Abstract S4-05: Exome sequencing identifies shift in TP53 and PIK3CA mutation status after paclitaxel-based neoadjuvant chemotherapy in breast cancer

Abstract

Abstract Purpose: The changed gene-expression profiles of breast cancer under neoadjuvant chemotherapy (NCT) have been described. However, it remains unclear whether chemotherapy affects somatic mutation status in breast cancer. We investigated the influence of paclitaxel-based chemotherapy on somatic mutations in tumor tissues from patients with breast cancer. Patients and Methods: Samples were derived from two cohorts: first, 296 patients who underwent paclitaxel-based NCT with matched pre- and post-chemotherapy tumor tissues; second, 81 patients who underwent paclitaxel-based chemotherapy with pre-chemotherapy tumor tissues. First, we performed whole exome sequencing (WES) to examine the exomes (100-fold coverage) of two paired basal-like breast cancer samples (pre-treatment tumor biopsies and post-treatment tumors). Shift in somatic mutation status was validated by Sanger sequencing and analyzed in an extension cohort of 296 patients. Furthermore, we performed microdissection and genetic heterogeneity analysis for samples from 81 patients who underwent paclitaxel-based chemotherapy. Somatic mutation status was determined to reveal potential impact of paclitaxel-based chemotherapy on mutation status. Results: Compared with post-treatment biopsies, the analysis of WES data identified and validated TP53 and PIK3CA — as significantly mutated genes in pre-treatment tumors with a mutation frequency of approximately 10% in an independent extension cohort of 296 paired samples of different molecular subtypes. Somatic mutations of TP53 or PIK3CA were detected in 24.3% of the pre-chemotherapy tumor samples (35 of 296 for TP53, 32 of 296 for PIK3CA, 5 of 296 for both genes, respectively) but in only 12.2% of the post-chemotherapy tumor samples (18 of 296 for TP53, 16 of 296 for PIK3CA, 2 of 296 for both genes, respectively). The decrease in mutation rate was statistically significant (P < 0.001). Patients with TP53/PIK3CA mutations switched from positive to negative after chemotherapy had better partial response than patients with no change or with a reverse change (P = .008). Furthermore, patients with TP53/PIK3CA mutations switched from positive to negative had improved disease-free survival (P = 0.018) and improved overall survival (P = 0.032) relative to patients with no change or with a reverse change. In the second cohort, 18.5% of the tumors (15 of 81) showed intratumoral heterogeneity of TP53 or PIK3CA somatic mutations, whereas 81.5% (66 of 81) were homogeneous, either with mutations of certain genes or not. Conclusion: Our data reveal the novel concept that significant evolution might occur during chemotherapy. Chemotherapy may reduce somatic mutation frequency in patients with breast cancer, likely the result of a preferential response of highly fit sub-clones without mutations of certain genes. In addition, the identification of somatic mutations of TP53 and PIK3CA as biomarkers for prediction of treatment response and prognosis might help us optimize choice for sequential therapy and improve patients’ survival. KEY WORDS: Exome sequencing; TP53; PIK3CA; neoadjuvant chemotherapy; breast cancer. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr S4-05.