Circulating-free DNA Mutation Associated with Response of Targeted Therapy in Human Epidermal Growth Factor Receptor 2-positive Metastatic Breast Cancer

Qing Ye, Fan Qi, Li Bian, Shao-Hua Zhang, Tao Wang, Ze-Fei Jiang, Qing Ye, Fan Qi, Li Bian, Shao-Hua Zhang, Tao Wang, Ze-Fei Jiang

Abstract

Background: The addition of anti-human epidermal growth factor receptor 2 (HER2)-targeted drugs, such as trastuzumab, lapatinib, and trastuzumab emtansine (T-DM1), to chemotherapy significantly improved prognosis of HER2-positive breast cancer patients. However, it was confused that metastatic patients vary in the response of targeted drug. Therefore, methods of accurately predicting drug response were really needed. To overcome the spatial and temporal limitations of biopsies, we aimed to develop a more sensitive and less invasive method of detecting mutations associated with anti-HER2 therapeutic response through circulating-free DNA (cfDNA).

Methods: From March 6, 2014 to December 10, 2014, 24 plasma samples from 20 patients with HER2-positive metastatic breast cancer who received systemic therapy were eligible. We used a panel for detection of hot-spot mutations from 50 oncogenes and tumor suppressor genes, and then used targeted next-generation sequencing (NGS) to identify somatic mutation of these samples in those 50 genes. Samples taken before their first trastuzumab administration and subsequently proven with clinical benefit were grouped into sensitive group. The others were collected after disease progression of the trastuzumab-based therapy and were grouped into the resistant group.

Results: A total of 486 single-nucleotide variants from 46 genes were detected. Of these 46 genes, phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), proto-oncogene c-Kit (KIT), and tumor protein p53 (TP53) were the most common mutated genes. Seven genes, including epidermal growth factor receptor (EGFR), G protein subunit alpha S (GNAS), HRas proto-oncogene (HRAS), mutL homolog 1 (MLH1), cadherin 1 (CDH1), neuroblastoma RAS viral oncogene homolog (NRAS), and NOTCH1, that only occurred m utations in the resistant group were associated with the resistance of targeted therapy. In addition, we detected a HER2 S855I mutation in two patients who had persistent benefits from anti-HER2 therapy.

Conclusion: Targeted NGS of cfDNA has potential clinical utility to detect biomarkers from HER2-targeted therapies.

Conflict of interest statement

There are no conflicts of interest.

Figures

Figure 1
Figure 1
The constitution ratio of 486 somatic mutations detected from 24 plasma samples. *Genes that owe less than 10 single-nucleotide variants (2%), those genes contain fibroblast growth factor receptor 1 (FGFR1), G protein subunit alpha q (GNAQ), RB transcriptional corepressor 1 (RB1), ABL proto-oncogene 1 (ABL1), B-Raf proto-oncogene (BRAF), fibroblast growth factor receptor 3 (FGFR3), guanine nucleotide-binding protein alpha stimulating (GNAS), HRas proto-oncogene (HRAS), fms-related tyrosine kinase 3 (FLT3), AKT serine/threonine kinase 1 (AKT), ret proto-oncogene (RET), cadherin 1 (CDH1), cyclin-dependent kinase inhibitor 2A (CDKN2A), ERBB2, enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2), isocitrate dehydrogenase 1 (IDH1), isocitrate dehydrogenase 2 (IDH2), MET proto-oncogene (MET), mutL homolog 1 (MLH1), neuroblastoma RAS viral oncogene homolog (NRAS), catenin beta 1 (CTNNB1), janus kinase 2 (JAK2), NOTCH1, protein tyrosine phosphatase nonreceptor type 11 (PTPN11), janus kinase 3 (JAK3), and MPL proto-oncogene (MPL).
Figure 2
Figure 2
Mutational prevalence of 24 human epidermal growth factor receptor 2-positive breast cancer patients’ plasma samples from 46 genes.
Figure 3
Figure 3
The landscape of the identified mutations in seven anti-human epidermal growth factor receptor 2-targeted therapy-resistant genes. The number shown in the box meant the mean allele frequency of the identified mutations in that gene. R: Resistant group. EGFR: Epidermal growth factor receptor; GNAS: Guanine nucleotide-binding protein alpha stimulating; HRAS: HRas proto-oncogene; MLH1: mutL homolog 1; CDH1: Cadherin 1; NRAS: Neuroblastoma RAS viral oncogene homolog.
Figure 4
Figure 4
The gene map of human epidermal growth factor receptor 2 p.S855I mutation identified in circulating-free DNA.
Figure 5
Figure 5
The clinical timeline for two metastatic breast cancer patients with the HER2 p.S855I mutation in cfDNA. (a and b) The clinical treatment history and the dramatic effect of containing anti-HER2 agents’ regimen in the Patient R2 and S2 with HER2 activating mutation, respectively. Values within each circle represent mutation frequency. Positron emission tomography/computed tomography scan showed the clinical complete response in the right breast tumor of patient S8 after eight cycles’ therapy. *TPH: Docetaxel, carboplatin, trastuzumab; RT: Radiotherapy; ANA: Anastrozole; G: Goserelin. †LX: Lapatinib, capecitabine. ‡TXH: Docetaxel, capecitabine, trastuzumab. §The pathological images showed the pathological complete response in the breast tumor of patient S8 after eight cycles’ therapy. HER2: Human epidermal growth factor receptor 2; cfDNA: Circulating-free DNA.

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