Pathway-Based Identification of Biomarkers for Targeted Therapeutics: Personalized Oncology with PI3K Pathway Inhibitors

Sci Transl Med 4 August 2010:
Vol. 2, Issue 43, p. 43ra55
DOI: 10.1126/scitranslmed.3001065
Research Article
Pathway-Based Identification of Biomarkers for Targeted Therapeutics: Personalized Oncology with PI3K Pathway Inhibitors
Jannik N. Andersen1,*, Sriram Sathyanarayanan1,*, Alessandra Di Bacco1, An Chi1, Theresa Zhang1, Albert H. Chen1, Brian Dolinski1, Manfred Kraus1, Brian Roberts1, William Arthur2, Rich A. Klinghoffer1,†, Diana Gargano1,‡, Lixia Li1, Igor Feldman1, Bethany Lynch1, John Rush3, Ronald C. Hendrickson4,§, Peter Blume-Jensen1,§|| and Cloud P. Paweletz1
+ Author Affiliations

1Merck Sharp & Dohme, Boston, MA 02115, USA.
2Merck Sharp & Dohme, North Wales, PA 19454, USA.
3Cell Signaling Technology, Danvers, MA 01923, USA.
4Merck Sharp & Dohme, Rahway, NJ 07065, USA.
§To whom correspondence should be addressed. E-mail: ronald_hendrickson@merck.com (R.C.H.); pblume-jensen@dsi.com (P.B.-J.)

Abstract
Although we have made great progress in understanding the complex genetic alterations that underlie human cancer, it has proven difficult to identify which molecularly targeted therapeutics will benefit which patients. Drug-specific modulation of oncogenic signaling pathways in specific patient subpopulations can predict responsiveness to targeted therapy. Here, we report a pathway-based phosphoprofiling approach to identify and quantify clinically relevant, drug-specific biomarkers for phosphatidylinositol 3-kinase (PI3K) pathway inhibitors that target AKT, phosphoinositide-dependent kinase 1 (PDK1), and PI3K–mammalian target of rapamycin (mTOR). We quantified 375 nonredundant PI3K pathway–relevant phosphopeptides, all containing AKT, PDK1, or mitogen-activated protein kinase substrate recognition motifs. Of these phosphopeptides, 71 were drug-regulated, 11 of them by all three inhibitors. Drug-modulated phosphoproteins were enriched for involvement in cytoskeletal reorganization (filamin, stathmin, dynamin, PAK4, and PTPN14), vesicle transport (LARP1, VPS13D, and SLC20A1), and protein translation (S6RP and PRAS40). We then generated phosphospecific antibodies against selected, drug-regulated phosphorylation sites that would be suitable as biomarker tools for PI3K pathway inhibitors. As proof of concept, we show clinical translation feasibility for an antibody against phospho-PRAS40Thr246. Evaluation of binding of this antibody in human cancer cell lines, a PTEN (phosphatase and tensin homolog deleted from chromosome 10)–deficient mouse prostate tumor model, and triple-negative breast tumor tissues showed that phospho-PRAS40Thr246 positively correlates with PI3K pathway activation and predicts AKT inhibitor sensitivity. In contrast to phosphorylation of AKTThr308, the phospho-PRAS40Thr246 epitope is highly stable in tissue samples and thus is ideal for immunohistochemistry. In summary, our study illustrates a rational approach for discovery of drug-specific biomarkers toward development of patient-tailored treatments.

Footnotes
↵* These authors contributed equally to this work.

↵† Present address: Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

↵‡ Present address: Biogen Idec, Cambridge, MA 02432, USA.

↵|| Present address: Daiichi Sankyo Research Institute, Daiichi Sankyo, Inc., Edison, NJ 08837, USA.

Citation: J. N. Andersen, S. Sathyanarayanan, A. Di Bacco, A. Chi, T. Zhang, A. H. Chen, B. Dolinski, M. Kraus, B. Roberts, W. Arthur, R. A. Klinghoffer, D. Gargano, L. Li, I. Feldman, B. Lynch, J. Rush, R. C. Hendrickson, P. Blume-Jensen, C. P. Paweletz, Pathway-based identification of biomarkers for targeted therapeutics: Personalized oncology with PI3K pathway inhibitors. Sci. Transl. Med. 2, 43ra55 (2010).

Copyright © 2010, American Association for the Advancement of Science
http://stm.sciencemag.org/content/2/43/43ra55.abstract