Abstract
The mutation pattern of breast cancer molecular subtypes is incompletely understood. The purpose of this study was to identify mutations in genes that may be targeted with currently available investigational drugs in the three major breast cancer subtypes (ER+/HER2−, HER2+, and Triple Negative). We extracted DNA from fine needle aspirations of 267 stage I–III breast cancers. These tumor specimens typically consisted of >80 % neoplastic cells. We examined 28 genes for 163 known cancer-related nucleic acid variations by Sequenom technology. We observed at least one mutation in 38 alleles corresponding to 15 genes in 108 (40 %) samples, including PIK3CA (16.1 % of all samples), FBXW7 (8 %), BRAF (3.0 %), EGFR (2.6 %), AKT1 and CTNNB1 (1.9 % each), KIT and KRAS (1.5 % each), and PDGFR-α (1.1 %). We also checked for the polymorphism in PHLPP2 that is known to activate AKT and it was found at 13.5 % of the patient samples. PIK3CA mutations were more frequent in estrogen receptor-positive cancers compared to triple negative breast cancer (TNBC) (19 vs. 8 %, p = 0.001). High frequency of PIK3CA mutations (28 %) were also found in HER2+ breast tumors. In TNBC, FBXW7 mutations were significantly more frequent compared to ER+ tumors (13 vs. 5 %, p = 0.037). We performed validation for all mutated alleles with allele-specific PCR or direct sequencing; alleles analyzed by two different sequencing techniques showed 95–100 % concordance for mutation status. In conclusion, different breast cancer subtypes harbor different type of mutations and approximately 40 % of tumors contained individually rare mutations in signaling pathways that can be potentially targeted with drugs. Simultaneous testing of many different mutations in a single needle biopsy is feasible and allows the design of prospective clinical trials that could test the functional importance of these mutations in the future.
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Acknowledgments
This study was supported by Grants from Associazione Italiana per la Ricerca sul Cancro (AIRC–Grant 6251) e Foundation Sandro Pitigliani (LS) and the Safeway Foundation and the Breast Cancer Research Foundation (WFS and LP), National Cancer Institute 1K23CA121994-01 (AMG), Susan G. Komen Foundation KGKG081099 (AMG, KSH).
Author Contributions
LP and LS designed the study, oversaw all of its conduct, and finalized the manuscript. LS and YQ carried out the analysis of data and performed statistical analysis, LS drafted the manuscript; BW and KS-H performed molecular studies on specimens. DJH, FAH, JO’Sm GH, JP, TV, HG, VV, GNH, AMG accrued patients to the study, made biopsy materials available for molecular analyis and provided clinical input. EJY maintained the clinical data base. WFS obtained many of the cancer biopsies for this study. ADL participated in the design and provided intellectual input into interpretation of results. GB provided intellectual input into interpretation of results. All authors have read and approved the final version.
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The authors declare no conflicting or competing commercial interests.
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Santarpia, L., Qi, Y., Stemke-Hale, K. et al. Mutation profiling identifies numerous rare drug targets and distinct mutation patterns in different clinical subtypes of breast cancers. Breast Cancer Res Treat 134, 333–343 (2012). https://doi.org/10.1007/s10549-012-2035-3
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DOI: https://doi.org/10.1007/s10549-012-2035-3