Evaluation of quantification and normalization strategies for phosphoprotein phosphatase affinity proteomics: application to breast cancer signaling
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ABSTRACT: Accurate quantification of proteomics data is essential for correctly characterizing signaling processes. We have recently developed a chemical proteomic strategy, phosphatase inhibitor beads and mass spectrometry (PIB-MS), to investigate endogenous phosphoprotein phosphatase (PPP) dephosphorylation signaling. Here, we compare the robustness and reproducibility of different quantification methods for optimal performance and ease of implementation. We then apply PIB-MS to an array of breast cancer (BC) cell lines to determine differences in PPP signaling between subtypes. BC is a leading cause of cancer death in women. There are three main subtypes: estrogen receptor-positive (ER+), human epidermal growth factor receptor two positive (HER2+), and triple-negative (TNBC). Furthermore, TNBC has few targeted therapies. Therefore, there is a need to identify novel means for treating breast cancers. Using PIB-MS, we distinguished between TNBC and Non-TNBC based on PPP holoenzyme composition. We identified an increase in PPP interactions with Hippo pathway proteins in TNBC. These interactions suggest that phosphatases in TNBC play an inhibitory role on the Hippo pathway and correlate with increased expression of YAP/TAZ target genes both in TNBC cell lines and in TNBC patients.
INSTRUMENT(S): Orbitrap Fusion Lumos, Q Exactive Plus
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: Arminja Kettenbach
PROVIDER: MSV000090020 | MassIVE | Fri Jul 29 17:54:00 BST 2022
SECONDARY ACCESSION(S): PXD035636
REPOSITORIES: MassIVE
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