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

Emmy D G Fleuren, Myrella Vlenterie, Winette T.A. Van Der Graaf, Melissa H.S. Hillebrandt-Roeffen, James Blackburn, Xiuquan Ma, Howard Chan, Mandy C. Magias, Anke Van Erp, Laurens Van Houdt, Sabri A.S. Cebeci, Amy Van De Ven, Uta E. Flucke, Erin E. Heyer, David M. Thomas, Christopher J Lord, Kieren D. Marini, Vijesh Vaghjiani, Tim R Mercer, Jason E. Cain & 3 others Jianmin Wu, Yvonne M.H. Versleijen-Jonkers, Roger J. Daly

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12 Citations (Scopus)

Abstract

Despite intensive multimodal 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 (ALKD2–17). Functional ALK dependency was confirmed in vitro and in vivo with selective inhibitors. Importantly, ALK immunopositivity was detected in 6 of 43 (14%) of SS patient specimens, one of which exhibited an ALK rearrangement. High PDGFRa 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 PDGFRa expression was detected in 58% and 84% of SS patients, respectively, with coexpression in 56%. Consequently, our integrated approach has led to the identification of ALK and MET as promising therapeutic targets in SS.

Original languageEnglish
Pages (from-to)4279-4292
Number of pages14
JournalCancer Research
Volume77
Issue number16
DOIs
Publication statusPublished - 15 Aug 2017

Cite this

Fleuren, E. D. G., Vlenterie, M., Van Der Graaf, W. T. A., Hillebrandt-Roeffen, M. H. S., Blackburn, J., Ma, X., ... Daly, R. J. (2017). Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes. Cancer Research, 77(16), 4279-4292. https://doi.org/10.1158/0008-5472.CAN-16-2550
Fleuren, Emmy D G ; Vlenterie, Myrella ; Van Der Graaf, Winette T.A. ; Hillebrandt-Roeffen, Melissa H.S. ; Blackburn, James ; Ma, Xiuquan ; Chan, Howard ; Magias, Mandy C. ; Van Erp, Anke ; Van Houdt, Laurens ; Cebeci, Sabri A.S. ; Van De Ven, Amy ; Flucke, Uta E. ; Heyer, Erin E. ; Thomas, David M. ; Lord, Christopher J ; Marini, Kieren D. ; Vaghjiani, Vijesh ; Mercer, Tim R ; Cain, Jason E. ; Wu, Jianmin ; Versleijen-Jonkers, Yvonne M.H. ; Daly, Roger J. / Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes. In: Cancer Research. 2017 ; Vol. 77, No. 16. pp. 4279-4292.
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title = "Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes",
abstract = "Despite intensive multimodal 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 (ALKD2–17). Functional ALK dependency was confirmed in vitro and in vivo with selective inhibitors. Importantly, ALK immunopositivity was detected in 6 of 43 (14{\%}) of SS patient specimens, one of which exhibited an ALK rearrangement. High PDGFRa 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 PDGFRa expression was detected in 58{\%} and 84{\%} of SS patients, respectively, with coexpression in 56{\%}. Consequently, our integrated approach has led to the identification of ALK and MET as promising therapeutic targets in SS.",
author = "Fleuren, {Emmy D G} and Myrella Vlenterie and {Van Der Graaf}, {Winette T.A.} and Hillebrandt-Roeffen, {Melissa H.S.} and James Blackburn and Xiuquan Ma and Howard Chan and Magias, {Mandy C.} and {Van Erp}, Anke and {Van Houdt}, Laurens and Cebeci, {Sabri A.S.} and {Van De Ven}, Amy and Flucke, {Uta E.} and Heyer, {Erin E.} and Thomas, {David M.} and Lord, {Christopher J} and Marini, {Kieren D.} and Vijesh Vaghjiani and Mercer, {Tim R} and Cain, {Jason E.} and Jianmin Wu and Versleijen-Jonkers, {Yvonne M.H.} and Daly, {Roger J.}",
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Fleuren, EDG, Vlenterie, M, Van Der Graaf, WTA, Hillebrandt-Roeffen, MHS, Blackburn, J, Ma, X, Chan, H, Magias, MC, Van Erp, A, Van Houdt, L, Cebeci, SAS, Van De Ven, A, Flucke, UE, Heyer, EE, Thomas, DM, Lord, CJ, Marini, KD, Vaghjiani, V, Mercer, TR, Cain, JE, Wu, J, Versleijen-Jonkers, YMH & Daly, RJ 2017, 'Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes', Cancer Research, vol. 77, no. 16, pp. 4279-4292. https://doi.org/10.1158/0008-5472.CAN-16-2550

Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes. / Fleuren, Emmy D G; Vlenterie, Myrella; Van Der Graaf, Winette T.A.; Hillebrandt-Roeffen, Melissa H.S.; Blackburn, James; Ma, Xiuquan; Chan, Howard; Magias, Mandy C.; Van Erp, Anke; Van Houdt, Laurens; Cebeci, Sabri A.S.; Van De Ven, Amy; Flucke, Uta E.; Heyer, Erin E.; Thomas, David M.; Lord, Christopher J; Marini, Kieren D.; Vaghjiani, Vijesh; Mercer, Tim R; Cain, Jason E.; Wu, Jianmin; Versleijen-Jonkers, Yvonne M.H.; Daly, Roger J.

In: Cancer Research, Vol. 77, No. 16, 15.08.2017, p. 4279-4292.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes

AU - Fleuren, Emmy D G

AU - Vlenterie, Myrella

AU - Van Der Graaf, Winette T.A.

AU - Hillebrandt-Roeffen, Melissa H.S.

AU - Blackburn, James

AU - Ma, Xiuquan

AU - Chan, Howard

AU - Magias, Mandy C.

AU - Van Erp, Anke

AU - Van Houdt, Laurens

AU - Cebeci, Sabri A.S.

AU - Van De Ven, Amy

AU - Flucke, Uta E.

AU - Heyer, Erin E.

AU - Thomas, David M.

AU - Lord, Christopher J

AU - Marini, Kieren D.

AU - Vaghjiani, Vijesh

AU - Mercer, Tim R

AU - Cain, Jason E.

AU - Wu, Jianmin

AU - Versleijen-Jonkers, Yvonne M.H.

AU - Daly, Roger J.

PY - 2017/8/15

Y1 - 2017/8/15

N2 - Despite intensive multimodal 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 (ALKD2–17). Functional ALK dependency was confirmed in vitro and in vivo with selective inhibitors. Importantly, ALK immunopositivity was detected in 6 of 43 (14%) of SS patient specimens, one of which exhibited an ALK rearrangement. High PDGFRa 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 PDGFRa expression was detected in 58% and 84% of SS patients, respectively, with coexpression in 56%. Consequently, our integrated approach has led to the identification of ALK and MET as promising therapeutic targets in SS.

AB - Despite intensive multimodal 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 (ALKD2–17). Functional ALK dependency was confirmed in vitro and in vivo with selective inhibitors. Importantly, ALK immunopositivity was detected in 6 of 43 (14%) of SS patient specimens, one of which exhibited an ALK rearrangement. High PDGFRa 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 PDGFRa expression was detected in 58% and 84% of SS patients, respectively, with coexpression in 56%. Consequently, our integrated approach has led to the identification of ALK and MET as promising therapeutic targets in SS.

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U2 - 10.1158/0008-5472.CAN-16-2550

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Fleuren EDG, Vlenterie M, Van Der Graaf WTA, Hillebrandt-Roeffen MHS, Blackburn J, Ma X et al. Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes. Cancer Research. 2017 Aug 15;77(16):4279-4292. https://doi.org/10.1158/0008-5472.CAN-16-2550