Phosphoproteome is one of key signatures to understand the differences of patient-derived cancer cell lines at the molecular level, pathway level and system level. We developed sensitive and high-throughput phosphoproteome and tyrosine phosphoproteome analysis platform and performed characterization of 35 esophageal squamous cell carcinoma cell lines.
We obtained phosphoproteome and phosphotyrosine-proteome profiles of thirty-five esophageal squamous cell carcinoma cells established from Japanese patients. Phosphopeptides were enriched by immobilized metal affinity chromatography (IMAC) and phosphotyrosine peptides were further purified by immuno precipitation using pY 1000 antibody. Peptides were labeled by TMT10 plex reagent and analyzed by Q Exactive plus instrument and MS data were processed by MaxQuant. Search results were filtered to a maximum false discovery rate (FDR) of 0.01 for proteins and peptides. Class I phosphorylation sites (localization probability, p > 0.75) were counted as identified sites/peptides.
We identified over 19000 phosphorylation sites including 1402 phosphorylation sites on tyrosine residue across thirty-five cell lines. Moreover 945 phosphorylation sites on protein kinases were quantified. Our preliminary results suggest that phosphorylation status is cell line specific and we observed subgroups in which EGFR, Met, Fyn, Trio or PTK2 are highly phosphorylated. We will present the results of cell viability assays using kinase inhibitors. Phosphoproteomic approach is applicable for characterizing the cellular kinase signaling status and classify subgroups of esophageal squamous cell carcinoma cells.
Phosphoproteome profiling is useful to characterize cellular signaling status and classify subgroups of esophageal squamous cell carcinoma cells.