1
|
Islam SA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, Alexandrov LB. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. CELL GENOMICS 2022; 2:None. [PMID: 36388765 PMCID: PMC9646490 DOI: 10.1016/j.xgen.2022.100179] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 04/10/2022] [Accepted: 08/31/2022] [Indexed: 12/09/2022]
Abstract
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.
Collapse
Affiliation(s)
- S.M. Ashiqul Islam
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yang Wu
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mike Vella
- NVIDIA Corporation, 2788 San Tomas Expressway, Santa Clara, CA 95051, USA
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Jon W. Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Peter Clapham
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sergey Senkin
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Yun Rose Li
- Departments of Radiation Oncology and Cancer Genetics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Laura Riva
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Andreas J. Gruber
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
- Department of Biology, University of Konstanz, Universitaetsstrasse 10, D-78464 Konstanz, Germany
| | - Christopher D. Steele
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | | | - Samuel W. Brady
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David J. Adams
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David C. Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Michael R. Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Steven G. Rozen
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| |
Collapse
|
2
|
DMPC/Chol liposomal copper CX5461 is therapeutically superior to a DSPC/Chol formulation. J Control Release 2022; 345:75-90. [DOI: 10.1016/j.jconrel.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 11/20/2022]
|
3
|
Zhou J, Gelot C, Pantelidou C, Li A, Yücel H, Davis RE, Farkkila A, Kochupurakkal B, Syed A, Shapiro GI, Tainer JA, Blagg BSJ, Ceccaldi R, D’Andrea AD. A first-in-class Polymerase Theta Inhibitor selectively targets Homologous-Recombination-Deficient Tumors. NATURE CANCER 2021; 2:598-610. [PMID: 34179826 PMCID: PMC8224818 DOI: 10.1038/s43018-021-00203-x] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA polymerase theta (POLθ) is synthetic lethal with Homologous Recombination (HR) deficiency and thus a candidate target for HR-deficient cancers. Through high-throughput small molecule screens we identified the antibiotic Novobiocin (NVB) as a specific POLθ inhibitor that selectively kills HR-deficient tumor cells in vitro and in vivo. NVB directly binds to the POLθ ATPase domain, inhibits its ATPase activity, and phenocopies POLθ depletion. NVB kills HR-deficient breast and ovarian tumors in GEMM, xenograft and PDX models. Increased POLθ levels predict NVB sensitivity, and BRCA-deficient tumor cells with acquired resistance to PARP inhibitors (PARPi) are sensitive to NVB in vitro and in vivo. Mechanistically, NVB-mediated cell death in PARPi-resistant cells arises from increased double-strand break end resection, leading to accumulation of single-strand DNA intermediates and non-functional RAD51 foci. Our results demonstrate that NVB may be useful alone or in combination with PARPi in treating HR-deficient tumors, including those with acquired PARPi resistance. (151/150).
Collapse
Affiliation(s)
- Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Camille Gelot
- Inserm U830, PSL Research University, Institut Curie, 75005, Paris, France
| | - Constantia Pantelidou
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Adam Li
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Hatice Yücel
- Inserm U830, PSL Research University, Institut Curie, 75005, Paris, France
| | - Rachel E. Davis
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Anniina Farkkila
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Bose Kochupurakkal
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Aleem Syed
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Geoffrey I. Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John A. Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brian S. J. Blagg
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Raphael Ceccaldi
- Inserm U830, PSL Research University, Institut Curie, 75005, Paris, France.,Corresponding authors: Alan D. D’Andrea, M.D., Director, Susan F. Smith Center for Women’s Cancers (SFSCWC), Director, Center for DNA Damage and Repair, Dana-Farber Cancer Institute, The Fuller-American Cancer Society Professor, Harvard Medical School, Phone: 617-632-2080, , Raphael Ceccaldi, Institut Curie, 75005, Paris, France, Phone: +33 (0)1 56 24 69 49,
| | - Alan D. D’Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA, USA.,Susan F. Smith Center for Women’s Cancers, Dana-Farber Cancer Institute, Boston, MA, USA.,Corresponding authors: Alan D. D’Andrea, M.D., Director, Susan F. Smith Center for Women’s Cancers (SFSCWC), Director, Center for DNA Damage and Repair, Dana-Farber Cancer Institute, The Fuller-American Cancer Society Professor, Harvard Medical School, Phone: 617-632-2080, , Raphael Ceccaldi, Institut Curie, 75005, Paris, France, Phone: +33 (0)1 56 24 69 49,
| |
Collapse
|
4
|
Wang Y, Park JYP, Pacis A, Denroche RE, Jang GH, Zhang A, Cuggia A, Domecq C, Monlong J, Raitses-Gurevich M, Grant RC, Borgida A, Holter S, Stossel C, Bu S, Masoomian M, Lungu IM, Bartlett JM, Wilson JM, Gao ZH, Riazalhosseini Y, Asselah J, Bouganim N, Cabrera T, Boucher LM, Valenti D, Biagi J, Greenwood CM, Polak P, Foulkes WD, Golan T, O'Kane GM, Fischer SE, Knox JJ, Gallinger S, Zogopoulos G. A Preclinical Trial and Molecularly Annotated Patient Cohort Identify Predictive Biomarkers in Homologous Recombination–deficient Pancreatic Cancer. Clin Cancer Res 2020; 26:5462-5476. [DOI: 10.1158/1078-0432.ccr-20-1439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/24/2020] [Accepted: 08/03/2020] [Indexed: 12/27/2022]
Abstract
Abstract
Purpose:
Pancreatic ductal adenocarcinoma (PDAC) arising in patients with a germline BRCA1 or BRCA2 (gBRCA) mutation may be sensitive to platinum and PARP inhibitors (PARPi). However, treatment stratification based on gBRCA mutational status alone is associated with heterogeneous responses.
Experimental Design:
We performed a seven-arm preclinical trial consisting of 471 mice, representing 12 unique PDAC patient-derived xenografts, of which nine were gBRCA mutated. From 179 patients whose PDAC was whole-genome and transcriptome sequenced, we identified 21 cases with homologous recombination deficiency (HRD), and investigated prognostic biomarkers.
Results:
We found that biallelic inactivation of BRCA1/BRCA2 is associated with genomic hallmarks of HRD and required for cisplatin and talazoparib (PARPi) sensitivity. However, HRD genomic hallmarks persisted in xenografts despite the emergence of therapy resistance, indicating the presence of a genomic scar. We identified tumor polyploidy and a low Ki67 index as predictors of poor cisplatin and talazoparib response. In patients with HRD PDAC, tumor polyploidy and a basal-like transcriptomic subtype were independent predictors of shorter survival. To facilitate clinical assignment of transcriptomic subtype, we developed a novel pragmatic two-marker assay (GATA6:KRT17).
Conclusions:
In summary, we propose a predictive and prognostic model of gBRCA-mutated PDAC on the basis of HRD genomic hallmarks, Ki67 index, tumor ploidy, and transcriptomic subtype.
Collapse
Affiliation(s)
- Yifan Wang
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Jin Yong Patrick Park
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Alain Pacis
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 3Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | | | - Gun Ho Jang
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Amy Zhang
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Adeline Cuggia
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Celine Domecq
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Jean Monlong
- 5Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Maria Raitses-Gurevich
- 6Pancreatic Cancer Translational Research Laboratory, Oncology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Robert C. Grant
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Ayelet Borgida
- 8Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Spring Holter
- 8Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Chani Stossel
- 6Pancreatic Cancer Translational Research Laboratory, Oncology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- 9Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Simeng Bu
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Mehdi Masoomian
- 10Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ilinca M. Lungu
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M.S. Bartlett
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 10Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Julie M. Wilson
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Zu-Hua Gao
- 11Department of Pathology, McGill University, Montreal, Quebec, Canada
| | | | - Jamil Asselah
- 12Department of Oncology, McGill University, Montreal, Quebec, Canada
| | | | - Tatiana Cabrera
- 13Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada
| | - Louis-Martin Boucher
- 13Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada
| | - David Valenti
- 13Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada
| | - James Biagi
- 14Department of Oncology, Queen's University, Kingston, Ontario, Canada
| | - Celia M.T. Greenwood
- 5Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- 12Department of Oncology, McGill University, Montreal, Quebec, Canada
- 15Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
- 16Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Paz Polak
- 17Icahn School of Medicine at Mount Sinai Hospital, New York, New York
| | - William D. Foulkes
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- 5Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Talia Golan
- 6Pancreatic Cancer Translational Research Laboratory, Oncology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- 9Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Grainne M. O'Kane
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Sandra E. Fischer
- 10Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer J. Knox
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Steven Gallinger
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - George Zogopoulos
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| |
Collapse
|
5
|
Mladenov E, Staudt C, Soni A, Murmann-Konda T, Siemann-Loekes M, Iliakis G. Strong suppression of gene conversion with increasing DNA double-strand break load delimited by 53BP1 and RAD52. Nucleic Acids Res 2020; 48:1905-1924. [PMID: 31832684 PMCID: PMC7038941 DOI: 10.1093/nar/gkz1167] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/30/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
In vertebrates, genomic DNA double-strand breaks (DSBs) are removed by non-homologous end-joining processes: classical non-homologous end-joining (c-NHEJ) and alternative end-joining (alt-EJ); or by homology-dependent processes: gene-conversion (GC) and single-strand annealing (SSA). Surprisingly, these repair pathways are not real alternative options restoring genome integrity with equal efficiency, but show instead striking differences in speed, accuracy and cell-cycle-phase dependence. As a consequence, engagement of one pathway may be associated with processing-risks for the genome absent from another pathway. Characterization of engagement-parameters and their consequences is, therefore, essential for understanding effects on the genome of DSB-inducing agents, such as ionizing-radiation (IR). Here, by addressing pathway selection in G2-phase, we discover regulatory confinements in GC with consequences for SSA- and c-NHEJ-engagement. We show pronounced suppression of GC with increasing DSB-load that is not due to RAD51 availability and which is delimited but not defined by 53BP1 and RAD52. Strikingly, at low DSB-loads, GC repairs ∼50% of DSBs, whereas at high DSB-loads its contribution is undetectable. Notably, with increasing DSB-load and the associated suppression of GC, SSA gains ground, while alt-EJ is suppressed. These observations explain earlier, apparently contradictory results and advance our understanding of logic and mechanisms underpinning the wiring between DSB repair pathways.
Collapse
Affiliation(s)
- Emil Mladenov
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen, Germany
| | - Christian Staudt
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen, Germany
| | - Aashish Soni
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen, Germany
| | - Tamara Murmann-Konda
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen, Germany
| | - Maria Siemann-Loekes
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen, Germany
| |
Collapse
|
6
|
The spectrum of genetic variants in hereditary pancreatic cancer includes Fanconi anemia genes. Fam Cancer 2019; 17:235-245. [PMID: 28687971 DOI: 10.1007/s10689-017-0019-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Approximately 5-10% of all pancreatic cancer patients carry a predisposing mutation in a known susceptibility gene. Since >90% of patients present with late stage disease, it is crucial to identify high risk individuals who may be amenable to early detection or other prevention. To explore the spectrum of hereditary pancreatic cancer susceptibility, we evaluated germline DNA from pancreatic cancer participants (n = 53) from a large hereditary cancer registry. For those without a known predisposition mutation gene (n = 49), germline next generation sequencing was completed using targeted capture for 706 candidate genes. We identified 16 of 53 participants (30%) with a pathogenic (P) or likely pathogenic (LP) variant that may be related to their hereditary pancreatic cancer predisposition; seven had mutations in genes associated with well-known cancer syndromes (13%) [ATM (2), BRCA2 (3), MSH2 (1), MSH6 (1)]. Many had mutations in Fanconi anemia complex genes [BRCA2 (3 participants), FANCF, FANCM]. Eight participants had rare protein truncating variants of uncertain significance with no other P or LP variants. Earlier age of pancreatic cancer diagnosis (57.5 vs 64.8 years) was indicative of possessing a P or LP variant, as was cancer family history (p values <0.0001). Our multigene panel approach for identifying known cancer predisposing genetic susceptibility in those at risk for hereditary pancreatic cancer may have direct applicability to clinical practice in cases with mutations in actionable genes. Future pancreatic cancer predisposition studies should include evaluation of the Fanconi anemia genes.
Collapse
|
7
|
Zemanek T, Melichar B, Lovecek M, Soucek P, Mohelnikova-Duchonova B. Biomarkers and pathways of chemoresistance and chemosensitivity for personalized treatment of pancreatic adenocarcinoma. Pharmacogenomics 2018; 20:113-127. [PMID: 30539680 DOI: 10.2217/pgs-2018-0073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pancreatic carcinoma is usually diagnosed late when treatment options are limited and is considered a chemo-resistant malignancy. However, early stage, good performance status and specific patient subgroup are thought to have a more favorable prognosis. Search for novel molecular biomarkers, which could predict treatment resistance, represents a major opportunity, but also a challenge in further research. This review summarizes most aspects of individualized therapy of pancreatic cancer including promising biomarkers, BRCA-deficient pancreatic cancer and its etiology. It may be estimated that nearly a third of metastatic pancreatic ductal adenocarcinoma patients could benefit from treatment other than gold standard chemotherapy. Thus, other aspects of an individualized approach concerning the main factors for the choice of the best therapy for individual pancreatic cancer patient (surgery and chemotherapy), as well as the future directions (target therapy and immunotherapy), are also addressed.
Collapse
Affiliation(s)
- Tomas Zemanek
- Department of Oncology, Faculty of Medicine & Dentistry, Palacky University Olomouc, University Hospital Olomouc, Czech Republic
| | - Bohuslav Melichar
- Department of Oncology, Faculty of Medicine & Dentistry, Palacky University Olomouc, University Hospital Olomouc, Czech Republic.,Institute of Molecular & Translational Medicine, Faculty of Medicine & Dentistry, Palacky University, Olomouc, Czech Republic
| | - Martin Lovecek
- Department of Surgery I, Faculty of Medicine & Dentistry, Palacky University, Olomouc, University Hospital Olomouc, Czech Republic
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Beatrice Mohelnikova-Duchonova
- Department of Oncology, Faculty of Medicine & Dentistry, Palacky University Olomouc, University Hospital Olomouc, Czech Republic.,Institute of Molecular & Translational Medicine, Faculty of Medicine & Dentistry, Palacky University, Olomouc, Czech Republic
| |
Collapse
|
8
|
TGF-βRII Knock-down in Pancreatic Cancer Cells Promotes Tumor Growth and Gemcitabine Resistance. Importance of STAT3 Phosphorylation on S727. Cancers (Basel) 2018; 10:cancers10080254. [PMID: 30065235 PMCID: PMC6116183 DOI: 10.3390/cancers10080254] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 01/05/2023] Open
Abstract
Pancreatic adenocarcinoma (PDAC) is one of the most deadly cancers in the Western world because of a lack of early diagnostic markers and efficient therapeutics. At the time of diagnosis, more than 80% of patients have metastasis or locally advanced cancer and are therefore not eligible for surgical resection. Pancreatic cancer cells also harbour a high resistance to chemotherapeutic drugs such as gemcitabine that is one of the main palliative treatments for PDAC. Proteins involved in TGF-β signaling pathway (SMAD4 or TGF-βRII) are frequently mutated in PDAC (50–80%). TGF-β signalling pathway plays antagonistic roles during carcinogenesis by initially inhibiting epithelial growth and later promoting the progression of advanced tumors and thus emerged as both tumor suppressor and oncogenic pathways. In order to decipher the role of TGF-β in pancreatic carcinogenesis and chemoresistance, we generated CAPAN-1 and CAPAN-2 cell lines knocked down for TGF-βRII (first actor of TGF-β signaling). The impact on biological properties of these TGF-βRII-KD cells was studied both in vitro and in vivo. We show that TGF-βRII silencing alters tumor growth and migration as well as resistance to gemcitabine. TGF-βRII silencing also leads to S727 STAT3 and S63 c-Jun phosphorylation, decrease of MRP3 and increase of MRP4 ABC transporter expression and induction of a partial EMT phenotype. These markers associated with TGF-β signaling pathways may thus appear as potent therapeutic tools to better treat/manage pancreatic cancer.
Collapse
|
9
|
Chatterjee G, Jimenez-Sainz J, Presti T, Nguyen T, Jensen RB. Distinct binding of BRCA2 BRC repeats to RAD51 generates differential DNA damage sensitivity. Nucleic Acids Res 2016; 44:5256-70. [PMID: 27084934 PMCID: PMC4914107 DOI: 10.1093/nar/gkw242] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/29/2016] [Indexed: 01/01/2023] Open
Abstract
BRCA2 is a multi-faceted protein critical for the proper regulation of homology-directed repair of DNA double-strand breaks. Elucidating the mechanistic features of BRCA2 is crucial for understanding homologous recombination and how patient-derived mutations impact future cancer risk. Eight centrally located BRC repeats in BRCA2 mediate binding and regulation of RAD51 on resected DNA substrates. Herein, we dissect the biochemical and cellular features of the BRC repeats tethered to the DNA binding domain of BRCA2. To understand how the BRC repeats and isolated domains of BRCA2 contribute to RAD51 binding, we analyzed both the biochemical and cellular properties of these proteins. In contrast to the individual BRC repeat units, we find that the BRC5-8 region potentiates RAD51-mediated DNA strand pairing and provides complementation functions exceeding those of BRC repeats 1-4. Furthermore, BRC5-8 can efficiently repair nuclease-induced DNA double-strand breaks and accelerate the assembly of RAD51 repair complexes upon DNA damage. These findings highlight the importance of the BRC5-8 domain in stabilizing the RAD51 filament and promoting homology-directed repair under conditions of cellular DNA damage.
Collapse
Affiliation(s)
- Gouri Chatterjee
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Judit Jimenez-Sainz
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Thomas Presti
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Tiffany Nguyen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| |
Collapse
|
10
|
Francis JC, Melchor L, Campbell J, Kendrick H, Wei W, Armisen-Garrido J, Assiotis I, Chen L, Kozarewa I, Fenwick K, Swain A, Smalley MJ, Lord CJ, Ashworth A. Whole-exome DNA sequence analysis of Brca2- and Trp53-deficient mouse mammary gland tumours. J Pathol 2015; 236:186-200. [PMID: 25692405 DOI: 10.1002/path.4517] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 02/03/2015] [Accepted: 02/11/2015] [Indexed: 01/08/2023]
Abstract
Germline mutations in the tumour suppressor BRCA2 predispose to breast, ovarian and a number of other human cancers. Brca2-deficient mouse models are used for preclinical studies but the pattern of genomic alterations in these tumours has not yet been described in detail. We have performed whole-exome DNA sequencing analysis of mouse mammary tumours from Blg-Cre Brca2(f/f) Trp53(f/f) animals, a model of BRCA2-deficient human cancer. We also used the sequencing data to estimate DNA copy number alterations in these tumours and identified a recurrent copy number gain in Met, which has been found amplified in other mouse mammary cancer models. Through a comparative genomic analysis, we identified several mouse Blg-Cre Brca2(f/f) Trp53(f/f) mammary tumour somatic mutations in genes that are also mutated in human cancer, but few of these genes have been found frequently mutated in human breast cancer. A more detailed analysis of these somatic mutations revealed a set of genes that are mutated in human BRCA2 mutant breast and ovarian tumours and that are also mutated in mouse Brca2-null, Trp53-null mammary tumours. Finally, a DNA deletion surrounded by microhomology signature found in human BRCA1/2-deficient cancers was not common in the genome of these mouse tumours. Although a useful model, there are some differences in the genomic landscape of tumours arising in Blg-Cre Brca2(f/f) Trp53(f/f) mice compared to human BRCA-mutated breast cancers. Therefore, this needs to be taken into account in the use of this model.
Collapse
MESH Headings
- Animals
- Antigens, CD/genetics
- Breast Neoplasms/genetics
- Chromosomal Proteins, Non-Histone/genetics
- DNA Copy Number Variations/genetics
- DNA, Neoplasm/genetics
- Disease Models, Animal
- Female
- Gene Knockout Techniques
- Genes, BRCA2/physiology
- Germ-Line Mutation/genetics
- Humans
- Mammary Neoplasms, Experimental/genetics
- Mice, Transgenic
- Mutation, Missense/genetics
- Ovarian Neoplasms/genetics
- Protein Serine-Threonine Kinases/genetics
- Receptors, Immunologic/genetics
- Sequence Analysis, DNA
- Signaling Lymphocytic Activation Molecule Family
- Tumor Suppressor Protein p53/deficiency
Collapse
Affiliation(s)
- Jeffrey C Francis
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK
| | - Lorenzo Melchor
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
| | - James Campbell
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK
| | - Howard Kendrick
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
| | - Wenbin Wei
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK
| | | | | | - Lina Chen
- Tumour Profiling Unit, Institute of Cancer Research, London, UK
| | - Iwanka Kozarewa
- Tumour Profiling Unit, Institute of Cancer Research, London, UK
| | - Kerry Fenwick
- Tumour Profiling Unit, Institute of Cancer Research, London, UK
| | - Amanda Swain
- Tumour Profiling Unit, Institute of Cancer Research, London, UK
| | - Matthew J Smalley
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
| | - Christopher J Lord
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
- The CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK
| |
Collapse
|
11
|
Scourzic L, Mouly E, Bernard OA. TET proteins and the control of cytosine demethylation in cancer. Genome Med 2015; 7:9. [PMID: 25632305 PMCID: PMC4308928 DOI: 10.1186/s13073-015-0134-6] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The discovery that ten-eleven translocation (TET) proteins are α-ketoglutarate-dependent dioxygenases involved in the conversion of 5-methylcytosines (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine and 5-carboxycytosine has revealed new pathways in the cytosine methylation and demethylation process. The description of inactivating mutations in TET2 suggests that cellular transformation is in part caused by the deregulation of this 5-mC conversion. The direct and indirect deregulation of methylation control through mutations in DNA methyltransferase and isocitrate dehydrogenase (IDH) genes, respectively, along with the importance of cytosine methylation in the control of normal and malignant cellular differentiation have provided a conceptual framework for understanding the early steps in cancer development. Here, we review recent advances in our understanding of the cytosine methylation cycle and its implication in cellular transformation, with an emphasis on TET enzymes and 5-hmC. Ongoing clinical trials targeting the activity of mutated IDH enzymes provide a proof of principle that DNA methylation is targetable, and will trigger further therapeutic applications aimed at controlling both early and late stages of cancer development.
Collapse
Affiliation(s)
- Laurianne Scourzic
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
| | - Enguerran Mouly
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
| | - Olivier A Bernard
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
| |
Collapse
|
12
|
Exome-wide somatic microsatellite variation is altered in cells with DNA repair deficiencies. PLoS One 2014; 9:e110263. [PMID: 25402475 PMCID: PMC4234249 DOI: 10.1371/journal.pone.0110263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/18/2014] [Indexed: 11/19/2022] Open
Abstract
Microsatellites (MST), tandem repeats of 1–6 nucleotide motifs, are mutational hot-spots with a bias for insertions and deletions (INDELs) rather than single nucleotide polymorphisms (SNPs). The majority of MST instability studies are limited to a small number of loci, the Bethesda markers, which are only informative for a subset of colorectal cancers. In this paper we evaluate non-haplotype alleles present within next-gen sequencing data to evaluate somatic MST variation (SMV) within DNA repair proficient and DNA repair defective cell lines. We confirm that alleles present within next-gen data that do not contribute to the haplotype can be reliably quantified and utilized to evaluate the SMV without requiring comparisons of matched samples. We observed that SMV patterns found in DNA repair proficient cell lines without DNA repair defects, MCF10A, HEK293 and PD20 RV:D2, had consistent patterns among samples. Further, we were able to confirm that changes in SMV patterns in cell lines lacking functional BRCA2, FANCD2 and mismatch repair were consistent with the different pathways perturbed. Using this new exome sequencing analysis approach we show that DNA instability can be identified in a sample and that patterns of instability vary depending on the impaired DNA repair mechanism, and that genes harboring minor alleles are strongly associated with cancer pathways. The MST Minor Allele Caller used for this study is available at https://github.com/zalmanv/MST_minor_allele_caller.
Collapse
|
13
|
Natrajan R, Mackay A, Lambros MB, Weigelt B, Wilkerson PM, Manie E, Grigoriadis A, A’Hern R, van der Groep P, Kozarewa I, Popova T, Mariani O, Turaljic S, Furney SJ, Marais R, Rodruigues DN, Flora AC, Wai P, Pawar V, McDade S, Carroll J, Stoppa-Lyonnet D, Green AR, Ellis IO, Swanton C, van Diest P, Delattre O, Lord CJ, Foulkes WD, Vincent-Salomon A, Ashworth A, Stern MH, Reis-Filho JS. A whole-genome massively parallel sequencing analysis of BRCA1 mutant oestrogen receptor-negative and -positive breast cancers. J Pathol 2012; 227:29-41. [PMID: 22362584 PMCID: PMC4976800 DOI: 10.1002/path.4003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 01/29/2012] [Accepted: 01/31/2012] [Indexed: 12/12/2022]
Abstract
BRCA1 encodes a tumour suppressor protein that plays pivotal roles in homologous recombination (HR) DNA repair, cell-cycle checkpoints, and transcriptional regulation. BRCA1 germline mutations confer a high risk of early-onset breast and ovarian cancer. In more than 80% of cases, tumours arising in BRCA1 germline mutation carriers are oestrogen receptor (ER)-negative; however, up to 15% are ER-positive. It has been suggested that BRCA1 ER-positive breast cancers constitute sporadic cancers arising in the context of a BRCA1 germline mutation rather than being causally related to BRCA1 loss-of-function. Whole-genome massively parallel sequencing of ER-positive and ER-negative BRCA1 breast cancers, and their respective germline DNAs, was used to characterize the genetic landscape of BRCA1 cancers at base-pair resolution. Only BRCA1 germline mutations, somatic loss of the wild-type allele, and TP53 somatic mutations were recurrently found in the index cases. BRCA1 breast cancers displayed a mutational signature consistent with that caused by lack of HR DNA repair in both ER-positive and ER-negative cases. Sequencing analysis of independent cohorts of hereditary BRCA1 and sporadic non-BRCA1 breast cancers for the presence of recurrent pathogenic mutations and/or homozygous deletions found in the index cases revealed that DAPK3, TMEM135, KIAA1797, PDE4D, and GATA4 are potential additional drivers of breast cancers. This study demonstrates that BRCA1 pathogenic germline mutations coupled with somatic loss of the wild-type allele are not sufficient for hereditary breast cancers to display an ER-negative phenotype, and has led to the identification of three potential novel breast cancer genes (ie DAPK3, TMEM135, and GATA4).
Collapse
Affiliation(s)
- Rachael Natrajan
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| | - Alan Mackay
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| | - Maryou B Lambros
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| | - Britta Weigelt
- Signal Transduction Laboratory, Cancer Research UK London Research
Institute, WC2A 3LY, UK
| | - Paul M Wilkerson
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| | - Elodie Manie
- Institut Curie, INSERM U830, 75248 Paris, France
| | - Anita Grigoriadis
- Breakthrough Research Unit, Bermondsey Wing, Guy’s Hospital,
London, SE1 9RT, UK
| | - Roger A’Hern
- CRUK Clinical Trials Unit, The Institute of Cancer Research, Sutton,
SM2 5NG, UK
| | | | - Iwanka Kozarewa
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| | | | - Odette Mariani
- Institut Curie, Department of Tumour Biology, 75248 Paris,
France
| | - Samra Turaljic
- Signal Transduction Team, Division of Cell and Molecular Biology,
The Institute of Cancer Research, London, SW3 6JB, UK
| | - Simon J Furney
- Signal Transduction Team, Division of Cell and Molecular Biology,
The Institute of Cancer Research, London, SW3 6JB, UK
| | - Richard Marais
- Signal Transduction Team, Division of Cell and Molecular Biology,
The Institute of Cancer Research, London, SW3 6JB, UK
| | - Daniel-Nava Rodruigues
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| | - Adriana C Flora
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| | - Patty Wai
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| | - Vidya Pawar
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| | - Simon McDade
- Centre for Cancer Research and Cell Biology, Queen’s
University, Belfast, BT9 7BL, Northern Ireland, UK
| | - Jason Carroll
- Nuclear Receptor Transcription Laboratory, Cancer Research UK
Cambridge Research Institute, Cambridge, CB2 0RE, UK
| | - Dominique Stoppa-Lyonnet
- Institut Curie, INSERM U830, 75248 Paris, France
- Institut Curie, Department of Tumour Biology, 75248 Paris,
France
| | - Andrew R Green
- Department of Histopathology, School of Molecular Medical Sciences,
University of Nottingham and Nottingham University Hospitals Trust, Nottingham, NG7
2UH, UK
| | - Ian O Ellis
- Department of Histopathology, School of Molecular Medical Sciences,
University of Nottingham and Nottingham University Hospitals Trust, Nottingham, NG7
2UH, UK
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK
London Research Institute, WC2A 3LY, UK
- UCL Cancer Institute, Huntley Street, London WC1E 6DD, UK
| | - Paul van Diest
- University Medical Centre Utrecht, 3584 CX Utrecht, The
Netherlands
| | | | - Christopher J Lord
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| | - William D Foulkes
- Program in Cancer Genetics, Departments of Human Genetics and
Oncology, McGill University, Montreal, QC, H2W 1S6, Canada
| | - Anne Vincent-Salomon
- Institut Curie, INSERM U830, 75248 Paris, France
- Institut Curie, Department of Tumour Biology, 75248 Paris,
France
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| | - Marc Henri Stern
- Institut Curie, INSERM U830, 75248 Paris, France
- Institut Curie, Department of Tumour Biology, 75248 Paris,
France
| | - Jorge S Reis-Filho
- The Breakthrough Breast Cancer Research Centre, The Institute of
Cancer Research, London, SW3 6JB, UK
| |
Collapse
|
14
|
Kozarewa I, Rosa-Rosa JM, Wardell CP, Walker BA, Fenwick K, Assiotis I, Mitsopoulos C, Zvelebil M, Morgan GJ, Ashworth A, J. C. A modified method for whole exome resequencing from minimal amounts of starting DNA. PLoS One 2012; 7:e32617. [PMID: 22403682 PMCID: PMC3293839 DOI: 10.1371/journal.pone.0032617] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Accepted: 01/30/2012] [Indexed: 01/09/2023] Open
Abstract
Next generation DNA sequencing (NGS) technologies have revolutionized the pace at which whole genome and exome sequences can be generated. However, despite these advances, many of the methods for targeted resequencing, such as the generation of high-depth exome sequences, are somewhat limited by the relatively large amounts of starting DNA that are normally required. In the case of tumour analysis this is particularly pertinent as many tumour biopsies often return submicrogram quantities of DNA, especially when tumours are microdissected prior to analysis. Here, we present a method for exome capture and resequencing using as little as 50 ng of starting DNA. The sequencing libraries generated by this minimal starting amount (MSA-Cap) method generate datasets that are comparable to standard amount (SA) whole exome libraries that use three micrograms of starting DNA. This method, which can be performed in most laboratories using commonly available reagents, has the potential to enhance large scale profiling efforts such as the resequencing of tumour exomes.
Collapse
Affiliation(s)
- Iwanka Kozarewa
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Juan Manuel Rosa-Rosa
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Christopher P. Wardell
- Haemato-Oncology Research Unit, The Institute of Cancer Research, Sutton, United Kingdom
| | - Brian A. Walker
- Haemato-Oncology Research Unit, The Institute of Cancer Research, Sutton, United Kingdom
| | - Kerry Fenwick
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Ioannis Assiotis
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Costas Mitsopoulos
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Marketa Zvelebil
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Gareth J. Morgan
- Haemato-Oncology Research Unit, The Institute of Cancer Research, Sutton, United Kingdom
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- Cancer Research UK, Gene Function Group, The Institute of Cancer Research, London, United Kingdom
| | - Christopher J.
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
- * E-mail:
| |
Collapse
|
15
|
Abstract
Genomic instability is one of the most pervasive characteristics of tumour cells and is probably the combined effect of DNA damage, tumour-specific DNA repair defects, and a failure to stop or stall the cell cycle before the damaged DNA is passed on to daughter cells. Although these processes drive genomic instability and ultimately the disease process, they also provide therapeutic opportunities. A better understanding of the cellular response to DNA damage will not only inform our knowledge of cancer development but also help to refine the classification as well as the treatment of the disease.
Collapse
Affiliation(s)
- Christopher J Lord
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK.
| | | |
Collapse
|