Development of diagnostic kit for in vitro diagnostics of the TP53 signature in early breast cancer

Abstract

Abstract Background Diagnostic tests based on gene expression signatures identified by transcriptome analyses have been developed and these have been used for predicting prognosis, recurrence and/or effect of anticancer drugs including endocrine therapies in clinical practice of breast cancer, ahead of other cancer types. We have previously reported that TP53 signature, which has the ability to determine TP53 mutation status, are an independent prognostic factor of breast cancer, and also shown that the TP53 signature has better predictability of prognosis and efficacy on chemotherapies than the TP53 mutation status and other known clinic-pathological factors. Objects The aim of this study is to develop the diagnostic kit for in vitro diagnostics based on the TP53 signature. Methods We adopted an nCounter system (NanoString) because it has robust ability to analyze a gene expression signature of the TP53 signature from a small amount of RNA derived from archival FFPE tissues. Results We have designed a specific probe set for IVD of the TP53 signature and programed a new algorithm to determine the status of TP53 signature from the identified expression data. The algorithm has the characteristic that is hard to be affected by the outliers than previous algorithm (the algorithm cannot be disclosed). Using this method, we determined status of TP53 signature of 220 stage I-II breast cancers. The predictability of recurrence by the IVD of the TP53 signature will be shown in this study. We are also conducting a retrospective-prospective analysis of over 500 breast cancers as the validation study of the IVD under cooperation of JBCRG, OOTR. From this study, the predictability of the pathological CR (pCR) after neoadjuvant chemotherapies and the prognosis by the IVD will be also shown. Conclusion The TP53 signature diagnostic kit is expected to be a clinically useful biomarker for prediction of prognosis, recurrence and efficacy of perioperative chemotherapy in breast cancer.