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McConechy MK, Talhouk A, Leung S, Chiu D, Yang W, Senz J, Reha-Krantz LJ, Lee CH, Huntsman DG, Gilks CB, McAlpine JN. Endometrial Carcinomas with POLE Exonuclease Domain Mutations Have a Favorable Prognosis. Clin Cancer Res 2016; 22:2865-73. [DOI: 10.1158/1078-0432.ccr-15-2233] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/04/2015] [Indexed: 11/16/2022]
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102
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Lebrec H, Brennan FR, Haggerty H, Herzyk D, Kamperschroer C, Maier CC, Ponce R, Preston BD, Weinstock D, Mellon RD. HESI/FDA workshop on immunomodulators and cancer risk assessment: Building blocks for a weight-of-evidence approach. Regul Toxicol Pharmacol 2015; 75:72-80. [PMID: 26743742 DOI: 10.1016/j.yrtph.2015.12.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 12/27/2015] [Indexed: 12/22/2022]
Abstract
Profound immunosuppression (e.g., AIDS, transplant therapy) is epidemiologically associated with an increased cancer risk, and often with oncogenic viruses. It is currently unclear how broadly this association translates to therapeutics that modulate immunity. A workshop co-sponsored by the FDA and HESI examined how perturbing the immune system may contribute to carcinogenesis, and highlighted priorities for improving non-clinical risk assessment of targeted immunomodulatory therapies. Conclusions from the workshop were as follows. 1) While profound altered immunity can promote tumorigenesis, not all components of the immune system are equally important in defense against or promotion of cancer and a similar cancer risk for all immunomodulatory molecules should not be assumed. 2) Rodent carcinogenicity studies have limitations and are generally not reliable predictors of cancer risk associated with immunosuppression. 3) Cancer risk needs to be evaluated based on mechanism-based weight-of-evidence, including data from immune function tests most relevant to tumor immunosurveillance or promotion. 4) Information from nonclinical experiments, clinical epidemiology and immunomodulatory therapeutics show that immunosurveillance involves a complex network of cells and mediators. To support a weight-of-evidence approach, an increased focus on understanding the quantitative relationship between changes in relevant immune function tests and cancer risk is needed.
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Affiliation(s)
- H Lebrec
- Amgen Inc, 1120 Veterans Blvd, South San Francisco, CA 94080, USA.
| | - F R Brennan
- UCB-Celltech, 208 Bath Road, Slough SL1 3WE, UK
| | - H Haggerty
- Bristol-Myers Squibb Company, 1 Squibb Dr., New Brunswick, NJ 08903, USA
| | - D Herzyk
- Merck & Co Inc, 770 Sumneytown Pike, PO Box 4, MS WP45-233, West Point, PA, USA
| | | | - C C Maier
- GlaxoSmithKline, 709 Swedeland Rd, King of Prussia, PA 19406, USA
| | - R Ponce
- Amgen Inc, 1120 Veterans Blvd, South San Francisco, CA 94080, USA
| | - B D Preston
- Amgen Inc, 1120 Veterans Blvd, South San Francisco, CA 94080, USA
| | - D Weinstock
- Janssen Research & Development, LLC, Welsh & McKean Roads, Spring House, PA 19477, USA
| | - R D Mellon
- Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
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103
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Ferguson LR, Chen H, Collins AR, Connell M, Damia G, Dasgupta S, Malhotra M, Meeker AK, Amedei A, Amin A, Ashraf SS, Aquilano K, Azmi AS, Bhakta D, Bilsland A, Boosani CS, Chen S, Ciriolo MR, Fujii H, Guha G, Halicka D, Helferich WG, Keith WN, Mohammed SI, Niccolai E, Yang X, Honoki K, Parslow VR, Prakash S, Rezazadeh S, Shackelford RE, Sidransky D, Tran PT, Yang ES, Maxwell CA. Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition. Semin Cancer Biol 2015; 35 Suppl:S5-S24. [PMID: 25869442 PMCID: PMC4600419 DOI: 10.1016/j.semcancer.2015.03.005] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 03/08/2015] [Accepted: 03/13/2015] [Indexed: 02/06/2023]
Abstract
Genomic instability can initiate cancer, augment progression, and influence the overall prognosis of the affected patient. Genomic instability arises from many different pathways, such as telomere damage, centrosome amplification, epigenetic modifications, and DNA damage from endogenous and exogenous sources, and can be perpetuating, or limiting, through the induction of mutations or aneuploidy, both enabling and catastrophic. Many cancer treatments induce DNA damage to impair cell division on a global scale but it is accepted that personalized treatments, those that are tailored to the particular patient and type of cancer, must also be developed. In this review, we detail the mechanisms from which genomic instability arises and can lead to cancer, as well as treatments and measures that prevent genomic instability or take advantage of the cellular defects caused by genomic instability. In particular, we identify and discuss five priority targets against genomic instability: (1) prevention of DNA damage; (2) enhancement of DNA repair; (3) targeting deficient DNA repair; (4) impairing centrosome clustering; and, (5) inhibition of telomerase activity. Moreover, we highlight vitamin D and B, selenium, carotenoids, PARP inhibitors, resveratrol, and isothiocyanates as priority approaches against genomic instability. The prioritized target sites and approaches were cross validated to identify potential synergistic effects on a number of important areas of cancer biology.
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Affiliation(s)
| | - Helen Chen
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada
| | - Andrew R Collins
- Department of Nutrition, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marisa Connell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada
| | - Giovanna Damia
- Department of Oncology, Instituti di Ricovero e Cura a Carattere Scientifico-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Santanu Dasgupta
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, United States
| | | | - Alan K Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Amr Amin
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates; Faculty of Science, Cairo University, Cairo, Egypt
| | - S Salman Ashraf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Katia Aquilano
- Department of Biology, Università di Roma Tor Vergata, Rome, Italy
| | - Asfar S Azmi
- Department of Biology, University of Rochester, Rochester, United States
| | - Dipita Bhakta
- School of Chemical and BioTechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - Alan Bilsland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Chandra S Boosani
- Department of BioMedical Sciences, Creighton University, Omaha, NE, United States
| | - Sophie Chen
- Department of Research & Development, Ovarian and Prostate Cancer Research Trust Laboratory, Guildford, Surrey, United Kingdom
| | | | - Hiromasa Fujii
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Gunjan Guha
- School of Chemical and BioTechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | | | - William G Helferich
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - W Nicol Keith
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sulma I Mohammed
- Department of Comparative Pathobiology and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Xujuan Yang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Kanya Honoki
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | | | - Satya Prakash
- School of Pharmacy, University College Cork, Cork, Ireland
| | - Sarallah Rezazadeh
- Department of Biology, University of Rochester, Rochester, United States
| | - Rodney E Shackelford
- Department of Pathology, Louisiana State University Health Shreveport, Shreveport, LA, United States
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Phuoc T Tran
- Departments of Radiation Oncology & Molecular Radiation Sciences, Oncology and Urology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Eddy S Yang
- Department of Radiation Oncology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, United States
| | - Christopher A Maxwell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada.
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104
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Aoude LG, Heitzer E, Johansson P, Gartside M, Wadt K, Pritchard AL, Palmer JM, Symmons J, Gerdes AM, Montgomery GW, Martin NG, Tomlinson I, Kearsey S, Hayward NK. POLE mutations in families predisposed to cutaneous melanoma. Fam Cancer 2015; 14:621-8. [PMID: 26251183 DOI: 10.1007/s10689-015-9826-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Germline mutations in the exonuclease domain of POLE have been shown to predispose to colorectal cancers and adenomas. POLE is an enzyme involved in DNA repair and chromosomal DNA replication. In order to assess whether such mutations might also predispose to cutaneous melanoma, we interrogated whole-genome and exome data from probands of 34 melanoma families lacking pathogenic mutations in known high penetrance melanoma susceptibility genes: CDKN2A, CDK4, BAP1, TERT, POT1, ACD and TERF2IP. We found a novel germline mutation, POLE p.(Trp347Cys), in a 7-case cutaneous melanoma family. Functional assays in S. pombe showed that this mutation led to an increased DNA mutation rate comparable to that seen with a Pol ε mutant with no exonuclease activity. We then performed targeted sequencing of POLE in 1243 cutaneous melanoma cases and found that a further ten probands had novel or rare variants in the exonuclease domain of POLE. Although this frequency is not significantly higher than that in unselected Caucasian controls, we observed multiple cancer types in the melanoma families, suggesting that some germline POLE mutations may predispose to a broad spectrum of cancers, including melanoma. In addition, we found the first mutation outside the exonuclease domain, p.(Gln520Arg), in a family with an extensive history of colorectal cancer.
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Affiliation(s)
- Lauren G Aoude
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.
| | - Ellen Heitzer
- Institut für Humangenetik, Medizinische Universität Graz, Harrachgasse 21, 8010, Graz, Austria
| | - Peter Johansson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Michael Gartside
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Karin Wadt
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Antonia L Pritchard
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Jane M Palmer
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Judith Symmons
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Grant W Montgomery
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory and Genomic Medicine Theme Oxford NIHR Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Stephen Kearsey
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
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105
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Formation of interference-sensitive meiotic cross-overs requires sufficient DNA leading-strand elongation. Proc Natl Acad Sci U S A 2015; 112:12534-9. [PMID: 26392549 DOI: 10.1073/pnas.1507165112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Meiosis halves diploid genomes to haploid and is essential for sexual reproduction in eukaryotes. Meiotic recombination ensures physical association of homologs and their subsequent accurate segregation and results in the redistribution of genetic variations among progeny. Most organisms have two classes of cross-overs (COs): interference-sensitive (type I) and -insensitive (type II) COs. DNA synthesis is essential for meiotic recombination, but whether DNA synthesis has a role in differentiating meiotic CO pathways is unknown. Here, we show that Arabidopsis POL2A, the homolog of the yeast DNA polymerase-ε (a leading-strand DNA polymerase), is required for plant fertility and meiosis. Mutations in POL2A cause reduced fertility and meiotic defects, including abnormal chromosome association, improper chromosome segregation, and fragmentation. Observation of prophase I cell distribution suggests that pol2a mutants likely delay progression of meiotic recombination. In addition, the residual COs in pol2a have reduced CO interference, and the double mutant of pol2a with mus81, which affects type II COs, displayed more severe defects than either single mutant, indicating that POL2A functions in the type I pathway. We hypothesize that sufficient leading-strand DNA elongation promotes formation of some type I COs. Given that meiotic recombination and DNA synthesis are conserved in divergent eukaryotes, this study and our previous study suggest a novel role for DNA synthesis in the differentiation of meiotic recombination pathways.
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106
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van Gool IC, Eggink FA, Freeman-Mills L, Stelloo E, Marchi E, de Bruyn M, Palles C, Nout RA, de Kroon CD, Osse EM, Klenerman P, Creutzberg CL, Tomlinson IPM, Smit VTHBM, Nijman HW, Bosse T, Church DN. POLE Proofreading Mutations Elicit an Antitumor Immune Response in Endometrial Cancer. Clin Cancer Res 2015; 21:3347-3355. [PMID: 25878334 PMCID: PMC4627582 DOI: 10.1158/1078-0432.ccr-15-0057] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/03/2015] [Indexed: 12/20/2022]
Abstract
PURPOSE Recent studies have shown that 7% to 12% of endometrial cancers are ultramutated due to somatic mutation in the proofreading exonuclease domain of the DNA replicase POLE. Interestingly, these tumors have an excellent prognosis. In view of the emerging data linking mutation burden, immune response, and clinical outcome in cancer, we investigated whether POLE-mutant endometrial cancers showed evidence of increased immunogenicity. EXPERIMENTAL DESIGN We examined immune infiltration and activation according to tumor POLE proofreading mutation in a molecularly defined endometrial cancer cohort including 47 POLE-mutant tumors. We sought to confirm our results by analysis of RNAseq data from the TCGA endometrial cancer series and used the same series to examine whether differences in immune infiltration could be explained by an enrichment of immunogenic neoepitopes in POLE-mutant endometrial cancers. RESULTS Compared with other endometrial cancers, POLE mutants displayed an enhanced cytotoxic T-cell response, evidenced by increased numbers of CD8(+) tumor-infiltrating lymphocytes and CD8A expression, enrichment for a tumor-infiltrating T-cell gene signature, and strong upregulation of the T-cell cytotoxic differentiation and effector markers T-bet, Eomes, IFNG, PRF, and granzyme B. This was accompanied by upregulation of T-cell exhaustion markers, consistent with chronic antigen exposure. In silico analysis confirmed that POLE-mutant cancers are predicted to display more antigenic neoepitopes than other endometrial cancers, providing a potential explanation for our findings. CONCLUSIONS Ultramutated POLE proofreading-mutant endometrial cancers are characterized by a robust intratumoral T-cell response, which correlates with, and may be caused by an enrichment of antigenic neopeptides. Our study provides a plausible mechanism for the excellent prognosis of these cancers.
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Affiliation(s)
- Inge C van Gool
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Florine A Eggink
- University of Groningen, University Medical Center Groningen, Department of Obstetrics and Gynecology, PO 30.001 9700 RB Groningen, The Netherlands
| | - Luke Freeman-Mills
- Molecular and Population Genetics Laboratory, The Wellcome Trust Centre for Human Genetics, University of Oxford. Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Ellen Stelloo
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Emanuele Marchi
- Immunity Theme, NIHR Oxford Comprehensive Biomedical Research Centre, The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK
| | - Marco de Bruyn
- University of Groningen, University Medical Center Groningen, Department of Obstetrics and Gynecology, PO 30.001 9700 RB Groningen, The Netherlands
| | - Claire Palles
- Molecular and Population Genetics Laboratory, The Wellcome Trust Centre for Human Genetics, University of Oxford. Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Remi A Nout
- Department of Clinical Oncology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Cor D de Kroon
- Department of Gynecology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Elisabeth M Osse
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Paul Klenerman
- Immunity Theme, NIHR Oxford Comprehensive Biomedical Research Centre, The Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK
| | - Carien L Creutzberg
- Department of Clinical Oncology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Ian PM Tomlinson
- Molecular and Population Genetics Laboratory, The Wellcome Trust Centre for Human Genetics, University of Oxford. Roosevelt Drive, Oxford, OX3 7BN, UK
- Genomic Medicine Theme, Oxford Comprehensive Biomedical Research Centre, The Wellcome Trust Centre for Human Genetics, University of Oxford. Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Vincent THBM Smit
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Hans W Nijman
- University of Groningen, University Medical Center Groningen, Department of Obstetrics and Gynecology, PO 30.001 9700 RB Groningen, The Netherlands
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - David N Church
- Molecular and Population Genetics Laboratory, The Wellcome Trust Centre for Human Genetics, University of Oxford. Roosevelt Drive, Oxford, OX3 7BN, UK
- Oxford Cancer Centre, Churchill Hospital, Old Road, Oxford OX3 9DU, UK
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107
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Bellido F, Pineda M, Aiza G, Valdés-Mas R, Navarro M, Puente DA, Pons T, González S, Iglesias S, Darder E, Piñol V, Soto JL, Valencia A, Blanco I, Urioste M, Brunet J, Lázaro C, Capellá G, Puente XS, Valle L. POLE and POLD1 mutations in 529 kindred with familial colorectal cancer and/or polyposis: review of reported cases and recommendations for genetic testing and surveillance. Genet Med 2015; 18:325-32. [PMID: 26133394 PMCID: PMC4823640 DOI: 10.1038/gim.2015.75] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/23/2015] [Indexed: 02/06/2023] Open
Abstract
Purpose: Germ-line mutations in the exonuclease domains of POLE and POLD1 have been recently associated with polyposis and colorectal cancer (CRC) predisposition. Here, we aimed to gain a better understanding of the phenotypic characteristics of this syndrome to establish specific criteria for POLE and POLD1 mutation screening and to help define the clinical management of mutation carriers. Genet Med18 4, 325–332. Methods: The exonuclease domains of POLE and POLD1 were studied in 529 kindred, 441 with familial nonpolyposis CRC and 88 with polyposis, by using pooled DNA amplification and massively parallel sequencing. Genet Med18 4, 325–332. Results: Seven novel or rare genetic variants were identified. In addition to the POLE p.L424V recurrent mutation in a patient with polyposis, CRC and oligodendroglioma, six novel or rare POLD1 variants (four of them, p.D316H, p.D316G, p.R409W, and p.L474P, with strong evidence for pathogenicity) were identified in nonpolyposis CRC families. Phenotypic data from these and previously reported POLE/POLD1 carriers point to an associated phenotype characterized by attenuated or oligo-adenomatous colorectal polyposis, CRC, and probably brain tumors. In addition, POLD1 mutations predispose to endometrial and breast tumors. Genet Med18 4, 325–332. Conclusion: Our results widen the phenotypic spectrum of the POLE/POLD1-associated syndrome and identify novel pathogenic variants. We propose guidelines for genetic testing and surveillance recommendations. Genet Med18 4, 325–332.
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Affiliation(s)
- Fernando Bellido
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Rafael Valdés-Mas
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Diana A Puente
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Tirso Pons
- Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Sara González
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Silvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Esther Darder
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGi, Girona, Spain
| | - Virginia Piñol
- Gastroenterology Department, Hospital Dr. Josep Trueta, Girona, Spain.,Medical Science Department, School of Medicine, University of Girona, Girona, Spain
| | - José Luís Soto
- Molecular Genetics Laboratory, Elche University Hospital, Elche, Spain
| | - Alfonso Valencia
- Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Ignacio Blanco
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO) and Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGi, Girona, Spain.,Medical Science Department, School of Medicine, University of Girona, Girona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Xose S Puente
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
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108
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Bellone S, Centritto F, Black J, Schwab C, English D, Cocco E, Lopez S, Bonazzoli E, Predolini F, Ferrari F, Silasi DA, Ratner E, Azodi M, Schwartz PE, Santin AD. Polymerase ε (POLE) ultra-mutated tumors induce robust tumor-specific CD4+ T cell responses in endometrial cancer patients. Gynecol Oncol 2015; 138:11-7. [PMID: 25931171 PMCID: PMC4469551 DOI: 10.1016/j.ygyno.2015.04.027] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/20/2015] [Indexed: 01/16/2023]
Abstract
OBJECTIVE Around 7-10% of endometrial carcinomas are characterized by polymerase-ε-(POLE) exonuclease-domain-mutations, an ultra-mutated-phenotype and a favorable prognosis. It is currently unknown whether POLE ultra-mutated-tumors are more immunogenic when compared to the other groups of endometrial cancers. METHODS We used autologous-dendritic-cells (DC) pulsed with whole-tumor-extracts to assess the level of CD8+ and CD4+ T-cell-activation induced by POLE-ultramutated (+) and POLE wild-type (-) endometrial cancer cells in vitro. T-lymphocyte-proliferations were evaluated using CFSE and/or ([3H])thymidine-incorporation-assays while the ability to specifically kill autologous-tumor-cells by cytotoxic-T-lymphocyte (CTL) was tested in standard 4-h-(51)Cr-cytotoxicity-assays. In order to correlate cytotoxic activity and proliferation by CD4+ and CD8+ T-lymphocytes, respectively, with a particular lymphoid subset, two-color-flow-cytometric analysis of intracellular-cytokine-expression (IFN-γ vs IL-4) at the single cell level was also performed. RESULTS DC-pulsed with tumor extracts were able to induce CTL-responses against autologous-tumor-cells in both POLE (+) and POLE (-) cancer patients (P=0.305). These CD8+ T-cell-populations were cytotoxic against tumor-cells but they did not lyse PHA-stimulated-autologous-lymphocytes or autologous-EBV-transformed-lymphoblastoid-control-cell-lines. In contrast, only POLE (+) tumor-lysate-pulsed-DC were able to induce significant proliferation and high IFN-γ expression (i.e., Th1-cytokine-bias) in autologous in vitro DC-stimulated CD4+ T-cells as well as naïve CD4+ and CD8+ T-cells from patients-peripheral-blood (P<0.05). CONCLUSIONS POLE ultra-mutated-tumors are significantly more immunogenic when compared to POLE (-) tumors, in particular to the helper arm of the immune system. These data lend support to the hypothesis that the better prognosis of patients with POLE (+) tumors may at least in part be linked to their enhanced immunogenicity.
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Affiliation(s)
- Stefania Bellone
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Floriana Centritto
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Jonathan Black
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Carlton Schwab
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Diana English
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Emiliano Cocco
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Salvatore Lopez
- Division of Gynecologic Oncology, University Campus Bio-Medico of Roma, Roma, Italy
| | - Elena Bonazzoli
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Federica Predolini
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Francesca Ferrari
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Dan-Arin Silasi
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Elena Ratner
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Masoud Azodi
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Peter E Schwartz
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA
| | - Alessandro D Santin
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, PO Box 208063, New Haven, CT 06520-8063, USA.
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109
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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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110
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St Charles JA, Liberti SE, Williams JS, Lujan SA, Kunkel TA. Quantifying the contributions of base selectivity, proofreading and mismatch repair to nuclear DNA replication in Saccharomyces cerevisiae. DNA Repair (Amst) 2015; 31:41-51. [PMID: 25996407 DOI: 10.1016/j.dnarep.2015.04.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/13/2015] [Accepted: 04/22/2015] [Indexed: 12/19/2022]
Abstract
Mismatches generated during eukaryotic nuclear DNA replication are removed by two evolutionarily conserved error correction mechanisms acting in series, proofreading and mismatch repair (MMR). Defects in both processes are associated with increased susceptibility to cancer. To better understand these processes, we have quantified base selectivity, proofreading and MMR during nuclear DNA replication in Saccharomyces cerevisiae. In the absence of proofreading and MMR, the primary leading and lagging strand replicases, polymerase ɛ and polymerase δ respectively, synthesize DNA in vivo with somewhat different error rates and specificity, and with apparent base selectivity that is more than 100 times higher than measured in vitro. Moreover, leading and lagging strand replication fidelity rely on a different balance between proofreading and MMR. On average, proofreading contributes more to replication fidelity than does MMR, but their relative contributions vary from nearly all proofreading of some mismatches to mostly MMR of other mismatches. Thus accurate replication of the two DNA strands results from a non-uniform and variable balance between error prevention, proofreading and MMR.
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Affiliation(s)
- Jordan A St Charles
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Sascha E Liberti
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Jessica S Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.
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111
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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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112
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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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113
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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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114
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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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115
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Erson-Omay EZ, Çağlayan AO, Schultz N, Weinhold N, Omay SB, Özduman K, Köksal Y, Li J, Serin Harmancı A, Clark V, Carrión-Grant G, Baranoski J, Çağlar C, Barak T, Coşkun S, Baran B, Köse D, Sun J, Bakırcıoğlu M, Moliterno Günel J, Pamir MN, Mishra-Gorur K, Bilguvar K, Yasuno K, Vortmeyer A, Huttner AJ, Sander C, Günel M. Somatic POLE mutations cause an ultramutated giant cell high-grade glioma subtype with better prognosis. Neuro Oncol 2015; 17:1356-64. [PMID: 25740784 DOI: 10.1093/neuonc/nov027] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/03/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Malignant high-grade gliomas (HGGs), including the most aggressive form, glioblastoma multiforme, show significant clinical and genomic heterogeneity. Despite recent advances, the overall survival of HGGs and their response to treatment remain poor. In order to gain further insight into disease pathophysiology by correlating genomic landscape with clinical behavior, thereby identifying distinct HGG molecular subgroups associated with improved prognosis, we performed a comprehensive genomic analysis. METHODS We analyzed and compared 720 exome-sequenced gliomas (136 from Yale, 584 from The Cancer Genome Atlas) based on their genomic, histological, and clinical features. RESULTS We identified a subgroup of HGGs (6 total, 4 adults and 2 children) that harbored a statistically significantly increased number of somatic mutations (mean = 9257.3 vs 76.2, P = .002). All of these "ultramutated" tumors harbored somatic mutations in the exonuclease domain of the polymerase epsilon gene (POLE), displaying a distinctive genetic profile, characterized by genomic stability and increased C-to-A transversions. Histologically, they all harbored multinucleated giant or bizarre cells, some with predominant infiltrating immune cells. One adult and both pediatric patients carried homozygous germline mutations in the mutS homolog 6 (MSH6) gene. In adults, POLE mutations were observed in patients younger than 40 years and were associated with a longer progression-free survival. CONCLUSIONS We identified a genomically, histologically, and clinically distinct subgroup of HGGs that harbored somatic POLE mutations and carried an improved prognosis. Identification of distinctive molecular and pathological HGG phenotypes has implications not only for improved classification but also for potential targeted treatments.
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Affiliation(s)
- E Zeynep Erson-Omay
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Ahmet Okay Çağlayan
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Nikolaus Schultz
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Nils Weinhold
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - S Bülent Omay
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Koray Özduman
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Yavuz Köksal
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Jie Li
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Akdes Serin Harmancı
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Victoria Clark
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Geneive Carrión-Grant
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Jacob Baranoski
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Caner Çağlar
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Tanyeri Barak
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Süleyman Coşkun
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Burçin Baran
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Doğan Köse
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Jia Sun
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Mehmet Bakırcıoğlu
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Jennifer Moliterno Günel
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - M Necmettin Pamir
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Ketu Mishra-Gorur
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Kaya Bilguvar
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Katsuhito Yasuno
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Alexander Vortmeyer
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Anita J Huttner
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Chris Sander
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
| | - Murat Günel
- Department of Neurosurgery, Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut (E.Z.E.-O., A.O.Ç., S.B.O., A.S.H., V.C., G.C.-G., J.B., C.Ç., T.B., S.C., B.B., M.B., J.M.G., K.M.-G., K.B., K.Y., M.G.); Department of Genetics, Yale School of Medicine, New Haven, Connecticut (K.B., M.G.); Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York (N.S., N.W., C.S.); Department of Neurosurgery, Acıbadem University School of Medicine, Istanbul, Turkey (K.O., M.N.P.); Division of Hematology and Oncology, Faculty of Medicine, Department of Pediatrics, Selçuk University, Konya, Turkey (Y.K., D.K.); Department of Pathology, Yale School of Medicine, New Haven, Connecticut (J.L., J.S., A.V., A.J.H.)
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Santin AD, Bellone S, Centritto F, Schlessinger J, Lifton R. Improved survival of patients with hypermutation in uterine serous carcinoma. Gynecol Oncol Rep 2015; 12:3-4. [PMID: 26076146 PMCID: PMC4442647 DOI: 10.1016/j.gore.2015.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/15/2015] [Indexed: 11/05/2022] Open
Abstract
Uterine serous carcinoma (USC) is an aggressive subtype of endometrial cancer. Mutations in DNA polymerase ε gene (POLE) are detected in a subset of USC and confer a strong mutator phenotype. USC patients diagnosed with POLE mutations experience a significantly better prognosis.
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117
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Ganai RA, Osterman P, Johansson E. Yeast DNA polymerase ϵ catalytic core and holoenzyme have comparable catalytic rates. J Biol Chem 2014; 290:3825-35. [PMID: 25538242 DOI: 10.1074/jbc.m114.615278] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The holoenzyme of yeast DNA polymerase ϵ (Pol ϵ) consists of four subunits: Pol2, Dpb2, Dpb3, and Dpb4. A protease-sensitive site results in an N-terminal proteolytic fragment of Pol2, called Pol2core, that consists of the catalytic core of Pol ϵ and retains both polymerase and exonuclease activities. Pre-steady-state kinetics showed that the exonuclease rates on single-stranded, double-stranded, and mismatched DNA were comparable between Pol ϵ and Pol2core. Single-turnover pre-steady-state kinetics also showed that the kpol of Pol ϵ and Pol2core were comparable when preloading the polymerase onto the primer-template before adding Mg(2+) and dTTP. However, a global fit of the data over six sequential nucleotide incorporations revealed that the overall polymerization rate and processivity were higher for Pol ϵ than for Pol2core. The largest difference between Pol ϵ and Pol2core was observed when challenged for the formation of a ternary complex and incorporation of the first nucleotide. Pol ϵ needed less than 1 s to incorporate a nucleotide, but several seconds passed before Pol2core incorporated detectable levels of the first nucleotide. We conclude that the accessory subunits and the C terminus of Pol2 do not influence the catalytic rate of Pol ϵ but facilitate the loading and incorporation of the first nucleotide by Pol ϵ.
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Affiliation(s)
- Rais A Ganai
- From the Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Pia Osterman
- From the Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Erik Johansson
- From the Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
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118
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Somatic mosaicism in the human genome. Genes (Basel) 2014; 5:1064-94. [PMID: 25513881 PMCID: PMC4276927 DOI: 10.3390/genes5041064] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/26/2014] [Accepted: 11/28/2014] [Indexed: 12/17/2022] Open
Abstract
Somatic mosaicism refers to the occurrence of two genetically distinct populations of cells within an individual, derived from a postzygotic mutation. In contrast to inherited mutations, somatic mosaic mutations may affect only a portion of the body and are not transmitted to progeny. These mutations affect varying genomic sizes ranging from single nucleotides to entire chromosomes and have been implicated in disease, most prominently cancer. The phenotypic consequences of somatic mosaicism are dependent upon many factors including the developmental time at which the mutation occurs, the areas of the body that are affected, and the pathophysiological effect(s) of the mutation. The advent of second-generation sequencing technologies has augmented existing array-based and cytogenetic approaches for the identification of somatic mutations. We outline the strengths and weaknesses of these techniques and highlight recent insights into the role of somatic mosaicism in causing cancer, neurodegenerative, monogenic, and complex disease.
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119
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Furusawa M. The disparity mutagenesis model predicts rescue of living things from catastrophic errors. Front Genet 2014; 5:421. [PMID: 25538731 PMCID: PMC4255596 DOI: 10.3389/fgene.2014.00421] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/17/2014] [Indexed: 01/24/2023] Open
Abstract
In animals including humans, mutation rates per generation exceed a perceived threshold, and excess mutations increase genetic load. Despite this, animals have survived without extinction. This is a perplexing problem for animal and human genetics, arising at the end of the last century, and to date still does not have a fully satisfactory explanation. Shortly after we proposed the disparity theory of evolution in 1992, the disparity mutagenesis model was proposed, which forms the basis for an explanation for an acceleration of evolution and species survival. This model predicts a significant increase of the mutation threshold values if the fidelity difference in replication between the lagging and leading strands is high enough. When applied to biological evolution, the model predicts that living things, including humans, might overcome the lethal effect of accumulated deleterious mutations and be able to survive. Artificially derived mutator strains of microorganisms, in which an enhanced lagging-strand-biased mutagenesis was introduced, showed unexpectedly high adaptability to severe environments. The implications of the striking behaviors shown by these disparity mutators will be discussed in relation to how living things with high mutation rates can avoid the self-defeating risk of excess mutations.
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Stenzinger A, Pfarr N, Endris V, Penzel R, Jansen L, Wolf T, Herpel E, Warth A, Klauschen F, Kloor M, Roth W, Bläker H, Chang-Claude J, Brenner H, Hoffmeister M, Weichert W. Mutations in POLE and survival of colorectal cancer patients--link to disease stage and treatment. Cancer Med 2014; 3:1527-38. [PMID: 25124163 PMCID: PMC4298379 DOI: 10.1002/cam4.305] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/10/2014] [Accepted: 06/24/2014] [Indexed: 12/14/2022] Open
Abstract
Recent molecular profiling studies reported a new class of ultramutated colorectal cancers (CRCs), which are caused by exonuclease domain mutations (EDMs) in DNA polymerase ϵ (POLE). Data on the clinical implications of these findings as to whether these mutations define a unique CRC entity with distinct clinical outcome are lacking. We performed Sanger sequencing of the POLE exonuclease domain in 431 well-characterized patients with microsatellite stable (MSS) CRCs of a population-based patient cohort. Mutation data were analyzed for associations with major epidemiological, clinical, genetic, and pathological parameters including overall survival (OS) and disease-specific survival (DSS). In 373 of 431 MSS CRC, all exons of the exonuclease domain were analyzable. Fifty-four mutations were identified in 46 of these samples (12.3%). Besides already reported EDMs, we detected many new mutations in exons 13 and 14 (corresponding to amino acids 410-491) as well as in exon 9 and exon 11 (corresponding to aa 268-303 and aa 341-369). However, we did not see any significant associations of EDMs with clinicopathological parameters, including sex, age, tumor location and tumor stage, CIMP, KRAS, and BRAF mutations. While with a median follow-up time of 5.0 years, survival analysis of the whole cohort revealed nonsignificantly different adjusted hazard ratios (HRs) of 1.35 (95% CI: 0.82-2.25) and 1.44 (0.81-2.58) for OS and DSS indicating slightly impaired survival of patients with EDMs, subgroup analysis for patients with stage III/IV disease receiving chemotherapy revealed a statistically significantly increased adjusted HR (1.87; 95%CI: 1.02-3.44). In conclusion, POLE EDMs do not appear to define an entirely new clinically distinct disease entity in CRC but may have prognostic or predictive implications in CRC subgroups, whose significance remains to be investigated in future studies.
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Affiliation(s)
| | - Nicole Pfarr
- Institute of Pathology, Heidelberg University HospitalGermany
| | - Volker Endris
- Institute of Pathology, Heidelberg University HospitalGermany
| | - Roland Penzel
- Institute of Pathology, Heidelberg University HospitalGermany
| | - Lina Jansen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ)Heidelberg, Germany
| | - Thomas Wolf
- Institute of Pathology, Heidelberg University HospitalGermany
- German Consortium for Translational Cancer Research (DKTK)Germany
| | - Esther Herpel
- Institute of Pathology, Heidelberg University HospitalGermany
| | - Arne Warth
- Institute of Pathology, Heidelberg University HospitalGermany
| | | | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University of HeidelbergHeidelberg, Germany
| | - Wilfried Roth
- Institute of Pathology, Heidelberg University HospitalGermany
| | - Hendrik Bläker
- Institute of Pathology, Charité University MedicineBerlin, Germany
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, German Cancer Research Center (DKFZ)Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ)Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK)Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ)Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Heidelberg University HospitalGermany
- German Consortium for Translational Cancer Research (DKTK)Germany
- National Center for Tumor Diseases (NCT)Heidelberg, Germany
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121
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Abstract
The mutator phenotype hypothesis proposes that the mutation rate of normal cells is insufficient to account for the large number of mutations found in human cancers. Consequently, human tumors exhibit an elevated mutation rate that increases the likelihood of a tumor acquiring advantageous mutations. The hypothesis predicts that tumors are composed of cells harboring hundreds of thousands of mutations, as opposed to a small number of specific driver mutations, and that malignant cells within a tumor therefore constitute a highly heterogeneous population. As a result, drugs targeting specific mutated driver genes or even pathways of mutated driver genes will have only limited anticancer potential. In addition, because the tumor is composed of such a diverse cell population, tumor cells harboring drug-resistant mutations will exist prior to the administration of any chemotherapeutic agent. We present recent evidence in support of the mutator phenotype hypothesis, major arguments against this concept, and discuss the clinical consequences of tumor evolution fueled by an elevated mutation rate. We also consider the therapeutic possibility of altering the rate of mutation accumulation. Most significantly, we contend that there is a need to fundamentally reconsider current approaches to personalized cancer therapy. We propose that targeting cellular pathways that alter the rate of mutation accumulation in tumors will ultimately prove more effective than attempting to identify and target mutant driver genes or driver pathways.
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Affiliation(s)
- Edward J Fox
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
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122
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Ghodgaonkar MM, Kehl P, Ventura I, Hu L, Bignami M, Jiricny J. Phenotypic characterization of missense polymerase-δ mutations using an inducible protein-replacement system. Nat Commun 2014; 5:4990. [PMID: 25241845 DOI: 10.1038/ncomms5990] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/14/2014] [Indexed: 01/12/2023] Open
Abstract
Next-generation sequencing has revolutionized the search for disease-causing genetic alterations. Unfortunately, the task of distinguishing the handful of causative mutations from rare variants remains daunting. We now describe an assay that permits the analysis of all types of mutations in any gene of choice through the generation of stable human cell lines, in which the endogenous protein has been inducibly replaced with its genetic variant. Here we studied the phenotype of variants of the essential replicative polymerase-δ carrying missense mutations in its active site, similar to those recently identified in familial colon cancer patients. We show that expression of the mutants but not the wild-type protein endows the engineered cells with a mutator phenotype and that the mutations affect the fidelity and/or the exonuclease activity of the isolated enzyme in vitro. This proof-of-principle study demonstrates the general applicability of this experimental approach in the study of genotype-phenotype correlations.
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Affiliation(s)
- Medini Manohar Ghodgaonkar
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Patrick Kehl
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Ilenia Ventura
- 1] Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland [2] Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome 11061, Italy
| | - Liyan Hu
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Margherita Bignami
- 1] Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland [2] Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome 11061, Italy
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, ETH Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
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123
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Konstantinopoulos PA, Matulonis UA. POLE mutations as an alternative pathway for microsatellite instability in endometrial cancer: implications for Lynch syndrome testing. Cancer 2014; 121:331-4. [PMID: 25224324 DOI: 10.1002/cncr.29057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 08/29/2014] [Indexed: 11/12/2022]
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124
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Billingsley CC, Cohn DE, Mutch DG, Stephens JA, Suarez AA, Goodfellow PJ. Polymerase ɛ (POLE) mutations in endometrial cancer: clinical outcomes and implications for Lynch syndrome testing. Cancer 2014; 121:386-94. [PMID: 25224212 DOI: 10.1002/cncr.29046] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/06/2014] [Accepted: 06/11/2014] [Indexed: 01/24/2023]
Abstract
BACKGROUND DNA polymerase ɛ (POLE) exonuclease domain mutations characterize a subtype of endometrial cancer (EC) with a markedly increased somatic mutational burden. POLE-mutant tumors were described as a molecular subtype with improved progression-free survival by The Cancer Genome Atlas. In this study, the frequency, spectrum, prognostic significance, and potential clinical application of POLE mutations were investigated in patients with endometrioid EC. METHODS Polymerase chain reaction amplification and Sanger sequencing were used to test for POLE mutations in 544 tumors. Correlations between demographic, survival, clinicopathologic, and molecular features were investigated. Statistical tests were 2-sided. RESULTS Thirty POLE mutations (5.6%) were identified. Mutations were associated with younger age (<60 years; P=.001). POLE mutations were detected in tumors with microsatellite stability (MSS) and microsatellite instability (MSI) at similar frequencies (5.9% and 5.2%, respectively) and were most common in tumors with MSI that lacked mutL homolog 1 (MLH1) methylation (P<.001). There was no association with progression-free survival (hazard ratio, 0.22; P=.127). CONCLUSIONS The discovery that mutations occur with equal frequency in MSS and MSI tumors and are most frequent in MSI tumors lacking MLH1 methylation has implications for Lynch syndrome screening and mutation testing. The current results indicate that POLE mutations are associated with somatic mutation in DNA mismatch repair genes in a subset of tumors. The absence of an association between POLE mutation and progression-free survival indicates that POLE mutation status is unlikely to be a clinically useful prognostic marker. However, POLE testing in MSI ECs could serve as a marker of somatic disease origin. Therefore, POLE tumor testing may be a valuable exclusionary criterion for Lynch syndrome gene testing.
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Affiliation(s)
- Caroline C Billingsley
- Department of Obstetrics and Gynecology, Division of Gynecology Oncology, The Ohio State University, College of Medicine, Columbus, Ohio
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125
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Abstract
Mutational heterogeneity must be taken into account when reconstructing evolutionary histories, calibrating molecular clocks, and predicting links between genes and disease. Selective pressures and various DNA transactions have been invoked to explain the heterogeneous distribution of genetic variation between species, within populations, and in tissue-specific tumors. To examine relationships between such heterogeneity and variations in leading- and lagging-strand replication fidelity and mismatch repair, we accumulated 40,000 spontaneous mutations in eight diploid yeast strains in the absence of selective pressure. We found that replicase error rates vary by fork direction, coding state, nucleosome proximity, and sequence context. Further, error rates and DNA mismatch repair efficiency both vary by mismatch type, responsible polymerase, replication time, and replication origin proximity. Mutation patterns implicate replication infidelity as one driver of variation in somatic and germline evolution, suggest mechanisms of mutual modulation of genome stability and composition, and predict future observations in specific cancers.
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126
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Abstract
Two sibling DNA polymerases synthesize most of the eukaryotic nuclear genome. A new study provides insights into the distinct protein interactions that deliver these replicases for asymmetric leading- and lagging-strand replication and reveals possible cross-talk between DNA replication and other cellular processes.
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Affiliation(s)
- Thomas A Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
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127
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Henninger EE, Pursell ZF. DNA polymerase ε and its roles in genome stability. IUBMB Life 2014; 66:339-51. [PMID: 24861832 DOI: 10.1002/iub.1276] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 05/02/2014] [Indexed: 12/14/2022]
Abstract
DNA Polymerase Epsilon (Pol ε) is one of three DNA Polymerases (along with Pol δ and Pol α) required for nuclear DNA replication in eukaryotes. Pol ε is comprised of four subunits, the largest of which is encoded by the POLE gene and contains the catalytic polymerase and exonuclease activities. The 3'-5' exonuclease proofreading activity is able to correct DNA synthesis errors and helps protect against genome instability. Recent cancer genome sequencing efforts have shown that 3% of colorectal and 7% of endometrial cancers contain mutations within the exonuclease domain of POLE and are associated with significantly elevated levels of single nucleotide substitutions (15-500 per Mb) and microsatellite stability. POLE mutations have also been found in other tumor types, though at lower frequency, suggesting roles in tumorigenesis more broadly in different tissue types. In addition to its proofreading activity, Pol ε contributes to genome stability through multiple mechanisms that are discussed in this review.
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Affiliation(s)
- Erin E Henninger
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
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128
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Mouradov D, Sloggett C, Jorissen RN, Love CG, Li S, Burgess AW, Arango D, Strausberg RL, Buchanan D, Wormald S, O'Connor L, Wilding JL, Bicknell D, Tomlinson IPM, Bodmer WF, Mariadason JM, Sieber OM. Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer. Cancer Res 2014; 74:3238-47. [PMID: 24755471 DOI: 10.1158/0008-5472.can-14-0013] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Human colorectal cancer cell lines are used widely to investigate tumor biology, experimental therapy, and biomarkers. However, to what extent these established cell lines represent and maintain the genetic diversity of primary cancers is uncertain. In this study, we profiled 70 colorectal cancer cell lines for mutations and DNA copy number by whole-exome sequencing and SNP microarray analyses, respectively. Gene expression was defined using RNA-Seq. Cell line data were compared with those published for primary colorectal cancers in The Cancer Genome Atlas. Notably, we found that exome mutation and DNA copy-number spectra in colorectal cancer cell lines closely resembled those seen in primary colorectal tumors. Similarities included the presence of two hypermutation phenotypes, as defined by signatures for defective DNA mismatch repair and DNA polymerase ε proofreading deficiency, along with concordant mutation profiles in the broadly altered WNT, MAPK, PI3K, TGFβ, and p53 pathways. Furthermore, we documented mutations enriched in genes involved in chromatin remodeling (ARID1A, CHD6, and SRCAP) and histone methylation or acetylation (ASH1L, EP300, EP400, MLL2, MLL3, PRDM2, and TRRAP). Chromosomal instability was prevalent in nonhypermutated cases, with similar patterns of chromosomal gains and losses. Although paired cell lines derived from the same tumor exhibited considerable mutation and DNA copy-number differences, in silico simulations suggest that these differences mainly reflected a preexisting heterogeneity in the tumor cells. In conclusion, our results establish that human colorectal cancer lines are representative of the main subtypes of primary tumors at the genomic level, further validating their utility as tools to investigate colorectal cancer biology and drug responses.
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Affiliation(s)
- Dmitri Mouradov
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Clare Sloggett
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Robert N Jorissen
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Christopher G Love
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Shan Li
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Antony W Burgess
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Diego Arango
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Robert L Strausberg
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Daniel Buchanan
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Samuel Wormald
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Liam O'Connor
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
| | - Jennifer L Wilding
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - David Bicknell
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Ian P M Tomlinson
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Walter F Bodmer
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - John M Mariadason
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Oliver M Sieber
- Authors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies Group, Queensland Institute of Medical Research, Herston, QLD, Australia; Group of Molecular Oncology, CIBBIM-Nanomedicine, Vall d'Hebron University Hospital, Research Institute (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron, 119-129, 08035 Barcelona; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN); Spain; Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; Ludwig Institute for Cancer Research Ltd., New York, New York; Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford; and Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, United KingdomAuthors' Affiliations: Ludwig Institute for Cancer Research; Systems Biology and Personalised Medicine Division; Structural Biology Division; Walter and Eliza Hall Institute of Medical Research; Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville; VLSCI Life Sciences Computation Centre, a collaboration between Melbourne, Monash and LaTrobe Universities, c/o The University of Melbourne, Carlton; Oncogenic Transcription Laboratory, Ludwig Institute for Cancer Research, Austin, VIC, Australia; Cancer and Population Studies
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Esteban-Jurado C, Garre P, Vila M, Lozano JJ, Pristoupilova A, Beltrán S, Abulí A, Muñoz J, Balaguer F, Ocaña T, Castells A, Piqué JM, Carracedo A, Ruiz-Ponte C, Bessa X, Andreu M, Bujanda L, Caldés T, Castellví-Bel S. New genes emerging for colorectal cancer predisposition. World J Gastroenterol 2014; 20:1961-1971. [PMID: 24587672 PMCID: PMC3934466 DOI: 10.3748/wjg.v20.i8.1961] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/20/2013] [Accepted: 01/15/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most frequent neoplasms and an important cause of mortality in the developed world. This cancer is caused by both genetic and environmental factors although 35% of the variation in CRC susceptibility involves inherited genetic differences. Mendelian syndromes account for about 5% of the total burden of CRC, with Lynch syndrome and familial adenomatous polyposis the most common forms. Excluding hereditary forms, there is an important fraction of CRC cases that present familial aggregation for the disease with an unknown germline genetic cause. CRC can be also considered as a complex disease taking into account the common disease-commom variant hypothesis with a polygenic model of inheritance where the genetic components of common complex diseases correspond mostly to variants of low/moderate effect. So far, 30 common, low-penetrance susceptibility variants have been identified for CRC. Recently, new sequencing technologies including exome- and whole-genome sequencing have permitted to add a new approach to facilitate the identification of new genes responsible for human disease predisposition. By using whole-genome sequencing, germline mutations in the POLE and POLD1 genes have been found to be responsible for a new form of CRC genetic predisposition called polymerase proofreading-associated polyposis.
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Kane DP, Shcherbakova PV. A common cancer-associated DNA polymerase ε mutation causes an exceptionally strong mutator phenotype, indicating fidelity defects distinct from loss of proofreading. Cancer Res 2014; 74:1895-901. [PMID: 24525744 DOI: 10.1158/0008-5472.can-13-2892] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Exonucleolytic proofreading and DNA mismatch repair (MMR) act in series to maintain high-fidelity DNA replication and to avoid mutagenesis. MMR defects elevate the overall mutation rate and are associated with increased cancer incidence. Hypermutable colorectal and endometrial tumors with functional MMR were recently reported to carry amino acid substitutions in the exonuclease domain of DNA polymerase ε (Polε). This created a notion that loss of the proofreading activity of Polε is an initiating cause of some sporadic human cancers. In this study, we identified a somatic P286R substitution in the conserved ExoI motif of Polε in a collection of 52 sporadic colorectal tumor specimens. This change has been repeatedly observed in colorectal and endometrial tumors in previous studies despite many possible ways to inactivate Polε proofreading. To understand the reasons for the recurrent appearance of the P286R variant, we characterized its functional consequences using the yeast model system. An analogous substitution in the yeast Polε produced an unusually strong mutator phenotype exceeding that of proofreading-deficient mutants by two orders of magnitude. This argues that the P286R mutation acts at some level other than loss of exonuclease to elevate cancer risk. Heterozygosity for the variant allele caused a strong mutator effect comparable with that of complete MMR deficiency, providing an explanation for why loss of heterozygosity is not required for the development of Polε-mutant human tumors.
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Affiliation(s)
- Daniel P Kane
- Authors' Affiliation: Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
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131
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Heitzer E, Tomlinson I. Replicative DNA polymerase mutations in cancer. Curr Opin Genet Dev 2014; 24:107-13. [PMID: 24583393 PMCID: PMC4003352 DOI: 10.1016/j.gde.2013.12.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 12/18/2022]
Abstract
Three DNA polymerases - Pol α, Pol δ and Pol ɛ - are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson-Crick base pairing and 3'exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to 'polymerase proofreading associated polyposis' (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an 'ultramutator' phenotype, with a dramatic increase in base substitutions.
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Affiliation(s)
- Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010 Graz, Austria.
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK; Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
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132
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Zou Y, Liu FY, Liu H, Wang F, Li W, Huang MZ, Huang Y, Yuan XQ, Xu XY, Huang OP, He M. Frequent POLE1 p.S297F mutation in Chinese patients with ovarian endometrioid carcinoma. Mutat Res 2014; 761:49-52. [PMID: 24472300 DOI: 10.1016/j.mrfmmm.2014.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 01/04/2014] [Accepted: 01/07/2014] [Indexed: 01/12/2023]
Abstract
The catalytic subunit of DNA polymerase epsilon (POLE1) functions primarily in nuclear DNA replication and repair. Recently, POLE1 mutations were detected frequently in colorectal and endometrial carcinomas while with lower frequency in several other types of cancer, and the p.P286R and p.V411L mutations were the potential mutation hotspots in human cancers. Nevertheless, the mutation frequency of POLE1 in ovarian cancer still remains largely unknown. Here, we screened a total of 251 Chinese samples with distinct subtypes of ovarian carcinoma for the presence of POLE1 hotspot mutations by direct sequencing. A heterozygous somatic POLE1 mutation, p.S297F (c.890C>T), but not p.P286R and p.V411L hotspot mutations observed in other cancer types, was identified in 3 out of 37 (8.1%) patients with ovarian endometrioid carcinoma; this mutation was evolutionarily highly conserved from Homo sapiens to Schizosaccharomyces. Of note, the POLE1 mutation coexisted with mutation in the ovarian cancer-associated PPP2R1A (protein phosphatase 2, regulatory subunit A, α) gene in a 46-year-old patient, who was also diagnosed with ectopic endometriosis in the benign ovary. In addition, a 45-year-old POLE1-mutated ovarian endometrioid carcinoma patient was also diagnosed with uterine leiomyoma while the remaining 52-year-old POLE1-mutated patient showed no additional distinctive clinical manifestation. In contrast to high frequency of POLE1 mutations in ovarian endometrioid carcinoma, no POLE1 mutations were identified in patients with other subtypes of ovarian carcinoma. Our results showed for the first time that the POLE1 p.S297F mutation, but not p.P286R and p.V411L hotspot mutations observed in other cancer types, was frequent in Chinese ovarian endometrioid carcinoma, but absent in other subtypes of ovarian carcinoma. These results implicated that POLE1 p.S297F mutation might be actively involved in the pathogenesis of ovarian endometrioid carcinoma, but might not be actively involved in other subtypes of ovarian carcinoma.
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Affiliation(s)
- Yang Zou
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China
| | - Fa-Ying Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China
| | - Huai Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China
| | - Feng Wang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China
| | - Wei Li
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China; Graduate School of Nanchang University, Nanchang, Jiangxi 330031, China
| | - Mei-Zhen Huang
- Graduate School of Nanchang University, Nanchang, Jiangxi 330031, China; Jiangxi Provincial Cancer Institute, Jiangxi Provincial Cancer Hospital, Nanchang, Jiangxi 330029, China
| | - Yan Huang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China; Graduate School of Nanchang University, Nanchang, Jiangxi 330031, China
| | - Xiao-Qun Yuan
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, China; Graduate School of Nanchang University, Nanchang, Jiangxi 330031, China
| | - Xiao-Yun Xu
- Graduate School of Nanchang University, Nanchang, Jiangxi 330031, China; Jiangxi Provincial Cancer Institute, Jiangxi Provincial Cancer Hospital, Nanchang, Jiangxi 330029, China
| | - Ou-Ping Huang
- Jiangxi Provincial Cancer Institute, Jiangxi Provincial Cancer Hospital, Nanchang, Jiangxi 330029, China.
| | - Ming He
- Department of Pharmacology & Molecular Therapeutics, Nanchang University School of Pharmaceutical Science, Nanchang 330006, China.
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Abstract
Genetic defects in DNA polymerase accuracy, proofreading, or mismatch repair (MMR) induce mutator phenotypes that accelerate adaptation of microbes and tumor cells. Certain combinations of mutator alleles synergistically increase mutation rates to levels that drive extinction of haploid cells. The maximum tolerated mutation rate of diploid cells is unknown. Here, we define the threshold for replication error-induced extinction (EEX) of diploid Saccharomyces cerevisiae. Double-mutant pol3 alleles that carry mutations for defective DNA polymerase-δ proofreading (pol3-01) and accuracy (pol3-L612M or pol3-L612G) induce strong mutator phenotypes in heterozygous diploids (POL3/pol3-01,L612M or POL3/pol3-01,L612G). Both pol3-01,L612M and pol3-01,L612G alleles are lethal in the homozygous state; cells with pol3-01,L612M divide up to 10 times before arresting at random stages in the cell cycle. Antimutator eex mutations in the pol3 alleles suppress this lethality (pol3-01,L612M,eex or pol3-01,L612G,eex). MMR defects synergize with pol3-01,L612M,eex and pol3-01,L612G,eex alleles, increasing mutation rates and impairing growth. Conversely, inactivation of the Dun1 S-phase checkpoint kinase suppresses strong pol3-01,L612M,eex and pol3-01,L612G,eex mutator phenotypes as well as the lethal pol3-01,L612M phenotype. Our results reveal that the lethal error threshold in diploids is 10 times higher than in haploids and likely determined by homozygous inactivation of essential genes. Pronounced loss of fitness occurs at mutation rates well below the lethal threshold, suggesting that mutator-driven cancers may be susceptible to drugs that exacerbate replication errors.
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135
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Agbor AA, Göksenin AY, LeCompte KG, Hans SH, Pursell ZF. Human Pol ε-dependent replication errors and the influence of mismatch repair on their correction. DNA Repair (Amst) 2013; 12:954-63. [PMID: 24051051 PMCID: PMC4520434 DOI: 10.1016/j.dnarep.2013.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 08/19/2013] [Accepted: 08/20/2013] [Indexed: 12/30/2022]
Abstract
Mutations in human DNA polymerase (Pol) ε, one of three eukaryotic Pols required for DNA replication, have recently been found associated with an ultramutator phenotype in tumors from somatic colorectal and endometrial cancers and in a familial colorectal cancer. Possibly, Pol ε mutations reduce the accuracy of DNA synthesis, thereby increasing the mutational burden and contributing to tumor development. To test this possibility in vivo, we characterized an active site mutant allele of human Pol ε that exhibits a strong mutator phenotype in vitro when the proofreading exonuclease activity of the enzyme is inactive. This mutant has a strong bias toward mispairs opposite template pyrimidine bases, particularly T • dTTP mispairs. Expression of mutant Pol ε in human cells lacking functional mismatch repair caused an increase in mutation rate primarily due to T • dTTP mispairs. Functional mismatch repair eliminated the increased mutagenesis. The results indicate that the mutant Pol ε causes replication errors in vivo, and is at least partially dominant over the endogenous, wild type Pol ε. Since tumors from familial and somatic colorectal patients arise with Pol ε mutations in a single allele, are microsatellite stable and have a large increase in base pair substitutions, our data are consistent with a Pol ε mutation requiring additional factors to promote tumor development.
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Affiliation(s)
- Anderson Ayuk Agbor
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - A. Yasemin Göksenin
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Kimberly G. LeCompte
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Samuel H. Hans
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Zachary F. Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
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A reversible histone H3 acetylation cooperates with mismatch repair and replicative polymerases in maintaining genome stability. PLoS Genet 2013; 9:e1003899. [PMID: 24204308 PMCID: PMC3812082 DOI: 10.1371/journal.pgen.1003899] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/06/2013] [Indexed: 01/06/2023] Open
Abstract
Mutations are a major driving force of evolution and genetic disease. In eukaryotes, mutations are produced in the chromatin environment, but the impact of chromatin on mutagenesis is poorly understood. Previous studies have determined that in yeast Saccharomyces cerevisiae, Rtt109-dependent acetylation of histone H3 on K56 is an abundant modification that is introduced in chromatin in S phase and removed by Hst3 and Hst4 in G2/M. We show here that the chromatin deacetylation on histone H3 K56 by Hst3 and Hst4 is required for the suppression of spontaneous gross chromosomal rearrangements, base substitutions, 1-bp insertions/deletions, and complex mutations. The rate of base substitutions in hst3Δ hst4Δ is similar to that in isogenic mismatch repair-deficient msh2Δ mutant. We also provide evidence that H3 K56 acetylation by Rtt109 is important for safeguarding DNA from small insertions/deletions and complex mutations. Furthermore, we reveal that both the deacetylation and acetylation on histone H3 K56 are involved in mutation avoidance mechanisms that cooperate with mismatch repair and the proofreading activities of replicative DNA polymerases in suppressing spontaneous mutagenesis. Our results suggest that cyclic acetylation and deacetylation of chromatin contribute to replication fidelity and play important roles in the protection of nuclear DNA from diverse spontaneous mutations. Mutations strongly predispose humans to cancer and many other diseases. Despite significant progress, we still do not fully understand the molecular mechanisms that protect us from mutations. Human DNA is part of a highly organized complex called chromatin. Chromatin regulates our development, metabolism, and behavior. Special enzymes modify chromatin by the addition and removal of chemical groups. Acetylation and deacetylation of chromatin have been conserved during evolution. The involvement of chromatin and its modifications in the protection of DNA from mutations is poorly understood. The yeast Saccharomyces cerevisiae is an excellent model for studying the connection between chromatin modifications and mutations. Using this model, we found that the deacetylation and acetylation of chromatin on histone H3 lysine 56 are required for preventing a wide range of spontaneous mutations. Future studies will determine whether acetylation and deacetylation of chromatin are involved in protecting DNA from mutations in human cells.
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137
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Grosch M, Grüner B, Spranger S, Stütz AM, Rausch T, Korbel JO, Seelow D, Nürnberg P, Sticht H, Lausch E, Zabel B, Winterpacht A, Tagariello A. Identification of a Ninein (NIN) mutation in a family with spondyloepimetaphyseal dysplasia with joint laxity (leptodactylic type)-like phenotype. Matrix Biol 2013; 32:387-92. [DOI: 10.1016/j.matbio.2013.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/30/2013] [Accepted: 05/01/2013] [Indexed: 12/29/2022]
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Role of DNA damage response pathways in preventing carcinogenesis caused by intrinsic replication stress. Oncogene 2013; 33:3688-95. [PMID: 23975433 PMCID: PMC3936004 DOI: 10.1038/onc.2013.339] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 12/11/2022]
Abstract
Defective DNA replication can result in genomic instability, cancer, and developmental defects. To understand the roles of DNA damage response (DDR) genes on carcinogenesis in mutants defective for core DNA replication components, we utilized the Mcm4Chaos3/Chaos3 (“Chaos3”) mouse model which, by virtue of an amino acid alteration in MCM4 that destabilizes the MCM2-7 DNA replicative helicase, has fewer dormant replication origins and an increased number of stalled replication forks. This leads to genomic instability and cancer in most Chaos3 mice. We found that animals doubly mutant for Chaos3 and components of the ATM double strand break response pathway (Atm, p21/Cdkn1a, Chk2/Chek2) had decreased tumor latency and/or increased tumor susceptibility. Tumor latency and susceptibility differed between genetic backgrounds and genders, with females demonstrating an overall greater cancer susceptibility to Atm and p21 deficiency than males. ATM deficiency was semilethal in the Chaos3 background and impaired embryonic fibroblast proliferation, suggesting that ATM drug inhibitors might be useful against tumors with DNA replication defects. Hypomorphism for the 9-1-1 component Hus1 did not affect tumor latency or susceptibility in Chaos3 animals, and tumors in these mice did not exhibit impaired ATR pathway signaling. These and other data indicate that under conditions of systemic replication stress, the ATM pathway is particularly important both for cancer suppression and viability during development.
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139
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Abaan OD, Polley EC, Davis SR, Zhu YJ, Bilke S, Walker RL, Pineda M, Gindin Y, Jiang Y, Reinhold WC, Holbeck SL, Simon RM, Doroshow JH, Pommier Y, Meltzer PS. The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology. Cancer Res 2013; 73:4372-82. [PMID: 23856246 DOI: 10.1158/0008-5472.can-12-3342] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The NCI-60 cell lines are the most frequently studied human tumor cell lines in cancer research. This panel has generated the most extensive cancer pharmacology database worldwide. In addition, these cell lines have been intensely investigated, providing a unique platform for hypothesis-driven research focused on enhancing our understanding of tumor biology. Here, we report a comprehensive analysis of coding variants in the NCI-60 panel of cell lines identified by whole exome sequencing, providing a list of possible cancer specific variants for the community. Furthermore, we identify pharmacogenomic correlations between specific variants in genes such as TP53, BRAF, ERBBs, and ATAD5 and anticancer agents such as nutlin, vemurafenib, erlotinib, and bleomycin showing one of many ways the data could be used to validate and generate novel hypotheses for further investigation. As new cancer genes are identified through large-scale sequencing studies, the data presented here for the NCI-60 will be an invaluable resource for identifying cell lines with mutations in such genes for hypothesis-driven research. To enhance the utility of the data for the greater research community, the genomic variants are freely available in different formats and from multiple sources including the CellMiner and Ingenuity websites.
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Affiliation(s)
- Ogan D Abaan
- Genetics Branch, Laboratory of Molecular Pharmacology, Center for Cancer Research, and Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, MD 20982, USA
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Church DN, Briggs SEW, Palles C, Domingo E, Kearsey SJ, Grimes JM, Gorman M, Martin L, Howarth KM, Hodgson SV, Kaur K, Taylor J, Tomlinson IPM. DNA polymerase ε and δ exonuclease domain mutations in endometrial cancer. Hum Mol Genet 2013; 22:2820-8. [PMID: 23528559 PMCID: PMC3690967 DOI: 10.1093/hmg/ddt131] [Citation(s) in RCA: 270] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/19/2013] [Indexed: 12/31/2022] Open
Abstract
Accurate duplication of DNA prior to cell division is essential to suppress mutagenesis and tumour development. The high fidelity of eukaryotic DNA replication is due to a combination of accurate incorporation of nucleotides into the nascent DNA strand by DNA polymerases, the recognition and removal of mispaired nucleotides (proofreading) by the exonuclease activity of DNA polymerases δ and ε, and post-replication surveillance and repair of newly synthesized DNA by the mismatch repair (MMR) apparatus. While the contribution of defective MMR to neoplasia is well recognized, evidence that faulty DNA polymerase activity is important in cancer development has been limited. We have recently shown that germline POLE and POLD1 exonuclease domain mutations (EDMs) predispose to colorectal cancer (CRC) and, in the latter case, to endometrial cancer (EC). Somatic POLE mutations also occur in 5-10% of sporadic CRCs and underlie a hypermutator, microsatellite-stable molecular phenotype. We hypothesized that sporadic ECs might also acquire somatic POLE and/or POLD1 mutations. Here, we have found that missense POLE EDMs with good evidence of pathogenic effects are present in 7% of a set of 173 endometrial cancers, although POLD1 EDMs are uncommon. The POLE mutations localized to highly conserved residues and were strongly predicted to affect proofreading. Consistent with this, POLE-mutant tumours were hypermutated, with a high frequency of base substitutions, and an especially large relative excess of G:C>T:A transversions. All POLE EDM tumours were microsatellite stable, suggesting that defects in either DNA proofreading or MMR provide alternative mechanisms to achieve genomic instability and tumourigenesis.
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Affiliation(s)
- David N Church
- Molecular and Population Genetics Laboratory, University of Oxford, Roosevelt Drive, Oxford OX3 7BN.
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141
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Briggs S, Tomlinson I. Germline and somatic polymerase ε and δ mutations define a new class of hypermutated colorectal and endometrial cancers. J Pathol 2013; 230:148-53. [PMID: 23447401 PMCID: PMC3709119 DOI: 10.1002/path.4185] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 02/20/2013] [Accepted: 02/22/2013] [Indexed: 12/28/2022]
Abstract
Polymerases ε and δ are the main enzymes that replicate eukaryotic DNA. Accurate replication occurs through Watson-Crick base pairing and also through the action of the polymerases' exonuclease (proofreading) domains. We have recently shown that germline exonuclease domain mutations (EDMs) of POLE and POLD1 confer a high risk of multiple colorectal adenomas and carcinoma (CRC). POLD1 mutations also predispose to endometrial cancer (EC). These mutations are associated with high penetrance and dominant inheritance, although the phenotype can be variable. We have named the condition polymerase proofreading-associated polyposis (PPAP). Somatic POLE EDMs have also been found in sporadic CRCs and ECs, although very few somatic POLD1 EDMs have been detected. Both the germline and the somatic DNA polymerase EDMs cause an 'ultramutated', apparently microsatellite-stable, type of cancer, sometimes leading to over a million base substitutions per tumour. Here, we present the evidence for POLE and POLD1 as important contributors to the pathogenesis of CRC and EC, and highlight some of the key questions in this emerging field.
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Affiliation(s)
- Sarah Briggs
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of OxfordRoosevelt Drive, Oxford, OX3 7BN, UK
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of OxfordRoosevelt Drive, Oxford, OX3 7BN, UK
- Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt DriveOxford, OX3 7BN, UK
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142
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Abstract
Our understanding of inherited risk factors for colorectal cancer (CRC) is incomplete. A new study reports the identification of germline CRC risk variants that adversely affect the proofreading function of DNA polymerases encoded by POLE and POLD1.
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143
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Dual role for mammalian DNA polymerase ζ in maintaining genome stability and proliferative responses. Proc Natl Acad Sci U S A 2013; 110:E687-96. [PMID: 23386725 DOI: 10.1073/pnas.1217425110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA polymerase ζ (polζ) is critical for bypass of DNA damage and the associated mutagenesis, but also has unique functions in mammals. It is required for embryonic development and for viability of hematopoietic cells, but, paradoxically, skin epithelia appear to survive polζ deletion. We wished to determine whether polζ functions in a tissue-specific manner and how polζ status influences skin tumorigenesis. Mice were produced in which Rev3L (the catalytic subunit of polζ) was deleted in tissues expressing keratin 5. Efficient epidermal deletion of Rev3L was tolerated but led to skin and hair abnormalities, accompanied by evidence of DNA breaks. Unchallenged mice developed tumors in keratin 5-expressing tissues with age, consistent with the chromosomal instability accompanying a polζ defect. Unexpectedly, mice with the Rev3L deletion were much more sensitive to UVB radiation than mice defective in other DNA repair genes. Following irradiation, polζ-defective mice failed to mount skin-regenerative responses and responded to stress by mobilizing melanocytes to the epidermis. However, they did not develop skin tumors after chronic UVB irradiation. To determine the proliferative potential of polζ-deficient skin epithelia, keratinocytes were isolated and examined. These keratinocytes harbored chromosomal gaps and breaks and exhibited a striking proliferation defect. These results can be unified by a model in which slowly dividing cells accumulate replication-associated DNA breaks but otherwise survive Rev3L deletion, but functional polζ is essential for responses requiring rapid proliferation, both in cell culture and in vivo. The results reveal a biological role for mammalian polζ in tolerating DNA damage and enabling proliferative responses in vivo.
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144
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Palles C, Cazier JB, Howarth KM, Domingo E, Jones AM, Broderick P, Kemp Z, Spain SL, Almeida EG, Salguero I, Sherborne A, Chubb D, Carvajal-Carmona LG, Ma Y, Kaur K, Dobbins S, Barclay E, Gorman M, Martin L, Kovac MB, Humphray S, Lucassen A, Holmes C, Bentley D, Donnelly P, Taylor J, Petridis C, Roylance R, Sawyer EJ, Kerr DJ, Clark S, Grimes J, Kearsey SE, Thomas HJW, McVean G, Houlston RS, Tomlinson I. Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat Genet 2013; 45:136-44. [PMID: 23263490 PMCID: PMC3785128 DOI: 10.1038/ng.2503] [Citation(s) in RCA: 732] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 11/28/2012] [Indexed: 12/11/2022]
Abstract
Many individuals with multiple or large colorectal adenomas or early-onset colorectal cancer (CRC) have no detectable germline mutations in the known cancer predisposition genes. Using whole-genome sequencing, supplemented by linkage and association analysis, we identified specific heterozygous POLE or POLD1 germline variants in several multiple-adenoma and/or CRC cases but in no controls. The variants associated with susceptibility, POLE p.Leu424Val and POLD1 p.Ser478Asn, have high penetrance, and POLD1 mutation was also associated with endometrial cancer predisposition. The mutations map to equivalent sites in the proofreading (exonuclease) domain of DNA polymerases ɛ and δ and are predicted to cause a defect in the correction of mispaired bases inserted during DNA replication. In agreement with this prediction, the tumors from mutation carriers were microsatellite stable but tended to acquire base substitution mutations, as confirmed by yeast functional assays. Further analysis of published data showed that the recently described group of hypermutant, microsatellite-stable CRCs is likely to be caused by somatic POLE mutations affecting the exonuclease domain.
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Affiliation(s)
- Claire Palles
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jean-Baptiste Cazier
- Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kimberley M Howarth
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Enric Domingo
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Angela M. Jones
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Peter Broderick
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Zoe Kemp
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sarah L Spain
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Estrella Guarino Almeida
- Dept. of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
| | - Israel Salguero
- Dept. of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
| | - Amy Sherborne
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Daniel Chubb
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Luis G Carvajal-Carmona
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Yusanne Ma
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Kulvinder Kaur
- Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sara Dobbins
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Ella Barclay
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Maggie Gorman
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Lynn Martin
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Michal B Kovac
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Research Group Human Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland
| | - Sean Humphray
- Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK
| | | | | | - Anneke Lucassen
- Wessex Regional Genetics, Princess Anne Hospital, Southampton SO16 5YA UK
| | - Christopher Holmes
- Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Department of Statistics, University of Oxford, South Parks Road, Oxford OX1 3TG, UK
| | - David Bentley
- Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK
| | - Peter Donnelly
- Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Department of Statistics, University of Oxford, South Parks Road, Oxford OX1 3TG, UK
| | - Jenny Taylor
- Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christos Petridis
- Guy’s, King’s, St Thomas’ Cancer Centre, Guy’s Hospital, London SE1 9RT, UK
| | - Rebecca Roylance
- Institute of Cancer, Bart’s and the London Medical School, Queen Mary College, University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Elinor J Sawyer
- Guy’s, King’s, St Thomas’ Cancer Centre, Guy’s Hospital, London SE1 9RT, UK
| | - David J. Kerr
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 7DU, UK
| | - Susan Clark
- Polyposis Registry, Imperial College School of Medicine, St Mark’s Hospital Watford Road, Harrow, HA1 3UJ, UK
| | - Jonathan Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Science Division, Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
| | - Stephen E Kearsey
- Dept. of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
| | - Huw JW Thomas
- Family Cancer Clinic, Imperial College School of Medicine, St Mark’s Hospital Watford Road, Harrow, HA1 3UJ, UK
| | - Gilean McVean
- Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Richard S Houlston
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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145
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Zhou W, Tan Y, Anderson DJ, Crist EM, Ruohola-Baker H, Salipante SJ, Horwitz MS. Use of somatic mutations to quantify random contributions to mouse development. BMC Genomics 2013; 14:39. [PMID: 23327737 PMCID: PMC3564904 DOI: 10.1186/1471-2164-14-39] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 01/11/2013] [Indexed: 01/14/2023] Open
Abstract
Background The C. elegans cell fate map, in which the lineage of its approximately 1000 cells is visibly charted beginning from the zygote, represents a developmental biology milestone. Nematode development is invariant from one specimen to the next, whereas in mammals, aspects of development are probabilistic, and development exhibits variation between even genetically identical individuals. Consequently, a single defined cell fate map applicable to all individuals cannot exist. Results To determine the extent to which patterns of cell lineage are conserved between different mice, we have employed the recently developed method of “phylogenetic fate mapping” to compare cell fate maps in siblings. In this approach, somatic mutations arising in individual cells are used to retrospectively deduce lineage relationships through phylogenetic and—as newly investigated here—related analytical approaches based on genetic distance. We have cataloged genomic mutations at an average of 110 mutation-prone polyguanine (polyG) tracts for about 100 cells clonally isolated from various corresponding tissues of each of two littermates of a hypermutable mouse strain. Conclusions We find that during mouse development, muscle and fat arise from a mixed progenitor cell pool in the germ layer, but, contrastingly, vascular endothelium in brain derives from a smaller source of progenitor cells. Additionally, formation of tissue primordia is marked by establishment of left and right lateral compartments, with restricted cell migration between divisions. We quantitatively demonstrate that development represents a combination of stochastic and deterministic events, offering insight into how chance influences normal development and may give rise to birth defects.
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Affiliation(s)
- Wenyu Zhou
- Department of Pathology, University of Washington, Box 358056, Seattle, WA 98195, USA
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146
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Emergence of DNA polymerase ε antimutators that escape error-induced extinction in yeast. Genetics 2013; 193:751-70. [PMID: 23307893 DOI: 10.1534/genetics.112.146910] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA polymerases (Pols) ε and δ perform the bulk of yeast leading- and lagging-strand DNA synthesis. Both Pols possess intrinsic proofreading exonucleases that edit errors during polymerization. Rare errors that elude proofreading are extended into duplex DNA and excised by the mismatch repair (MMR) system. Strains that lack Pol proofreading or MMR exhibit a 10- to 100-fold increase in spontaneous mutation rate (mutator phenotype), and inactivation of both Pol δ proofreading (pol3-01) and MMR is lethal due to replication error-induced extinction (EEX). It is unclear whether a similar synthetic lethal relationship exists between defects in Pol ε proofreading (pol2-4) and MMR. Using a plasmid-shuffling strategy in haploid Saccharomyces cerevisiae, we observed synthetic lethality of pol2-4 with alleles that completely abrogate MMR (msh2Δ, mlh1Δ, msh3Δ msh6Δ, or pms1Δ mlh3Δ) but not with partial MMR loss (msh3Δ, msh6Δ, pms1Δ, or mlh3Δ), indicating that high levels of unrepaired Pol ε errors drive extinction. However, variants that escape this error-induced extinction (eex mutants) frequently emerged. Five percent of pol2-4 msh2Δ eex mutants encoded second-site changes in Pol ε that reduced the pol2-4 mutator phenotype between 3- and 23-fold. The remaining eex alleles were extragenic to pol2-4. The locations of antimutator amino-acid changes in Pol ε and their effects on mutation spectra suggest multiple mechanisms of mutator suppression. Our data indicate that unrepaired leading- and lagging-strand polymerase errors drive extinction within a few cell divisions and suggest that there are polymerase-specific pathways of mutator suppression. The prevalence of suppressors extragenic to the Pol ε gene suggests that factors in addition to proofreading and MMR influence leading-strand DNA replication fidelity.
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147
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Pachlopnik Schmid J, Lemoine R, Nehme N, Cormier-Daire V, Revy P, Debeurme F, Debré M, Nitschke P, Bole-Feysot C, Legeai-Mallet L, Lim A, de Villartay JP, Picard C, Durandy A, Fischer A, de Saint Basile G. Polymerase ε1 mutation in a human syndrome with facial dysmorphism, immunodeficiency, livedo, and short stature ("FILS syndrome"). ACTA ACUST UNITED AC 2012; 209:2323-30. [PMID: 23230001 PMCID: PMC3526359 DOI: 10.1084/jem.20121303] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Homozygous missense mutations in POLE1 caused an inherited disorder characterized by facial dysmorphism, immunodeficiency, livedo, and short stature. DNA polymerase ε (Polε) is a large, four-subunit polymerase that is conserved throughout the eukaryotes. Its primary function is to synthesize DNA at the leading strand during replication. It is also involved in a wide variety of fundamental cellular processes, including cell cycle progression and DNA repair/recombination. Here, we report that a homozygous single base pair substitution in POLE1 (polymerase ε 1), encoding the catalytic subunit of Polε, caused facial dysmorphism, immunodeficiency, livedo, and short stature (“FILS syndrome”) in a large, consanguineous family. The mutation resulted in alternative splicing in the conserved region of intron 34, which strongly decreased protein expression of Polε1 and also to a lesser extent the Polε2 subunit. We observed impairment in proliferation and G1- to S-phase progression in patients’ T lymphocytes. Polε1 depletion also impaired G1- to S-phase progression in B lymphocytes, chondrocytes, and osteoblasts. Our results evidence the developmental impact of a Polε catalytic subunit deficiency in humans and its causal relationship with a newly recognized, inherited disorder.
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148
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Prindle MJ, Loeb LA. DNA polymerase delta in DNA replication and genome maintenance. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:666-82. [PMID: 23065663 PMCID: PMC3694620 DOI: 10.1002/em.21745] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/09/2012] [Accepted: 09/12/2012] [Indexed: 05/12/2023]
Abstract
The eukaryotic genome is in a constant state of modification and repair. Faithful transmission of the genomic information from parent to daughter cells depends upon an extensive system of surveillance, signaling, and DNA repair, as well as accurate synthesis of DNA during replication. Often, replicative synthesis occurs over regions of DNA that have not yet been repaired, presenting further challenges to genomic stability. DNA polymerase δ (pol δ) occupies a central role in all of these processes: catalyzing the accurate replication of a majority of the genome, participating in several DNA repair synthetic pathways, and contributing structurally to the accurate bypass of problematic lesions during translesion synthesis. The concerted actions of pol δ on the lagging strand, pol ϵ on the leading strand, associated replicative factors, and the mismatch repair (MMR) proteins results in a mutation rate of less than one misincorporation per genome per replication cycle. This low mutation rate provides a high level of protection against genetic defects during development and may prevent the initiation of malignancies in somatic cells. This review explores the role of pol δ in replication fidelity and genome maintenance.
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Affiliation(s)
- Marc J Prindle
- Department of Pathology, The Joseph Gottstien Memorial Cancer Research Laboratory, University of Washington, Seattle, WA 98195-7705, USA
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149
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Menezes MR, Sweasy JB. Mouse models of DNA polymerases. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:645-665. [PMID: 23001998 DOI: 10.1002/em.21731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 08/01/2012] [Accepted: 08/07/2012] [Indexed: 06/01/2023]
Abstract
In 1956, Arthur Kornberg discovered the mechanism of the biological synthesis of DNA and was awarded the Nobel Prize in Physiology or Medicine in 1959 for this contribution, which included the isolation and characterization of Escherichia coli DNA polymerase I. Now there are 15 known DNA polymerases in mammalian cells that belong to four different families. These DNA polymerases function in many different cellular processes including DNA replication, DNA repair, and damage tolerance. Several biochemical and cell biological studies have provoked a further investigation of DNA polymerase function using mouse models in which polymerase genes have been altered using gene-targeting techniques. The phenotypes of mice harboring mutant alleles reveal the prominent role of DNA polymerases in embryogenesis, prevention of premature aging, and cancer suppression.
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Affiliation(s)
- Miriam R Menezes
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
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150
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Waisertreiger ISR, Liston VG, Menezes MR, Kim HM, Lobachev KS, Stepchenkova EI, Tahirov TH, Rogozin IB, Pavlov YI. Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:699-724. [PMID: 23055184 PMCID: PMC3893020 DOI: 10.1002/em.21735] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/13/2012] [Accepted: 08/15/2012] [Indexed: 06/01/2023]
Abstract
The rate of mutations in eukaryotes depends on a plethora of factors and is not immediately derived from the fidelity of DNA polymerases (Pols). Replication of chromosomes containing the anti-parallel strands of duplex DNA occurs through the copying of leading and lagging strand templates by a trio of Pols α, δ and ϵ, with the assistance of Pol ζ and Y-family Pols at difficult DNA template structures or sites of DNA damage. The parameters of the synthesis at a given location are dictated by the quality and quantity of nucleotides in the pools, replication fork architecture, transcription status, regulation of Pol switches, and structure of chromatin. The result of these transactions is a subject of survey and editing by DNA repair.
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Affiliation(s)
- Irina S.-R. Waisertreiger
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Victoria G. Liston
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Miriam R. Menezes
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Hyun-Min Kim
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, U.S.A
| | - Elena I. Stepchenkova
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Saint Petersburg Branch of Vavilov Institute of General Genetics, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
| | - Tahir H. Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
| | - Igor B. Rogozin
- National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, U.S.A
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | - Youri. I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, ESH 7009, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, U.S.A
- Department of Genetics, Saint Petersburg University, Universitetskaya emb. 7/9, St Petersburg, 199034, Russia
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