51. Abstract P2-06-07: Exome sequencing identifies somatic mutations in basal-like breast cancer before and after neoadjuvant chemotherapy
- Author
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K-D Yu, Y-Z Jiang, and Z-M Shao
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Cancer Research ,Chemotherapy ,Oncology ,Somatic cell ,medicine.medical_treatment ,Cancer research ,medicine ,Biology ,Bioinformatics ,Exome sequencing ,Basal-Like Breast Cancer - Abstract
Purpose: Among the five breast cancer subtypes, basal-like breast cancers (BLBCs) have drawn much attention, because they are associated with poor clinicopathological features, lack of effective treatment targets, and have poor prognosis. We designed the experiment to test the hypothesis that significant mutational evolution of BLBCs might occur during chemotherapy. Methods: We performed exome sequencing (100-fold coverage) to examine the exomes of 11 paired BLBC samples (pretreatment tumor biopsies and posttreatment tumors). The molecular subtype of BLBC was proven by gene-expression profile as well as by immunohistochemistry assay. Firstly, we sequenced the tumor genomic DNA obtained before and after neoadjuvant chemotherapy and their matched normal breast tissues. After analyzing and comparing potential somatic single nucleotide variations (SNVs) and insertions & deletions (indels), we focused on the functional mutations in certain genes or pathways. Furthermore, after validation of the mutations by Sanger sequencing, we investigated their biological functions (e.g. drug-resistance, cell proliferation, etc.). Results: Compared with pretreatment biopsies, analysis of whole-exome sequence data identified and validated TEKT4 (tektin 4) — a constitutive protein of microtubules in cilia, flagella, basal bodies and centrioles — as a significantly mutated gene in posttreatment tumors with a mutation frequency of approximately 17.6% in an independent extension cohort of 84 paired BLBC samples. TEKT4 mutations are biologically relevant, as ectopic expression of mutant TEKT4 increased paclitaxel resistance of BLBC cell lines both in vitro and in vivo. Additionally, compared with the normal breast tissues, 16 significantly mutated genes were identified and validated in the paired cancer samples, including TP53, ARID1A, BEND5, LCT, COL4A4, GAP43, COL6A6, LOC728369, STAP1, KCNK17, LZTS2, TST, IL9R, HDLBP, RASL11A and FAM22D. These genes have functions that could be broadly grouped into five biological classes: (i) MAPK signaling, (ii) PI3K/AKT signaling, (iii) cell cycle, (iv) metabolism and (v) loss of genome stability. Conclusion: Our data reveal the novel concept that significant evolution might occur during chemotherapy and mutational heterogeneity could be a property of BLBCs. In addition, the identification of somatic mutations as biomarkers for pCR (pathologic complete remission) prediction and prognosis might help us optimize choice for sequential therapy and improve patients' survival. Prospective clinical trials based on these findings might illustrate the drug-resistant mechanism and identify resistance pathways that can be exploited for therapeutic selection. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-06-07.
- Published
- 2012
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