AIM: The aim of this study was to identify markers that have the potential to predict BKM120 (a pan-class I PI3K inhibitor) effectiveness in triple negative breast cancer.

INTRODUCTION: Triple negative breast cancer is an aggressive subtype that constitutes circa 20% of all breast cancers. This subtype of breast cancer is defined by its lack of estrogen-, progesterone- and HER2/neu expression. Since these are the operative receptors for targeted breast cancer therapies, current standard treatment instead centers on conventional cytotoxic chemotherapy. Unfortunately, the majority of triple negative breast cancer patients does not have meaningful response, and new therapeutic agents are needed. The PI3K/Akt/mTOR axis is often dysregulated in breast cancer, and clinical trials are ongoing for several inhibitors targeting this pathway. Differential analysis of the global proteome and phosphoproteome of BKM120-treated responsive and resistant tumors may identify markers, patterns and pathways associated with clinical response to support precision therapy.

MATERIALS AND METHODS: We collected tumor material from triple negative breast cancer xenografts propagated in the mammary fat pads of NOD SCID mice after BKM120 treatment. Long term (∼30 days) treatment was performed to assess growth rates and sensitivity to the drug. For mass spectrometry analyses, tumor material from 6 different mouse models across 5 treatment conditions was lysed and digested into peptides. Samples were labeled with TMT6-plex reagents, and analyzed together with one reference sample in a total of 6 TMT6-plex experiments. To increase proteome coverage, sample complexity was reduced using high-pH reversed-phase separation, and phospho-peptides were enriched using immobilized metal affinity chromatography. All samples were analyzed on a Q Exactive mass spectrometer.

RESULTS AND DATA ANALYSES: Cumulatively, >19,000 proteins were identified, with an average of >10,000 proteins and >21,000 phosphosites per sample. The 6 mice showed a continuum of response to the drug from highly sensitive to highly resistant. Pearson correlation analysis was used to identify proteins and phosphosites that correlate to this response gradient, while moderate t-tests were used to identify commonly regulated markers. Preliminary analyses indicate several interesting proteins and phospho-sites, some pertaining to the PI3K/Akt pathway. Further canonical pathways were detected using Gene Set Enrichment Analysis on a sample-by sample basis and additional network and pathway analyses were performed using the network analysis program GeNets, as well as Ingenuity Pathway Analysis.

Citation Format: Filip O. Mundt*, Cynthia Ma*, Philipp Mertins, Zhanfang Guo, Matthew Meyer, Jana Qiao, DR Mani, Karl Clauser, Shunqiang Li, Kuan Huang, Jason Held, Sherri Davies, Kelly Ruggles, Li Ding, Michael Gillette, David Fenyo, Reid Townsend, Matthew Ellis, Steven A. Carr. Effects of PI3K/Akt pathway inhibition on global proteome levels and phosphorylation signaling in patient-derived xenograft models of triple negative breast cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C200.