Journal: Nature Communications
Article Title: In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer
Figure Lengend Snippet: Kinases driving the profiles of the relapsed cases. a Example of a chart of normalized enrichment scores (NESs) (left) obtained for CLK1 from the relative abundance of its phosphorylated substrates in either the relapsed or the non-relapsed cases (right)—or kinase set enrichment analysis (KSEAS). Each substrate (phosphopeptide) is represented in the KSEA as a vertical black line. The proteins to which they map are represented in the right column by their encoding genes, adjacent to the site at which phosphorylation was detected. In this column, a larger or shorter horizontal bar depicts, for each substrate, the Log 2 -fold regulation in the relapsed (blue) versus non-relapsed (red) cases. b Two phosphatase (DUSP6 and PP2C-δ) and 9 kinase domains were enriched in the relapsed cases. The finding of an enriched phosphatase domain can be accounted for by the presence of a high concentration of a substrate for that phosphatase in a specific subgroup of patient tumors or cell lines. The in silico tool cannot predict whether a phosphatase is functional based on the absence of phosphorylation of its putative substrates; however, it can predict which upstream kinases or phosphatases can bind (and phosphorylate or cleave) an identified substrate. P -values and false discovery rates (FDR) are depicted for each kinase or phosphatase. Although most KSEAS show a low FDR, a relaxed FDR boundary (up to 0.25) was allowed to ensure as little information loss as possible in the mass spectrometry-to-immunohistochemistry translation step
Article Snippet: Deparafinization and antigen retrieval (cell conditioning) were performed on DISCOVERY XT automated slide staining system using validated reagents (Ventana Medical Systems, Inc.).
Techniques: Concentration Assay, In Silico, Functional Assay, Mass Spectrometry, Immunohistochemistry