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Sipos O, Tovey H, Quist J, Haider S, Nowinski S, Gazinska P, Kernaghan S, Toms C, Maguire S, Orr N, Linn SC, Owen J, Gillett C, Pinder SE, Bliss JM, Tutt A, Cheang MCU, Grigoriadis A. Assessment of structural chromosomal instability phenotypes as biomarkers of carboplatin response in triple negative breast cancer: the TNT trial. Ann Oncol 2021; 32:58-65. [PMID: 33098992 PMCID: PMC7784666 DOI: 10.1016/j.annonc.2020.10.475] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 03/23/2020] [Revised: 08/05/2020] [Accepted: 10/13/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND In the TNT trial of triple negative breast cancer (NCT00532727), germline BRCA1/2 mutations were present in 28% of carboplatin responders. We assessed quantitative measures of structural chromosomal instability (CIN) to identify a wider patient subgroup within TNT with preferential benefit from carboplatin over docetaxel. PATIENTS AND METHODS Copy number aberrations (CNAs) were established from 135 formalin-fixed paraffin-embedded primary carcinomas using Illumina OmniExpress SNP-arrays. Seven published [allelic imbalanced CNA (AiCNA); allelic balanced CNA (AbCNA); copy number neutral loss of heterozygosity (CnLOH); number of telomeric allelic imbalances (NtAI); BRCA1-like status; percentage of genome altered (PGA); homologous recombination deficiency (HRD) scores] and two novel [Shannon diversity index (SI); high-level amplifications (HLAMP)] CIN-measurements were derived. HLAMP was defined based on the presence of at least one of the top 5% amplified cytobands located on 1q, 8q and 10p. Continuous CIN-measurements were divided into tertiles. All nine CIN-measurements were used to analyse objective response rate (ORR) and progression-free survival (PFS). RESULTS Patients with tumours without HLAMP had a numerically higher ORR and significantly longer PFS in the carboplatin (C) than in the docetaxel (D) arm [56% (C) versus 29% (D), PHLAMP,quiet = 0.085; PFS 6.1 months (C) versus 4.1 months (D), Pinteraction/HLAMP = 0.047]. In the carboplatin arm, patients with tumours showing intermediate telomeric NtAI and AiCNA had higher ORR [54% (C) versus 20% (D), PNtAI,intermediate = 0.03; 62% (C) versus 33% (D), PAiCNA,intermediate = 0.076]. Patients with high AiCNA and PGA had shorter PFS in the carboplatin arm [3.4 months (high) versus 5.7 months (low/intermediate); and 3.8 months (high) versus 5.6 months (low/intermediate), respectively; Pinteraction/AiCNA = 0.027, Padj.interaction/AiCNA = 0.125 and Pinteraction/PGA = 0.053, Padj.interaction/PGA = 0.176], whilst no difference was observed in the docetaxel arm. CONCLUSIONS Patients with tumours lacking HLAMP and demonstrating intermediate CIN-measurements formed a subgroup benefitting from carboplatin relative to docetaxel treatment within the TNT trial. This suggests a complex and paradoxical relationship between the extent of genomic instability in primary tumours and treatment response in the metastatic setting.
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Affiliation(s)
- O Sipos
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - H Tovey
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - J Quist
- Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, UK; School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - S Haider
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - S Nowinski
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - P Gazinska
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - S Kernaghan
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - C Toms
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - S Maguire
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - N Orr
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - S C Linn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - J Owen
- King's Health Partners Cancer Biobank, London, UK
| | - C Gillett
- King's Health Partners Cancer Biobank, London, UK
| | - S E Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - J M Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - A Tutt
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK; Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, UK; School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK
| | - M C U Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, UK
| | - A Grigoriadis
- Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, UK; School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, UK.
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Sipos O, Tovey H, Quist J, Haider S, Nowinski S, Gazinska P, Kernaghan S, Toms C, Timms KM, Lanchbury JS, Linn SC, Pinder SE, Bliss JM, Tutt A, Cheang MC, Grigoriadis A. Abstract P1-06-07: Characterization of chromosomal instability in the TNT trial: A randomized phase III trial of carboplatin compared with docetaxel for patients with metastatic or recurrent locally advanced triple negative or BRCA1/2 breast cancer (CRUK/07/012). Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p1-06-07] [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
A distinctive trait of triple negative breast cancer (TNBC) is the acquisition of genome wide highly aberrant copy number states, which is more evident in metastatic settings. The level of copy number alterations can be characterized by quantitative estimates of chromosomal instability, such as allelic imbalanced copy number aberrations, telomeric allelic imbalance (NtAI), homologous recombination deficiency (HRD) score, referred here as genomic scars. Several of these scars are reported as being indicative of BRCAness and potential predictive and/or prognostic biomarkers of chemotherapy response, currently mostly demonstrated in neoadjuvant settings in TNBC.
Aims
Using several genomic scar measures, we aim to capture chromosomal instability and test their predictive and prognostic value in metastatic or recurrent locally advanced triple negative or BRCA1/2 mutated breast cancer in the TNT trial.
Methods
Patients recruited to TNT (n=376) had ER-/PR-/Her2- breast cancer or were germline BRCA mutation carriers. Genome-wide copy numbers (CN) were derived from FFPE samples including primary tumours and positive lymph nodes (n=183, docetaxel=93, carboplatin=90; BRCA1 mut=25). Genomic scars were generated using ASCAT (Van loo et al., PNAS 2010) CN profiles. HRD scores were established by Myriad Genetics, Inc. assay (n=272). BRCA1-like classifier was applied as described in Schouten et al., Mol Onc 2015. Shannon diversity index was calculated using ASCAT raw CN profiles. Association of genomic scars with PAM50 subtypes and BRCA1 deficiency status were evaluated using Kruskal-Wallis test; p-values were adjusted for multiple comparisons (Dunn's test). Statistical significance was defined as p<0.05. Association of genomic scars with objective tumour response rate (ORR) and Progression Free Survival (PFS) was assessed using logistic regression and restricted mean survival analysis, respectively.
Results
HRD and NtAI scores were higher in basal like samples compared to non-basal like (median diff. HRD=11.5, p=0.005; NtAI=3, p=0.04). HRD (p=2e-14) and NtAI (p=0.003) scores were also higher in BRCA1 deficient (BRCA1 germline/somatic mutant or BRCA1 methylated) samples compared to non-deficient. Using the BRCA1-like classifier, 42 out of 50 BRCA1 deficient samples and 93 out of 133 BRCA1 non-deficient/undetermined samples were identified as BRCA1-like. The Shannon diversity index, measuring CN heterogeneity, clustered samples into 3 groups. Analysis of ORR showed non-significant trends to preferential response rates with docetaxel in cluster 1 and 3. Membership of cluster 2 predicted higher ORR to carboplatin over docetaxel (interaction p=0.017). PFS indicated a treatment effect in cluster 2, but not in cluster 1 or 3; there was no evidence of interaction between subgroups and treatment (p=0.15).
Conclusions
Our results suggest that the overall heterogeneity of the copy number landscape is a promising area for seeking predictive/prognostic biomarkers in metastatic TNBC, and combined with other modalities of high-dimensional omics data could provide essential treatment response information.
Citation Format: Sipos O, Tovey H, Quist J, Haider S, Nowinski S, Gazinska P, Kernaghan S, Toms C, Timms KM, Lanchbury JS, Linn SC, Pinder SE, Bliss JM, Tutt A, Cheang MC, Grigoriadis A, On behalf of the TNT Trial Management Group and Investigators. Characterization of chromosomal instability in the TNT trial: A randomized phase III trial of carboplatin compared with docetaxel for patients with metastatic or recurrent locally advanced triple negative or BRCA1/2 breast cancer (CRUK/07/012) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-06-07.
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Affiliation(s)
- O Sipos
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - H Tovey
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - J Quist
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - S Haider
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - S Nowinski
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - P Gazinska
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - S Kernaghan
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - C Toms
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - KM Timms
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - JS Lanchbury
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - SC Linn
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - SE Pinder
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - JM Bliss
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - A Tutt
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - MC Cheang
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
| | - A Grigoriadis
- The Institute of Cancer Research, The Breast Cancer Now Toby Robins Research Centre, London, United Kingdom; The Institute of Cancer Research, Clinical Trials & Statistics Unit (ICR-CTSU), London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Breast Cancer Now Research Unit, Cancer Bioinformatics, London, United Kingdom; King's College London, Faculty of Life Sciences and Medicine, School of Cancer & Pharmaceutical Sciences, Cancer Bioinformatics, London, United Kingdom; Myriad Genetics, Inc., Salt Lake City, UT; Netherlands Cancer Institute, Amsterdam, Netherlands; King's College London, King's Health Partners Cancer Biobank, London, United Kingdom
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