Activating PIK3CA Mutations Induce an Epidermal Growth Factor Receptor (EGFR)/Extracellular Signal-regulated Kinase (ERK) Paracrine Signaling Axis in Basal-like Breast Cancer

Mutations in PIK3CA, the gene encoding the p110α catalytic subunit of phosphoinositide 3-kinase (PI3K) have been shown to transform human mammary epithelial cells (MECs). These mutations are present in all breast cancer subtypes, including basal-like breast cancer (BLBC). Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified 72 protein expression changes in human basal-like MECs with knock-in E545K or H1047R PIK3CA mutations versus isogenic MECs with wild-type PIK3CA. Several of these were secreted proteins, cell surface receptors or ECM interacting molecules and were required for growth of PIK3CA mutant cells as well as adjacent cells with wild-type PIK3CA. The proteins identified by MS were enriched among human BLBC cell lines and pointed to a PI3K-dependent amphiregulin/EGFR/ERK signaling axis that is activated in BLBC. Proteins induced by PIK3CA mutations correlated with EGFR signaling and reduced relapse-free survival in BLBC. Treatment with EGFR inhibitors reduced growth of PIK3CA mutant BLBC cell lines and murine mammary tumors driven by a PIK3CA mutant transgene, all together suggesting that PIK3CA mutations promote tumor growth in part by inducing protein changes that activate EGFR.

Abstract B015: Knock-in of PIK3CA mutations in MCF10A mammary epithelial cells modifies their proteomic profile to resemble basal-like breast cancer and stimulate EGFR-dependent cell proliferation

PIK3CA, the gene encoding the p110α catalytic subunit of phosphatidylinositol-3 kinase (PI3K), is frequently mutated in breast cancer. Activating mutations in PIK3CA are known to transform mammary epithelial cells (MECs). Genomic knock-in of the two most frequent hot-spot PIK3CA mutations (E545K or H1047R) into MCF10A MECs resulted in growth factor-independent proliferation. Shotgun LC-MS/MS mass spectrometry analysis of wild type, E545K and H1047R MCF10A cell lysates revealed 73 proteins uniquely altered in the both mutant cell lines compared to wild type cells. KEGG pathway analysis demonstrated that PIK3CA mutant cells have elevated levels of proteins involved in focal adhesion, ECM-receptor interactions and actin cytoskeleton regulation. Nearly half the proteins upregulated in the mutant cells are secreted or involved in extracellular matrix (ECM) processing or signaling. The EGFR ligand amphiregulin was five-fold higher in the conditioned media harvested from PIK3CA mutant cells as compared to wild type cells. The conditioned media of PIK3CA mutant cells, but not that of wild-type cells, was sufficient to stimulate proliferation and EGFR phosphorylation in wild type MCF10A cells. Proliferation and EGFR activation were inhibited with an amphiregulin-neutralizing antibody or with EGFR neutralizing antibodies and kinase inhibitors. PIK3CA mutant cells downregulated PTPRF, a receptor tyrosine phosphatase. EGFR signaling and proliferation were stimulated in wild type cells when PTPRF was downregulated with siRNA, suggesting that PIK3CA mutant MCF10A cells activate EGFR-dependent proliferation by suppression of a negative regulatory phosphatase and increased secretion of amphiregulin.

The expression of transglutaminase 2, peroxidasin, fibronectin, integrin α5, laminin β3, laminin γ2, thrombospondin and EphA2, eight proteins upregulated in PIK3CA mutant MCF10A cells, was evaluated in a panel of breast cancer cell lines. All eight proteins were more highly expressed in basal-like compared to luminal-like breast cancer cell lines. The expression of PTPRF, which is decreased in PIK3CA mutant MCF10A cells, was lower in basal-like cell lines. Interrogation of microarray data demonstrated that the RNA signal of proteins upregulated in mutant PIK3CA MCF10A cells correlated with decreased relapse-free survival in basal-like, but not in luminal-like breast cancer. siRNA-mediated silencing of peroxidasin, laminin γ2, EphA2, integrin β1 or amphiregulin reduced the proliferation of PIK3CA mutant MCF10A cells, suggesting that these proteins are necessary for maintenance of the transformed phenotype. siRNA-mediated silencing of peroxidasin and EphA2 proteins also reduces the proliferation of basal-like breast cancer cells. Our proteomic analysis of PIK3CA mutant MCF10A cells revealed mechanisms of autocrine and paracrine induced proliferation and alterations mostly limited to basal-like breast cancer cells. These may serve as therapeutic targets in this subtype of breast cancer.

Citation Format: Christian D. Young, Lisa J. Zimmerman, Corbin A. Whitwell, Ariella B. Hanker, Thomas Stricker, Dana M. Brantley-Sieders, Ben Ho Park, Daniel C. Liebler, Rebecca S. Cook, Carlos L. Arteaga. Knock-in of PIK3CA mutations in MCF10A mammary epithelial cells modifies their proteomic profile to resemble basal-like breast cancer and stimulate EGFR-dependent cell proliferation. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr B015.

Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS)

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities.