Identification of mutation patterns and circulating tumour DNA-derived prognostic markers in advanced breast cancer patients

Hao Liao, Jiayang Zhang, Tiantian Zheng, Xiaoran Liu, Jianxin Zhong, Bin Shao, Xiaoxi Dong, Xiaohong Wang, Pan Du, Bonnie L King, Shidong Jia, Jianjun Yu, Huiping Li, Hao Liao, Jiayang Zhang, Tiantian Zheng, Xiaoran Liu, Jianxin Zhong, Bin Shao, Xiaoxi Dong, Xiaohong Wang, Pan Du, Bonnie L King, Shidong Jia, Jianjun Yu, Huiping Li

Abstract

Background: The correlations between circulating tumour DNA (ctDNA)-derived genomic markers and treatment response and survival outcome in Chinese patients with advanced breast cancer (ABC) have not been extensively characterized.

Methods: Blood samples from 141 ABC patients who underwent first-line standard treatment in Peking University Cancer Hospital were collected. A next-generation sequencing based liquid biopsy assay (PredicineCARE) was used to detect somatic mutations and copy number variations (CNVs) in ctDNA. A subset of matched blood samples and tumour tissue biopsies were compared to evaluate the concordance.

Results: Overall, TP53 (44.0%) and PIK3CA (28.4%) were the top two altered genes. Frequent CNVs included amplifications of ERBB2 (24.8%) and FGFR1 (8.5%) and deletions of CDKN2A (3.5%). PIK3CA/TP53 and FGFR1/2/3 variants were associated with drug resistance in hormone receptor-positive (HR +) and human epidermal growth factor receptor 2-positive (HER2 +) patients. The comparison of genomic variants across matched tumour tissue and ctDNA samples revealed a moderate to high concordance that was gene dependent. Triple-negative breast cancer (TNBC) patients harbouring TP53 or PIK3CA alterations had a shorter overall survival than those without corresponding mutations (P = 0.03 and 0.008). A high ctDNA fraction was correlated with a shorter progression-free survival (PFS) (P = 0.005) in TNBC patients. High blood-based tumor mutation burden (bTMB) was associated with a shorter PFS for HER2 + and TNBC patients (P = 0.009 and 0.05). Moreover, disease monitoring revealed several acquired genomic variants such as ESR1 mutations, CDKN2A deletions, and FGFR1 amplifications.

Conclusions: This study revealed the molecular profiles of Chinese patients with ABC and the clinical validity of ctDNA-derived markers, including the ctDNA fraction and bTMB, for predicting treatment response, prognosis, and disease progression.

Trial registration: ClinicalTrials.gov ID: NCT03792529. Registered January 3rd 2019, https://ichgcp.net/clinical-trials-registry/NCT03792529 .

Keywords: Advanced breast cancer; Next generation sequencing; Survival outcomes; Tumor mutation burden; ctDNA fraction.

Conflict of interest statement

The authors have no conflicts of interest to disclose.

© 2022. The Author(s).

Figures

Fig. 1
Fig. 1
CtDNA mutation profile of Chinese ABC patients and the distribution of variations among different IHC subtypes. A Somatic mutation landscape of 141 Chinese ABC patients. The bar chart above the heatmap shows the ctDNA fractions of all baseline samples in the cohort. In the heatmap, the top bars depict the number of mutations a patient carried and the bars below denote different IHC subtypes. Each column represents one patient, and each row represents one gene. The text on the left represents gene names. The values on the right represent the mutation rates of these genes. Distributions of (B) the top 10 somatic mutations and (C) the top 10 CNVs among the three IHC subtypes. ABC, advanced breast cancer; ctDNA, circulating tumour DNA; IHC, immunohistochemistry; CNVs, copy number variations
Fig. 2
Fig. 2
Concordance analysis of mutations between plasma and tissue samples. Concordance of (A) SNVs and (B) CNVs between tissue samples and plasma ctDNA. In the matrices, the top bar charts depict the number of mutations. The text below represents patient identities, and the text on the left represents gene names. Coloured triangles in the squares indicate mutations. If a square was filled with two coloured triangles, the same mutation was detected in the corresponding patient's plasma and tissue. Overlapping (C) PIK3CA SNVs, (D) TP53 SNVs, and (E) ERBB2 CNVs between tissue and plasma ctDNA. SNVs, single nucleotide variations; CNVs, copy number variations; ctDNA, circulating tumour DNA
Fig. 3
Fig. 3
Oncoplots for drug-sensitive and drug-resistant (A) HR + samples, (B) HER2 + samples, and (C) TNBC samples. The green bars below the heatmap indicate samples collected from patients who are sensitive to treatment, while the orange bars indicate samples collected from patients who are resistant to treatment. Different colours of squares denote different types of mutations. Red represents SNVs/Indels, blue represents amplifications, and green represents deletions. Survival analyses of OS (D) between patients with or without TP53 mutations and (E) between patients with or without PIK3CA mutations. F Comparison of ctDNA fractions among the three IHC subtypes. The black lines represent the median of each group. HR + , hormone receptor-positive; HER2 + , human epidermal growth factor receptor 2-positive; TNBC, triple-negative breast cancer; SNVs, single nucleotide variations; Indels, insertions and deletions; OS, overall survival; ctDNA, circulating tumour DNA; IHC, immunohistochemistry
Fig. 4
Fig. 4
Survival analyses of (A) PFS and (B) OS among the three IHC subtypes. C Comparison of bTMB among the three IHC subtypes. D Comparison of bTMB between HER2 + drug-sensitive and drug-resistant samples. The black lines represent the median of each group. Survival analyses of (E) PFS and (F) OS between patients with low and high bTMB. PFS, progression-free survival; OS, overall survival; IHC, immunohistochemistry; bTMB, blood-based tumour mutation burden; HER2 + , human epidermal growth factor receptor 2-positive
Fig. 5
Fig. 5
Survival analyses of PFS (A) between TNBC patients with low and high ctDNA fractions, (B) between HER2 + patients with low and high bTMB, and (C) between TNBC patients with low and high bTMB. PFS, progression-free survival; TNBC, triple-negative breast cancer; ctDNA, circulating tumour DNA; HER2 + , human epidermal growth factor receptor 2-positive; bTMB, blood-based tumour mutation burden

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