A systems biology case study of ovarian cancer drug resistance.
In ovarian cancer treatment, the chemotherapy drug cisplatin often induce drug resistance after prolonged use, causing cancer relapse and the eventual deaths of patients. Cisplatin-induced drug resistance is known to involve a complex set of cellular changes but its molecular mechanism(s) remain unclear. In this study, we designed a systems biology approach to examine global protein level and network level changes by comparing Proteomics profiles between cisplatin-resistant cell lines and cisplatin-sensitive cell lines. First, we used an experimental proteomics method based on a Label-free Liquid Chromatography / Mass Spectrometry (LC/MS) platform to obtain a list of 119 proteins that are differentially expressed in the samples. Second, we expanded these proteins into a cisplatin-resistant activated sub-network, which consists of 1230 proteins in 1111 protein interactions. An examination of network topology features reveals the activated responses in the network are closely coupled. Third, we examined sub-network proteins using Gene Ontology categories. We found significant enrichment of proton-transporting ATPase and ATP synthase complexes in addition to protein binding proteins. Fourth, we examined sub-network protein interaction function categories using 2-dimensional visualization matrixes. We found that significant cellular physiological responses arise from endogenous, abiotic, and stress-related signals, which correlates well with known facts that internalized cisplatin cause DNA damage and induce cell stress. Fifth and finally, we developed a new visual representation structure for display of activated sub-networks using functional categories as network nodes and their crosstalk as network edges. This type of sub-network further shows that while cell communication and cell growth are generally important to tumor mechanisms, molecular regulation of cell differentiation and development caused by responses to genomic-wide stress seem to be more relevant to the acquisition of drug resistance.
Chen
Jake Y
JY
Indiana University School of Informatics, Indiana University/Purdue University Indianapolis, Indianapolis, IN 46202, USA. jakechen@iupui.edu
Shen
Changyu
C
Yan
Zhong
Z
Brown
Dawn P G
DP
Wang
Mu
M
D000970:Antineoplastic Agents / Q000494:pharmacology; D002853:Chromatography, Liquid / Q000379:methods; D002945:Cisplatin / Q000494:pharmacology; D019295:Computational Biology / Q000379:methods*; D019008:Drug Resistance, Neoplasm; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D016678:Genome; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D015233:Models, Statistical; D010051:Ovarian Neoplasms / Q000188:drug therapy* / Q000473:pathology*; D040901:Proteomics / Q000379:methods; D012984:Software; D049490:Systems Biology / Q000379:methods*
D000970:Antineoplastic Agents; D002945:Cisplatin