title: Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells.
abstract: Kinases determine the phenotypes of many cancer cells, but the frequency with which individual kinases are activated in primary tumors remains largely unknown. We used a computational approach, termed kinase-substrate enrichment analysis (KSEA), to systematically infer the activation of given kinase pathways from mass spectrometry-based phosphoproteomic analysis of acute myeloid leukemia (AML) cells. Experiments conducted in cell lines validated the approach and, furthermore, revealed that DNA-dependent protein kinase (DNA-PK) was activated as a result of inhibiting the phosphoinositide 3-kinase (PI3K)-mammalian target of rapamycin (mTOR) signaling pathway. Application of KSEA to primary AML cells identified PI3K, casein kinases (CKs), cyclin-dependent kinases (CDKs), and p21-activated kinases (PAKs) as the kinase substrate groups most frequently enriched in this cancer type. Substrates phosphorylated by extracellular signal-regulated kinase (ERK) and cell division cycle 7 (CDC7) were enriched in primary AML cells that were resistant to inhibition of PI3K-mTOR signaling, whereas substrates of the kinases Abl, Lck, Src, and CDK1 were increased in abundance in inhibitor-sensitive cells. Modeling based on the abundances of these substrate groups accurately predicted sensitivity to a dual PI3K and mTOR inhibitor in two independent sets of primary AML cells isolated from patients. Thus, our study demonstrates KSEA as an untargeted method for the systematic profiling of kinase pathway activities and for increasing our understanding of diseases caused by the dysregulation of signaling pathways.
authors.affiliation: Analytical Signalling Group, Centre for Cell Signalling, Barts Cancer Institute, Queen Mary University of London, London EC1B 6BQ, UK. pedro.cutillas@imperial.ac.uk
authors.forename: Pedro
authors.initials: P
authors.lastname: Casado
authors.forename: Juan-Carlos
authors.initials: JC
authors.lastname: Rodriguez-Prados
authors.forename: Sabina C
authors.initials: SC
authors.lastname: Cosulich
authors.forename: Sylvie
authors.initials: S
authors.lastname: Guichard
authors.forename: Bart
authors.initials: B
authors.lastname: Vanhaesebroeck
authors.forename: Simon
authors.initials: S
authors.lastname: Joel
authors.forename: Pedro R
authors.initials: PR
authors.lastname: Cutillas
mesh_terms: D019295:Computational Biology / Q000379:methods*; D051747:DNA-Activated Protein Kinase / Q000378:metabolism*; D004789:Enzyme Activation / Q000235:genetics / Q000502:physiology*; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000201:enzymology*; D013058:Mass Spectrometry / Q000379:methods; D008954:Models, Biological; D019869:Phosphatidylinositol 3-Kinases / Q000378:metabolism; D010766:Phosphorylation; D040901:Proteomics / Q000379:methods; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology*; D013379:Substrate Specificity; D058570:TOR Serine-Threonine Kinases / Q000378:metabolism
chemical_list: D051747:DNA-Activated Protein Kinase; D019869:Phosphatidylinositol 3-Kinases; D058570:TOR Serine-Threonine Kinases; C546842:MTOR protein, human