1
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Casimir L, Zimmer S, Racine-Brassard F, Jacques PÉ, Maréchal A. The mutational impact of Illudin S on human cells. DNA Repair (Amst) 2023; 122:103433. [PMID: 36566616 DOI: 10.1016/j.dnarep.2022.103433] [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: 08/09/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Illudin S (ILS) is a fungal sesquiterpene secondary metabolite with potent genotoxic and cytotoxic properties. Early genetic studies and more recent genome-wide CRISPR screens showed that Illudin-induced lesions are preferentially repaired by transcription-coupled nucleotide excision repair (TC-NER) with some contribution from post-replication repair pathways. In line with these results, Irofulven, a semi-synthetic ILS analog was recently shown to be particularly effective on cell lines and patient-derived xenografts with impaired NER (e.g. ERCC2/3 mutations), raising hope that ILS-derived molecules may soon enter the clinic. Despite the therapeutic potential of ILS and its analogs, we still lack a global understanding of their mutagenic potential. Here, we characterize the mutational signatures associated with chronic exposure to ILS in human cells. ILS treatment rapidly stalls DNA replication and transcription, leading to the activation of the replication stress response and the accumulation of DNA damage. Novel single and double base substitution signatures as well as a characteristic indel signature indicate that ILS treatment preferentially alkylates purine residues and induces oxidative stress, confirming prior in vitro data. Many mutation contexts exhibit a strong transcriptional strand bias, highlighting the contribution of TC-NER to the repair of ILS lesions. Finally, collateral mutations are also observed in response to ILS, suggesting a contribution of translesion synthesis pathways to ILS tolerance. Accordingly, ILS treatment led to the rapid recruitment of the Y-family DNA polymerase kappa onto chromatin, supporting its preferential use for ILS lesion bypass. Altogether, our work provides the first global assessment of the genomic impact of ILS, demonstrating the contribution of multiple DNA repair pathways to ILS resistance and mutagenicity.
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Affiliation(s)
- Lisa Casimir
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Samuel Zimmer
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Félix Racine-Brassard
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
| | - Alexandre Maréchal
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
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2
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A natural mutator allele shapes mutation spectrum variation in mice. Nature 2022; 605:497-502. [PMID: 35545679 DOI: 10.1038/s41586-022-04701-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 03/25/2022] [Indexed: 12/12/2022]
Abstract
Although germline mutation rates and spectra can vary within and between species, common genetic modifiers of the mutation rate have not been identified in nature1. Here we searched for loci that influence germline mutagenesis using a uniquely powerful resource: a panel of recombinant inbred mouse lines known as the BXD, descended from the laboratory strains C57BL/6J (B haplotype) and DBA/2J (D haplotype). Each BXD lineage has been maintained by brother-sister mating in the near absence of natural selection, accumulating de novo mutations for up to 50 years on a known genetic background that is a unique linear mosaic of B and D haplotypes2. We show that mice inheriting D haplotypes at a quantitative trait locus on chromosome 4 accumulate C>A germline mutations at a 50% higher rate than those inheriting B haplotypes, primarily owing to the activity of a C>A-dominated mutational signature known as SBS18. The B and D quantitative trait locus haplotypes encode different alleles of Mutyh, a DNA repair gene that underlies the heritable cancer predisposition syndrome that causes colorectal tumors with a high SBS18 mutation load3,4. Both B and D Mutyh alleles are present in wild populations of Mus musculus domesticus, providing evidence that common genetic variation modulates germline mutagenesis in a model mammalian species.
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3
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Liu C, Zhou S, Bai W, Shi L, Li X. Protective effect of food derived nutrients on cisplatin nephrotoxicity and its mechanism. Food Funct 2022; 13:4839-4860. [PMID: 35416186 DOI: 10.1039/d1fo04391a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Platinum-based metal complexes, especially cisplatin (cis-diamminedichloroplatinum II, CDDP), possess strong anticancer properties and a broad anticancer spectrum. However, the clinical application of CDDP has been limited by its side effects including nephrotoxicity, ototoxicity, and neurotoxicity. Furthermore, the therapeutic effects of current clinical protocols are imperfect. Accordingly, it is essential to identify key targets and effective clinical protocols to restrict CDDP-induced nephrotoxicity. Herein, we first analyzed the relevant molecular mechanisms during the process of CDDP-induced nephrotoxicity including oxidative stress, apoptosis, and inflammation. Evidence from current studies was collected and potential targets and clinical protocols are summarized. The evidence indicates an efficacious role of nutrition-based substances in CDDP-induced renal injury.
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Affiliation(s)
- Chaofan Liu
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, PR China.
| | - Sajin Zhou
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, PR China.
| | - Weibin Bai
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, PR China.
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, PR China.
| | - Xiaoling Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, PR China.
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4
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Póti Á, Szikriszt B, Gervai JZ, Chen D, Szüts D. Characterisation of the spectrum and genetic dependence of collateral mutations induced by translesion DNA synthesis. PLoS Genet 2022; 18:e1010051. [PMID: 35130276 PMCID: PMC8870599 DOI: 10.1371/journal.pgen.1010051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/24/2022] [Accepted: 01/21/2022] [Indexed: 11/18/2022] Open
Abstract
Translesion DNA synthesis (TLS) is a fundamental damage bypass pathway that utilises specialised polymerases with relaxed template specificity to achieve replication through damaged DNA. Misinsertions by low fidelity TLS polymerases may introduce additional mutations on undamaged DNA near the original lesion site, which we termed collateral mutations. In this study, we used whole genome sequencing datasets of chicken DT40 and several human cell lines to obtain evidence for collateral mutagenesis in higher eukaryotes. We found that cisplatin and UVC radiation frequently induce close mutation pairs within 25 base pairs that consist of an adduct-associated primary and a downstream collateral mutation, and genetically linked their formation to TLS activity involving PCNA ubiquitylation and polymerase κ. PCNA ubiquitylation was also indispensable for close mutation pairs observed amongst spontaneously arising base substitutions in cell lines with disrupted homologous recombination. Collateral mutation pairs were also found in melanoma genomes with evidence of UV exposure. We showed that collateral mutations frequently copy the upstream base, and extracted a base substitution signature that describes collateral mutagenesis in the presented dataset regardless of the primary mutagenic process. Using this mutation signature, we showed that collateral mutagenesis creates approximately 10–20% of non-paired substitutions as well, underscoring the importance of the process. DNA base substitutions are the most common form of genomic mutations, formed both spontaneously and in response to environmental mutagens. One of the main mechanisms of base substitution mutagenesis is translesion synthesis, a process that relies on specialised DNA polymerases to replicate damaged DNA templates. In addition to incorrect base insertions at the site of lesions in the template, translesion polymerases may also generate ‘collateral’ mutations away from the lesion due to their lower accuracy in selecting the correct incoming nucleotide. In this study, we surveyed the whole genome sequence of experimental cell clones to examine the extent and genetic dependence of collateral mutagenesis in higher eukaryotes. Looking for close mutation pairs, we found that collateral mutations frequently occur near primary lesions generated by cisplatin or ultraviolet radiation in chicken and human cells, but are restricted to a short distance of approximately 25 base pairs. By analysing their sequence context, we showed that collateral mutations can also occur near correctly bypassed primary lesions and may be responsible for a considerable proportion of all base substitution mutations.
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Affiliation(s)
- Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | | | - Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- * E-mail:
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5
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Seplyarskiy VB, Sunyaev S. The origin of human mutation in light of genomic data. Nat Rev Genet 2021; 22:672-686. [PMID: 34163020 DOI: 10.1038/s41576-021-00376-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 02/05/2023]
Abstract
Despite years of active research into the role of DNA repair and replication in mutagenesis, surprisingly little is known about the origin of spontaneous human mutation in the germ line. With the advent of high-throughput sequencing, genome-scale data have revealed statistical properties of mutagenesis in humans. These properties include variation of the mutation rate and spectrum along the genome at different scales in relation to epigenomic features and dependency on parental age. Moreover, mutations originated in mothers are less frequent than mutations originated in fathers and have a distinct genomic distribution. Statistical analyses that interpret these patterns in the context of known biochemistry can provide mechanistic models of mutagenesis in humans.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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6
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Wu PS, Grosser J, Cameron DP, Baranello L, Ström L. Deficiency of Polη in Saccharomyces cerevisiae reveals the impact of transcription on damage-induced cohesion. PLoS Genet 2021; 17:e1009763. [PMID: 34499654 PMCID: PMC8454932 DOI: 10.1371/journal.pgen.1009763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/21/2021] [Accepted: 08/05/2021] [Indexed: 11/18/2022] Open
Abstract
The structural maintenance of chromosome (SMC) complex cohesin mediates sister chromatid cohesion established during replication, and damage-induced cohesion formed in response to DSBs post-replication. The translesion synthesis polymerase Polη is required for damage-induced cohesion through a hitherto unknown mechanism. Since Polη is functionally associated with transcription, and transcription triggers de novo cohesion in Schizosaccharomyces pombe, we hypothesized that transcription facilitates damage-induced cohesion in Saccharomyces cerevisiae. Here, we show dysregulated transcriptional profiles in the Polη null mutant (rad30Δ), where genes involved in chromatin assembly and positive transcription regulation were downregulated. In addition, chromatin association of RNA polymerase II was reduced at promoters and coding regions in rad30Δ compared to WT cells, while occupancy of the H2A.Z variant (Htz1) at promoters was increased in rad30Δ cells. Perturbing histone exchange at promoters inactivated damage-induced cohesion, similarly to deletion of the RAD30 gene. Conversely, altering regulation of transcription elongation suppressed the deficient damage-induced cohesion in rad30Δ cells. Furthermore, transcription inhibition negatively affected formation of damage-induced cohesion. These results indicate that the transcriptional deregulation of the Polη null mutant is connected with its reduced capacity to establish damage-induced cohesion. This also suggests a linkage between regulation of transcription and formation of damage-induced cohesion after replication.
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Affiliation(s)
- Pei-Shang Wu
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Jan Grosser
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Donald P. Cameron
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Laura Baranello
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Lena Ström
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
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7
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Bezalel-Buch R, Cheun YK, Roy U, Schärer OD, Burgers PM. Bypass of DNA interstrand crosslinks by a Rev1-DNA polymerase ζ complex. Nucleic Acids Res 2020; 48:8461-8473. [PMID: 32633759 PMCID: PMC7470978 DOI: 10.1093/nar/gkaa580] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/18/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022] Open
Abstract
DNA polymerase ζ (Pol ζ) and Rev1 are essential for the repair of DNA interstrand crosslink (ICL) damage. We have used yeast DNA polymerases η, ζ and Rev1 to study translesion synthesis (TLS) past a nitrogen mustard-based interstrand crosslink (ICL) with an 8-atom linker between the crosslinked bases. The Rev1-Pol ζ complex was most efficient in complete bypass synthesis, by 2-3 fold, compared to Pol ζ alone or Pol η. Rev1 protein, but not its catalytic activity, was required for efficient TLS. A dCMP residue was faithfully inserted across the ICL-G by Pol η, Pol ζ, and Rev1-Pol ζ. Rev1-Pol ζ, and particularly Pol ζ alone showed a tendency to stall before the ICL, whereas Pol η stalled just after insertion across the ICL. The stalling of Pol η directly past the ICL is attributed to its autoinhibitory activity, caused by elongation of the short ICL-unhooked oligonucleotide (a six-mer in our study) by Pol η providing a barrier to further elongation of the correct primer. No stalling by Rev1-Pol ζ directly past the ICL was observed, suggesting that the proposed function of Pol ζ as an extender DNA polymerase is also required for ICL repair.
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Affiliation(s)
- Rachel Bezalel-Buch
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Young K Cheun
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Upasana Roy
- Department of Chemistry, Stony Brook University, Stony Book, NY 11794, USA.,Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA
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8
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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: 114] [Impact Index Per Article: 28.5] [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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9
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Saini N, Sterling JF, Sakofsky CJ, Giacobone CK, Klimczak LJ, Burkholder AB, Malc EP, Mieczkowski PA, Gordenin DA. Mutation signatures specific to DNA alkylating agents in yeast and cancers. Nucleic Acids Res 2020; 48:3692-3707. [PMID: 32133535 PMCID: PMC7144945 DOI: 10.1093/nar/gkaa150] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 01/28/2023] Open
Abstract
Alkylation is one of the most ubiquitous forms of DNA lesions. However, the motif preferences and substrates for the activity of the major types of alkylating agents defined by their nucleophilic substitution reactions (SN1 and SN2) are still unclear. Utilizing yeast strains engineered for large-scale production of single-stranded DNA (ssDNA), we probed the substrate specificity, mutation spectra and signatures associated with DNA alkylating agents. We determined that SN1-type agents preferably mutagenize double-stranded DNA (dsDNA), and the mutation signature characteristic of the activity of SN1-type agents was conserved across yeast, mice and human cancers. Conversely, SN2-type agents preferably mutagenize ssDNA in yeast. Moreover, the spectra and signatures derived from yeast were detectable in lung cancers, head and neck cancers and tumors from patients exposed to SN2-type alkylating chemicals. The estimates of mutation loads associated with the SN2-type alkylation signature were higher in lung tumors from smokers than never-smokers, pointing toward the mutagenic activity of the SN2-type alkylating carcinogens in cigarettes. In summary, our analysis of mutations in yeast strains treated with alkylating agents, as well as in whole-exome and whole-genome-sequenced tumors identified signatures highly specific to alkylation mutagenesis and indicate the pervasive nature of alkylation-induced mutagenesis in cancers.
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Affiliation(s)
- Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Joan F Sterling
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Cynthia J Sakofsky
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Camille K Giacobone
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Adam B Burkholder
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Ewa P Malc
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Piotr A Mieczkowski
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC 27709, USA
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10
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Pich O, Muiños F, Lolkema MP, Steeghs N, Gonzalez-Perez A, Lopez-Bigas N. The mutational footprints of cancer therapies. Nat Genet 2019; 51:1732-1740. [PMID: 31740835 PMCID: PMC6887544 DOI: 10.1038/s41588-019-0525-5] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/30/2019] [Indexed: 12/02/2022]
Abstract
Some cancer therapies damage DNA and cause mutations both in cancer and healthy cells of the patient. Therapy-induced mutations may underlie some of the long-term and late side effects of treatments, such as mental disabilities, organ toxicities and secondary neoplasms. Currently we ignore the mutation burden caused by different cancer treatments. Here we identify mutational signatures, or footprints of six widely-used anti-cancer therapies across more than 3,500 metastatic tumors originating from different organs. These include previously known and new mutational signatures generated by platinum-based drugs, and a novel signature of nucleoside metabolic inhibitors. Exploiting these mutational footprints, we estimate the contribution of different treatments to the mutation burden of tumors and their risk of contributing coding and potential driver mutations in the genome. The mutational footprints identified here allow for precisely assessing the mutational risk of different cancer therapies to understand their long-term side effects.
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Affiliation(s)
- Oriol Pich
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Martijn Paul Lolkema
- Department of Medical Oncology, Erasmus Medical Center Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Neeltje Steeghs
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine 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, Barcelona, Spain.
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11
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Skowron MA, Petzsch P, Hardt K, Wagner N, Beier M, Stepanow S, Drechsler M, Rieder H, Köhrer K, Niegisch G, Hoffmann MJ, Schulz WA. Distinctive mutational spectrum and karyotype disruption in long-term cisplatin-treated urothelial carcinoma cell lines. Sci Rep 2019; 9:14476. [PMID: 31597922 PMCID: PMC6785536 DOI: 10.1038/s41598-019-50891-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 09/09/2019] [Indexed: 12/12/2022] Open
Abstract
The DNA-damaging compound cisplatin is broadly employed for cancer chemotherapy. The mutagenic effects of cisplatin on cancer cell genomes are poorly studied and might even contribute to drug resistance. We have therefore analyzed mutations and chromosomal alterations in four cisplatin-resistant bladder cancer cell lines (LTTs) by whole-exome-sequencing and array-CGH. 720–7479 genes in the LTTs contained point mutations, with a characteristic mutational signature. Only 53 genes were mutated in all LTTs, including the presumed cisplatin exporter ATP7B. Chromosomal alterations were characterized by segmented deletions and gains leading to severely altered karyotypes. The few chromosomal changes shared among LTTs included gains involving the anti-apoptotic BCL2L1 gene and losses involving the NRF2 regulator KEAP1. Overall, the extent of genomic changes paralleled cisplatin treatment concentrations. In conclusion, bladder cancer cell lines selected for cisplatin-resistance contain abundant and characteristic drug-induced genomic changes. Cisplatin treatment may therefore generate novel tumor genomes during patient treatment.
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Affiliation(s)
- Margaretha A Skowron
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Patrick Petzsch
- Biological and Medical Research Center (BMFZ), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Karin Hardt
- Institute for Human Genetics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nicholas Wagner
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Manfred Beier
- Institute for Human Genetics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stefanie Stepanow
- Biological and Medical Research Center (BMFZ), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Matthias Drechsler
- Institute for Human Genetics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Harald Rieder
- Institute for Human Genetics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Karl Köhrer
- Biological and Medical Research Center (BMFZ), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Günter Niegisch
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michèle J Hoffmann
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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12
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Proteasome inhibition prevents cell death induced by the chemotherapeutic agent cisplatin downstream of DNA damage. DNA Repair (Amst) 2019; 73:28-33. [DOI: 10.1016/j.dnarep.2018.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 01/07/2023]
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Chang EYC, Novoa CA, Aristizabal MJ, Coulombe Y, Segovia R, Chaturvedi R, Shen Y, Keong C, Tam AS, Jones SJM, Masson JY, Kobor MS, Stirling PC. RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability. J Cell Biol 2017; 216:3991-4005. [PMID: 29042409 PMCID: PMC5716281 DOI: 10.1083/jcb.201703168] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/16/2017] [Accepted: 09/18/2017] [Indexed: 01/01/2023] Open
Abstract
Sgs1, the orthologue of human Bloom's syndrome helicase BLM, is a yeast DNA helicase functioning in DNA replication and repair. We show that SGS1 loss increases R-loop accumulation and sensitizes cells to transcription-replication collisions. Yeast lacking SGS1 accumulate R-loops and γ-H2A at sites of Sgs1 binding, replication pausing regions, and long genes. The mutation signature of sgs1Δ reveals copy number changes flanked by repetitive regions with high R-loop-forming potential. Analysis of BLM in Bloom's syndrome fibroblasts or by depletion of BLM from human cancer cells confirms a role for Sgs1/BLM in suppressing R-loop-associated genome instability across species. In support of a potential direct effect, BLM is found physically proximal to DNA:RNA hybrids in human cells, and can efficiently unwind R-loops in vitro. Together, our data describe a conserved role for Sgs1/BLM in R-loop suppression and support an increasingly broad view of DNA repair and replication fork stabilizing proteins as modulators of R-loop-mediated genome instability.
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Affiliation(s)
| | - Carolina A Novoa
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | | | - Yan Coulombe
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Romulo Segovia
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Richa Chaturvedi
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Yaoqing Shen
- Michael Smith Genome Sciences Centre, Vancouver, Canada
| | - Christelle Keong
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada .,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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