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Liebal UW, Phan ANT, Sudhakar M, Raman K, Blank LM. Machine Learning Applications for Mass Spectrometry-Based Metabolomics. Metabolites 2020; 10:E243. [PMID: 32545768 PMCID: PMC7345470 DOI: 10.3390/metabo10060243] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
The metabolome of an organism depends on environmental factors and intracellular regulation and provides information about the physiological conditions. Metabolomics helps to understand disease progression in clinical settings or estimate metabolite overproduction for metabolic engineering. The most popular analytical metabolomics platform is mass spectrometry (MS). However, MS metabolome data analysis is complicated, since metabolites interact nonlinearly, and the data structures themselves are complex. Machine learning methods have become immensely popular for statistical analysis due to the inherent nonlinear data representation and the ability to process large and heterogeneous data rapidly. In this review, we address recent developments in using machine learning for processing MS spectra and show how machine learning generates new biological insights. In particular, supervised machine learning has great potential in metabolomics research because of the ability to supply quantitative predictions. We review here commonly used tools, such as random forest, support vector machines, artificial neural networks, and genetic algorithms. During processing steps, the supervised machine learning methods help peak picking, normalization, and missing data imputation. For knowledge-driven analysis, machine learning contributes to biomarker detection, classification and regression, biochemical pathway identification, and carbon flux determination. Of important relevance is the combination of different omics data to identify the contributions of the various regulatory levels. Our overview of the recent publications also highlights that data quality determines analysis quality, but also adds to the challenge of choosing the right model for the data. Machine learning methods applied to MS-based metabolomics ease data analysis and can support clinical decisions, guide metabolic engineering, and stimulate fundamental biological discoveries.
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Affiliation(s)
- Ulf W. Liebal
- Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany;
| | - An N. T. Phan
- Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany;
| | - Malvika Sudhakar
- Department of Biotechnology, Bhupat and Juoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India; (M.S.); (K.R.)
- Initiative for Biological Systems Engineering, IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Juoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India; (M.S.); (K.R.)
- Initiative for Biological Systems Engineering, IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Lars M. Blank
- Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany;
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Wei R, Li P, He F, Wei G, Zhou Z, Su Z, Ni T. Comprehensive analysis reveals distinct mutational signature and its mechanistic insights of alcohol consumption in human cancers. Brief Bioinform 2020; 22:5841903. [PMID: 32480415 DOI: 10.1093/bib/bbaa066] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Alcohol consumption is a critical risk factor for multiple types of cancer. A genome can be attacked and acquire numerous somatic mutations in the environment of alcohol exposure. Mutational signature has the capacity illustrating the complex somatic mutation patterns in cancer genome. Recent studies have discovered distinct mutational signatures associating with alcohol consumption in liver and esophageal cancers. However, their prevalence among diverse cancers, impact of genetic background and origin of alcohol-induced mutational signatures remain unclear. By a comprehensive bioinformatics analysis on somatic mutations from patients of four cancer types with drinking information, we identified nine mutational signatures (signatures B-J), among which signature J (similar to COSMIC signature 16) was distinctive to alcohol drinking. Signature J was associated with HNSC, ESCA and LIHC but not PAAD. Interestingly, patients with mutated allele rs1229984 in ADH1B had lower level of signature J while mutated allele rs671 in ALDH2 exhibited higher signature J abundance, suggesting acetaldehyde is one cause of signature J. Intriguingly, somatic mutations of three potential cancer driver genes (TP53, CUL3 and NSD1) were found the critical contributors for increased mutational load of signature J in alcohol consumption patients. Furthermore, signature J was enriched with early accumulated clonal mutations compared to mutations derived from late tumor growth. This study systematically characterized alcohol-related mutational signature and indicated mechanistic insights into the prevalence, origin and gene-environment interaction regarding the risk oncogenic mutations associated with alcohol intake.
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Volkova NV, Meier B, González-Huici V, Bertolini S, Gonzalez S, Vöhringer H, Abascal F, Martincorena I, Campbell PJ, Gartner A, Gerstung M. Mutational signatures are jointly shaped by DNA damage and repair. Nat Commun 2020; 11:2169. [PMID: 32358516 PMCID: PMC7195458 DOI: 10.1038/s41467-020-15912-7] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 03/26/2020] [Indexed: 02/08/2023] Open
Abstract
Cells possess an armamentarium of DNA repair pathways to counter DNA damage and prevent mutation. Here we use C. elegans whole genome sequencing to systematically quantify the contributions of these factors to mutational signatures. We analyse 2,717 genomes from wild-type and 53 DNA repair defective backgrounds, exposed to 11 genotoxins, including UV-B and ionizing radiation, alkylating compounds, aristolochic acid, aflatoxin B1, and cisplatin. Combined genotoxic exposure and DNA repair deficiency alters mutation rates or signatures in 41% of experiments, revealing how different DNA alterations induced by the same genotoxin are mended by separate repair pathways. Error-prone translesion synthesis causes the majority of genotoxin-induced base substitutions, but averts larger deletions. Nucleotide excision repair prevents up to 99% of point mutations, almost uniformly across the mutation spectrum. Our data show that mutational signatures are joint products of DNA damage and repair and suggest that multiple factors underlie signatures observed in cancer genomes.
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Affiliation(s)
- Nadezda V Volkova
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10, 1SD, UK
| | - Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, Scotland
| | - Víctor González-Huici
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, Scotland
- Institute for Research in Biomedicine (IRB Barcelona), Parc Científic de Barcelona, 08028, Barcelona, Spain
| | - Simone Bertolini
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, Scotland
| | - Santiago Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10, 1SD, UK
- Institute for Research in Biomedicine (IRB Barcelona), Parc Científic de Barcelona, 08028, Barcelona, Spain
| | - Harald Vöhringer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10, 1SD, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Haematology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, DD1 5EH, Scotland.
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 689-798, Republic of Korea.
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 689-798, Republic of Korea.
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10, 1SD, UK.
- European Molecular Biology Laboratory, Genome Biology Unit, 69177, Heidelberg, Germany.
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Melki PN, Korenjak M, Zavadil J. Experimental investigations of carcinogen-induced mutation spectra: Innovation, challenges and future directions. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2020; 853:503195. [PMID: 32522347 DOI: 10.1016/j.mrgentox.2020.503195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 11/18/2022]
Abstract
Recent years have witnessed an expansion of mutagenesis research focusing on experimentally modeled genome-scale mutational signatures of carcinogens and of endogenous processes. Experimental mutational signatures can explain etiologic links to patterns found in human tumors that may be linked to same exposures, and can serve as biomarkers of exposure history and may even provide insights on causality. A number of innovative exposure models have been employed and reported, based on cells cultured in monolayers or in 3-D, on organoids, induced pluripotent stem cells, non-mammalian organisms, microorganisms and rodent bioassays. Here we discuss some of the latest developments and pros and cons of these experimental systems used in mutational signature analysis. Integrative designs that bring together multiple exposure systems (in vitro, in vivo and in silico pan-cancer data mining) started emerging as powerful tools to identify robust mutational signatures of the tested cancer risk agents. We further propose that devising a new generation of cell-based models is warranted to streamline systematic testing of carcinogen effects on the cell genomes, while seeking to increasingly supplant animal with non-animal systems to address relevant ethical issues and accentuate the 3R principles. We conclude that the knowledge accumulating from the growing body of signature modelling investigations has considerable power to advance cancer etiology studies and to support cancer prevention efforts through streamlined characterization of cancer-causing agents and the recognition of their specific effects.
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Affiliation(s)
- Pamela N Melki
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France
| | - Michael Korenjak
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France
| | - Jiri Zavadil
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France.
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Schrenk D, Bignami M, Bodin L, Chipman JK, del Mazo J, Grasl‐Kraupp B, Hogstrand C, Hoogenboom L(R, Leblanc J, Nebbia CS, Nielsen E, Ntzani E, Petersen A, Sand S, Schwerdtle T, Vleminckx C, Marko D, Oswald IP, Piersma A, Routledge M, Schlatter J, Baert K, Gergelova P, Wallace H. Risk assessment of aflatoxins in food. EFSA J 2020; 18:e06040. [PMID: 32874256 PMCID: PMC7447885 DOI: 10.2903/j.efsa.2020.6040] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
EFSA was asked to deliver a scientific opinion on the risks to public health related to the presence of aflatoxins in food. The risk assessment was confined to aflatoxin B1 (AFB1), AFB2, AFG1, AFG2 and AFM1. More than 200,000 analytical results on the occurrence of aflatoxins were used in the evaluation. Grains and grain-based products made the largest contribution to the mean chronic dietary exposure to AFB1 in all age classes, while 'liquid milk' and 'fermented milk products' were the main contributors to the AFM1 mean exposure. Aflatoxins are genotoxic and AFB1 can cause hepatocellular carcinomas (HCCs) in humans. The CONTAM Panel selected a benchmark dose lower confidence limit (BMDL) for a benchmark response of 10% of 0.4 μg/kg body weight (bw) per day for the incidence of HCC in male rats following AFB1 exposure to be used in a margin of exposure (MOE) approach. The calculation of a BMDL from the human data was not appropriate; instead, the cancer potencies estimated by the Joint FAO/WHO Expert Committee on Food Additives in 2016 were used. For AFM1, a potency factor of 0.1 relative to AFB1 was used. For AFG1, AFB2 and AFG2, the in vivo data are not sufficient to derive potency factors and equal potency to AFB1 was assumed as in previous assessments. MOE values for AFB1 exposure ranged from 5,000 to 29 and for AFM1 from 100,000 to 508. The calculated MOEs are below 10,000 for AFB1 and also for AFM1 where some surveys, particularly for the younger age groups, have an MOE below 10,000. This raises a health concern. The estimated cancer risks in humans following exposure to AFB1 and AFM1 are in-line with the conclusion drawn from the MOEs. The conclusions also apply to the combined exposure to all five aflatoxins.
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56
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Koh G, Zou X, Nik-Zainal S. Mutational signatures: experimental design and analytical framework. Genome Biol 2020; 21:37. [PMID: 32059681 PMCID: PMC7023746 DOI: 10.1186/s13059-020-1951-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/30/2020] [Indexed: 12/21/2022] Open
Abstract
Mutational signatures provide a powerful alternative for understanding the pathophysiology of cancer. Currently, experimental efforts aimed at validating and understanding the etiologies of cancer-derived mutational signatures are underway. In this review, we highlight key aspects of mutational signature experimental design and describe the analytical framework. We suggest guidelines and quality control measures for handling whole-genome sequencing data for mutational signature analyses and discuss pitfalls in interpretation. We envision that improved next-generation sequencing technologies and molecular cell biology approaches will usher in the next generation of studies into the etiologies and mechanisms of mutational patterns uncovered in cancers.
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Affiliation(s)
- Gene Koh
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Xueqing Zou
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Serena Nik-Zainal
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK.
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0XZ, UK.
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57
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Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SMA, Lopez-Bigas N, Klimczak LJ, McPherson JR, Morganella S, Sabarinathan R, Wheeler DA, Mustonen V, Getz G, Rozen SG, Stratton MR. The repertoire of mutational signatures in human cancer. Nature 2020; 578:94-101. [PMID: 32025018 PMCID: PMC7054213 DOI: 10.1038/s41586-020-1943-3] [Citation(s) in RCA: 1873] [Impact Index Per Article: 468.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/18/2019] [Indexed: 01/27/2023]
Abstract
Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature1. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium2 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses3-15, enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated-but distinct-DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer.
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Affiliation(s)
- Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, Department of Bioengineering, Moores Cancer Center, University of California, San Diego, CA, USA
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas J Haradhvala
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Mi Ni Huang
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Alvin Wei Tian Ng
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Yang Wu
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Arnoud Boot
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Kyle R Covington
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), Durham, NC, USA
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, Department of Bioengineering, Moores Cancer Center, University of California, San Diego, CA, USA
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine, Department of Bioengineering, Moores Cancer Center, University of California, San Diego, CA, USA
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences (NIEHS), Durham, NC, USA
| | - John R McPherson
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | | | - Radhakrishnan Sabarinathan
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ville Mustonen
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Steven G Rozen
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore.
- SingHealth, Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, Singapore.
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58
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Salk JJ, Kennedy SR. Next-Generation Genotoxicology: Using Modern Sequencing Technologies to Assess Somatic Mutagenesis and Cancer Risk. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:135-151. [PMID: 31595553 PMCID: PMC7003768 DOI: 10.1002/em.22342] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 05/09/2023]
Abstract
Mutations have a profound effect on human health, particularly through an increased risk of carcinogenesis and genetic disease. The strong correlation between mutagenesis and carcinogenesis has been a driving force behind genotoxicity research for more than 50 years. The stochastic and infrequent nature of mutagenesis makes it challenging to observe and to study. Indeed, decades have been spent developing increasingly sophisticated assays and methods to study these low-frequency genetic errors, in hopes of better predicting which chemicals may be carcinogens, understanding their mode of action, and informing guidelines to prevent undue human exposure. While effective, widely used genetic selection-based technologies have a number of limitations that have hampered major advancements in the field of genotoxicity. Emerging new tools, in the form of enhanced next-generation sequencing platforms and methods, are changing this paradigm. In this review, we discuss rapidly evolving sequencing tools and technologies, such as error-corrected sequencing and single cell analysis, which we anticipate will fundamentally reshape the field. In addition, we consider a variety emerging applications for these new technologies, including the detection of DNA adducts, inference of mutational processes based on genomic site and local sequence contexts, and evaluation of genome engineering fidelity, as well as other cutting-edge challenges for the next 50 years of environmental and molecular mutagenesis research. Environ. Mol. Mutagen. 61:135-151, 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)
- Jesse J. Salk
- Department of Medicine, Division of Medical OncologyUniversity of Washington School of MedicineSeattleWashington
- TwinStrand BiosciencesSeattleWashington
| | - Scott R. Kennedy
- Department of PathologyUniversity of WashingtonSeattleWashington
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Recognition of DNA adducts by edited and unedited forms of DNA glycosylase NEIL1. DNA Repair (Amst) 2019; 85:102741. [PMID: 31733589 DOI: 10.1016/j.dnarep.2019.102741] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/18/2022]
Abstract
Pre-mRNA encoding human NEIL1 undergoes editing by adenosine deaminase ADAR1 that converts a single adenosine to inosine, and this conversion results in an amino acid change of lysine 242 to arginine. Previous investigations of the catalytic efficiencies of the two forms of the enzyme revealed differential release of thymine glycol (ThyGly) from synthetic oligodeoxynucleotides, with the unedited form, NEIL1 K242 being ≈30-fold more efficient than the edited NEIL1 K242R. In contrast, when these enzymes were reacted with oligodeoxynucleotides containing guanidinohydantoin or spiroiminohydantoin, the edited K242R form was ≈3-fold more efficient than the unedited NEIL1. However, no prior studies have investigated the efficiencies of these two forms of NEIL1 on either high-molecular weight DNA containing multiple oxidatively-induced base damages, or oligodeoxynucleotides containing a bulky alkylated formamidopyrimidine. To understand the extent of changes in substrate recognition, γ-irradiated calf thymus DNA was treated with either edited or unedited NEIL1 and the released DNA base lesions analyzed by gas chromatography-tandem mass spectrometry. Of all the measured DNA lesions, imidazole ring-opened 4,6-diamino-5-formamidopyrimidine (FapyAde) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua) were preferentially released by both NEIL1 enzymes with K242R being ≈1.3 and 1.2-fold more efficient than K242 on excision of FapyAde and FapyGua, respectively. Consistent with the prior literature, large differences (≈7.5 to 12-fold) were measured in the excision of ThyGly from genomic DNA by the unedited versus edited NEIL1. In contrast, the edited NEIL1 was more efficient (≈3 to 5-fold) on release of 5-hydroxycytosine. Excision kinetics on DNA containing a site-specific aflatoxin B1-FapyGua adduct revealed an ≈1.4-fold higher rate by the unedited NEIL1. Molecular modeling provides insight into these differential substrate specificities. The results of this study and in particular, the comparison of substrate specificities of unedited and edited NEIL1 using biologically and clinically important base lesions, are critical for defining its role in preservation of genomic integrity.
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60
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Korenjak M, Zavadil J. Experimental identification of cancer driver alterations in the era of pan-cancer genomics. Cancer Sci 2019; 110:3622-3629. [PMID: 31594033 PMCID: PMC6890429 DOI: 10.1111/cas.14210] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 09/22/2019] [Accepted: 10/03/2019] [Indexed: 12/30/2022] Open
Abstract
Rapidly accumulating data from large-scale cancer genomics studies have been generating important information about genes and their somatic alterations underlying cell transformation, cancer onset and tumor progression. However, these events are usually defined by using computational techniques, whereas the understanding of their actual functional roles and impact typically warrants validation by experimental means. Critical information has been obtained from targeted genetic perturbation (gene knockout) studies conducted in animals, yet these investigations are cost-prohibitive and time-consuming. In addition, the 3R principles (replacement, reduction, refinement) have been set in place to reduce animal use burden and are increasingly observed in many areas of biomedical research. Consequently, the focus has shifted to new designs of innovative cell-based experimental models of cell immortalization and transformation in which the critical cancer driver events can be introduced by mutagenic insult and studied functionally, at the level of critical phenotypic readouts. From these efforts, primary cell-based selective barrier-bypass models of cell immortalization have emerged as an attractive system that allows studies of the functional relevance of acquired mutations as well as their role as candidate cancer driver events. In this review, we provide an overview of various experimental systems linking carcinogen exposure-driven cell transformation with the study of cancer driver events. We further describe the advantages and disadvantages of the currently available cell-based models while outlining future directions for in vitro modeling and functional testing of cancer driver events.
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Affiliation(s)
- Michael Korenjak
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Jiri Zavadil
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
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61
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Christensen S, Van der Roest B, Besselink N, Janssen R, Boymans S, Martens JWM, Yaspo ML, Priestley P, Kuijk E, Cuppen E, Van Hoeck A. 5-Fluorouracil treatment induces characteristic T>G mutations in human cancer. Nat Commun 2019; 10:4571. [PMID: 31594944 PMCID: PMC6783534 DOI: 10.1038/s41467-019-12594-8] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/16/2019] [Indexed: 12/15/2022] Open
Abstract
5-Fluorouracil (5-FU) is a chemotherapeutic drug commonly used for the treatment of solid cancers. It is proposed that 5-FU interferes with nucleotide synthesis and incorporates into DNA, which may have a mutational impact on both surviving tumor and healthy cells. Here, we treat intestinal organoids with 5-FU and find a highly characteristic mutational pattern that is dominated by T>G substitutions in a CTT context. Tumor whole genome sequencing data confirms that this signature is also identified in vivo in colorectal and breast cancer patients who have received 5-FU treatment. Taken together, our results demonstrate that 5-FU is mutagenic and may drive tumor evolution and increase the risk of secondary malignancies. Furthermore, the identified signature shows a strong resemblance to COSMIC signature 17, the hallmark signature of treatment-naive esophageal and gastric tumors, which indicates that distinct endogenous and exogenous triggers can converge onto highly similar mutational signatures.
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Affiliation(s)
- Sharon Christensen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Bastiaan Van der Roest
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer institute, Erasmus University Medical Center, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Marie-Laure Yaspo
- Max Planck Institute for Molecular Genetics, Ihnestraße 63, 14195, Berlin, Germany
| | | | - Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands.
- Hartwig Medical Foundation, Science Park 408, 1098 XH, Amsterdam, The Netherlands.
| | - Arne Van Hoeck
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
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Zavadil J, Rozen SG. Experimental Delineation of Mutational Signatures Is an Essential Tool in Cancer Epidemiology and Prevention. Chem Res Toxicol 2019; 32:2153-2155. [PMID: 31509385 DOI: 10.1021/acs.chemrestox.9b00339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Advances in experimental modeling of the mutational signatures of environmental exposures and endogenous mutagenic processes will elucidate the role of mutagenesis in cancer, facilitate carcinogen classification, and enable new molecular cancer epidemiology studies.
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Affiliation(s)
- Jiri Zavadil
- Molecular Mechanisms and Biomarkers Group, Mechanisms of Carcinogenesis Section , International Agency for Research on Cancer/World Health Organization , 150 cours Albert Thomas , 69008 Lyon , France
| | - Steven G Rozen
- Duke-NUS Centre for Computational Biology and Cancer and Stem Cell Biology Program , Duke-NUS Medical School Singapore , 8 College Road , Singapore 169857 , Republic of Singapore
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63
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Jager M, Blokzijl F, Kuijk E, Bertl J, Vougioukalaki M, Janssen R, Besselink N, Boymans S, de Ligt J, Pedersen JS, Hoeijmakers J, Pothof J, van Boxtel R, Cuppen E. Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer. Genome Res 2019; 29:1067-1077. [PMID: 31221724 PMCID: PMC6633256 DOI: 10.1101/gr.246223.118] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 06/07/2019] [Indexed: 12/24/2022]
Abstract
Nucleotide excision repair (NER) is one of the main DNA repair pathways that protect cells against genomic damage. Disruption of this pathway can contribute to the development of cancer and accelerate aging. Mutational characteristics of NER-deficiency may reveal important diagnostic opportunities, as tumors deficient in NER are more sensitive to certain treatments. Here, we analyzed the genome-wide somatic mutational profiles of adult stem cells (ASCs) from NER-deficient Ercc1 -/Δ mice. Our results indicate that NER-deficiency increases the base substitution load twofold in liver but not in small intestinal ASCs, which coincides with the tissue-specific aging pathology observed in these mice. Moreover, NER-deficient ASCs of both tissues show an increased contribution of Signature 8 mutations, which is a mutational pattern with unknown etiology that is recurrently observed in various cancer types. The scattered genomic distribution of the base substitutions indicates that deficiency of global-genome NER (GG-NER) underlies the observed mutational consequences. In line with this, we observe increased Signature 8 mutations in a GG-NER-deficient human organoid culture, in which XPC was deleted using CRISPR-Cas9 gene-editing. Furthermore, genomes of NER-deficient breast tumors show an increased contribution of Signature 8 mutations compared with NER-proficient tumors. Elevated levels of Signature 8 mutations could therefore contribute to a predictor of NER-deficiency based on a patient's mutational profile.
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Affiliation(s)
- Myrthe Jager
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Francis Blokzijl
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Johanna Bertl
- Department of Molecular Medicine, Aarhus University, 8200 Aarhus N, Denmark
| | | | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Joep de Ligt
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | | | | | - Joris Pothof
- Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Ruben van Boxtel
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
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64
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Enrichment of AT-TA transversion at 5'-CAG-3' motif is not a unique mutational signature of aristolochic acid. SCIENCE CHINA-LIFE SCIENCES 2019; 62:974-977. [PMID: 31187304 DOI: 10.1007/s11427-019-9566-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
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65
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Steenwyk JL, Opulente DA, Kominek J, Shen XX, Zhou X, Labella AL, Bradley NP, Eichman BF, Čadež N, Libkind D, DeVirgilio J, Hulfachor AB, Kurtzman CP, Hittinger CT, Rokas A. Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLoS Biol 2019; 17:e3000255. [PMID: 31112549 PMCID: PMC6528967 DOI: 10.1371/journal.pbio.3000255] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
Cell-cycle checkpoints and DNA repair processes protect organisms from potentially lethal mutational damage. Compared to other budding yeasts in the subphylum Saccharomycotina, we noticed that a lineage in the genus Hanseniaspora exhibited very high evolutionary rates, low Guanine-Cytosine (GC) content, small genome sizes, and lower gene numbers. To better understand Hanseniaspora evolution, we analyzed 25 genomes, including 11 newly sequenced, representing 18/21 known species in the genus. Our phylogenomic analyses identify two Hanseniaspora lineages, a faster-evolving lineage (FEL), which began diversifying approximately 87 million years ago (mya), and a slower-evolving lineage (SEL), which began diversifying approximately 54 mya. Remarkably, both lineages lost genes associated with the cell cycle and genome integrity, but these losses were greater in the FEL. E.g., all species lost the cell-cycle regulator WHIskey 5 (WHI5), and the FEL lost components of the spindle checkpoint pathway (e.g., Mitotic Arrest-Deficient 1 [MAD1], Mitotic Arrest-Deficient 2 [MAD2]) and DNA-damage-checkpoint pathway (e.g., Mitosis Entry Checkpoint 3 [MEC3], RADiation sensitive 9 [RAD9]). Similarly, both lineages lost genes involved in DNA repair pathways, including the DNA glycosylase gene 3-MethylAdenine DNA Glycosylase 1 (MAG1), which is part of the base-excision repair pathway, and the DNA photolyase gene PHotoreactivation Repair deficient 1 (PHR1), which is involved in pyrimidine dimer repair. Strikingly, the FEL lost 33 additional genes, including polymerases (i.e., POLymerase 4 [POL4] and POL32) and telomere-associated genes (e.g., Repressor/activator site binding protein-Interacting Factor 1 [RIF1], Replication Factor A 3 [RFA3], Cell Division Cycle 13 [CDC13], Pbp1p Binding Protein [PBP2]). Echoing these losses, molecular evolutionary analyses reveal that, compared to the SEL, the FEL stem lineage underwent a burst of accelerated evolution, which resulted in greater mutational loads, homopolymer instabilities, and higher fractions of mutations associated with the common endogenously damaged base, 8-oxoguanine. We conclude that Hanseniaspora is an ancient lineage that has diversified and thrived, despite lacking many otherwise highly conserved cell-cycle and genome integrity genes and pathways, and may represent a novel, to our knowledge, system for studying cellular life without them.
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Affiliation(s)
- Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Dana A Opulente
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin, United States of America
| | - Jacek Kominek
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin, United States of America
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Abigail L Labella
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Noah P Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Neža Čadež
- University of Ljubljana Biotechnical Faculty, Department of Food Science and Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, Universidad Nacional del Comahue-CONICET, San Carlos de Bariloche, Río Negro, Argentina
| | - Jeremy DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, Illinois, United States of America
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cletus P Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, Illinois, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin, United States of America
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
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66
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Leichsenring J, Kazdal D, Ploeger C, Allgäuer M, Endris V, Volckmar AL, Neumann O, Kirchner M, Penzel R, Rempel E, Budczies J, Schirmacher P, Fröhling S, Stenzinger A. [From panel diagnostics to comprehensive genomic analysis : Infobesity or empowerment?]. DER PATHOLOGE 2019; 40:235-242. [PMID: 31089797 DOI: 10.1007/s00292-019-0608-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Precision oncology is obtaining a central role in the therapy of malignant diseases. The indication for targeted therapy is based on the identification of molecular targets for which next-generation sequencing (NGS) is commonly used nowadays. All approved predictive biomarkers and molecular targets, including gene fusions and copy number alterations, can be identified depending on panel design and method applied. Some clinical scenarios, however, may require more holistic genomic approaches, such as whole-genome/whole-exome and transcriptome analysis, which must be embedded in a clinical trial. Here, key aspects and applications of each method are summarized and discussed.
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Affiliation(s)
- J Leichsenring
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - D Kazdal
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - C Ploeger
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - M Allgäuer
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - V Endris
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - A-L Volckmar
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - O Neumann
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - M Kirchner
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - R Penzel
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - E Rempel
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - J Budczies
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - P Schirmacher
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - S Fröhling
- Abteilung Translationale Medizinische Onkologie, Nationales Centrum für Tumorerkrankungen (NCT) Heidelberg und Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Deutschland
| | - A Stenzinger
- Pathologisches Institut, Molekularpathologisches Zentrum, Universitätsklinikum Heidelberg, Heidelberg, Deutschland.
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67
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McCullough AK, Lloyd RS. Mechanisms underlying aflatoxin-associated mutagenesis - Implications in carcinogenesis. DNA Repair (Amst) 2019; 77:76-86. [PMID: 30897375 PMCID: PMC6959417 DOI: 10.1016/j.dnarep.2019.03.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 01/07/2023]
Abstract
Chronic dietary exposure to aflatoxin B1 (AFB1), concomitant with hepatitis B infection is associated with a significant increased risk for hepatocellular carcinomas (HCCs) in people living in Southeast Asia and sub-Saharan Africa. Human exposures to AFB1 occur through the consumption of foods that are contaminated with pervasive molds, including Aspergillus flavus. Even though dietary exposures to aflatoxins constitute the second largest global environmental risk factor for cancer development, there are still significant questions concerning the molecular mechanisms driving carcinogenesis and what factors may modulate an individual's risk for HCC. The objective of this review is to summarize key discoveries that established the association of chronic inflammation (most commonly associated with hepatitis B viral (HBV) infection) and environmental exposures to aflatoxin with increased HCC risk. Special emphasis will be given to recent investigations that have: 1) refined the aflatoxin-associated mutagenic signature, 2) expanded the DNA repair mechanisms that limit mutagenesis via adduct removal prior to replication-induced mutagenesis, 3) implicated a specific DNA polymerase in the error-prone bypass and resulting mutagenesis, and 4) identified human polymorphic variants that may modulate individual susceptibility to aflatoxin-induced cancers. Collectively, these investigations revealed that specific sequence contexts are differentially resistant against, or prone to, aflatoxin-induced mutagenesis and that these associations are remarkably similar between in vitro and in vivo analyses. These recent investigations also established DNA polymerase ζ as the major polymerase that confers the G to T transversion signature. Additionally, although the nucleotide excision repair (NER) pathway has been previously shown to repair aflatoxin-induced DNA adducts, recent murine data demonstrated that NEIL1-initiated base excision repair was significantly more important than NER relative to the removal of the highly mutagenic AFB1-Fapy-dG adducts. These data suggest that inactivating polymorphic variants of NEIL1 could be a potential driver of HCCs in aflatoxin-exposed populations.
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Affiliation(s)
- Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States; Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97239, United States.
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68
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Zhivagui M, Ng AWT, Ardin M, Churchwell MI, Pandey M, Renard C, Villar S, Cahais V, Robitaille A, Bouaoun L, Heguy A, Guyton KZ, Stampfer MR, McKay J, Hollstein M, Olivier M, Rozen SG, Beland FA, Korenjak M, Zavadil J. Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans. Genome Res 2019; 29:521-531. [PMID: 30846532 PMCID: PMC6442384 DOI: 10.1101/gr.242453.118] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/01/2019] [Indexed: 02/06/2023]
Abstract
Humans are frequently exposed to acrylamide, a probable human carcinogen found in commonplace sources such as most heated starchy foods or tobacco smoke. Prior evidence has shown that acrylamide causes cancer in rodents, yet epidemiological studies conducted to date are limited and, thus far, have yielded inconclusive data on association of human cancers with acrylamide exposure. In this study, we experimentally identify a novel and unique mutational signature imprinted by acrylamide through the effects of its reactive metabolite glycidamide. We next show that the glycidamide mutational signature is found in a full one-third of approximately 1600 tumor genomes corresponding to 19 human tumor types from 14 organs. The highest enrichment of the glycidamide signature was observed in the cancers of the lung (88% of the interrogated tumors), liver (73%), kidney (>70%), bile duct (57%), cervix (50%), and, to a lesser extent, additional cancer types. Overall, our study reveals an unexpectedly extensive contribution of acrylamide-associated mutagenesis to human cancers.
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Affiliation(s)
- Maria Zhivagui
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Alvin W T Ng
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
| | - Maude Ardin
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Mona I Churchwell
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
| | - Manuraj Pandey
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Claire Renard
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Stephanie Villar
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Alexis Robitaille
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Liacine Bouaoun
- Environment and Radiation Section, International Agency for Research on Cancer, Lyon 69008, France
| | - Adriana Heguy
- Department of Pathology and Genome Technology Center, New York University, Langone Medical Center, New York, New York 10016, USA
| | - Kathryn Z Guyton
- IARC Monographs Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Martha R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - James McKay
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Monica Hollstein
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
- Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany
- Faculty of Medicine and Health, University of Leeds, LIGHT Laboratories, Leeds LS2 9JT, United Kingdom
| | - Magali Olivier
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Steven G Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
| | - Frederick A Beland
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
| | - Michael Korenjak
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Jiri Zavadil
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
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69
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Chen J, Zhu J, Wang G, Groopman JD, Kensler TW. Qidong: a crucible for studies on liver cancer etiology and prevention. Cancer Biol Med 2019; 16:24-37. [PMID: 31119044 PMCID: PMC6528445 DOI: 10.20892/j.issn.2095-3941.2018.0394] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Qidong (Jiangsu, China) has been of interest to cancer epidemiologists and biologists because, until recently, it was an endemic area for liver cancer, having amongst the highest incidence rates in the world. The establishment of the Qidong Cancer Registry together with the Qidong Liver Cancer Institute in 1972 has charted the patterns of liver cancer incidence and mortality in a stable population throughout a period of enormous economic, social, and environmental changes as well as of improvements in health care delivery. Updated incidence trends in Qidong are described. Notably, the China age-standardized incidence rate for liver cancer has dropped by over 50% in the past several decades. Molecular epidemiologic and genomic deep sequencing studies have affirmed that infection with hepatitis B virus as well as dietary exposure to aflatoxins through contamination of dietary staples such as corn, and to microcystins – blue-green algal toxins found in ditch and pond water – were likely important etiologic factors that account for the high incidence of liver cancer in this region. Public health initiatives to facilitate universal vaccination of newborns against HBV and to improve drinking water sources in this rural area, as well as economic and social mandates serendipitously facilitating dietary diversity, have led to precipitous declines in exposures to these etiologic factors, concomitantly driving substantive declines in the liver cancer incidence seen now in Qidong. In this regard, Qidong serves as a template for the global impact that a package of intervention strategies may exert on cancer burden.
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Affiliation(s)
- Jianguo Chen
- Department of Epidemiology, Qidong Liver Cancer Institute, Qidong 226200, China.,Department of Epidemiology, Tumor Hospital, Nantong University, Nantong 226361, China
| | - Jian Zhu
- Department of Epidemiology, Qidong Liver Cancer Institute, Qidong 226200, China
| | - Gaoren Wang
- Department of Epidemiology, Tumor Hospital, Nantong University, Nantong 226361, China
| | - John D Groopman
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore 21205, MD, USA
| | - Thomas W Kensler
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore 21205, MD, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle 98109, WA 98109, USA
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70
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Nassar AH, Umeton R, Kim J, Lundgren K, Harshman L, Van Allen EM, Preston M, Dong F, Bellmunt J, Mouw KW, Choueiri TK, Sonpavde G, Kwiatkowski DJ. Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites. Clin Cancer Res 2018; 25:2458-2470. [PMID: 30593515 DOI: 10.1158/1078-0432.ccr-18-3147] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/17/2018] [Accepted: 12/21/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE The purpose of this study is to characterize the mutational landscape across the spectrum of urothelial carcinoma (UC) to identify mutational features and potential therapeutic targets. EXPERIMENTAL DESIGN Using targeted exome sequencing (n = 237 genes), we analyzed the mutation spectra of 82 low-grade nonmuscle-invasive bladder cancers (LG-NMIBC), 126 high-grade (HG) NMIBC, 199 muscle-invasive bladder cancers (MIBC), 10 LG-upper tract urothelial cancers (LG-UTUC), and 55 HG-UTUC. RESULTS FGFR3 and KDM6A mutations were significantly more common in LG-NMIBC (72% and 44%, respectively) versus other bladder subtypes. FGFR3 alterations were also enriched in LG-UTUC versus HG-UTUC tumors (80% vs. 16%). In contrast, TP53 and RB1 mutations were significantly more frequent in all 3 HG urothelial carcinoma subtypes than in LG-NIMBC (45%-58% vs. 4%; 9%-22% vs. 0; respectively). Among LG-NMIBC tumors, KDM6A mutations were more common in women than in men (71% vs. 38%). HG-NMIBC and MIBC had higher tumor mutational burden (TMB) than LG-NMIBC (P = 0.001 and P < 0.01, respectively). DNA-damage repair (DDR) alterations were associated with a higher TMB in HG-NMIBC and MIBC tumors, and these two tumor types were also enriched for an APOBEC mutational signature compared with LG-NMIBC and HG-UTUC. Alterations in FGFR3, PIK3CA, and EP300 correlated with worse overall survival in HG-UTUC and occurred concurrently. CONCLUSIONS Our analysis suggests that a fraction of MIBCs likely arise from precursor lesions other than LG-NMIBC. KDM6A mutations are twice as common in women with LG-NIMBC than those in men. DDR gene mutations and APOBEC mutagenesis drive mutations in HG-NMIBC and MIBC. UTUC has a distinct mutation profile from bladder cancer.
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Affiliation(s)
- Amin H Nassar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Renato Umeton
- Department of Informatics, Dana-Farber Cancer Institute, Boston, Massachusetts.,Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jaegil Kim
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kevin Lundgren
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lauren Harshman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Mark Preston
- Department of Urology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Joaquim Bellmunt
- Department of Medical Oncology, IMIM-Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Guru Sonpavde
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David J Kwiatkowski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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71
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Minko IG, Christov PP, Li L, Stone MP, McCullough AK, Lloyd RS. Processing of N 5-substituted formamidopyrimidine DNA adducts by DNA glycosylases NEIL1 and NEIL3. DNA Repair (Amst) 2018; 73:49-54. [PMID: 30448017 DOI: 10.1016/j.dnarep.2018.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 12/29/2022]
Abstract
A variety of agents cause DNA base alkylation damage, including the known hepatocarcinogen aflatoxin B1 (AFB1) and chemotherapeutic drugs derived from nitrogen mustard (NM). The N7 site of guanine is the primary site of alkylation, with some N7-deoxyguanosine adducts undergoing imidazole ring-opening to stable mutagenic N5-alkyl formamidopyrimidine (Fapy-dG) adducts. These adducts exist as a mixture of canonical β- and unnatural α-anomeric forms. The β species are predominant in double-stranded (ds) DNA. Recently, we have demonstrated that the DNA glycosylase NEIL1 can initiate repair of AFB1-Fapy-dG adducts both in vitro and in vivo, with Neil1-/- mice showing an increased susceptibility to AFB1-induced hepatocellular carcinoma. Here, we hypothesized that NEIL1 could excise NM-Fapy-dG and that NEIL3, a closely related DNA glycosylase, could excise both NM-Fapy-dG and AFB1-Fapy-dG. Product formation from the reaction of human NEIL1 with ds oligodeoxynucleotides containing a unique NM-Fapy-dG followed a bi-component exponential function under single turnover conditions. Thus, two adduct conformations were differentially recognized by hNEIL1. The excision rate of the major form (∼13.0 min-1), presumed to be the β-anomer, was significantly higher than that previously reported for 5-hydroxycytosine, 5-hydroxyuracil, thymine glycol (Tg), and AFB1-Fapy-dG. Product generation from the minor form was much slower (∼0.4 min-1), likely reflecting the rate of conversion of the α anomer into the β anomer. Mus musculus NEIL3 (MmuNEIL3Δ324) excised NM-Fapy-dG from single-stranded (ss) DNA (turnover rate of ∼0.4 min-1), but not from ds DNA. Product formation from ss substrate was incomplete, presumably because of a substantial presence of the α anomer. MmuNEIL3Δ324 could not initiate repair of AFB1-Fapy-dG in either ds or ss DNA. Overall, the data suggest that both NEIL1 and NEIL3 may protect cells against cytotoxic and mutagenic effects of NM-Fapy-dG, but NEIL1 may have a unique role in initiation of base excision repair of AFB1-Fapy-dG.
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Affiliation(s)
- Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States
| | - Plamen P Christov
- Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN 37235, United States
| | - Liang Li
- Department of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Michael P Stone
- Department of Chemistry and Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, United States; Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97239, United States.
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72
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Phillips DH. Mutational spectra and mutational signatures: Insights into cancer aetiology and mechanisms of DNA damage and repair. DNA Repair (Amst) 2018; 71:6-11. [PMID: 30236628 PMCID: PMC6219445 DOI: 10.1016/j.dnarep.2018.08.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Reporter gene assays, in which a single mutation from each experiment can contribute to the assembly of a mutation spectrum for an agent, have provided the basis for understanding the mutational processes induced by mutagenic agents and for providing clues to the origins of mutations in human tumours. More recently exome and whole genome sequencing of human tumours has revealed distinct patterns of mutation that could provide additional clues for the causative origins of cancer. This can be tested by examining the mutational signatures induced in experimental systems by putative cancer-causing agents. Such signatures are now being generated in vitro in a number of different mutagen-exposed cellular systems. Results reveal that mutagens induce characteristic mutation signatures that, in some cases, match signatures found in human tumours. Proof of principle has been established with mutational signatures generated by simulated sunlight and aristolochic acid, which match those signatures found in human melanomas and urothelial cancers, respectively. In an analysis of somatic mutations in cancers for which tobacco smoking confers an elevated risk, it was found that smoking is associated with increased mutation burdens of multiple different mutational signatures, which contribute to different extents in different tissues. One of these signatures, mainly found in tissues directly exposed to tobacco smoke, is attributable to misreplication of DNA damage caused by tobacco carcinogens. Others likely reflect indirect activation of DNA editing by APOBEC cytidine deaminases and of an endogenous clock-like mutational process. The results are consistent with the proposition that smoking increases cancer risk by increasing the somatic mutation load although direct evidence for this mechanism is lacking in some cancer types. Thus, next generation sequencing of exomes or whole genomes is providing new insights into processes underlying the causes of human cancer.
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Affiliation(s)
- David H Phillips
- MRC-PHE Centre for Environment and Health, King's College London, UK; NIHR Health Protection Research Unit in Health Impact of Environmental Hazards at King's College London in Partnership with Public Health England, Department of Analytical, Environmental and Forensic Sciences, School of Public Health and Environmental Sciences, Faculty of Life Sciences and Medicine, King's College London, UK.
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73
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Fedeles BI, Essigmann JM. Impact of DNA lesion repair, replication and formation on the mutational spectra of environmental carcinogens: Aflatoxin B 1 as a case study. DNA Repair (Amst) 2018; 71:12-22. [PMID: 30309820 DOI: 10.1016/j.dnarep.2018.08.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In a multicellular organism, somatic mutations represent a permanent record of the past chemical and biochemical perturbations experienced by a cell in its local microenvironment. Akin to a perpetual recording device, with every replication, genomic DNA accumulates mutations in patterns that reflect: i) the sequence context-dependent formation of DNA damage, due to environmental or endogenous reactive species, including spontaneous processes; ii) the activity of DNA repair pathways, which, depending on the type of lesion, can erase, ignore or exacerbate the mutagenic consequences of that DNA damage; and iii) the choice of replication machinery that synthesizes the nascent genomic copy. These three factors result in a richly contoured sequence context-dependent mutational spectrum that, from appearances, is distinct for most individual forms of DNA damage. Such a mutagenic legacy, if appropriately decoded, can reveal the local history of genome-altering events such as chemical or pathogen exposures, metabolic stress, and inflammation, which in turn can provide an indication of the underlying causes and mechanisms of genetic disease. Modern tools have positioned us to develop a deep mechanistic understanding of the cellular factors and pathways that modulate a mutational process and, in turn, provide opportunities for better diagnostic and prognostic biomarkers, better exposure risk assessment and even actionable therapeutic targets. The goal of this Perspective is to present a bottom-up, lesion-centric framework of mutagenesis that integrates the contributions of lesion replication, lesion repair and lesion formation to explain the complex mutational spectra that emerge in the genome following exposure to mutagens. The mutational spectra of the well-studied hepatocarcinogen aflatoxin B1 are showcased here as specific examples, but the implications are meant to be generalizable.
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Affiliation(s)
- Bogdan I Fedeles
- Departments of Biological Engineering, Chemistry and The Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - John M Essigmann
- Departments of Biological Engineering, Chemistry and The Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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74
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A genome-wide mutation analysis method enabling high-throughput identification of chemical mutagen signatures. Sci Rep 2018; 8:9583. [PMID: 29942026 PMCID: PMC6018237 DOI: 10.1038/s41598-018-27755-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 06/08/2018] [Indexed: 12/17/2022] Open
Abstract
Trinucleotide mutational signatures extracted from cancer genomes provide clues useful in understanding the roles of mutagens and mutagenic mechanisms in cancer development. The lack of a simple method for genome-wide analysis of alterations induced by mutagens hampers the identification of trinucleotide signatures of mutagen exposure and evaluation of their relationships with human cancers. Here, we describe a novel approach to facilitate analysis of chemically induced mutations in bacterial cells by detection of increased frequencies of base substitutions after mutagen exposure, using paired-end overlapping next-generation sequencing. DNA samples from Salmonella typhimurium strain TA100, exposed to three alkylating agents, ethylnitrosourea (ENU), methylnitrosourea (MNU), and ethyl methansulphonate (EMS), were analysed. The G:C > A:T mutation frequency was increased in all samples, whereas A:T base pair substitution frequencies were increased specifically in samples exposed to ENU, consistent with previous reports. Mutation patterns in the context of 96 possible trinucleotide formats in these samples exhibited a sharp peak corresponding to an NpCpY consensus sequence, which is similar to the mutational signature of alkylating agents in human cancer. These results indicate that our approach can be useful in facilitating the understanding of mechanisms underlying chemical mutagenicity and for identification of unknown causal mutagens in human cancer.
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75
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Ng AWT, Poon SL, Huang MN, Lim JQ, Boot A, Yu W, Suzuki Y, Thangaraju S, Ng CCY, Tan P, Pang ST, Huang HY, Yu MC, Lee PH, Hsieh SY, Chang AY, Teh BT, Rozen SG. Aristolochic acids and their derivatives are widely implicated in liver cancers in Taiwan and throughout Asia. Sci Transl Med 2018; 9:9/412/eaan6446. [PMID: 29046434 DOI: 10.1126/scitranslmed.aan6446] [Citation(s) in RCA: 243] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/31/2017] [Accepted: 09/25/2017] [Indexed: 12/21/2022]
Abstract
Many traditional pharmacopeias include Aristolochia and related plants, which contain nephrotoxins and mutagens in the form of aristolochic acids and similar compounds (collectively, AA). AA is implicated in multiple cancer types, sometimes with very high mutational burdens, especially in upper tract urothelial cancers (UTUCs). AA-associated kidney failure and UTUCs are prevalent in Taiwan, but AA's role in hepatocellular carcinomas (HCCs) there remains unexplored. Therefore, we sequenced the whole exomes of 98 HCCs from two hospitals in Taiwan and found that 78% showed the distinctive mutational signature of AA exposure, accounting for most of the nonsilent mutations in known cancer driver genes. We then searched for the AA signature in 1400 HCCs from diverse geographic regions. Consistent with exposure through known herbal medicines, 47% of Chinese HCCs showed the signature, albeit with lower mutation loads than in Taiwan. In addition, 29% of HCCs from Southeast Asia showed the signature. The AA signature was also detected in 13 and 2.7% of HCCs from Korea and Japan as well as in 4.8 and 1.7% of HCCs from North America and Europe, respectively, excluding one U.S. hospital where 22% of 87 "Asian" HCCs had the signature. Thus, AA exposure is geographically widespread. Asia, especially Taiwan, appears to be much more extensively affected, which is consistent with other evidence of patterns of AA exposure. We propose that additional measures aimed at primary prevention through avoidance of AA exposure and investigation of possible approaches to secondary prevention are warranted.
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Affiliation(s)
- Alvin W T Ng
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
| | - Song Ling Poon
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Mi Ni Huang
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jing Quan Lim
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore 169610, Singapore.,Lymphoma Genomic Translational Research Laboratory, Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Arnoud Boot
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Willie Yu
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Yuka Suzuki
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Saranya Thangaraju
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Cedric C Y Ng
- Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Patrick Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,SingHealth/Duke-NUS Precision Medicine Institute, Singapore 169609, Singapore.,Genome Institute of Singapore, Singapore 138672, Singapore
| | - See-Tong Pang
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital, Linkou, Taoyuan 33305, Taiwan
| | - Hao-Yi Huang
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan 33305, Taiwan
| | - Ming-Chin Yu
- Department of General Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan 33305, Taiwan
| | - Po-Huang Lee
- Department of Surgery, National Taiwan University, Taipei 10051, Taiwan
| | - Sen-Yung Hsieh
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan 33305, Taiwan.
| | - Alex Y Chang
- Johns Hopkins Singapore, Singapore 308433, Singapore.
| | - Bin T Teh
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore. .,Laboratory of Cancer Epigenome, Division of Medical Science, National Cancer Centre Singapore, Singapore 169610, Singapore.,SingHealth/Duke-NUS Precision Medicine Institute, Singapore 169609, Singapore.,Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Steven G Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore. .,Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore.,SingHealth/Duke-NUS Precision Medicine Institute, Singapore 169609, Singapore
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76
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Tomkova M, Schuster-Böckler B. DNA Modifications: Naturally More Error Prone? Trends Genet 2018; 34:627-638. [PMID: 29853204 DOI: 10.1016/j.tig.2018.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/22/2018] [Accepted: 04/27/2018] [Indexed: 12/31/2022]
Abstract
Epigenetic DNA modifications are essential for normal cell function in vertebrates, but they can also be hotspots of mutagenesis. Methylcytosine in particular has long been known to be less stable than other nucleotides and spontaneously deaminates to thymine. Beyond this well-established phenomenon, however, the influence of epigenetic marks on mutagenesis has recently become an active field of investigation. In this review, we summarize current knowledge of the interactions between different DNA modifications and other mutagenic processes. External mutagens, such as UV light or smoking carcinogens, affect modified cytosines differently from unmodified ones, and modified cytosine can in some cases be protective rather than mutagenic. Notably, cell-intrinsic processes, such as DNA replication, also appear to influence the mutagenesis of modified cytosines. Altogether, evidence is accumulating to show that epigenetic changes have a profound influence on tissue-specific mutation accumulation.
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Affiliation(s)
- Marketa Tomkova
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Benjamin Schuster-Böckler
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK.
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77
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In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors. Genome Res 2018; 28:654-665. [PMID: 29632087 PMCID: PMC5932606 DOI: 10.1101/gr.230219.117] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 03/13/2018] [Indexed: 12/18/2022]
Abstract
Cisplatin reacts with DNA and thereby likely generates a characteristic pattern of somatic mutations, called a mutational signature. Despite widespread use of cisplatin in cancer treatment and its role in contributing to secondary malignancies, its mutational signature has not been delineated. We hypothesize that cisplatin's mutational signature can serve as a biomarker to identify cisplatin mutagenesis in suspected secondary malignancies. Knowledge of which tissues are at risk of developing cisplatin-induced secondary malignancies could lead to guidelines for noninvasive monitoring for secondary malignancies after cisplatin chemotherapy. We performed whole genome sequencing of 10 independent clones of cisplatin-exposed MCF-10A and HepG2 cells and delineated the patterns of single and dinucleotide mutations in terms of flanking sequence, transcription strand bias, and other characteristics. We used the mSigAct signature presence test and nonnegative matrix factorization to search for cisplatin mutagenesis in hepatocellular carcinomas and esophageal adenocarcinomas. All clones showed highly consistent patterns of single and dinucleotide substitutions. The proportion of dinucleotide substitutions was high: 8.1% of single nucleotide substitutions were part of dinucleotide substitutions, presumably due to cisplatin's propensity to form intra- and interstrand crosslinks between purine bases in DNA. We identified likely cisplatin exposure in nine hepatocellular carcinomas and three esophageal adenocarcinomas. All hepatocellular carcinomas for which clinical data were available and all esophageal cancers indeed had histories of cisplatin treatment. We experimentally delineated the single and dinucleotide mutational signature of cisplatin. This signature enabled us to detect previous cisplatin exposure in human hepatocellular carcinomas and esophageal adenocarcinomas with high confidence.
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78
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Mutational and epigenetic signatures in cancer tissue linked to environmental exposures and lifestyle. Curr Opin Oncol 2018; 30:61-67. [DOI: 10.1097/cco.0000000000000418] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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