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Proteomic Analysis of Matched Formalin-Fixed, Paraffin-Embedded Specimens in Patients with Advanced Serous Ovarian Carcinoma
Division of Gynecologic Oncology, Magee-Womens Hospital of UPMC, Pittsburgh, PA 15213, USA
Biomedical Mass Spectrometry Center for the Health Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
Departments of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
Women's Cancer Research Center, Pittsburgh, PA 15213, USA
University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
* Author to whom correspondence should be addressed.
Received: 25 July 2013; in revised form: 8 October 2013 / Accepted: 8 October 2013 / Published: 17 October 2013
Abstract: Objective: The biology of high grade serous ovarian carcinoma (HGSOC) is poorly understood. Little has been reported on intratumoral homogeneity or heterogeneity of primary HGSOC tumors and their metastases. We evaluated the global protein expression profiles of paired primary and metastatic HGSOC from formalin-fixed, paraffin-embedded (FFPE) tissue samples. Methods: After IRB approval, six patients with advanced HGSOC were identified with tumor in both ovaries at initial surgery. Laser capture microdissection (LCM) was used to extract tumor for protein digestion. Peptides were extracted and analyzed by reversed-phase liquid chromatography coupled to a linear ion trap mass spectrometer. Tandem mass spectra were searched against the UniProt human protein database. Differences in protein abundance between samples were assessed and analyzed by Ingenuity Pathway Analysis software. Immunohistochemistry (IHC) for select proteins from the original and an additional validation set of five patients was performed. Results: Unsupervised clustering of the abundance profiles placed the paired specimens adjacent to each other. IHC H-score analysis of the validation set revealed a strong correlation between paired samples for all proteins. For the similarly expressed proteins, the estimated correlation coefficients in two of three experimental samples and all validation samples were statistically significant (p < 0.05). The estimated correlation coefficients in the experimental sample proteins classified as differentially expressed were not statistically significant. Conclusion: A global proteomic screen of primary HGSOC tumors and their metastatic lesions identifies tumoral homogeneity and heterogeneity and provides preliminary insight into these protein profiles and the cellular pathways they constitute.
Keywords: serous ovarian carcinoma; proteomics; laser capture microdissection
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Smith, A.L.; Sun, M.; Bhargava, R.; Stewart, N.A.; Flint, M.S.; Bigbee, W.L.; Krivak, T.C.; Strange, M.A.; Cooper, K.L.; Zorn, K.K. Proteomic Analysis of Matched Formalin-Fixed, Paraffin-Embedded Specimens in Patients with Advanced Serous Ovarian Carcinoma. Proteomes 2013, 1, 240-253.
Smith AL, Sun M, Bhargava R, Stewart NA, Flint MS, Bigbee WL, Krivak TC, Strange MA, Cooper KL, Zorn KK. Proteomic Analysis of Matched Formalin-Fixed, Paraffin-Embedded Specimens in Patients with Advanced Serous Ovarian Carcinoma. Proteomes. 2013; 1(3):240-253.
Smith, Ashlee L.; Sun, Mai; Bhargava, Rohit; Stewart, Nicolas A.; Flint, Melanie S.; Bigbee, William L.; Krivak, Thomas C.; Strange, Mary A.; Cooper, Kristine L.; Zorn, Kristin K. 2013. "Proteomic Analysis of Matched Formalin-Fixed, Paraffin-Embedded Specimens in Patients with Advanced Serous Ovarian Carcinoma." Proteomes 1, no. 3: 240-253.