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Sokolova A, Johnstone KJ, McCart Reed AE, Simpson PT, Lakhani SR. Hereditary breast cancer: syndromes, tumour pathology and molecular testing. Histopathology 2023; 82:70-82. [PMID: 36468211 PMCID: PMC10953374 DOI: 10.1111/his.14808] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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: 08/01/2022] [Revised: 09/12/2022] [Accepted: 09/18/2022] [Indexed: 12/09/2022]
Abstract
Hereditary factors account for a significant proportion of breast cancer risk. Approximately 20% of hereditary breast cancers are attributable to pathogenic variants in the highly penetrant BRCA1 and BRCA2 genes. A proportion of the genetic risk is also explained by pathogenic variants in other breast cancer susceptibility genes, including ATM, CHEK2, PALB2, RAD51C, RAD51D and BARD1, as well as genes associated with breast cancer predisposition syndromes - TP53 (Li-Fraumeni syndrome), PTEN (Cowden syndrome), CDH1 (hereditary diffuse gastric cancer), STK11 (Peutz-Jeghers syndrome) and NF1 (neurofibromatosis type 1). Polygenic risk, the cumulative risk from carrying multiple low-penetrance breast cancer susceptibility alleles, is also a well-recognised contributor to risk. This review provides an overview of the established breast cancer susceptibility genes as well as breast cancer predisposition syndromes, highlights distinct genotype-phenotype correlations associated with germline mutation status and discusses molecular testing and therapeutic implications in the context of hereditary breast cancer.
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Affiliation(s)
- A Sokolova
- Sullivan and Nicolaides PathologyBrisbane
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - K J Johnstone
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
- Pathology Queensland, The Royal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
| | - A E McCart Reed
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - P T Simpson
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - S R Lakhani
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
- Pathology Queensland, The Royal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
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Ramarao-Milne P, Kondrashova O, Patch AM, Nones K, Koufariotis LT, Newell F, Addala V, Lakis V, Holmes O, Leonard C, Wood S, Xu Q, Mukhopadhyay P, Naeini MM, Steinfort D, Williamson JP, Bint M, Pahoff C, Nguyen PT, Twaddell S, Arnold D, Grainge C, Basirzadeh F, Fielding D, Dalley AJ, Chittoory H, Simpson PT, Aoude LG, Bonazzi VF, Patel K, Barbour AP, Fennell DA, Robinson BW, Creaney J, Hollway G, Pearson JV, Waddell N. Comparison of actionable events detected in cancer genomes by whole-genome sequencing, in silico whole-exome and mutation panels. ESMO Open 2022; 7:100540. [PMID: 35849877 PMCID: PMC9463385 DOI: 10.1016/j.esmoop.2022.100540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 06/07/2022] [Accepted: 06/19/2022] [Indexed: 12/14/2022] Open
Abstract
Background Next-generation sequencing is used in cancer research to identify somatic and germline mutations, which can predict sensitivity or resistance to therapies, and may be a useful tool to reveal drug repurposing opportunities between tumour types. Multigene panels are used in clinical practice for detecting targetable mutations. However, the value of clinical whole-exome sequencing (WES) and whole-genome sequencing (WGS) for cancer care is less defined, specifically as the majority of variants found using these technologies are of uncertain significance. Patients and methods We used the Cancer Genome Interpreter and WGS in 726 tumours spanning 10 cancer types to identify drug repurposing opportunities. We compare the ability of WGS to detect actionable variants, tumour mutation burden (TMB) and microsatellite instability (MSI) by using in silico down-sampled data to mimic WES, a comprehensive sequencing panel and a hotspot mutation panel. Results We reveal drug repurposing opportunities as numerous biomarkers are shared across many solid tumour types. Comprehensive panels identify the majority of approved actionable mutations, with WGS detecting more candidate actionable mutations for biomarkers currently in clinical trials. Moreover, estimated values for TMB and MSI vary when calculated from WGS, WES and panel data, and are dependent on whether all mutations or only non-synonymous mutations were used. Our results suggest that TMB and MSI thresholds should not only be tumour-dependent, but also be sequencing platform-dependent. Conclusions There is a large opportunity to repurpose cancer drugs, and these data suggest that comprehensive sequencing is an invaluable source of information to guide clinical decisions by facilitating precision medicine and may provide a wealth of information for future studies. Furthermore, the sequencing and analysis approach used to estimate TMB may have clinical implications if a hard threshold is used to indicate which patients may respond to immunotherapy. Genome analysis revealed that treatment biomarkers are shared across solid tumours, highlighting repurposing opportunities. Comprehensive panels detect most known biomarkers; however, WGS detects more biomarkers for treatments in clinical trials. TMB is well correlated between sequencing methods, but absolute values vary and are dependent on mutation types considered.
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Affiliation(s)
- P Ramarao-Milne
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | - O Kondrashova
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - A-M Patch
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - K Nones
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - L T Koufariotis
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - F Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - V Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - V Lakis
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - O Holmes
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - C Leonard
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - S Wood
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Q Xu
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - P Mukhopadhyay
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - M M Naeini
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - D Steinfort
- Department of Thoracic Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | - J P Williamson
- Department of Thoracic Medicine, Liverpool Hospital Sydney, Sydney, Australia
| | - M Bint
- Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, Australia
| | - C Pahoff
- Department of Respiratory Medicine, Gold Coast University Hospital, Southport, Australia
| | - P T Nguyen
- Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, Australia
| | - S Twaddell
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - D Arnold
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - C Grainge
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - F Basirzadeh
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - D Fielding
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - A J Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - H Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - P T Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - L G Aoude
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - V F Bonazzi
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - K Patel
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - A P Barbour
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia; Upper Gastro-intestinal Surgical Unit, Department of Surgery, Princess Alexandra Hospital, Brisbane, Australia
| | - D A Fennell
- Cancer Research UK Centre Leicester, University of Leicester & University Hospitals of Leicester NHS Trust, Leicester, UK
| | - B W Robinson
- National Centre for Asbestos Related Disease, Institute of Respiratory Health, University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - J Creaney
- National Centre for Asbestos Related Disease, Institute of Respiratory Health, University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - G Hollway
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - J V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - N Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
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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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4
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McCart Reed AE, Kalaw E, Nones K, Bettington M, Lim M, Bennett J, Johnstone K, Kutasovic JR, Kazakoff S, Xu QC, Saunus JM, Reid LE, Black D, Niland C, Ferguson K, Gresshoff I, Raghavendra A, Liu JC, Kalinowski L, Reid AS, Davidson M, Pearson JV, Yamaguchi R, Harris G, Tse G, Papadimos D, Pathmanathan R, Pathmanathan N, Tan PH, Fox S, O'Toole S, Waddell N, Simpson PT, Lakhani SR. Abstract P3-08-03: Dissecting the heterogeneity of metaplastic breast cancer: A morphological, immunohistochemical and genomic analysis of a large cohort. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p3-08-03] [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
Although rare, Metaplastic Breast Carcinomas (MBC) account for significant global breast cancer mortality. This subgroup is extremely heterogeneous and by definition exhibits metaplastic change to squamous and/or mesenchymal elements, including but not limited to spindle, squamous, chondroid, osseous and rhabdomyoid elements. The WHO working group recognizes that the current classification is inadequate and in the interim, has suggested a purely descriptive classification. The mixed epithelial-mesenchymal morphology has led to speculation that MBC represent 'stem cell tumours'; in support of this, MBC have been shown to have a CD44+/CD24-/low phenotype. Clinically, patients present with tumours that are larger (higher stage), have increased likelihood of distant metastases at presentation and overall, have a reduced 5-year survival rate compared to Invasive Carcinoma-NST. Hence, this is a unique subtype with poor outcome but without a robust classification or understanding of the biology to aid clinical management. We present a detailed morphological, immunohistochemical and genomic analysis of a large series of MBC (n=347), as amassed through the Asia-Pacific MBC consortium. We consider our morphological dissection using the WHO subtyping guidelines and show that an increasing number of phenotypes in a mixed MBC (classified as WHO_1) significantly associates with a poor prognosis. Immunohistochemical analysis showed that a pure spindle (WHO_5) is significantly less likely to express vimentin, CK5/6, CK14, and CK19 than a mixed WHO_1 with spindle features. Similarly, a WHO_1 with chondroid features is less likely to express EGFR than WHO_1 with chondroid features and rhabdoid or osseous differentiation. Across the cohort, positivity for the AE1/3 antibody and a lack of EGFR expression both significantly associate with a better outcome. We report no significant association between patient age at diagnosis and breast cancer specific survival, nor between age and specific WHO MBC subtypes. We report a significant association between WHO_1 types and increasing tumour grade, and also between tumour size and grade, with tumour size being a highly significant prognostic indicator in this cohort. Our exome sequencing confirms a significant enrichment for TP53 and PTEN mutations in MBC, and intriguingly for concurrent mutations of TP53, PTEN and PIK3CA. A novel enrichment for NF1 mutations is also presented. In summary, we provide a thorough assessment of a large cohort of MBC, including morphology, survival, IHC and exome sequencing, and present our analysis contextualized by the WHO guidelines, extending the existing knowledge base of this rare tumour type.
Citation Format: McCart Reed AE, Kalaw E, Nones K, Bettington M, Lim M, Bennett J, Johnstone K, Kutasovic JR, Kazakoff S, Xu QC, Saunus JM, Reid LE, Black D, Niland C, Ferguson K, Gresshoff I, Raghavendra A, Liu JC, Kalinowski L, Reid AS, Davidson M, Pearson JV, Yamaguchi R, Harris G, Tse G, Papadimos D, Pathmanathan R, Pathmanathan N, Tan PH, Fox S, O'Toole S, Waddell N, Simpson PT, Lakhani SR. Dissecting the heterogeneity of metaplastic breast cancer: A morphological, immunohistochemical and genomic analysis of a large cohort [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 P3-08-03.
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Affiliation(s)
- AE McCart Reed
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - E Kalaw
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - K Nones
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - M Bettington
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - M Lim
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - J Bennett
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - K Johnstone
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - JR Kutasovic
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - S Kazakoff
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - QC Xu
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - JM Saunus
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - LE Reid
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - D Black
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - C Niland
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - K Ferguson
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - I Gresshoff
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - A Raghavendra
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - JC Liu
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - L Kalinowski
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - AS Reid
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - M Davidson
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - JV Pearson
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - R Yamaguchi
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - G Harris
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - G Tse
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - D Papadimos
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - R Pathmanathan
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - N Pathmanathan
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - PH Tan
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - S Fox
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - S O'Toole
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - N Waddell
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - PT Simpson
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, Sydney, Australia
| | - SR Lakhani
- University of Queensland, Brisbane, Australia; QIMR Berghofer Medical Research Institute, Brisbane, Australia; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia; Kurume University School of Medicine, Kurume, Japan; Canterbury Health Laboratories, Christchurch, New Zealand; Prince of Wales Hospital, Hong Kong, Hong Kong; Sullivan Nicolaides Pathology, Brisbane, Australia; Sime Darby Medical Centre, Selangor, Malaysia; Westmead Breast Cancer Institute; University of Sydney, Sydney, Australia; Singapore General Hospital, Singapore, Singapore; Peter MacCallum Cancer Centre, Melbourne, Australia; Garvan Institute of Medical Research and the Kinghorn Cancer Centre, 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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McCart Reed AE, Kutasovic JR, Nones K, da Silva L, Melville L, Jayanthan J, Vargas AC, Reid LE, Saunus JM, Cummings MM, Porter A, Evans E, Waddell N, Lakhani SR, Simpson PT. Abstract P1-07-08: Mixed ductal-lobular carcinomas of the breast: Abrogated cell adhesion in the clonal evolution from ductal to lobular morphology. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p1-07-08] [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
Mixed ductal-lobular carcinomas (MDL) display both ductal and lobular morphology, and are a clear example of intratumour morphological heterogeneity. The evolution of MDL carcinomas is not well understood. There is a paucity of data surrounding the genetic origin of the different morphological compartments and it remains to be seen whether the coincident presentation of these distinct morphological entities represents two independent tumours that have collided (so called 'collision tumours'), or whether they arise from a common clone. We propose that clonal progression during the evolution of these tumours is associated with a change in phenotype. To address this, a cohort of 82 MDLs was studied for clinical, morphological and molecular features. Key findings include: i) MDLs more frequently co-exist with ductal carcinoma in situ (DCIS) than lobular carcinoma in situ (LCIS); ii) the E-cadherin-catenin complex was recurrently normal in the ductal component but aberrantly localised in the lobular component of the same tumour; iii) E-cadherin deregulation in the lobular component was almost always aberrantly located to the cytoplasm, conversely classic ILCs are typically completely negative for this molecule; iv) epithelial to mesenchymal transition marker expression was not associated with E-cadherin deregulation. Comparative Genomic Hybridsation (CGH) and exome sequencing was performed to investigate clonal relationships between the different intratumour morphologies and identify mechanisms underlying the change in phenotype. Our analysis revealed that i) all morphological components within a case are clonally related; ii) divergence of the morphological components may occur early during tumour evolution (where both DCIS and LCIS are present) or later during tumour progression (cases with only DCIS detectible); and iii) mutations were identified in genes such as CDH1 and ESR1, and other breast cancer driver genes. Together, these data strongly support the concept that the disparate morphological components of these mixed tumours are clonally related, and are not the result of a collision event. Furthermore, we show that lobular morphology can arise via a 'ductal' pathway of tumour progression. The mechanisms driving the change in phenotype are yet to be fully elucidated, but there is significant intertumour heterogeneity and each case may utilise a unique molecular mechanism.
Citation Format: McCart Reed AE, Kutasovic JR, Nones K, da Silva L, Melville L, Jayanthan J, Vargas AC, Reid LE, Saunus JM, Cummings MM, Porter A, Evans E, Waddell N, Lakhani SR, Simpson PT. Mixed ductal-lobular carcinomas of the breast: Abrogated cell adhesion in the clonal evolution from ductal to lobular morphology [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-07-08.
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Affiliation(s)
- AE McCart Reed
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - JR Kutasovic
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - K Nones
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - L da Silva
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - L Melville
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - J Jayanthan
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - AC Vargas
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - LE Reid
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - JM Saunus
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - MM Cummings
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - A Porter
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - E Evans
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - N Waddell
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - SR Lakhani
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
| | - PT Simpson
- The University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD, Australia; QIMR Clive Berghofer Medical Research Institute, Brisbane, QLD, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; The University of Queensland, School of Medicine, Brisbane, QLD, Australia; The Wesley Breast Clinic, The Wesley Hospital, Brisbane, Brisbane, QLD, Australia
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Srihari S, Singla J, Wong L, Simpson PT, Khanna KK, Ragan MA. Abstract PD6-05: Identifying genetic vulnerabilities in cancers driven by defects in DNA-damage response. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-pd6-05] [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
Although defects in cancer susceptibility genes within the DNA-damage response (DDR) machinery including BRCA1 and BRCA2 account for only 5-10% of all breast cancer cases, these defects are highly penetrant and significantly increase the risk of breast (60-80%) and also ovarian (35%) cancers [1]. Together with defects in the DNA-damage sensor ATM, apoptosis effector TP53, and PTEN and CDH1 with roles in regulation of DDR, these account for considerable proportions of sporadic breast (63%) and ovarian (85%) cancers. To compensate for these DDR defects and to avoid cell death triggered from a genomic catastrophe, cancer cells rewire their DDR network while also selecting (during clonal expansion) the optimal combination of oncogenic events. Deciphering these combinations of events would aid in mapping the vulnerabilities of cancer cells harbouring defects in DDR.
While there have been several studies screening for essentiality of genes across DDR-deficient cell-lines, the essential genes so identified are either restricted only to these cell-line models or are not frequently (over)expressed in cancers. Here, we observe that oncogenic events that are mutually exclusive to DDR defects in large proportions of cancers constitute the (clonally) selected combinations that are amenable to cancer-cell survival, and therefore by systematically mining for these events, we infer vulnerability genes that if targeted in conjunction with DDR defects could induce a genomic catastrophe and trigger cancer-cell death.
Using data from DNA copy-number and mRNA-expression profiles we infer vulnerability genes that are mutually exclusive to defects in six DDR genes ATM, BRCA1, BRCA2, CDH1, PTEN and TP53 across four cancers (total 3980 samples) – breast (2029), prostate (623), ovarian (828) and uterine (500) from The Cancer Genome Atlas. Interestingly, across the four cancers these vulnerability genes form the most combinations with BRCA2 (59.02%), followed by CDH1 (24.59%), PTEN (8.20%) and TP53 (8.19%) at p<0.01 (1-hypergeometric test), whereas these show distinct patterns within the individual cancers: combinations dominated by CDH1 (90%) in breast, PTEN (78.38%) and BRCA2 (16.82%) in prostate, and BRCA1 (71.94%) and TP53 (16.21%) in ovarian cancers. Validation using GARP (Gene Activity Rank Profile)-score data from essentiality screens [2] from ten breast cancer cell lines (HCC1143, HCC1187, HCC1395, HCC1419, HCC1428, HCC1500, HCC1806, HCC1954, HCC38, MCF7) which harbour defects in at least one of the six DDR genes shows remarkable agreement between the GARP rankings and our inferred vulnerabilities. Our inferred genes are significantly enriched (p<0.0001 X2 test) in the top quartile of the entire set of profiled (∼16000) essential genes in these screens. Moreover, Kaplan-Meier analysis using survival data from 1000 breast cancer patients shows considerable overexpression of these genes (e.g. TLK2 in 37% luminal cases) which correlates significantly (TLK2: p<0.0006; Grade 3 hazard ratio 2.5) with poor prognosis. Experimental validation of these genes using single- and double knockout with DDR in breast cancer cell lines is currently underway.
[1] Liu & Srihari et al., Nucl Acids Res 2014, 42(10):6106-27.
[2] Marcotte et al., Cancer Discov 2012, 2(2):172-89.
Citation Format: Srihari S, Singla J, Wong L, Simpson PT, Khanna KK, Ragan MA. Identifying genetic vulnerabilities in cancers driven by defects in DNA-damage response. [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 PD6-05.
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Affiliation(s)
- S Srihari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia; Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; National University of Singapore, Singapore; The University of Queensland, Centre for Clinical Research and School of Medicine, Brisbane, Queensland, Australia; QIMR-Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - J Singla
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia; Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; National University of Singapore, Singapore; The University of Queensland, Centre for Clinical Research and School of Medicine, Brisbane, Queensland, Australia; QIMR-Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - L Wong
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia; Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; National University of Singapore, Singapore; The University of Queensland, Centre for Clinical Research and School of Medicine, Brisbane, Queensland, Australia; QIMR-Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - PT Simpson
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia; Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; National University of Singapore, Singapore; The University of Queensland, Centre for Clinical Research and School of Medicine, Brisbane, Queensland, Australia; QIMR-Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - KK Khanna
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia; Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; National University of Singapore, Singapore; The University of Queensland, Centre for Clinical Research and School of Medicine, Brisbane, Queensland, Australia; QIMR-Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - MA Ragan
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia; Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; National University of Singapore, Singapore; The University of Queensland, Centre for Clinical Research and School of Medicine, Brisbane, Queensland, Australia; QIMR-Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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Al-Ejeh F, Simpson PT, Saunus JM, Klein K, Kalimutho M, Shi W, Miranda M, Kutasovic J, Raghavendra A, Madore J, Reid L, Krause L, Chenevix-Trench G, Lakhani SR, Khanna KK. Meta-analysis of the global gene expression profile of triple-negative breast cancer identifies genes for the prognostication and treatment of aggressive breast cancer. Oncogenesis 2014; 3:e124. [PMID: 25347059 PMCID: PMC4216904 DOI: 10.1038/oncsis.2014.41] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Tilch E, Seidens T, Cocciardi S, Reid LE, Byrne D, Simpson PT, Vargas AC, Cummings MC, Fox SB, Lakhani SR, Chenevix Trench G. Mutations in EGFR, BRAF and RAS are rare in triple-negative and basal-like breast cancers from Caucasian women. Breast Cancer Res Treat 2013; 143:385-92. [DOI: 10.1007/s10549-013-2798-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 11/27/2013] [Indexed: 12/24/2022]
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Al-Ejeh F, Miranda M, Simpson PT, Chenevix-Trench G, Lakhani SR, Khanna KK. Abstract P6-10-06: Rational combination therapy against triple-negative breast cancer. Cancer Res 2012. [DOI: 10.1158/0008-5472.sabcs12-p6-10-06] [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: Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with higher incidence of recurrence, more distant metastasis, and poorer survival. This subtype is also characterized by complex genomes where little of their genomes remain at normal copy number but without high, focal copy number amplifications. At the transciptome level, the majority of TNBC (∼75%) are classified as basal-like breast cancer (BLBC) according to the five intrinsic subtypes. Despite considerable genomic and gene expression characterization of TNBC, proteomic and phospho-proteomic investigations of this disease are limited with no available targeted therapies in clinical use.
Methods & Results: We used the Kinex™ antibody array (http://www.kinexus.ca/) to interrogate protein/phosphoproteins levels in 43 primary breast cancer biopsies (16 TNBC, 16 ER/PR positive and 11 HER2-positive) and 16 breast cancer cell lines. Unsupervised hierarchical clustering of protein/phosphoprotein levels revealed two subgroups of TNBC in comparison to other subtypes. Western blotting and Proteome Profiler™ Arrays (R&D Systems) were used to validate deregulated proteins/phosphoproteins in TNBC. Pathway analysis revealed that one subgroup of TNBC exploits overlapping and cross-talking networks for survival. These signaling networks are downstream from elevated activation of EGFR, integrins and Insulin-like growth factor 1 receptor (IGF1R).
Targeted molecular inhibitors of activated kinases in these pathways showed specificity against basal-like/TNBC cell lines compared to other subtypes in vitro. These activated kinases/networks represent druggable targets for the treatment of TNBC but may be limited by compensatory effect of the complex cross-talking signaling networks.
To overcome compensatory downstream signaling that would limit the inhibition of a given pathway; we developed EGFR-targeted radioimmunotherapy (RIT) strategy to systemically deliver cytotoxic loads of beta particles (177Lu) that would kill targeted cells and surrounding cells by crossfire effect. The combination of EGFR-directed RIT with chemotherapy and PARP inhibition successfully treated orthotopic and metastatic TNBC models established from cell lines and patient-derived xenografts. The superior efficacy of this triple-agent combination therapy is explained by enhanced DNA damage and reduced DNA repair response, higher apoptotic cell death and the elimination of putative breast cancer stem cells.
Conclusion: Proteomic analysis of TNBC provides a powerful tool to elucidate druggable signaling networks with therapeutic potential. TNBC utilizes complex interacting signaling networks and rational combination therapies are required for effective therapy.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-10-06.
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Affiliation(s)
- F Al-Ejeh
- Queensland Institute of Medical Research, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia
| | - M Miranda
- Queensland Institute of Medical Research, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia
| | - PT Simpson
- Queensland Institute of Medical Research, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia
| | - G Chenevix-Trench
- Queensland Institute of Medical Research, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia
| | - SR Lakhani
- Queensland Institute of Medical Research, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia
| | - KK Khanna
- Queensland Institute of Medical Research, Brisbane, QLD, Australia; The University of Queensland, Brisbane, QLD, Australia
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Simpson PT, Reis-Filho JS, Lambros MBK, Jones C, Steele D, Mackay A, Iravani M, Fenwick K, Dexter T, Jones A, Reid L, Da Silva L, Shin SJ, Hardisson D, Ashworth A, Schmitt FC, Palacios J, Lakhani SR. Molecular profiling pleomorphic lobular carcinomas of the breast: evidence for a common molecular genetic pathway with classic lobular carcinomas. J Pathol 2008; 215:231-44. [DOI: 10.1002/path.2358] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Kar S, Markey K, Simpson PT, Bellei C, Green JS, Nagel SR, Kneip S, Carroll DC, Dromey B, Willingale L, Clark EL, McKenna P, Najmudin Z, Krushelnick K, Norreys P, Clarke RJ, Neely D, Borghesi M, Zepf M. Dynamic control of laser-produced proton beams. Phys Rev Lett 2008; 100:105004. [PMID: 18352198 DOI: 10.1103/physrevlett.100.105004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Indexed: 05/26/2023]
Abstract
The emission characteristics of intense laser driven protons are controlled using ultrastrong (of the order of 10(9) V/m) electrostatic fields varying on a few ps time scale. The field structures are achieved by exploiting the high potential of the target (reaching multi-MV during the laser interaction). Suitably shaped targets result in a reduction in the proton beam divergence, and hence an increase in proton flux while preserving the high beam quality. The peak focusing power and its temporal variation are shown to depend on the target characteristics, allowing for the collimation of the inherently highly divergent beam and the design of achromatic electrostatic lenses.
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Affiliation(s)
- S Kar
- The Queen's University of Belfast, Belfast BT7 1NN, United Kingdom
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13
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Carroll DC, McKenna P, Lundh O, Lindau F, Wahlström CG, Bandyopadhyay S, Pepler D, Neely D, Kar S, Simpson PT, Markey K, Zepf M, Bellei C, Evans RG, Redaelli R, Batani D, Xu MH, Li YT. Active manipulation of the spatial energy distribution of laser-accelerated proton beams. Phys Rev E Stat Nonlin Soft Matter Phys 2007; 76:065401. [PMID: 18233889 DOI: 10.1103/physreve.76.065401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 09/28/2007] [Indexed: 05/25/2023]
Abstract
The spatial energy distributions of beams of protons accelerated by ultrahigh intensity (>10(19)Wcm2) picosecond laser pulse interactions with thin foil targets are investigated. Using separate, low intensity (<10(13)Wcm2) nanosecond laser pulses, focused onto the front surface of the target foil prior to the arrival of the high intensity pulse, it is demonstrated that the proton beam profile can be actively manipulated. In particular, results obtained with an annular intensity distribution at the focus of the low intensity beam are presented, showing smooth proton beams with a sharp circular boundary at all energies, which represents a significant improvement in the beam quality compared to irradiation with the picosecond beam alone.
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Affiliation(s)
- D C Carroll
- SUPA, Department of Physics, University of Strathclyde, Glasgow G4 0NG, United Kingdom
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Dromey B, Kar S, Bellei C, Carroll DC, Clarke RJ, Green JS, Kneip S, Markey K, Nagel SR, Simpson PT, Willingale L, McKenna P, Neely D, Najmudin Z, Krushelnick K, Norreys PA, Zepf M. Bright multi-keV harmonic generation from relativistically oscillating plasma surfaces. Phys Rev Lett 2007; 99:085001. [PMID: 17930952 DOI: 10.1103/physrevlett.99.085001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Indexed: 05/25/2023]
Abstract
The first evidence of x-ray harmonic radiation extending to 3.3 A, 3.8 keV (order n>3200) from petawatt class laser-solid interactions is presented, exhibiting relativistic limit efficiency scaling (eta approximately n{-2.5}-n{-3}) at multi-keV energies. This scaling holds up to a maximum order, n{RO} approximately 8{1/2}gamma;{3}, where gamma is the relativistic Lorentz factor, above which the first evidence of an intensity dependent efficiency rollover is observed. The coherent nature of the generated harmonics is demonstrated by the highly directional beamed emission, which for photon energy hnu>1 keV is found to be into a cone angle approximately 4 degrees , significantly less than that of the incident laser cone (20 degrees ).
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Affiliation(s)
- B Dromey
- Department of Physics and Astronomy, Queens University, Belfast, UK
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15
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McKenna P, Carroll DC, Clarke RJ, Evans RG, Ledingham KWD, Lindau F, Lundh O, McCanny T, Neely D, Robinson APL, Robson L, Simpson PT, Wahlström CG, Zepf M. Lateral electron transport in high-intensity laser-irradiated foils diagnosed by ion emission. Phys Rev Lett 2007; 98:145001. [PMID: 17501281 DOI: 10.1103/physrevlett.98.145001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2006] [Indexed: 05/15/2023]
Abstract
An experimental investigation of lateral electron transport in thin metallic foil targets irradiated by ultraintense (>or=10(19) W/cm2) laser pulses is reported. Two-dimensional spatially resolved ion emission measurements are used to quantify electric-field generation resulting from electron transport. The measurement of large electric fields ( approximately 0.1 TV/m) millimeters from the laser focus reveals that lateral energy transport continues long after the laser pulse has decayed. Numerical simulations confirm a very strong enhancement of electron density and electric field at the edges of the target.
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Affiliation(s)
- P McKenna
- SUPA, Department of Physics, University of Strathclyde, Glasgow G4 0NG, United Kingdom
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Reis-Filho JS, Milanezi F, Steele D, Savage K, Simpson PT, Nesland JM, Pereira EM, Lakhani SR, Schmitt FC. Metaplastic breast carcinomas are basal-like tumours. Histopathology 2006; 49:10-21. [PMID: 16842242 DOI: 10.1111/j.1365-2559.2006.02467.x] [Citation(s) in RCA: 258] [Impact Index Per Article: 14.3] [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: 12/31/2022]
Abstract
AIMS Recently, an immunohistochemical panel comprising antibodies against HER2, oestrogen receptor (ER), epidermal growth factor receptor (EGFR) and cytokeratin (CK) 5/6 was reported to identify basal-like breast carcinomas, as defined by cDNA microarrays. Our aim was to analyse a series of metaplastic breast carcinomas (MBCs) using this panel plus two other basal markers (CK14 and p63) and progesterone receptor (PR), to define how frequently MBCs show a basal-like immunophenotype. METHODS AND RESULTS Sixty-five cases were retrieved from the pathology archives of the authors' institutions and reviewed by three of the authors. Immunohistochemistry with antibodies for HER2, ER, EGFR, CK5/6, CK14 and p63 was performed according to standard methods. All but six cases (91%) showed the typical immunoprofile of basal-like tumours (ER- and HER2-, EGFR+ and/or CK5/6+). When CK14 and p63 were added to the panel, two additional cases could be classified as basal-like. The majority of MBCs lacked PR, except 4/19 (21%) carcinomas with squamous metaplasia. CONCLUSIONS Our results demonstrate that MBCs show a basal-like phenotype, regardless of the type of metaplastic elements. Moreover, as these neoplasms frequently overexpress EGFR (57%), patients with MBC may benefit from treatment with anti-EGFR drugs.
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Affiliation(s)
- J S Reis-Filho
- The Breakthrough Toby Robins Breast Cancer Research Centre, Institute of Cancer Research, London, UK.
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Reis-Filho JS, Pinheiro C, Lambros MBK, Milanezi F, Carvalho S, Savage K, Simpson PT, Jones C, Swift S, Mackay A, Reis RM, Hornick JL, Pereira EM, Baltazar F, Fletcher CDM, Ashworth A, Lakhani SR, Schmitt FC. EGFR amplification and lack of activating mutations in metaplastic breast carcinomas. J Pathol 2006; 209:445-53. [PMID: 16739104 DOI: 10.1002/path.2004] [Citation(s) in RCA: 204] [Impact Index Per Article: 11.3] [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: 01/06/2023]
Abstract
Metaplastic breast carcinomas are reported to harbour epidermal growth factor receptor (EGFR) overexpression in up to 80% of the cases, but EGFR gene amplification is the underlying genetic mechanism in around one-third of these. In this study, EGFR gene amplification as defined by chromogenic in situ hybridization and protein overexpression was examined in a cohort of 47 metaplastic breast carcinomas. Furthermore, the presence of activating EGFR mutations in exons 18, 19, 20, and 21 was investigated. Thirty-two cases showed EGFR overexpression and of these, 11 (34%) harboured EGFR gene amplification. In addition, EGFR amplification showed a statistically significant association with EGFR overexpression (p < 0.0094) and was restricted to carcinomas with homologous metaplasia. Ten cases, five with and five without EGFR amplification, were subjected to microarray-based CGH, which demonstrated that EGFR copy number gain may occur by amplification of a discrete genomic region or by gains of the short arm of chromosome 7 with a breakpoint near the EGFR gene locus, the minimal region of amplification mapping to EGFR, LANCL2, and SEC61G. No activating EGFR mutations were identified, suggesting that this is unlikely to be a common alternative underlying genetic mechanism for EGFR expression in metaplastic breast carcinomas. Given that metaplastic breast carcinomas are resistant to conventional chemotherapy or hormone therapy regimens and that tumours with EGFR amplification are reported to be sensitive to EGFR tyrosine kinase inhibitors, these findings indicate that further studies are warranted to explore EGFR tyrosine kinase inhibitors as potential therapeutic agents for metaplastic breast carcinomas harbouring amplification of 7p11.2.
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Affiliation(s)
- J S Reis-Filho
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK.
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