Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer

Abstract

Our understanding of the molecular determinants of cancer is still inadequate because of cancer heterogeneity. Here, using epithelial ovarian cancer (EOC) as a model system, we analyzed a minute amount of patient-derived epithelial cells from either healthy or cancerous tissues by single-shot mass-spectrometry-based phosphoproteomics. Using a multi-disciplinary approach, we demonstrated that primary cells recapitulate tissue complexity and represent a valuable source of differentially expressed proteins and phosphorylation sites that discriminate cancer from healthy cells. Furthermore, we uncovered kinase signatures associated with EOC. In particular, CDK7 targets were characterized in both EOC primary cells and ovarian cancer cell lines. We showed that CDK7 controls cell proliferation and that pharmacological inhibition of CDK7 selectively represses EOC cell proliferation. Our approach defines the molecular landscape of EOC, paving the way for efficient therapeutic approaches for patients. Finally, we highlight the potential of phosphoproteomics to identify clinically relevant and druggable pathways in cancer.

Keywords: CDK7; EOC; OSE; POLR2A; THZ1; alternative splicing; fimbriae; ovarian cancer; phosphoproteomics; quantitative proteomics.

Graphical abstract

Figure 1

Proteomics of Patient-Derived Epithelial Cells Reveals Good Coverage of Phosphorylated Sites (A) Workflow of the proteomics analysis of epithelial cells derived from FTE, OSE, and EOC (see also Figure S1, Table S1, and Supplemental Experimental Procedures). (B) Numbers of identified proteins (blue) and phosphorylated sites (pink) in the 13 samples analyzed in this study. Data are presented as mean ± SD. (C) Unsupervised clustering of the phosphoproteome dataset shows separation between tumor and healthy samples. (D) Heatmap of the Pearson’s correlation (R²) of the phosphoproteome data shows good overall reproducibility among samples deriving from the same tissue (highlighted by black boxes). Numbers and letters indicate individual samples or technical replicates, respectively, according to Table S1. See also Figures S1 and S2 and Tables S1, S2, and S3.

Figure 2

Proteomic Analysis Discloses Differentially Expressed Proteins (A) 3D-PCA of all the proteins quantified in independent samples for each tissue. Missing values have not been considered. (B) Hierarchical clustering of the proteins differentially expressed in four independent samples derived from each of the three cell types. The identified clusters 1–4 are highlighted on the right and separated by a black line. Protein intensity is presented on the logarithmic scale with intensity below and above the mean color-coded in blue and red, respectively. The proteins highlighted in the different clusters were selected for further validation. (C) Lysates from three independent samples derived from each tissue (see Table S1) were subjected to WB analysis with the indicated antibodies. Vinculin was used as loading control. The experiment was repeated twice with analogous results. (D) The two histograms show the intensity of the staining for PHGDH (top) and KCTD12 (bottom) in normal OSE, FTE, serous adenocarcinomas, and metastasis (number of samples: 15 OSE, 18 fimbriae, 84 serous adenocarcinomas, and 34 metastases). Data are presented as mean ± SD. ^∗p < 0.001 compared to OSE (Wilcoxon test). See also Table S2.

Figure 3

The Phosphoproteomes of EOC and Healthy Tissues Are Different (A) 3D-PCA of all the phosphorylated sites of independent samples for each tissue. Missing values have not been considered. (B and C) KEGG pathways analysis (B) and biological processes (GO terms BP) (C) enriched in EOC samples. The analysis included 1,026 sites. (D) Network of the phosphorylated sites of EOC samples belonging to the enriched pathways shown in (B), based on STRING and visualized in Cytoscape. The Cytoscape plug-in MCODE revealed enriched networks of phosphorylated proteins of the spliceosome and actin cytoskeleton. See also Table S3.

Figure 4

The EOC Phosphoproteome Is Enriched in Proteins Belonging to Spliceosome (A) Hierarchical clustering of the 792 phosphorylated sites differentially expressed in four independent samples derived from each of the three cell types. The three clusters termed A–C are highlighted on the right and separated by a black line. The intensity of phosphorylated sites is presented on the logarithmic scale with intensity below and above the mean color-coded in blue and red, respectively. (B) Biological Processes (GO term) enriched in each of the three clusters. (C) Sequence motif analysis of the ± six-amino-acid residues flanking the regulated phosphorylation site identified in cluster C compared to cluster A. (D) Kinases substrate motif enriched in cluster C. (E) Network of proteins belonging to the GO term spliceosome (cluster C; Table S4) based on STRING and visualized in Cytoscape. Proteins whose phosphorylated sites were found in the PCA analysis (Figure 3A) are represented with a pink border; transcription factors and kinases are color-coded in light blue and pink, respectively. The light blue and pink clouds surrounding two distinct groups of proteins are based on the comparison of this dataset with the analysis of splicing components shown in Papasaikas et al. (2015). The color of the text is based on the sequence motif analysis shown in (F). (F) Sequence motif analysis of the ± six-amino-acid residues flanking the 100 phosphorylation sites belonging to the GO term spliceosome enriched in cluster C. See also Figures S3 and S4 and Tables S4 and S5.

Figure 5

Phosphoproteomics Identifies CDK7-Associated Proteins (A) Lysates from three independent samples derived from each tissue (see Table S1) were subjected to immunoblotting with the indicated antibodies. Tubulin was used as loading control. The experiment was repeated three times with analogous results. (B) OVCAR3 cells treated with DMSO (control), the CDK7 inhibitor THZ1, or the MEK inhibitor U0126 were subjected to immunoblotting with the indicated antibodies. THZ1, but not U0126, inhibits POLR2A phosphorylation. Tubulin was used as loading control. Lanes 1–3 represent independent biological replicates. (C) Hierarchical clustering of proteins differentially phosphorylated upon treatment with the CDK7 or MEK inhibitor. The four identified clusters are highlighted on the left and separated by a black line. Protein intensity is presented on the logarithmic scale with treated/control intensity below and above the mean colored-coded in red and blue, respectively. (D) Sequence motif analysis of the ± six-amino-acid residues flanking the phosphorylated site identified among the CDK7-associated (top) or MEK-associated (bottom) proteins. (E) GO term biological processes enriched in the CDK7 or MEK cluster. (F) List of the phosphorylated sites of POLR2A identified in OVCAR3 that are CDK7 regulated and/or found in patient-derived cells. CTD, C-terminal domain of POLR2A. S2 and S5 refer to the position of the phosphorylated serine in the repetitive stretch of amino acids found in the CTD of POLR2A. (G) Network based on STRING and visualized in Cytoscape of the CDK7-associated proteins (from C). Only the proteins also found in patient-derived cells are shown on the left. For a complete list, see Figure S6 and Table S6. CDK7-associated proteins enriched in the POLR2A cluster are shown on the right. See also Figures S5 and S6 and Table S6.

Figure 6

CDK7 Inhibition Affects the Proliferation of Ovarian Cancer Cells (A) Lysates from different ovarian cancer cell lines, either untreated or treated with DMSO, the PI3K inhibitor LY294002, or the CDK7 inhibitor THZ1 for 4 hr were subjected to immunoblotting with the indicated antibodies. Vinculin was used as loading control. The experiment was repeated three times with analogous results. (B) Cell proliferation of ovarian cancer cells treated for 72 hr with the indicated inhibitors. Data represent the mean ± SEM of three experiments. ^∗p value < 0.05 compared to untreated cells or cells treated with DMSO. Black line represents untreated cells at time 0. (C) Cell proliferation of cancer cells of different origin treated for 72 hr with THZ1 or DMSO as indicated. Data represent the mean ± SEM of three experiments. Black line represents untreated cells at time 0. (D) Lysates from OVCAR3, COV318, or COV362 cells, either not transfected or transfected with two different siRNA sequences against CDK7 or with a control siRNA, were subjected to immunoblotting with the indicated antibodies. (E) Cell proliferation of EOC cell lines treated as in (D) for 72 hr. Data represent the mean ± SEM of three experiments. ^∗p < 0.05 compared to untreated cells or cells treated with control siRNA. Black line represents untreated cells at time 0.