Where academic tradition
meets the exciting future

You are here: TUCS > PUBLICATIONS > Publication Search > Label-Free Quantitative Phosph...

Label-Free Quantitative Phosphoproteomics with Novel Pairwise Abundance Normalization Reveals Synergistic RAS and CIP2A Signaling

Otto Kauko, Teemu D. Laajala, Mikael Jumppanen, Petteri Hintsanen, Veronika Suni, Pekka Haapaniemi, Garry Corthals, Tero Aittokallio, Jukka Westermarck, Susumu Y. Imanishi, Label-Free Quantitative Phosphoproteomics with Novel Pairwise Abundance Normalization Reveals Synergistic RAS and CIP2A Signaling. Scientific Reports 5(13099), , 2015.

http://dx.doi.org/10.1038/srep13099

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.

BibTeX entry:

@ARTICLE{jKaLaJuHiSuHaCoAiWeIm15a,
  title = {Label-Free Quantitative Phosphoproteomics with Novel Pairwise Abundance Normalization Reveals Synergistic RAS and CIP2A Signaling},
  author = {Kauko, Otto and Laajala, Teemu D. and Jumppanen, Mikael and Hintsanen, Petteri and Suni, Veronika and Haapaniemi, Pekka and Corthals, Garry and Aittokallio, Tero and Westermarck, Jukka and Imanishi, Susumu Y.},
  journal = {Scientific Reports},
  volume = {5},
  number = {13099},
  pages = {     },
  year = {2015},
}

Belongs to TUCS Research Unit(s): Biomathematics Research Unit (BIOMATH)

Publication Forum rating of this publication: level 2

Edit publication