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Guasch MB, Krapivsky PL, Antal T. Error-induced extinction in a multi-type critical birth-death process. J Math Biol 2024; 89:36. [PMID: 39222150 PMCID: PMC11369052 DOI: 10.1007/s00285-024-02134-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 07/02/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024]
Abstract
Extreme mutation rates in microbes and cancer cells can result in error-induced extinction (EEX), where every descendant cell eventually acquires a lethal mutation. In this work, we investigate critical birth-death processes with n distinct types as a birth-death model of EEX in a growing population. Each type-i cell divides independently ( i ) → ( i ) + ( i ) or mutates ( i ) → ( i + 1 ) at the same rate. The total number of cells grows exponentially as a Yule process until a cell of type-n appears, which cell type can only divide or die at rate one. This makes the whole process critical and hence after the exponentially growing phase eventually all cells die with probability one. We present large-time asymptotic results for the general n-type critical birth-death process. We find that the mass function of the number of cells of type-k has algebraic and stationary tail( size ) - 1 - χ k , withχ k = 2 1 - k , for k = 2 , ⋯ , n , in sharp contrast to the exponential tail of the first type. The same exponents describe the tail of the asymptotic survival probability( time ) - ξ k . We present applications of the results for studying extinction due to intolerable mutation rates in biological populations.
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Affiliation(s)
- Meritxell Brunet Guasch
- School of Mathematics and Maxwell Institute for Mathematical Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UK.
| | - P L Krapivsky
- Department of Physics, Boston University, Boston, MA, 02215, USA
- Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Tibor Antal
- School of Mathematics and Maxwell Institute for Mathematical Sciences, University of Edinburgh, Edinburgh, EH9 3FD, UK
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2
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Ambrosini M, Rousseau B, Manca P, Artz O, Marabelle A, André T, Maddalena G, Mazzoli G, Intini R, Cohen R, Cercek A, Segal NH, Saltz L, Varghese AM, Yaeger R, Nusrat M, Goldberg Z, Ku GY, El Dika I, Margalit O, Grinshpun A, Murtaza Kasi P, Schilsky R, Lutfi A, Shacham-Shmueli E, Khan Afghan M, Weiss L, Westphalen CB, Conca V, Decker B, Randon G, Elez E, Fakih M, Schrock AB, Cremolini C, Jayachandran P, Overman MJ, Lonardi S, Pietrantonio F. Immune checkpoint inhibitors for POLE or POLD1 proofreading-deficient metastatic colorectal cancer. Ann Oncol 2024; 35:643-655. [PMID: 38777726 DOI: 10.1016/j.annonc.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND POLE and POLD1 proofreading deficiency (POLE/D1pd) define a rare subtype of ultramutated metastatic colorectal cancer (mCRC; over 100 mut/Mb). Disease-specific data about the activity and efficacy of immune checkpoint inhibitors (ICIs) in POLE/D1pd mCRC are lacking and it is unknown whether outcomes may be different from mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) mCRCs treated with ICIs. PATIENTS AND METHODS In this global study, we collected 27 patients with mCRC harboring POLE/D1 mutations leading to proofreading deficiency and treated with anti-programmed cell death-ligand 1 alone +/- anti-cytotoxic T-lymphocyte antigen-4 agents. We collected clinicopathological and genomic characteristics, response, and survival outcomes after ICIs of POLE/D1pd mCRC and compared them with a cohort of 610 dMMR/MSI-H mCRC patients treated with ICIs. Further genomic analyses were carried out in an independent cohort of 7241 CRCs to define POLE and POLD1pd molecular profiles and mutational signatures. RESULTS POLE/D1pd was associated with younger age, male sex, fewer RAS/BRAF driver mutations, and predominance of right-sided colon cancers. Patients with POLE/D1pd mCRC showed a significantly higher overall response rate (ORR) compared to dMMR/MSI-H mCRC (89% versus 54%; P = 0.01). After a median follow-up of 24.9 months (interquartile range: 11.3-43.0 months), patients with POLE/D1pd showed a significantly superior progression-free survival (PFS) compared to dMMR/MSI-H mCRC [hazard ratio (HR) = 0.24, 95% confidence interval (CI) 0.08-0.74, P = 0.01] and superior overall survival (OS) (HR = 0.38, 95% CI 0.12-1.18, P = 0.09). In multivariable analyses including the type of DNA repair defect, POLE/D1pd was associated with significantly improved PFS (HR = 0.17, 95% CI 0.04-0.69, P = 0.013) and OS (HR = 0.24, 95% CI 0.06-0.98, P = 0.047). Molecular profiling showed that POLE/D1pd tumors have higher tumor mutational burden (TMB). Responses were observed in both subtypes and were associated with the intensity of POLE/D1pd signature. CONCLUSIONS Patients with POLE/D1pd mCRC showed more favorable outcomes compared to dMMR/MSI-H mCRC to treatment with ICIs in terms of tumor response and survival.
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Affiliation(s)
- M Ambrosini
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - B Rousseau
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - P Manca
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Memorial Sloan Kettering Cancer Center, New York, USA
| | - O Artz
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - A Marabelle
- Department of Therapeutic Innovation and Phase 1 clinical trials, Inserm, Gustave Roussy, Université Paris Saclay, Villejuif
| | - T André
- Sorbonne Université and Department of Medical Oncology, Hôpital Saint Antoine, Paris, France
| | - G Maddalena
- Istituto Oncologico Veneto, IRCCS, Padua, Italy
| | - G Mazzoli
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - R Intini
- Istituto Oncologico Veneto, IRCCS, Padua, Italy
| | - R Cohen
- Sorbonne Université and Department of Medical Oncology, Hôpital Saint Antoine, Paris, France
| | - A Cercek
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - N H Segal
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - L Saltz
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - A M Varghese
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - R Yaeger
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - M Nusrat
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - Z Goldberg
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - G Y Ku
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - I El Dika
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - O Margalit
- Oncology Department, Sheba Medical Center and Tel-Aviv University Medicine Faculty, Tel-Aviv
| | - A Grinshpun
- Sharett Institute of Oncology, Hadassah Medical Center, and Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - A Lutfi
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City
| | - E Shacham-Shmueli
- Oncology Department, Sheba Medical Center and Tel-Aviv University Medicine Faculty, Tel-Aviv
| | - M Khan Afghan
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City
| | - L Weiss
- Department of Internal Medicine III and Comprehensive Cancer Center, Klinikum Grosshadern, University Hospital, Ludwig Maximilian University of Munich, Munich; German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - C B Westphalen
- Department of Internal Medicine III and Comprehensive Cancer Center, Klinikum Grosshadern, University Hospital, Ludwig Maximilian University of Munich, Munich; German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - V Conca
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - B Decker
- Foundation Medicine, Cambridge, USA
| | - G Randon
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - E Elez
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - M Fakih
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte
| | - A B Schrock
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - C Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - P Jayachandran
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles
| | - M J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Lonardi
- Istituto Oncologico Veneto, IRCCS, Padua, Italy
| | - F Pietrantonio
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
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Németh E, Szüts D. The mutagenic consequences of defective DNA repair. DNA Repair (Amst) 2024; 139:103694. [PMID: 38788323 DOI: 10.1016/j.dnarep.2024.103694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Multiple separate repair mechanisms safeguard the genome against various types of DNA damage, and their failure can increase the rate of spontaneous mutagenesis. The malfunction of distinct repair mechanisms leads to genomic instability through different mutagenic processes. For example, defective mismatch repair causes high base substitution rates and microsatellite instability, whereas homologous recombination deficiency is characteristically associated with deletions and chromosome instability. This review presents a comprehensive collection of all mutagenic phenotypes associated with the loss of each DNA repair mechanism, drawing on data from a variety of model organisms and mutagenesis assays, and placing greatest emphasis on systematic analyses of human cancer datasets. We describe the latest theories on the mechanism of each mutagenic process, often explained by reliance on an alternative repair pathway or the error-prone replication of unrepaired, damaged DNA. Aided by the concept of mutational signatures, the genomic phenotypes can be used in cancer diagnosis to identify defective DNA repair pathways.
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Affiliation(s)
- Eszter Németh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
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Chung WH. Signification and Application of Mutator and Antimutator Phenotype-Induced Genetic Variations in Evolutionary Adaptation and Cancer Therapeutics. J Microbiol 2023; 61:1013-1024. [PMID: 38100001 DOI: 10.1007/s12275-023-00091-z] [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: 10/09/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 01/11/2024]
Abstract
Mutations present a dichotomy in their implications for cellular processes. They primarily arise from DNA replication errors or damage repair processes induced by environmental challenges. Cumulative mutations underlie genetic variations and drive evolution, yet also contribute to degenerative diseases such as cancer and aging. The mutator phenotype elucidates the heightened mutation rates observed in malignant tumors. Evolutionary adaptation, analogous to bacterial and eukaryotic systems, manifests through mutator phenotypes during changing environmental conditions, highlighting the delicate balance between advantageous mutations and their potentially detrimental consequences. Leveraging the genetic tractability of Saccharomyces cerevisiae offers unique insights into mutator phenotypes and genome instability akin to human cancers. Innovative reporter assays in yeast model organisms enable the detection of diverse genome alterations, aiding a comprehensive analysis of mutator phenotypes. Despite significant advancements, our understanding of the intricate mechanisms governing spontaneous mutation rates and preserving genetic integrity remains incomplete. This review outlines various cellular pathways affecting mutation rates and explores the role of mutator genes and mutation-derived phenotypes, particularly prevalent in malignant tumor cells. An in-depth comprehension of mutator and antimutator activities in yeast and higher eukaryotes holds promise for effective cancer control strategies.
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Affiliation(s)
- Woo-Hyun Chung
- College of Pharmacy, Duksung Women's University, Seoul, 01369, Republic of Korea.
- Innovative Drug Center, Duksung Women's University, Seoul, 01369, Republic of Korea.
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5
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Strauss JD, Pursell ZF. Replication DNA polymerases, genome instability and cancer therapies. NAR Cancer 2023; 5:zcad033. [PMID: 37388540 PMCID: PMC10304742 DOI: 10.1093/narcan/zcad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/24/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023] Open
Abstract
It has been over a decade since the initial identification of exonuclease domain mutations in the genes encoding the catalytic subunits of replication DNA polymerases ϵ and δ (POLE and POLD1) in tumors from highly mutated endometrial and colorectal cancers. Interest in studying POLE and POLD1 has increased significantly since then. Prior to those landmark cancer genome sequencing studies, it was well documented that mutations in replication DNA polymerases that reduced their DNA synthesis accuracy, their exonuclease activity or their interactions with other factors could lead to increased mutagenesis, DNA damage and even tumorigenesis in mice. There are several recent, well-written reviews of replication DNA polymerases. The aim of this review is to gather and review in some detail recent studies of DNA polymerases ϵ and δ as they pertain to genome instability, cancer and potential therapeutic treatments. The focus here is primarily on recent informative studies on the significance of mutations in genes encoding their catalytic subunits (POLE and POLD1), mutational signatures, mutations in associated genes, model organisms, and the utility of chemotherapy and immune checkpoint inhibition in polymerase mutant tumors.
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Affiliation(s)
- Juliet D Strauss
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70118 LA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70118 LA, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, 70118 LA, USA
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6
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Sui Y, Epstein A, Dominska M, Zheng DQ, Petes T, Klein H. Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides. Nucleic Acids Res 2022; 50:6890-6902. [PMID: 35748861 PMCID: PMC9262587 DOI: 10.1093/nar/gkac536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022] Open
Abstract
Ribonucleotides can be incorporated into DNA during replication by the replicative DNA polymerases. These aberrant DNA subunits are efficiently recognized and removed by Ribonucleotide Excision Repair, which is initiated by the heterotrimeric enzyme RNase H2. While RNase H2 is essential in higher eukaryotes, the yeast Saccharomyces cerevisiae can survive without RNase H2 enzyme, although the genome undergoes mutation, recombination and other genome instability events at an increased rate. Although RNase H2 can be considered as a protector of the genome from the deleterious events that can ensue from recognition and removal of embedded ribonucleotides, under conditions of high ribonucleotide incorporation and retention in the genome in a RNase H2-negative strain, sudden introduction of active RNase H2 causes massive DNA breaks and genome instability in a condition which we term 'ribodysgenesis'. The DNA breaks and genome instability arise solely from RNase H2 cleavage directed to the ribonucleotide-containing genome. Survivors of ribodysgenesis have massive loss of heterozygosity events stemming from recombinogenic lesions on the ribonucleotide-containing DNA, with increases of over 1000X from wild-type. DNA breaks are produced over one to two divisions and subsequently cells adapt to RNase H2 and ribonucleotides in the genome and grow with normal levels of genome instability.
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Affiliation(s)
- Yang Sui
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan 316021, China,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anastasiya Epstein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dao-Qiong Zheng
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan 316021, China,Hainan Institute of Zhejiang University, Sanya 572000, China,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hannah L Klein
- To whom correspondence should be addressed. Tel: +1 212 263 5778;
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Yao Z, Wang Q, Dai Z. Recent Advances in Directed Yeast Genome Evolution. J Fungi (Basel) 2022; 8:635. [PMID: 35736118 PMCID: PMC9225242 DOI: 10.3390/jof8060635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
Saccharomyces cerevisiae, as a Generally Recognized as Safe (GRAS) fungus, has become one of the most widely used chassis cells for industrial applications and basic research. However, owing to its complex genetic background and intertwined metabolic networks, there are still many obstacles that need to be overcome in order to improve desired traits and to successfully link genotypes to phenotypes. In this context, genome editing and evolutionary technology have rapidly progressed over the last few decades to facilitate the rapid generation of tailor-made properties as well as for the precise determination of relevant gene targets that regulate physiological functions, including stress resistance, metabolic-pathway optimization and organismal adaptation. Directed genome evolution has emerged as a versatile tool to enable researchers to access desired traits and to study increasingly complicated phenomena. Here, the development of directed genome evolutions in S. cerevisiae is reviewed, with a focus on different techniques driving evolutionary engineering.
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Affiliation(s)
- Zhen Yao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China;
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Qinhong Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China;
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Zongjie Dai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China;
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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8
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Lamb NA, Bard JE, Loll-Krippleber R, Brown GW, Surtees JA. Complex mutation profiles in mismatch repair and ribonucleotide reductase mutants reveal novel repair substrate specificity of MutS homolog (MSH) complexes. Genetics 2022; 221:6605222. [PMID: 35686905 PMCID: PMC9339293 DOI: 10.1093/genetics/iyac092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/24/2022] [Indexed: 12/30/2022] Open
Abstract
Determining mutation signatures is standard for understanding the etiology of human tumors and informing cancer treatment. Multiple determinants of DNA replication fidelity prevent mutagenesis that leads to carcinogenesis, including the regulation of free deoxyribonucleoside triphosphate pools by ribonucleotide reductase and repair of replication errors by the mismatch repair system. We identified genetic interactions between rnr1 alleles that skew and/or elevate deoxyribonucleoside triphosphate levels and mismatch repair gene deletions. These defects indicate that the rnr1 alleles lead to increased mutation loads that are normally acted upon by mismatch repair. We then utilized a targeted deep-sequencing approach to determine mutational profiles associated with mismatch repair pathway defects. By combining rnr1 and msh mutations to alter and/or increase deoxyribonucleoside triphosphate levels and alter the mutational load, we uncovered previously unreported specificities of Msh2-Msh3 and Msh2-Msh6. Msh2-Msh3 is uniquely able to direct the repair of G/C single-base deletions in GC runs, while Msh2-Msh6 specifically directs the repair of substitutions that occur at G/C dinucleotides. We also identified broader sequence contexts that influence variant profiles in different genetic backgrounds. Finally, we observed that the mutation profiles in double mutants were not necessarily an additive relationship of mutation profiles in single mutants. Our results have implications for interpreting mutation signatures from human tumors, particularly when mismatch repair is defective.
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Affiliation(s)
- Natalie A Lamb
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jonathan E Bard
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA,University at Buffalo Genomics and Bioinformatics Core, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Raphael Loll-Krippleber
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jennifer A Surtees
- Corresponding author: Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Rm 4215, 955 Main Street, Buffalo, NY 14203, USA.
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9
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Zhou ZX, Lujan SA, Burkholder AB, St. Charles J, Dahl J, Farrell CE, Williams JS, Kunkel TA. How asymmetric DNA replication achieves symmetrical fidelity. Nat Struct Mol Biol 2021; 28:1020-1028. [PMID: 34887558 PMCID: PMC8815454 DOI: 10.1038/s41594-021-00691-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/22/2021] [Indexed: 11/09/2022]
Abstract
Accurate DNA replication of an undamaged template depends on polymerase selectivity for matched nucleotides, exonucleolytic proofreading of mismatches, and removal of remaining mismatches via DNA mismatch repair (MMR). DNA polymerases (Pols) δ and ε have 3'-5' exonucleases into which mismatches are partitioned for excision in cis (intrinsic proofreading). Here we provide strong evidence that Pol δ can extrinsically proofread mismatches made by itself and those made by Pol ε, independently of both Pol δ's polymerization activity and MMR. Extrinsic proofreading across the genome is remarkably efficient. We report, with unprecedented accuracy, in vivo contributions of nucleotide selectivity, proofreading, and MMR to the fidelity of DNA replication in Saccharomyces cerevisiae. We show that extrinsic proofreading by Pol δ improves and balances the fidelity of the two DNA strands. Together, we depict a comprehensive picture of how nucleotide selectivity, proofreading, and MMR cooperate to achieve high and symmetrical fidelity on the two strands.
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Affiliation(s)
- Zhi-Xiong Zhou
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Scott A. Lujan
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Adam B. Burkholder
- Integrative Bioinformatics Support Group, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Jordan St. Charles
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Joseph Dahl
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Corinne E. Farrell
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Jessica S. Williams
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Thomas A. Kunkel
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
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10
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Abstract
Choosing and optimizing treatment strategies for cancer requires
capturing its complex dynamics sufficiently well for understanding but
without being overwhelmed. Mathematical models are essential to
achieve this understanding, and we discuss the challenge of choosing
the right level of complexity to address the full range of tumor
complexity from growth, the generation of tumor heterogeneity, and
interactions within tumors and with treatments and the tumor
microenvironment. We discuss the differences between conceptual and
descriptive models, and compare the use of predator-prey models,
evolutionary game theory, and dynamic precision medicine approaches in
the face of uncertainty about mechanisms and parameter values.
Although there is of course no one-size-fits-all approach, we conclude
that broad and flexible thinking about cancer, based on combined
modeling approaches, will play a key role in finding creative and
improved treatments.
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Affiliation(s)
- Robert A Beckman
- Departments of Oncology and Biostatistics, Bioinformatics, & Biomathematics, Lombardi Comprehensive Cancer Center and Innovation Center for Biomedical Informatics, 12231Georgetown University Medical Center, Washington, DC, USA
| | - Irina Kareva
- Mathematical and Computational Sciences Center, School of Human Evolution and Social Change, 7864Arizona State University, Tempe, AZ, USA
| | - Frederick R Adler
- School of Biological Sciences, 415772University of Utah, Salt Lake City, UT, USA.,Department of Mathematics, 415772University of Utah, Salt Lake City, UT, USA
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11
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Rate volatility and asymmetric segregation diversify mutation burden in cells with mutator alleles. Commun Biol 2021; 4:21. [PMID: 33398111 PMCID: PMC7782790 DOI: 10.1038/s42003-020-01544-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022] Open
Abstract
Mutations that compromise mismatch repair (MMR) or DNA polymerase ε or δ exonuclease domains produce mutator phenotypes capable of fueling cancer evolution. Here, we investigate how combined defects in these pathways expands genetic heterogeneity in cells of the budding yeast, Saccharomyces cerevisiae, using a single-cell resolution approach that tallies all mutations arising from individual divisions. The distribution of replication errors present in mother cells after the initial S-phase was broader than expected for a single uniform mutation rate across all cell divisions, consistent with volatility of the mutator phenotype. The number of mismatches that then segregated to the mother and daughter cells co-varied, suggesting that each division is governed by a different underlying genome-wide mutation rate. The distribution of mutations that individual cells inherit after the second S-phase is further broadened by the sequential actions of semiconservative replication and mitotic segregation of chromosomes. Modeling suggests that this asymmetric segregation may diversify mutation burden in mutator-driven tumors. Dowsett et al use a single-cell resolution approach to analyse the distribution of mutations across several divisions in yeast diploid strains mutated in mismatch repair and polymerase delta proofreading. They find that the underlying mutation rate varies from one division to another, and that new mutations segregate unequally between sister chromatids at each division, expanding genetic heterogeneity in the population.
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12
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He J, Ouyang W, Zhao W, Shao L, Li B, Liu B, Wang D, Han-Zhang H, Zhang Z, Shao L, Li W. Distinctive genomic characteristics in POLE/POLD1-mutant cancers can potentially predict beneficial clinical outcomes in patients who receive immune checkpoint inhibitor. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:129. [PMID: 33569431 PMCID: PMC7867935 DOI: 10.21037/atm-20-7553] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Mutations in POLE /POLD1 proofreading domain can cause deficiencies in DNA repair, conferring ultramutated cancer phenotypes. Preliminary clinical studies have revealed an association between POLE/POLD1 mutations and beneficial clinical outcomes to immune checkpoint inhibitor (ICI) therapy This study aims to investigate the genomic characteristics of POLE/POLD-mutant tumors and the prognostic value of POLE/POLD mutation for ICI treatment. Methods Genomic data of 21,074 patients with 23 cancer types were retrieved from Burning Rock variant database (BR VarDB). The prevalence and spectra of POLE and POLD1 mutations were assessed and compared with that in The Cancer Genome Atlas (TCGA) samples. The correlations of POLE/POLD1 mutation with tumor mutational burden (TMB) and microsatellite instability (MSI) were investigated. The prognostic value of POLE/POLD1 mutations was also explored in 2,487 ICI-treated patients from published studies. Results BR VarDB samples displayed a similar mutational prevalence of POLE (3.2% vs. 3.2%) and POLD1 (1.4% vs. 1.6%, P=0.248) versusTCGA samples, but a slightly lower frequency of POLE and POLD1 co-mutations (0.21% vs. 0.43%, P<0.001). POLE/POLD1-mutant tumors harbored increased TCT→TAT and TCG→TTG transversions, and genomic signatures associated with DNA mismatch repair (MMR) deficiency and ultra-hypermuation. Furthermore, tumors with POLE/POLD1 proofreading mutation showed a significantly higher TMB than tumors with non-proofreading mutations (P<0.01), although both possessed a higher TMB than POLE/POLD1 wild-type (WT) tumors (P<0.0001 and P<0.0001, respectively). MSI was commonly observed in tumors harboring dominant clone of POLE/POLD1 mutation (10.2%), but occurred rarely in POLE/POLD1 WT tumors (0.5%) and tumors with accumulating sub-cloned POLE/POLD1 mutation (0%). Survival analysis revealed that POLE/POLD1 mutation was not independently correlated with longer survival after adjusting for TMB and other factors (HR =0.86, P=0.372). However, patients harboring POLE/POLD1 mutation demonstrated a higher response rate than patients with POLE/ POLD1 WT tumors (35.2% vs. 19.6%, P=0.0165). Conclusions We delineated distinctive genomic characteristics in POLE/POLD1-mutant tumors, suggesting the potential predictive role of POLE/POLD1 mutations, especially those in the proofreading domain, for beneficial outcomes of immunotherapy. Our results also suggest that MSI caused by a loss-of-function mutation in the MMR pathway tends to result from POLE/POLD1 proofreading deficiency in POLE/POLD1-mutant tumors with MSI.
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Affiliation(s)
- Junjun He
- Key Laboratory of Pancreatic Disease Research of Zhejiang Province, First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Ouyang
- Department of Oncology, Zhuzhou Central Hospital, Xiangya School of Medicine, Central South University, Zhuzhou, China
| | - Wugan Zhao
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lin Shao
- Burning Rock Biotech, Guangzhou, China
| | - Bing Li
- Burning Rock Biotech, Guangzhou, China
| | - Bihao Liu
- Department of Urology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Dejuan Wang
- Department of Urology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | | | | | | | - Wencai Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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13
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Pavlov YI, Zhuk AS, Stepchenkova EI. DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer. Cancers (Basel) 2020; 12:E3489. [PMID: 33255191 PMCID: PMC7760166 DOI: 10.3390/cancers12123489] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
Recent studies on tumor genomes revealed that mutations in genes of replicative DNA polymerases cause a predisposition for cancer by increasing genome instability. The past 10 years have uncovered exciting details about the structure and function of replicative DNA polymerases and the replication fork organization. The principal idea of participation of different polymerases in specific transactions at the fork proposed by Morrison and coauthors 30 years ago and later named "division of labor," remains standing, with an amendment of the broader role of polymerase δ in the replication of both the lagging and leading DNA strands. However, cancer-associated mutations predominantly affect the catalytic subunit of polymerase ε that participates in leading strand DNA synthesis. We analyze how new findings in the DNA replication field help elucidate the polymerase variants' effects on cancer.
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Affiliation(s)
- Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia;
| | - Anna S. Zhuk
- International Laboratory of Computer Technologies, ITMO University, 197101 Saint Petersburg, Russia;
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia;
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, 199034 Saint Petersburg, Russia
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14
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Bulock CR, Xing X, Shcherbakova PV. Mismatch repair and DNA polymerase δ proofreading prevent catastrophic accumulation of leading strand errors in cells expressing a cancer-associated DNA polymerase ϵ variant. Nucleic Acids Res 2020; 48:9124-9134. [PMID: 32756902 PMCID: PMC7498342 DOI: 10.1093/nar/gkaa633] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/13/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022] Open
Abstract
Substitutions in the exonuclease domain of DNA polymerase ϵ cause ultramutated human tumors. Yeast and mouse mimics of the most common variant, P286R, produce mutator effects far exceeding the effect of Polϵ exonuclease deficiency. Yeast Polϵ-P301R has increased DNA polymerase activity, which could underlie its high mutagenicity. We aimed to understand the impact of this increased activity on the strand-specific role of Polϵ in DNA replication and the action of extrinsic correction systems that remove Polϵ errors. Using mutagenesis reporters spanning a well-defined replicon, we show that both exonuclease-deficient Polϵ (Polϵ-exo−) and Polϵ-P301R generate mutations in a strictly strand-specific manner, yet Polϵ-P301R is at least ten times more mutagenic than Polϵ-exo− at each location analyzed. Thus, the cancer variant remains a dedicated leading-strand polymerase with markedly low accuracy. We further show that P301R substitution is lethal in strains lacking Polδ proofreading or mismatch repair (MMR). Heterozygosity for pol2-P301R is compatible with either defect but causes strong synergistic increases in the mutation rate, indicating that Polϵ-P301R errors are corrected by Polδ proofreading and MMR. These data reveal the unexpected ease with which polymerase exchange occurs in vivo, allowing Polδ exonuclease to prevent catastrophic accumulation of Polϵ-P301R-generated errors on the leading strand.
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Affiliation(s)
- Chelsea R Bulock
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Xuanxuan Xing
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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15
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Spontaneous Polyploids and Antimutators Compete During the Evolution of Saccharomyces cerevisiae Mutator Cells. Genetics 2020; 215:959-974. [PMID: 32513814 PMCID: PMC7404223 DOI: 10.1534/genetics.120.303333] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 05/22/2020] [Indexed: 02/02/2023] Open
Abstract
Mutations affecting DNA polymerase exonuclease domains or mismatch repair (MMR) generate "mutator" phenotypes capable of driving tumorigenesis. Cancers with both defects exhibit an explosive increase in mutation burden that appears to reach a threshold, consistent with selection acting against further mutation accumulation. In Saccharomyces cerevisiae haploid yeast, simultaneous defects in polymerase proofreading and MMR select for "antimutator" mutants that suppress the mutator phenotype. We report here that spontaneous polyploids also escape this "error-induced extinction" and routinely outcompete antimutators in evolved haploid cultures. We performed similar experiments to explore how diploid yeast adapt to the mutator phenotype. We first evolved cells with homozygous mutations affecting polymerase δ proofreading and MMR, which we anticipated would favor tetraploid emergence. While tetraploids arose with a low frequency, in most cultures, a single antimutator clone rose to prominence carrying biallelic mutations affecting the polymerase mutator alleles. Variation in mutation rate between subclones from the same culture suggests that there exists continued selection pressure for additional antimutator alleles. We then evolved diploid yeast modeling MMR-deficient cancers with the most common heterozygous exonuclease domain mutation (POLE-P286R). Although these cells grew robustly, within 120 generations, all subclones carried truncating or nonsynonymous mutations in the POLE-P286R homologous allele (pol2-P301R) that suppressed the mutator phenotype as much as 100-fold. Independent adaptive events in the same culture were common. Our findings suggest that analogous tumor cell populations may adapt to the threat of extinction by polyclonal mutations that neutralize the POLE mutator allele and preserve intratumoral genetic diversity for future adaptation.
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16
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Birtwell D, Luebeck G, Maley CC. The evolution of metapopulation dynamics and the number of stem cells in intestinal crypts and other tissue structures in multicellular bodies. Evol Appl 2020; 13:1771-1783. [PMID: 32821281 PMCID: PMC7428809 DOI: 10.1111/eva.13069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/04/2022] Open
Abstract
Carcinogenesis is a process of somatic evolution. Previous models of stem and transient amplifying cells in epithelial proliferating units like colonic crypts showed that intermediate numbers of stem cells in a crypt should optimally prevent progression to cancer. If a stem cell population is too small, it is easy for a mutator mutation to drift to fixation. If it is too large, it is easy for selection to drive cell fitness enhancing carcinogenic mutations to fixation. Here, we show that a multiscale microsimulation, that captures both within-crypt and between-crypt evolutionary dynamics, leads to a different conclusion. Epithelial tissues are metapopulations of crypts. We measured time to initiation of a neoplasm, implemented as inactivation of both alleles of a tumor suppressor gene. In our model, time to initiation is dependent on the spread of mutator clones in the crypts. The proportion of selectively beneficial and deleterious mutations in somatic cells is unknown and so was explored with a parameter. When the majority of non-neutral mutations are deleterious, the fitness of mutator clones tends to decline. When crypts are maintained by few stem cells, intercrypt competition tends to remove crypts with fixed mutators. When there are many stem cells within a crypt, there is virtually no crypt turnover, but mutator clones are suppressed by within-crypt competition. If the majority of non-neutral mutations are beneficial to the clone, then these results are reversed and intermediate-sized crypts provide the most protection against initiation. These results highlight the need to understand the dynamics of turnover and the mechanisms that control homeostasis, both at the level of stem cells within proliferative units and at the tissue level of competing proliferative units. Determining the distribution of fitness effects of somatic mutations will also be crucial to understanding the dynamics of tumor initiation and progression.
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Affiliation(s)
- David Birtwell
- Norris Comprehensive Cancer CenterUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Georg Luebeck
- Public Health Sciences DivisionFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Carlo C. Maley
- Arizona Cancer Evolution CenterBiodesign Institute and School of Life SciencesArizona State UniversityTempeAZUSA
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17
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Li HD, Lu C, Zhang H, Hu Q, Zhang J, Cuevas IC, Sahoo SS, Aguilar M, Maurais EG, Zhang S, Wang X, Akbay EA, Li GM, Li B, Koduru P, Ly P, Fu YX, Castrillon DH. A PoleP286R mouse model of endometrial cancer recapitulates high mutational burden and immunotherapy response. JCI Insight 2020; 5:138829. [PMID: 32699191 DOI: 10.1172/jci.insight.138829] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/10/2020] [Indexed: 12/18/2022] Open
Abstract
Cancer is instigated by mutator phenotypes, including deficient mismatch repair and p53-associated chromosomal instability. More recently, a distinct class of cancers was identified with unusually high mutational loads due to heterozygous amino acid substitutions (most commonly P286R) in the proofreading domain of DNA polymerase ε, the leading strand replicase encoded by POLE. Immunotherapy has revolutionized cancer treatment, but new model systems are needed to recapitulate high mutational burdens characterizing human cancers and permit study of mechanisms underlying clinical responses. Here, we show that activation of a conditional LSL-PoleP286R allele in endometrium is sufficient to elicit in all animals endometrial cancers closely resembling their human counterparts, including very high mutational burden. Diverse investigations uncovered potentially novel aspects of Pole-driven tumorigenesis, including secondary p53 mutations associated with tetraploidy, and cooperation with defective mismatch repair through inactivation of Msh2. Most significantly, there were robust antitumor immune responses with increased T cell infiltrates, accelerated tumor growth following T cell depletion, and unfailing clinical regression following immune checkpoint therapy. This model predicts that human POLE-driven cancers will prove consistently responsive to immune checkpoint blockade. Furthermore, this is a robust and efficient approach to recapitulate in mice the high mutational burdens and immune responses characterizing human cancers.
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Affiliation(s)
| | | | - He Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | | | | | | | | | | | | | | | | | - Esra A Akbay
- Department of Pathology.,Simmons Comprehensive Cancer Center
| | - Guo-Min Li
- Department of Radiation Oncology.,Advanced Imaging Research Center
| | - Bo Li
- Simmons Comprehensive Cancer Center.,Lyda Hill Department of Bioinformatics.,Department of Immunology
| | | | - Peter Ly
- Department of Pathology.,Simmons Comprehensive Cancer Center.,Department of Cell Biology, and
| | - Yang-Xin Fu
- Department of Pathology.,Simmons Comprehensive Cancer Center.,Department of Immunology
| | - Diego H Castrillon
- Department of Pathology.,Simmons Comprehensive Cancer Center.,Department of Obstetrics & Gynecology, UT Southwestern Medical Center, Dallas, Texas, USA
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18
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Abstract
Polδ and Polε are the two major replicative polymerases in eukaryotes, but their precise roles at the replication fork remain a subject of debate. A bulk of data supports a model where Polε and Polδ synthesize leading and lagging DNA strands, respectively. However, this model has been difficult to reconcile with the fact that mutations in Polδ have much stronger consequences for genome stability than equivalent mutations in Polε. We provide direct evidence for a long-entertained idea that Polδ can proofread errors made by Polε in addition to its own errors, thus, making a more prominent contribution to mutation avoidance. This paper provides an essential advance in the understanding of the mechanism of eukaryotic DNA replication. During eukaryotic replication, DNA polymerases ε (Polε) and δ (Polδ) synthesize the leading and lagging strands, respectively. In a long-known contradiction to this model, defects in the fidelity of Polε have a much weaker impact on mutagenesis than analogous Polδ defects. It has been previously proposed that Polδ contributes more to mutation avoidance because it proofreads mismatches created by Polε in addition to its own errors. However, direct evidence for this model was missing. We show that, in yeast, the mutation rate increases synergistically when a Polε nucleotide selectivity defect is combined with a Polδ proofreading defect, demonstrating extrinsic proofreading of Polε errors by Polδ. In contrast, combining Polδ nucleotide selectivity and Polε proofreading defects produces no synergy, indicating that Polε cannot correct errors made by Polδ. We further show that Polδ can remove errors made by exonuclease-deficient Polε in vitro. These findings illustrate the complexity of the one-strand–one-polymerase model where synthesis appears to be largely divided, but Polδ proofreading operates on both strands.
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19
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Sidorova A, Levashova N, Garaeva A, Tverdislov V. A percolation model of natural selection. Biosystems 2020; 193-194:104120. [PMID: 32092352 DOI: 10.1016/j.biosystems.2020.104120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/29/2020] [Accepted: 02/15/2020] [Indexed: 12/13/2022]
Abstract
A new approach has been proposed and developed: the selection of optimal variants in the evolutionary mutation flow is considered as an analogue of a percolation filter. Interaction of mutations in a series of generations and random processes of drift determine the collective behavior of nodes (individuals - carriers and converters of mutations) and bonds (mutations) in the space of percolation lattice. It is shown that the choice of the development trajectory at the population level depends on the spectrum of supporting and prohibiting mutations under the influence of conjugate deterministic and random factors. From the point of view of the fluctuation-bifurcation process, new concepts of the lower and upper thresholds of the percolation selection grid are defined in the hierarchical structure of speciation. The upper threshold determines the state of self-organized criticality, which, when overcome, leads to irreversible self-organization processes in the population caused by the accumulation of mutations.
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Affiliation(s)
- Alla Sidorova
- Department of Biophysics, Faculty of Physics, M.V.Lomonosov Moscow State University. Moscow, 119991, Russia.
| | - Natalia Levashova
- Department of Mathematics, Faculty of Physics, M.V.Lomonosov Moscow State University. Moscow, 119991, Russia.
| | - Anastasia Garaeva
- Department of Biophysics, Faculty of Physics, M.V.Lomonosov Moscow State University. Moscow, 119991, Russia.
| | - Vsevolod Tverdislov
- Department of Biophysics, Faculty of Physics, M.V.Lomonosov Moscow State University. Moscow, 119991, Russia.
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20
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Schmidt TT, Sharma S, Reyes GX, Gries K, Gross M, Zhao B, Yuan JH, Wade R, Chabes A, Hombauer H. A genetic screen pinpoints ribonucleotide reductase residues that sustain dNTP homeostasis and specifies a highly mutagenic type of dNTP imbalance. Nucleic Acids Res 2019; 47:237-252. [PMID: 30462295 PMCID: PMC6326808 DOI: 10.1093/nar/gky1154] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022] Open
Abstract
The balance and the overall concentration of intracellular deoxyribonucleoside triphosphates (dNTPs) are important determinants of faithful DNA replication. Despite the established fact that changes in dNTP pools negatively influence DNA replication fidelity, it is not clear why certain dNTP pool alterations are more mutagenic than others. As intracellular dNTP pools are mainly controlled by ribonucleotide reductase (RNR), and given the limited number of eukaryotic RNR mutations characterized so far, we screened for RNR1 mutations causing mutator phenotypes in Saccharomyces cerevisiae. We identified 24 rnr1 mutant alleles resulting in diverse mutator phenotypes linked in most cases to imbalanced dNTPs. Among the identified rnr1 alleles the strongest mutators presented a dNTP imbalance in which three out of the four dNTPs were elevated (dCTP, dTTP and dGTP), particularly if dGTP levels were highly increased. These rnr1 alleles caused growth defects/lethality in DNA replication fidelity-compromised backgrounds, and caused strong mutator phenotypes even in the presence of functional DNA polymerases and mismatch repair. In summary, this study pinpoints key residues that contribute to allosteric regulation of RNR’s overall activity or substrate specificity. We propose a model that distinguishes between different dNTP pool alterations and provides a mechanistic explanation why certain dNTP imbalances are particularly detrimental.
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Affiliation(s)
- Tobias T Schmidt
- DNA Repair Mechanisms and Cancer, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany.,Faculty of Bioscience, Heidelberg University, Heidelberg D-69120, Germany
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå SE-901 87 Sweden
| | - Gloria X Reyes
- DNA Repair Mechanisms and Cancer, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany
| | - Kerstin Gries
- DNA Repair Mechanisms and Cancer, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany
| | - Maike Gross
- DNA Repair Mechanisms and Cancer, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany
| | - Boyu Zhao
- DNA Repair Mechanisms and Cancer, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany.,Faculty of Bioscience, Heidelberg University, Heidelberg D-69120, Germany
| | - Jui-Hung Yuan
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg D-69118, Germany
| | - Rebecca Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg D-69118, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg D-69120, Germany.,Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg D-69120, Germany
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå SE-901 87 Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå SE-901 87, Sweden
| | - Hans Hombauer
- DNA Repair Mechanisms and Cancer, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany
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21
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Abstract
We recently developed an orthogonal replication system (OrthoRep) in yeast that allows for the rapid continuous mutagenesis of a special plasmid without mutating the genome. Although OrthoRep has been successfully applied to evolve several proteins and enzymes, the generality of OrthoRep has not yet been systematically studied. Here, we show that OrthoRep is fully compatible with all Saccharomyces cerevisiae strains tested, demonstrate that the orthogonal plasmid can encode genetic material of at least 22 kb, and report a CRISPR/Cas9-based method for expedient genetic manipulations of OrthoRep. It was previously reported that the replication system upon which OrthoRep is based is only stable in respiration-deficient S. cerevisiae strains that have lost their mitochondrial genome (ρ0 strains). However, here we trace this biological incompatibility to the activity of the dispensable toxin/antitoxin system encoded on the wild-type orthogonal plasmid. Since the toxin/antitoxin system is replaced by genes of interest in any OrthoRep application, OrthoRep is a generally compatible platform for continuous in vivo evolution in S. cerevisiae.
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Affiliation(s)
- Alex A. Javanpour
- Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, California 92697, United States
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22
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Tam AS, Stirling PC. Splicing, genome stability and disease: splice like your genome depends on it! Curr Genet 2019; 65:905-912. [PMID: 30953124 DOI: 10.1007/s00294-019-00964-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/21/2022]
Abstract
The spliceosome has been implicated in genome maintenance for decades. Recently, a surge in discoveries in cancer has suggested that the oncogenic mechanism of spliceosomal defects may involve defective genome stability. The action of the core spliceosome prevents R-loop accumulation, and regulates the expression of genome stability factors. At the same time, specific spliceosomal components have non-canonical functions in genome maintenance. Here we review these different models, highlighting their discovery in different model systems, and describing their potential impact on human disease states.
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Affiliation(s)
- Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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23
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Park VS, Pursell ZF. POLE proofreading defects: Contributions to mutagenesis and cancer. DNA Repair (Amst) 2019; 76:50-59. [PMID: 30818169 PMCID: PMC6467506 DOI: 10.1016/j.dnarep.2019.02.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/14/2022]
Abstract
DNA polymerases are uniquely poised to contribute to the elevated mutation burdens seen in many human tumors. These mutations can arise through a number of different polymerase-dependent mechanisms, including intrinsic errors made using template DNA and precursor dNTPs free from chemical modifications, misinsertion events opposite chemically damaged template DNA or insertion events using modified nucleotides. While specific DNA repair polymerases have been known to contribute to tumorigenesis, the role of replication polymerases in mutagenesis in human disease has come into sharp focus over the last decade. This review describes how mutations in these replication DNA polymerases help to drive mutagenesis and tumor development, with particular attention to DNA polymerase epsilon. Recent studies using cancer genome sequencing, mutational signature analyses, yeast and mouse models, and the influence of mismatch repair on tumors with DNA polymerase mutations are discussed.
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Affiliation(s)
- Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA, USA.
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24
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Lee MB, Dowsett IT, Carr DT, Wasko BM, Stanton SG, Chung MS, Ghodsian N, Bode A, Kiflezghi MG, Uppal PA, Grayden KA, Elala YC, Tang TT, Tran NHB, Tran THB, Diep AB, Hope M, Promislow DEL, Kennedy SR, Kaeberlein M, Herr AJ. Defining the impact of mutation accumulation on replicative lifespan in yeast using cancer-associated mutator phenotypes. Proc Natl Acad Sci U S A 2019; 116:3062-3071. [PMID: 30718408 PMCID: PMC6386679 DOI: 10.1073/pnas.1815966116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Mutations accumulate within somatic cells and have been proposed to contribute to aging. It is unclear what level of mutation burden may be required to consistently reduce cellular lifespan. Human cancers driven by a mutator phenotype represent an intriguing model to test this hypothesis, since they carry the highest mutation burdens of any human cell. However, it remains technically challenging to measure the replicative lifespan of individual mammalian cells. Here, we modeled the consequences of cancer-related mutator phenotypes on lifespan using yeast defective for mismatch repair (MMR) and/or leading strand (Polε) or lagging strand (Polδ) DNA polymerase proofreading. Only haploid mutator cells with significant lifetime mutation accumulation (MA) exhibited shorter lifespans. Diploid strains, derived by mating haploids of various genotypes, carried variable numbers of fixed mutations and a range of mutator phenotypes. Some diploid strains with fewer than two mutations per megabase displayed a 25% decrease in lifespan, suggesting that moderate numbers of random heterozygous mutations can increase mortality rate. As mutation rates and burdens climbed, lifespan steadily eroded. Strong diploid mutator phenotypes produced a form of genetic anticipation with regard to aging, where the longer a lineage persisted, the shorter lived cells became. Using MA lines, we established a relationship between mutation burden and lifespan, as well as population doubling time. Our observations define a threshold of random mutation burden that consistently decreases cellular longevity in diploid yeast cells. Many human cancers carry comparable mutation burdens, suggesting that while cancers appear immortal, individual cancer cells may suffer diminished lifespan due to accrued mutation burden.
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Affiliation(s)
- Mitchell B Lee
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Ian T Dowsett
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
- Molecular Medicine and Mechanisms of Disease Program, University of Washington, Seattle, WA 98195-7705
| | - Daniel T Carr
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Brian M Wasko
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
- Department of Biology and Biotechnology, University of Houston-Clear Lake, Houston, TX 77058
| | - Sarah G Stanton
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Michael S Chung
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Niloufar Ghodsian
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Anna Bode
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Michael G Kiflezghi
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
- Molecular Medicine and Mechanisms of Disease Program, University of Washington, Seattle, WA 98195-7705
| | - Priya A Uppal
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | | | - Yordanos C Elala
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Thao T Tang
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Ngoc H B Tran
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Thu H B Tran
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Anh B Diep
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Michael Hope
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Daniel E L Promislow
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
- Department of Biology, University of Washington, Seattle, WA, 98195-1800
| | - Scott R Kennedy
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Alan J Herr
- Department of Pathology, University of Washington, Seattle, WA 98195-7705;
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25
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Rationally designed perturbation factor drives evolution in Saccharomyces cerevisiae for industrial application. ACTA ACUST UNITED AC 2018; 45:869-880. [DOI: 10.1007/s10295-018-2057-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/14/2018] [Indexed: 10/28/2022]
Abstract
Abstract
Saccharomyces cerevisiae strains with favorable characteristics are preferred for application in industries. However, the current ability to reprogram a yeast cell on the genome scale is limited due to the complexity of yeast ploids. In this study, a method named genome replication engineering-assisted continuous evolution (GREACE) was proved efficient in engineering S. cerevisiae with different ploids. Through iterative cycles of culture coupled with selection, GREACE could continuously improve the target traits of yeast by accumulating beneficial genetic modification in genome. The application of GREACE greatly improved the tolerance of yeast against acetic acid compared with their parent strain. This method could also be employed to improve yeast aroma profile and the phenotype could be stably inherited to the offspring. Therefore, GREACE method was efficient in S. cerevisiae engineering and it could be further used to evolve yeast with other specific characteristics.
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26
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Haradhvala NJ, Kim J, Maruvka YE, Polak P, Rosebrock D, Livitz D, Hess JM, Leshchiner I, Kamburov A, Mouw KW, Lawrence MS, Getz G. Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair. Nat Commun 2018; 9:1746. [PMID: 29717118 PMCID: PMC5931517 DOI: 10.1038/s41467-018-04002-4] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/26/2018] [Indexed: 12/19/2022] Open
Abstract
Fidelity of DNA replication is maintained using polymerase proofreading and the mismatch repair pathway. Tumors with loss of function of either mechanism have elevated mutation rates with characteristic mutational signatures. Here we report that tumors with concurrent loss of both polymerase proofreading and mismatch repair function have mutational patterns that are not a simple sum of the signatures of the individual alterations, but correspond to distinct, previously unexplained signatures: COSMIC database signatures 14 and 20. We then demonstrate that in all five cases in which the chronological order of events could be determined, polymerase epsilon proofreading alterations precede the defect in mismatch repair. Overall, we illustrate that multiple distinct mutational signatures can result from different combinations of a smaller number of mutational processes (of either damage or repair), which can influence the interpretation and discovery of mutational signatures. Polymerase proofreading and the mismatch repair pathway maintain the fidelity of DNA replication. Here the authors show that tumors with concurrent loss of function of both pathways lead to mutation signatures that are not simply a sum of the signatures found in tumors involving single alteration.
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Affiliation(s)
- N J Haradhvala
- Department of Pathology and Cancer Center, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA.,Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
| | - J Kim
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
| | - Y E Maruvka
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
| | - P Polak
- Department of Pathology and Cancer Center, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA.,Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA.,Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - D Rosebrock
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
| | - D Livitz
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
| | - J M Hess
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
| | - I Leshchiner
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
| | - A Kamburov
- Department of Pathology and Cancer Center, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA.,Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA.,Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - K W Mouw
- Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.,Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, 450 Brookline Ave, HIM 350, Boston, MA, 02215, USA
| | - M S Lawrence
- Department of Pathology and Cancer Center, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA.,Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA.,Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - G Getz
- Department of Pathology and Cancer Center, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA. .,Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA. .,Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.
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27
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Lee MB, Kaeberlein M. Translational Geroscience: From invertebrate models to companion animal and human interventions. TRANSLATIONAL MEDICINE OF AGING 2018; 2:15-29. [PMID: 32368707 PMCID: PMC7198054 DOI: 10.1016/j.tma.2018.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Translational geroscience is an interdisciplinary field descended from basic gerontology that seeks to identify, validate, and clinically apply interventions to maximize healthy, disease-free lifespan. In this review, we describe a research pipeline for the identification and validation of lifespan extending interventions. Beginning in invertebrate model systems, interventions are discovered and then characterized using other invertebrate model systems (evolutionary translation), models of genetic diversity, and disease models. Vertebrate model systems, particularly mice, can then be utilized to validate interventions in mammalian systems. Collaborative, multi-site efforts, like the Interventions Testing Program (ITP), provide a key resource to assess intervention robustness in genetically diverse mice. Mouse disease models provide a tool to understand the broader utility of longevity interventions. Beyond mouse models, we advocate for studies in companion pets. The Dog Aging Project is an exciting example of translating research in dogs, both to develop a model system and to extend their healthy lifespan as a goal in itself. Finally, we discuss proposed and ongoing intervention studies in humans, unmet needs for validating interventions in humans, and speculate on how differences in survival among human populations may influence intervention efficacy.
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Affiliation(s)
- Mitchell B. Lee
- Department of Pathology, University of Washington, Seattle, WA USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA USA
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28
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Beckman RA, Loeb LA. Evolutionary dynamics and significance of multiple subclonal mutations in cancer. DNA Repair (Amst) 2017; 56:7-15. [PMID: 28652129 DOI: 10.1016/j.dnarep.2017.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
For the last 40 years the authors have collaborated on trying to understand the complexities of human cancer by formulating testable mathematical models that are based on mutation accumulation in human malignancies. We summarize the concepts encompassed by multiple mutations in human cancers in the context of source, accumulation during carcinogenesis and tumor progression, and therapeutic consequences. We conclude that the efficacious treatment of human cancer by targeted therapy will involve individualized, uniquely directed specific agents singly and in simultaneous combinations, and take into account the importance of targeting resistant subclonal mutations, particularly those subclones with alterations in DNA repair genes, DNA polymerase, and other genes required to maintain genetic stability.
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Affiliation(s)
- Robert A Beckman
- Departments of Oncology and Biostatistics, Bioinformatics, & Biomathematics, Lombardi Comprehensive Cancer Center and Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC 20007 USA
| | - Lawrence A Loeb
- Joseph Gottstein Memorial Cancer Research Laboratory, Departments of Pathology and Biochemistry, University of Washington School of Medicine, Seattle, WA, 98195 USA.
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29
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Normally lethal amino acid substitutions suppress an ultramutator DNA Polymerase δ variant. Sci Rep 2017; 7:46535. [PMID: 28417960 PMCID: PMC5394481 DOI: 10.1038/srep46535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/22/2017] [Indexed: 02/06/2023] Open
Abstract
In yeast, the pol3-01,L612M double mutant allele, which causes defects in DNA polymerase delta (Pol δ) proofreading (pol3-01) and nucleotide selectivity (pol3-L612M), confers an “ultramutator” phenotype that rapidly drives extinction of haploid and diploid MMR-proficient cells. Here, we investigate antimutator mutations that encode amino acid substitutions in Pol δ that suppress this lethal phenotype. We find that most of the antimutator mutations individually suppress the pol3-01 and pol3-L612M mutator phenotypes. The locations of many of the amino acid substitutions in Pol δ resemble those of previously identified antimutator substitutions; however, two novel mutations encode substitutions (R674G and Q697R) of amino acids in the fingers domain that coordinate the incoming dNTP. These mutations are lethal without pol3-L612M and markedly change the mutation spectra produced by the pol3-01,L612M mutator allele, suggesting that they alter nucleotide selection to offset the pol3-L612M mutator phenotype. Consistent with this hypothesis, mutations and drug treatments that perturb dNTP pool levels disproportionately influence the viability of pol3-L612M,R674G and pol3-L612M,Q697R cells. Taken together, our findings suggest that mutation rate can evolve through genetic changes that alter the balance of dNTP binding and dissociation from DNA polymerases.
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30
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Alterations in cellular metabolism triggered by URA7 or GLN3 inactivation cause imbalanced dNTP pools and increased mutagenesis. Proc Natl Acad Sci U S A 2017; 114:E4442-E4451. [PMID: 28416670 DOI: 10.1073/pnas.1618714114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic DNA replication fidelity relies on the concerted action of DNA polymerase nucleotide selectivity, proofreading activity, and DNA mismatch repair (MMR). Nucleotide selectivity and proofreading are affected by the balance and concentration of deoxyribonucleotide (dNTP) pools, which are strictly regulated by ribonucleotide reductase (RNR). Mutations preventing DNA polymerase proofreading activity or MMR function cause mutator phenotypes and consequently increased cancer susceptibility. To identify genes not previously linked to high-fidelity DNA replication, we conducted a genome-wide screen in Saccharomyces cerevisiae using DNA polymerase active-site mutants as a "sensitized mutator background." Among the genes identified in our screen, three metabolism-related genes (GLN3, URA7, and SHM2) have not been previously associated to the suppression of mutations. Loss of either the transcription factor Gln3 or inactivation of the CTP synthetase Ura7 both resulted in the activation of the DNA damage response and imbalanced dNTP pools. Importantly, these dNTP imbalances are strongly mutagenic in genetic backgrounds where DNA polymerase function or MMR activity is partially compromised. Previous reports have shown that dNTP pool imbalances can be caused by mutations altering the allosteric regulation of enzymes involved in dNTP biosynthesis (e.g., RNR or dCMP deaminase). Here, we provide evidence that mutations affecting genes involved in RNR substrate production can cause dNTP imbalances, which cannot be compensated by RNR or other enzymatic activities. Moreover, Gln3 inactivation links nutrient deprivation to increased mutagenesis. Our results suggest that similar genetic interactions could drive mutator phenotypes in cancer cells.
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31
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Loeb LA. Human Cancers Express a Mutator Phenotype: Hypothesis, Origin, and Consequences. Cancer Res 2017; 76:2057-9. [PMID: 27197248 DOI: 10.1158/0008-5472.can-16-0794] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 03/15/2016] [Indexed: 11/16/2022]
Abstract
The mutator phenotype hypothesis was postulated more than 40 years ago. It was based on the multiple enzymatic steps required to precisely replicate the 6 billion bases in the human genome each time a normal cell divides. A reduction in this accuracy during tumor progression could be responsible for the striking heterogeneity of malignant cells within a tumor and for the rapidity by which cancers become resistant to therapy. Cancer Res; 76(8); 2057-9. ©2016 AACRSee related article by Loeb et al. Cancer Res. 1974;34:2311-21.
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Affiliation(s)
- Lawrence A Loeb
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington. Department of Biochemistry, University of Washington School of Medicine, Seattle, Washington.
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32
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Hypermutation signature reveals a slippage and realignment model of translesion synthesis by Rev3 polymerase in cisplatin-treated yeast. Proc Natl Acad Sci U S A 2017; 114:2663-2668. [PMID: 28223526 DOI: 10.1073/pnas.1618555114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Gene-gene or gene-drug interactions are typically quantified using fitness as a readout because the data are continuous and easily measured in high throughput. However, to what extent fitness captures the range of other phenotypes that show synergistic effects is usually unknown. Using Saccharomyces cerevisiae and focusing on a matrix of DNA repair mutants and genotoxic drugs, we quantify 76 gene-drug interactions based on both mutation rate and fitness and find that these parameters are not connected. Independent of fitness defects, we identified six cases of synthetic hypermutation, where the combined effect of the drug and mutant on mutation rate was greater than predicted. One example occurred when yeast lacking RAD1 were exposed to cisplatin, and we characterized this interaction using whole-genome sequencing. Our sequencing results indicate mutagenesis by cisplatin in rad1Δ cells appeared to depend almost entirely on interstrand cross-links at GpCpN motifs. Interestingly, our data suggest that the following base on the template strand dictates the addition of the mutated base. This result differs from cisplatin mutation signatures in XPF-deficient Caenorhabditis elegans and supports a model in which translesion synthesis polymerases perform a slippage and realignment extension across from the damaged base. Accordingly, DNA polymerase ζ activity was essential for mutagenesis in cisplatin-treated rad1Δ cells. Together these data reveal the potential to gain new mechanistic insights from nonfitness measures of gene-drug interactions and extend the use of mutation accumulation and whole-genome sequencing analysis to define DNA repair mechanisms.
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33
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Risks at the DNA Replication Fork: Effects upon Carcinogenesis and Tumor Heterogeneity. Genes (Basel) 2017; 8:genes8010046. [PMID: 28117753 PMCID: PMC5295039 DOI: 10.3390/genes8010046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 12/27/2022] Open
Abstract
The ability of all organisms to copy their genetic information via DNA replication is a prerequisite for cell division and a biological imperative of life. In multicellular organisms, however, mutations arising from DNA replication errors in the germline and somatic cells are the basis of genetic diseases and cancer, respectively. Within human tumors, replication errors additionally contribute to mutator phenotypes and tumor heterogeneity, which are major confounding factors for cancer therapeutics. Successful DNA replication involves the coordination of many large-scale, complex cellular processes. In this review, we focus on the roles that defects in enzymes that normally act at the replication fork and dysregulation of enzymes that inappropriately damage single-stranded DNA at the fork play in causing mutations that contribute to carcinogenesis. We focus on tumor data and experimental evidence that error-prone variants of replicative polymerases promote carcinogenesis and on research indicating that the primary target mutated by APOBEC (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like) cytidine deaminases is ssDNA present at the replication fork. Furthermore, we discuss evidence from model systems that indicate replication stress and other cancer-associated metabolic changes may modulate mutagenic enzymatic activities at the replication fork.
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34
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Canonical DNA Repair Pathways Influence R-Loop-Driven Genome Instability. J Mol Biol 2016; 429:3132-3138. [PMID: 27452366 DOI: 10.1016/j.jmb.2016.07.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/05/2016] [Accepted: 07/12/2016] [Indexed: 12/22/2022]
Abstract
DNA repair defects create cancer predisposition in humans by fostering a higher rate of mutations. While DNA repair is quite well characterized, recent studies have identified previously unrecognized relationships between DNA repair and R-loop-mediated genome instability. R-loops are three-stranded nucleic acid structures in which RNA binds to genomic DNA to displace a loop of single-stranded DNA. Mutations in homologous recombination, nucleotide excision repair, crosslink repair, and DNA damage checkpoints have all now been linked to formation and function of transcription-coupled R-loops. This perspective will summarize recent literature linking DNA repair to R-loop-mediated genomic instability and discuss how R-loops may contribute to mutagenesis in DNA-repair-deficient cancers.
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35
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Nicolas E, Golemis EA, Arora S. POLD1: Central mediator of DNA replication and repair, and implication in cancer and other pathologies. Gene 2016; 590:128-41. [PMID: 27320729 PMCID: PMC4969162 DOI: 10.1016/j.gene.2016.06.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 02/06/2023]
Abstract
The evolutionarily conserved human polymerase delta (POLD1) gene encodes the large p125 subunit which provides the essential catalytic activities of polymerase δ (Polδ), mediated by 5′–3′ DNA polymerase and 3′–5′ exonuclease moieties. POLD1 associates with three smaller subunits (POLD2, POLD3, POLD4), which together with Replication Factor C and Proliferating Nuclear Cell Antigen constitute the polymerase holoenzyme. Polδ function is essential for replication, with a primary role as the replicase for the lagging strand. Polδ also has an important proofreading ability conferred by the exonuclease activity, which is critical for ensuring replicative fidelity, but also serves to repair DNA lesions arising as a result of exposure to mutagens. Polδ has been shown to be important for multiple forms of DNA repair, including nucleotide excision repair, double strand break repair, base excision repair, and mismatch repair. A growing number of studies in the past decade have linked germline and sporadic mutations in POLD1 and the other subunits of Polδ with human pathologies. Mutations in Polδ in mice and humans lead to genomic instability, mutator phenotype and tumorigenesis. The advent of genome sequencing techniques has identified damaging mutations in the proofreading domain of POLD1 as the underlying cause of some inherited cancers, and suggested that mutations in POLD1 may influence therapeutic management. In addition, mutations in POLD1 have been identified in the developmental disorders of mandibular hypoplasia, deafness, progeroid features and lipodystrophy and atypical Werner syndrome, while changes in expression or activity of POLD1 have been linked to senescence and aging. Intriguingly, some recent evidence suggests that POLD1 function may also be altered in diabetes. We provide an overview of critical Polδ activities in the context of these pathologic conditions.
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Affiliation(s)
- Emmanuelle Nicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sanjeevani Arora
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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36
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Rayner E, van Gool IC, Palles C, Kearsey SE, Bosse T, Tomlinson I, Church DN. A panoply of errors: polymerase proofreading domain mutations in cancer. Nat Rev Cancer 2016; 16:71-81. [PMID: 26822575 DOI: 10.1038/nrc.2015.12] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although it has long been recognized that the exonucleolytic proofreading activity intrinsic to the replicative DNA polymerases Pol δ and Pol ε is essential for faithful replication of DNA, evidence that defective DNA polymerase proofreading contributes to human malignancy has been limited. However, recent studies have shown that germline mutations in the proofreading domains of Pol δ and Pol ε predispose to cancer, and that somatic Pol ε proofreading domain mutations occur in multiple sporadic tumours, where they underlie a phenotype of 'ultramutation' and favourable prognosis. In this Review, we summarize the current understanding of the mechanisms and consequences of polymerase proofreading domain mutations in human malignancies, and highlight the potential utility of these variants as novel cancer biomarkers and therapeutic targets.
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Affiliation(s)
- Emily Rayner
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Inge C van Gool
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Claire Palles
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Stephen E Kearsey
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - David N Church
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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37
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Uchimura A, Higuchi M, Minakuchi Y, Ohno M, Toyoda A, Fujiyama A, Miura I, Wakana S, Nishino J, Yagi T. Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice. Genome Res 2015; 25:1125-34. [PMID: 26129709 PMCID: PMC4509997 DOI: 10.1101/gr.186148.114] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 05/30/2015] [Indexed: 12/19/2022]
Abstract
The germline mutation rate is an important parameter that affects the amount of genetic variation and the rate of evolution. However, neither the rate of germline mutations in laboratory mice nor the biological significance of the mutation rate in mammalian populations is clear. Here we studied genome-wide mutation rates and the long-term effects of mutation accumulation on phenotype in more than 20 generations of wild-type C57BL/6 mice and mutator mice, which have high DNA replication error rates. We estimated the base-substitution mutation rate to be 5.4 × 10−9 (95% confidence interval = 4.6 × 10−9–6.5 × 10−9) per nucleotide per generation in C57BL/6 laboratory mice, about half the rate reported in humans. The mutation rate in mutator mice was 17 times that in wild-type mice. Abnormal phenotypes were 4.1-fold more frequent in the mutator lines than in the wild-type lines. After several generations, the mutator mice reproduced at substantially lower rates than the controls, exhibiting low pregnancy rates, lower survival rates, and smaller litter sizes, and many of the breeding lines died out. These results provide fundamental information about mouse genetics and reveal the impact of germline mutation rates on phenotypes in a mammalian population.
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Affiliation(s)
- Arikuni Uchimura
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Mayumi Higuchi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Yohei Minakuchi
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Mizuki Ohno
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Ikuo Miura
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BioResource Center, Tsukuba 305-0074, Japan
| | - Shigeharu Wakana
- Technology and Development Team for Mouse Phenotype Analysis, Japan Mouse Clinic, RIKEN BioResource Center, Tsukuba 305-0074, Japan
| | - Jo Nishino
- Department of Biostatistics, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
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38
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Kennedy SR, Schultz EM, Chappell TM, Kohrn B, Knowels GM, Herr AJ. Volatility of Mutator Phenotypes at Single Cell Resolution. PLoS Genet 2015; 11:e1005151. [PMID: 25868109 PMCID: PMC4395103 DOI: 10.1371/journal.pgen.1005151] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 03/17/2015] [Indexed: 11/22/2022] Open
Abstract
Mutator phenotypes accelerate the evolutionary process of neoplastic transformation. Historically, the measurement of mutation rates has relied on scoring the occurrence of rare mutations in target genes in large populations of cells. Averaging mutation rates over large cell populations assumes that new mutations arise at a constant rate during each cell division. If the mutation rate is not constant, an expanding mutator population may contain subclones with widely divergent rates of evolution. Here, we report mutation rate measurements of individual cell divisions of mutator yeast deficient in DNA polymerase ε proofreading and base-base mismatch repair. Our data are best fit by a model in which cells can assume one of two distinct mutator states, with mutation rates that differ by an order of magnitude. In error-prone cell divisions, mutations occurred on the same chromosome more frequently than expected by chance, often in DNA with similar predicted replication timing, consistent with a spatiotemporal dimension to the hypermutator state. Mapping of mutations onto predicted replicons revealed that mutations were enriched in the first half of the replicon as well as near termination zones. Taken together, our findings show that individual genome replication events exhibit an unexpected volatility that may deepen our understanding of the evolution of mutator-driven malignancies. Mutations fuel microbial evolution and cancer. Cells with an increased rate of mutation are said to have a “mutator phenotype” and adapt more rapidly than non-mutator cells. Our study utilizes a novel way of measuring mutation rates of individual cell divisions to show that mutator cells can adopt one of two mutation rates that differ tenfold in magnitude. This mutator volatility suggests that the rates of mutation accumulation may vary widely within the same clone of mutator cells. Understanding how to modulate the mutator state may provide an avenue to treat certain cancers.
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Affiliation(s)
- Scott R. Kennedy
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Eric M. Schultz
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Thomas M. Chappell
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Brendan Kohrn
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Gary M. Knowels
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Alan J. Herr
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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dNTP pool levels modulate mutator phenotypes of error-prone DNA polymerase ε variants. Proc Natl Acad Sci U S A 2015; 112:E2457-66. [PMID: 25827226 DOI: 10.1073/pnas.1422948112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mutator phenotypes create genetic diversity that fuels tumor evolution. DNA polymerase (Pol) ε mediates leading strand DNA replication. Proofreading defects in this enzyme drive a number of human malignancies. Here, using budding yeast, we show that mutator variants of Pol ε depend on damage uninducible (Dun)1, an S-phase checkpoint kinase that maintains dNTP levels during a normal cell cycle and up-regulates dNTP synthesis upon checkpoint activation. Deletion of DUN1 (dun1Δ) suppresses the mutator phenotype of pol2-4 (encoding Pol ε proofreading deficiency) and is synthetically lethal with pol2-M644G (encoding altered Pol ε base selectivity). Although pol2-4 cells cycle normally, pol2-M644G cells progress slowly through S-phase. The pol2-M644G cells tolerate deletions of mediator of the replication checkpoint (MRC) 1 (mrc1Δ) and radiation sensitive (Rad) 9 (rad9Δ), which encode mediators of checkpoint responses to replication stress and DNA damage, respectively. The pol2-M644G mutator phenotype is partially suppressed by mrc1Δ but not rad9Δ; neither deletion suppresses the pol2-4 mutator phenotype. Thus, checkpoint activation augments the Dun1 effect on replication fidelity but is not required for it. Deletions of genes encoding key Dun1 targets that negatively regulate dNTP synthesis, suppress the dun1Δ pol2-M644G synthetic lethality and restore the mutator phenotype of pol2-4 in dun1Δ cells. DUN1 pol2-M644G cells have constitutively high dNTP levels, consistent with checkpoint activation. In contrast, pol2-4 and POL2 cells have similar dNTP levels, which decline in the absence of Dun1 and rise in the absence of the negative regulators of dNTP synthesis. Thus, dNTP pool levels correlate with Pol ε mutator severity, suggesting that treatments targeting dNTP pools could modulate mutator phenotypes for therapy.
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Colon cancer-associated mutator DNA polymerase δ variant causes expansion of dNTP pools increasing its own infidelity. Proc Natl Acad Sci U S A 2015; 112:E2467-76. [PMID: 25827231 DOI: 10.1073/pnas.1422934112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Defects in DNA polymerases δ (Polδ) and ε (Polε) cause hereditary colorectal cancer and have been implicated in the etiology of some sporadic colorectal and endometrial tumors. We previously reported that the yeast pol3-R696W allele mimicking a human cancer-associated variant, POLD1-R689W, causes a catastrophic increase in spontaneous mutagenesis. Here, we describe the mechanism of this extraordinary mutator effect. We found that the mutation rate increased synergistically when the R696W mutation was combined with defects in Polδ proofreading or mismatch repair, indicating that pathways correcting DNA replication errors are not compromised in pol3-R696W mutants. DNA synthesis by purified Polδ-R696W was error-prone, but not to the extent that could account for the unprecedented mutator phenotype of pol3-R696W strains. In a search for cellular factors that augment the mutagenic potential of Polδ-R696W, we discovered that pol3-R696W causes S-phase checkpoint-dependent elevation of dNTP pools. Abrogating this elevation by strategic mutations in dNTP metabolism genes eliminated the mutator effect of pol3-R696W, whereas restoration of high intracellular dNTP levels restored the mutator phenotype. Further, the use of dNTP concentrations present in pol3-R696W cells for in vitro DNA synthesis greatly decreased the fidelity of Polδ-R696W and produced a mutation spectrum strikingly similar to the spectrum observed in vivo. The results support a model in which (i) faulty synthesis by Polδ-R696W leads to a checkpoint-dependent increase in dNTP levels and (ii) this increase mediates the hypermutator effect of Polδ-R696W by facilitating the extension of mismatched primer termini it creates and by promoting further errors that continue to fuel the mutagenic pathway.
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Replicative DNA polymerase δ but not ε proofreads errors in Cis and in Trans. PLoS Genet 2015; 11:e1005049. [PMID: 25742645 PMCID: PMC4351087 DOI: 10.1371/journal.pgen.1005049] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 02/02/2015] [Indexed: 01/18/2023] Open
Abstract
It is now well established that in yeast, and likely most eukaryotic organisms, initial DNA replication of the leading strand is by DNA polymerase ε and of the lagging strand by DNA polymerase δ. However, the role of Pol δ in replication of the leading strand is uncertain. In this work, we use a reporter system in Saccharomyces cerevisiae to measure mutation rates at specific base pairs in order to determine the effect of heterozygous or homozygous proofreading-defective mutants of either Pol ε or Pol δ in diploid strains. We find that wild-type Pol ε molecules cannot proofread errors created by proofreading-defective Pol ε molecules, whereas Pol δ can not only proofread errors created by proofreading-defective Pol δ molecules, but can also proofread errors created by Pol ε-defective molecules. These results suggest that any interruption in DNA synthesis on the leading strand is likely to result in completion by Pol δ and also explain the higher mutation rates observed in Pol δ-proofreading mutants compared to Pol ε-proofreading defective mutants. For strains reverting via AT→GC, TA→GC, CG→AT, and GC→AT mutations, we find in addition a strong effect of gene orientation on mutation rate in proofreading-defective strains and demonstrate that much of this orientation dependence is due to differential efficiencies of mispair elongation. We also find that a 3′-terminal 8 oxoG, unlike a 3′-terminal G, is efficiently extended opposite an A and is not subject to proofreading. Proofreading mutations have been shown to result in tumor formation in both mice and humans; the results presented here can help explain the properties exhibited by those proofreading mutants. Many DNA polymerases are able to proofread their errors: after incorporation of a wrong base, the resulting mispair invokes an exonuclease activity of the polymerase that removes the mispaired base and allows replication to continue. Elimination of the proofreading activity thus results in much higher mutation rates. We demonstrate that the two major replicative DNA polymerases in yeast, Pol δ and Pol ε, have different proofreading abilities. In diploid cells, Pol ε is not able to proofread errors created by other Pol ε molecules, whereas Pol δ can proofread not only errors created by other Pol δ molecules but also errors created by Pol ε molecules. We also find that mispaired bases not corrected by proofreading have much different likelihoods of being extended, depending on the particular base-base mismatch. In humans, defects in Pol δ or Pol ε proofreading can lead to cancer, and these results help explain the formation of those tumors and the finding that Pol ε mutants seem to be found as frequently, or more so, in human tumors as Pol δ mutants.
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Darmawan H, Harrison M, Reha-Krantz LJ. DNA polymerase 3'→5' exonuclease activity: Different roles of the beta hairpin structure in family-B DNA polymerases. DNA Repair (Amst) 2015; 29:36-46. [PMID: 25753811 DOI: 10.1016/j.dnarep.2015.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 11/26/2022]
Abstract
Proofreading by the bacteriophage T4 and RB69 DNA polymerases requires a β hairpin structure that resides in the exonuclease domain. Genetic, biochemical and structural studies demonstrate that the phage β hairpin acts as a wedge to separate the primer-end from the template strand in exonuclease complexes. Single amino acid substitutions in the tip of the hairpin or deletion of the hairpin prevent proofreading and create "mutator" DNA polymerases. There is little known, however, about the function of similar hairpin structures in other family B DNA polymerases. We present mutational analysis of the yeast (Saccharomyces cerevisiae) DNA polymerase δ hairpin. Deletion of the DNA polymerase δ hairpin (hpΔ) did not significantly reduce DNA replication fidelity; thus, the β hairpin structure in yeast DNA polymerase δ is not essential for proofreading. However, replication efficiency was reduced as indicated by a slow growth phenotype. In contrast, the G447D amino acid substitution in the tip of the hairpin increased frameshift mutations and sensitivity to hydroxyurea (HU). A chimeric yeast DNA polymerase δ was constructed in which the T4 DNA polymerase hairpin (T4hp) replaced the yeast DNA polymerase δ hairpin; a strong increase in frameshift mutations was observed and the mutant strain was sensitive to HU and to the pyrophosphate analog, phosphonoacetic acid (PAA). But all phenotypes - slow growth, HU-sensitivity, PAA-sensitivity, and reduced fidelity, were observed only in the absence of mismatch repair (MMR), which implicates a role for MMR in mediating DNA polymerase δ replication problems. In comparison, another family B DNA polymerase, DNA polymerase ɛ, has only an atrophied hairpin with no apparent function. Thus, while family B DNA polymerases share conserved motifs and general structural features, the β hairpin has evolved to meet specific needs.
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Affiliation(s)
- Hariyanto Darmawan
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9
| | - Melissa Harrison
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9
| | - Linda J Reha-Krantz
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9.
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Church DN, Stelloo E, Nout RA, Valtcheva N, Depreeuw J, ter Haar N, Noske A, Amant F, Tomlinson IPM, Wild PJ, Lambrechts D, Jürgenliemk-Schulz IM, Jobsen JJ, Smit VTHBM, Creutzberg CL, Bosse T. Prognostic significance of POLE proofreading mutations in endometrial cancer. J Natl Cancer Inst 2015; 107:402. [PMID: 25505230 PMCID: PMC4301706 DOI: 10.1093/jnci/dju402] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/26/2014] [Accepted: 10/29/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Current risk stratification in endometrial cancer (EC) results in frequent over- and underuse of adjuvant therapy, and may be improved by novel biomarkers. We examined whether POLE proofreading mutations, recently reported in about 7% of ECs, predict prognosis. METHODS We performed targeted POLE sequencing in ECs from the PORTEC-1 and -2 trials (n = 788), and analyzed clinical outcome according to POLE status. We combined these results with those from three additional series (n = 628) by meta-analysis to generate multivariable-adjusted, pooled hazard ratios (HRs) for recurrence-free survival (RFS) and cancer-specific survival (CSS) of POLE-mutant ECs. All statistical tests were two-sided. RESULTS POLE mutations were detected in 48 of 788 (6.1%) ECs from PORTEC-1 and-2 and were associated with high tumor grade (P < .001). Women with POLE-mutant ECs had fewer recurrences (6.2% vs 14.1%) and EC deaths (2.3% vs 9.7%), though, in the total PORTEC cohort, differences in RFS and CSS were not statistically significant (multivariable-adjusted HR = 0.43, 95% CI = 0.13 to 1.37, P = .15; HR = 0.19, 95% CI = 0.03 to 1.44, P = .11 respectively). However, of 109 grade 3 tumors, 0 of 15 POLE-mutant ECs recurred, compared with 29 of 94 (30.9%) POLE wild-type cancers; reflected in statistically significantly greater RFS (multivariable-adjusted HR = 0.11, 95% CI = 0.001 to 0.84, P = .03). In the additional series, there were no EC-related events in any of 33 POLE-mutant ECs, resulting in a multivariable-adjusted, pooled HR of 0.33 for RFS (95% CI = 0.12 to 0.91, P = .03) and 0.26 for CSS (95% CI = 0.06 to 1.08, P = .06). CONCLUSION POLE proofreading mutations predict favorable EC prognosis, independently of other clinicopathological variables, with the greatest effect seen in high-grade tumors. This novel biomarker may help to reduce overtreatment in EC.
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Affiliation(s)
- David N Church
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Ellen Stelloo
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Remi A Nout
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Nadejda Valtcheva
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Jeroen Depreeuw
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Natalja ter Haar
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Aurelia Noske
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Frederic Amant
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Ian P M Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ).
| | - Peter J Wild
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Diether Lambrechts
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Ina M Jürgenliemk-Schulz
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Jan J Jobsen
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Vincent T H B M Smit
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Carien L Creutzberg
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
| | - Tjalling Bosse
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (DNC, IPMT); Oxford Cancer Centre, Churchill Hospital, Oxford, UK (DNC); Department of Pathology (ES, NtH, VTHBMS, TB) and Department of Clinical Oncology (RAN, CLC), Leiden University Medical Center, Leiden, the Netherlands; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland (NV, AN, PJW); Vesalius Research Center (VRC), VIB, Leuven, Belgium (JD, DL); Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Belgium (FA, DL); Department of Obstetrics & Gynecology, Division of Gynecologic Oncology, University Hospitals Gasthuisberg, Leuven, Belgium (FA); Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK (IPMT); Department of Radiation Oncology, University Medical Centrum Utrecht, the Netherlands (IMJS); Department of Radiation Oncology, Medisch Spectrum Twente, Enschede, the Netherlands (JJJ)
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