Integrative proteomic analysis of serum and peritoneal fluids helps identify proteins that are up-regulated in serum of women with ovarian cancer

Abstract

Background: We used intensive modern proteomics approaches to identify predictive proteins in ovary cancer. We identify up-regulated proteins in both serum and peritoneal fluid. To evaluate the overall performance of the approach we track the behavior of 20 validated markers across these experiments.

Methodology: Mass spectrometry based quantitative proteomics following extensive protein fractionation was used to compare serum of women with serous ovarian cancer to healthy women and women with benign ovarian tumors. Quantitation was achieved by isotopically labeling cysteine amino acids. Label-free mass spectrometry was used to compare peritoneal fluid taken from women with serous ovarian cancer and those with benign tumors. All data were integrated and annotated based on whether the proteins have been previously validated using antibody-based assays.

Findings: We selected 54 quantified serum proteins and 358 peritoneal fluid proteins whose case-control differences exceeded a predefined threshold. Seventeen proteins were quantified in both materials and 14 are extracellular. Of 19 validated markers that were identified all were found in cancer peritoneal fluid and a subset of 7 were quantified in serum, with one of these proteins, IGFBP1, newly validated here.

Conclusion: Proteome profiling applied to symptomatic ovarian cancer cases identifies a large number of up-regulated serum proteins, many of which are or have been confirmed by immunoassays. The number of currently known validated markers is highest in peritoneal fluid, but they make up a higher percentage of the proteins observed in both serum and peritoneal fluid, suggesting that the 10 additional markers in this group may be high quality candidates.

Figure 1. Log2 serum protein ratios from both IPAS experiments.

Green points represent proteins up-regulated in both experiments. Blue points represent proteins up-regulated in one experiment and not observed in the other. *Benchmark marker validated by ELISA assay; **New marker validated by ELISA assay.

Figure 2. Comparison of peptide counts from peritoneal fluid experiments.

Red points are up-regulated in SOC serum. Blue points are proteins observed in ovarian cancer ascitic fluid by Kuk et al . Benchmark proteins are labeled. Points above green dashed line are considered up-regulated in peritoneal fluid.

Figure 3. Comparison by log2 ratio of serum to peritoneal ascites fluid.

Proteins up-regulated in both fluids are colored blue. *Benchmark marker validated by ELISA assay; **New marker validated by ELISA assay.

Figure 4. IGFBP1 ROC curves.

SOC vs HA is shown in black and SOC vs BST in blue.