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System-Level Analysis of the Effects of RPTPs on Cellular Signaling Networks

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Protein Tyrosine Phosphatases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2743))


Tyrosine phosphorylation regulates signaling network activity downstream of receptor tyrosine kinase (RTK) activation. Receptor protein tyrosine phosphatases (RPTPs) serve to dephosphorylate RTKs and their proximal adaptor proteins, thus serving to modulate RTK activity. While the general function of RPTPs is well understood, the direct and indirect substrates for each RPTP are poorly characterized. Here we describe a method, quantitative phosphotyrosine phosphoproteomics, that enables the identification of specific phosphorylation sites whose phosphorylation levels are altered by the expression and activity of a given RPTP. In a proof-of-concept application, we use this method to highlight several direct or indirect substrate phosphorylation sites for PTPRJ, also known as DEP1, and show their quantitative phosphorylation in the context of wild-type PTPRJ compared to a mutant form of PTPRJ with increased activity, in EGF-stimulated cells. This method is generally applicable to define the signaling network effects of each RPTP in cells or tissues under different physiological conditions.

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This work was supported in part by grants from the National Institutes of Health, including U01CA238720 and R01GM139998, as well as support from the Center for Precision Cancer Medicine in the Koch Institute for Integrative Research at MIT.

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Correspondence to Forest M. White .

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© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Gerritsen, J., Rizzo, S., Thévenin, D., White, F.M. (2024). System-Level Analysis of the Effects of RPTPs on Cellular Signaling Networks. In: Thévenin, D., P. Müller, J. (eds) Protein Tyrosine Phosphatases. Methods in Molecular Biology, vol 2743. Humana, New York, NY.

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3568-1

  • Online ISBN: 978-1-0716-3569-8

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