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Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes


Despite intensive multi-modal treatment of sarcomas, a heterogeneous group of malignant tumors arising from connective tissue, survival remains poor. Candidate-based targeted treatments have demonstrated limited clinical success, urging an unbiased and comprehensive analysis of oncogenic signaling networks to reveal therapeutic targets and personalized treatment strategies. Here we applied mass spectrometry-based phosphoproteomic profiling to the largest and most heterogeneous set of sarcoma cell lines characterized to date and identified novel tyrosine phosphorylation patterns, enhanced tyrosine kinases in specific subtypes, and potential driver kinases. ALK was identified as a novel driver in the Aska-SS synovial sarcoma (SS) cell line via expression of an ALK variant with a large extracellular domain deletion (ALKDelta2-17). Functional ALK dependency was confirmed in vitro and in vivo with selective inhibitors. Importantly, ALK immunopositivity was detected in 6/43 (14%) of SS patient specimens, one of which exhibited an ALK rearrangement. High PDGFRalpha phosphorylation also characterized SS cell lines, which was accompanied by enhanced MET activation in Yamato-SS cells. Although Yamato-SS cells were sensitive to crizotinib (ALK/MET-inhibitor) but not pazopanib (VEGFR/PDGFR-inhibitor) monotherapy in vitro, synergistic effects were observed upon drug combination. In vivo, both drugs were individually effective, with pazopanib efficacy likely attributable to reduced angiogenesis. MET or PDGFRalpha expression was detected in 58% and 84% of SS patients, respectively, with co-expression in 56%. Consequently, our integrated approach has led to the identification of ALK and MET as promising therapeutic targets in SS.

Type Journal
ISBN 1538-7445 (Electronic) 0008-5472 (Linking)
Authors Fleuren, E. D. G.; Vlenterie, M.; van der Graaf, W.; Hillebrandt-Roeffen, M. H. S.; Blackburn, J.; Ma, X.; Chan, H.; Magias, M. C.; van Erp, A.; van Houdt, L.; Cebeci, S.; van de Ven, A.; Flucke, U. E.; Heyer, E. E.; Thomas, D. M.; Lord, C. J.; Marini, K. D.; Vaghjiani, V.; Mercer, T.; Cain, J. E.; Wu, J.; Versleijen-Jonkers, Y. M. H.; Daly, R. J.
Responsible Garvan Author Prof David Thomas
Published Date 2017-08-15
Published Volume 77
Published Issue 16
Published Pages 4279-4292
Status Published in-print
DOI 10.1158/0008-5472.CAN-16-2550
URL link to publisher's version