Protein profiling of ovarian cancers by immunohistochemistry to identify potential target pathways

BACKGROUND: To determine the protein expression profile (PEP) of primary and recurrent ovarian cancer patients in order to predict therapeutic targets for chemotherapy. METHODS: Tissue samples were submitted for PEP in two formats, including formalin-fixed paraffin-embedded tissue for immunohistochemistry (IHC) and fresh frozen tissue for oligonucleotide microarray (MA) gene expression assays. Specimens were analyzed for 18 protein markers and 88 MA genes. A series of Generalized Linear Models (GLM) was used to predict the proportion of positive results by histology for each biomarker. RESULTS: Four hundred and twenty-eight specimens were analyzed for IHC and 67 specimens for MA analysis. The majority of specimens, 82%, were serous histology and 35.3% of specimens were poorly differentiated. Sixty percent of specimens were advanced stage, 62% were from a primary diagnosis, and 53% were obtained from a metastatic site. BCRP, ER, MGMT, and RRM1 proteins were overexpressed in 85%, 47%, 93%, and 47% of serous carcinomas, respectively. The MGMT and RRM1 biomarkers were significantly overexpressed in serous (p < .001) and endometrioid (p = .01) histologies when compared to clear cell histology. MGMT was significantly elevated in 93% of serous and endometrioid samples, compared to 62% of samples with clear cell histology. Those proteins most often underexpressed included Her2/neu, SPARC, and c-kit, seen in less than 1%, 4%, and 5% of specimens, respectively. CONCLUSIONS: PEP is a reliable and effective way of analyzing ovarian cancer specimens. PEP target identification does not appear to vary significantly with site evaluated, ovarian or other abdominal pelvic tissue, or primary versus recurrent disease. Variability in the expression of drug targets, including BCRP, ER, MGMT, and RRM1 could impact decision making pertaining to which therapeutic strategies carry the best chances for controlling disease. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/2053-6844-1-4) contains supplementary material, which is available to authorized users.