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Axelsson J, LeBlanc D, Shojaeisaadi H, Meier MJ, Fitzgerald DM, Nachmanson D, Carlson J, Golubeva A, Higgins J, Smith T, Lo FY, Pilsner R, Williams A, Salk J, Marchetti F, Yauk C. Frequency and spectrum of mutations in human sperm measured using duplex sequencing correlate with trio-based de novo mutation analyses. Sci Rep 2024; 14:23134. [PMID: 39379474 PMCID: PMC11461794 DOI: 10.1038/s41598-024-73587-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 09/18/2024] [Indexed: 10/10/2024] Open
Abstract
De novo mutations (DNMs) are drivers of genetic disorders. However, the study of DNMs is hampered by technological limitations preventing accurate quantification of ultra-rare mutations. Duplex Sequencing (DS) theoretically has < 1 error/billion base-pairs (bp). To determine the DS utility to quantify and characterize DNMs, we analyzed DNA from blood and spermatozoa from six healthy, 18-year-old Swedish men using the TwinStrand DS mutagenesis panel (48 kb spanning 20 genic and intergenic loci). The mean single nucleotide variant mutation frequency (MF) was 1.2 × 10- 7 per bp in blood and 2.5 × 10- 8 per bp in sperm, with the most common base substitution being C > T. Blood MF and substitution spectrum were similar to those reported in blood cells with an orthogonal method. The sperm MF was in the same order of magnitude and had a strikingly similar spectrum to DNMs from publicly available whole genome sequencing data from human pedigrees (1.2 × 10- 8 per bp). DS revealed much larger numbers of insertions and deletions in sperm over blood, driven by an abundance of putative extra-chromosomal circular DNAs. The study indicates the strong potential of DS to characterize human DNMs to inform factors that contribute to disease susceptibility and heritable genetic risks.
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Affiliation(s)
- Jonatan Axelsson
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
- Reproductive Medicine Centre, Skåne University Hospital, Malmö, Sweden.
- Department of Translational Medicine, Lund University, Malmö, Sweden.
- Department of Laboratory Medicine, Lund University, Lund, Sweden.
| | - Danielle LeBlanc
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | | | - Matthew J Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | | | | | | | | | | | | | - Fang Yin Lo
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | - Richard Pilsner
- Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, USA
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Jesse Salk
- TwinStrand Biosciences, Inc., Seattle, WA, USA
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Carole Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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2
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Wang Y, Le Y, Harris KL, Chen Y, Li X, Faske J, Wynne RA, Mittelstaedt RA, Cao X, Miranda-Colon J, Elkins L, Muskhelishvili L, Davis K, Mei N, Sun W, Robison TW, Heflich RH, Parsons BL. Repeat treatment of organotypic airway cultures with ethyl methanesulfonate causes accumulation of somatic cell mutations without expansion of bronchial-carcinoma-specific cancer driver mutations. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 897:503786. [PMID: 39054009 DOI: 10.1016/j.mrgentox.2024.503786] [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: 03/06/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/27/2024]
Abstract
The human in vitro organotypic air-liquid-interface (ALI) airway tissue model is structurally and functionally similar to the human large airway epithelium and, as a result, is being used increasingly for studying the toxicity of inhaled substances. Our previous research demonstrated that DNA damage and mutagenesis can be detected in human airway tissue models under conditions used to assess general and respiratory toxicity endpoints. Expanding upon our previous proof-of-principle study, human airway epithelial tissue models were treated with 6.25-100 µg/mL ethyl methanesulfonate (EMS) for 28 days, followed by a 28-day recovery period. Mutagenesis was evaluated by Duplex Sequencing (DS), and clonal expansion of bronchial-cancer-specific cancer-driver mutations (CDMs) was investigated by CarcSeq to determine if both mutation-based endpoints can be assessed in the same system. Additionally, DNA damage and tissue-specific responses were analyzed during the treatment and following the recovery period. EMS exposure led to time-dependent increases in mutagenesis over the 28-day treatment period, without expansion of clones containing CDMs; the mutation frequencies remained elevated following the recovery. EMS also produced an increase in DNA damage measured by the CometChip and MultiFlow assays and the elevated levels of DNA damage were reduced (but not eliminated) following the recovery period. Cytotoxicity and most tissue-function changes induced by EMS treatment recovered to control levels, the exception being reduced proliferating cell frequency. Our results indicate that general, respiratory-tissue-specific and genotoxicity endpoints increased with repeat EMS dosing; expansion of CDM clones, however, was not detected using this repeat treatment protocol. DISCLAIMER: This article reflects the views of its authors and does not necessarily reflect those of the U.S. Food and Drug Administration. Any mention of commercial products is for clarification only and is not intended as approval, endorsement, or recommendation.
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Affiliation(s)
- Yiying Wang
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Yuan Le
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Kelly L Harris
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Ying Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Xilin Li
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Jennifer Faske
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Rebecca A Wynne
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Roberta A Mittelstaedt
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Xuefei Cao
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Jaime Miranda-Colon
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Lana Elkins
- Toxicologic Pathology Associates, Jefferson, AR 72079, USA
| | | | - Kelly Davis
- Toxicologic Pathology Associates, Jefferson, AR 72079, USA
| | - Nan Mei
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Wei Sun
- Division of Pharmacology/Toxicology for Immunology & Inflammation, Office of Immunology and Inflammation, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Timothy W Robison
- Division of Pharmacology/Toxicology for Immunology & Inflammation, Office of Immunology and Inflammation, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
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3
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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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4
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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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5
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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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6
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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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7
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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: 2] [Impact Index Per Article: 2.0] [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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8
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Smith JT, Noren Hooten N, Mode NA, Zonderman AB, Ezike N, Kaushal S, Evans MK. Frailty, sex, and poverty are associated with DNA damage and repair in frail, middle-aged urban adults. DNA Repair (Amst) 2023; 129:103530. [PMID: 37437502 PMCID: PMC10807508 DOI: 10.1016/j.dnarep.2023.103530] [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: 12/09/2022] [Revised: 04/17/2023] [Accepted: 06/27/2023] [Indexed: 07/14/2023]
Abstract
Frailty is an age-related syndrome characterized by reduced recovery from stressors and increased risks of morbidity and mortality. Although frailty is usually studied in those over 65 years, our previous work showed that frailty is both present and a risk factor for premature mortality in midlife. We identified altered gene expression patterns and biological pathways associated with inflammation in frailty. Evidence suggests DNA oxidation damage related to inflammation accumulates with age, and that DNA repair capacity (DRC) declines with age and age-related conditions. We hypothesized that inter-individual differences in DNA oxidation damage and DRC are associated with frailty status and poverty level. Using the CometChip assay, we assessed baseline single-strand breaks and hydrogen peroxide (H2O2)-induced DNA oxidation damage and DRC in non-frail and frail middle-aged African American and White individuals with household incomes above and below poverty. Analysis of baseline single-strand breaks showed no associations with frailty, poverty, race, or sex. However, we identified an interaction between frailty and poverty in H2O2-induced DNA oxidation damage. We also identified interactions between sex and frailty as well as sex and poverty status with DRC. The social determinant of health, poverty, associates with DRC in men. Baseline DNA damage, H2O2-induced DNA damage as well as DRC were associated with serum cytokine levels. IL-10 levels were inversely associated with baseline DNA damage as well as H2O2-induced DNA damage, DRC was altered by IL-4 levels and sex, and by TNF-α levels in the context of sex and poverty status. This is the first evidence that DRC may be influenced by poverty status at midlife. Our data show that social determinants of health should be considered in examining biological pathways through which disparate age-related health outcomes become manifest.
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Affiliation(s)
- Jessica T Smith
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Nicole Noren Hooten
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Nicolle A Mode
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Ngozi Ezike
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
| | - Simran Kaushal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States.
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9
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Lynch AM, Zanoni TB, Salk JJ, Martincorena I, Young RR, Kucab J, Valentine CC, Yauk C, Escobar PA, Witt KL, Frötschl R, Reed SH, Ashford A. Next Generation Sequencing Workshop at the Royal Society of Medicine (London, May 2022): how genomics is on the path to modernizing genetic toxicology. Mutagenesis 2023; 38:192-200. [PMID: 37300447 PMCID: PMC10687350 DOI: 10.1093/mutage/gead012] [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: 03/19/2023] [Indexed: 06/12/2023] Open
Abstract
The use of error-corrected Next Generation Sequencing (ecNG) to determine mutagenicity has been a subject of growing interest and potentially a disruptive technology that could supplement, and in time, replace current testing paradigms in preclinical safety assessment. Considering this, a Next Generation Sequencing Workshop was held at the Royal Society of Medicine in London in May 2022, supported by the United Kingdom Environmental Mutagen Society (UKEMS) and TwinStrand Biosciences (WA, USA), to discuss progress and future applications of this technology. In this meeting report, the invited speakers provide an overview of the Workshop topics covered and identify future directions for research. In the area of somatic mutagenesis, several speakers reviewed recent progress made with correlating ecNGS to classic in vivo transgenic rodent mutation assays as well as exploring the use of this technology directly in humans and animals, and in complex organoid models. Additionally, ecNGS has been used for detecting off-target effects of gene editing tools and emerging data suggest ecNGS potential to measure clonal expansion of cells carrying mutations in cancer driver genes as an early marker of carcinogenic potential and for direct human biomonitoring. As such, the workshop demonstrated the importance of raising awareness and support for advancing the science of ecNGS for mutagenesis, gene editing, and carcinogenesis research. Furthermore, the potential of this new technology to contribute to advances in drug and product development and improve safety assessment was extensively explored.
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Affiliation(s)
- Anthony M Lynch
- GSK R&D, Stevenage, United Kingdom
- School of Medicine, Swansea University, Swansea, United Kingdom
| | | | - Jesse J Salk
- TwinStrand Biosciences, Seattle, WA, United States
- Division of Medical Oncology, University of Washington, Seattle, WA, United States
- Fred Hutch Cancer Center, Seattle, WA, United States
| | - Inigo Martincorena
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Jill Kucab
- Genetic and Environmental Toxicology, King’s College, London, United Kingdom
| | | | - Carole Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | | | - Kristine L Witt
- National Institute of Environmental Health Sciences, Division of Translational Toxicology, Research Triangle Park, NC, United States
| | - Roland Frötschl
- Federal Institute for Drugs and Medical Devices (Bundesinstitiut für Arzneimittel und Medizinprodukte), Bonn, Germany
| | - Simon H Reed
- School of Medicine, Division of Cancer and Genetics, Cardiff University, Cardiff, CF14 4XN, United Kingdom
| | - Anne Ashford
- Safety Innovation, Safety Sciences, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
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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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11
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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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12
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Wilson TE, Ahmed S, Higgins J, Salk J, Glover T. svCapture: efficient and specific detection of very low frequency structural variant junctions by error-minimized capture sequencing. NAR Genom Bioinform 2023; 5:lqad042. [PMID: 37181851 PMCID: PMC10167630 DOI: 10.1093/nargab/lqad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/15/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Error-corrected sequencing of genomic targets enriched by probe-based capture has become a standard approach for detecting single-nucleotide variants (SNVs) and small insertion/deletions (indels) present at very low variant allele frequencies. Less attention has been given to comparable strategies for rare structural variant (SV) junctions, where different error mechanisms must be addressed. Working from samples with known SV properties, we demonstrate that duplex sequencing (DuplexSeq), which demands confirmation of variants on both strands of a source DNA molecule, eliminates false SV junctions arising from chimeric PCR. DuplexSeq could not address frequent intermolecular ligation artifacts that arise during Y-adapter addition prior to strand denaturation without requiring multiple source molecules. In contrast, tagmentation libraries coupled with data filtering based on strand family size greatly reduced both artifact classes and enabled efficient and specific detection of single-molecule SV junctions. The throughput of SV capture sequencing (svCapture) and base-level accuracy of DuplexSeq provided detailed views of the microhomology profile and limited occurrence of de novo SNVs near the junctions of hundreds of newly created SVs, suggesting end joining as a possible formation mechanism. The open source svCapture pipeline enables rare SV detection as a routine addition to SNVs/indels in properly prepared capture sequencing libraries.
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Affiliation(s)
- Thomas E Wilson
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Samreen Ahmed
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jake Higgins
- TwinStrand Biosciences Inc., Seattle, WA 98121, USA
| | - Jesse J Salk
- TwinStrand Biosciences Inc., Seattle, WA 98121, USA
| | - Thomas W Glover
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
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13
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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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14
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Munakata S, Watanabe T, Takahashi T, Kimuro S, Ishimori K, Hashizume T. Development of a micronucleus test using the EpiAirway™ organotypic human airway model. Genes Environ 2023; 45:14. [PMID: 37046355 PMCID: PMC10099928 DOI: 10.1186/s41021-023-00269-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND The use of organotypic human tissue models in genotoxicity has increased as an alternative to animal testing. Genotoxicity is generally examined using a battery of in vitro assays such as Ames and micronucleus (MN) tests that cover gene mutations and structural and numerical chromosome aberrations. At the 7th International Workshop on Genotoxicity Testing, working group members agreed that the skin models have reached an advanced stage of maturity, while further efforts in liver and airway models are needed [Pfuhler et al., Mutat. Res. 850-851 (2020) 503135]. Organotypic human airway model is composed of fully differentiated and functional respiratory epithelium. However, because cell proliferation in organotypic airway models is thought to be less active, assessing their MN-inducing potential is an issue, even in the cytokinesis-blocking approach using cytochalasin B (CB) [Wang et al., Environ. Mol. Mutagen. 62 (2021) 306-318]. Here, we developed a MN test using EpiAirway™ in which epidermal growth factor (EGF) was included as a stimulant of cell division. RESULTS By incubating EpiAirway™ tissue with medium containing various concentrations of CB, we found that the percentage of binucleated cells (%BNCs) almost plateaued at 3 μg/mL CB for 72 h incubation. Additionally, we confirmed that EGF stimulation with CB incubation produced an additional increase in %BNCs with a peak at 5 ng/mL EGF. Transepithelial electrical resistance measurement and tissue histology revealed that CB incubation caused the reduced barrier integrity and cyst formation in EpiAirway™. Adenylate kinase assay confirmed that the cytotoxicity increased with each day of culture in the CB incubation period with EGF stimulation. These results indicated that chemical treatment should be conducted prior to CB incubation. Under these experimental conditions, it was confirmed that the frequency of micronucleated cells was dose-dependently increased by apical applications of two clastogens, mitomycin C and methyl methanesulfonate, and an aneugen, colchicine, at the subcytotoxic concentrations assessed in %BNCs. CONCLUSIONS Well-studied genotoxicants demonstrated capability in an organotypic human airway model as a MN test system. For further utilization, investigations of aerosol exposure, repeating exposure protocol, and metabolic activation are required.
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Affiliation(s)
- Satoru Munakata
- Scientific Product Assessment Center, Japan Tobacco Inc, 6-2, Umegaoka, Aoba-Ku, Yokohama, Kanagawa, 227-8512, Japan
| | - Taku Watanabe
- Scientific Product Assessment Center, Japan Tobacco Inc, 6-2, Umegaoka, Aoba-Ku, Yokohama, Kanagawa, 227-8512, Japan
| | - Tomohiro Takahashi
- Scientific Product Assessment Center, Japan Tobacco Inc, 6-2, Umegaoka, Aoba-Ku, Yokohama, Kanagawa, 227-8512, Japan
| | - Shiori Kimuro
- Scientific Product Assessment Center, Japan Tobacco Inc, 6-2, Umegaoka, Aoba-Ku, Yokohama, Kanagawa, 227-8512, Japan
| | - Kanae Ishimori
- Scientific Product Assessment Center, Japan Tobacco Inc, 6-2, Umegaoka, Aoba-Ku, Yokohama, Kanagawa, 227-8512, Japan
| | - Tsuneo Hashizume
- Scientific Product Assessment Center, Japan Tobacco Inc, 6-2, Umegaoka, Aoba-Ku, Yokohama, Kanagawa, 227-8512, Japan.
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15
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Error-corrected next-generation sequencing to advance nonclinical genotoxicity and carcinogenicity testing. Nat Rev Drug Discov 2023; 22:165-166. [PMID: 36646809 DOI: 10.1038/d41573-023-00014-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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16
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Beal MA, Audebert M, Barton-Maclaren T, Battaion H, Bemis JC, Cao X, Chen C, Dertinger SD, Froetschl R, Guo X, Johnson G, Hendriks G, Khoury L, Long AS, Pfuhler S, Settivari RS, Wickramasuriya S, White P. Quantitative in vitro to in vivo extrapolation of genotoxicity data provides protective estimates of in vivo dose. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2023; 64:105-122. [PMID: 36495195 DOI: 10.1002/em.22521] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Genotoxicity assessment is a critical component in the development and evaluation of chemicals. Traditional genotoxicity assays (i.e., mutagenicity, clastogenicity, and aneugenicity) have been limited to dichotomous hazard classification, while other toxicity endpoints are assessed through quantitative determination of points-of-departures (PODs) for setting exposure limits. The more recent higher-throughput in vitro genotoxicity assays, many of which also provide mechanistic information, offer a powerful approach for determining defined PODs for potency ranking and risk assessment. In order to obtain relevant human dose context from the in vitro assays, in vitro to in vivo extrapolation (IVIVE) models are required to determine what dose would elicit a concentration in the body demonstrated to be genotoxic using in vitro assays. Previous work has demonstrated that application of IVIVE models to in vitro bioactivity data can provide PODs that are protective of human health, but there has been no evaluation of how these models perform with in vitro genotoxicity data. Thus, the Genetic Toxicology Technical Committee, under the Health and Environmental Sciences Institute, conducted a case study on 31 reference chemicals to evaluate the performance of IVIVE application to genotoxicity data. The results demonstrate that for most chemicals considered here (20/31), the PODs derived from in vitro data and IVIVE are health protective relative to in vivo PODs from animal studies. PODs were also protective by assay target: mutations (8/13 chemicals), micronuclei (9/12), and aneugenicity markers (4/4). It is envisioned that this novel testing strategy could enhance prioritization, rapid screening, and risk assessment of genotoxic chemicals.
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Affiliation(s)
- Marc A Beal
- Bureau of Chemical Safety, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Marc Audebert
- Toxalim UMR1331, Toulouse University, INRAE, Toulouse, France
| | - Tara Barton-Maclaren
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Hannah Battaion
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | | | - Xuefei Cao
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Connie Chen
- Health and Environmental Sciences Institute, Washington, District of Columbia, USA
| | | | | | - Xiaoqing Guo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | | | | | - Alexandra S Long
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Stefan Pfuhler
- Global Product Stewardship, Procter & Gamble, Cincinnati, Ohio, USA
| | - Raja S Settivari
- Mammalian Toxicology Center, Corteva Agriscience, Newark, Delaware, USA
| | - Shamika Wickramasuriya
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Paul White
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
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17
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Miranda JA, Alund AW, Yan J, McKinzie PB, Dobrovolsky VN, Revollo JR. Genome-wide detection of ultralow-frequency substitution mutations in cultures of mouse lymphoma L5178Y cells and Caenorhabditis elegans worms by PacBio sequencing. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2022; 63:68-75. [PMID: 35224786 DOI: 10.1002/em.22473] [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: 11/22/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
Many conventional genetic toxicology assays require specialized cell cultures or animals and can only detect mutations that inactivate the function of a reporter gene. These limitations make such assays incompatible with many toxicological models but could be overcome by the development of techniques capable of directly detecting genome-wide somatic mutations through DNA sequencing. PacBio sequencing can generate almost error-free consensus reads by repeatedly inspecting both DNA strands from circularized molecules (a method known as PacBio HiFi). In this study, we show that PacBio HiFi can detect genome-wide ultralow-frequency substitution mutations in cultures of mouse lymphoma L5178Y cells and Caenorhabditis elegans worms. The mutation frequencies (MFs) of unexposed samples in both models were ~1 × 10-7 mutations per base pair. Compared to these controls, PacBio HiFi detected MF increases of 23-fold in cultures of L5178Y cells exposed to 5 mM ethyl methanosulfonate (EMS) for 4 h, and 5-, 12-, and 29-fold in cultures of C. elegans worms exposed to 12.5, 25, and 50 mM EMS for 4 h, respectively. In both models, the mutation spectra of controls were diverse, while those derived from EMS-exposed samples were dominated by C:G → T:A transitions. To validate these results, clone sequencing analyses were performed on the same cultures of L5178Y cells. The results obtained by clone sequencing and PacBio HiFi were almost identical. Our results suggest that PacBio sequencing could be used for the detection, quantitation, and characterization of mutations in any DNA-containing sample, including those that are not compatible with conventional mutation detection approaches.
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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
| | - Alexander W Alund
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Jian Yan
- 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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18
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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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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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