Comparison of the Mutation Profiles of Triple-Negative Breast Cancers and Hormone Receptor-Positive/Human Epidermal Growth Factor Receptor 2-Negative Breast Cancers at the T2N0-1M0 Stage

BackgroundTriple-negative breast cancer (TNBC) has higher loco-regional recurrence and visceral metastasis compared to other breast cancer subtypes; however, little is known about the molecular pathogenesis and therapeutic targets of TNBC. Therefore, we compared the mutation profiles of early TNBC with those of hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2) breast cancer using a customized next-generation sequencing capture panel.MethodsDNA was obtained from the primary tumor tissues of 34 patients diagnosed with pT2N0-1M0 HR+/HER2 breast cancer or TNBC. To enrich the 48 breast cancer-associated genes, 21,192 probes were designed using the SureSelect design tool. After library preparation using the SureSelect XT kit (Agilent), paired-end DNA sequencing was performed on a HiSeq platform (Illumina). The mean depth of the target regions was 1,766 (×). The subsequent output containing genetic variation was analyzed using a pipeline of bioinformatics tools. Significant mutations with allele frequencies of more than 30% were checked for their germline counterparts in the peripheral blood. Circulating cell-free nucleic acids were extracted and analyzed with a therascreen® PIK3CA RGQ PCR kit (QIAGEN).ResultsSignificant mutations were found in TP53, PIK3CA, AR, BRCA1, PTEN, BRCA2, BRIP2, KIT, MET, AKT1, ALK, BARD1, BRAF, CD274, ERBB2, FGFR1, IDH2, NOTCH1, RET, and STK11 (in descending order of occurrence). TP53 mutations were identified in the TNBC group more frequently than in the HR+/HER2 group (p=0.003). The presence of TP53 mutations was associated with a higher tumor grade (p=0.008), p53 positivity (p<0.0001), and a higher (≥15) Ki-67 index (p=0.004). PIK3CA was the most frequently mutated gene in HR+/HER2 breast cancer (8/22, 36.4%), but not in TNBC (1/12, 8.3%). However, circulating cell-free PIK3CA mutations were not detected in either group. ConclusionsThe TP53 mutation is associated with higher tumor grade and Ki-67 expression in both groups, and with larger tumor size in TNBC, but not in HR+/HER2– breast cancer. In the foundation of TP53 mutation, concomitant mutation numbers are proportional to tumor size, reflecting clonal progression. Breast cancer-associated mutations such as those in TP53 and PIK3CA have different biological implications for the proliferation and clonal diversification of these two distinct groups of breast cancer.