title: Evolution of network biomarkers from early to late stage bladder cancer samples.
abstract: We use a systems biology approach to construct protein-protein interaction networks (PPINs) for early and late stage bladder cancer. By comparing the networks of these two stages, we find that both networks showed very significantly different mechanisms. To obtain the differential network structures between cancer and noncancer PPINs, we constructed cancer PPIN and noncancer PPIN network structures for the two bladder cancer stages using microarray data from cancer cells and their adjacent noncancer cells, respectively. With their carcinogenesis relevance values (CRVs), we identified 152 and 50 significant proteins and their PPI networks (network markers) for early and late stage bladder cancer by statistical assessment. To investigate the evolution of network biomarkers in the carcinogenesis process, primary pathway analysis showed that the significant pathways of early stage bladder cancer are related to ordinary cancer mechanisms, while the ribosome pathway and spliceosome pathway are most important for late stage bladder cancer. Their only intersection is the ubiquitin mediated proteolysis pathway in the whole stage of bladder cancer. The evolution of network biomarkers from early to late stage can reveal the carcinogenesis of bladder cancer. The findings in this study are new clues specific to this study and give us a direction for targeted cancer therapy, and it should be validated in vivo or in vitro in the future.
authors.affiliation: Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
authors.forename: Yung-Hao
authors.identifier: 0000-0001-5448-2269
authors.initials: YH
authors.lastname: Wong
authors.affiliation: Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
authors.forename: Cheng-Wei
authors.identifier: 0000-0002-5883-4812
authors.initials: CW
authors.lastname: Li
authors.affiliation: Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
authors.forename: Bor-Sen
authors.identifier: 0000-0003-1644-6106
authors.initials: BS
authors.lastname: Chen
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics* / Q000378:metabolism; D063646:Carcinogenesis / Q000235:genetics / Q000473:pathology; D030541:Databases, Genetic; D006801:Humans; D009363:Neoplasm Proteins / Q000378:metabolism; D009367:Neoplasm Staging; D060066:Protein Interaction Maps; D015398:Signal Transduction; D013997:Time Factors; D001749:Urinary Bladder Neoplasms / Q000235:genetics* / Q000473:pathology*
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins