title: Proteome of formalin-fixed paraffin-embedded pancreatic ductal adenocarcinoma and lymph node metastases.
abstract: Pancreatic ductal adenocarcinoma (PDAC) is a major cause of cancer-related death, largely due to metastatic disease. To better understand PDAC metastatic spread and identify novel therapeutic targets, we analysed the proteome of primary tumours and matched lymph node (LN) metastases. As frozen specimens of metastatic lesions are scarce, we examined formalin-fixed paraffin-embedded (FFPE) tissues. This poses technical challenges because of the cross-linkages induced by fixation. Using laser capture microdissection (PALM system), we isolated malignant epithelia from seven FFPE primary PDAC tumours and matched LN metastases. Following dissection, samples were analysed in duplicate using Multidimensional Protein Identification Technology (MudPIT); this resulted in the identification of 1504 proteins, 854 of which were common to all samples analysed. Comparison of the obtained proteins with data from previous proteomics studies on pancreatic tissue, pancreatic juice, serum, and urine resulted in a less than 30% overlap, indicating that our study has substantially expanded the current database of proteins expressed in this malignancy. Statistical analysis further showed that 115/854 proteins (13.5%) were significantly differentially expressed (g-value ≥ 3.8). Two proteins, S100P and 14-3-3 sigma, with highly significant g-values were confirmed to be significantly differentially expressed (S100P: p = 0.05 and 14-3-3 sigma: p < 0.001) in a larger series of 55 cases of matched primary PDAC and LN metastases using immunohistochemistry. Thus, laser capture microdissection of FFPE tissue coupled with downstream proteomic analysis is a valid approach for the investigation of metastatic PDAC. This is the first study to establish and compare the protein composition of primary PDAC and matched LN metastases, and has resulted in the identification of several potential epithelial-specific therapeutic targets, including 14-3-3 sigma and S100P.
authors.affiliation: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.
authors.forename: Kalnisha
authors.initials: K
authors.lastname: Naidoo
authors.forename: Richard
authors.initials: R
authors.lastname: Jones
authors.forename: Branko
authors.initials: B
authors.lastname: Dmitrovic
authors.forename: Nilukshi
authors.initials: N
authors.lastname: Wijesuriya
authors.forename: Hemant
authors.initials: H
authors.lastname: Kocher
authors.forename: Ian R
authors.initials: IR
authors.lastname: Hart
authors.forename: Tatjana
authors.initials: T
authors.lastname: Crnogorac-Jurcevic
mesh_terms: D048948:14-3-3 Proteins / Q000032:analysis; D014408:Biomarkers, Tumor / Q000032:analysis*; D002135:Calcium-Binding Proteins / Q000032:analysis; D021441:Carcinoma, Pancreatic Ductal / Q000737:chemistry* / Q000556:secondary; D005092:Exonucleases / Q000032:analysis; D005095:Exoribonucleases; D005404:Fixatives; D005557:Formaldehyde; D006801:Humans; D007150:Immunohistochemistry; D061346:Laser Capture Microdissection; D008198:Lymph Nodes / Q000737:chemistry* / Q000473:pathology; D008207:Lymphatic Metastasis; D009363:Neoplasm Proteins / Q000032:analysis*; D010190:Pancreatic Neoplasms / Q000737:chemistry* / Q000473:pathology; D016612:Paraffin Embedding; D011379:Prognosis; D040901:Proteomics / Q000379:methods; D053719:Tandem Mass Spectrometry; D016707:Tissue Fixation / Q000379:methods*
chemical_list: D048948:14-3-3 Proteins; D014408:Biomarkers, Tumor; D002135:Calcium-Binding Proteins; D005404:Fixatives; D009363:Neoplasm Proteins; C103003:S100P protein, human; D005557:Formaldehyde; D005092:Exonucleases; D005095:Exoribonucleases; C413442:SFN protein, human