Quantitative proteomics identifies conserved proteins and altered regulation of mucin-16 in low grade serous ovarian cancers

Low-grade serous ovarian carcinoma (LGSOC) is a rare and largely chemoresistant subtype of epithelial ovarian cancer. Unlike treatment for high-grade serous ovarian cancer (HGSOC), management options for LGSOC patients are limited, in part, due to a lack of deep molecular characterization of this disease. To address this limitation, we aimed to define highly conserved proteome alterations in LGSOC by performing deep quantitative proteomic analysis of tumors collected from LGSOC and HGSOC patients or normal fallopian tube tissues and validating proteins within two independent proteomic datasets of LGSOC and HGSOC tumors.

Formalin-fixed, paraffin-embedded LGSOC (n = 12), HGSOC (n = 24), and FT (n = 12) tissues underwent pressure-assisted trypsin digestion followed by quantitative proteomic analyses using a multiplex, tandem-mass tag (TMT11) workflow and high-resolution mass spectrometry. Proteome alterations between LGSOC and HGSOC tumors were validated against two independent proteome datasets generated from LGSOC (n = 25) and HGSOC (n = 49) tumors. Mucin-16 (MUC16/CA125) was assessed in LGSOC and HGSOC tumors by immunohistochemistry and reviewed by three independent pathologists.

Our efforts identified 275 protein alterations conserved between LGSOC and HGSOC tumors that exhibit high quantitative correlation between discovery and validation cohorts (Spearman Rho ≥ 0.82, P < 1E-4). Conserved proteins elevated in LGSOC tumors were enriched for pathways regulating cell adhesion and defective cellular apoptosis signaling and candidates mapping as putative drug targets included 5'-nucleotidase/ cluster of differentiation 73 (NT5E/CD73). We also identified MUC16 (CA125) as significantly elevated in LGSOC versus HGSOC tumors and confirmed this by immunohistochemistry analysis. We further find that MUC16 exhibits a more apical versus membrane-staining pattern in LGSOC tumors, suggesting unique regulation of MUC16 in this disease subtype.

Our efforts define highly conserved protein alterations distinguishing LGSOC from HGSOC tumors, including CD73, as well as the novel identification that MUC16 is elevated and exhibits more apical staining pattern in LGSOC tumor tissues. These findings deepen our molecular understanding of LGSOC and provide unique insights into highly conserved proteome alterations in LGSOC tumors.