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.

A framework for transcriptome-wide association studies in breast cancer in diverse study populations

“…Two of these 4 TWAS-identified genes have strong functional evidence in breast cancer survival literature. Mutations in AURKA and PIK3CA have previously been shown to be significantly associated with breast cancer survival rates [31][32][33]. Less is known about the involvement of SER-PINB5 and CAPN13 in breast cancer survival, though they have been identified in studies into breast cancer progression [48][49][50][51][52].…”

“…4c). Of these 4 loci, associations with survival have been reported with SNPs near the same chromosomal region as AURKA, PIK3CA, and SERPINB5 [8,[31][32][33][34][35], though none of these reported SNPs were utilized in constructing the GReX of this gene. Furthermore, the GReX of these four genes were not significantly correlated (P > 0.05 for all pairwise Spearman correlation tests), and the sets of SNPs used in constructing the GReX of these four genes had no pairwise intersections, providing evidence that their independent association with breast cancer-specific survival was not a pleiotropic effect from shared or correlated SNPs.…”

Targeting the PI3K/AKT/mTOR Signaling Pathway in Lung Cancer: An Update Regarding Potential Drugs and Natural Products

“…Deregulation of the PI3K/AKT/mTOR signaling pathway by either the mutation or amplification of genes involved in the PI3K pathway, loss of the tumor suppressor PTEN, or overactivation of RTKs, has been observed in various cancer cells, contributing to tumor progression and metastasis [ 48 , 49 , 50 , 51 ]. PIK3CA , the gene encoding the catalytic subunit of the PI3Kα isoform, is frequently mutated in various human cancers, including breast, ovarian and lung cancers [ 52 , 53 , 54 ]. Two hotspot E542K and E545K mutations in the p110 subunit alter the conformation of PI3Kα, in which an active site of PI3Kα is exposed at the membrane and is subsequently activated [ 55 , 56 ].…”

Use of Liquid Biopsy to Detect <i>PIK3CA</i> Mutation in Metastatic Breast Cancer

“…PIK3CA is associated with tumor progression and has a high mutation rate in breast (21-35%), colorectal (13-32%), and endometrial (24-32%) cancers 2 3 4 . There are three established mutation hot-spots, namely E545K, E542K, and H1047R/L, which are responsible for 70-80% of all PIK3CA mutations 5 . The prevalence of PIK3CA mutation is high in the luminal and HER2-enriched breast cancer types, but low in the TN type 2 .…”