Fig 1.
Overall overview of our study.
(A) Prostate cell lines used in the present study. AR: Androgen Receptor. (B) Prostate cancer progression over time, from localized asymptomatic castration-sensitive to metastatic castration-resistant disease. (C) SILAC Cell line culture preparation, Spike-in and Mass Spectrometry analysis of the proteomes and phosphoproteomes. Figure adapted from [19] (D) Hierarchical clustering of the proteomes and (E) phosphoproteomes normalized expression data in the four cell lines.
Fig 2.
Functional enrichments of proteins up- and downregulated in PC cell lines.
Bar graphs represent relative fold change of Gene Ontology Biological Processes among (A) LNCaP, (B) DU145, (C) PC3 upregulated proteins (red bars) and downregulated proteins (green bars), as compared to PNT1A cells. Significance is represented in the dot plot by –log (P-values).
Fig 3.
Functional enrichments of protein resistance biomarkers.
(A) Bar graphs represent relative fold change of Gene Ontology Biological Processes among proteins upregulated (red bars) and downregulated (green bars) in Castration Resistant cell lines DU145 and PC3 as compared to castration-sensitive LNCaP cell line. Significance is represented in the dot plot by –log (P-values). (B) Clustered heatmap of ROMA pathway analysis. The color intensities correspond to the values of the scores of each signaling pathway (red, upregulated; green, downregulated).
Fig 4.
Network of CR biomarker interactions.
Proteins (boxes) and phosphosites (triangles) significantly upregulated or downregulated in the CR context are mapped in red or green, respectively, with color intensities related to fold-changes. For visualization purposes, the expression values correspond to the mean of the expression of PC3 and DU145 cell lines. Proteins and phosphosites identified only in CR (DU145 and PC3) or CS (LNCaP) cells lines are squared in red and green, respectively.