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PIK3CA mutation profiling in patients with breast cancer, using a highly sensitive detection system.

ABSTRACT: PIK3CA mutations are common activating mutations associated with breast cancer (occurring in 20-30% of all cases) and are potent predictive markers for responses to PI3K inhibitors. Thus, it is important to develop sensitive methods to detect these mutations. We established a novel detection method using a quenching probe (QP) system to identify PIK3CA mutations, using DNA from 309 breast cancer tissues. In a developmental cohort, we determined the optimal detection threshold of the QP system with human tumor DNA from 119 freshly frozen tumor samples. We found a 96% concordance rate with the QP system between DNA from 26 matching fresh-frozen specimens and formalin-fixed paraffin-embedded (FFPE) specimens from the same patients, and known PIK3CA mutation status in the developmental cohort. In a validation cohort, we evaluated whether the threshold for judging mutations using the QP system with frozen specimen-derived DNA was applicable with FFPE-derived DNA. In the validation cohort, 30 DNA samples from 190 FFPE-derived DNA samples with known PIK3CA mutation status were analyzed by direct sequencing (DS) and droplet digital PCR, in a blinded manner. The sensitivity and specificity of the droplet digital PCR results were 100% and 100% (QP system), and 60% and 100% (DS), respectively. We also analyzed the relationship between clinical outcomes and the PIK3CA mutational status of 309 breast cancer samples, including the developmental cohort and validation cohort samples. Multivariate analysis suggested that PIK3CA mutations, especially H1047R, were prognostic factors of relapse-free survival. Our novel detection system could be more useful than DS for detecting clinical PIK3CA mutations.

SUBMITTER: Shimoi T

PROVIDER: S-EPMC6113507 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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PIK3CA mutation profiling in patients with breast cancer, using a highly sensitive detection system.

Shimoi Tatsunori T Hamada Akinobu A Yamagishi Marifu M Hirai Mitsuharu M Yoshida Masayuki M Nishikawa Tadaaki T Sudo Kazuki K Shimomura Akihiko A Noguchi Emi E Yunokawa Mayu M Yonemori Kan K Shimizu Chikako C Kinoshita Takayuki T Fukuda Takahiro T Fujiwara Yasuhiro Y Tamura Kenji K

Cancer science 20180728 8

PIK3CA mutations are common activating mutations associated with breast cancer (occurring in 20-30% of all cases) and are potent predictive markers for responses to PI3K inhibitors. Thus, it is important to develop sensitive methods to detect these mutations. We established a novel detection method using a quenching probe (QP) system to identify PIK3CA mutations, using DNA from 309 breast cancer tissues. In a developmental cohort, we determined the optimal detection threshold of the QP system wi ...[more]

PMID: 29906308

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Project description:The rapidly evolving nature of antibody drug development has resulted in technologies that generate vast numbers (hundreds to thousands) of lead antibody candidates during early discovery. These candidates must be rapidly pared down to identify the most drug-like candidates for in-depth analysis of their safety and efficacy, which can only be performed on a limited number of antibodies due to time and resource requirements. One key biophysical property of successful antibody therapeutics is high specificity, defined as low levels of nonspecific binding or polyspecificity. Although there has been some progress in developing assays for detecting antibody polyspecificity, most of these assays are limited by poor sensitivity or assay formats that require proprietary antibody surface display methods, and some of these assays use complex and poorly defined polyspecificity reagents. Here we report the PolySpecificity Particle (PSP) assay, a sensitive flow cytometry assay for evaluating antibody nonspecific interactions that overcomes previous limitations and can be used for evaluating diverse types of IgGs, multispecific antibodies and Fc-fusion proteins. Our approach uses micron-sized magnetic beads coated with Protein A to capture antibodies at extremely dilute concentrations (<0.02 mg/mL). Flow cytometry analysis of polyspecificity reagent binding to these conjugates results in sensitive detection of differences in nonspecific interactions for clinical-stage antibodies. Our PSP assay strongly discriminates between antibodies with different levels of polyspecificity using previously reported polyspecificity reagents that are either well-defined proteins or highly complex protein mixtures. Moreover, we also find that a unique reagent, namely ovalbumin, results in the best assay sensitivity and specificity. Importantly, our assay is much more sensitive than standard assays such as ELISAs. We expect that our simple, sensitive, and high-throughput PSP assay will accelerate the development of safe and effective antibody therapeutics.

Dataset Information

PIK3CA mutation profiling in patients with breast cancer, using a highly sensitive detection system.

Publications

PIK3CA mutation profiling in patients with breast cancer, using a highly sensitive detection system.

Similar Datasets

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