Proteomics

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Co-expression analysis of label-free proteomics data reveals prognostic biomarkers in pancreatic ductal adenocarcinoma

ABSTRACT: Despite extensive biological and clinical studies, including comprehensive genomics and transcriptomics analysis, pancreatic ductal adenocarcinoma (PDAC) remains a devastating disease, with poor survival and no effective therapies to date. Correlation networks are emerging as a powerful approach to infer tumor biology and to prioritize candidate genes as biomarkers or drug targets. In this study we applied a weighted co-expression analysis to the functionally relevant proteome of 20 surgically resected patients with PDAC. We obtained twelve modules with overlapping yet distinct biology, which implicated metabolism and ECM complexes in several modules. Notably, one module enriched for metabolic processes and epithelial-mesenchymal-transition (EMT) was significantly associated with overall survival (p=0.01) and was validated in public RNA data (p=0.02). The prognostic value of three proteins (SPTBN1, KHSRP and PYGL) belonging to this module was confirmed using immunohistochemistry in a cohort of 82 radically resected patients.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Pancreatic Ductal Cell, Pancreatic Ductal Adenocarcinoma Cell

DISEASE(S): Pancreatic Ductal Carcinoma

SUBMITTER: Sander Piersma  

LAB HEAD: Connie Ramona Jimenez

PROVIDER: PXD015744 | Pride | 2020-09-01

REPOSITORIES: Pride

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QE1_180417_OPL1022_TLL_PDAC_tumor_A1.raw Raw
QE1_180417_OPL1022_TLL_PDAC_tumor_A2.raw Raw
QE1_180417_OPL1022_TLL_PDAC_tumor_A3.raw Raw
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Co-expression analysis of pancreatic cancer proteome reveals biology and prognostic biomarkers.

Mantini G G   Vallés A M AM   Le Large T Y S TYS   Capula M M   Funel N N   Pham T V TV   Piersma S R SR   Kazemier G G   Bijlsma M F MF   Giovannetti E E   Jimenez C R CR  

Cellular oncology (Dordrecht, Netherlands) 20200829 6

<h4>Purpose</h4>Despite extensive biological and clinical studies, including comprehensive genomic and transcriptomic profiling efforts, pancreatic ductal adenocarcinoma (PDAC) remains a devastating disease, with a poor survival and limited therapeutic options. The goal of this study was to assess co-expressed PDAC proteins and their associations with biological pathways and clinical parameters.<h4>Methods</h4>Correlation network analysis is emerging as a powerful approach to infer tumor biology  ...[more]

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