Assessment of structural chromosomal instability phenotypes as biomarkers of carboplatin response in triple negative breast cancer: the TNT trial

O Sipos, H Tovey, J Quist, S Haider, S Nowinski, P Gazinska, S Kernaghan, C Toms, S Maguire, N Orr, S C Linn, J Owen, C Gillett, S E Pinder, J M Bliss, A Tutt, M C U Cheang, A Grigoriadis, O Sipos, H Tovey, J Quist, S Haider, S Nowinski, P Gazinska, S Kernaghan, C Toms, S Maguire, N Orr, S C Linn, J Owen, C Gillett, S E Pinder, J M Bliss, A Tutt, M C U Cheang, A Grigoriadis

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.

Keywords: allelic imbalance; carboplatin; genomic instability; metastatic triple negative breast cancer.

Conflict of interest statement

Disclosure AT, HT, MCUC, SK, PG, AG, SEP and JMB report that their institutional departments have received grants from Breast Cancer Now and/or Cancer Research UK and other support for costs or consumables in this research from Myriad Genetics Inc. and NanoString Technologies Inc. during the conduct of the TNT trial. Furthermore, the salary of HT has been part supported by educational grants from Merck Sharp & Dohme Ltd and Pfizer Inc. MCUC has a patent: US Patent No. 9,631,239 with royalties paid. SCL received institutional research support funding from Agendia, Amgen, AstraZeneca, Eurocept, Genentech, Roche, Sanofi and Tesaro. SCL is an advisory board member for Cergentis, IBM, Novartis, Pfizer, Roche and Sanofi. JMB also reports grants and non-financial support from AstraZeneca, Novartis, Janssen-Cilag, Merck Sharpe & Dohme, Pfizer, Roche, and Clovis Oncology outside the submitted work. All remaining authors have declared no conflicts of interest.

Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.

Figures

Figure 1
Figure 1
CONSORT diagram showing the number of evaluable primary tumour samples. Samples with ambiguous BRCA1/2 deficiency status (n = 21) were excluded when the associations of CIN-measurements with BRCA1/2 mutation and BRCA1 methylation status were examined.
Figure 2
Figure 2
Overview of the characterisation of the CIN-measurements among the primary tumour samples (n = 135). (A) Frequency of copy number gains and losses across the whole genome in the TNT copy number subset (n = 135). CNAs were determined based on ASCAT copy number estimates of the primary tumour samples. (B) Summary of the CIN-measurements of the primary tumour samples. The samples are ordered according to the PGA score within the HLAMP groups. The bar plot shows the PGA values for each sample. The coloured bars display the association with BRCA1/2 mutation and BRCA1 methylation status: burgundy – BRCA1/2 mutation, dark blue – BRCA1 methylation, green – both BRCA1/2 mutation and BRCA1 methylation. The displayed covariates include HLAMP group, Shannon diversity index group, BRCA1-like status and HRD status. NtAI, AiCNA, AbCNA, CnLOH values are displayed as z-scores. Tumour purity (estimated by ASCAT algorithm) is shown as quartiles (0% representing the lowest quartile with samples of lowest tumour purity). BRCA1/2 mutational status and BRCA1 methylation status are displayed together with loss of heterozygosity status for the patients with mutation or methylation of BRCA1 or BRCA2. Bottom panel shows the identified DNA damage response (DDR)-related germline variants other than BRCA1/2. Triangles mark non-triple negative samples with BRCA1/2 mutation. (C) Comparison of the distribution of the CIN-measurements among the BRCA1/2 deficiency subgroups: AiCNA, AbCNA, CnLOH, NtAI, PGA are displayed on boxplots; HLAMP, Shannon index (SI), BRCA1-like and HRD status are displayed on stacked bar plots. The somatic BRCA1 mutated cases are coloured in burgundy on the boxplots for the continuous variables, and the number of somatic BRCA1 mutated cases in each subgroup of the categorical CIN-measurements are displayed next to the bar plots. P values of Kruskal–Wallis rank sum tests for AiCNA, AbCNA, CnLOH, NtAI and PGA and Fisher's exact tests for HLAMP, SI, BRCA1-like and HRD are shown. The P values are corrected for multiple comparisons by the Benjamini–Hochberg method. AbCNA, allelic balanced CNA; AiCNA, allelic imbalanced CNA; CnLOH, copy number neutral loss of heterozygosity; HLAMP, high-level amplifications; HRD, homologous recombination deficiency; MET, BRCA1 promoter methylated; MUT, BRCA1/2 mutated; NtAI, number of telomeric allelic imbalances; PGA, percentage of genome altered; WT, BRCA1/2 wild-type.
Figure 3
Figure 3
Objective response rate (ORR) in the carboplatin and docetaxel treatment arms across (A) NtAI, (B) AiCNA and (C) HLAMP subgroups (low, intermediate, high, as defined by tertiles for NtAI and AiCNA; and quiet, low, high for HLAMP). Ninety-five per cent confidence intervals, Fisher's exact test P values and percentage of subjects who responded to treatment in the group are shown on the bar plots. Kaplan–Meier survival plots showing the progression-free survival (PFS) in the carboplatin and docetaxel arms between the (D) HLAMP, (E) AiCNA and (F) PGA subgroups. P values of likelihood ratio tests for interaction between the CIN-measurements and treatment group are shown with and without adjustment for clinical covariates. N at risk (events) shows the number of subjects who remain in the analysis set at a given time point and the number of PFS events reported between time points.

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