Novel prognostic protein markers of resectable pancreatic cancer identified by coupled shotgun and targeted proteomics using formalin‐fixed paraffin‐embedded tissues

Abstract

Pancreatic cancer is among the most lethal malignancies worldwide. We aimed to identify novel prognostic markers by applying mass spectrometry (MS)-based proteomic analysis to formalin-fixed paraffin-embedded (FFPE) tissues. Resectable, node positive pancreatic ductal adenocarcinoma (PDAC) with poor (n 5 4) and better (n 5 4) outcomes, based on survival duration, with essentially the same clinicopathological backgrounds, and noncancerous pancreatic ducts (n 5 5) were analyzed. Cancerous and noncancerous cells collected from FFPE tissue sections by laser microdissection (LMD) were processed for liquid chromatography (LC)-tandem MS (MS/MS). Candidate proteins were identified by semiquantitative comparison and then analyzed quantitatively using selected reaction monitoring (SRM)-based MS. To confirm the associations between candidate proteins and outcomes, we immunohistochemically analyzed a cohort of 87 cases. In result, totally 1,229 proteins were identified and 170 were selected as candidate proteins for SRM-based targeted proteomics. Fourteen proteins overexpressed in cancerous as compared to noncancerous tissue showed different expressions in the poor and better outcome groups. Among these proteins, we found that three novel proteins ECH1, OLFM4 and STML2 were overexpressed in poor group than in better group, and that one known protein GTR1 was expressed reciprocally. Kaplan-Meier analysis showed high expressions of all four proteins to correlate with significantly worse overall survival (p < 0.05). In conclusion, we identified four proteins as candidates of prognostic marker of PDAC. The combination of shotgun proteomics verified by SRM and validated by immunohistochemistry resulted in the prognostic marker discovery that will contribute the understanding of PDAC biology and therapeutic development.

Enoyl-coenzyme A hydratase in cancer

“…outcome PDAC. These results further confirmed by IHC showing Ech overexpression in the poor outcome group [9]. There were no significant correlations between the expression of Ech and clinicopathological parameters like tumor location, tumor size, lymph node or distant metastasis at the time of resection.…”

“…Majority of exocrine pancreatic cancers are pancreatic ductal adenocarcinoma (PDAC). Studies of pancreatic cancer using serum/plasma and tissue samples are few [8,9].…”

Plasma olfactomedin 4 level in peripheral blood and its association with clinical features of breast cancer

“…It has been previously reported that pancreatic cancer with higher OLFM4 gene expression has increased malignant behavior and invasive capacity as well as the ability to metastasize more easily (30). OLFM4 expression is upregulated in early colorectal and gastric cancer but downregulated in progressive or advanced tumors (2,31).…”

Quantitative Targeted Proteomics of Pancreatic Cancer: Deoxycytidine Kinase Protein Level Correlates to Progression-Free Survival of Patients Receiving Gemcitabine Treatment

“…Takadate et al identified Nm23/nucleoside diphosphate kinase-A as a dFdC-sensitivity marker by means of comprehensive proteome analysis in dissected pancreatic cancer tissues. 17 However, other molecules included in Fig. 1 were not found in that study.…”