Exome Sequencing Identified Mutation Shift During Neoadjuvant Chemotherapy In Breast Cancer

Purpose:The changed gene-expression profiles of breast cancer under neoadjuvant chemotherapy (NCT) have been described. However, it remains unclear whether chemotherapy affects mutation status in breast cancer. In our study, we investigated the influence of chemotherapy on mutation status in breast cancer.Methods:We performed microdissection and 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). Furthermore, shift in mutation status was validated by Sanger sequencing and analyzed in independent extension cohorts. To determine the phenotype of these mutations, we functionally characterized the mutations using protein structure analysis, in vitro kinase assays, cell culture, and xenograft experiments.Results:Compared with pre-treatment biopsies, WES identified the enrichment of two TEKT4 germline variations in post-treatment tumors with a frequency of approximately 10% in an independent extension cohort of 84 paired samples. Tektin4 (encoded by TEKT4) associates closely with rubulin in doublet microtubules and helps stabilize these structures. These two TEKT4 variations in a high cis linkage were biologically relevant, as the ectopic expression of variant TEKT4 deregulated the microtubule stability, antagonized the paclitaxel-induced stabilizing effect of microtubules, and increased paclitaxel resistance. Furthermore, TEKT4 variations were associated with reduced disease-free survival (DFS) and overall survival (OS) compared with wild-type TEKT4 in patients undergoing paclitaxel-based chemotherapy. Furthermore, the analysis of WES data also revealed the loss of somatic mutations in TP53 and PIK3CA in tumor tissues after NCT. In the extension cohort, somatic mutations in TP53 or PIK3CA were identified in 24.8% of the pre-NCT tumor samples but in only 12.1% of the post-NCT tumor samples (P< 0.001). Patients with initial TP53 and PIK3CA mutations who became negative for the mutations after NCT had a higher Miller-Payne score, improved DFS and improved OS than those with no change or the opposite change.Conclusion:Our data reveal the novel concept that mutation shift might occur during chemotherapy. Furthermore, the enrichment of variations in TEKT4 and the loss of somatic mutations in TP53 and PIK3CA may be translated to biomarkers for prognosis via further verification, which may optimize the choice of sequential therapy and improve patient survival.