Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergetic RAS and CIP2A signaling

Journal article


Kauko, Otto, Laajala, Teemu Daniel, Jumppanen, Mikael, Hintsanen, Petteri, Suni, Veronika, Haapaniemi, Pekka, Corthals, Garry, Aittokallio, Tero, Westermarck, Jukka and Imanishi, Susumu Y.. (2015) Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergetic RAS and CIP2A signaling. Scientific Reports. 5, pp. 1 - 17. https://doi.org/10.1038/srep13099
AuthorsKauko, Otto, Laajala, Teemu Daniel, Jumppanen, Mikael, Hintsanen, Petteri, Suni, Veronika, Haapaniemi, Pekka, Corthals, Garry, Aittokallio, Tero, Westermarck, Jukka and Imanishi, Susumu Y.
Abstract

Hyperactivated RAS drives progression of many human malignancies. However, oncogenic activity of RAS is dependent on simultaneous inactivation of protein phosphatase 2A (PP2A) activity. Although PP2A is known to regulate some of the RAS effector pathways, it has not been systematically assessed how these proteins functionally interact. Here we have analyzed phosphoproteomes regulated by either RAS or PP2A, by phosphopeptide enrichment followed by mass-spectrometry-based label-free quantification. To allow data normalization in situations where depletion of RAS or PP2A inhibitor CIP2A causes a large uni-directional change in the phosphopeptide abundance, we developed a novel normalization strategy, named pairwise normalization. This normalization is based on adjusting phosphopeptide abundances measured before and after the enrichment. The superior performance of the pairwise normalization was verified by various independent methods. Additionally, we demonstrate how the selected normalization method influences the downstream analyses and interpretation of pathway activities. Consequently, bioinformatics analysis of RAS and CIP2A regulated phosphoproteomes revealed a significant overlap in their functional pathways. This is most likely biologically meaningful as we observed a synergistic survival effect between CIP2A and RAS expression as well as KRAS activating mutations in TCGA pan-cancer data set and synergistic relationship between CIP2A and KRAS depletion in colony growth assays.

Year2015
JournalScientific Reports
Journal citation5, pp. 1 - 17
PublisherNature Publishing Group
ISSN2045-2322
Digital Object Identifier (DOI)https://doi.org/10.1038/srep13099
Open accessOpen access
Page range1 - 17
Research GroupMary MacKillop Institute for Health Research
Publisher's version
License
Place of publicationUnited Kingdom
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https://acuresearchbank.acu.edu.au/item/89933/label-free-quantitative-phosphoproteomics-with-novel-pairwise-abundance-normalization-reveals-synergetic-ras-and-cip2a-signaling

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