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Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells.

Chavez JD, Hoopmann MR, Weisbrod CR, Takara K, Bruce JE - PLoS ONE (2011)

Bottom Line: Unfortunately mRNA levels do not always correlate with protein expression levels due to post-transcriptional changes in protein abundance.A total of 856 proteins were identified and quantified, with 374 displaying significantly altered expression levels between the cell lines.Several of these proteins have been previously implicated in resistance towards platinum-based and other drugs, while many represent new potential markers or therapeutic targets.

View Article: PubMed Central - PubMed

Affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.

ABSTRACT
Cisplatin along with other platinum based drugs are some of the most widely used chemotherapeutic agents. However drug resistance is a major problem for the successful chemotherapeutic treatment of cancer. Current evidence suggests that drug resistance is a multifactorial problem due to changes in the expression levels and activity of a wide number of proteins. A majority of the studies to date have quantified mRNA levels between drug resistant and drug sensitive cell lines. Unfortunately mRNA levels do not always correlate with protein expression levels due to post-transcriptional changes in protein abundance. Therefore global quantitative proteomics screens are needed to identify the protein targets that are differentially expressed in drug resistant cell lines. Here we employ a quantitative proteomics technique using stable isotope labeling with amino acids in cell culture (SILAC) coupled with mass spectrometry to quantify changes in protein levels between cisplatin resistant (HeLa/CDDP) and sensitive HeLa cells in an unbiased fashion. A total of 856 proteins were identified and quantified, with 374 displaying significantly altered expression levels between the cell lines. Expression level data was then integrated with a network of protein-protein interactions, and biological pathways to obtain a systems level view of proteome changes which occur with cisplatin resistance. Several of these proteins have been previously implicated in resistance towards platinum-based and other drugs, while many represent new potential markers or therapeutic targets.

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Related in: MedlinePlus

Expression level and protein interaction network analysis.Protein interaction network generated with STRING 8.3 [56] and visualized with Cytoscape [57] consisting of 803 proteins connected by 1174 protein-protein interactions. The 134 proteins with significantly increased expression levels (p<0.01) of at least 1.25 fold in cisplatin resistant HeLa cells are shown in red. Major clusters of interacting proteins include those involved in metabolic energy production, protein folding, and cellular signaling. The 147 proteins with significantly decreased expression levels (p<0.01) of at least 1.25 fold in cisplatin resistant HeLa cells are shown in green. Major clusters of interacting proteins include the 40S and 60S ribosomal proteins and ribonucleoproteins. Interactive Cytoscape networks are included as Dataset S1.
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pone-0019892-g004: Expression level and protein interaction network analysis.Protein interaction network generated with STRING 8.3 [56] and visualized with Cytoscape [57] consisting of 803 proteins connected by 1174 protein-protein interactions. The 134 proteins with significantly increased expression levels (p<0.01) of at least 1.25 fold in cisplatin resistant HeLa cells are shown in red. Major clusters of interacting proteins include those involved in metabolic energy production, protein folding, and cellular signaling. The 147 proteins with significantly decreased expression levels (p<0.01) of at least 1.25 fold in cisplatin resistant HeLa cells are shown in green. Major clusters of interacting proteins include the 40S and 60S ribosomal proteins and ribonucleoproteins. Interactive Cytoscape networks are included as Dataset S1.

Mentions: The protein interaction network shown in Figure 4 contains 803 proteins and 1174 protein-protein interactions. An interactive version of this Cytoscape network is provided in Dataset S1. Several clusters of related functional classes of proteins are visible in this network including ribosomal proteins, ribonucleoproteins, metabolic and energy producing proteins, and proteins involved in redox homeostasis and protein folding. To identify the relevant biological pathways that were altered due to cisplatin resistance, BiNGO [14] was used to find GO biological pathway and molecular function terms that were enriched among the differentially expressed proteins in the network. In total 208 biological pathway terms and 109 molecular function terms were associated with proteins identified with increased expression, while 101 biological pathway terms and 18 molecular function terms were associated with proteins identified with decreased expression. Enriched biological pathways for proteins identified with increased expression include the metabolism of carbohydrates, metabolism of NADH and NADPH, regulation of apoptosis, protein folding, and maintenance of cellular homeostasis. Enriched biological pathways for proteins identified with decreased expression include ribosomal assembly and RNA processing, gene expression, and translation. A complete list of the enriched GO biological pathway and molecular function terms for the proteins with altered expression levels can be viewed in Table S2.


Quantitative proteomic and interaction network analysis of cisplatin resistance in HeLa cells.

Chavez JD, Hoopmann MR, Weisbrod CR, Takara K, Bruce JE - PLoS ONE (2011)

Expression level and protein interaction network analysis.Protein interaction network generated with STRING 8.3 [56] and visualized with Cytoscape [57] consisting of 803 proteins connected by 1174 protein-protein interactions. The 134 proteins with significantly increased expression levels (p<0.01) of at least 1.25 fold in cisplatin resistant HeLa cells are shown in red. Major clusters of interacting proteins include those involved in metabolic energy production, protein folding, and cellular signaling. The 147 proteins with significantly decreased expression levels (p<0.01) of at least 1.25 fold in cisplatin resistant HeLa cells are shown in green. Major clusters of interacting proteins include the 40S and 60S ribosomal proteins and ribonucleoproteins. Interactive Cytoscape networks are included as Dataset S1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102677&req=5

pone-0019892-g004: Expression level and protein interaction network analysis.Protein interaction network generated with STRING 8.3 [56] and visualized with Cytoscape [57] consisting of 803 proteins connected by 1174 protein-protein interactions. The 134 proteins with significantly increased expression levels (p<0.01) of at least 1.25 fold in cisplatin resistant HeLa cells are shown in red. Major clusters of interacting proteins include those involved in metabolic energy production, protein folding, and cellular signaling. The 147 proteins with significantly decreased expression levels (p<0.01) of at least 1.25 fold in cisplatin resistant HeLa cells are shown in green. Major clusters of interacting proteins include the 40S and 60S ribosomal proteins and ribonucleoproteins. Interactive Cytoscape networks are included as Dataset S1.
Mentions: The protein interaction network shown in Figure 4 contains 803 proteins and 1174 protein-protein interactions. An interactive version of this Cytoscape network is provided in Dataset S1. Several clusters of related functional classes of proteins are visible in this network including ribosomal proteins, ribonucleoproteins, metabolic and energy producing proteins, and proteins involved in redox homeostasis and protein folding. To identify the relevant biological pathways that were altered due to cisplatin resistance, BiNGO [14] was used to find GO biological pathway and molecular function terms that were enriched among the differentially expressed proteins in the network. In total 208 biological pathway terms and 109 molecular function terms were associated with proteins identified with increased expression, while 101 biological pathway terms and 18 molecular function terms were associated with proteins identified with decreased expression. Enriched biological pathways for proteins identified with increased expression include the metabolism of carbohydrates, metabolism of NADH and NADPH, regulation of apoptosis, protein folding, and maintenance of cellular homeostasis. Enriched biological pathways for proteins identified with decreased expression include ribosomal assembly and RNA processing, gene expression, and translation. A complete list of the enriched GO biological pathway and molecular function terms for the proteins with altered expression levels can be viewed in Table S2.

Bottom Line: Unfortunately mRNA levels do not always correlate with protein expression levels due to post-transcriptional changes in protein abundance.A total of 856 proteins were identified and quantified, with 374 displaying significantly altered expression levels between the cell lines.Several of these proteins have been previously implicated in resistance towards platinum-based and other drugs, while many represent new potential markers or therapeutic targets.

View Article: PubMed Central - PubMed

Affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.

ABSTRACT
Cisplatin along with other platinum based drugs are some of the most widely used chemotherapeutic agents. However drug resistance is a major problem for the successful chemotherapeutic treatment of cancer. Current evidence suggests that drug resistance is a multifactorial problem due to changes in the expression levels and activity of a wide number of proteins. A majority of the studies to date have quantified mRNA levels between drug resistant and drug sensitive cell lines. Unfortunately mRNA levels do not always correlate with protein expression levels due to post-transcriptional changes in protein abundance. Therefore global quantitative proteomics screens are needed to identify the protein targets that are differentially expressed in drug resistant cell lines. Here we employ a quantitative proteomics technique using stable isotope labeling with amino acids in cell culture (SILAC) coupled with mass spectrometry to quantify changes in protein levels between cisplatin resistant (HeLa/CDDP) and sensitive HeLa cells in an unbiased fashion. A total of 856 proteins were identified and quantified, with 374 displaying significantly altered expression levels between the cell lines. Expression level data was then integrated with a network of protein-protein interactions, and biological pathways to obtain a systems level view of proteome changes which occur with cisplatin resistance. Several of these proteins have been previously implicated in resistance towards platinum-based and other drugs, while many represent new potential markers or therapeutic targets.

Show MeSH
Related in: MedlinePlus