Identifying Circulating Tumor DNA Mutation Profiles in Metastatic Breast Cancer Patients with Multiline Resistance

Zhe-Yu Hu, Ning Xie, Can Tian, Xiaohong Yang, Liping Liu, Jing Li, Huawu Xiao, Hui Wu, Jun Lu, Jianxiang Gao, Xuming Hu, Min Cao, Zhengrong Shui, Mengjia Xiao, Yu Tang, Qiongzhi He, Lianpeng Chang, Xuefeng Xia, Xin Yi, Qianjin Liao, Quchang Ouyang, Zhe-Yu Hu, Ning Xie, Can Tian, Xiaohong Yang, Liping Liu, Jing Li, Huawu Xiao, Hui Wu, Jun Lu, Jianxiang Gao, Xuming Hu, Min Cao, Zhengrong Shui, Mengjia Xiao, Yu Tang, Qiongzhi He, Lianpeng Chang, Xuefeng Xia, Xin Yi, Qianjin Liao, Quchang Ouyang

Abstract

Purpose: In cancer patients, tumor gene mutations contribute to drug resistance and treatment failure. In patients with metastatic breast cancer (MBC), these mutations increase after multiline treatment, thereby decreasing treatment efficiency. The aim of this study was to evaluate gene mutation patterns in MBC patients to predict drug resistance and disease progression.

Method: A total of 68 MBC patients who had received multiline treatment were recruited. Circulating tumor DNA (ctDNA) mutations were evaluated and compared among hormone receptor (HR)/human epidermal growth factor receptor 2 (HER2) subgroups.

Results: The baseline gene mutation pattern (at the time of recruitment) varied among HR/HER2 subtypes. BRCA1 and MED12 were frequently mutated in triple negative breast cancer (TNBC) patients, PIK3CA and FAT1 mutations were frequent in HR+ patients, and PIK3CA and ERBB2 mutations were frequent in HER2+ patients. Gene mutation patterns also varied in patients who progressed within either 3 months or 3-6 months of chemotherapy treatment. For example, in HR+ patients who progressed within 3 months of treatment, the frequency of TERT mutations significantly increased. Other related mutations included FAT1 and NOTCH4. In HR+ patients who progressed within 3-6 months, PIK3CA, TP53, MLL3, ERBB2, NOTCH2, and ERS1 were the candidate mutations. This suggests that different mechanisms underlie disease progression at different times after treatment initiation. In the COX model, the ctDNA TP53 + PIK3CA gene mutation pattern successfully predicted progression within 6 months.

Conclusion: ctDNA gene mutation profiles differed among HR/HER2 subtypes of MBC patients. By identifying mutations associated with treatment resistance, we hope to improve therapy selection for MBC patients who received multiline treatment.

Keywords: Circulating tumor DNA (ctDNA); Drug resistance; Gene mutation pattern; HR/HER2 subtype; Metastatic breast cancer; Progression-free survival.

Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Figures

Fig. 1
Fig. 1
Circulating tumor DNA (ctDNA) gene mutation profiles (top) and patient demographic/clinical data (bottom).
Fig. 2
Fig. 2
Tumor mutation burden (TMB) for different metastatic breast cancer subtypes. A. TMB comparison among the different HR/HER2 subtypes: ER/PR+, HER2+, and triple negative breast cancer (TNBC). B. Number of mutated circulating tumor DNA (ctDNA) genes and their maximum frequency in each patient among the four HR/HER2 subtypes.
Fig. 3
Fig. 3
Ranking circulating tumor DNA (ctDNA) gene mutations increased in triple negative breast cancer (TNBC), HR+, and HER2+ patients with progression. A. ctDNA gene mutations increased in patients who had progression within 3 months of treatment. B. ctDNA gene mutations increased in patients who had progression within 3–6 months. C. Ranking of ctDNA mutations increased in patients who had progression within 3 months. D. Ranking of ctDNA gene mutations increased in patients who had progression within 3–6 months.
Fig. 4
Fig. 4
Receiver operating characteristics (ROC) curves for four joint models of TP53, PIK3CA, ERBB2, BRCA1, and CDK12 mutations in predicting progression-free survival.
Fig. 5
Fig. 5
Kaplan-Meier curves for progression-free survival probabilities stratified by circulating tumor DNA (ctDNA) mutations, TP53 (A), PIK3CA (B),TP53/PIK3CA (C), ERBB2 (D),BCRA1 (E), and CDK12 (F).
Fig. S2
Fig. S2
Mutation hotspot for TP53 and PIK3CAcirculating tumor DNA (ctDNA) genes in recruited patients (A and C) and in previous publications (B and D).
Fig. S3
Fig. S3
Four patients showed increased mutation frequency by ctDNA analysis but did not did not exhibit progression via image analysis. These metastatic tumors were detected by computed tomography (CT). Pink arrows indicated the metastatic target lesions in CT images at the time of circulating tumor DNA (ctDNA) testing. A–D panels represents the image and ctDNA changes for patients #1–#4 listed in Table S6C, respectively.

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