Pathway-based Identification of Biomarkers for Targeted Therapeutics: Personalized Oncology With PI3K Pathway Inhibitors

Sci Transl Med. 2010 Aug 4;2(43):43ra55. doi: 10.1126/scitranslmed.3001065.


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-PRAS40(Thr246). 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-PRAS40(Thr246) positively correlates with PI3K pathway activation and predicts AKT inhibitor sensitivity. In contrast to phosphorylation of AKT(Thr308), the phospho-PRAS40(Thr246) 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing
  • Animals
  • Basophils / drug effects
  • Basophils / enzymology
  • Biomarkers, Tumor / metabolism*
  • Breast Neoplasms / enzymology
  • Breast Neoplasms / pathology
  • Cell Line, Tumor
  • Computational Biology
  • Cytoskeletal Proteins / metabolism
  • Enzyme Activation / drug effects
  • Epitopes / immunology
  • Humans
  • Lung Neoplasms / enzymology
  • Lung Neoplasms / pathology
  • Mice
  • Neoplasms / drug therapy*
  • Neoplasms / enzymology
  • Neoplasms / pathology
  • PTEN Phosphohydrolase / metabolism
  • Phosphatidylinositol 3-Kinase / metabolism
  • Phosphoinositide-3 Kinase Inhibitors*
  • Phosphoproteins / metabolism
  • Phosphoserine / metabolism
  • Precision Medicine*
  • Protein Kinase Inhibitors / pharmacology*
  • Protein Kinase Inhibitors / therapeutic use*
  • Protein Stability / drug effects
  • Protein Transport / drug effects
  • Proto-Oncogene Proteins c-akt / metabolism
  • Signal Transduction / drug effects*
  • Subcellular Fractions / drug effects
  • Subcellular Fractions / metabolism
  • Substrate Specificity / drug effects
  • Up-Regulation / drug effects


  • AKT1S1 protein, human
  • Adaptor Proteins, Signal Transducing
  • Biomarkers, Tumor
  • Cytoskeletal Proteins
  • Epitopes
  • Phosphoinositide-3 Kinase Inhibitors
  • Phosphoproteins
  • Protein Kinase Inhibitors
  • Phosphoserine
  • Phosphatidylinositol 3-Kinase
  • Proto-Oncogene Proteins c-akt
  • PTEN Phosphohydrolase
  • PTEN protein, human