High-Throughput Mutation Profiling Changes before and 3 Weeks after Chemotherapy in Newly Diagnosed Breast Cancer Patients

Abstract

Background: Changes in tumor DNA mutation status during chemotherapy can provide insights into tumor biology and drug resistance. The purpose of this study is to analyse the presence or absence of mutations in cancer-related genes using baseline breast tumor samples and those obtained after exposure to one cycle of chemotherapy to determine if any differences exist, and to correlate these differences with clinical and pathological features.

Methods: Paired breast tumor core biopsies obtained pre- and post-first cycle doxorubicin (n = 18) or docetaxel (n = 22) in treatment-naïve breast cancer patients were analysed for 238 mutations in 19 cancer-related genes by the Sequenom Oncocarta assay.

Results: Median age of patients was 48 years (range 32-64); 55% had estrogen receptor-positive tumors, and 60% had tumor reduction ≥25% after cycle 1. Mutations were detected in 10/40 (25%) pre-treatment and 11/40 (28%) post-treatment samples. Four mutation pattern categories were identified based on tumor mutation status pre- → post-treatment: wildtype (WT)→WT, n = 24; mutant (MT)→MT, n = 5; MT→WT, n = 5; WT→MT, n = 6. Overall, the majority of tumors were WT at baseline (30/40, 75%), of which 6/30 (20%) acquired new mutations after chemotherapy. Pre-treatment mutations were predominantly in PIK3CA (8/10, 80%), while post-treatment mutations were distributed in PIK3CA, EGFR, PDGFRA, ABL1 and MET. All 6 WT→MT cases were treated with docetaxel. Higher mutant allele frequency in baseline MT tumors (n = 10; PIK3CA mutations n = 8) correlated with less tumor reduction after cycle 1 chemotherapy (R = -0.667, p = 0.035). No other associations were observed between mutation pattern category with treatment, clinicopathological features, and tumor response or survival.

Conclusion: Tumor mutational profiles can change as quickly as after one cycle of chemotherapy in breast cancer. Understanding of these changes can provide insights on potential therapeutic options in residual resistant tumors.

Trial registration: ClinicalTrials.gov NCT00212082.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1. CONSORT flow chart in which the number of paired samples with data available for Sequenom analysis are shown.

Fig 2. Oncogenic mutations detected pre- and post-chemotherapy.

Representative chromatograms of (A) PIK3CA E542K in a MT→MT case HOB045, (B) EGFR S768I in a MT→WT case HOB035, and (C) MET Y1230C detected in a WT→MT case HOB090. The expected positions for the unextended primer (UEP) and the nucleotide and mutation status (mutant [MT] or wildtype [WT]) based on the size of the extension products are indicated above the gray vertical dashed lines.

Fig 3. Correlation between percentage allele frequency and post-cycle 1 tumor response of at least 25%.

Fig 4. Progression-free and overall survival between the WT→WT subgroup versus combination of other mutation pattern subgroups.

(A) Progression-free survival and (B) overall survival of the WT→WT subgroup and a combination of other mutation pattern subgroups (MT→MT, MT→WT, WT→MT). Bold line: WT→WT subgroup; broken line: combination of the other mutation subgroups MT→MT, MT→WT, WT→MT.