Dataset Information

Phosphoproteome profiling reveals molecular mechanisms of growth factor mediated kinase inhibitor resistance in cancer cells

ABSTRACT: Although substantial progress has been made regarding the use of molecularly targeted cancer therapies, resistance almost invariably develops and presents a major clinical challenge. To evade the selective pressure of kinase inhibitors, cells often activate bypass signaling tracks and become intrinsically resistant. Apart from intrinsic cellular adaptation, the tumor microenvironment can rescue cancer cells by growth factor mediated induction of pro-survival signaling. We show that EGFR inhibition by Gefitinib is counteracted by several growth factors notably FGF2 and we assessed the global consequences of FGF2-mediated Gefitinib resistance at the proteome and phosphoproteome level. Multiplexed tandem mass tag (TMT) peptide labeling in conjunction with high resolution tandem mass spectrometry allowed the identification and quantification of ~22,000 phosphopeptides and ~8,800 proteins in biological triplicates without missing values. The data shows that Gefitinib treated cells are forced into developing intrinsic resistance by reprogramming of the proteome and phosphoproteome, whereas co-treatment with FGF2 largely reverted these changes to resemble the molecular composition of untreated cells. Simultaneous small molecule EGFR and FGFR inhibition overcomes FGF2 induced Gefitinib resistance and the phosphoproteomic experiments further prioritized the RAS/MEK/ERK axis as well as the PI3K/mTOR axis for combination treatment. Consequently, the MEK inhibitor Trametinib prevented FGF2-mediated survival of EGFR inhibitor resistant cells when used in combination with Gefitinib. Surprisingly, the pase II PI3K/mTOR inhibitor GSK2126458 reversed resistance mediated by all four growth factors tested, making it an interesting candidate for targeting the survival signals provided by the tumor microenvironment.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Squamous Cell Carcinoma

SUBMITTER: Heiner Koch

LAB HEAD: Bernhard Kuster

PROVIDER: PXD004007 | Pride | 2022-03-01

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	RAWphosphoproteome.zip	Other
	RAWproteome.zip	Other
	highconfidenphosphopeptidespectra.pdf	Pdf
	searchresultsphosphoproteome.zip	Other
	spectraforproteinsidentifiedwithlessthantwouniquepeptides.pdf	Pdf

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Publications

Phosphoproteome Profiling Reveals Molecular Mechanisms of Growth-Factor-Mediated Kinase Inhibitor Resistance in EGFR-Overexpressing Cancer Cells.

Koch Heiner H Wilhelm Mathias M Ruprecht Benjamin B Beck Scarlet S Frejno Martin M Klaeger Susan S Kuster Bernhard B

Journal of proteome research 20161116 12

Although substantial progress has been made regarding the use of molecularly targeted cancer therapies, resistance almost invariably develops and presents a major clinical challenge. The tumor microenvironment can rescue cancer cells from kinase inhibitors by growth-factor-mediated induction of pro-survival pathways. Here we show that epidermal growth factor receptor (EGFR) inhibition by Gefitinib is counteracted by growth factors, notably FGF2, and we assessed the global molecular consequences ...[more]

PMID: 27794612

Similar Datasets

Project description:Despite initial and often dramatic responses of epidermal growth factor receptor (EGFR)-addicted lung tumors to the EGFR-specific tyrosine kinase inhibitors (TKIs), gefitinib and erlotinib, nearly all develop resistance and relapse. To explore novel mechanisms mediating acquired resistance, we employed non-small-cell lung cancer (NSCLC) cell lines bearing activating mutations in EGFR and rendered them resistant to EGFR-specific TKIs through chronic adaptation in tissue culture. In addition to previously observed resistance mechanisms including EGFR-T790M 'gate-keeper' mutations and MET amplification, a subset of the seven chronically adapted NSCLC cell lines including HCC4006, HCC2279 and H1650 cells exhibited marked induction of fibroblast growth factor (FGF) 2 and FGF receptor 1 (FGFR1) mRNA and protein. Also, adaptation to EGFR-specific TKIs was accompanied by an epithelial to mesenchymal transition (EMT) as assessed by changes in CDH1, VIM, ZEB1 and ZEB2 expression and altered growth properties in Matrigel. In adapted cell lines exhibiting increased FGF2 and FGFR1 expression, measures of growth and signaling, but not EMT, were blocked by FGFR-specific TKIs, an FGF-ligand trap and FGFR1 silencing with RNAi. In parental HCC4006 cells, cell growth was strongly inhibited by gefitinib, although drug-resistant clones progress within 10 days. Combined treatment with gefitinib and AZD4547, an FGFR-specific TKI, prevented the outgrowth of drug-resistant clones. Thus, induction of FGF2 and FGFR1 following chronic adaptation to EGFR-specific TKIs provides a novel autocrine receptor tyrosine kinase-driven bypass pathway in a subset of lung cancer cell lines that are initially sensitive to EGFR-specific TKIs. The findings support FGFR-specific TKIs as potentially valuable additions to existing targeted therapeutic strategies with EGFR-specific TKIs to prevent or delay acquired resistance in EGFR-driven NSCLC. Examination of mRNA levels in DMSO and gefitinib-resistant cultures of HCC4006 and HCC827. Each group has two replicates.