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Hollis RL, Meynert AM, Michie CO, Rye T, Churchman M, Hallas-Potts A, Croy I, McCluggage WG, Williams AR, Bartos C, Iida Y, Okamoto A, Dougherty B, Barrett JC, March R, Matakidou A, Roxburgh P, Semple CA, Harkin DP, Kennedy R, Herrington CS, Gourley C. Multiomic Characterization of High-Grade Serous Ovarian Carcinoma Enables High-Resolution Patient Stratification. Clin Cancer Res 2022; 28:3546-3556. [PMID: 35696721 PMCID: PMC9662902 DOI: 10.1158/1078-0432.ccr-22-0368] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/13/2022] [Accepted: 06/09/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE High-grade serous ovarian carcinoma (HGSOC) is the most common ovarian cancer type; most patients experience disease recurrence that accumulates chemoresistance, leading to treatment failure. Genomic and transcriptomic features have been associated with differential outcome and treatment response. However, the relationship between events at the gene sequence, copy number, and gene-expression levels remains poorly defined. EXPERIMENTAL DESIGN We perform multiomic characterization of a large HGSOC cohort (n = 362) with detailed clinical annotation to interrogate the relationship between patient subgroups defined by specific molecular events. RESULTS BRCA2-mutant (BRCA2m) and EMSY-overexpressing cases demonstrated prolonged survival [multivariable hazard ratios (HR) 0.40 and 0.51] and significantly higher first- and second-line chemotherapy response rate. CCNE1-gained (CCNE1g) cases demonstrated underrepresentation of FIGO stage IV cases, with shorter survival but no significant difference in treatment response. We demonstrate marked overlap between the TCGA- and Tothill-derived subtypes. IMR/C2 cases displayed higher BRCA1/2m frequency (25.5%, 32.5%) and significantly greater immune cell infiltration, whereas PRO/C5 cases had the highest CCNE1g rate (23.9%, 22.2%) and were uniformly low in immune cell infiltration. The survival benefit for cases with aberrations in homologous recombination repair (HRR) genes was apparent across all transcriptomic subtypes (HR range, 0.48-0.68). There was significant co-occurrence of RB loss and HRR gene aberrations; RB loss was further associated with favorable survival within HRR-aberrant cases (multivariable HR, 0.50). CONCLUSIONS These data paint a high-resolution picture of the molecular landscape in HGSOC, better defining patients who may benefit most from specific molecular therapeutics and highlighting those for whom novel treatment strategies are needed to improve outcomes.
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Affiliation(s)
- Robert L. Hollis
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Corresponding Author: Robb L. Hollis, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, Scotland, UK. E-mail:
| | - Alison M. Meynert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Caroline O. Michie
- Edinburgh Cancer Centre, Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Tzyvia Rye
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Amelia Hallas-Potts
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ian Croy
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | | | - Clare Bartos
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Yasushi Iida
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- The Jikei University School of Medicine, Tokyo, Japan
| | - Aikou Okamoto
- The Jikei University School of Medicine, Tokyo, Japan
| | - Brian Dougherty
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - J. Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - Ruth March
- Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Athena Matakidou
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Patricia Roxburgh
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Belfast, UK
- Beatson West of Scotland Cancer Centre, Glasgow, UK
| | - Colin A. Semple
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - D. Paul Harkin
- Almac Diagnostics, Craigavon, UK
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Richard Kennedy
- Almac Diagnostics, Craigavon, UK
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - C. Simon Herrington
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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2
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Parkes EE, Savage KI, Lioe T, Boyd C, Halliday S, Walker SM, Lowry K, Knight L, Buckley NE, Grogan A, Logan GE, Clayton A, Hurwitz J, Kirk SJ, Xu J, Sidi FA, Humphries MP, Bingham V, James JA, James CR, Paul Harkin D, Kennedy RD, McIntosh SA. Activation of a cGAS-STING-mediated immune response predicts response to neoadjuvant chemotherapy in early breast cancer. Br J Cancer 2022; 126:247-258. [PMID: 34728791 PMCID: PMC8770594 DOI: 10.1038/s41416-021-01599-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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] [Received: 02/08/2021] [Revised: 09/21/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The DNA-damage immune-response (DDIR) signature is an immune-driven gene expression signature retrospectively validated as predicting response to anthracycline-based therapy. This feasibility study prospectively evaluates the use of this assay to predict neoadjuvant chemotherapy response in early breast cancer. METHODS This feasibility study assessed the integration of a novel biomarker into clinical workflows. Tumour samples were collected from patients receiving standard of care neoadjuvant chemotherapy (FEC + /-taxane and anti-HER2 therapy as appropriate) at baseline, mid- and post-chemotherapy. Baseline DDIR signature scores were correlated with pathological treatment response. RNA sequencing was used to assess chemotherapy/response-related changes in biologically linked gene signatures. RESULTS DDIR signature reports were available within 14 days for 97.8% of 46 patients (13 TNBC, 16 HER2 + ve, 27 ER + HER2-ve). Positive scores predicted response to treatment (odds ratio 4.67 for RCB 0-1 disease (95% CI 1.13-15.09, P = 0.032)). DDIR positivity correlated with immune infiltration and upregulated immune-checkpoint gene expression. CONCLUSIONS This study validates the DDIR signature as predictive of response to neoadjuvant chemotherapy which can be integrated into clinical workflows, potentially identifying a subgroup with high sensitivity to anthracycline chemotherapy. Transcriptomic data suggest induction with anthracycline-containing regimens in immune restricted, "cold" tumours may be effective for immune priming. TRIAL REGISTRATION Not applicable (non-interventional study). CRUK Internal Database Number 14232.
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Affiliation(s)
- Eileen E Parkes
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Kienan I Savage
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Tong Lioe
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Clinton Boyd
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Sophia Halliday
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Steven M Walker
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Keith Lowry
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Laura Knight
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Niamh E Buckley
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Andrena Grogan
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Gemma E Logan
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Alison Clayton
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Jane Hurwitz
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Stephen J Kirk
- South Eastern Health and Social Care Trust, Ulster Hospital, Upper Newtownards Road, BT 16 1RH, Dundonald, UK
| | - Jiamei Xu
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Fatima Abdullahi Sidi
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Matthew P Humphries
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Victoria Bingham
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Jaqueline A James
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Colin R James
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - D Paul Harkin
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Richard D Kennedy
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Stuart A McIntosh
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK.
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK.
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3
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Lappin KM, Barros EM, Jhujh SS, Irwin GW, McMillan H, Liberante FG, Latimer C, LaBonte MJ, Mills KI, Harkin DP, Stewart GS, Savage KI. CANCER-ASSOCIATED SF3B1 MUTATIONS CONFER A BRCA-LIKE CELLULAR PHENOTYPE AND SYNTHETIC LETHALITY TO PARP INHIBITORS. Cancer Res 2022; 82:819-830. [DOI: 10.1158/0008-5472.can-21-1843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/12/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
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Turkington RC, Knight LA, Blayney JK, Secrier M, Douglas R, Parkes EE, Sutton EK, Stevenson L, McManus D, Halliday S, McCavigan AM, Logan GE, Walker SM, Steele CJ, Perner J, Bornschein J, MacRae S, Miremadi A, McCarron E, McQuaid S, Arthur K, James JA, Eatock MM, O'Neill R, Noble F, Underwood TJ, Harkin DP, Salto-Tellez M, Fitzgerald RC, Kennedy RD. Immune activation by DNA damage predicts response to chemotherapy and survival in oesophageal adenocarcinoma. Gut 2019; 68:1918-1927. [PMID: 30852560 PMCID: PMC6839732 DOI: 10.1136/gutjnl-2018-317624] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Current strategies to guide selection of neoadjuvant therapy in oesophageal adenocarcinoma (OAC) are inadequate. We assessed the ability of a DNA damage immune response (DDIR) assay to predict response following neoadjuvant chemotherapy in OAC. DESIGN Transcriptional profiling of 273 formalin-fixed paraffin-embedded prechemotherapy endoscopic OAC biopsies was performed. All patients were treated with platinum-based neoadjuvant chemotherapy and resection between 2003 and 2014 at four centres in the Oesophageal Cancer Clinical and Molecular Stratification consortium. CD8 and programmed death ligand 1 (PD-L1) immunohistochemical staining was assessed in matched resection specimens from 126 cases. Kaplan-Meier and Cox proportional hazards regression analysis were applied according to DDIR status for recurrence-free survival (RFS) and overall survival (OS). RESULTS A total of 66 OAC samples (24%) were DDIR positive with the remaining 207 samples (76%) being DDIR negative. DDIR assay positivity was associated with improved RFS (HR: 0.61; 95% CI 0.38 to 0.98; p=0.042) and OS (HR: 0.52; 95% CI 0.31 to 0.88; p=0.015) following multivariate analysis. DDIR-positive patients had a higher pathological response rate (p=0.033), lower nodal burden (p=0.026) and reduced circumferential margin involvement (p=0.007). No difference in OS was observed according to DDIR status in an independent surgery-alone dataset.DDIR-positive OAC tumours were also associated with the presence of CD8+ lymphocytes (intratumoural: p<0.001; stromal: p=0.026) as well as PD-L1 expression (intratumoural: p=0.047; stromal: p=0.025). CONCLUSION The DDIR assay is strongly predictive of benefit from DNA-damaging neoadjuvant chemotherapy followed by surgical resection and is associated with a proinflammatory microenvironment in OAC.
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Affiliation(s)
- Richard C Turkington
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | - Jaine K Blayney
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Maria Secrier
- Genetics Institute, University College London, London, UK
| | - Rosalie Douglas
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Eileen E Parkes
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Eilis K Sutton
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Leanne Stevenson
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Damian McManus
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - Sophia Halliday
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | | | | | | | - Juliane Perner
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jan Bornschein
- Translational Gastroenterology Unit, John Radcliffe Hospital Oxford University Hospitals NHS Trust, Oxford, UK
| | | | - Ahmad Miremadi
- Department of Histopathology, Addenbrookes Hospital, Cambridge, UK
| | - Eamon McCarron
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - Stephen McQuaid
- Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, Belfast, UK
| | - Kenneth Arthur
- Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, Belfast, UK
| | - Jacqueline A James
- Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, Belfast, UK
| | - Martin M Eatock
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
- Department of Medical Oncology, Belfast Health and Social Care Trust, Belfast, UK
| | - Robert O'Neill
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, UK
| | - Fergus Noble
- Department of Surgery, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | | | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | - Richard D Kennedy
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
- Almac Diagnostics Ltd, Craigavon, UK
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5
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Hollis RL, Churchman M, Michie CO, Rye T, Knight L, McCavigan A, Perren T, Williams ARW, McCluggage WG, Kaplan RS, Jayson GC, Oza A, Harkin DP, Herrington CS, Kennedy R, Gourley C. High EMSY expression defines a BRCA-like subgroup of high-grade serous ovarian carcinoma with prolonged survival and hypersensitivity to platinum. Cancer 2019; 125:2772-2781. [PMID: 31154673 PMCID: PMC6771827 DOI: 10.1002/cncr.32079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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] [Received: 10/23/2018] [Revised: 01/11/2019] [Accepted: 01/15/2019] [Indexed: 11/14/2022]
Abstract
BACKGROUND Approximately half of high-grade serous ovarian carcinomas (HGSOCs) demonstrate homologous recombination repair (HR) pathway defects, resulting in a distinct clinical phenotype comprising hypersensitivity to platinum, superior clinical outcome, and greater sensitivity to poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitors. EMSY, which is known to be amplified in breast and ovarian cancers, encodes a protein reported to bind and inactivate BRCA2. Thus, EMSY overexpression may mimic BRCA2 mutation, resulting in HR deficiency. However, to our knowledge, the phenotypic consequences of EMSY overexpression in HGSOC patients has not been explored. METHODS Here we investigate the impact of EMSY expression on clinical outcome and sensitivity to platinum-based chemotherapy using available data from transcriptomically characterized HGSOC cohorts. RESULTS High EMSY expression was associated with better clinical outcome in a cohort of 265 patients with HGSOC from Edinburgh (overall survival multivariable hazard ratio, 0.58 [95% CI, 0.38-0.88; P = .011] and progression-free survival multivariable hazard ratio, 0.62 [95% CI, 0.40-0.96; P = .030]). Superior outcome also was demonstrated in the Medical Research Council ICON7 clinical trial and multiple publicly available data sets. Patients within the Edinburgh cohort who had high EMSY expression were found to demonstrate greater rates of complete response to multiple platinum-containing chemotherapy regimens (radiological complete response rate of 44.4% vs 12.5% at second exposure; P = .035) and corresponding prolonged time to disease progression (median, 151.5 days vs 60.5 days after third platinum exposure; P = .004). CONCLUSIONS Patients with HGSOCs demonstrating high EMSY expression appear to experience prolonged survival and greater platinum sensitivity, reminiscent of BRCA-mutant cases. These data are consistent with the notion that EMSY overexpression may render HGSOCs HR deficient.
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Affiliation(s)
- Robert L. Hollis
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Caroline O. Michie
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Tzyvia Rye
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | | | | | - Timothy Perren
- St. James's Institute of OncologySt. James's University HospitalLeedsUnited Kingdom
| | | | - W. Glenn McCluggage
- Center for Cancer Research and Cell BiologyQueen's University of BelfastBelfastUnited Kingdom
- Department of PathologyBelfast Health and Social Care TrustBelfastUnited Kingdom
| | - Richard S. Kaplan
- Medical Research Council Clinical Trials Unit at University College LondonLondonUnited Kingdom
| | - Gordon C. Jayson
- Division of Molecular and Clinical Cancer SciencesUniversity of ManchesterManchesterUnited Kingdom
| | - Amit Oza
- Cancer Clinical Research Unit, Division of Medical Oncology and Hematology, Princess Margaret Cancer CentreUniversity of TorontoTorontoOntarioCanada
| | - D. Paul Harkin
- Almac DiagnosticsCraigavonUnited Kingdom
- Center for Cancer Research and Cell BiologyQueen's University of BelfastBelfastUnited Kingdom
| | - C. Simon Herrington
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
- Department of PathologyUniversity of EdinburghEdinburghUnited Kingdom
- Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Richard Kennedy
- Almac DiagnosticsCraigavonUnited Kingdom
- Center for Cancer Research and Cell BiologyQueen's University of BelfastBelfastUnited Kingdom
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
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6
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Jain S, Lyons CA, Walker SM, McQuaid S, Hynes SO, Mitchell DM, Pang B, Logan GE, McCavigan AM, O'Rourke D, McArt DG, McDade SS, Mills IG, Prise KM, Knight LA, Steele CJ, Medlow PW, Berge V, Katz B, Loblaw DA, Harkin DP, James JA, O'Sullivan JM, Kennedy RD, Waugh DJ. Validation of a Metastatic Assay using biopsies to improve risk stratification in patients with prostate cancer treated with radical radiation therapy. Ann Oncol 2019; 29:215-222. [PMID: 29045551 PMCID: PMC5834121 DOI: 10.1093/annonc/mdx637] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Background Radiotherapy is an effective treatment of intermediate/high-risk locally advanced prostate cancer, however, >30% of patients relapse within 5 years. Clinicopathological parameters currently fail to identify patients prone to systemic relapse and those whom treatment intensification may be beneficial. The purpose of this study was to independently validate the performance of a 70-gene Metastatic Assay in a cohort of diagnostic biopsies from patients treated with radical radiotherapy and androgen deprivation therapy. Patients and methods A bridging cohort of prostate cancer diagnostic biopsy specimens was profiled to enable optimization of the Metastatic Assay threshold before further independent clinical validation in a cohort of diagnostic biopsies from patients treated with radical radiotherapy and androgen deprivation therapy. Multivariable Cox proportional hazard regression analysis was used to assess assay performance in predicting biochemical failure-free survival (BFFS) and metastasis-free survival (MFS). Results Gene expression analysis was carried out in 248 patients from the independent validation cohort and the Metastatic Assay applied. Ten-year MFS was 72% for Metastatic Assay positive patients and 94% for Metastatic Assay negative patients [HR = 3.21 (1.35–7.67); P = 0.003]. On multivariable analysis the Metastatic Assay remained predictive for development of distant metastases [HR = 2.71 (1.11–6.63); P = 0.030]. The assay retained independent prognostic performance for MFS when assessed with the Cancer of the Prostate Assessment Score (CAPRA) [HR = 3.23 (1.22–8.59); P = 0.019] whilst CAPRA itself was not significant [HR = 1.88, (0.52–6.77); P = 0.332]. A high concordance [100% (61.5–100)] for the assay result was noted between two separate foci taken from 11 tumours, whilst Gleason score had low concordance. Conclusions The Metastatic Assay demonstrated significant prognostic performance in patients treated with radical radiotherapy both alone and independent of standard clinical and pathological variables. The Metastatic Assay could have clinical utility when deciding upon treatment intensification in high-risk patients. Genomic and clinical data are available as a public resource.
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Affiliation(s)
- S Jain
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK
| | - C A Lyons
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK
| | - S M Walker
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK.,Almac Diagnostics, Seagoe Industrial Estate, Craigavon, UK
| | - S McQuaid
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK
| | - S O Hynes
- Department of Pathology, University Hospital Galway, Galway, Ireland
| | - D M Mitchell
- Northern Ireland Cancer Centre, Belfast City Hospital, Belfast, UK
| | - B Pang
- Department of Pathology, National University Cancer Institute, Singapore
| | - G E Logan
- Almac Diagnostics, Seagoe Industrial Estate, Craigavon, UK
| | - A M McCavigan
- Almac Diagnostics, Seagoe Industrial Estate, Craigavon, UK
| | - D O'Rourke
- Department of Pathology, Belfast City Hospital, Belfast, UK
| | - D G McArt
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK
| | - S S McDade
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK
| | - I G Mills
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK
| | - K M Prise
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK
| | - L A Knight
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK.,Almac Diagnostics, Seagoe Industrial Estate, Craigavon, UK
| | - C J Steele
- Almac Diagnostics, Seagoe Industrial Estate, Craigavon, UK
| | - P W Medlow
- Almac Diagnostics, Seagoe Industrial Estate, Craigavon, UK
| | - V Berge
- Department of Urology, Oslo University Hospital, Oslo, Norway
| | - B Katz
- Department of Urology, Oslo University Hospital, Oslo, Norway
| | - D A Loblaw
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada
| | - D P Harkin
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK.,Almac Diagnostics, Seagoe Industrial Estate, Craigavon, UK
| | - J A James
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK
| | - J M O'Sullivan
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK
| | - R D Kennedy
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK.,Almac Diagnostics, Seagoe Industrial Estate, Craigavon, UK
| | - D J Waugh
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK
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7
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Campbell AM, Morris M, Gallagher R, Boyd R, Carson H, Harkin DP, Wielogorska E, Elliott C, Savage KI, McIntosh SA. Chemoprevention in BRCA1 mutation carriers (CIBRAC): protocol for an open allocation crossover feasibility trial assessing mechanisms of chemoprevention with goserelin and anastrozole versus tamoxifen and acceptability of treatment. BMJ Open 2018; 8:e023115. [PMID: 30580266 PMCID: PMC6318512 DOI: 10.1136/bmjopen-2018-023115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION BRCA1 mutation carriers have a significant lifetime risk of breast cancer, with their primary risk-reduction option being bilateral mastectomy. Preclinical work from our laboratory demonstrated that in BRCA1-deficient breast cells, oestrogen and its metabolites are capable of driving DNA damage and subsequent genomic instability, which are well-defined early events in BRCA1-related cancers. Based on this, we hypothesise that a chemopreventive approach which reduces circulating oestrogen levels may reduce DNA damage and genomic instability, thereby providing an alternative to risk-reducing surgery. METHODS AND ANALYSIS 12 premenopausal women with pathogenic BRCA1 mutations and no previous risk-reducing surgery will be recruited from family history clinics. Participants will be allocated 1:1 to two arms. All will undergo baseline breast biopsies, blood and urine sampling, and quality of life questionnaires. Group A will receive goserelin 3.6 mg/28 days by subcutaneous injection, plus oral anastrozole 1 mg/day, for 12 weeks. Group B will receive oral tamoxifen 20 mg/day for 12 weeks. Following treatment, both groups will provide repeat biopsies, blood and urine samples, and questionnaires. Following a 1-month washout period, the groups will cross over, group A receiving tamoxifen and group B goserelin and anastrozole for a further 12 weeks. After treatment, biopsies, blood and urine samples, and questionnaires will be repeated. DNA damage will be assessed in core biopsies, while blood and urine samples will be used to measure oestrogen metabolite and DNA adduct levels. ETHICS AND DISSEMINATION This study has ethical approval from the Office for Research Ethics Committees Northern Ireland (16/NI/0055) and the Medicines and Healthcare products Regulatory Agency (MHRA) (reference: 32485/0032/001-0001). The investigational medicinal products used in this trial are licensed and in common use, with well-documented safety information. Dissemination of results will be via high-impact journals and relevant national/international conferences. A copy of the results will be offered to the participants and be made available to patient support groups. TRIAL REGISTRATION NUMBER EudraCT: 2016-001087-11; Pre-results.
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Affiliation(s)
- Aideen M Campbell
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Melanie Morris
- Northern Ireland Cancer Trials Network, Belfast City Hospital, Belfast, UK
| | - Rebecca Gallagher
- Northern Ireland Cancer Trials Network, Belfast City Hospital, Belfast, UK
| | - Ruth Boyd
- Northern Ireland Cancer Trials Network, Belfast City Hospital, Belfast, UK
| | | | - D Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | - Christopher Elliott
- Institute for Global Food Security, Advanced ASSET Centre, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Kienan I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Stuart A McIntosh
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
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8
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Reilly E, McCavigan A, Walker SM, McCabe N, Parkes E, Harkin DP, Kennedy RD, Knight LA. Exploration of the cGAS-STING pathway in prostate cancer. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.5075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Emma Reilly
- Almac Diagnostics, Craigavon, United Kingdom
| | | | | | | | - Eileen Parkes
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom
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9
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Johnston R, D'Costa Z, Ray S, Gorski J, Harkin DP, Mullan P, Panov KI. The identification of a novel role for BRCA1 in regulating RNA polymerase I transcription. Oncotarget 2018; 7:68097-68110. [PMID: 27589844 PMCID: PMC5356541 DOI: 10.18632/oncotarget.11770] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/24/2016] [Indexed: 12/22/2022] Open
Abstract
The unrestrained proliferation of cancer cells requires a high level of ribosome biogenesis. The first stage of ribosome biogenesis is the transcription of the large ribosomal RNAs (rRNAs); the structural and functional components of the ribosome. Transcription of rRNA is carried out by RNA polymerase I (Pol-I) and its associated holoenzyme complex.Here we report that BRCA1, a nuclear phosphoprotein, and a known tumour suppressor involved in variety of cellular processes such as DNA damage response, transcriptional regulation, cell cycle control and ubiquitylation, is associated with rDNA repeats, in particular with the regulatory regions of the rRNA gene.We demonstrate that BRCA1 interacts directly with the basal Pol-I transcription factors; upstream binding factor (UBF), selectivity factor-1 (SL1) as well as interacting with RNA Pol-I itself. We show that in response to DNA damage, BRCA1 occupancy at the rDNA repeat is decreased and the observed BRCA1 interactions with the Pol-I transcription machinery are weakened.We propose, therefore, that there is a rDNA associated fraction of BRCA1 involved in DNA damage dependent regulation of Pol-I transcription, regulating the stability and formation of the Pol-I holoenzyme during initiation and/or elongation in response to DNA damage.
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Affiliation(s)
- Rebecca Johnston
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Zenobia D'Costa
- The Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7BL, UK.,Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Swagat Ray
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, UK.,Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Julia Gorski
- The Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - D Paul Harkin
- The Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Paul Mullan
- The Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Konstantin I Panov
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, UK.,The Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7BL, UK
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10
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Reilly E, McCavigan A, Walker SM, McCabe N, Parkes E, Harkin DP, Kennedy RD, Knight LA. Exploration of the cGAS-STING pathway in prostate cancer. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.5_suppl.103] [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: 11/20/2022] Open
Abstract
103 Background: Recent studies have demonstrated limited success of immune checkpoint therapies in unselected prostate cancer. We therefore assessed an immune based DNA Damage Repair Deficiency (DDRD) assay, that we have previously reported represents activation of the cGAS STING pathway, in the TCGA prostate cancer dataset to investigate the presence of targetable immune biology in prostate cancer. In addition we applied a second assay (the prostate cancer metastatic signature-PCM) that predicts the risk of metastatic recurrence for early prostate cancer, in order to assess if immune therapy could have a role in treating high risk disease. Methods: 498 samples with RNA sequencing data were scored with the PCM and DDRD assays. Integrative analysis was performed on 488 samples with RNA sequencing, promoter site methylation, somatic mutation and somatic copy number variation. Gene expression of n = 6 immune checkpoint targets was investigated with the subgroups identified using T-tests. The prevalence of immune infiltration in each subgroup was tested by applying a cut off to the leukocyte fraction. Cox proportional hazards regression analysis of 441 patients was assessed for biochemical recurrence. Results: Integrative analysis identified four patient subgroups characterised primarily by variances in copy number and genomic mutation. One of these subgroups ‘Metastatic-like DDRD’ had significantly higher PCM scores and DDRD immune scores compared to the other subgroups (p < 2E-12). This subgroup of patients showed elevated leukocyte fraction and expression of immune checkpoint genes: CD274 (PDL1), CTLA4, ICOS, IDO1, HAVCR2 (TIM3) & LAG3 (p < 2E-6). Genomic instability with amplification of 8q and a larger prevalence of somatic mutations including that of TP53 was also detected in this subgroup. These patients had an increased risk of biochemical relapse in both univariate (p < 2E-5) and multivariate (p < 0.008) analysis. Conclusions: We identified a poor prognostic subgroup, representing 17% of early prostate cancer patients that are at increased risk of developing metastatic disease and present with targetable immune biology. These patients may represent a viable target population for immune checkpoint and DNA damaging therapies in prostate cancer.
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Affiliation(s)
- Emma Reilly
- Almac Diagnostics, Craigavon, United Kingdom
| | | | | | | | - Eileen Parkes
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom
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11
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McGivern N, El-Helali A, Mullan P, McNeish IA, Paul Harkin D, Kennedy RD, McCabe N. Activation of MAPK signalling results in resistance to saracatinib (AZD0530) in ovarian cancer. Oncotarget 2018; 9:4722-4736. [PMID: 29435137 PMCID: PMC5797008 DOI: 10.18632/oncotarget.23524] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/01/2017] [Indexed: 02/06/2023] Open
Abstract
SRC tyrosine kinase is frequently overexpressed and activated in late-stage, poor prognosis ovarian tumours, and preclinical studies have supported the use of targeted SRC inhibitors in the treatment of this disease. The SAPPROC trial investigated the addition of the SRC inhibitor saracatinib (AZD0530) to weekly paclitaxel for the treatment of platinum resistant ovarian cancer; however, this drug combination did not provide any benefit to progression free survival (PFS) of women with platinum resistant disease. In this study we aimed to identify mechanisms of resistance to SRC inhibitors in ovarian cancer cells. Using two complementary strategies; a targeted tumour suppressor gene siRNA screen, and a phospho-receptor tyrosine kinase array, we demonstrate that activation of MAPK signalling, via a reduction in NF1 (neurofibromin) expression or overexpression of HER2 and the insulin receptor, can drive resistance to AZD0530. Knockdown of NF1 in two ovarian cancer cell lines resulted in resistance to AZD0530, and was accompanied with activated MEK and ERK signalling. We also show that silencing of HER2 and the insulin receptor can partially resensitize AZD0530 resistant cells, which was associated with decreased phosphorylation of MEK and ERK. Furthermore, we demonstrate a synergistic effect of combining SRC and MEK inhibitors in both AZD0530 sensitive and resistant cells, and that MEK inhibition is sufficient to completely resensitize AZD0530 resistant cells. This work provides a preclinical rationale for the combination of SRC and MEK inhibitors in the treatment of ovarian cancer, and also highlights the need for biomarker driven patient selection for clinical trials.
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Affiliation(s)
- Niamh McGivern
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Northern Ireland, UK
| | - Aya El-Helali
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Northern Ireland, UK
| | - Paul Mullan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Northern Ireland, UK
| | - Iain A. McNeish
- Institute of Cancer Sciences, University of Glasgow, Scotland, UK
| | - D. Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Northern Ireland, UK
- Almac Diagnostics, 19 Seagoe Industrial Estate, Craigavon, Northern Ireland, UK
| | - Richard D. Kennedy
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Northern Ireland, UK
- Almac Diagnostics, 19 Seagoe Industrial Estate, Craigavon, Northern Ireland, UK
| | - Nuala McCabe
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Northern Ireland, UK
- Almac Diagnostics, 19 Seagoe Industrial Estate, Craigavon, Northern Ireland, UK
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12
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Bankhead P, Fernández JA, McArt DG, Boyle DP, Li G, Loughrey MB, Irwin GW, Harkin DP, James JA, McQuaid S, Salto-Tellez M, Hamilton PW. Integrated tumor identification and automated scoring minimizes pathologist involvement and provides new insights to key biomarkers in breast cancer. J Transl Med 2018; 98:15-26. [PMID: 29251737 DOI: 10.1038/labinvest.2017.131] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [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] [Received: 06/04/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 02/07/2023] Open
Abstract
Digital image analysis (DIA) is becoming central to the quantitative evaluation of tissue biomarkers for discovery, diagnosis and therapeutic selection for the delivery of precision medicine. In this study, automated DIA using a new purpose-built software platform (QuPath) is applied to a cohort of 293 breast cancer patients to score five biomarkers in tissue microarrays (TMAs): ER, PR, HER2, Ki67 and p53. This software is able to measure IHC expression following fully automated tumor recognition in the same immunohistochemical (IHC)-stained tissue section, as part of a rapid workflow to ensure objectivity and accelerate biomarker analysis. The digital scores produced by QuPath were compared with manual scores by a pathologist and shown to have a good level of concordance in all cases (Cohen's κ>0.6), and almost perfect agreement for the clinically relevant biomarkers ER, PR and HER2 (κ>0.86). To assess prognostic value, cutoff thresholds could be applied to both manual and automated scores using the QuPath software, and survival analysis performed for 5-year overall survival. DIA was shown to be capable of replicating the statistically significant stratification of patients achieved using manual scoring across all biomarkers (P<0.01, log-rank test). Furthermore, the image analysis scores were shown to consistently lead to statistical significance across a wide range of potential cutoff thresholds, indicating the robustness of the method, and identify sub-populations of cases exhibiting different expression patterns within the p53 and Ki67 data sets that warrant further investigation. These findings have demonstrated QuPath's suitability for fast, reproducible, high-throughput TMA analysis across a range of important biomarkers. This was achieved using our tumor recognition algorithms for IHC-stained sections, trained interactively without the need for any additional tumor recognition markers, for example, cytokeratin, to obtain greater insight into the relationship between biomarker expression and clinical outcome applicable to a range of cancer types.
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Affiliation(s)
- Peter Bankhead
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - José A Fernández
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Darragh G McArt
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - David P Boyle
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Gerald Li
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Maurice B Loughrey
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Gareth W Irwin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - D Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Jacqueline A James
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Stephen McQuaid
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Manuel Salto-Tellez
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Peter W Hamilton
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
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13
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Vohhodina J, Barros EM, Savage AL, Liberante FG, Manti L, Bankhead P, Cosgrove N, Madden AF, Harkin DP, Savage KI. The RNA processing factors THRAP3 and BCLAF1 promote the DNA damage response through selective mRNA splicing and nuclear export. Nucleic Acids Res 2017; 45:12816-12833. [PMID: 29112714 PMCID: PMC5728405 DOI: 10.1093/nar/gkx1046] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 10/03/2017] [Accepted: 10/19/2017] [Indexed: 12/18/2022] Open
Abstract
mRNA splicing and export plays a key role in the regulation of gene expression, with recent evidence suggesting an additional layer of regulation of gene expression and cellular function through the selective splicing and export of genes within specific pathways. Here we describe a role for the RNA processing factors THRAP3 and BCLAF1 in the regulation of the cellular DNA damage response (DDR) pathway, a key pathway involved in the maintenance of genomic stability and the prevention of oncogenic transformation. We show that loss of THRAP3 and/or BCLAF1 leads to sensitivity to DNA damaging agents, defective DNA repair and genomic instability. Additionally, we demonstrate that this phenotype can be at least partially explained by the role of THRAP3 and BCLAF1 in the selective mRNA splicing and export of transcripts encoding key DDR proteins, including the ATM kinase. Moreover, we show that cancer associated mutations within THRAP3 result in deregulated processing of THRAP3/BCLAF1-regulated transcripts and consequently defective DNA repair. Taken together, these results suggest that THRAP3 and BCLAF1 mutant tumors may be promising targets for DNA damaging chemotherapy.
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Affiliation(s)
- Jekaterina Vohhodina
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Eliana M. Barros
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Abigail L. Savage
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Fabio G. Liberante
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Lorenzo Manti
- Dipartimento di Fisica ‘E Pancini’, Università di Napoli Federico II, Monte S. Angelo, 80126 Napoli, Italy
| | - Peter Bankhead
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Nicola Cosgrove
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin 2, D02 YN77, Ireland
| | - Angelina F. Madden
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - D. Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Kienan I. Savage
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
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14
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Niedzwiecki D, Frankel WL, Venook AP, Ye X, Friedman PN, Goldberg RM, Mayer RJ, Colacchio TA, Mulligan JM, Davison TS, O'Brien E, Kerr P, Johnston PG, Kennedy RD, Harkin DP, Schilsky RL, Bertagnolli MM, Warren RS, Innocenti F. Reply to L. Casadaban et al. J Clin Oncol 2017; 35:1373-1374. [PMID: 28113023 DOI: 10.1200/jco.2016.71.2646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Donna Niedzwiecki
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Wendy L Frankel
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alan P Venook
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Xing Ye
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Paula N Friedman
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Richard M Goldberg
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Robert J Mayer
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Thomas A Colacchio
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jude Marie Mulligan
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Timothy S Davison
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Eamonn O'Brien
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Peter Kerr
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Patrick G Johnston
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Richard D Kennedy
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - D Paul Harkin
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Richard L Schilsky
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Monica M Bertagnolli
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Robert S Warren
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Federico Innocenti
- Donna Niedzwiecki, Duke University, Durham, NC; Wendy L. Frankel, The Ohio State University, Columbus, OH; Alan P. Venook, University of California, San Francisco, San Francisco, CA; Xing Ye, Duke University, Durham, NC; Paula N. Friedman, Northwestern University, Chicago, IL; Richard M. Goldberg, The Ohio State University, Columbus, OH; Robert J. Mayer, Dana-Farber Cancer Institute, Boston, MA; Thomas A. Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, and Peter Kerr, Almac Diagnostics, Craigavon, United Kingdom; Patrick G. Johnston, Queen's University, Belfast, United Kingdom; Richard D. Kennedy and D. Paul Harkin, Almac Diagnostics, Craigavon, United Kingdom; Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Robert S. Warren, University of California, San Francisco, San Francisco, CA; and Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC
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15
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Parkes EE, Walker SM, Taggart LE, McCabe N, Knight LA, Wilkinson R, McCloskey KD, Buckley NE, Savage KI, Salto-Tellez M, McQuaid S, Harte MT, Mullan PB, Harkin DP, Kennedy RD. Activation of STING-Dependent Innate Immune Signaling By S-Phase-Specific DNA Damage in Breast Cancer. J Natl Cancer Inst 2016; 109:2905926. [PMID: 27707838 PMCID: PMC5441301 DOI: 10.1093/jnci/djw199] [Citation(s) in RCA: 309] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 07/29/2016] [Indexed: 11/14/2022] Open
Abstract
Background Previously we identified a DNA damage response-deficient (DDRD) molecular subtype within breast cancer. A 44-gene assay identifying this subtype was validated as predicting benefit from DNA-damaging chemotherapy. This subtype was defined by interferon signaling. In this study, we address the mechanism of this immune response and its possible clinical significance. Methods We used immunohistochemistry (IHC) to characterize immune infiltration in 184 breast cancer samples, of which 65 were within the DDRD subtype. Isogenic cell lines, which represent DDRD-positive and -negative, were used to study the effects of chemokine release on peripheral blood mononuclear cell (PBMC) migration and the mechanism of immune signaling activation. Finally, we studied the association between the DDRD subtype and expression of the immune-checkpoint protein PD-L1 as detected by IHC. All statistical tests were two-sided. Results We found that DDRD breast tumors were associated with CD4+ and CD8+ lymphocytic infiltration (Fisher's exact test P < .001) and that DDRD cells expressed the chemokines CXCL10 and CCL5 3.5- to 11.9-fold more than DNA damage response-proficient cells (P < .01). Conditioned medium from DDRD cells statistically significantly attracted PBMCs when compared with medium from DNA damage response-proficient cells (P < .05), and this was dependent on CXCL10 and CCL5. DDRD cells demonstrated increased cytosolic DNA and constitutive activation of the viral response cGAS/STING/TBK1/IRF3 pathway. Importantly, this pathway was activated in a cell cycle-specific manner. Finally, we demonstrated that S-phase DNA damage activated expression of PD-L1 in a STING-dependent manner. Conclusions We propose a novel mechanism of immune infiltration in DDRD tumors, independent of neoantigen production. Activation of this pathway and associated PD-L1 expression may explain the paradoxical lack of T-cell-mediated cytotoxicity observed in DDRD tumors. We provide a rationale for exploration of DDRD in the stratification of patients for immune checkpoint-based therapies.
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Affiliation(s)
- Eileen E Parkes
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Steven M Walker
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Laura E Taggart
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Nuala McCabe
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Laura A Knight
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Richard Wilkinson
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Karen D McCloskey
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Niamh E Buckley
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Kienan I Savage
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Manuel Salto-Tellez
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Stephen McQuaid
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Mary T Harte
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Paul B Mullan
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - D Paul Harkin
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
| | - Richard D Kennedy
- Affiliations of authors: Centre for Cancer Research and Cell Biology (EEP, SMW, LET, NM, RW, KDM, NEB, KIS, MST, SM, MTH, PBM, DPH, RDK) and Northern Ireland Molecular Pathology Laboratory (MST, SM), Queens University Belfast, Northern Ireland; Almac Diagnostics, Craigavon, Northern Ireland (SMW, LET, NM, LH, DPH, RDK)
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16
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Blayney JK, Davison T, McCabe N, Walker S, Keating K, Delaney T, Greenan C, Williams AR, McCluggage WG, Capes-Davis A, Harkin DP, Gourley C, Kennedy RD. Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line. Nucleic Acids Res 2016; 44:e137. [PMID: 27353327 PMCID: PMC5041471 DOI: 10.1093/nar/gkw578] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/17/2016] [Accepted: 06/16/2016] [Indexed: 01/03/2023] Open
Abstract
Here, we describe gene expression compositional assignment (GECA), a powerful, yet simple method based on compositional statistics that can validate the transfer of prior knowledge, such as gene lists, into independent data sets, platforms and technologies. Transcriptional profiling has been used to derive gene lists that stratify patients into prognostic molecular subgroups and assess biomarker performance in the pre-clinical setting. Archived public data sets are an invaluable resource for subsequent in silico validation, though their use can lead to data integration issues. We show that GECA can be used without the need for normalising expression levels between data sets and can outperform rank-based correlation methods. To validate GECA, we demonstrate its success in the cross-platform transfer of gene lists in different domains including: bladder cancer staging, tumour site of origin and mislabelled cell lines. We also show its effectiveness in transferring an epithelial ovarian cancer prognostic gene signature across technologies, from a microarray to a next-generation sequencing setting. In a final case study, we predict the tumour site of origin and histopathology of epithelial ovarian cancer cell lines. In particular, we identify and validate the commonly-used cell line OVCAR-5 as non-ovarian, being gastrointestinal in origin. GECA is available as an open-source R package.
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Affiliation(s)
- Jaine K Blayney
- Centre for Cancer Research and Cell Biology, Queen's University, Belfast, BT9 7BL, UK
| | - Timothy Davison
- Centre for Cancer Research and Cell Biology, Queen's University, Belfast, BT9 7BL, UK Almac Diagnostics, Craigavon, BT63 5QD, UK
| | - Nuala McCabe
- Centre for Cancer Research and Cell Biology, Queen's University, Belfast, BT9 7BL, UK Almac Diagnostics, Craigavon, BT63 5QD, UK
| | - Steven Walker
- Centre for Cancer Research and Cell Biology, Queen's University, Belfast, BT9 7BL, UK Almac Diagnostics, Craigavon, BT63 5QD, UK
| | | | | | - Caroline Greenan
- Centre for Cancer Research and Cell Biology, Queen's University, Belfast, BT9 7BL, UK Almac Diagnostics, Craigavon, BT63 5QD, UK
| | - Alistair R Williams
- Department of Pathology, The University of Edinburgh, Royal Infirmary of Edinburgh, EH16 4SA, UK
| | - W Glenn McCluggage
- Centre for Cancer Research and Cell Biology, Queen's University, Belfast, BT9 7BL, UK Department of Pathology, Belfast Health and Social Care Trust, Belfast, BT12 6BA, UK
| | - Amanda Capes-Davis
- CellBank Australia, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - D Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University, Belfast, BT9 7BL, UK Almac Diagnostics, Craigavon, BT63 5QD, UK
| | - Charlie Gourley
- Edinburgh Cancer Research Centre, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XR, UK
| | - Richard D Kennedy
- Centre for Cancer Research and Cell Biology, Queen's University, Belfast, BT9 7BL, UK Almac Diagnostics, Craigavon, BT63 5QD, UK
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17
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Niedzwiecki D, Frankel WL, Venook AP, Ye X, Friedman PN, Goldberg RM, Mayer RJ, Colacchio TA, Mulligan JM, Davison TS, O'Brien E, Kerr P, Johnston PG, Kennedy RD, Harkin DP, Schilsky RL, Bertagnolli MM, Warren RS, Innocenti F. Association Between Results of a Gene Expression Signature Assay and Recurrence-Free Interval in Patients With Stage II Colon Cancer in Cancer and Leukemia Group B 9581 (Alliance). J Clin Oncol 2016; 34:3047-53. [PMID: 27432924 PMCID: PMC5012711 DOI: 10.1200/jco.2015.65.4699] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [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: 01/01/2023] Open
Abstract
PURPOSE Conventional staging methods are inadequate to identify patients with stage II colon cancer (CC) who are at high risk of recurrence after surgery with curative intent. ColDx is a gene expression, microarray-based assay shown to be independently prognostic for recurrence-free interval (RFI) and overall survival in CC. The objective of this study was to further validate ColDx using formalin-fixed, paraffin-embedded specimens collected as part of the Alliance phase III trial, C9581. PATIENTS AND METHODS C9581 evaluated edrecolomab versus observation in patients with stage II CC and reported no survival benefit. Under an initial case-cohort sampling design, a randomly selected subcohort (RS) comprised 514 patients from 901 eligible patients with available tissue. Forty-nine additional patients with recurrence events were included in the analysis. Final analysis comprised 393 patients: 360 RS (58 events) and 33 non-RS events. Risk status was determined for each patient by ColDx. The Self-Prentice method was used to test the association between the resulting ColDx risk score and RFI adjusting for standard prognostic variables. RESULTS Fifty-five percent of patients (216 of 393) were classified as high risk. After adjustment for prognostic variables that included mismatch repair (MMR) deficiency, ColDx high-risk patients exhibited significantly worse RFI (multivariable hazard ratio, 2.13; 95% CI, 1.3 to 3.5; P < .01). Age and MMR status were marginally significant. RFI at 5 years for patients classified as high risk was 82% (95% CI, 79% to 85%), compared with 91% (95% CI, 89% to 93%) for patients classified as low risk. CONCLUSION ColDx is associated with RFI in the C9581 subsample in the presence of other prognostic factors, including MMR deficiency. ColDx could be incorporated with the traditional clinical markers of risk to refine patient prognosis.
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Affiliation(s)
- Donna Niedzwiecki
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA.
| | - Wendy L Frankel
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Alan P Venook
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Xing Ye
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Paula N Friedman
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Richard M Goldberg
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Robert J Mayer
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Thomas Anthony Colacchio
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Jude Marie Mulligan
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Timothy S Davison
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Eamonn O'Brien
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Peter Kerr
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Patrick G Johnston
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Richard D Kennedy
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - D Paul Harkin
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Richard L Schilsky
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Monica M Bertagnolli
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Robert S Warren
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
| | - Federico Innocenti
- Donna Niedzwiecki and Xing Ye, Duke University, Durham; Federico Innocenti, University of North Carolina at Chapel Hill, Chapel Hill, NC; Wendy L. Frankel and Richard M. Goldberg, The Ohio State University, Columbus, OH; Alan P. Venook and Robert S. Warren, University of California-San Francisco, San Francisco, CA; Paula N. Friedman, The University of Chicago, Chicago, IL; Robert J. Mayer, Dana-Farber Cancer Institute; Monica M. Bertagnolli, Brigham and Women's Hospital, Boston, MA; Thomas Anthony Colacchio, Dartmouth-Hitchcock Medical Center, Lebanon, NH; Jude Marie Mulligan, Timothy S. Davison, Eamonn O'Brien, Peter Kerr, Richard D. Kennedy, and D. Paul Harkin, Almac Diagnostics, Craigavon; Patrick G. Johnston, Queen's University, Belfast, Northern Ireland; and Richard L. Schilsky, American Society of Clinical Oncology, Alexandria, VA
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Parkes EE, Walker SM, McCabe N, Taggart LE, Hill L, Buckley NE, Savage KI, Salto-Tellez M, McQuaid S, Harte MT, Mullan PB, Harkin DP, Kennedy RD. Abstract 4000: A DNA damage response deficiency (DDRD) group in breast cancer is associated with activation of the STING innate immune pathway and PD-L1 expression. Immunology 2016. [DOI: 10.1158/1538-7445.am2016-4000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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19
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Tsantoulis P, Hill LA, Walker SM, Wirapati P, Graham DM, Wilson RH, Coyle V, Delorenzi M, Harkin DP, Kennedy RD, Tejpar S. Association of a specific innate immune response to DNA damage with DNA repair deficient colorectal cancers. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.3035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | - Richard H. Wilson
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
| | - Victoria Coyle
- Queen's Univeristy Belfast, Centre for Cancer and Cell Biology, Belfast, United Kingdom
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20
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Vohhodina J, Harkin DP, Savage KI. Dual roles of DNA repair enzymes in RNA biology/post-transcriptional control. Wiley Interdiscip Rev RNA 2016; 7:604-19. [PMID: 27126972 DOI: 10.1002/wrna.1353] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 12/12/2022]
Abstract
Despite consistent research into the molecular principles of the DNA damage repair pathway for almost two decades, it has only recently been found that RNA metabolism is very tightly related to this pathway, and the two ancient biochemical mechanisms act in alliance to maintain cellular genomic integrity. The close links between these pathways are well exemplified by examining the base excision repair pathway, which is now well known for dual roles of many of its members in DNA repair and RNA surveillance, including APE1, SMUG1, and PARP1. With additional links between these pathways steadily emerging, this review aims to provide a summary of the emerging roles for DNA repair proteins in the post-transcriptional regulation of RNAs. WIREs RNA 2016, 7:604-619. doi: 10.1002/wrna.1353 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jekaterina Vohhodina
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - D Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Kienan I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
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21
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Beirne JP, Irwin GW, McIntosh SA, Harley IJG, Harkin DP. The molecular and genetic basis of inherited cancer risk in gynaecology. ACTA ACUST UNITED AC 2015. [DOI: 10.1111/tog.12213] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- James P Beirne
- Northern Ireland Gynaecological Cancer Centre; Belfast City Hospital; Belfast Health and Social Care Trust; Belfast, Northern Ireland and Gynaecological Cancer Research Focus Group; Centre for Cancer Research and Cell Biology; Queens University; Belfast Northern Ireland
| | - Gareth W Irwin
- Northern Ireland Regional Breast Unit, Belfast City Hospital; Belfast Health and Social Care Trust; Belfast; Northern Ireland and Breast Cancer Research Focus Group; Centre for Cancer Research and Cell Biology; Queens University; Belfast Northern Ireland
| | - Stuart A McIntosh
- Northern Ireland Regional Breast Unit, Belfast City Hospital; Belfast Health and Social Care Trust; Belfast; Northern Ireland and Breast Cancer Research Focus Group; Centre for Cancer Research and Cell Biology; Queens University; Belfast Northern Ireland
| | - Ian JG Harley
- Northern Ireland Gynaecological Cancer Centre; Belfast City Hospital; Belfast Health and Social Care Trust; Belfast, Northern Ireland and Gynaecological Cancer Research Focus Group; Centre for Cancer Research and Cell Biology; Queens University; Belfast Northern Ireland
| | - D Paul Harkin
- Breast Cancer Research Focus Group; Centre for Cancer Research and Cell Biology; Queens University; Belfast Northern Ireland
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22
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McCabe N, Hanna C, Walker SM, Gonda D, Li J, Wikstrom K, Savage KI, Butterworth KT, Chen C, Harkin DP, Prise KM, Kennedy RD. Mechanistic Rationale to Target PTEN-Deficient Tumor Cells with Inhibitors of the DNA Damage Response Kinase ATM. Cancer Res 2015; 75:2159-65. [DOI: 10.1158/0008-5472.can-14-3502] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/24/2015] [Indexed: 11/16/2022]
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23
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McArt DG, Blayney JK, Boyle DP, Irwin GW, Moran M, Hutchinson RA, Bankhead P, Kieran D, Wang Y, Dunne PD, Kennedy RD, Mullan PB, Harkin DP, Catherwood MA, James JA, Salto-Tellez M, Hamilton PW. PICan: An integromics framework for dynamic cancer biomarker discovery. Mol Oncol 2015; 9:1234-40. [PMID: 25814194 DOI: 10.1016/j.molonc.2015.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/23/2014] [Accepted: 02/05/2015] [Indexed: 02/05/2023] Open
Abstract
Modern cancer research on prognostic and predictive biomarkers demands the integration of established and emerging high-throughput technologies. However, these data are meaningless unless carefully integrated with patient clinical outcome and epidemiological information. Integrated datasets hold the key to discovering new biomarkers and therapeutic targets in cancer. We have developed a novel approach and set of methods for integrating and interrogating phenomic, genomic and clinical data sets to facilitate cancer biomarker discovery and patient stratification. Applied to a known paradigm, the biological and clinical relevance of TP53, PICan was able to recapitulate the known biomarker status and prognostic significance at a DNA, RNA and protein levels.
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Affiliation(s)
- Darragh G McArt
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Jaine K Blayney
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - David P Boyle
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Gareth W Irwin
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Michael Moran
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Ryan A Hutchinson
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Peter Bankhead
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Declan Kieran
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Yinhai Wang
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Richard D Kennedy
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Paul B Mullan
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - D Paul Harkin
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Mark A Catherwood
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Jacqueline A James
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom.
| | - Peter W Hamilton
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom.
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24
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D'Costa ZC, Higgins C, Ong CW, Irwin GW, Boyle D, McArt DG, McCloskey K, Buckley NE, Crawford NT, Thiagarajan L, Murray JT, Kennedy RD, Mulligan KA, Harkin DP, Waugh DJJ, Scott CJ, Salto-Tellez M, Williams R, Mullan PB. TBX2 represses CST6 resulting in uncontrolled legumain activity to sustain breast cancer proliferation: a novel cancer-selective target pathway with therapeutic opportunities. Oncotarget 2015; 5:1609-20. [PMID: 24742492 PMCID: PMC4057604 DOI: 10.18632/oncotarget.1707] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
TBX2 is an oncogenic transcription factor known to drive breast cancer proliferation. We have identified the cysteine protease inhibitor Cystatin 6 (CST6) as a consistently repressed TBX2 target gene, co-repressed through a mechanism involving Early Growth Response 1 (EGR1). Exogenous expression of CST6 in TBX2-expressing breast cancer cells resulted in significant apoptosis whilst non-tumorigenic breast cells remained unaffected. CST6 is an important tumor suppressor in multiple tissues, acting as a dual protease inhibitor of both papain-like cathepsins and asparaginyl endopeptidases (AEPs) such as Legumain (LGMN). Mutation of the CST6 LGMN-inhibitory domain completely abrogated its ability to induce apoptosis in TBX2-expressing breast cancer cells, whilst mutation of the cathepsin-inhibitory domain or treatment with a pan-cathepsin inhibitor had no effect, suggesting that LGMN is the key oncogenic driver enzyme. LGMN activity assays confirmed the observed growth inhibitory effects were consistent with CST6 inhibition of LGMN. Knockdown of LGMN and the only other known AEP enzyme (GPI8) by siRNA confirmed that LGMN was the enzyme responsible for maintaining breast cancer proliferation. CST6 did not require secretion or glycosylation to elicit its cell killing effects, suggesting an intracellular mode of action. Finally, we show that TBX2 and CST6 displayed reciprocal expression in a cohort of primary breast cancers with increased TBX2 expression associating with increased metastases. We have also noted that tumors with altered TBX2/CST6 expression show poor overall survival. This novel TBX2-CST6-LGMN signaling pathway, therefore, represents an exciting opportunity for the development of novel therapies to target TBX2 driven breast cancers.
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Affiliation(s)
- Zenobia C D'Costa
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
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25
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Savage KI, Harkin DP. BRCA1, a 'complex' protein involved in the maintenance of genomic stability. FEBS J 2014; 282:630-46. [PMID: 25400280 DOI: 10.1111/febs.13150] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [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: 09/18/2014] [Revised: 11/10/2014] [Accepted: 11/13/2014] [Indexed: 12/15/2022]
Abstract
BRCA1 is a major breast and ovarian cancer susceptibility gene, with mutations in this gene predisposing women to a very high risk of developing breast and ovarian tumours. BRCA1 primarily functions to maintain genomic stability via critical roles in DNA repair, cell cycle checkpoint control, transcriptional regulation, apoptosis and mRNA splicing. As a result, BRCA1 mutations often result in defective DNA repair, genomic instability and sensitivity to DNA damaging agents. BRCA1 carries out these different functions through its ability to interact, and form complexes with, a vast array of proteins involved in multiple cellular processes, all of which are considered to contribute to its function as a tumour suppressor. This review discusses and highlights recent research into the functions of BRCA1-related protein complexes and their roles in maintaining genomic stability and tumour suppression.
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Affiliation(s)
- Kienan I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
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26
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Boyle DP, McArt DG, Irwin G, Wilhelm-Benartzi CS, Lioe TF, Sebastian E, McQuaid S, Hamilton PW, James JA, Mullan PB, Catherwood MA, Harkin DP, Salto-Tellez M. The prognostic significance of the aberrant extremes of p53 immunophenotypes in breast cancer. Histopathology 2014; 65:340-52. [PMID: 24612173 DOI: 10.1111/his.12398] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [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: 12/18/2013] [Accepted: 02/19/2014] [Indexed: 01/12/2023]
Abstract
AIMS The utility of p53 as a prognostic assay has been elusive. The aims of this study were to describe a novel, reproducible scoring system and assess the relationship between differential p53 immunohistochemistry (IHC) expression patterns, TP53 mutation status and patient outcomes in breast cancer. METHODS AND RESULTS Tissue microarrays were used to study p53 IHC expression patterns: expression was defined as extreme positive (EP), extreme negative (EN), and non-extreme (NE; intermediate patterns). Overall survival (OS) was used to define patient outcome. A representative subgroup (n = 30) showing the various p53 immunophenotypes was analysed for TP53 hotspot mutation status (exons 4-9). Extreme expression of any type occurred in 176 of 288 (61%) cases. As compared with NE expression, EP expression was significantly associated (P = 0.039) with poorer OS. In addition, as compared with NE expression, EN expression was associated (P = 0.059) with poorer OS. Combining cases showing either EP or EN expression better predicted OS than either pattern alone (P = 0.028). This combination immunophenotype was significant in univariate but not multivariate analysis. In subgroup analysis, six substitution exon mutations were detected, all corresponding to extreme IHC phenotypes. Five missense mutations corresponded to EP staining, and the nonsense mutation corresponded to EN staining. No mutations were detected in the NE group. CONCLUSIONS Patients with extreme p53 IHC expression have a worse OS than those with NE expression. Accounting for EN as well as EP expression improves the prognostic impact. Extreme expression positively correlates with nodal stage and histological grade, and negatively with hormone receptor status. Extreme expression may relate to specific mutational status.
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Affiliation(s)
- David P Boyle
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
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27
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Gourley C, McCavigan A, Perren T, Paul J, Michie CO, Churchman M, Williams A, McCluggage WG, Parmar M, Kaplan RS, Hill LA, Halfpenny IA, O'Brien EJ, Raji O, Deharo S, Davison T, Johnston P, Keating KE, Harkin DP, Kennedy RD. Molecular subgroup of high-grade serous ovarian cancer (HGSOC) as a predictor of outcome following bevacizumab. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.5502] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Charlie Gourley
- Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | | | - Timothy Perren
- St James's Institute of Oncology, St. James's University Hospital, Leeds, United Kingdom
| | - James Paul
- University of Glasgow, Glasgow, United Kingdom
| | | | - Michael Churchman
- University of Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | | | - W. Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | | | | | | | | | | | - Olaide Raji
- Almac Diagnostics, Craigavon, Northern Ireland
| | | | | | - Patrick Johnston
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland
| | | | | | - Richard D. Kennedy
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
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28
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Ahdesmäki M, Lancashire L, Proutski V, Wilson C, Davison TS, Harkin DP, Kennedy RD. Model selection for prognostic time-to-event gene signature discovery with applications in early breast cancer data. Stat Appl Genet Mol Biol 2014; 12:619-35. [PMID: 24077567 DOI: 10.1515/sagmb-2012-0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Model selection between competing models is a key consideration in the discovery of prognostic multigene signatures. The use of appropriate statistical performance measures as well as verification of biological significance of the signatures is imperative to maximise the chance of external validation of the generated signatures. Current approaches in time-to-event studies often use only a single measure of performance in model selection, such as logrank test p-values, or dichotomise the follow-up times at some phase of the study to facilitate signature discovery. In this study we improve the prognostic signature discovery process through the application of the multivariate partial Cox model combined with the concordance index, hazard ratio of predictions, independence from available clinical covariates and biological enrichment as measures of signature performance. The proposed framework was applied to discover prognostic multigene signatures from early breast cancer data. The partial Cox model combined with the multiple performance measures were used in both guiding the selection of the optimal panel of prognostic genes and prediction of risk within cross validation without dichotomising the follow-up times at any stage. The signatures were successfully externally cross validated in independent breast cancer datasets, yielding a hazard ratio of 2.55 [1.44, 4.51] for the top ranking signature.
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29
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Savage KI, Matchett KB, Barros EM, Cooper KM, Irwin GW, Gorski JJ, Orr KS, Vohhodina J, Kavanagh JN, Madden AF, Powell A, Manti L, McDade SS, Park BH, Prise KM, McIntosh SA, Salto-Tellez M, Richard DJ, Elliott CT, Harkin DP. BRCA1 deficiency exacerbates estrogen-induced DNA damage and genomic instability. Cancer Res 2014; 74:2773-2784. [PMID: 24638981 DOI: 10.1158/0008-5472.can-13-2611] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Germline mutations in BRCA1 predispose carriers to a high incidence of breast and ovarian cancers. BRCA1 functions to maintain genomic stability through critical roles in DNA repair, cell-cycle arrest, and transcriptional control. A major question has been why BRCA1 loss or mutation leads to tumors mainly in estrogen-regulated tissues, given that BRCA1 has essential functions in all cell types. Here, we report that estrogen and estrogen metabolites can cause DNA double-strand breaks (DSB) in estrogen receptor-α-negative breast cells and that BRCA1 is required to repair these DSBs to prevent metabolite-induced genomic instability. We found that BRCA1 also regulates estrogen metabolism and metabolite-mediated DNA damage by repressing the transcription of estrogen-metabolizing enzymes, such as CYP1A1, in breast cells. Finally, we used a knock-in human cell model with a heterozygous BRCA1 pathogenic mutation to show how BRCA1 haploinsufficiency affects these processes. Our findings provide pivotal new insights into why BRCA1 mutation drives the formation of tumors in estrogen-regulated tissues, despite the general role of BRCA1 in DNA repair in all cell types.
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Affiliation(s)
- Kienan I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Kyle B Matchett
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Eliana M Barros
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Kevin M Cooper
- Institute for Global Food Security, Queen's University Belfast, 30 Malone Rd, Belfast BT9 5BN, UK
| | - Gareth W Irwin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Julia J Gorski
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Katy S Orr
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Jekaterina Vohhodina
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Joy N Kavanagh
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Angelina F Madden
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Alexander Powell
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK.,Institute for Global Food Security, Queen's University Belfast, 30 Malone Rd, Belfast BT9 5BN, UK
| | - Lorenzo Manti
- Radiation Biophysics Laboratory, Department of Physics, University of Naples Federico II, Via Cinthia-80126 Naples, Italy
| | - Simon S McDade
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Ben Ho Park
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Kevin M Prise
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Stuart A McIntosh
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
| | - Derek J Richard
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, 4059, Brisbane, Australia
| | - Christopher T Elliott
- Institute for Global Food Security, Queen's University Belfast, 30 Malone Rd, Belfast BT9 5BN, UK
| | - D Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Rd, Belfast BT9 7BL, UK
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30
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Mulligan JM, Hill LA, Deharo S, Irwin G, Boyle D, Keating KE, Raji OY, McDyer FA, O'Brien E, Bylesjo M, Quinn JE, Lindor NM, Mullan PB, James CR, Walker SM, Kerr P, James J, Davison TS, Proutski V, Salto-Tellez M, Johnston PG, Couch FJ, Paul Harkin D, Kennedy RD. Identification and validation of an anthracycline/cyclophosphamide-based chemotherapy response assay in breast cancer. J Natl Cancer Inst 2014; 106:djt335. [PMID: 24402422 PMCID: PMC3906990 DOI: 10.1093/jnci/djt335] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background There is no method routinely used to predict response to anthracycline and cyclophosphamide–based chemotherapy in the clinic; therefore patients often receive treatment for breast cancer with no benefit. Loss of the Fanconi anemia/BRCA (FA/BRCA) DNA damage response (DDR) pathway occurs in approximately 25% of breast cancer patients through several mechanisms and results in sensitization to DNA-damaging agents. The aim of this study was to develop an assay to detect DDR-deficient tumors associated with loss of the FA/BRCA pathway, for the purpose of treatment selection. Methods DNA microarray data from 21 FA patients and 11 control subjects were analyzed to identify genetic processes associated with a deficiency in DDR. Unsupervised hierarchical clustering was then performed using 60 BRCA1/2 mutant and 47 sporadic tumor samples, and a molecular subgroup was identified that was defined by the molecular processes represented within FA patients. A 44-gene microarray-based assay (the DDR deficiency assay) was developed to prospectively identify this subgroup from formalin-fixed, paraffin-embedded samples. All statistical tests were two-sided. Results In a publicly available independent cohort of 203 patients, the assay predicted complete pathologic response vs residual disease after neoadjuvant DNA-damaging chemotherapy (5-fluorouracil, anthracycline, and cyclophosphamide) with an odds ratio of 3.96 (95% confidence interval [Cl] =1.67 to 9.41; P = .002). In a new independent cohort of 191 breast cancer patients treated with adjuvant 5-fluorouracil, epirubicin, and cyclophosphamide, a positive assay result predicted 5-year relapse-free survival with a hazard ratio of 0.37 (95% Cl = 0.15 to 0.88; P = .03) compared with the assay negative population. Conclusions A formalin-fixed, paraffin-embedded tissue-based assay has been developed and independently validated as a predictor of response and prognosis after anthracycline/cyclophosphamide–based chemotherapy in the neoadjuvant and adjuvant settings. These findings warrant further validation in a prospective clinical study.
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Affiliation(s)
- Jude M Mulligan
- Affiliations of authors: Almac Diagnostics, Craigavon, UK (JMM, LAH, SD, KEK, OYR, FAM, EO, MB, SMW, PK, TSD, VP, PGJ, DPH, RDK); Centre for Cancer Research and Cell Biology, Queen' s University Belfast, Belfast, UK (GI, DB, JEQ, PBM, CRJ, JJ, TSD, MS-T, PGJ, DPH, RDK); Department of Health Science Research, Mayo Clinic, Scottsdale, AZ (NML); Department of Medical Genetics, Mayo Clinic, Rochester, MN (FJC)
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31
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Niedzwiecki D, Frankel W, Venook AP, Ye X, Friedman PN, Goldberg RM, Mayer RJ, Colacchio TA, Kennedy RD, Davison T, O'Brien EJ, Mulligan J, Johnston PG, Harkin DP, Schilsky RL, Bertagnolli MM, Innocenti F. Association between ColDx assay result and recurrence-free interval in stage II colon cancer patients on CALGB (Alliance) 9581. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.3_suppl.455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
455 Background: Only 15-25% of pts with stage II colon cancer (CC) experience recurrence and conventional staging methods neither allow accurate identification of low (L) and high-risk (H) subgroups nor predict benefit of adjuvant chemotherapy. The ColDx assay (Almac Diagnostics) is a 634-probeset gene expression signature shown to be independently prognostic for recurrence-free interval (RFI). The objective of this study was to assess the ability of ColDx to classify stage II CC pts at L- and H-risk of relapse. Methods: This validation study was conducted using formalin fixed paraffin embedded biospecimens and clinical data from CALGB 9581, a phase III trial of edrecolomab v. observation in pts with normal risk, stage II CC. 1,454 CALGB 9,581 pts met eligibility criteria. A case-cohort sampling design was used to randomly select (RS) 514 pts from 901 eligible pts with available tissue; supplemented by 49 non-RS recurrent pts (total 563). Risk status for each pt was based on a positive or negative ColDx score using a pre-specified cutpoint, 0.4377. The Self Prentice method was used to test the association between ColDx categories and RFI (distant recurrence or death due to primary disease). Results: Initial results in 563 pts were erroneous due to a quality failure in a batch of reagent. 524 samples were re-labeled, re-ordered, and re-assayed using reagents that passed quality control (36 samples had insufficient material; 95 failed ColDx QC). Final analysis comprised 393 pts, 360 RS (58 events; 16%); 33 non-RS events. 216 pts (55%) were predicted H (62 events); 177 (45%) pts were predicted L (29 events). H pts exhibited significantly worse RFI (univariable hazard ratio (HR), 2.0; 95% CI, 1.3-3.3; p < 0.01). ColDx remained significant after adjustment for prognostic factors; HR, 2.1 (95% CI, 1.3-3.4; p < 0.01). Conclusions: The ColDx assay result is associated with RFI in the CALGB 9,581 sub-sample and is independent from other prognostic factors, including MSI. Further investigation is needed to establish the role of this classifier in guiding treatment decisions in this patient population.
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Affiliation(s)
| | | | | | | | | | - Richard M. Goldberg
- The Ohio State University Comprehensive Cancer Center - Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH
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32
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Buckley NE, Nic An tSaoir CB, Blayney JK, Oram LC, Crawford NT, D’Costa ZC, Quinn JE, Kennedy RD, Harkin DP, Mullan PB. BRCA1 is a key regulator of breast differentiation through activation of Notch signalling with implications for anti-endocrine treatment of breast cancers. Nucleic Acids Res 2013; 41:8601-14. [PMID: 23863842 PMCID: PMC3794588 DOI: 10.1093/nar/gkt626] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 06/24/2013] [Accepted: 06/26/2013] [Indexed: 12/17/2022] Open
Abstract
Here, we show for the first time, that the familial breast/ovarian cancer susceptibility gene BRCA1 activates the Notch pathway in breast cells by transcriptional upregulation of Notch ligands and receptors in both normal and cancer cells. We demonstrate through chromatin immunoprecipitation assays that BRCA1 is localized to a conserved intronic enhancer region within the Notch ligand Jagged-1 (JAG1) gene, an event requiring ΔNp63. We propose that this BRCA1/ΔNp63-mediated induction of JAG1 may be important the regulation of breast stem/precursor cells, as knockdown of all three proteins resulted in increased tumoursphere growth and increased activity of stem cell markers such as Aldehyde Dehydrogenase 1 (ALDH1). Knockdown of Notch1 and JAG1 phenocopied BRCA1 knockdown resulting in the loss of Estrogen Receptor-α (ER-α) expression and other luminal markers. A Notch mimetic peptide could activate an ER-α promoter reporter in a BRCA1-dependent manner, whereas Notch inhibition using a γ-secretase inhibitor reversed this process. We demonstrate that inhibition of Notch signalling resulted in decreased sensitivity to the anti-estrogen drug Tamoxifen but increased expression of markers associated with basal-like breast cancer. Together, these findings suggest that BRCA1 transcriptional upregulation of Notch signalling is a key event in the normal differentiation process in breast tissue.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Paul B. Mullan
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, 97 Lisburn Road, Belfast BT7 9BL, UK
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33
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Mulligan JM, Hill LA, Deharo S, Keating KE, Raji O, McDyer FA, James J, Irwin G, Boyle D, Quinn JE, Mullan PB, James CR, Salto-Tellez M, Davison TS, Johnston P, Couch FJ, Harkin DP, Kennedy RD. Identification and validation of an assay predictive of response and prognosis following anthracycline-based chemotherapy for early breast cancer. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.tps11120] [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: 11/20/2022] Open
Abstract
TPS11120 Background: Currently there is no biomarker to predict specific benefit from DNA-damaging anthracycline and cyclophosphamide-based chemotherapy in the clinic. Loss of the Fanconi anemia/BRCA (FA/BRCA) DNA-damage response pathway occurs in approximately 25% of breast cancer and results in sensitivity to DNA-damaging agents. We therefore developed an assay to detect loss of the FA/BRCA pathway, for the purpose of predicting benefit from chemotherapy. Methods: 21 FA patient samples were analyzed to identify genetic processes associated with loss of the FA/BRCA pathway. Unsupervised hierarchical clustering was then performed using 60 BRCA1/2 mutant and 47 sporadic tumor samples and a molecular subgroup was identified that was defined by the molecular processes representing loss of the FA/BRCA pathway. A 44-gene DNA Damage response deficient (DDRD) assay was developed that could identify this subgroup from formalin fixed, paraffin embedded (FFPE) samples in the clinic. Results: In a publicly available independent cohort of 204 patients, the assay predicted response to neoadjuvant DNA-damaging chemotherapy (5-fluorouracil, anthracycline and cyclophosphamide) with an odds ratio of 4.01, (95% Cl:1.69-9.54). We also analysed samples from an independent cohort of 114 node-negative breast cancer patients treated with adjuvant 5-fluorouracil, epirubicin and cyclophosphamide treatment at the Northern Ireland Cancer Centre. The DDRD assay significantly predicted 5-year relapse free survival with a hazard ratio of 0.27 (95% Cl:0.10-0.83). The assay was not predictive of survival in patients who did not receive chemotherapy. Conclusions: An FFPE tissue-based assay that detects loss of the FA/BRCA pathway has been developed and independently validated as a predictor of response and prognosis following DNA damaging anthracycline/cyclophosphamide-based chemotherapy in the neoadjuvant and adjuvant settings.
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Affiliation(s)
| | | | | | | | - Olaide Raji
- Almac Diagnostics, Craigavon, Northern Ireland
| | | | | | - Gareth Irwin
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, Northern Ireland
| | - David Boyle
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, Northern Ireland
| | | | | | | | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, Northern Ireland
| | | | - Patrick Johnston
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, Northern Ireland
| | | | | | - Richard D. Kennedy
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, Northern Ireland
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Harte MT, Gorski JJ, Savage KI, Purcell JW, Barros EM, Burn PM, McFarlane C, Mullan PB, Kennedy RD, Perkins ND, Harkin DP. NF-κB is a critical mediator of BRCA1-induced chemoresistance. Oncogene 2013; 33:713-723. [PMID: 23435429 PMCID: PMC3917825 DOI: 10.1038/onc.2013.10] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 12/13/2012] [Accepted: 12/14/2012] [Indexed: 12/17/2022]
Abstract
BRCA1 mediates resistance to apoptosis in response to DNA damaging agents, causing BRCA1 wild-type tumours to be significantly more resistant to DNA damage than their mutant counterparts. In this study we demonstrate that following treatment with the DNA damaging agents etoposide or camptothecin, BRCA1 is required for the activation of NF-κB, and that BRCA1 and NF-κB cooperate to regulate the expression of the NF-κB antiapoptotic targets BCL2 and XIAP. We show that BRCA1 and the NF-κB subunit p65/RelA associate constitutively, whereas the p50 NF-κB subunit associates with BRCA1 only upon DNA damage treatment. Consistent with this BRCA1 and p65 are present constitutively on the promoters of BCL2 and XIAP whereas p50 is recruited to these promoters only in damage treated cells. Importantly, we demonstrate that the recruitment of p50 onto the promoters of BCL2 and XIAP is dependent upon BRCA1, but independent of its NF-κB partner subunit p65. The functional relevance of NF-κB activation by BRCA1 in response to etoposide and camptothecin is demonstrated by the significantly reduced survival of BRCA1 wild type cells upon NF-κB inhibition. This study identifies a novel BRCA1-p50 complex, and demonstrates for the first time that NF-κB is required for BRCA1 mediated resistance to DNA damage. It reveals a functional interdependence between BRCA1 and NF-κB, further elucidating the role played by NF-κB in mediating cellular resistance of BRCA1 wild-type tumours to DNA damaging agents.
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Affiliation(s)
- Mary T Harte
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, UK BT9 7BL
| | - Julia J Gorski
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, UK BT9 7BL
| | - Kienan I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, UK BT9 7BL
| | | | - Eliana M Barros
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, UK BT9 7BL
| | - Philip M Burn
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, UK BT9 7BL
| | - Cheryl McFarlane
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, UK BT9 7BL
| | - Paul B Mullan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, UK BT9 7BL
| | - Richard D Kennedy
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, UK BT9 7BL
| | | | - D Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, UK BT9 7BL
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35
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Tkocz D, Crawford NT, Buckley NE, Berry FB, Kennedy RD, Gorski JJ, Harkin DP, Mullan PB. BRCA1 and GATA3 corepress FOXC1 to inhibit the pathogenesis of basal-like breast cancers. Oncogene 2012; 31:3667-78. [PMID: 22120723 DOI: 10.1038/onc.2011.531] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [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] [Received: 06/12/2011] [Revised: 09/21/2011] [Accepted: 10/18/2011] [Indexed: 12/24/2022]
Abstract
In this study we describe a novel interaction between the breast/ovarian tumor suppressor gene BRCA1 and the transcription factor GATA3, an interaction, which is important for normal breast differentiation. We show that the BRCA1-GATA3 interaction is important for the repression of genes associated with triple-negative and basal-like breast cancer (BLBCs) including FOXC1, and that GATA3 interacts with a C-terminal region of BRCA1. We demonstrate that FOXC1 is an essential survival factor maintaining the proliferation of BLBCs cell lines. We define the mechanistic basis of this corepression and identify the GATA3-binding site within the FOXC1 distal promoter region. We show that BRCA1 and GATA3 interact on the FOXC1 promoter and that BRCA1 requires GATA3 for recruitment to this region. This interaction requires fully functional BRCA1 as a mutant BRCA1 protein is unable to localize to the FOXC1 promoter or repress FOXC1 expression. We demonstrate that this BRCA1-GATA3 repression complex is not a FOXC1-specific phenomenon as a number of other genes associated with BLBCs such as FOXC2, CXCL1 and p-cadherin were also repressed in a similar manner. Finally, we demonstrate the importance of our findings by showing that loss of GATA3 expression or aberrant FOXC1 expression contributes to the drug resistance and epithelial-to-mesenchymal transition-like phenotypes associated with aggressive BLBCs.
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Affiliation(s)
- D Tkocz
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
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36
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McCabe N, Walker SM, Goffard N, Wikstrom K, Greenan C, McLean E, McDyer FA, Keating KE, James I, Harrison T, Mullan PB, Harkin DP, Chen C, Kennedy RD. Activation of and dependence on ataxia telangiectasia mutated kinase in PTEN-deficient tumor cells. J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.15_suppl.10553] [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: 11/20/2022] Open
Abstract
10553 Background: Loss of PTEN function has been widely reported to cause up-regulation of the PI3K/AKT signalling pathway resulting in increased cell growth, proliferation and survival. More recently it has been reported that PTEN null cells demonstrate genomic instability and have increased production of reactive oxygen species (ROS) and oxidative stress induced DNA damage. Ataxia Telangiectasia Mutated (ATM) is the primary response kinase, which responds to stalled DNA replication and DNA double strand breaks due to oxidative DNA damage. Methods: A metagene representing ATM activation was generated from cell line data and used to perform hierarchical clustering analysis of public DNA microarray profiling datasets of breast cancer, ovarian cancer and glioblastoma with known PTEN IHC/mutation status. Furthermore, we ask if ATM activation may be therapeutically exploited in PTEN null tumours using ATM specific siRNA and compounds in 2 PTEN isogenic cell line model systems. Results: We show that PTEN null cells have elevated levels of ROS, DNA damage and have endogenous activation of ATM, an enzyme important in responding to DNA damage resulting from oxidative stress. We hypothesised that PTEN deficient tumours may rely on ATM enzyme for survival. To investigate this we generated a 189-gene list representing ATM activation and used this to perform hierarchical clustering analysis of a breast cancer DNA microarray dataset. This list was able to significantly cluster tumours with known loss of PTEN expression (p=0.004). Furthermore, this gene list was able to segregate PTEN null/mutant tumours from PTEN wild-type tumours in 2 independent datasets of glioblastoma and ovarian cancer (p=0.015 and p=0.012). In addition, we found that inhibition of ATM using the selective inhibitor KU-55933 caused DNA damage, cell cycle arrest and apoptosis specifically in PTEN deficient cells when compared to PTEN wild-type cells. Conclusions: These observations suggest that ATM may represent a therapeutic target in PTEN deficient tumours and furthermore ATM activation may be the basis of a biomarker of PTEN status in human cancers.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Iain James
- Almac Discovery, Craigavon, United Kingdom
| | | | | | | | - Clark Chen
- University of California, San Diego, San Diego, CA
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37
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Busacca S, Sheaff M, Arthur K, Gray SG, O'Byrne KJ, Richard DJ, Soltermann A, Opitz I, Pass H, Harkin DP, Quinn JE, Fennell DA. BRCA1 is an essential mediator of vinorelbine-induced apoptosis in mesothelioma. J Pathol 2012; 227:200-8. [DOI: 10.1002/path.3979] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 11/21/2011] [Accepted: 12/10/2011] [Indexed: 12/22/2022]
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38
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McCabe N, Walker SM, Goffard N, Wikstrom K, Greenan C, Delaney T, McCarthy M, McDyer F, Hill L, Deharo S, Proutski V, Keating K, Mullan P, Harkin DP, Kennedy RD. P5-01-12: Identification of an ATM Activation Subtype in PTEN Mutant Breast Tumours. Cancer Res 2011. [DOI: 10.1158/0008-5472.sabcs11-p5-01-12] [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 PTEN is frequently lost in cancer cells through genetic mutation or epigenetic silencing. Loss of PTEN function has been widely reported to cause up-regulation of the PI3K/AKT signalling pathway resulting in increased cell growth, proliferation and survival. More recently it has been reported that PTEN null cells demonstrate genomic instability through increased ROS and oxidative stress induced DNA damage. The aim of this study was to identify a biomarker for PTEN status in human breast cancers.
Materials and Methods A metagene representing ATM activation was generated from public cell line data of AT fibroblasts treated with gamma-irradiation. This was used to perform hierarchical clustering analysis of a public DNA microarray profiling dataset with known PTEN IHC status. The metagene was validated in PTEN wildtype and null breast cancer cell lines.
Results We found that PTEN null cells have elevated levels of ROS and furthermore activation of the DNA damage signalling kinase, ATM. In agreement with this, the ATM metagene signature correlated with PTEN mutation in breast cancer tumours. Scoring of PTEN wildtype and null breast cancer cell lines using the metagene correlated with ATM activation and sensitivity to inhibition of ATM. Furthermore we show that inhibition of ATM caused DNA damage, cell cycle arrest and apoptosis in PTEN deficient cells suggesting a novel therapeutic strategy.
Conclusion These observations suggest that ATM may represent a therapeutic target in PTEN deficient tumours and furthermore ATM activation may also be an important biomarker of PTEN mutation or loss in breast cancer.
Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-01-12.
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Affiliation(s)
- N McCabe
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - SM Walker
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - N Goffard
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - K Wikstrom
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - C Greenan
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - T Delaney
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - M McCarthy
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - F McDyer
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - L Hill
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - S Deharo
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - V Proutski
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - K Keating
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - P Mullan
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - DP Harkin
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
| | - RD Kennedy
- 1Almac Diagnostics, Craigavon, United Kingdom; Queens University Belfast, Belfast, United Kingdom
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Gorski JJ, Savage KI, Mulligan JM, McDade SS, Blayney JK, Ge Z, Harkin DP. Profiling of the BRCA1 transcriptome through microarray and ChIP-chip analysis. Nucleic Acids Res 2011; 39:9536-48. [PMID: 21880590 PMCID: PMC3239190 DOI: 10.1093/nar/gkr679] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 07/27/2011] [Accepted: 08/01/2011] [Indexed: 11/16/2022] Open
Abstract
A role for BRCA1 in the direct and indirect regulation of transcription is well established. However, a comprehensive view of the degree to which BRCA1 impacts transcriptional regulation on a genome-wide level has not been defined. We performed genome-wide expression profiling and ChIP-chip analysis, comparison of which revealed that although BRCA1 depletion results in transcriptional changes in 1294 genes, only 44 of these are promoter bound by BRCA1. However, 27% of these transcripts were linked to transcriptional regulation possibly explaining the large number of indirect transcriptional changes observed by microarray analysis. We show that no specific consensus sequence exists for BRCA1 DNA binding but rather demonstrate the presence of a number of known and novel transcription factor (TF)- binding sites commonly found on BRCA1 bound promoters. Co-immunoprecipitations confirmed that BRCA1 interacts with a number of these TFs including AP2-α, PAX2 and ZF5. Finally, we show that BRCA1 is bound to a subset of promoters of genes that are not altered by BRCA1 loss, but are transcriptionally regulated in a BRCA1-dependent manner upon DNA damage. These data suggest a model, whereby BRCA1 is present on defined promoters as part of an inactive complex poised to respond to various genotoxic stimuli.
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Affiliation(s)
- Julia J Gorski
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7BL and ALMAC Diagnostics, Craigavon BT63 5QD, UK.
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Kennedy RD, Bylesjo M, Kerr P, Davison T, Black JM, Kay EW, Holt RJ, Proutski V, Ahdesmaki M, Farztdinov V, Goffard N, Hey P, McDyer F, Mulligan K, Mussen J, O'Brien E, Oliver G, Walker SM, Mulligan JM, Wilson C, Winter A, O'Donoghue D, Mulcahy H, O'Sullivan J, Sheahan K, Hyland J, Dhir R, Bathe OF, Winqvist O, Manne U, Shanmugam C, Ramaswamy S, Leon EJ, Smith WI, McDermott U, Wilson RH, Longley D, Marshall J, Cummins R, Sargent DJ, Johnston PG, Harkin DP. Development and independent validation of a prognostic assay for stage II colon cancer using formalin-fixed paraffin-embedded tissue. J Clin Oncol 2011; 29:4620-6. [PMID: 22067406 DOI: 10.1200/jco.2011.35.4498] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Current prognostic factors are poor at identifying patients at risk of disease recurrence after surgery for stage II colon cancer. Here we describe a DNA microarray-based prognostic assay using clinically relevant formalin-fixed paraffin-embedded (FFPE) samples. PATIENTS AND METHODS A gene signature was developed from a balanced set of 73 patients with recurrent disease (high risk) and 142 patients with no recurrence (low risk) within 5 years of surgery. RESULTS The 634-probe set signature identified high-risk patients with a hazard ratio (HR) of 2.62 (P < .001) during cross validation of the training set. In an independent validation set of 144 samples, the signature identified high-risk patients with an HR of 2.53 (P < .001) for recurrence and an HR of 2.21 (P = .0084) for cancer-related death. Additionally, the signature was shown to perform independently from known prognostic factors (P < .001). CONCLUSION This gene signature represents a novel prognostic biomarker for patients with stage II colon cancer that can be applied to FFPE tumor samples.
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Affiliation(s)
- Richard D Kennedy
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Northern Ireland, United Kingdom
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41
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Paul I, Savage KI, Blayney JK, Lamers E, Gately K, Kerr K, Sheaff M, Arthur K, Richard DJ, Hamilton PW, James JA, O'Byrne KJ, Harkin DP, Quinn JE, Fennell DA. PARP inhibition induces BAX/BAK-independent synthetic lethality of BRCA1-deficient non-small cell lung cancer. J Pathol 2011; 224:564-74. [PMID: 21706479 DOI: 10.1002/path.2925] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 04/07/2011] [Accepted: 04/13/2011] [Indexed: 01/09/2023]
Abstract
Evasion of apoptosis contributes to both tumourigenesis and drug resistance in non-small cell lung carcinoma (NSCLC). The pro-apoptotic BCL-2 family proteins BAX and BAK are critical regulators of mitochondrial apoptosis. New strategies for targeting NSCLC in a mitochondria-independent manner should bypass this common mechanism of apoptosis block. BRCA1 mutation frequency in lung cancer is low; however, decreased BRCA1 mRNA and protein expression levels have been reported in a significant proportion of lung adenocarcinomas. BRCA1 mutation/deficiency confers a defect in homologous recombination DNA repair that has been exploited by synthetic lethality through inhibition of PARP (PARPi) in breast and ovarian cells; however, it is not known whether this same synthetic lethal mechanism exists in NSCLC cells. Additionally, it is unknown whether the mitochondrial apoptotic pathway is required for BRCA1/PARPi-mediated synthetic lethality. Here we demonstrate that silencing of BRCA1 expression by RNA interference sensitizes NSCLC cells to PARP inhibition. Importantly, this sensitivity was not attenuated in cells harbouring mitochondrial apoptosis block induced by co-depletion of BAX and BAK. Furthermore, we demonstrate that BRCA1 inhibition cannot override platinum resistance, which is often mediated by loss of mitochondrial apoptosis signalling, but can still sensitize to PARP inhibition. Finally we demonstrate the existence of a BRCA1-deficient subgroup (11-19%) of NSCLC patients by analysing BRCA1 protein levels using immunohistochemistry in two independent primary NSCLC cohorts. Taken together, the existence of BRCA1-immunodeficient NSCLC suggests that this molecular subgroup could be effectively targeted by PARP inhibitors in the clinic and that PARP inhibitors could be used for the treatment of BRCA1-immunodeficient, platinum-resistant tumours.
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Affiliation(s)
- Ian Paul
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
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42
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Buckley NE, Conlon SJ, Jirstrom K, Kay EW, Crawford NT, O'Grady A, Sheehan K, Mc Dade SS, Wang CW, McCance DJ, Johnston PG, Kennedy RD, Harkin DP, Mullan PB. The DeltaNp63 proteins are key allies of BRCA1 in the prevention of basal-like breast cancer. Cancer Res 2011; 71:1933-44. [PMID: 21363924 DOI: 10.1158/0008-5472.can-10-2717] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [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: 11/16/2022]
Abstract
Little is known about the origin of basal-like breast cancers, an aggressive disease that is highly similar to BRCA1-mutant breast cancers. p63 family proteins that are structurally related to the p53 suppressor protein are known to function in stem cell regulation and stratified epithelia development in multiple tissues, and p63 expression may be a marker of basal-like breast cancers. Here we report that ΔNp63 isoforms of p63 are transcriptional targets for positive regulation by BRCA1. Our analyses of breast cancer tissue microarrays and BRCA1-modulated breast cancer cell lines do not support earlier reports that p63 is a marker of basal-like or BRCA1 mutant cancers. Nevertheless, we found that BRCA1 interacts with the specific p63 isoform ΔNp63γ along with transcription factor isoforms AP-2α and AP-2γ. BRCA1 required ΔNp63γ and AP-2γ to localize to an intronic enhancer region within the p63 gene to upregulate transcription of the ΔNp63 isoforms. In mammary stem/progenitor cells, siRNA-mediated knockdown of ΔNp63 expression resulted in genomic instability, increased cell proliferation, loss of DNA damage checkpoint control, and impaired growth control. Together, our findings establish that transcriptional upregulation of ΔNp63 proteins is critical for BRCA1 suppressor function and that defects in BRCA1-ΔNp63 signaling are key events in the pathogenesis of basal-like breast cancer.
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Affiliation(s)
- Niamh E Buckley
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
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43
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Murray MM, Buckley N, Harkin DP. Activin B functions downstream of BRCA1 in stem cell maintenance. Breast Cancer Res 2010. [PMCID: PMC2875563 DOI: 10.1186/bcr2498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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44
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Lamers E, McDyer FA, Mulligan JM, Couch F, Savage KI, O'Brien NE, Mullan PB, Kennedy RD, Harkin DP, Quinn JE. Microarray based expression profiling of BRCA1 mutated human tumours using a breast-specific platform to identify a profile of BRCA1 deficiency. Breast Cancer Res 2010. [PMCID: PMC2875606 DOI: 10.1186/bcr2541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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45
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Walker SM, McGoohan C, Mcdyer F, Oliver GR, McCabe N, Deharo S, Johnston PG, Harkin DP, Kennedy RD. Abstract 1153: The development and utilization of a novel DNA microarray platform for biomarker and target identification in advanced prostate cancer. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-1153] [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
Prostate cancer is the second leading cause of cancer-related deaths in men; specifically one in six men are diagnosed with prostate cancer in their lifetime. The use of serum prostate-specific antigen (PSA) levels has been lauded as a huge step forward in the diagnosis and treatment of prostate cancer, however since it's implemenatation as a biomarker it has become apparent that the numbers of deaths from prostate cancer has only decreased slightly. Therefore the identification of new biomarkers and treatments for highly invasive/metastatic prostate cancers is of a high priority.
We sought to identify new biomarkers and drug targets by performing DNA microarray analysis of prostate tumour samples and normal prostate tissue samples. To further these goals we developed a specific array platform, this array was based upon extensive sequencing of prostate tumour samples and contains approximately 90,000 probesets many of which are specific to prostate cancer.
We then utilized this technology to profile a series of fresh high Gleason score primary prostate tumour samples and normal prostate samples. We identified approximately 1,600 transcripts and many associated functionally relevant pathways that were significantly differentially expressed in the prostate tumour samples when compared with the normal prostate samples. Encouragingly we also identified several transcripts which are known to be specifically expressed in prostate cancer including prostate cancer antigen 3 (PCA3), α-methylacyl-coA-racemase AKA 2-methylacyl-CoA 2-epimerase (AMACR) and members of the olfactory receptor family 51, thereby demonstrating that this approach was producing reliable information. Additionally to these transcripts 34% of the 1,600 was annotated as being unique to the prostate cancer disease specific array when compared to available generic microarrays, thereby representing novel potential biomarkers and drug targets. Functional analysis of these unique transcripts annotated many to apoptotic processes, DNA repair and cellular proliferation amongst others. This content may be highly relevant to biomarker and target development for advanced prostate cancer.
In conclusion we have developed a novel prostate cancer disease specific array, we have utilized this platform to profiled a series of prostate tumour and normal samples identifying several novel transcripts associated with advanced prostate cancer. Functional annotation of these unique transcripts associated many with processes know to be deregulated in cancer. We believe that this approach demonstrates the utility of this novel platform for the discovery of clinical biomarkers and novel drug targets from tumour tissue.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1153.
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Tejpar S, Bertagnolli M, Bosman F, Lenz HJ, Garraway L, Waldman F, Warren R, Bild A, Collins-Brennan D, Hahn H, Harkin DP, Kennedy R, Ilyas M, Morreau H, Proutski V, Swanton C, Tomlinson I, Delorenzi M, Fiocca R, Van Cutsem E, Roth A. Prognostic and predictive biomarkers in resected colon cancer: current status and future perspectives for integrating genomics into biomarker discovery. Oncologist 2010; 15:390-404. [PMID: 20350999 PMCID: PMC3227961 DOI: 10.1634/theoncologist.2009-0233] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The number of agents that are potentially effective in the adjuvant treatment of locally advanced resectable colon cancer is increasing. Consequently, it is important to ascertain which subgroups of patients will benefit from a specific treatment. Despite more than two decades of research into the molecular genetics of colon cancer, there is a lack of prognostic and predictive molecular biomarkers with proven utility in this setting. A secondary objective of the Pan European Trials in Adjuvant Colon Cancer-3 trial, which compared irinotecan in combination with 5-fluorouracil and leucovorin in the postoperative treatment of stage III and stage II colon cancer patients, was to undertake a translational research study to assess a panel of putative prognostic and predictive markers in a large colon cancer patient cohort. The Cancer and Leukemia Group B 89803 trial, in a similar design, also investigated the use of prognostic and predictive biomarkers in this setting. In this article, the authors, who are coinvestigators from these trials and performed similar investigations of biomarker discovery in the adjuvant treatment of colon cancer, review the current status of biomarker research in this field, drawing on their experiences and considering future strategies for biomarker discovery in the postgenomic era.
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Affiliation(s)
- Sabine Tejpar
- Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium.
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Harte MT, O'Brien GJ, Ryan NM, Gorski JJ, Savage KI, Crawford NT, Mullan PB, Harkin DP. BRD7, a subunit of SWI/SNF complexes, binds directly to BRCA1 and regulates BRCA1-dependent transcription. Cancer Res 2010; 70:2538-47. [PMID: 20215511 DOI: 10.1158/0008-5472.can-09-2089] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [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
We carried out a yeast two-hybrid screen using a BRCA1 bait composed of amino acids 1 to 1142 and identified BRD7 as a novel binding partner of BRCA1. This interaction was confirmed by coimmunoprecipitation of endogenous BRCA1 and BRD7 in T47D and HEK-293 cells. BRD7 is a bromodomain containing protein, which is a subunit of PBAF-specific Swi/Snf chromatin remodeling complexes. To determine the functional consequences of the BRCA1-BRD7 interaction, we investigated the role of BRD7 in BRCA1-dependent transcription using microarray-based expression profiling. We found that a variety of targets were coordinately regulated by BRCA1 and BRD7, such as estrogen receptor alpha (ERalpha). Depletion of BRD7 or BRCA1 in either T47D or MCF7 cells resulted in loss of expression of ERalpha at both the mRNA and protein level, and this loss of ERalpha was reflected in resistance to the antiestrogen drug fulvestrant. We show that BRD7 is present, along with BRCA1 and Oct-1, on the ESR1 promoter (the gene which encodes ERalpha). Depletion of BRD7 prevented the recruitment of BRCA1 and Oct-1 to the ESR1 promoter; however, it had no effect on the recruitment of the other Swi/Snf subunits BRG1, BAF155, and BAF57 or on RNA polymerase II recruitment. These results support a model whereby the regulation of ERalpha transcription by BRD7 is mediated by its recruitment of BRCA1 and Oct-1 to the ESR1 promoter.
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Affiliation(s)
- Mary T Harte
- Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, Northern Ireland, United Kingdom.
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48
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Gorski JJ, James CR, Quinn JE, Stewart GE, Staunton KC, Buckley NE, McDyer FA, Kennedy RD, Wilson RH, Mullan PB, Harkin DP. BRCA1 transcriptionally regulates genes associated with the basal-like phenotype in breast cancer. Breast Cancer Res Treat 2009; 122:721-31. [PMID: 19882246 DOI: 10.1007/s10549-009-0565-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [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] [Received: 06/11/2009] [Accepted: 09/17/2009] [Indexed: 01/16/2023]
Abstract
Expression profiling of BRCA1-deficient tumours has identified a pattern of gene expression similar to basal-like breast tumours. In this study, we examine whether a BRCA1-dependent transcriptional mechanism may underpin the link between BRCA1 and basal-like phenotype. In methods section, the mRNA and protein were harvested from a number of BRCA1 mutant and wild-type breast cancer cell lines and from matched isogenic controls. Microarray-based expression profiling was used to identify potential BRCA1-regulated transcripts. These gene targets were then validated (by in silico analysis of tumour samples) by real-time PCR and Western blot analysis. Chromatin immunoprecipitation (ChIP) assays were used to confirm recruitment of BRCA1 to specific promoters. In results, we demonstrate that functional BRCA1 represses the expression of cytokeratins 5(KRT5) and 17(KRT17) and p-Cadherin (CDH3) in HCC1937 and T47D breast cancer cell lines at both mRNA and protein level. ChIP assays demonstrate that BRCA1 is recruited to the promoters of KRT5, KRT17 and CDH3, and re-ChIP assays confirm that BRCA1 is recruited independently to form c-Myc and Sp1 complexes on the CDH3 promoter. We show that siRNA-mediated inhibition of endogenous c-Myc (and not Sp1) results in a marked increase in CDH3 expression analogous to that observed following the inhibition of endogenous BRCA1. The data provided suggest a model whereby BRCA1 and c-Myc form a repressor complex on the promoters of specific basal genes and represent a potential mechanism to explain the observed overexpression of key basal markers in BRCA1-deficient tumours.
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Affiliation(s)
- Julia J Gorski
- Department of Oncology, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7BL, N. Ireland, UK.
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Quinn JE, Carser JE, James CR, Kennedy RD, Harkin DP. BRCA1 and implications for response to chemotherapy in ovarian cancer. Gynecol Oncol 2009; 113:134-42. [DOI: 10.1016/j.ygyno.2008.12.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 12/05/2008] [Accepted: 12/09/2008] [Indexed: 01/05/2023]
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Abstract
Breast cancer 1 (BRCA1) was initially identified as one of the genes conferring genetic predisposition to both breast and ovarian cancer. One of the interesting aspects of BRCA1-linked cancers is the observed specificity for estrogen-responsive tissues such as breast and ovary. Recent advances in our understanding of BRCA1-linked breast cancers have revealed a complex relationship between BRCA1 and estrogen receptor alpha (ERalpha) signaling. Estrogen stimulation increases expression of BRCA1 at the mRNA and protein level and conversely BRCA1 functions to both induce ERalpha mRNA expression and act as a negative regulator of ERalpha signaling. Here, we review the relationship between BRCA1 and ERalpha and discuss the use of antiestrogen therapies such as tamoxifen and aromatase inhibitors in the treatment of BRCA1 mutation carriers.
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Affiliation(s)
- Julia J Gorski
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland
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