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Luen SJ, Viale G, Nik-Zainal S, Savas P, Kammler R, Dell'Orto P, Biasi O, Degasperi A, Brown LC, Láng I, MacGrogan G, Tondini C, Bellet M, Villa F, Bernardo A, Ciruelos E, Karlsson P, Neven P, Climent M, Müller B, Jochum W, Bonnefoi H, Martino S, Davidson NE, Geyer C, Chia SK, Ingle JN, Coleman R, Solbach C, Thürlimann B, Colleoni M, Coates AS, Goldhirsch A, Fleming GF, Francis PA, Speed TP, Regan MM, Loi S. Genomic characterisation of hormone receptor-positive breast cancer arising in very young women. Ann Oncol 2023; 34:397-409. [PMID: 36709040 PMCID: PMC10619213 DOI: 10.1016/j.annonc.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/14/2022] [Accepted: 01/15/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Very young premenopausal women diagnosed with hormone receptor-positive, human epidermal growth factor receptor 2-negative (HR+HER2-) early breast cancer (EBC) have higher rates of recurrence and death for reasons that remain largely unexplained. PATIENTS AND METHODS Genomic sequencing was applied to HR+HER2- tumours from patients enrolled in the Suppression of Ovarian Function Trial (SOFT) to determine genomic drivers that are enriched in young premenopausal women. Genomic alterations were characterised using next-generation sequencing from a subset of 1276 patients (deep targeted sequencing, n = 1258; whole-exome sequencing in a young-age, case-control subsample, n = 82). We defined copy number (CN) subgroups and assessed for features suggestive of homologous recombination deficiency (HRD). Genomic alteration frequencies were compared between young premenopausal women (<40 years) and older premenopausal women (≥40 years), and assessed for associations with distant recurrence-free interval (DRFI) and overall survival (OS). RESULTS Younger women (<40 years, n = 359) compared with older women (≥40 years, n = 917) had significantly higher frequencies of mutations in GATA3 (19% versus 16%) and CN amplifications (CNAs) (47% versus 26%), but significantly lower frequencies of mutations in PIK3CA (32% versus 47%), CDH1 (3% versus 9%), and MAP3K1 (7% versus 12%). Additionally, they had significantly higher frequencies of features suggestive of HRD (27% versus 21%) and a higher proportion of PIK3CA mutations with concurrent CNAs (23% versus 11%). Genomic features suggestive of HRD, PIK3CA mutations with CNAs, and CNAs were associated with significantly worse DRFI and OS compared with those without these features. These poor prognostic features were enriched in younger patients: present in 72% of patients aged <35 years, 54% aged 35-39 years, and 40% aged ≥40 years. Poor prognostic features [n = 584 (46%)] versus none [n = 692 (54%)] had an 8-year DRFI of 84% versus 94% and OS of 88% versus 96%. Younger women (<40 years) had the poorest outcomes: 8-year DRFI 74% versus 85% and OS 80% versus 93%, respectively. CONCLUSION These results provide insights into genomic alterations that are enriched in young women with HR+HER2- EBC, provide rationale for genomic subgrouping, and highlight priority molecular targets for future clinical trials.
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Affiliation(s)
- S J Luen
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - G Viale
- International Breast Cancer Study Group Central Pathology Office, IEO European Institute of Oncology IRCCS, University of Milan, Milan, Italy
| | - S Nik-Zainal
- Department of Medical Genetics & MRC Cancer Unit, The Clinical School, University of Cambridge, Cambridge, UK
| | - P Savas
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - R Kammler
- International Breast Cancer Study Group, Coordinating Center, Central Pathology Office, Bern, Switzerland
| | - P Dell'Orto
- International Breast Cancer Study Group Central Pathology Office, Department of Pathology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - O Biasi
- Division of Pathology and Laboratory Medicine, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - A Degasperi
- Department of Medical Genetics & MRC Cancer Unit, The Clinical School, University of Cambridge, Cambridge, UK
| | - L C Brown
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - I Láng
- Istenhegyi Health Center Oncology Clinic, National Institute of Oncology, Budapest, Hungary
| | - G MacGrogan
- Biopathology Department, Institut Bergonié Comprehensive Cancer Centre, Bordeaux, France
| | - C Tondini
- Osp. Papa Giovanni XXIII, Bergamo, Italy
| | - M Bellet
- Vall d'Hebron Institute of Oncology (VHIO) and Vall d'Hebron University Hospital, Barcelona, Spain
| | - F Villa
- Oncology Unit, Department of Oncology, Alessandro Manzoni Hospital, ASST Lecco, Lecco, Italy
| | - A Bernardo
- ICS Maugeri IRCCS, Medical Oncology Unit of Pavia Institute, Italy
| | - E Ciruelos
- University Hospital 12 de Octubre, Madrid, Spain
| | - P Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - P Neven
- Gynecologic Oncology and Multidisciplinary Breast Center, University Hospitals UZ-Leuven, KU Leuven, Leuven, Belgium
| | - M Climent
- Instituto Valenciano de Oncologia, Valencia, Spain
| | - B Müller
- Chilean Cooperative Group for Oncologic Research (GOCCHI), Santiago, Chile
| | - W Jochum
- Institute of Pathology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland; Swiss Group for Clinical Cancer Research (SAKK), Berne, Switzerland
| | - H Bonnefoi
- Institut Bergonié Comprehensive Cancer Centre, Université de Bordeaux, INSERM U1218, Bordeaux, France; European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
| | - S Martino
- The Angeles Clinic and Research Institute, Santa Monica, USA
| | - N E Davidson
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, USA
| | - C Geyer
- Houston Methodist Cancer Center, NRG Oncology, Houston, USA
| | - S K Chia
- BC Cancer and Canadian Cancer Trials Group, Vancouver, Canada
| | - J N Ingle
- Mayo Clinic, Rochester, Minnesota, USA
| | - R Coleman
- National Institute for Health Research (NIHR) Cancer Research Network, University of Sheffield, Sheffield, UK
| | - C Solbach
- Breast Center, University Hospital, Goethe University Frankfurt, Frankfurt, Germany
| | - B Thürlimann
- Swiss Group for Clinical Cancer Research (SAKK), Berne, Switzerland; Breast Center, Kantonsspital, St. Gallen, Switzerland
| | - M Colleoni
- Division of Medical Senology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - A S Coates
- International Breast Cancer Study Group and University of Sydney, Sydney, Australia
| | - A Goldhirsch
- International Breast Cancer Study Group (IBCSG), Bern Switzerland and IEO European Institute of Oncology IRCCS, Milan, Italy
| | - G F Fleming
- Section of Hematology Oncology, The University of Chicago, Chicago, USA
| | - P A Francis
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - T P Speed
- Bioinformatics Division, Walter and Eliza Hall Institute, Melbourne, Australia
| | - M M Regan
- Division of Biostatistics, International Breast Cancer Study Group Statistical Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - S Loi
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.
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Nik-Zainal S. Abstract MS1-2: Genomics of DNA repair defects in breast cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-ms1-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
While driver mutations in cancer genomes were the focus of cancer research for a long time, passenger mutational signatures - the imprints of DNA damage and DNA repair processes that have been operative during tumorigenesis - are also biologically informative. In this lecture, I provide an update of what has been uncovered in breast cancers in relation to genomic imprints of DNA repair defects and showcase how we have developed computational applications that we hope to translate toward clinical utility.
Citation Format: S Nik-Zainal. Genomics of DNA repair defects in breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr MS1-2.
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Affiliation(s)
- S Nik-Zainal
- University of Cambridge, Cambridge, United Kingdom
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3
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Guffanti F, Alvisi MF, Anastasia A, Ricci F, Chiappa M, Llop-Guevara A, Serra V, Fruscio R, Degasperi A, Nik-Zainal S, Bani MR, Lupia M, Giavazzi R, Rulli E, Damia G. Basal expression of RAD51 foci predicts olaparib response in patient-derived ovarian cancer xenografts. Br J Cancer 2022; 126:120-128. [PMID: 34732853 PMCID: PMC8727677 DOI: 10.1038/s41416-021-01609-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/07/2021] [Accepted: 10/21/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The search for biomarkers to evaluate ovarian cancer (OC) homologous recombination (HR) function and predict the response to therapy is an urgent clinical need to improve the selection of patients who could benefit from platinum- and olaparib (poly-ADP ribose polymerase inhibitors, PARPi)-based therapies. METHODS We used a large collection of OC patient-derived xenografts (PDXs) (n = 47) and evaluated their HR status based on BRCA1/2 mutations, BRCA1 promoter methylation and the HRDetect score. RAD51 foci were quantified in formalin-fixed, paraffin-embedded untreated tumour specimens by immunofluorescence and the messenger RNA expression of 21 DNA repair genes by real-time PCR. RESULTS Tumour HR deficiency predicted both platinum and olaparib responses. The basal level of RAD51 foci evaluated in geminin-positive/replicating cells strongly inversely correlated with olaparib response (p = 0.011); in particular, the lower the foci score, the greater the sensitivity to olaparib, while low RAD51 foci score seems to associate with platinum activity. CONCLUSIONS The basal RAD51 foci score is a candidate predictive biomarker of olaparib response in OC patients as it can be easily translatable in a clinical setting. Moreover, the findings corroborate the importance of OC-PDXs as a reliable tool to identify and validate biomarkers of response to therapy.
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Affiliation(s)
- F. Guffanti
- grid.4527.40000000106678902Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - M F Alvisi
- grid.4527.40000000106678902Laboratory of Methodology for Clinical Research, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - A. Anastasia
- grid.4527.40000000106678902Laboratory of Cancer Metastasis Therapeutics, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - F. Ricci
- grid.4527.40000000106678902Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - M. Chiappa
- grid.4527.40000000106678902Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - A. Llop-Guevara
- grid.411083.f0000 0001 0675 8654Experimental Therapeutics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - V. Serra
- grid.411083.f0000 0001 0675 8654Experimental Therapeutics Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - R. Fruscio
- grid.7563.70000 0001 2174 1754Clinic of Obstetrics and Gynecology, Department of Medicine and Surgery, San Gerardo Hospital, University of Milan Bicocca, Monza, Italy
| | - A. Degasperi
- grid.5335.00000000121885934MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ UK ,grid.120073.70000 0004 0622 5016Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke’s Treatment Centre, Addenbrooke’s Hospital, Box 238, Cambridge, CB2 0QQ UK
| | - S. Nik-Zainal
- grid.5335.00000000121885934MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ UK ,grid.120073.70000 0004 0622 5016Academic Laboratory of Medical Genetics, Lv 6 Addenbrooke’s Treatment Centre, Addenbrooke’s Hospital, Box 238, Cambridge, CB2 0QQ UK
| | - M R Bani
- grid.4527.40000000106678902Laboratory of Cancer Metastasis Therapeutics, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - M. Lupia
- grid.15667.330000 0004 1757 0843Unit of Gynecological Oncology Research, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - R. Giavazzi
- grid.4527.40000000106678902Laboratory of Cancer Metastasis Therapeutics, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - E. Rulli
- grid.4527.40000000106678902Laboratory of Methodology for Clinical Research, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - G. Damia
- grid.4527.40000000106678902Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
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Serra Elizalde V, Llop-Guevara A, Pearson A, Cruz C, Castroviejo-Bermejo M, Chopra N, Tovey H, Toms C, Kriplani D, Gevensleben H, Roylance R, Chan S, Tutt A, Skene A, Evans A, Davies H, Bliss J, Nik-Zainal S, Balmaña J, Turner N. 1O Detection of homologous recombination repair deficiency (HRD) in treatment-naive early triple-negative breast cancer (TNBC) by RAD51 foci and comparison with DNA-based tests. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Miller RE, Leary A, Scott CL, Serra V, Lord CJ, Bowtell D, Chang DK, Garsed DW, Jonkers J, Ledermann JA, Nik-Zainal S, Ray-Coquard I, Shah SP, Matias-Guiu X, Swisher EM, Yates LR. ESMO recommendations on predictive biomarker testing for homologous recombination deficiency and PARP inhibitor benefit in ovarian cancer. Ann Oncol 2020; 31:1606-1622. [PMID: 33004253 DOI: 10.1016/j.annonc.2020.08.2102] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Homologous recombination repair deficiency (HRD) is a frequent feature of high-grade serous ovarian, fallopian tube and peritoneal carcinoma (HGSC) and is associated with sensitivity to PARP inhibitor (PARPi) therapy. HRD testing provides an opportunity to optimise PARPi use in HGSC but methodologies are diverse and clinical application remains controversial. MATERIALS AND METHODS To define best practice for HRD testing in HGSC the ESMO Translational Research and Precision Medicine Working Group launched a collaborative project that incorporated a systematic review approach. The main aims were to (i) define the term 'HRD test'; (ii) provide an overview of the biological rationale and the level of evidence supporting currently available HRD tests; (iii) provide recommendations on the clinical utility of HRD tests in clinical management of HGSC. RESULTS A broad range of repair genes, genomic scars, mutational signatures and functional assays are associated with a history of HRD. Currently, the clinical validity of HRD tests in ovarian cancer is best assessed, not in terms of biological HRD status per se, but in terms of PARPi benefit. Clinical trials evidence supports the use of BRCA mutation testing and two commercially available assays that also incorporate genomic instability for identifying subgroups of HGSCs that derive different magnitudes of benefit from PARPi therapy, albeit with some variation by clinical scenario. These tests can be used to inform treatment selection and scheduling but their use is limited by a failure to consistently identify a subgroup of patients who derive no benefit from PARPis in most studies. Existing tests lack negative predictive value and inadequately address the complex and dynamic nature of the HRD phenotype. CONCLUSIONS Currently available HRD tests are useful for predicting likely magnitude of benefit from PARPis but better biomarkers are urgently needed to better identify current homologous recombination proficiency status and stratify HGSC management.
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Affiliation(s)
- R E Miller
- Department of Medical Oncology, University College London, London, UK; Department of Medical Oncology, St Bartholomew's Hospital, London, UK
| | - A Leary
- Department of Medicine and INSERM U981, Gustave Roussy Cancer Center, Université Paris-Saclay, Paris, France
| | - C L Scott
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | - V Serra
- Experimental Therapeutics Group Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - C J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - D Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | - D K Chang
- Glasgow Precision Oncology Laboratory, Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - D W Garsed
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | - J Jonkers
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J A Ledermann
- UCL Cancer Institute, University College London, London, UK
| | - S Nik-Zainal
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK; MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - I Ray-Coquard
- Centre Leon Berard, Lyon, France; University Claude Bernard Groupe University of Lyon, France
| | - S P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - X Matias-Guiu
- Departments of Pathology, Hospital U Arnau de Vilanova and Hospital U de Bellvitge, Universities of Lleida and Barcelona, Irblleida, Idibell, Ciberonc, Barcelona, Spain
| | - E M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - L R Yates
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge; Guy's Cancer Centre, Guys and St Thomas' NHS Foundation Trust, London, UK.
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7
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Nones K, Johnson J, Newell F, Patch AM, Thorne H, Kazakoff SH, de Luca XM, Parsons MT, Ferguson K, Reid LE, McCart Reed AE, Srihari S, Lakis V, Davidson AL, Mukhopadhyay P, Holmes O, Xu Q, Wood S, Leonard C, Beesley J, Harris JM, Barnes D, Degasperi A, Ragan MA, Spurdle AB, Khanna KK, Lakhani SR, Pearson JV, Nik-Zainal S, Chenevix-Trench G, Waddell N, Simpson PT. Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers. Ann Oncol 2019; 30:1071-1079. [PMID: 31090900 PMCID: PMC6637375 DOI: 10.1093/annonc/mdz132] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) is a powerful method for revealing the diversity and complexity of the somatic mutation burden of tumours. Here, we investigated the utility of tumour and matched germline WGS for understanding aetiology and treatment opportunities for high-risk individuals with familial breast cancer. PATIENTS AND METHODS We carried out WGS on 78 paired germline and tumour DNA samples from individuals carrying pathogenic variants in BRCA1 (n = 26) or BRCA2 (n = 22) or from non-carriers (non-BRCA1/2; n = 30). RESULTS Matched germline/tumour WGS and somatic mutational signature analysis revealed patients with unreported, dual pathogenic germline variants in cancer risk genes (BRCA1/BRCA2; BRCA1/MUTYH). The strategy identified that 100% of tumours from BRCA1 carriers and 91% of tumours from BRCA2 carriers exhibited biallelic inactivation of the respective gene, together with somatic mutational signatures suggestive of a functional deficiency in homologous recombination. A set of non-BRCA1/2 tumours also had somatic signatures indicative of BRCA-deficiency, including tumours with BRCA1 promoter methylation, and tumours from carriers of a PALB2 pathogenic germline variant and a BRCA2 variant of uncertain significance. A subset of 13 non-BRCA1/2 tumours from early onset cases were BRCA-proficient, yet displayed complex clustered structural rearrangements associated with the amplification of oncogenes and pathogenic germline variants in TP53, ATM and CHEK2. CONCLUSIONS Our study highlights the role that WGS of matched germline/tumour DNA and the somatic mutational signatures can play in the discovery of pathogenic germline variants and for providing supporting evidence for variant pathogenicity. WGS-derived signatures were more robust than germline status and other genomic predictors of homologous recombination deficiency, thus impacting the selection of platinum-based or PARP inhibitor therapy. In this first examination of non-BRCA1/2 tumours by WGS, we illustrate the considerable heterogeneity of these tumour genomes and highlight that complex genomic rearrangements may drive tumourigenesis in a subset of cases.
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Affiliation(s)
- K Nones
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J Johnson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - F Newell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - A M Patch
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - H Thorne
- kConFab Investigators, The Peter MacCallum Cancer Centre, Melbourne, VIC; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC
| | - S H Kazakoff
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - X M de Luca
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - M T Parsons
- Molecular Cancer Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - K Ferguson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - L E Reid
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - A E McCart Reed
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - S Srihari
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD
| | - V Lakis
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - A L Davidson
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD; Faculty of Medicine, The University of Queensland, Brisbane, QLD
| | - P Mukhopadhyay
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - O Holmes
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - Q Xu
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S Wood
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - C Leonard
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J Beesley
- Cancer Genetics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J M Harris
- Faculty of Health, School Biomedical Science - Queensland University of Technology, Brisbane, QLD, Australia
| | - D Barnes
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge
| | - A Degasperi
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge; Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, UK
| | - M A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD
| | - A B Spurdle
- Molecular Cancer Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - K K Khanna
- Signal Transduction Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S R Lakhani
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD; Royal Brisbane & Women's Hospital, Pathology Queensland, Brisbane, QLD, Australia
| | - J V Pearson
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S Nik-Zainal
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge; Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, UK
| | - G Chenevix-Trench
- Cancer Genetics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - N Waddell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD.
| | - P T Simpson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD.
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Simpson P, Nones K, Johnson J, Newell F, Patch AM, Thorne H, Kazakoff S, De Luca X, Parsons M, Ferguson K, Reid L, McCart Reed A, Srihari S, Lakis V, Davidson A, Mukhopadhyay P, Holmes O, Xu Q, Wood S, Leonard C, Beasley J, Degasperi A, Nik-Zainal S, Ragan M, Spurdle A, Khanna KK, Lakhani S, Pearson J, Chenevix-Trench G, Waddell N. Abstract P5-10-01: Using whole genome sequencing and somatic mutation signatures to unravel insight into familial breast cancer aetiology. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p5-10-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Approximately 10-15% of breast cancers are associated with a strong family history of disease. Pathogenic variants in BRCA1, BRCA2 or other moderate to highly penetrant susceptibility genes (e.g. TP53, ATM, CHEK2, PALB2 and PTEN) account for a number of breast cancer families. However, for over 50% of families the underlying genetic contribution to their risk remains unknown (termed here as non-BRCA1/2). This has a profound impact for how individuals and their families are managed in the clinic. We applied whole genome sequencing (WGS) to determine whether somatic mutation analysis can reveal insight into the aetiology of familial breast cancer. The full repertoire of somatic mutations was evaluated in 26 BRCA1, 22 BRCA2 and 32 non-BRCA1/2 tumours; including SNPs, indels, copy number changes and structural rearrangements, and mutational signatures. Genomes were also analysed using the HRD Index and HRDetect, as predictors of homologous recombination deficiency. BRCA1, BRCA2 and non-BRCA1/2 tumours exhibited a different burden of mutations, a different spectrum of mutational signatures and different telomere length. Based on collective patterns of mutation signatures, tumours were classified as 'BRCA1-like', 'BRCA2-like' or 'non-BRCA1/2-like' with a 15% rate of tumour re-classification from their original clinical BRCA status. The results demonstrate the power of WGS to differentiate between BRCA1 and BRCA2 driven tumours; in the identification of double-pathogenic germline mutation carriers based on the resulting somatic mutation signature; and in the interpretation of BRCA unclassified variants. WGS of tumour genomes reveals fascinating insights into tumour aetiology and could compliment current genetic testing of breast cancer families.
Citation Format: Simpson P, Nones K, Johnson J, Newell F, Patch A-M, Thorne H, Kazakoff S, De Luca X, Parsons M, Ferguson K, Reid L, McCart Reed A, Srihari S, Lakis V, Davidson A, Mukhopadhyay P, Holmes O, Xu Q, Wood S, Leonard C, Beasley J, Degasperi A, Nik-Zainal S, Ragan M, Spurdle A, Khanna KK, Lakhani S, Pearson J, Chenevix-Trench G, Waddell N. Using whole genome sequencing and somatic mutation signatures to unravel insight into familial breast cancer aetiology [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-10-01.
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Affiliation(s)
- P Simpson
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - K Nones
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - J Johnson
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - F Newell
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - A-M Patch
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - H Thorne
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - S Kazakoff
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - X De Luca
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - M Parsons
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - K Ferguson
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - L Reid
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - A McCart Reed
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - S Srihari
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - V Lakis
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - A Davidson
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - P Mukhopadhyay
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - O Holmes
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - Q Xu
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - S Wood
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - C Leonard
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - J Beasley
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - A Degasperi
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - S Nik-Zainal
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - M Ragan
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - A Spurdle
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - KK Khanna
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - S Lakhani
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - J Pearson
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - G Chenevix-Trench
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
| | - N Waddell
- The University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia; University of Cambridge, Cambridge, United Kingdom; Westmead Institute for Medical Research, Sydney, Australia
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Głodzik D, Purdie C, Rye IH, Simpson PT, Staaf J, Span PN, Russnes HG, Nik-Zainal S. Mutational mechanisms of amplifications revealed by analysis of clustered rearrangements in breast cancers. Ann Oncol 2018; 29:2223-2231. [PMID: 30252041 PMCID: PMC6290883 DOI: 10.1093/annonc/mdy404] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Complex clusters of rearrangements are a challenge in interpretation of cancer genomes. Some clusters of rearrangements demarcate clear amplifications of driver oncogenes but others are less well understood. A detailed analysis of rearrangements within these complex clusters could reveal new insights into selection and underlying mutational mechanisms. Patients and methods Here, we systematically investigate rearrangements that are densely clustered in individual tumours in a cohort of 560 breast cancers. Applying an agnostic approach, we identify 21 hotspots where clustered rearrangements recur across cancers. Results Some hotspots coincide with known oncogene loci including CCND1, ERBB2, ZNF217, chr8:ZNF703/FGFR1, IGF1R, and MYC. Others contain cancer genes not typically associated with breast cancer: MCL1, PTP4A1, and MYB. Intriguingly, we identify clustered rearrangements that physically connect distant hotspots. In particular, we observe simultaneous amplification of chr8:ZNF703/FGFR1 and chr11:CCND1 where deep analysis reveals that a chr8-chr11 translocation is likely to be an early, critical, initiating event. Conclusions We present an overview of complex rearrangements in breast cancer, highlighting a potential new way for detecting drivers and revealing novel mechanistic insights into the formation of two common amplicons.
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Affiliation(s)
- D Głodzik
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Wellcome Trust Sanger Institute, Hinxton, Cambridge
| | - C Purdie
- Department of Pathology, Ninewells Hospital & Medical School, Dundee, UK
| | - I H Rye
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - P T Simpson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - J Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - P N Span
- Department of Radiation Oncology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - H G Russnes
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - S Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge; Academic Department of Medical Genetics, The Clinical School University of Cambridge, Cambridge, UK.
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De Mattos-Arruda L, Sammut S, Ross E, Bashford-Rogers R, Greenstein E, Rueda O, Nik-Zainal S, Markowetz F, Seoane J, Caldas C. 11 The heterogeneous genomic and immune landscapes of lethal metastatic breast cancer. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Degasperi A, Amarante TD, Zou X, Morganella S, Glodzik D, Davies H, Nik-Zainal S. PO-339 Implications of organ-wise extraction of cancer mutational signatures using 2577 whole genomes. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Wesseling J, Thompson A, Nik-Zainal S, Futreal A, Hwang S, Jonkers J, Lips E, Rea D. Abstract P4-15-13: When is cancer not really cancer? The PREvent ductal carcinoma in situ invasive overtreatment now (PRECISION)* initiative. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p4-15-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Ductal carcinoma in situ (DCIS) now represents 20-25% of all breast neoplasia due to large-scale detection by widely adopted population-based breast cancer screening programs. As a result, thousands of women are confronted with DCIS each year: more than 8,000 in the UK, 2,500 in the Netherlands, and some 50,000 in the US. Conventional management includes surgery, supplemented by radiotherapy and/or endocrine therapy, but overtreats the majority of DCIS as ˜1% recur annually and breast cancer mortality is ˜3% at 20 years. Uncertainty as to which DCIS lesions will progress to invasive cancer or, after excision, which will return with recurrent DCIS or invasive breast cancer drives this overtreatment. This urges us to learn how to distinguish DCIS that may progress to invasive breast cancer from the majority of indolent DCIS. Such distinction may be best achieved by synergistic international collaboration between leading global experts from various disciplines, driven by the essential input from patient voices as full members of the research team.
Aim
PRECISION (PREvent ductal Carcinoma In Situ Invasive Overtreatment Now) aims to save thousands of women with low risk DCIS the burden of intensive inappropriate treatment of DCIS (surgery, radiation therapy, hormonal therapies) through the discovery of new data and development of novel tests that promote informed and shared decision-making between patients and clinicians, without compromising the excellent outcomes for DCIS management presently achieved.
Methods
First, three large DCIS cohorts and supplementary resources will be collected enabling in depth molecular studies. Second, extensive genomic characterization, immune profiling and imaging analysis will be performed. In vivo and in vitro modeling will be performed to study the biology of DCIS in detail. Finally, all clinical, immune, and molecular data will be incorporated into a clinical risk prediction model. This risk prediction model will be validated in three prospective randomized DCIS trials in the US (COMET trial), UK (LORIS trial), and mainland Europe (LORD trial).
How the results of this research will be used
The discoveries from our laboratory studies, including a risk stratification model, will be cross-validated in three prospective trials of DCIS active surveillance versus conventional treatment (the COMET, LORIS and LORD trials). As such, the main result of this study will be that we can identify a group of women for which active surveillance for DCIS could be a safer alternative to intensive treatment. Ultimately, this may also contribute to a more reassuring perception of risk regarding non-life threatening precancerous lesions in general, reducing anxiety and preserving quality of life.
* The PRECISION Team is a Cancer Research UK Grand Challenge Award 2017 winning team and will be jointly funded by Cancer Research UK and the Dutch Cancer Society.
Citation Format: Wesseling J, Thompson A, Nik-Zainal S, Futreal A, Hwang S, Jonkers J, Lips E, Rea D, On Behalf of the PRECISION Team. When is cancer not really cancer? The PREvent ductal carcinoma in situ invasive overtreatment now (PRECISION)* initiative [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-15-13.
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Affiliation(s)
- J Wesseling
- Netherlands Cancer Institute; MD Anderson Cancer Center; Welcome Trust Sanger Institute; Duke University; University of Birmingham
| | - A Thompson
- Netherlands Cancer Institute; MD Anderson Cancer Center; Welcome Trust Sanger Institute; Duke University; University of Birmingham
| | - S Nik-Zainal
- Netherlands Cancer Institute; MD Anderson Cancer Center; Welcome Trust Sanger Institute; Duke University; University of Birmingham
| | - A Futreal
- Netherlands Cancer Institute; MD Anderson Cancer Center; Welcome Trust Sanger Institute; Duke University; University of Birmingham
| | - S Hwang
- Netherlands Cancer Institute; MD Anderson Cancer Center; Welcome Trust Sanger Institute; Duke University; University of Birmingham
| | - J Jonkers
- Netherlands Cancer Institute; MD Anderson Cancer Center; Welcome Trust Sanger Institute; Duke University; University of Birmingham
| | - E Lips
- Netherlands Cancer Institute; MD Anderson Cancer Center; Welcome Trust Sanger Institute; Duke University; University of Birmingham
| | - D Rea
- Netherlands Cancer Institute; MD Anderson Cancer Center; Welcome Trust Sanger Institute; Duke University; University of Birmingham
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Nik-Zainal S. Abstract PL2: Advances in the understanding and the applications of mutational signatures in human cells. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-pl2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A cancer genome is an historical account of the mutagenic activity that has occurred throughout the development of the tumour. Indeed, every mutation matters. While driver mutations were the main focus of cancer research for a long time, passenger mutational signatures, the imprints of DNA damage and DNA repair processes that have been operative during tumorigenesis, are also biologically informative.
We previously outlined the methods for identifying and quantifying base substitution mutational signatures present in primary human cancers. Recently, the intellectual framework of mutational signatures was extended to include six novel rearrangement signatures. Exploring this in >2,500 whole genome sequenced tumours of multiple tumour types, reveals how our early (and rather simplistic) thinking of mutational signatures, requires critical re-evaluation. There are more nuances than previously appreciated.
Diving into the detail of individual mutational signatures, we reveal intriguing mechanistic insights into the DNA damage and repair processes that mark the landscape of cancer genomes. In some instances, our findings invite more thoughtful consideration of that relatively binary distinction between drivers and passengers. Furthermore, we demonstrate why our whole genome profiling methods could assist in taking things to a clinical level, with mutational signatures forming an additional weapon in the arsenal of cancer diagnostics and therapeutic stratification, in the modern war against cancer.
Finally, we validate cancer mutational signatures using cell-based model systems and arrive at new realisations (unpublished). This powerful approach (humbles the analyst and) emphasises how biological exploration of big data still relies indispensably on experimental work to truly advance understanding.
Citation Format: Nik-Zainal S. Advances in the understanding and the applications of mutational signatures in human cells [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PL2.
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Affiliation(s)
- S Nik-Zainal
- The Wellcome Trust Sanger Institute, Cambridge, UNITED KINGDOM
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Desmedt C, Fornili M, Detours V, van den Eynden G, Salgado R, Maetens M, Brown D, Nik-Zainal S, Sotiriou C, Biganzoli E. Abstract P1-05-02: Genomic, transcriptomic and immune features of breast cancer according to the patient's body mass index at diagnosis. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p1-05-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
This abstract was withdrawn by the authors.
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Affiliation(s)
- C Desmedt
- Institut Jules Bordet - Université Libre de Bruxelles; University of Milan- Istituto Nazionale Tumori; ICGC Breast Cancer Working Group; Université Libre de Bruxelles; Wellcome Trust Sanger Institute
| | - M Fornili
- Institut Jules Bordet - Université Libre de Bruxelles; University of Milan- Istituto Nazionale Tumori; ICGC Breast Cancer Working Group; Université Libre de Bruxelles; Wellcome Trust Sanger Institute
| | - V Detours
- Institut Jules Bordet - Université Libre de Bruxelles; University of Milan- Istituto Nazionale Tumori; ICGC Breast Cancer Working Group; Université Libre de Bruxelles; Wellcome Trust Sanger Institute
| | - G van den Eynden
- Institut Jules Bordet - Université Libre de Bruxelles; University of Milan- Istituto Nazionale Tumori; ICGC Breast Cancer Working Group; Université Libre de Bruxelles; Wellcome Trust Sanger Institute
| | - R Salgado
- Institut Jules Bordet - Université Libre de Bruxelles; University of Milan- Istituto Nazionale Tumori; ICGC Breast Cancer Working Group; Université Libre de Bruxelles; Wellcome Trust Sanger Institute
| | - M Maetens
- Institut Jules Bordet - Université Libre de Bruxelles; University of Milan- Istituto Nazionale Tumori; ICGC Breast Cancer Working Group; Université Libre de Bruxelles; Wellcome Trust Sanger Institute
| | - D Brown
- Institut Jules Bordet - Université Libre de Bruxelles; University of Milan- Istituto Nazionale Tumori; ICGC Breast Cancer Working Group; Université Libre de Bruxelles; Wellcome Trust Sanger Institute
| | - S Nik-Zainal
- Institut Jules Bordet - Université Libre de Bruxelles; University of Milan- Istituto Nazionale Tumori; ICGC Breast Cancer Working Group; Université Libre de Bruxelles; Wellcome Trust Sanger Institute
| | - C Sotiriou
- Institut Jules Bordet - Université Libre de Bruxelles; University of Milan- Istituto Nazionale Tumori; ICGC Breast Cancer Working Group; Université Libre de Bruxelles; Wellcome Trust Sanger Institute
| | - E Biganzoli
- Institut Jules Bordet - Université Libre de Bruxelles; University of Milan- Istituto Nazionale Tumori; ICGC Breast Cancer Working Group; Université Libre de Bruxelles; Wellcome Trust Sanger Institute
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Martens JWM, Smid M, Rodríguez-González G, Sieuwerts AM, Prager-Van der Smissen WJC, Van Der Vlugt - Daane M, Van Galen A, Nik-Zainal S, Staaf J, Brinkman AB, Van de Vijver MJ, Richardson AL, Berentsen K, Caldas C, Butler A, Martin S, Davies HD, Debets R, Meijer-Van Gelder ME, Van Deurzen CHM, Ramakrishna MR, Ringnér M, Viari A, Birney E, Børresen-Dale AL, Stunnenberg HG, Stratton M, Foekens JA. Abstract P6-08-10: Mutational signatures impact the breast cancer transcriptome and distinguish mitotic from immune response pathways. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p6-08-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A comprehensive whole genome analysis of a large breast cancer cohort of 560 cases (Nik-Zainal et al, submitted 2015) reports novel and existing DNA substitution and rearrangement signatures next a comprehensive list of events driving the breast cancer cell to its malignant potency. In the current study, we linked the observed genetic diversity to the breast cancer transcriptome for 260 cases for which whole genome and whole transcriptome data were both available.
Cluster analysis of the global gene expression showed the familiar view of a coherent basal-like and a heterogeneous luminal subgroup. New and previously reported1 subtype-specific aberrations with concordant expression changes were found in TP53, PIK3CA, PTEN, CCND1, CDH1 and GATA3, and mutations in PIK3CA, PTEN, AKT1 and AKT2 were mutually exclusive confirming they are active in the same pathway in breast cancer.
Integrating the identified DNA substitutions signatures with the transcriptome, we observed that the total number of substitutions in a cancer, irrespective of substitution type, was positively associated with cell cycle regulated gene expression and with adverse outcome.
In addition and more remarkably, we observed that the number substitution of two substitution signatures2 particularly associated with immune-response specific gene expression, with increased amount of tumor infiltrating lymphocytes and with a better outcome. These two signatures comprised 1) mutations of the APOBEC-type (predominant C>G in a TCN context), and 2) mutations which lacks specific features but which are strongly associated with genetic and epigenetic inactivating aberrations in BRCA1 and BRCA2.
Thus, while earlier reports3-5 imply that the sheer number of driver events triggers an immune-response, we refine this statement by observing that substitutions of a particular type are much very effective in doing so explaining the superior outcome of cancer having these particular types of substitutions. This result also implies that purposefully augmenting T-cell reactivity against amino-acid substitutions resulting from either of these two DNA substitution types could potentially improve immunotherapies in breast cancer.
1. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (2012).
2. Alexandrov, L.B., et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
3. Rizvi, N.A., et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348, 124-128 (2015).
4. Schumacher, T.N. & Schreiber, R.D. Neoantigens in cancer immunotherapy. Science 348, 69-74 (2015).
5. Snyder, A., et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med 371, 2189-2199 (2014).
Citation Format: Martens JWM, Smid M, Rodríguez-González G, Sieuwerts AM, Prager-Van der Smissen WJC, Van Der Vlugt - Daane M, Van Galen A, Nik-Zainal S, Staaf J, Brinkman AB, Van de Vijver MJ, Richardson AL, Berentsen K, Caldas C, Butler A, Martin S, Davies HD, Debets R, Meijer-Van Gelder ME, Van Deurzen CHM, Ramakrishna MR, Ringnér M, Viari A, Birney E, Børresen-Dale A-L, Stunnenberg HG, Stratton M, Foekens JA. Mutational signatures impact the breast cancer transcriptome and distinguish mitotic from immune response pathways. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-08-10.
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Affiliation(s)
- JWM Martens
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - M Smid
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - G Rodríguez-González
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - AM Sieuwerts
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - WJC Prager-Van der Smissen
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - M Van Der Vlugt - Daane
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - A Van Galen
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - S Nik-Zainal
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - J Staaf
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - AB Brinkman
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - MJ Van de Vijver
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - AL Richardson
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - K Berentsen
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - C Caldas
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - A Butler
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - S Martin
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - HD Davies
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - R Debets
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - ME Meijer-Van Gelder
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - CHM Van Deurzen
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - MR Ramakrishna
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - M Ringnér
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - A Viari
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - E Birney
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - A-L Børresen-Dale
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - HG Stunnenberg
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - M Stratton
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
| | - JA Foekens
- Erasmus MC, Rotterdam, Netherlands; Wellcome Trust Sanger Institute, Hinxton, United Kingdom; Lund University, Lund, Sweden; Radboud University Nijmegen, Nijmegen, Netherlands; Academic Medical Center Amsterdam, Amsterdam, Netherlands; Dana-Farber Cancer Institute, Boston, MA; University of Cambridge, Cambridge, United Kingdom; Synergie Lyon Cancer, Lyon, France; European Bioinformatics Institute, Hinxton, United Kingdom; University of Oslo, Oslo, Norway
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Ramakrishna M, Davies H, Nik-Zainal S, Martin S, Campbell P, Stratton M. 462: Mutational characterisation of 400 breast cancers genomes. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50413-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Papaemmanuil E, Cazzola M, Boultwood J, Malcovati L, Vyas P, Bowen D, Pellagatti A, Wainscoat JS, Hellstrom-Lindberg E, Gambacorti-Passerini C, Godfrey AL, Rapado I, Cvejic A, Rance R, McGee C, Ellis P, Mudie LJ, Stephens PJ, McLaren S, Massie CE, Tarpey PS, Varela I, Nik-Zainal S, Davies HR, Shlien A, Jones D, Raine K, Hinton J, Butler AP, Teague JW, Baxter EJ, Score J, Galli A, Della Porta MG, Travaglino E, Groves M, Tauro S, Munshi NC, Anderson KC, El-Naggar A, Fischer A, Mustonen V, Warren AJ, Cross NCP, Green AR, Futreal PA, Stratton MR, Campbell PJ. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N Engl J Med 2011; 365:1384-95. [PMID: 21995386 PMCID: PMC3322589 DOI: 10.1056/nejmoa1103283] [Citation(s) in RCA: 928] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Myelodysplastic syndromes are a diverse and common group of chronic hematologic cancers. The identification of new genetic lesions could facilitate new diagnostic and therapeutic strategies. METHODS We used massively parallel sequencing technology to identify somatically acquired point mutations across all protein-coding exons in the genome in 9 patients with low-grade myelodysplasia. Targeted resequencing of the gene encoding RNA splicing factor 3B, subunit 1 (SF3B1), was also performed in a cohort of 2087 patients with myeloid or other cancers. RESULTS We identified 64 point mutations in the 9 patients. Recurrent somatically acquired mutations were identified in SF3B1. Follow-up revealed SF3B1 mutations in 72 of 354 patients (20%) with myelodysplastic syndromes, with particularly high frequency among patients whose disease was characterized by ring sideroblasts (53 of 82 [65%]). The gene was also mutated in 1 to 5% of patients with a variety of other tumor types. The observed mutations were less deleterious than was expected on the basis of chance, suggesting that the mutated protein retains structural integrity with altered function. SF3B1 mutations were associated with down-regulation of key gene networks, including core mitochondrial pathways. Clinically, patients with SF3B1 mutations had fewer cytopenias and longer event-free survival than patients without SF3B1 mutations. CONCLUSIONS Mutations in SF3B1 implicate abnormalities of messenger RNA splicing in the pathogenesis of myelodysplastic syndromes. (Funded by the Wellcome Trust and others.).
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Affiliation(s)
- E Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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Nik-Zainal S, Skepper JN, Hockaday A, Huang CL. Cardiac glycosides inhibit detubulation in amphibian skeletal muscle fibres exposed to osmotic shock. J Muscle Res Cell Motil 1999; 20:45-53. [PMID: 10360233 DOI: 10.1023/a:1005494114976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
It has recently been suggested that the 'vacuolation' of the transverse tubular system that follows the imposition of an osmotic shock is a component process in the eventual 'detubulation' of amphibian skeletal muscle. However, such a hypothesis requires net fluid transfers from the intracellular space into the lumina of the transverse tubules against the prevailing transmembrane osmotic gradients. The present experiments tested the effects of cardiac glycosides on the consequences of established osmotic protocols known reliably to achieve high levels of both detubulation and vacuolation in Rana temporaria sartorius muscle. Tubular isolation (detubulation) was assessed through electrophysiological observations of the abolition or otherwise of the after-depolarisation components of muscle action potentials. Vacuolation was assessed by stereological estimation of the volume fraction of muscle that was occupied by fluorescence-labelled vacuoles observed using confocal microscopy. Introduction of ouabain in the osmotic shock solutions sharply reduced such measures of vacuolation from 48.5 +/- 3.6% (mean +/- SEM; n = 70) to 12.1 +/- 2.7% (n = 190) of the total fibre volume. This was accompanied by sharp reductions in the incidence of detubulation (detubulation index reduced from 96.3 +/- 2.6% to 0.0 +/- 0.0%). The presence of ouabain was critical at the osmotic shock stage in the procedures at which the hypertonic glycerol-containing solutions were replaced by isotonic Ca(2+)-Mg(2+)-Ringer solutions. Finally, the alternative cardiac glycosides, strophanthidine and digoxin, exerted similar effects. These findings support a scheme in which the osmotic shock initiates a metabolically dependent fluid expulsion. This distends the transverse tubules into vacuoles that in turn lead to fibre detubulation.
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Affiliation(s)
- S Nik-Zainal
- Physiological Laboratory, University of Cambridge, UK
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