Figure 2

Proteome and phosphoproteome analyses on colonic tissue colonized by SGG UCN34 or SGM over 12 weeks reveals a pro-tumoral shift specific to SGG UCN34. (a) Sample preparation for proteome and phosphoproteome LC–MS analysis. All samples were collected at the end of the AOM-induced CRC model. Tissue samples were from macroscopically tumor-free colon sections for SGM and SGG UCN34 groups and from colon tumors found in this experiment only for the SGG UCN34 group. Proteins were extracted by urea lysis and trypsin digestion. For phosphoproteome MS analysis a phosphopeptide enrichment step was added. All samples were processed by label free LC–MS/MS analysis. (b) Principal component analysis (PCA) of proteome samples in 3D representation. (c) PCA of phosphoproteome samples in 3D representation. Proteome and phosphoproteome analyses were done using myProMS web server⁶⁵. (d) Top disease and bio functions (IPA) of proteome and phosphoproteome changes between SGG UCN34 and SGM. The diseases and functions analysis identified biological functions and/or diseases that were most significant from the data set. Data sets used in this analysis were proteins or phosphoproteins differentially expressed between SGG UCN34 and SGM detected in macroscopically tumor-free colonic tissue. Molecules indicate the number of proteins or phosphoproteins associated with indicated diseases and disorders. A right-tailed Fisher’s Exact Test was used to calculate a p value determining the probability that each biological function and/or disease assigned to that data set is due to chance alone.