UK
| | | | - Meagan B Myers
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Alisa Vespa
- Pharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - George E Johnson
- Swansea University Medical School, Swansea University, Swansea, Wales, UK
| | - Paul A White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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2
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Dertinger SD, Briggs E, Hussien Y, Bryce SM, Avlasevich SL, Conrad A, Johnson GE, Williams A, Bemis JC. Visualization strategies to aid interpretation of high-dimensional genotoxicity data. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65:156-178. [PMID: 38757760 PMCID: PMC11178453 DOI: 10.1002/em.22604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
This article describes a range of high-dimensional data visualization strategies that we have explored for their ability to complement machine learning algorithm predictions derived from MultiFlow® assay results. For this exercise, we focused on seven biomarker responses resulting from the exposure of TK6 cells to each of 126 diverse chemicals over a range of concentrations. Obviously, challenges associated with visualizing seven biomarker responses were further complicated whenever there was a desire to represent the entire 126 chemical data set as opposed to results from a single chemical. Scatter plots, spider plots, parallel coordinate plots, hierarchical clustering, principal component analysis, toxicological prioritization index, multidimensional scaling, t-distributed stochastic neighbor embedding, and uniform manifold approximation and projection are each considered in turn. Our report provides a comparative analysis of these techniques. In an era where multiplexed assays and machine learning algorithms are becoming the norm, stakeholders should find some of these visualization strategies useful for efficiently and effectively interpreting their high-dimensional data.
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Affiliation(s)
| | | | - Yusuf Hussien
- Institute of Life Sciences, Swansea University, Swansea, UK
| | | | | | - Adam Conrad
- Litron Laboratories, Rochester, New York, USA
| | | | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
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3
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Johnson MTJ, Arif I, Marchetti F, Munshi-South J, Ness RW, Szulkin M, Verrelli BC, Yauk CL, Anstett DN, Booth W, Caizergues AE, Carlen EJ, Dant A, González J, Lagos CG, Oman M, Phifer-Rixey M, Rennison DJ, Rosenberg MS, Winchell KM. Effects of urban-induced mutations on ecology, evolution and health. Nat Ecol Evol 2024; 8:1074-1086. [PMID: 38641700 DOI: 10.1038/s41559-024-02401-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/13/2024] [Indexed: 04/21/2024]
Abstract
Increasing evidence suggests that urbanization is associated with higher mutation rates, which can affect the health and evolution of organisms that inhabit cities. Elevated pollution levels in urban areas can induce DNA damage, leading to de novo mutations. Studies on mutations induced by urban pollution are most prevalent in humans and microorganisms, whereas studies of non-human eukaryotes are rare, even though increased mutation rates have the potential to affect organisms and their populations in contemporary time. Our Perspective explores how higher mutation rates in urban environments could impact the fitness, ecology and evolution of populations. Most mutations will be neutral or deleterious, and higher mutation rates associated with elevated pollution in urban populations can increase the risk of cancer in humans and potentially other species. We highlight the potential for urban-driven increased deleterious mutational loads in some organisms, which could lead to a decline in population growth of a wide diversity of organisms. Although beneficial mutations are expected to be rare, we argue that higher mutation rates in urban areas could influence adaptive evolution, especially in organisms with short generation times. Finally, we explore avenues for future research to better understand the effects of urban-induced mutations on the fitness, ecology and evolution of city-dwelling organisms.
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Affiliation(s)
- Marc T J Johnson
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada.
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada.
| | - Irtaqa Arif
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Jason Munshi-South
- Department of Biology and Louis Calder Center, Fordham University, Armonk, NY, USA
| | - Rob W Ness
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Marta Szulkin
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Brian C Verrelli
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel N Anstett
- Department of Plant Biology, Department of Entomology, Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Warren Booth
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Aude E Caizergues
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Elizabeth J Carlen
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, MO, USA
| | - Anthony Dant
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona, Spain
| | - César González Lagos
- Departamento de Ciencias, Facultad de Artes Liberales, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Madeleine Oman
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | | | - Diana J Rennison
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Michael S Rosenberg
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
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4
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Seo JE, Le Y, Revollo J, Miranda-Colon J, Xu H, McKinzie P, Mei N, Chen T, Heflich RH, Zhou T, Robison T, Bonzo JA, Guo X. Evaluating the mutagenicity of N-nitrosodimethylamine in 2D and 3D HepaRG cell cultures using error-corrected next generation sequencing. Arch Toxicol 2024; 98:1919-1935. [PMID: 38584193 PMCID: PMC11106104 DOI: 10.1007/s00204-024-03731-4] [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: 11/12/2023] [Accepted: 03/07/2024] [Indexed: 04/09/2024]
Abstract
Human liver-derived metabolically competent HepaRG cells have been successfully employed in both two-dimensional (2D) and 3D spheroid formats for performing the comet assay and micronucleus (MN) assay. In the present study, we have investigated expanding the genotoxicity endpoints evaluated in HepaRG cells by detecting mutagenesis using two error-corrected next generation sequencing (ecNGS) technologies, Duplex Sequencing (DS) and High-Fidelity (HiFi) Sequencing. Both HepaRG 2D cells and 3D spheroids were exposed for 72 h to N-nitrosodimethylamine (NDMA), followed by an additional incubation for the fixation of induced mutations. NDMA-induced DNA damage, chromosomal damage, and mutagenesis were determined using the comet assay, MN assay, and ecNGS, respectively. The 72-h treatment with NDMA resulted in concentration-dependent increases in cytotoxicity, DNA damage, MN formation, and mutation frequency in both 2D and 3D cultures, with greater responses observed in the 3D spheroids compared to 2D cells. The mutational spectrum analysis showed that NDMA induced predominantly A:T → G:C transitions, along with a lower frequency of G:C → A:T transitions, and exhibited a different trinucleotide signature relative to the negative control. These results demonstrate that the HepaRG 2D cells and 3D spheroid models can be used for mutagenesis assessment using both DS and HiFi Sequencing, with the caveat that severe cytotoxic concentrations should be avoided when conducting DS. With further validation, the HepaRG 2D/3D system may become a powerful human-based metabolically competent platform for genotoxicity testing.
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Affiliation(s)
- Ji-Eun Seo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Yuan Le
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Javier Revollo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Jaime Miranda-Colon
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Hannah Xu
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Page McKinzie
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Nan Mei
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Tong Zhou
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, MD, 20855, USA
| | - Timothy Robison
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Jessica A Bonzo
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Xiaoqing Guo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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Kopp B, Khawam A, Di Perna K, Lenart D, Vinette M, Silva R, Zanoni TB, Rore C, Guenigault G, Richardson E, Kostrzewski T, Boswell A, Van P, Valentine Iii C, Salk J, Hamel A. Liver-on-chip model and application in predictive genotoxicity and mutagenicity of drugs. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 896:503762. [PMID: 38821675 DOI: 10.1016/j.mrgentox.2024.503762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 06/02/2024]
Abstract
Currently, there is no test system, whether in vitro or in vivo, capable of examining all endpoints required for genotoxicity evaluation used in pre-clinical drug safety assessment. The objective of this study was to develop a model which could assess all the required endpoints and possesses robust human metabolic activity, that could be used in a streamlined, animal-free manner. Liver-on-chip (LOC) models have intrinsic human metabolic activity that mimics the in vivo environment, making it a preferred test system. For our assay, the LOC was assembled using primary human hepatocytes or HepaRG cells, in a MPS-T12 plate, maintained under microfluidic flow conditions using the PhysioMimix® Microphysiological System (MPS), and co-cultured with human lymphoblastoid (TK6) cells in transwells. This system allows for interaction between two compartments and for the analysis of three different genotoxic endpoints, i.e. DNA strand breaks (comet assay) in hepatocytes, chromosome loss or damage (micronucleus assay) and mutation (Duplex Sequencing) in TK6 cells. Both compartments were treated at 0, 24 and 45 h with two direct genotoxicants: methyl methanesulfonate (MMS) and ethyl methanesulfonate (EMS), and two genotoxicants requiring metabolic activation: benzo[a]pyrene (B[a]P) and cyclophosphamide (CP). Assessment of cytochrome activity, RNA expression, albumin, urea and lactate dehydrogenase production, demonstrated functional metabolic capacities. Genotoxicity responses were observed for all endpoints with MMS and EMS. Increases in the micronucleus and mutations (MF) frequencies were also observed with CP, and %Tail DNA with B[a]P, indicating the metabolic competency of the test system. CP did not exhibit an increase in the %Tail DNA, which is in line with in vivo data. However, B[a]P did not exhibit an increase in the % micronucleus and MF, which might require an optimization of the test system. In conclusion, this proof-of-principle experiment suggests that LOC-MPS technology is a promising tool for in vitro hazard identification genotoxicants.
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Affiliation(s)
- B Kopp
- Charles River Laboratories Montreal ULC, Canada
| | - A Khawam
- Charles River Laboratories Montreal ULC, Canada
| | - K Di Perna
- Charles River Laboratories Montreal ULC, Canada
| | - D Lenart
- Charles River Laboratories Montreal ULC, Canada
| | - M Vinette
- Charles River Laboratories Montreal ULC, Canada
| | - R Silva
- CN Bio Innovations, Cambridge, United Kingdom
| | - T B Zanoni
- TwinStrand Biosciences, Seattle, United States
| | - C Rore
- CN Bio Innovations, Cambridge, United Kingdom
| | | | | | | | - A Boswell
- TwinStrand Biosciences, Seattle, United States
| | - P Van
- TwinStrand Biosciences, Seattle, United States
| | | | - J Salk
- TwinStrand Biosciences, Seattle, United States
| | - A Hamel
- Charles River Laboratories Montreal ULC, Canada.
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6
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Minko I, Luzadder M, Vartanian V, Rice SM, Nguyen M, Sanchez-Contreras M, Van P, Kennedy S, McCullough A, Lloyd R. Frequencies and spectra of aflatoxin B 1-induced mutations in liver genomes of NEIL1-deficient mice as revealed by duplex sequencing. NAR MOLECULAR MEDICINE 2024; 1:ugae006. [PMID: 38779538 PMCID: PMC11105970 DOI: 10.1093/narmme/ugae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/18/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
Increased risk for the development of hepatocellular carcinoma (HCC) is driven by a number of etiological factors including hepatitis viral infection and dietary exposures to foods contaminated with aflatoxin-producing molds. Intracellular metabolic activation of aflatoxin B1 (AFB1) to a reactive epoxide generates highly mutagenic AFB1-Fapy-dG adducts. Previously, we demonstrated that repair of AFB1-Fapy-dG adducts can be initiated by the DNA glycosylase NEIL1 and that male Neil1-/- mice were significantly more susceptible to AFB1-induced HCC relative to wild-type mice. To investigate the mechanisms underlying this enhanced carcinogenesis, WT and Neil1-/- mice were challenged with a single, 4 mg/kg dose of AFB1 and frequencies and spectra of mutations were analyzed in liver DNAs 2.5 months post-injection using duplex sequencing. The analyses of DNAs from AFB1-challenged mice revealed highly elevated mutation frequencies in the nuclear genomes of both males and females, but not the mitochondrial genomes. In both WT and Neil1-/- mice, mutation spectra were highly similar to the AFB1-specific COSMIC signature SBS24. Relative to wild-type, the NEIL1 deficiency increased AFB1-induced mutagenesis with concomitant elevated HCCs in male Neil1-/- mice. Our data establish a critical role of NEIL1 in limiting AFB1-induced mutagenesis and ultimately carcinogenesis.
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Affiliation(s)
- Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Michael M Luzadder
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Vladimir L Vartanian
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Sean P M Rice
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
- School of Public Health, Oregon Health & Science University - Portland State University, Portland, OR, USA
| | - Megan M Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Phu Van
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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7
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Sahib S, Yan J, Chen T. Application of duplex sequencing to evaluate mutagenicity of aristolochic acid and methapyrilene in Fisher 344 rats. Food Chem Toxicol 2024; 185:114512. [PMID: 38342231 DOI: 10.1016/j.fct.2024.114512] [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: 11/06/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/13/2024]
Abstract
Duplex sequencing (DS) is an error-corrected next-generation sequencing (NGS) method that can overcome notorious high error rate from the process of NGS and detect ultralow-frequency mutations. In this study, we evaluated the mutagenicity of aristolochic acid, a known genotoxic carcinogen, and methapyrilene, a known nongenotoxic carcinogen using DS. Four male Fisher 344 rats were treated with aristolochic acid, methapyrilene, or the vehicle control for 6 weeks, liver tissues were collected one day after the treatment, and the DNA was isolated for analysis. The mutation frequency for the aristolochic acid-treated group was significantly increased over the vehicle control (44-fold), whereas no significant difference in the mutation frequency was observed between the methapyrilene-treated and the control groups. The primary type of mutation induced by aristolochic acid was A:T > T:A transversion, which occurred frequently at ApT sites, whereas the major type of mutation in the control and methapyrilene-treated groups was G:C > A:T transition, which occurred frequently at CpG sites. These findings are consistent with previously published data obtained with other in vivo mutation assays. Thus, our results suggest that the DS mutation assay is a promising technology for assessing mutagenicity of chemicals in vivo.
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Affiliation(s)
- Seaab Sahib
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Jian Yan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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8
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Demir E, Kacew S. Environmental Toxicology and Human Health. Int J Mol Sci 2023; 25:555. [PMID: 38203725 PMCID: PMC10779361 DOI: 10.3390/ijms25010555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Humans and animals may be exposed on a continuous daily basis to a mixture of environmental contaminants that may act on several organ systems through differing mechanisms [...].
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Affiliation(s)
- Esref Demir
- Department of Medical Services and Techniques, Medical Laboratory Techniques Programme, Vocational School of Health Services, Antalya Bilim University, 07190 Antalya, Turkey
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Sam Kacew
- Institute of Population Health, R. Samuel McLaughlin Centre for Population Health Risk Assessment, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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Beal MA, Chen G, Dearfield KL, Gi M, Gollapudi B, Heflich RH, Horibata K, Long AS, Lovell DP, Parsons BL, Pfuhler S, Wills J, Zeller A, Johnson G, White PA. Interpretation of in vitro concentration-response data for risk assessment and regulatory decision-making: Report from the 2022 IWGT quantitative analysis expert working group meeting. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2023. [PMID: 38115239 DOI: 10.1002/em.22582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/15/2023] [Accepted: 12/16/2023] [Indexed: 12/21/2023]
Abstract
Quantitative risk assessments of chemicals are routinely performed using in vivo data from rodents; however, there is growing recognition that non-animal approaches can be human-relevant alternatives. There is an urgent need to build confidence in non-animal alternatives given the international support to reduce the use of animals in toxicity testing where possible. In order for scientists and risk assessors to prepare for this paradigm shift in toxicity assessment, standardization and consensus on in vitro testing strategies and data interpretation will need to be established. To address this issue, an Expert Working Group (EWG) of the 8th International Workshop on Genotoxicity Testing (IWGT) evaluated the utility of quantitative in vitro genotoxicity concentration-response data for risk assessment. The EWG first evaluated available in vitro methodologies and then examined the variability and maximal response of in vitro tests to estimate biologically relevant values for the critical effect sizes considered adverse or unacceptable. Next, the EWG reviewed the approaches and computational models employed to provide human-relevant dose context to in vitro data. Lastly, the EWG evaluated risk assessment applications for which in vitro data are ready for use and applications where further work is required. The EWG concluded that in vitro genotoxicity concentration-response data can be interpreted in a risk assessment context. However, prior to routine use in regulatory settings, further research will be required to address the remaining uncertainties and limitations.
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Affiliation(s)
- Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Guangchao Chen
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment (RIVM), Utrecht, the Netherlands
| | - Kerry L Dearfield
- Retired from US Environmental Protection Agency and US Department of Agriculture, Washington, DC, USA
| | - Min Gi
- Department of Environmental Risk Assessment, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | | | - Robert H Heflich
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Katsuyoshi Horibata
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - David P Lovell
- St George's Medical School, University of London, London, UK
| | - Barbara L Parsons
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Stefan Pfuhler
- Global Product Stewardship - Human Safety, Procter & Gamble, Cincinnati, Ohio, USA
| | - John Wills
- Genetic Toxicology and Photosafety, GSK Research & Development, Stevenage, UK
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - George Johnson
- Swansea University Medical School, Swansea University, Swansea, UK
| | - Paul A White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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10
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You X, Cao Y, Suzuki T, Shao J, Zhu B, Masumura K, Xi J, Liu W, Zhang X, Luan Y. Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing. Nucleic Acids Res 2023; 51:e109. [PMID: 37870450 PMCID: PMC10681716 DOI: 10.1093/nar/gkad909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023] Open
Abstract
Error-corrected next-generation sequencing (ecNGS) is an emerging technology for accurately measuring somatic mutations. Here, we report paired-end and complementary consensus sequencing (PECC-Seq), a high-accuracy ecNGS approach for genome-wide somatic mutation detection. We characterize a novel 2-aminoimidazolone lesion besides 7,8-dihydro-8-oxoguanine and the resulting end-repair artifacts originating from NGS library preparation that obscure the sequencing accuracy of NGS. We modify library preparation protocol for the enzymatic removal of end-repair artifacts and improve the accuracy of our previously developed duplex consensus sequencing method. Optimized PECC-Seq shows an error rate of <5 × 10-8 with consensus bases compressed from approximately 25 Gb of raw sequencing data, enabling the accurate detection of low-abundance somatic mutations. We apply PECC-Seq to the quantification of in vivo mutagenesis. Compared with the classic gpt gene mutation assay using gpt delta transgenic mice, PECC-Seq exhibits high sensitivity in quantitatively measuring dose-dependent mutagenesis induced by Aristolochic acid I (AAI). Moreover, PECC-Seq specifically characterizes the distinct genome-wide mutational signatures of AAI, Benzo[a]pyrene, N-Nitroso-N-ethylurea and N-nitrosodiethylamine and reveals the mutational signature of Quinoline in common mouse models. Overall, our findings demonstrate that high-accuracy PECC-Seq is a promising tool for genome-wide somatic mutagenesis quantification and for in vivo mutagenicity testing.
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Affiliation(s)
- Xinyue You
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yiyi Cao
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Takayoshi Suzuki
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Jie Shao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, The Chinese Academy of Sciences, Beijing 100085, China; The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Benzhan Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, The Chinese Academy of Sciences, Beijing 100085, China; The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kenichi Masumura
- Division of Risk Assessment, National Institute of Health Sciences, Kawasaki 210-9501, Japan
| | - Jing Xi
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Weiying Liu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xinyu Zhang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Luan
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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11
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Smith-Roe SL, Hobbs CA, Hull V, Todd Auman J, Recio L, Streicker MA, Rivas MV, Pratt GA, Lo FY, Higgins JE, Schmidt EK, Williams LN, Nachmanson D, Valentine Iii CC, Salk JJ, Witt KL. Adopting duplex sequencing technology for genetic toxicity testing: A proof-of-concept mutagenesis experiment with N-ethyl-N-nitrosourea (ENU)-exposed rats. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 891:503669. [PMID: 37770135 PMCID: PMC10539650 DOI: 10.1016/j.mrgentox.2023.503669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 09/30/2023]
Abstract
Duplex sequencing (DS) is an error-corrected next-generation sequencing method in which molecular barcodes informatically link PCR-copies back to their source DNA strands, enabling computational removal of errors in consensus sequences. The resulting background of less than one artifactual mutation per 107 nucleotides allows for direct detection of somatic mutations. TwinStrand Biosciences, Inc. has developed a DS-based mutagenesis assay to sample the rat genome, which can be applied to genetic toxicity testing. To evaluate this assay for early detection of mutagenesis, a time-course study was conducted using male Hsd:Sprague Dawley SD rats (3 per group) administered a single dose of 40 mg/kg N-ethyl-N-nitrosourea (ENU) via gavage, with mutation frequency (MF) and spectrum analyzed in stomach, bone marrow, blood, and liver tissues at 3 h, 24 h, 7 d, and 28 d post-exposure. Significant increases in MF were observed in ENU-exposed rats as early as 24 h for stomach (site of contact) and bone marrow (a highly proliferative tissue) and at 7 d for liver and blood. The canonical, mutational signature of ENU was established by 7 d post-exposure in all four tissues. Interlaboratory analysis of a subset of samples from different tissues and time points demonstrated remarkable reproducibility for both MF and spectrum. These results demonstrate that MF and spectrum can be evaluated successfully by directly sequencing targeted regions of DNA obtained from various tissues, a considerable advancement compared to currently used in vivo gene mutation assays.
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Affiliation(s)
| | - Cheryl A Hobbs
- Integrated Laboratory Systems, LLC (An Inotiv Company), Research Triangle Park, NC, USA
| | - Victoria Hull
- Integrated Laboratory Systems, LLC (An Inotiv Company), Research Triangle Park, NC, USA
| | - J Todd Auman
- Integrated Laboratory Systems, LLC (An Inotiv Company), Research Triangle Park, NC, USA
| | - Leslie Recio
- Integrated Laboratory Systems, LLC (An Inotiv Company), Research Triangle Park, NC, USA
| | - Michael A Streicker
- Integrated Laboratory Systems, LLC (An Inotiv Company), Research Triangle Park, NC, USA
| | - Miriam V Rivas
- Integrated Laboratory Systems, LLC (An Inotiv Company), Research Triangle Park, NC, USA
| | | | - Fang Yin Lo
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | | | | | | | | | | | | | - Kristine L Witt
- Division of Translational Toxicology, NIEHS, Research Triangle Park, NC, USA
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12
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Menz J, Götz ME, Gündel U, Gürtler R, Herrmann K, Hessel-Pras S, Kneuer C, Kolrep F, Nitzsche D, Pabel U, Sachse B, Schmeisser S, Schumacher DM, Schwerdtle T, Tralau T, Zellmer S, Schäfer B. Genotoxicity assessment: opportunities, challenges and perspectives for quantitative evaluations of dose-response data. Arch Toxicol 2023; 97:2303-2328. [PMID: 37402810 PMCID: PMC10404208 DOI: 10.1007/s00204-023-03553-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023]
Abstract
Genotoxicity data are mainly interpreted in a qualitative way, which typically results in a binary classification of chemical entities. For more than a decade, there has been a discussion about the need for a paradigm shift in this regard. Here, we review current opportunities, challenges and perspectives for a more quantitative approach to genotoxicity assessment. Currently discussed opportunities mainly include the determination of a reference point (e.g., a benchmark dose) from genetic toxicity dose-response data, followed by calculation of a margin of exposure (MOE) or derivation of a health-based guidance value (HBGV). In addition to new opportunities, major challenges emerge with the quantitative interpretation of genotoxicity data. These are mainly rooted in the limited capability of standard in vivo genotoxicity testing methods to detect different types of genetic damage in multiple target tissues and the unknown quantitative relationships between measurable genotoxic effects and the probability of experiencing an adverse health outcome. In addition, with respect to DNA-reactive mutagens, the question arises whether the widely accepted assumption of a non-threshold dose-response relationship is at all compatible with the derivation of a HBGV. Therefore, at present, any quantitative genotoxicity assessment approach remains to be evaluated case-by-case. The quantitative interpretation of in vivo genotoxicity data for prioritization purposes, e.g., in connection with the MOE approach, could be seen as a promising opportunity for routine application. However, additional research is needed to assess whether it is possible to define a genotoxicity-derived MOE that can be considered indicative of a low level of concern. To further advance quantitative genotoxicity assessment, priority should be given to the development of new experimental methods to provide a deeper mechanistic understanding and a more comprehensive basis for the analysis of dose-response relationships.
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Affiliation(s)
- Jakob Menz
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany.
| | - Mario E Götz
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Ulrike Gündel
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Rainer Gürtler
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Kristin Herrmann
- Department of Pesticides Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Stefanie Hessel-Pras
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Carsten Kneuer
- Department of Pesticides Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Franziska Kolrep
- Department of Safety in the Food Chain, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Dana Nitzsche
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Ulrike Pabel
- Department of Safety in the Food Chain, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Benjamin Sachse
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Sebastian Schmeisser
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - David M Schumacher
- Department of Safety in the Food Chain, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Tanja Schwerdtle
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Tewes Tralau
- Department of Pesticides Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Sebastian Zellmer
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Bernd Schäfer
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
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13
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Miranda JA, Fenner K, McKinzie PB, Dobrovolsky VN, Revollo JR. Unbiased whole genome detection of ultrarare off-target mutations in genome-edited cell populations by HiFi sequencing. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2023; 64:374-381. [PMID: 37488781 DOI: 10.1002/em.22566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/13/2023] [Accepted: 07/23/2023] [Indexed: 07/26/2023]
Abstract
DNA base editors (BEs) composed of a nuclease-deficient Cas9 fused to a DNA-modifying enzyme can achieve on-target mutagenesis without creating double-strand DNA breaks (DSBs). As a result, BEs generate far less DNA damage than traditional nuclease-proficient Cas9 systems, which do rely on the creation of DSBs to achieve on-target mutagenesis. The inability of BEs to create DSBs makes the detection of their undesired off-target effects very difficult. PacBio HiFi sequencing can efficiently detect ultrarare mutations resulting from chemical mutagenesis in whole genomes with a sensitivity ~1 × 10-8 mutations per base pair. In this proof-of-principle study, we evaluated whether this technique could also detect the on- and off-target mutations generated by a cytosine-to-thymine (C>T) BE targeting the LacZ gene in Escherichia coli (E. coli). HiFi sequencing detected on-target mutant allele fractions ranging from ~7% to ~63%, depending on the single-guide RNA (sgRNA) used, while no on-target mutations were detected in controls lacking the BE. The presence of the BE resulted in a ~3-fold increase in mutation frequencies compared to controls lacking the BE, irrespective of the sgRNA used. These increases were mostly composed of C:G>T:A substitutions distributed throughout the genome. Our results demonstrate that HiFi sequencing can efficiently identify on- and off-target mutations in cell populations that have undergone genome editing.
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Affiliation(s)
- Jaime A Miranda
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Kristina Fenner
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Page B McKinzie
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Vasily N Dobrovolsky
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Javier R Revollo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
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14
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Dodge AE, LeBlanc DPM, Zhou G, Williams A, Meier MJ, Van P, Lo FY, Valentine Iii CC, Salk JJ, Yauk CL, Marchetti F. Duplex sequencing provides detailed characterization of mutation frequencies and spectra in the bone marrow of MutaMouse males exposed to procarbazine hydrochloride. Arch Toxicol 2023; 97:2245-2259. [PMID: 37341741 PMCID: PMC10322784 DOI: 10.1007/s00204-023-03527-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/17/2023] [Indexed: 06/22/2023]
Abstract
Mutagenicity testing is an essential component of health safety assessment. Duplex Sequencing (DS), an emerging high-accuracy DNA sequencing technology, may provide substantial advantages over conventional mutagenicity assays. DS could be used to eliminate reliance on standalone reporter assays and provide mechanistic information alongside mutation frequency (MF) data. However, the performance of DS must be thoroughly assessed before it can be routinely implemented for standard testing. We used DS to study spontaneous and procarbazine (PRC)-induced mutations in the bone marrow (BM) of MutaMouse males across a panel of 20 diverse genomic targets. Mice were exposed to 0, 6.25, 12.5, or 25 mg/kg-bw/day for 28 days by oral gavage and BM sampled 42 days post-exposure. Results were compared with those obtained using the conventional lacZ viral plaque assay on the same samples. DS detected significant increases in mutation frequencies and changes to mutation spectra at all PRC doses. Low intra-group variability within DS samples allowed for detection of increases at lower doses than the lacZ assay. While the lacZ assay initially yielded a higher fold-change in mutant frequency than DS, inclusion of clonal mutations in DS mutation frequencies reduced this discrepancy. Power analyses suggested that three animals per dose group and 500 million duplex base pairs per sample is sufficient to detect a 1.5-fold increase in mutations with > 80% power. Overall, we demonstrate several advantages of DS over classical mutagenicity assays and provide data to support efforts to identify optimal study designs for the application of DS as a regulatory test.
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Affiliation(s)
- Annette E Dodge
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Danielle P M LeBlanc
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Gu Zhou
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Phu Van
- TwinStrand Biosciences Inc., Seattle, Washington, USA
| | - Fang Yin Lo
- TwinStrand Biosciences Inc., Seattle, Washington, USA
| | | | - Jesse J Salk
- TwinStrand Biosciences Inc., Seattle, Washington, USA
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.
- Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada.
- Department of Biology, Carleton University, Ottawa, Ontario, Canada.
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15
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Marchetti F, Cardoso R, Chen CL, Douglas GR, Elloway J, Escobar PA, Harper T, Heflich RH, Kidd D, Lynch AM, Myers MB, Parsons BL, Salk JJ, Settivari RS, Smith-Roe SL, Witt KL, Yauk CL, Young R, Zhang S, Minocherhomji S. Error-corrected next generation sequencing - Promises and challenges for genotoxicity and cancer risk assessment. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108466. [PMID: 37643677 DOI: 10.1016/j.mrrev.2023.108466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/12/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Error-corrected Next Generation Sequencing (ecNGS) is rapidly emerging as a valuable, highly sensitive and accurate method for detecting and characterizing mutations in any cell type, tissue or organism from which DNA can be isolated. Recent mutagenicity and carcinogenicity studies have used ecNGS to quantify drug-/chemical-induced mutations and mutational spectra associated with cancer risk. ecNGS has potential applications in genotoxicity assessment as a new readout for traditional models, for mutagenesis studies in 3D organotypic cultures, and for detecting off-target effects of gene editing tools. Additionally, early data suggest that ecNGS can measure clonal expansion of mutations as a mechanism-agnostic early marker of carcinogenic potential and can evaluate mutational load directly in human biomonitoring studies. In this review, we discuss promising applications, challenges, limitations, and key data initiatives needed to enable regulatory testing and adoption of ecNGS - including for advancing safety assessment, augmenting weight-of-evidence for mutagenicity and carcinogenicity mechanisms, identifying early biomarkers of cancer risk, and managing human health risk from chemical exposures.
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Affiliation(s)
| | | | - Connie L Chen
- Health and Environmental Sciences Institute, Washington, DC, USA.
| | | | - Joanne Elloway
- Safety Sciences, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | - Tod Harper
- Amgen Research, Amgen Inc, Thousand Oaks, CA, USA
| | - Robert H Heflich
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | - Darren Kidd
- Labcorp Early Development Laboratories Limited, Harrogate, North Yorkshire, UK
| | | | - Meagan B Myers
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | - Barbara L Parsons
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | | | | | | | - Kristine L Witt
- NIEHS, Division of the National Toxicology Program, Research Triangle Park, NC, USA
| | | | - Robert Young
- MilliporeSigma, Rockville, MD, USA; Current: Consultant, Bethesda, MD, USA
| | | | - Sheroy Minocherhomji
- Amgen Research, Amgen Inc, Thousand Oaks, CA, USA; Current: Eli Lilly and Company, Indianapolis, IN, USA
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16
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Menon V, Brash DE. Next-generation sequencing methodologies to detect low-frequency mutations: "Catch me if you can". MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108471. [PMID: 37716438 PMCID: PMC10843083 DOI: 10.1016/j.mrrev.2023.108471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023]
Abstract
Mutations, the irreversible changes in an organism's DNA sequence, are present in tissues at a variant allele frequency (VAF) ranging from ∼10-8 per bp for a founder mutation to ∼10-3 for a histologically normal tissue sample containing several independent clones - compared to 1%- 50% for a heterozygous tumor mutation or a polymorphism. The rarity of these events poses a challenge for accurate clinical diagnosis and prognosis, toxicology, and discovering new disease etiologies. Standard Next-Generation Sequencing (NGS) technologies report VAFs as low as 0.5% per nt, but reliably observing rarer precursor events requires additional sophistication to measure ultralow-frequency mutations. We detail the challenge; define terms used to characterize the results, which vary between laboratories and sometimes conflict between biologists and bioinformaticists; and describe recent innovations to improve standard NGS methodologies including: single-strand consensus sequence methods such as Safe-SeqS and SiMSen-Seq; tandem-strand consensus sequence methods such as o2n-Seq and SMM-Seq; and ultrasensitive parent-strand consensus sequence methods such as DuplexSeq, PacBio HiFi, SinoDuplex, OPUSeq, EcoSeq, BotSeqS, Hawk-Seq, NanoSeq, SaferSeq, and CODEC. Practical applications are also noted. Several methods quantify VAF down to 10-5 at a nt and mutation frequency (MF) in a target region down to 10-7 per nt. By expanding to > 1 Mb of sites never observed twice, thus forgoing VAF, other methods quantify MF < 10-9 per nt or < 15 errors per haploid genome. Clonal expansion cannot be directly distinguished from independent mutations by sequencing, so it is essential for a paper to report whether its MF counted only different mutations - the minimum independent-mutation frequency MFminI - or all mutations observed including recurrences - the larger maximum independent-mutation frequency MFmaxI which may reflect clonal expansion. Ultrasensitive methods reveal that, without their use, even mutations with VAF 0.5-1% are usually spurious.
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Affiliation(s)
- Vijay Menon
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA.
| | - Douglas E Brash
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA; Department of Dermatology, Yale School of Medicine, New Haven, CT 06520-8059, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520-8028, USA.
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17
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Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
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Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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18
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Cho E, Swartz CD, Williams A, V Rivas M, Recio L, Witt KL, Schmidt EK, Yaplee J, Smith TH, Van P, Lo FY, Valentine CC, Salk JJ, Marchetti F, Smith-Roe SL, Yauk CL. Error-corrected duplex sequencing enables direct detection and quantification of mutations in human TK6 cells with strong inter-laboratory consistency. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 889:503649. [PMID: 37491114 PMCID: PMC10395007 DOI: 10.1016/j.mrgentox.2023.503649] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 07/27/2023]
Abstract
Error-corrected duplex sequencing (DS) enables direct quantification of low-frequency mutations and offers tremendous potential for chemical mutagenicity assessment. We investigated the utility of DS to quantify induced mutation frequency (MF) and spectrum in human lymphoblastoid TK6 cells exposed to a prototypical DNA alkylating agent, N-ethyl-N-nitrosourea (ENU). Furthermore, we explored appropriate experimental parameters for this application, and assessed inter-laboratory reproducibility. In two independent experiments in two laboratories, TK6 cells were exposed to ENU (25-200 µM) and DNA was sequenced 48, 72, and 96 h post-exposure. A DS mutagenicity panel targeting twenty 2.4-kb regions distributed across the genome was used to sample diverse, genome-representative sequence contexts. A significant increase in MF that was unaffected by time was observed in both laboratories. Concentration-response in the MF from the two laboratories was strongly positively correlated (r = 0.97). C:G>T:A, T:A>C:G, T:A>A:T, and T:A>G:C mutations increased in consistent, concentration-dependent manners in both laboratories, with high proportions of C:G>T:A at all time points. The consistent results across the three time points suggest that 48 h may be sufficient for mutation analysis post-exposure. The target sites responded similarly between the two laboratories and revealed a higher average MF in intergenic regions. These results, demonstrating remarkable reproducibility across time and laboratory for both MF and spectrum, support the high value of DS for characterizing chemical mutagenicity in both research and regulatory evaluation.
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Affiliation(s)
- Eunnara Cho
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada
| | | | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | | | - Leslie Recio
- Inotiv-RTP, Research Triangle Park, NC, USA; Scitovation, Research Triangle Park, NC, USA
| | - Kristine L Witt
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | | | | | | | - Phu Van
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | - Fang Yin Lo
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | | | | | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Stephanie L Smith-Roe
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada; Department of Biology, University of Ottawa, Ottawa, ON, Canada.
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19
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Smith-Roe SL, Hobbs CA, Hull V, Auman JT, Recio L, Streicker MA, Rivas MV, Pratt GA, Lo FY, Higgins JE, Schmidt EK, Williams LN, Nachmanson D, Valentine CC, Salk JJ, Witt KL. Adopting Duplex Sequencing™ Technology for Genetic Toxicity Testing: A Proof-of-Concept Mutagenesis Experiment with N-Ethyl-N-Nitrosourea (ENU)-Exposed Rats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539833. [PMID: 37214853 PMCID: PMC10197591 DOI: 10.1101/2023.05.08.539833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Duplex sequencing (DuplexSeq) is an error-corrected next-generation sequencing (ecNGS) method in which molecular barcodes informatically link PCR-copies back to their source DNA strands, enabling computational removal of errors by comparing grouped strand sequencing reads. The resulting background of less than one artifactual mutation per 10 7 nucleotides allows for direct detection of somatic mutations. TwinStrand Biosciences, Inc. has developed a DuplexSeq-based mutagenesis assay to sample the rat genome, which can be applied to genetic toxicity testing. To evaluate this assay for early detection of mutagenesis, a time-course study was conducted using male Hsd:Sprague Dawley SD rats (3 per group) administered a single dose of 40 mg/kg N-ethyl-N-nitrosourea (ENU) via gavage, with mutation frequency (MF) and spectrum analyzed in stomach, bone marrow, blood, and liver tissues at 3 h, 24 h, 7 d, and 28 d post-exposure. Significant increases in MF were observed in ENU-exposed rats as early as 24 h for stomach (site of contact) and bone marrow (a highly proliferative tissue) and at 7 d for liver and blood. The canonical, mutational signature of ENU was established by 7 d post-exposure in all four tissues. Interlaboratory analysis of a subset of samples from different tissues and time points demonstrated remarkable reproducibility for both MF and spectrum. These results demonstrate that MF and spectrum can be evaluated successfully by directly sequencing targeted regions of DNA obtained from various tissues, a considerable advancement compared to currently used in vivo gene mutation assays. HIGHLIGHTS DuplexSeq is an ultra-accurate NGS technology that directly quantifies mutationsENU-dependent mutagenesis was detected 24 h post-exposure in proliferative tissuesMultiple tissues exhibited the canonical ENU mutation spectrum 7 d after exposureResults obtained with DuplexSeq were highly concordant between laboratoriesThe Rat-50 Mutagenesis Assay is promising for applications in genetic toxicology.
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Affiliation(s)
| | - Cheryl A. Hobbs
- Integrated Laboratory Systems, LLC (an Inotiv company), Research Triangle Park, NC
| | - Victoria Hull
- Integrated Laboratory Systems, LLC (an Inotiv company), Research Triangle Park, NC
| | - J. Todd Auman
- Integrated Laboratory Systems, LLC (an Inotiv company), Research Triangle Park, NC
| | - Leslie Recio
- Integrated Laboratory Systems, LLC (an Inotiv company), Research Triangle Park, NC
| | - Michael A. Streicker
- Integrated Laboratory Systems, LLC (an Inotiv company), Research Triangle Park, NC
| | - Miriam V. Rivas
- Integrated Laboratory Systems, LLC (an Inotiv company), Research Triangle Park, NC
| | | | | | | | | | | | | | | | | | - Kristine L. Witt
- Division of Translational Toxicology, NIEHS, Research Triangle Park, NC
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20
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Das S, Babu A, Medha T, Ramanathan G, Mukherjee AG, Wanjari UR, Murali R, Kannampuzha S, Gopalakrishnan AV, Renu K, Sinha D, George Priya Doss C. Molecular mechanisms augmenting resistance to current therapies in clinics among cervical cancer patients. Med Oncol 2023; 40:149. [PMID: 37060468 PMCID: PMC10105157 DOI: 10.1007/s12032-023-01997-9] [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: 01/23/2023] [Accepted: 03/10/2023] [Indexed: 04/16/2023]
Abstract
Cervical cancer (CC) is the fourth leading cause of cancer death (~ 324,000 deaths annually) among women internationally, with 85% of these deaths reported in developing regions, particularly sub-Saharan Africa and Southeast Asia. Human papillomavirus (HPV) is considered the major driver of CC, and with the availability of the prophylactic vaccine, HPV-associated CC is expected to be eliminated soon. However, female patients with advanced-stage cervical cancer demonstrated a high recurrence rate (50-70%) within two years of completing radiochemotherapy. Currently, 90% of failures in chemotherapy are during the invasion and metastasis of cancers related to drug resistance. Although molecular target therapies have shown promising results in the lab, they have had little success in patients due to the tumor heterogeneity fueling resistance to these therapies and bypass the targeted signaling pathway. The last two decades have seen the emergence of immunotherapy, especially immune checkpoint blockade (ICB) therapies, as an effective treatment against metastatic tumors. Unfortunately, only a small subgroup of patients (< 20%) have benefited from this approach, reflecting disease heterogeneity and manifestation with primary or acquired resistance over time. Thus, understanding the mechanisms driving drug resistance in CC could significantly improve the quality of medical care for cancer patients and steer them to accurate, individualized treatment. The rise of artificial intelligence and machine learning has also been a pivotal factor in cancer drug discovery. With the advancement in such technology, cervical cancer screening and diagnosis are expected to become easier. This review will systematically discuss the different tumor-intrinsic and extrinsic mechanisms CC cells to adapt to resist current treatments and scheme novel strategies to overcome cancer drug resistance.
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Affiliation(s)
- Soumik Das
- School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Achsha Babu
- School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Tamma Medha
- School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Gnanasambandan Ramanathan
- School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Anirban Goutam Mukherjee
- School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Uddesh Ramesh Wanjari
- School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Reshma Murali
- School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Sandra Kannampuzha
- School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | | | - Kaviyarasi Renu
- Department of Biochemistry, Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600077, Tamil Nadu, India
| | - Debottam Sinha
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
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21
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Coppedè F. Genes and the Environment in Cancer: Focus on Environmentally Induced DNA Methylation Changes. Cancers (Basel) 2023; 15:cancers15041019. [PMID: 36831363 PMCID: PMC9953779 DOI: 10.3390/cancers15041019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Cancer has traditionally been viewed as a genetic disorder resulting from the accumulation of gene mutations, chromosomal rearrangements, and aneuploidies in somatic cells [...].
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy; ; Tel.: +39-050-2218544
- Interdepartmental Research Center of Biology and Pathology of Aging, University of Pisa, 56126 Pisa, Italy
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22
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Zhivagui M, Hoda A, Valenzuela N, Yeh YY, Dai J, He Y, Nandi SP, Otlu B, Van Houten B, Alexandrov LB. DNA damage and somatic mutations in mammalian cells after irradiation with a nail polish dryer. Nat Commun 2023; 14:276. [PMID: 36650165 PMCID: PMC9845303 DOI: 10.1038/s41467-023-35876-8] [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: 02/07/2021] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
Ultraviolet A light is commonly emitted by UV-nail polish dryers with recent reports suggesting that long-term use may increase the risk for developing skin cancer. However, no experimental evaluation has been conducted to reveal the effect of radiation emitted by UV-nail polish dryers on mammalian cells. Here, we show that irradiation by a UV-nail polish dryer causes high levels of reactive oxygen species, consistent with 8-oxo-7,8-dihydroguanine damage and mitochondrial dysfunction. Analysis of somatic mutations reveals a dose-dependent increase of C:G>A:T substitutions in irradiated samples with mutagenic patterns similar to mutational signatures previously attributed to reactive oxygen species. In summary, this study demonstrates that radiation emitted by UV-nail polish dryers can both damage DNA and permanently engrave mutations on the genomes of primary mouse embryonic fibroblasts, human foreskin fibroblasts, and human epidermal keratinocytes.
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Affiliation(s)
- Maria Zhivagui
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Areebah Hoda
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
| | | | - Yi-Yu Yeh
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
| | - Jason Dai
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Shuvro P Nandi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Burcak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Bennett Van Houten
- UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA. .,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA. .,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA.
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23
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Javaid M, Khan S, Haleem A, Rab S. Adoption of modern technologies for implementing industry 4.0: an integrated MCDM approach. BENCHMARKING-AN INTERNATIONAL JOURNAL 2022. [DOI: 10.1108/bij-01-2021-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
PurposeModern technologies are seen as an essential component of the fourth industrial revolution (industry 4.0) and their adoption is vital to transform the existing manufacturing system into industry 4.0-based manufacturing system. Therefore, the primary objective of this research explores the barriers of modern technology adoption and their mitigating solutions in order to align with Industry 4.0 objectives.Design/methodology/approachBarriers to adopting modern technologies and respective mitigating solutions are identified from the available literature. Further, these barriers are ranked with the help of expert opinions by using the BWM method appropriately. The identified solutions are ranked using the combined compromise solution (CoCoSo) method.FindingsSeveral modern technologies and their capabilities are recognised to support the industry 4.0-based manufacturing systems. This study identifies 22 barriers to the effective adoption of modern technologies in manufacturing and 14 solutions to overcome these barriers. Change management, the high initial cost of technology and appropriate support infrastructure are the most significant barriers. The most prominent solutions to overcome the most considerable barriers are ‘supportive research, development and commercialisation environment’, ‘updated policy and effective implementation’ and ‘capacity building through training’ that are the top three solutions that need to be addressed.Research limitations/implicationsThe barriers and solutions of modern technology adoption are obtained through a comprehensive literature review, so there is a chance to ignore some significant barriers and their solutions. Furthermore, ranking barriers and solutions is done with expert opinion, which is not free from biases.Practical implicationsThis identification and prioritisation of barriers will help managers to understand the barriers so they can better prepare themselves. Furthermore, the suggested solutions to overcome these barriers are helpful for the managers and could be strategically adopted through optimal resource utilisation.Originality/valueThis study proposes a framework to identify and analyse the significant barriers and solutions to adopting modern technologies in the manufacturing system. It might be helpful for manufacturing organisations that are willing to transform their manufacturing system into industry 4.0.
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24
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Leuthner T, Benzing L, Kohrn B, Bergemann C, Hipp M, Hershberger K, Mello D, Sokolskyi T, Stevenson K, Merutka I, Seay S, Gregory S, Kennedy S, Meyer J. Resistance of mitochondrial DNA to cadmium and Aflatoxin B1 damage-induced germline mutation accumulation in C. elegans. Nucleic Acids Res 2022; 50:8626-8642. [PMID: 35947695 PMCID: PMC9410910 DOI: 10.1093/nar/gkac666] [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: 12/13/2021] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 01/12/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is prone to mutation in aging and over evolutionary time, yet the processes that regulate the accumulation of de novo mtDNA mutations and modulate mtDNA heteroplasmy are not fully elucidated. Mitochondria lack certain DNA repair processes, which could contribute to polymerase error-induced mutations and increase susceptibility to chemical-induced mtDNA mutagenesis. We conducted error-corrected, ultra-sensitive Duplex Sequencing to investigate the effects of two known nuclear genome mutagens, cadmium and Aflatoxin B1, on germline mtDNA mutagenesis in Caenorhabditis elegans. Detection of thousands of mtDNA mutations revealed pervasive heteroplasmy in C. elegans and that mtDNA mutagenesis is dominated by C:G → A:T mutations generally attributed to oxidative damage. However, there was no effect of either exposure on mtDNA mutation frequency, spectrum, or trinucleotide context signature despite a significant increase in nuclear mutation rate after aflatoxin B1 exposure. Mitophagy-deficient mutants pink-1 and dct-1 accumulated significantly higher levels of mtDNA damage compared to wild-type C. elegans after exposures. However, there were only small differences in mtDNA mutation frequency, spectrum, or trinucleotide context signature compared to wild-type after 3050 generations, across all treatments. These findings suggest mitochondria harbor additional previously uncharacterized mechanisms that regulate mtDNA mutational processes across generations.
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Affiliation(s)
- Tess C Leuthner
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Laura Benzing
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Michael J Hipp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Danielle F Mello
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Tymofii Sokolskyi
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Kevin Stevenson
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Ilaria R Merutka
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Sarah A Seay
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA,Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Joel N Meyer
- To whom correspondence should be addressed. Tel: +1 919 613 8109;
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25
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Miranda JA, McKinzie PB, Dobrovolsky VN, Revollo JR. Evaluation of the mutagenic effects of Molnupiravir and N4-hydroxycytidine in bacterial and mammalian cells by HiFi sequencing. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2022; 63:320-328. [PMID: 36181379 DOI: 10.1002/em.22510] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/09/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Molnupiravir (MOV) is used to treat COVID-19. In cells, MOV is converted to the ribonucleoside analog N4-hydroxycytidine (NHC) and incorporated into the SARS-CoV-2 RNA genome during its replication, resulting in RNA mutations. The widespread accumulation of such mutations inhibits SARS-CoV-2 propagation. Although safety assessments by many regulatory agencies across the world have concluded that the genotoxic risks associated with the clinical use of MOV are low, concerns remain that it could induce DNA mutations in patients, particularly because numerous in vitro studies have shown that NHC is a DNA mutagen. In this study, we used HiFi sequencing, a technique that can detect ultralow-frequency substitution mutations in whole genomes, to evaluate the mutagenic effects of MOV in E. coli and of MOV and NHC in mouse lymphoma L5178Y cells and human lymphoblastoid TK6 cells. In all models, exposure to these compounds increased genome-wide mutation frequencies in a dose-dependent manner, and these increases were mainly composed of A:T → G:C transitions. The NHC exposure concentrations used for mammalian cells were comparable to those observed in the plasma of humans who received clinical doses of MOV.
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Affiliation(s)
- Jaime A Miranda
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Page B McKinzie
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Vasily N Dobrovolsky
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Javier R Revollo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
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26
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Alekseenko A, Wang J, Barrett D, Pelechano V. OPUSeq simplifies detection of low-frequency DNA variants and uncovers fragmentase-associated artifacts. NAR Genom Bioinform 2022; 4:lqac048. [PMID: 35769342 PMCID: PMC9235115 DOI: 10.1093/nargab/lqac048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Detection of low-frequency DNA variants (below 1%) is becoming increasingly important in biomedical research and clinical practice, but is challenging to do with standard sequencing approaches due to high error rates. The use of double-stranded unique molecular identifiers (dsUMIs) allows correction of errors by comparing reads arising from the same original DNA duplex. However, the implementation of such approaches is still challenging. Here, we present a novel method, one-pot dsUMI sequencing (OPUSeq), which allows incorporation of dsUMIs in the same reaction as the library PCR. This obviates the need for adapter pre-synthesis or additional enzymatic steps. OPUSeq can be incorporated into standard DNA library preparation approaches and coupled with hybridization target capture. We demonstrate successful error correction and detection of variants down to allele frequency of 0.01%. Using OPUSeq, we also show that the use of enzymatic fragmentation can lead to the appearance of spurious double-stranded variants, interfering with detection of variant fractions below 0.1%.
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Affiliation(s)
- Alisa Alekseenko
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Donal Barrett
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
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27
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Christopher Corton J, Mitchell CA, Auerbach S, Bushel JP, Ellinger-Ziegelbauer H, Escobar PA, Froetschl R, Harrill AH, Johnson K, Klaunig JE, Pandiri AR, Podtelezhnikov AA, Rager JE, Tanis KQ, van der Laan JW, Vespa A, Yauk CL, Pettit SD, Sistare FD. A Collaborative Initiative to Establish Genomic Biomarkers for Assessing Tumorigenic Potential to Reduce Reliance on Conventional Rodent Carcinogenicity Studies. Toxicol Sci 2022; 188:4-16. [PMID: 35404422 PMCID: PMC9238304 DOI: 10.1093/toxsci/kfac041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
There is growing recognition across broad sectors of the scientific community that use of genomic biomarkers has the potential to reduce the need for conventional rodent carcinogenicity studies of industrial chemicals, agrochemicals, and pharmaceuticals through a weight-of-evidence approach. These biomarkers fall into 2 major categories: (1) sets of gene transcripts that can identify distinct tumorigenic mechanisms of action; and (2) cancer driver gene mutations indicative of rapidly expanding growth-advantaged clonal cell populations. This call-to-action article describes a collaborative approach launched to develop and qualify biomarker gene expression panels that measure widely accepted molecular pathways linked to tumorigenesis and their activation levels to predict tumorigenic doses of chemicals from short-term exposures. Growing evidence suggests that application of such biomarker panels in short-term exposure rodent studies can identify both tumorigenic hazard and tumorigenic activation levels for chemical-induced carcinogenicity. In the future, this approach will be expanded to include methodologies examining mutations in key cancer driver gene mutation hotspots as biomarkers of both genotoxic and nongenotoxic chemical tumor risk. Analytical, technical, and biological validation studies of these complementary genomic tools are being undertaken by multisector and multidisciplinary collaborative teams within the Health and Environmental Sciences Institute. Success from these efforts will facilitate the transition from current heavy reliance on conventional 2-year rodent carcinogenicity studies to more rapid animal- and resource-sparing approaches for mechanism-based carcinogenicity evaluation supporting internal and regulatory decision-making.
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Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | | | - Scott Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - J Pierre Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | | | - Patricia A Escobar
- Safety Assessment and Laboratory Animal Resources, Merck Sharp & Dohme Corp, West Point, PA, USA
| | - Roland Froetschl
- BfArM-Bundesinstitut für Arzneimittel und Medizinprodukte, Federal Institute for Drugs and Medical Devices, Kurt-Georg-Kiesinger-Allee 3, Bonn, Germany
| | - Alison H Harrill
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | | | - James E Klaunig
- Laboratory of Investigative Toxicology and Pathology, Department of Environmental and Occupational Health, Indiana School of Public Health, Indiana University, Bloomington, IN, USA
| | - Arun R Pandiri
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | | | - Julia E Rager
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Keith Q Tanis
- Safety Assessment and Laboratory Animal Resources, Merck Sharp & Dohme Corp, West Point, PA, USA
| | - Jan Willem van der Laan
- Section on Pharmacology, Toxicology and Kinetics, Medicines Evaluation Board, Utrecht, The Netherlands
| | - Alisa Vespa
- Therapeutic Products Directorate, Health Canada, Ottawa, Canada
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Syril D Pettit
- Health and Environmental Sciences Institute, Washington, DC, USA
| | - Frank D Sistare
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
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28
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Cho E, Allemang A, Audebert M, Chauhan V, Dertinger S, Hendriks G, Luijten M, Marchetti F, Minocherhomji S, Pfuhler S, Roberts DJ, Trenz K, Yauk CL. AOP report: Development of an adverse outcome pathway for oxidative DNA damage leading to mutations and chromosomal aberrations. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2022; 63:118-134. [PMID: 35315142 PMCID: PMC9322445 DOI: 10.1002/em.22479] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/18/2022] [Indexed: 05/22/2023]
Abstract
The Genetic Toxicology Technical Committee (GTTC) of the Health and Environmental Sciences Institute (HESI) is developing adverse outcome pathways (AOPs) that describe modes of action leading to potentially heritable genomic damage. The goal was to enhance the use of mechanistic information in genotoxicity assessment by building empirical support for the relationships between relevant molecular initiating events (MIEs) and regulatory endpoints in genetic toxicology. Herein, we present an AOP network that links oxidative DNA damage to two adverse outcomes (AOs): mutations and chromosomal aberrations. We collected empirical evidence from the literature to evaluate the key event relationships between the MIE and the AOs, and assessed the weight of evidence using the modified Bradford-Hill criteria for causality. Oxidative DNA damage is constantly induced and repaired in cells given the ubiquitous presence of reactive oxygen species and free radicals. However, xenobiotic exposures may increase damage above baseline levels through a variety of mechanisms and overwhelm DNA repair and endogenous antioxidant capacity. Unrepaired oxidative DNA base damage can lead to base substitutions during replication and, along with repair intermediates, can also cause DNA strand breaks that can lead to mutations and chromosomal aberrations if not repaired adequately. This AOP network identifies knowledge gaps that could be filled by targeted studies designed to better define the quantitative relationships between key events, which could be leveraged for quantitative chemical safety assessment. We anticipate that this AOP network will provide the building blocks for additional genotoxicity-associated AOPs and aid in designing novel integrated testing approaches for genotoxicity.
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Affiliation(s)
- Eunnara Cho
- Environmental Health Science and Research BureauHealth CanadaOttawaOntarioCanada
- Department of BiologyCarleton UniversityOttawaOntarioCanada
| | | | | | - Vinita Chauhan
- Consumer and Clinical Radiation Protection BureauHealth CanadaOttawaOntarioCanada
| | | | | | - Mirjam Luijten
- Centre for Health ProtectionNational Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - Francesco Marchetti
- Environmental Health Science and Research BureauHealth CanadaOttawaOntarioCanada
- Department of BiologyCarleton UniversityOttawaOntarioCanada
| | - Sheroy Minocherhomji
- Amgen Research, Translational Safety and Bioanalytical SciencesAmgen Inc.Thousand OaksCaliforniaUSA
| | | | | | | | - Carole L. Yauk
- Environmental Health Science and Research BureauHealth CanadaOttawaOntarioCanada
- Department of BiologyCarleton UniversityOttawaOntarioCanada
- Department of BiologyUniversity of OttawaOttawaOntarioCanada
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29
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Waters MD, Warren S, Hughes C, Lewis P, Zhang F. Human genetic risk of treatment with antiviral nucleoside analog drugs that induce lethal mutagenesis: The special case of molnupiravir. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2022; 63:37-63. [PMID: 35023215 DOI: 10.1002/em.22471] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/28/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
This review considers antiviral nucleoside analog drugs, including ribavirin, favipiravir, and molnupiravir, which induce genome error catastrophe in SARS-CoV or SARS-CoV-2 via lethal mutagenesis as a mode of action. In vitro data indicate that molnupiravir may be 100 times more potent as an antiviral agent than ribavirin or favipiravir. Molnupiravir has recently demonstrated efficacy in a phase 3 clinical trial. Because of its anticipated global use, its relative potency, and the reported in vitro "host" cell mutagenicity of its active principle, β-d-N4-hydroxycytidine, we have reviewed the development of molnupiravir and its genotoxicity safety evaluation, as well as the genotoxicity profiles of three congeners, that is, ribavirin, favipiravir, and 5-(2-chloroethyl)-2'-deoxyuridine. We consider the potential genetic risks of molnupiravir on the basis of all available information and focus on the need for additional human genotoxicity data and follow-up in patients treated with molnupiravir and similar drugs. Such human data are especially relevant for antiviral NAs that have the potential of permanently modifying the genomes of treated patients and/or causing human teratogenicity or embryotoxicity. We conclude that the results of preclinical genotoxicity studies and phase 1 human clinical safety, tolerability, and pharmacokinetics are critical components of drug safety assessments and sentinels of unanticipated adverse health effects. We provide our rationale for performing more thorough genotoxicity testing prior to and within phase 1 clinical trials, including human PIG-A and error corrected next generation sequencing (duplex sequencing) studies in DNA and mitochondrial DNA of patients treated with antiviral NAs that induce genome error catastrophe via lethal mutagenesis.
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Affiliation(s)
- Michael D Waters
- Michael Waters Consulting USA, Hillsborough, North Carolina, USA
| | | | - Claude Hughes
- Duke University Medical Center, Durham, North Carolina, USA
| | | | - Fengyu Zhang
- Global Clinical and Translational Research Institute, Bethesda, Maryland, USA
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Beal MA, Gagne M, Kulkarni SA, Patlewicz G, Thomas RS, Barton-Maclaren TS. Implementing in vitro bioactivity data to modernize priority setting of chemical inventories. ALTEX 2022; 39:123-139. [PMID: 34818430 PMCID: PMC8973434 DOI: 10.14573/altex.2106171] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/22/2021] [Indexed: 01/03/2023]
Abstract
Internationally, there are thousands of existing and newly introduced chemicals in commerce, highlighting the ongoing importance of innovative approaches to identify emerging chemicals of concern. For many chemicals, there is a paucity of hazard and exposure data. Thus, there is a crucial need for efficient and robust approaches to address data gaps and support risk-based prioritization. Several studies have demonstrated the utility of in vitro bioactivity data from the ToxCast program in deriving points of departure (PODs). ToxCast contains data for nearly 1,400 endpoints per chemical, and the bioactivity concentrations, indicative of potential adverse outcomes, can be converted to human-equivalent PODs using high-throughput toxicokinetics (HTTK) modeling. However, data gaps need to be addressed for broader application: the limited chemical space of HTTK and quantitative high-throughput screening data. Here we explore the applicability of in silico models to address these data needs. Specifically, we used ADMET predictor for HTTK predictions and a generalized read-across approach to predict ToxCast bioactivity potency. We applied these models to profile 5,801 chemicals on Canada’s Domestic Substances List (DSL). To evaluate the approach’s performance, bioactivity PODs were compared with in vivo results from the EPA Toxicity Values database for 1,042 DSL chemicals. Comparisons demonstrated that the bioactivity PODs, based on ToxCast data or read-across, were conservative for 95% of the chemicals. Comparing bioactivity PODs to human exposure estimates supports the identification of chemicals of potential interest for further work. The bioactivity workflow shows promise as a powerful screening tool to support effective triaging of chemical inventories.
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Affiliation(s)
- Marc A. Beal
- Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Matthew Gagne
- Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Sunil A. Kulkarni
- Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Grace Patlewicz
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Russell S. Thomas
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
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Leuthner TC, Meyer JN. Mitochondrial DNA Mutagenesis: Feature of and Biomarker for Environmental Exposures and Aging. Curr Environ Health Rep 2021; 8:294-308. [PMID: 34761353 PMCID: PMC8826492 DOI: 10.1007/s40572-021-00329-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2021] [Indexed: 01/12/2023]
Abstract
PURPOSE OF REVIEW Mitochondrial dysfunction is a hallmark of aging. Mitochondrial genome (mtDNA) instability contributes to mitochondrial dysfunction, and mtDNA mutagenesis may contribute to aging. However, the origin of mtDNA mutations remains somewhat controversial. The goals of this review are to introduce and review recent literature on mtDNA mutagenesis and aging, address recent animal and epidemiological evidence for the effects of chemicals on mtDNA damage and mutagenesis, propose hypotheses regarding the contribution of environmental toxicant exposure to mtDNA mutagenesis in the context of aging, and suggest future directions and approaches for environmental health researchers. RECENT FINDINGS Stressors such as pollutants, pharmaceuticals, and ultraviolet radiation can damage the mitochondrial genome or disrupt mtDNA replication, repair, and organelle homeostatic processes, potentially influencing the rate of accumulation of mtDNA mutations. Accelerated mtDNA mutagenesis could contribute to aging, diseases of aging, and sensitize individuals with pathogenic mtDNA variants to stressors. We propose three potential mechanisms of toxicant-induced effects on mtDNA mutagenesis over lifespan: (1) increased de novo mtDNA mutations, (2) altered frequencies of mtDNA mutations, or (3) both. There are remarkably few studies that have investigated the impact of environmental chemical exposures on mtDNA instability and mutagenesis, and even fewer in the context of aging. More studies are warranted because people are exposed to tens of thousands of chemicals, and are living longer. Finally, we suggest that toxicant-induced mtDNA damage and mutational signatures may be a sensitive biomarker for some exposures.
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Affiliation(s)
- Tess C Leuthner
- Nicholas School of the Environment, 9 Circuit Dr, Box 90328, Duke University, NC, 27708, USA
| | - Joel N Meyer
- Nicholas School of the Environment, 9 Circuit Dr, Box 90328, Duke University, NC, 27708, USA.
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32
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Otsubo Y, Matsumura S, Ikeda N, Yamane M. Single-strand specific nuclease enhances accuracy of error-corrected sequencing and improves rare mutation-detection sensitivity. Arch Toxicol 2021; 96:377-386. [PMID: 34767040 PMCID: PMC8748355 DOI: 10.1007/s00204-021-03185-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022]
Abstract
Error-corrected sequences (ECSs) that utilize double-stranded DNA sequences are useful in detecting mutagen-induced mutations. However, relatively higher frequencies of G:C > T:A (1 × 10−7 bp) and G:C > C:G (2 × 10−7 bp) errors decrease the accuracy of detection of rare G:C mutations (approximately 10−7 bp). Oxidized guanines in single-strand (SS) overhangs generated after shearing could serve as the source of these errors. To remove these errors, we first computationally discarded up to 20 read bases corresponding to the ends of the DNA fragments. Error frequencies decreased proportionately with trimming length; however, the results indicated that they were not sufficiently removed. To efficiently remove SS overhangs, we evaluated three mechanistically distinct SS-specific nucleases (S1 Nuclease, mung bean nuclease, and RecJf exonuclease) and found that they were more efficient than computational trimming. Consequently, we established Jade-Seq™, an ECS protocol with S1 Nuclease treatment, which reduced G:C > T:A and G:C > C:G errors to 0.50 × 10−7 bp and 0.12 × 10−7 bp, respectively. This was probably because S1 Nuclease removed SS regions, such as gaps and nicks, depending on its wide substrate specificity. Subsequently, we evaluated the mutation-detection sensitivity of Jade-Seq™ using DNA samples from TA100 cells exposed to 3-methylcholanthrene and 7,12-dimethylbenz[a]anthracene, which contained the rare G:C > T:A mutation (i.e., 2 × 10−7 bp). Fold changes of G:C > T:A compared to the vehicle control were 1.2- and 1.3-times higher than those of samples without S1 Nuclease treatment, respectively. These findings indicate the potential of Jade-Seq™ for detecting rare mutations and determining the mutagenicity of environmental mutagens.
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Affiliation(s)
- Yuki Otsubo
- R&D Safety Science Research, Kao Corporation, 3-25-14 Tono-machi, Kawasaki-ku, Kawasaki City, Kanagawa, 210-0821, Japan
| | - Shoji Matsumura
- R&D Safety Science Research, Kao Corporation, 3-25-14 Tono-machi, Kawasaki-ku, Kawasaki City, Kanagawa, 210-0821, Japan.
| | - Naohiro Ikeda
- R&D Safety Science Research, Kao Corporation, 3-25-14 Tono-machi, Kawasaki-ku, Kawasaki City, Kanagawa, 210-0821, Japan
| | - Masayuki Yamane
- R&D Safety Science Research, Kao Corporation, 2606 Akabane, Ichikai-Machi, Haga-Gun, Tochigi, 321-3497, Japan
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Tice RR, Bassan A, Amberg A, Anger LT, Beal MA, Bellion P, Benigni R, Birmingham J, Brigo A, Bringezu F, Ceriani L, Crooks I, Cross K, Elespuru R, Faulkner DM, Fortin MC, Fowler P, Frericks M, Gerets HHJ, Jahnke GD, Jones DR, Kruhlak NL, Lo Piparo E, Lopez-Belmonte J, Luniwal A, Luu A, Madia F, Manganelli S, Manickam B, Mestres J, Mihalchik-Burhans AL, Neilson L, Pandiri A, Pavan M, Rider CV, Rooney JP, Trejo-Martin A, Watanabe-Sailor KH, White AT, Woolley D, Myatt GJ. In Silico Approaches In Carcinogenicity Hazard Assessment: Current Status and Future Needs. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 20. [PMID: 35368437 DOI: 10.1016/j.comtox.2021.100191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Historically, identifying carcinogens has relied primarily on tumor studies in rodents, which require enormous resources in both money and time. In silico models have been developed for predicting rodent carcinogens but have not yet found general regulatory acceptance, in part due to the lack of a generally accepted protocol for performing such an assessment as well as limitations in predictive performance and scope. There remains a need for additional, improved in silico carcinogenicity models, especially ones that are more human-relevant, for use in research and regulatory decision-making. As part of an international effort to develop in silico toxicological protocols, a consortium of toxicologists, computational scientists, and regulatory scientists across several industries and governmental agencies evaluated the extent to which in silico models exist for each of the recently defined 10 key characteristics (KCs) of carcinogens. This position paper summarizes the current status of in silico tools for the assessment of each KC and identifies the data gaps that need to be addressed before a comprehensive in silico carcinogenicity protocol can be developed for regulatory use.
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Affiliation(s)
- Raymond R Tice
- RTice Consulting, Hillsborough, North Carolina, 27278, USA
| | | | - Alexander Amberg
- Sanofi Preclinical Safety, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Lennart T Anger
- Genentech, Inc., South San Francisco, California, 94080, USA
| | - Marc A Beal
- Healthy Environments and Consumer Safety Branch, Health Canada, Government of Canada, Ottawa, Ontario, Canada K1A 0K9
| | | | | | - Jeffrey Birmingham
- GlaxoSmithKline, David Jack Centre for R&D, Ware, Hertfordshire, SG12 0DP, United Kingdom
| | - Alessandro Brigo
- Roche Pharmaceutical Research & Early Development, Pharmaceutical Sciences, Roche Innovation, Center Basel, F. Hoffmann-La Roche Ltd, CH-4070, Basel, Switzerland
| | | | - Lidia Ceriani
- Humane Society International, 1000 Brussels, Belgium
| | - Ian Crooks
- British American Tobacco (Investments) Ltd, GR&D Centre, Southampton, SO15 8TL, United Kingdom
| | | | - Rosalie Elespuru
- Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, Maryland, 20993, USA
| | - David M Faulkner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marie C Fortin
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey, 08855, USA
| | - Paul Fowler
- FSTox Consulting (Genetic Toxicology), Northamptonshire, United Kingdom
| | | | | | - Gloria D Jahnke
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | | | - Naomi L Kruhlak
- Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, Maryland, 20993, USA
| | - Elena Lo Piparo
- Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | - Juan Lopez-Belmonte
- Cuts Ice Ltd Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | - Amarjit Luniwal
- North American Science Associates (NAMSA) Inc., Minneapolis, Minnesota, 55426, USA
| | - Alice Luu
- Healthy Environments and Consumer Safety Branch, Health Canada, Government of Canada, Ottawa, Ontario, Canada K1A 0K9
| | - Federica Madia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Serena Manganelli
- Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | | | - Jordi Mestres
- IMIM Institut Hospital Del Mar d'Investigacions Mèdiques and Universitat Pompeu Fabra, Doctor Aiguader 88, Parc de Recerca Biomèdica, 08003 Barcelona, Spain; and Chemotargets SL, Baldiri Reixac 4, Parc Científic de Barcelona, 08028, Barcelona, Spain
| | | | - Louise Neilson
- Broughton Nicotine Services, Oak Tree House, Earby, Lancashire, BB18 6JZ United Kingdom
| | - Arun Pandiri
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | | | - Cynthia V Rider
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | - John P Rooney
- Integrated Laboratory Systems, LLC., Morrisville, North Carolina, 27560, USA
| | | | - Karen H Watanabe-Sailor
- School of Mathematical and Natural Sciences, Arizona State University, West Campus, Glendale, Arizona, 85306, USA
| | - Angela T White
- GlaxoSmithKline, David Jack Centre for R&D, Ware, Hertfordshire, SG12 0DP, United Kingdom
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Revollo JR, Miranda JA, Dobrovolsky VN. PacBio sequencing detects genome-wide ultra-low-frequency substitution mutations resulting from exposure to chemical mutagens. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2021; 62:438-445. [PMID: 34424574 DOI: 10.1002/em.22462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Genetic toxicology uses several assays to identity mutagens and protects the public. Most of these assays, however, rely on reporter genes, can only measure mutation indirectly based on phenotype, and often require specific cell lines or animal models-features that impede their integration with existing and emerging toxicological models, such as organoids. In this study, we show that PacBio Single-Molecule, Real-Time (PB SMRT) sequencing identified substitution mutations caused by chemical mutagens in Escherichia coli by generating nearly error-free consensus reads after repeatedly inspecting both strands of circular DNA molecules. Using DNA from E. coli exposed to ethyl methanosulfonate (EMS) or N-ethyl-N-nitrosourea (ENU), PB SMRT sequencing detected mutation frequencies (MFs) and spectra comparable to those obtained by clone-sequencing from the same exposures. The optimized background MF of PB SMRT sequencing was ≤ 1 × 10-7 mutations per base pair (mut/bp).
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Affiliation(s)
- Javier R Revollo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Jaime A Miranda
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Vasily N Dobrovolsky
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
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35
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McKim KL, Myers MB, Harris KL, Gong B, Xu J, Parsons BL. CarcSeq Measurement of Rat Mammary Cancer Driver Mutations and Relation to Spontaneous Mammary Neoplasia. Toxicol Sci 2021; 182:142-158. [PMID: 33822199 DOI: 10.1093/toxsci/kfab040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The ability to deduce carcinogenic potential from subchronic, repeat dose rodent studies would constitute a major advance in chemical safety assessment and drug development. This study investigated an error-corrected NGS method (CarcSeq) for quantifying cancer driver mutations (CDMs) and deriving a metric of clonal expansion predictive of future neoplastic potential. CarcSeq was designed to interrogate subsets of amplicons encompassing hotspot CDMs applicable to a variety of cancers. Previously, normal human breast DNA was analyzed by CarcSeq and metrics based on mammary-specific CDMs were correlated with tissue donor age, a surrogate of breast cancer risk. Here we report development of parallel methodologies for rat. The utility of the rat CarcSeq method for predicting neoplastic potential was investigated by analyzing mammary tissue of 16-week-old untreated rats with known differences in spontaneous mammary neoplasia (Fischer 344, Wistar Han, and Sprague Dawley). Hundreds of mutants with mutant fractions ≥ 10-4 were quantified in each strain, most were recurrent mutations, and 42.5% of the nonsynonymous mutations have human homologs. Mutants in the mammary-specific target of the most tumor-sensitive strain (Sprague Dawley) showed the greatest nonsynonymous/synonymous mutation ratio, indicative of positive selection consistent with clonal expansion. For the mammary-specific target (Hras, Pik3ca, and Tp53 amplicons), median absolute deviation correlated with percentages of rats that develop spontaneous mammary neoplasia at 104 weeks (Pearson r = 1.0000, 1-tailed p = .0010). Therefore, this study produced evidence CarcSeq analysis of spontaneously occurring CDMs can be used to derive an early metric of clonal expansion relatable to long-term neoplastic outcome.
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Affiliation(s)
| | | | | | - Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, USA
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Harris KL, McKim KL, Myers MB, Gong B, Xu J, Parsons BL. Assessment of clonal expansion using CarcSeq measurement of lung cancer driver mutations and correlation with mouse strain- and sex-related incidence of spontaneous lung neoplasia. Toxicol Sci 2021; 184:1-14. [PMID: 34373914 DOI: 10.1093/toxsci/kfab098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Quantification of variation in levels of spontaneously occurring cancer driver mutations (CDMs) was developed to assess clonal expansion and predict future risk of neoplasm development. Specifically, an error-corrected next generation sequencing method, CarcSeq, and a mouse CarcSeq panel (analogous to human and rat panels) were developed and used to quantify low-frequency mutations in a panel of amplicons enriched in hotspot CDMs. Mutations in a subset of panel amplicons, Braf, Egfr, Kras, Stk11 and Tp53, were related to incidence of lung neoplasms at two years. This was achieved by correlating median absolute deviation (MAD) from the overall median mutant fraction (MF) measured in the lung DNA of 16-week-old male and female, B6C3F1 and CD-1 mice (10 mice/sex/strain) with percentages of spontaneous alveolar/bronchioloalveolar adenomas and carcinomas reported in bioassay control groups. 1,586 mouse lung mutants with MFs >1 x 10-4 were recovered. The ratio of non-synonymous to synonymous mutations was used to assess the proportion of recovered mutations conferring a positive selective advantage. The greatest ratio was observed in what is considered the most lung tumor-sensitive model examined, male B6C3F1 mice. Of the recurrent, non-synonymous mouse mutations recovered, 55.5% have been reported in human tumors, with many located in or around the mouse equivalent of human cancer hotspot codons. MAD for the same subset of amplicons measured in normal human lung DNA samples showed a correlation of moderate strength and borderline significance) with age (a cancer risk factor), as well as age-related cumulative lung cancer risk, suggesting MAD may inform species extrapolation.
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Affiliation(s)
- Kelly L Harris
- U.S. Food and Drug Administration, National Center for Toxicological Research, Division of Genetic and Molecular Toxicology, 3900 NCTR Rd, Jefferson, AR, 72079
| | - Karen L McKim
- U.S. Food and Drug Administration, National Center for Toxicological Research, Division of Genetic and Molecular Toxicology, 3900 NCTR Rd, Jefferson, AR, 72079
| | - Meagan B Myers
- U.S. Food and Drug Administration, National Center for Toxicological Research, Division of Genetic and Molecular Toxicology, 3900 NCTR Rd, Jefferson, AR, 72079
| | - Binsheng Gong
- U.S. Food and Drug Administration, National Center for Toxicological Research, Division of Bioinformatics and Biostatistics, 3900 NCTR Rd, Jefferson, AR, 72079
| | - Joshua Xu
- U.S. Food and Drug Administration, National Center for Toxicological Research, Division of Bioinformatics and Biostatistics, 3900 NCTR Rd, Jefferson, AR, 72079
| | - Barbara L Parsons
- U.S. Food and Drug Administration, National Center for Toxicological Research, Division of Genetic and Molecular Toxicology, 3900 NCTR Rd, Jefferson, AR, 72079
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Wang Y, Mittelstaedt RA, Wynne R, Chen Y, Cao X, Muskhelishvili L, Davis K, Robison TW, Sun W, Schmidt EK, Smith TH, Norgaard ZK, Valentine CC, Yaplee J, Williams LN, Salk JJ, Heflich RH. Genetic toxicity testing using human in vitro organotypic airway cultures: Assessing DNA damage with the CometChip and mutagenesis by Duplex Sequencing. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2021; 62:306-318. [PMID: 34050964 PMCID: PMC8251634 DOI: 10.1002/em.22444] [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] [Received: 02/19/2021] [Revised: 05/05/2021] [Accepted: 05/15/2021] [Indexed: 05/10/2023]
Abstract
The organotypic human air-liquid-interface (ALI) airway tissue model has been used as an in vitro cell culture system for evaluating the toxicity of inhaled substances. ALI airway cultures are highly differentiated, which has made it challenging to evaluate genetic toxicology endpoints. In the current study, we assayed DNA damage with the high-throughput CometChip assay and quantified mutagenesis with Duplex Sequencing, an error-corrected next-generation sequencing method capable of detecting a single mutation per 107 base pairs. Fully differentiated human ALI airway cultures were treated from the basolateral side with 6.25 to 100 μg/mL ethyl methanesulfonate (EMS) over a period of 28 days. CometChip assays were conducted after 3 and 28 days of treatment, and Duplex Sequencing after 28 days of treatment. Treating the airway cultures with EMS resulted in time- and concentration-dependent increases in DNA damage and a concentration-dependent increase in mutant frequency. The mutations observed in the EMS-treated cultures were predominantly C → T transitions and exhibited a unique trinucleotide signature relative to the negative control. Measurement of physiological endpoints indicated that the EMS treatments had no effect on anti-p63-positive basal cell frequency, but produced concentration-responsive increases in cytotoxicity and perturbations in cell morphology, along with concentration-responsive decreases in culture viability, goblet cell and anti-Ki67-positive proliferating cell frequency, cilia beating frequency, and mucin secretion. The results indicate that a unified 28-day study can be used to measure several important safety endpoints in physiologically relevant human in vitro ALI airway cultures, including DNA damage, mutagenicity, and tissue-specific general toxicity.
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Affiliation(s)
- Yiying Wang
- U.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansasUSA
| | - Roberta A. Mittelstaedt
- U.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansasUSA
| | - Rebecca Wynne
- U.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansasUSA
| | - Ying Chen
- U.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansasUSA
| | - Xuefei Cao
- U.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansasUSA
| | | | - Kelly Davis
- Toxicologic Pathology AssociatesJeffersonArkansasUSA
| | - Timothy W. Robison
- U.S. Food and Drug Administration, Center for Drug Evaluation and ResearchSilver SpringMarylandUSA
| | - Wei Sun
- U.S. Food and Drug Administration, Center for Drug Evaluation and ResearchSilver SpringMarylandUSA
| | | | | | | | | | | | | | | | - Robert H. Heflich
- U.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansasUSA
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Diaz G S, LeBlanc DP, Gagné R, Behan NA, Wong A, Marchetti F, MacFarlane AJ. Folate Intake Alters Mutation Frequency and Profiles in a Tissue- and Dose-Specific Manner in MutaMouse Male Mice. J Nutr 2021; 151:800-809. [PMID: 33693772 DOI: 10.1093/jn/nxaa402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/09/2020] [Accepted: 11/20/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND While cancer is common, its incidence varies widely by tissue. These differences are attributable to variable risk factors, such as environmental exposure, genetic inheritance, and lifetime number of stem cell divisions in a tissue. Folate deficiency is generally associated with increased risk for colorectal cancer (CRC) and acute lymphocytic leukemia (ALL). Conversely, high folic acid (FA) intake has also been associated with higher CRC risk. OBJECTIVE Our objective was to compare the effect of folate intake on mutant frequency (MF) and types of mutations in the colon and bone marrow of mice. METHODS Five-week-old MutaMouse male mice were fed a deficient (0 mg FA/kg), control (2 mg FA/kg), or supplemented (8 mg FA/kg) diet for 20 wk. Tissue MF was assessed using the lacZ mutant assay and comparisons made by 2-factor ANOVA. LacZ mutant plaques were sequenced using next-generation sequencing, and diet-specific mutation profiles within each tissue were compared by Fisher's exact test. RESULTS In the colon, the MF was 1.5-fold and 1.3-fold higher in mice fed the supplemented diet compared with mice fed the control (P = 0.001) and deficient (P = 0.008) diets, respectively. This contrasted with the bone marrow MF in the same mice where the MF was 1.7-fold and 1.6-fold higher in mice fed the deficient diet compared with mice fed the control (P = 0.02) and supplemented (P = 0.03) diets, respectively. Mutation profiles and signatures (mutation context) were tissue-specific. CONCLUSIONS Our data indicate that dietary folate intake affects mutagenesis in a tissue- and dose-specific manner in mice. Mutation profiles were generally tissue- but not dose-specific, suggesting that altered cellular folate status appears to interact with endogenous mutagenic mechanisms in each tissue to create a permissive context in which specific mutation types accumulate. These data illuminate potential mechanisms underpinning differences in observed associations between folate intake/status and cancer.
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Affiliation(s)
- Stephanie Diaz G
- Nutrition Research Division, Health Canada, Ottawa, Canada.,Department of Biology, Carleton University, Ottawa, Canada
| | | | - Remi Gagné
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | | | - Alex Wong
- Department of Biology, Carleton University, Ottawa, Canada
| | - Francesco Marchetti
- Department of Biology, Carleton University, Ottawa, Canada.,Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Amanda J MacFarlane
- Nutrition Research Division, Health Canada, Ottawa, Canada.,Department of Biology, Carleton University, Ottawa, Canada
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Kirby C, Baig A, Avlasevich SL, Torous DK, Tian S, Singh P, Bemis JC, Saubermann LJ, Dertinger SD. Dextran sulfate sodium mouse model of inflammatory bowel disease evaluated for systemic genotoxicity via blood micronucleus and Pig-a gene mutation assays. Mutagenesis 2020; 35:161-167. [PMID: 32050029 DOI: 10.1093/mutage/geaa006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/24/2020] [Indexed: 12/31/2022] Open
Abstract
Inflammatory bowel disease (IBD) is an important risk factor for gastrointestinal cancers. Inflammation and other carcinogenesis-related effects at distal, tissue-specific sites require further study. In order to better understand if systemic genotoxicity is associated with IBD, we exposed mice to dextran sulfate sodium salt (DSS) and measured the incidence of micronucleated cells (MN) and Pig-a mutant phenotype cells in blood erythrocyte populations. In one study, 8-week-old male CD-1 mice were exposed to 0, 1, 2, 3 or 4% w/v DSS in drinking water. The 4-week in-life period was divided into four 1-week intervals-alternately on then off DSS treatment. Low volume blood samples were collected for MN analysis at the end of each week, and cardiac blood samples were collected at the end of the 4-week period for Pig-a analyses. The two highest doses of DSS were observed to induce significant increases in reticulocyte frequencies. Even so, no statistically significant treatment-related effects on the genotoxicity biomarkers were evident. While one high-dose mouse showed modestly elevated MN frequencies during the DSS treatment cycles, it also exhibited exceptionally high reticulocyte frequencies (e.g. 18.7% at the end of the second DSS cycle). In a second study, mice were treated with 0 or 4% DSS for 9-18 consecutive days. Exposure was continued until rectal bleeding or morbidity was evident, at which point the treatment was terminated and blood was collected for MN analysis. The Pig-a assay was conducted on samples collected 29 days after the start of treatment. The initial blood specimens showed highly elevated reticulocyte frequencies in DSS-exposed mice (mean ± SEM = 1.75 ± 0.10% vs. 13.04 ± 3.66% for 0 vs. 4% mice, respectively). Statistical analyses showed no treatment-related effect on MN or Pig-a mutant frequencies. Even so, the incidence of MN versus reticulocytes in the DSS-exposed mice were positively correlated (linear fit R2 = 0.657, P = 0.0044). Collectively, these results suggest that in the case of the DSS CD-1 mouse model, systemic effects include stress erythropoiesis but not remarkable genotoxicity. To the extent MN may have been slightly elevated in a minority of individual mice, these effects appear to be secondary, likely attributable to stimulated erythropoiesis.
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Affiliation(s)
| | - Ayesha Baig
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY
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Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing. Proc Natl Acad Sci U S A 2020; 117:33414-33425. [PMID: 33318186 PMCID: PMC7776782 DOI: 10.1073/pnas.2013724117] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Error-corrected next-generation sequencing (ecNGS) can be used to rapidly detect and quantify the in vivo mutagenic impact of environmental exposures or endogenous processes in any tissue, from any species, at any genomic location. The greater speed, higher scalability, richer data outputs, and cross-species and cross-locus applicability of ecNGS compared to existing methods make it a powerful new tool for mutational research, regulatory safety testing, and emerging clinical applications. The ability to accurately measure mutations is critical for basic research and identifying potential drug and chemical carcinogens. Current methods for in vivo quantification of mutagenesis are limited because they rely on transgenic rodent systems that are low-throughput, expensive, prolonged, and do not fully represent other species such as humans. Next-generation sequencing (NGS) is a conceptually attractive alternative for detecting mutations in the DNA of any organism; however, the limit of resolution for standard NGS is poor. Technical error rates (∼1 × 10−3) of NGS obscure the true abundance of somatic mutations, which can exist at per-nucleotide frequencies ≤1 × 10−7. Using duplex sequencing, an extremely accurate error-corrected NGS (ecNGS) technology, we were able to detect mutations induced by three carcinogens in five tissues of two strains of mice within 31 d following exposure. We observed a strong correlation between mutation induction measured by duplex sequencing and the gold-standard transgenic rodent mutation assay. We identified exposure-specific mutation spectra of each compound through trinucleotide patterns of base substitution. We observed variation in mutation susceptibility by genomic region, as well as by DNA strand. We also identified a primordial marker of carcinogenesis in a cancer-predisposed strain of mice, as evidenced by clonal expansions of cells carrying an activated oncogene, less than a month after carcinogen exposure. These findings demonstrate that ecNGS is a powerful method for sensitively detecting and characterizing mutagenesis and the early clonal evolutionary hallmarks of carcinogenesis. Duplex sequencing can be broadly applied to basic mutational research, regulatory safety testing, and emerging clinical applications.
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Albertini RJ, Kaden DA. Mutagenicity monitoring in humans: Global versus specific origin of mutations. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 786:108341. [PMID: 33339577 DOI: 10.1016/j.mrrev.2020.108341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 01/19/2023]
Abstract
An underappreciated aspect of human mutagenicity biomonitoring is tissue specificity reflected in different assays, especially those that measure events that can only occur in developing bone marrow (BM) cells. Reviewed here are 9 currently-employed human mutagenicity biomonitoring assays. Several assays measure chromosome-level events in circulating T-lymphocytes (T-cells), i.e., traditional analyses of aberrations, translocation studies involving chromosome painting and fluorescence in situ hybridization (FISH) and determinations of micronuclei (MN). Other T-cell assays measure gene mutations. i.e., hypoxanthine-guanine phosphoriboslytransferase (HPRT) and phosphoribosylinositol glycan class A (PIGA). In addition to the T-cell assays, also reviewed are those assays that measure events in peripheral blood cells that necessarily arose in BM cells, i.e., MN in reticulocytes; glycophorin A (GPA) gene mutations in red blood cells (RBCs), and PIGA gene mutations in RBC or granulocytes. This review considers only cell culture- or cytometry-based assays to describe endpoints measured, methods, optimal sampling times, and sample summaries of typical quantitative and qualitative results. However, to achieve its intended focus on the target cells where events occur, kinetics of the cells of peripheral blood that derive at some point from precursor cells are reviewed to identify body sites and tissues where the genotoxic events originate. Kinetics indicate that in normal adults, measured events in T-cells afford global assessments of in vivo mutagenicity but are not specific for BM effects. Therefore, an agent's capacity for inducing mutations in BM cells cannot be reliably inferred from T-cell assays as the magnitude of effect in BM, if any, is unknown. By contrast, chromosome or gene level mutations measured in RBCs/reticulocytes or granulocytes must originate in BM cells, i.e. in RBC or granulocyte precursors, thereby making them specific indicators for effects in BM. Assays of mutations arising directly in BM cells may quantitatively reflect the mutagenicity of potential leukemogenic agents.
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Affiliation(s)
- Richard J Albertini
- University of Vermont, 111 Colchester Avenue, Burlington, VT 05401, United States
| | - Debra A Kaden
- Ramboll US Consulting, Inc., 101 Federal Street, Suite 1900, Boston, MA 02110, United States.
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Kripke M, Brody JG, Hawk E, Hernandez AB, Hoppin PJ, Jacobs MM, Rudel RA, Rebbeck TR. Rethinking Environmental Carcinogenesis. Cancer Epidemiol Biomarkers Prev 2020; 29:1870-1875. [PMID: 33004408 DOI: 10.1158/1055-9965.epi-20-0541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/07/2020] [Accepted: 06/11/2020] [Indexed: 11/16/2022] Open
Abstract
The 2010 report of the President's Cancer Panel concluded that the burden of cancer from chemical exposures is substantial, while the programs for testing and regulation of carcinogens remain inadequate. New research on the role of early life exposures and the ability of chemicals to act via multiple biological pathways, including immunosuppression, inflammation, and endocrine disruption as well as mutagenesis, further supports the potential for chemicals and chemical mixtures to influence disease. Epidemiologic observations, such as higher leukemia incidence in children living near roadways and industrial sources of air pollution, and new in vitro technologies that decode carcinogenesis at the molecular level, illustrate the diverse evidence that primary prevention of some cancers may be achieved by reducing harmful chemical exposures. The path forward requires cross-disciplinary approaches, increased environmental research investment, system-wide collaboration to develop safer economic alternatives, and community engagement to support evidence-informed action. Engagement by cancer researchers to integrate environmental risk factors into prevention initiatives holds tremendous promise for reducing the rates of disease.See all articles in this CEBP Focus section, "Environmental Carcinogenesis: Pathways to Prevention."
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Affiliation(s)
- Margaret Kripke
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Ernest Hawk
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Polly J Hoppin
- University of Massachusetts Lowell and Lowell Center for Sustainable Production, Lowell, Massachusetts
| | - Molly M Jacobs
- University of Massachusetts Lowell and Lowell Center for Sustainable Production, Lowell, Massachusetts
| | | | - Timothy R Rebbeck
- Dana-Farber Cancer Institute and Harvard TH Chan School of Public Health, Boston, Massachusetts.
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Minocherhomji S, Liu Y, He YD, Fielden MR. Biomarkers of genome instability in normal mammalian genomes following drug-induced replication stress. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:770-785. [PMID: 32078182 DOI: 10.1002/em.22364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/03/2020] [Accepted: 02/16/2020] [Indexed: 06/10/2023]
Abstract
Genome instability is a hallmark of most human cancers and is exacerbated following replication stress. However, the effects that drugs/xenobiotics have in promoting genome instability including chromosomal structural rearrangements in normal cells are not currently assessed in the genetic toxicology battery. Here, we show that drug-induced replication stress leads to increased genome instability in vitro using proliferating primary human cells as well as in vivo in rat bone marrow (BM) and duodenum (DD). p53-binding protein 1 (53BP1, biomarker of DNA damage repair) nuclear bodies were increased in a dose-dependent manner in normal proliferating human mammary epithelial fibroblasts following treatment with compounds traditionally classified as either genotoxic (hydralazine) and nongenotoxic (low-dose aphidicolin, duvelisib, idelalisib, and amiodarone). Comparatively, no increases in 53BP1 nuclear bodies were observed in nonproliferating cells. Negative control compounds (mannitol, alosteron, diclofenac, and zonisamide) not associated with cancer risk did not induce 53BP1 nuclear bodies in any cell type. Finally, we studied the in vivo genomic consequences of drug-induced replication stress in rats treated with 10 mg/kg of cyclophosphamide for up to 14 days followed by polymerase chain reaction-free whole genome sequencing (30X coverage) of BM and DD cells. Cyclophosphamide induced chromosomal structural rearrangements at an average of 90 genes, including 40 interchromosomal/intrachromosomal translocations, within 2 days of treatment. Collectively, these data demonstrate that this drug-induced genome instability test (DiGIT) can reveal potential adverse effects of drugs not otherwise informed by standard genetic toxicology testing batteries. These efforts are aligned with the food and drug administration's (FDA's) predictive toxicology roadmap initiative.
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Affiliation(s)
- Sheroy Minocherhomji
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Inc., Thousand Oaks, California
| | - Yang Liu
- Genome Analysis Unit, Amgen Research, Amgen Inc., Thousand Oaks, California
| | - Yudong D He
- Genome Analysis Unit, Amgen Research, Amgen Inc., Thousand Oaks, California
| | - Mark R Fielden
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Inc., Thousand Oaks, California
- Expansion Therapeutics, San Diego, California
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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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Godschalk RWL, Yauk CL, van Benthem J, Douglas GR, Marchetti F. In utero Exposure to Genotoxicants Leading to Genetic Mosaicism: An Overlooked Window of Susceptibility in Genetic Toxicology Testing? ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:55-65. [PMID: 31743493 PMCID: PMC6973016 DOI: 10.1002/em.22347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/14/2019] [Accepted: 11/17/2019] [Indexed: 05/08/2023]
Abstract
In utero development represents a sensitive window for the induction of mutations. These mutations may subsequently expand clonally to populate entire organs or anatomical structures. Although not all adverse mutations will affect tissue structure or function, there is growing evidence that clonally expanded genetic mosaics contribute to various monogenic and complex diseases, including cancer. We posit that genetic mosaicism is an underestimated potential health problem that is not fully addressed in the current regulatory genotoxicity testing paradigm. Genotoxicity testing focuses exclusively on adult exposures and thus may not capture the complexity of genetic mosaicisms that contribute to human disease. Numerous studies have shown that conversion of genetic damage into mutations during early developmental exposures can result in much higher mutation burdens than equivalent exposures in adults in certain tissues. Therefore, we assert that analysis of genetic effects caused by in utero exposures should be considered in the current regulatory testing paradigm, which is possible by harmonization with current reproductive/developmental toxicology testing strategies. This is particularly important given the recent proposed paradigm change from simple hazard identification to quantitative mutagenicity assessment. Recent developments in sequencing technologies offer practical tools to detect mutations in any tissue or species. In addition to mutation frequency and spectrum, these technologies offer the opportunity to characterize the extent of genetic mosaicism following exposure to mutagens. Such integration of new methods with existing toxicology guideline studies offers the genetic toxicology community a way to modernize their testing paradigm and to improve risk assessment for vulnerable populations. Environ. Mol. Mutagen. 61:55-65, 2020. © 2019 The Authors. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Roger W. L. Godschalk
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM)Maastricht UniversityMaastrichtThe Netherlands
| | - Carole L. Yauk
- Mechanistic Studies DivisionEnvironmental Health Science and Research Bureau, Health CanadaOttawaK1A 0K9OntarioCanada
| | - Jan van Benthem
- Center for Health ProtectionNational Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - George R. Douglas
- Mechanistic Studies DivisionEnvironmental Health Science and Research Bureau, Health CanadaOttawaK1A 0K9OntarioCanada
| | - Francesco Marchetti
- Mechanistic Studies DivisionEnvironmental Health Science and Research Bureau, Health CanadaOttawaK1A 0K9OntarioCanada
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Hanawalt P, Sweasy J. Mechanistic understanding of cellular responses to genomic stress. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:25-33. [PMID: 31793074 DOI: 10.1002/em.22349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Within the past half century we have learned of multiple pathways for repairing damaged DNA, based upon the intrinsic redundancy of information in its complementary double strands. Mechanistic details of these pathways have provided insights into environmental and endogenous threats to genomic stability. Studies on bacterial responses to ultraviolet light led to the discovery of excision repair, as well as the inducible SOS response to DNA damage. Similar responses in eukaryotes promote upregulation of error-prone translesion DNA polymerases. Recent advances in this burgeoning field include duplex DNA sequencing to provide strikingly accurate profiling of mutational signatures, analyses of gene expression patterns in single cells, CRISPR/Cas9 to generate changes at precise genomic positions, novel roles for RNA in gene expression and DNA repair, phase-separated aqueous environments for specialized cellular transactions, and DNA lesions as epigenetic signals for gene expression. The Environmental Mutagenesis and Genomics Society (EMGS), through the broad range of expertise in its membership, stands at the crossroad of basic understanding of mechanisms for genomic maintenance and the field of genetic toxicology, with the need for regulation of exposures to toxic substances. Our future challenges include devising strategies and technologies to identify individuals who are susceptible to specific genomic stresses, along with basic research on the underlying mechanisms of cellular stress responses that promote disease-causing mutations. As the science moves forward it should also be a responsibility for the EMGS to expand its outreach programs for the enlightenment and benefit of all humans and the biosphere. Environ. Mol. Mutagen. 61:25-33, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Philip Hanawalt
- Department of Biology, Stanford University, Stanford, California
| | - Joann Sweasy
- University of Arizona Cancer Center, Tucson, Arizona
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47
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Heflich RH, Johnson GE, Zeller A, Marchetti F, Douglas GR, Witt KL, Gollapudi BB, White PA. Mutation as a Toxicological Endpoint for Regulatory Decision-Making. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:34-41. [PMID: 31600846 DOI: 10.1002/em.22338] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/09/2019] [Accepted: 09/14/2019] [Indexed: 05/23/2023]
Abstract
Mutations induced in somatic cells and germ cells are responsible for a variety of human diseases, and mutation per se has been considered an adverse health concern since the early part of the 20th Century. Although in vitro and in vivo somatic cell mutation data are most commonly used by regulatory agencies for hazard identification, that is, determining whether or not a substance is a potential mutagen and carcinogen, quantitative mutagenicity dose-response data are being used increasingly for risk assessments. Efforts are currently underway to both improve the measurement of mutations and to refine the computational methods used for evaluating mutation data. We recommend continuing the development of these approaches with the objective of establishing consensus regarding the value of including the quantitative analysis of mutation per se as a required endpoint for comprehensive assessments of toxicological risk. Environ. Mol. Mutagen. 61:34-41, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Robert H Heflich
- U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas
| | | | - Andreas Zeller
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - George R Douglas
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Kristine L Witt
- National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | | | - Paul A White
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
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