Classification of Cancer Cell Lines Using an Automated Two-dimensional Liquid Mapping Method with Hierarchical Clustering Techniques

Wang, Yanfei; Wu, Rong; Cho, Kathleen R.; Shedden, Kerby; Barder, Timothy J.; Lubman, David M.

doi:10.1074/mcp.t500023-mcp200

Cited by 23 publications

(23 citation statements)

References 28 publications

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“…The human ovarian cancer cell lines: SK-OV-3 (adenocarcinoma), CaOV-3 (adenocarcinoma), and ES-2 (clear cell carcinoma) were chosen because of their extensive prior use and characterization [25][26][27][28][29][30]. The cell lines were obtained from the American Tissue Culture Collection The in vitro test system has previously been described in detail [31][32][33].…”

Section: Methodsmentioning

confidence: 99%

The histone deacetylase inhibitor panobinostat demonstrates marked synergy with conventional chemotherapeutic agents in human ovarian cancer cell lines

et al. 2010

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Although platinum based therapy has improved short term survival of patients with metastatic ovarian cancer, the majority of patients continue to relapse and eventually die of their disease. Currently, a plethora of agents are in development, but how to combine them to enhance efficacy remains largely empiric. We have used short in vitro culture of defined cell lines with application of promising agents and analysis for cell death using a MTT assay to identify potentially useful combinations. Using median effect analysis, curve shift analysis and apoptosis assays, we can identify when agents are synergistic or antagonistic when applied together. Up to three agents can be studied in combination. Using three cell lines: SK-OV3, CaOV-3, and ES-2 (a clear cell tumor), we have identified that panobinostat (LBH-589), a broad histone deacetylase inhibitor in clinical trials, demonstrates global synergy with gemcitabine, with paclitaxel, and additive to synergistic effects with 5'DFUR. The triplet of panobinostat, doxorubicin, and carboplatin is especially synergistic in these cell lines. These effects are cytotoxic and not cytostatic. As all these agents are used clinically, we have identified combinations which warrant further investigation.

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Section: Methodsmentioning

confidence: 99%

The histone deacetylase inhibitor panobinostat demonstrates marked synergy with conventional chemotherapeutic agents in human ovarian cancer cell lines

et al. 2010

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“…This is reflective of the differential protein expression between Barrett metaplasia and esophageal adenocarcinoma that we demonstrated for several individual proteins. Although our findings require extensive validation in larger independent sets of tissue samples, this high throughput approach may have broad potential for tumor identification and classification as we have demonstrated previously in other tissue types (34) and as others have suggested for a variety of proteomics strategies (35,36).…”

Section: Proteomics Of Esophageal Adenocarcinomamentioning

confidence: 99%

Comparative Proteomics Analysis of Barrett Metaplasia and Esophageal Adenocarcinoma Using Two-dimensional Liquid Mass Mapping

Zhao

Chang

et al. 2007

Molecular & Cellular Proteomics

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Esophageal adenocarcinoma, currently the seventh leading cause of cancer-related death, has been associated with the presence of Barrett metaplasia. The malignant potential of Barrett metaplasia is evidenced by ultimate progression of this condition to invasive adenocarcinoma. We utilized liquid phase separation of proteins with chromatofocusing in the first dimension and nonporous reverse phase HPLC in the second dimension followed by ESI-TOF mass spectrometry to identify proteins differentially expressed in six Barrett metaplasia samples as compared with six esophageal adenocarcinoma samples; all six Barrett samples were obtained from the identical six patients from whom we obtained the esophageal adenocarcinoma tissue. Approximately 300 protein bands were detected by mass mappings, and 38 differentially expressed proteins were identified by LC-MS/MS. The false positive rates of the peptide identifications were evaluated by reversed database searching. Among the proteins that were identified, Rho GDP dissociation inhibitor 2, ␣-enolase, Lamin A/C, and nucleoside-diphosphate kinase A were demonstrated to be up-regulated in both mRNA and protein expression in esophageal adenocarcinomas relative to Barrett metaplasia. Candidate proteins were examined at the mRNA level using high density oligonucleotide microarrays. The cellular expression patterns were verified in both esophageal adenocarcinomas and in Barrett metaplasia by immunohistochemistry. These differentially expressed proteins may have utility as useful candidate markers of esophageal adenocarcinoma. Molecular & Cellular Proteomics 6:987-999, 2007.Esophageal adenocarcinoma is increasing rapidly in Western countries and is currently the seventh leading cause of cancer-related death (1). Esophageal adenocarcinoma has been associated with the presence of Barrett metaplasia, a condition in which the normal squamous epithelium of the esophagus is replaced by columnar epithelium. The malignant potential of this condition is evidenced by the progression of Barrett metaplasia to low grade dysplasia, high grade dysplasia, and ultimately to invasive adenocarcinoma. The risk of developing adenocarcinoma is 30 -125 times higher in people who have Barrett metaplasia than people who do not. The prognosis of patients with esophageal adenocarcinoma remains poor with overall 5-year survival rates of only 5-15% (1). Unfortunately patients often present with regionally advanced disease (2). Given the poor prognosis associated with esophageal adenocarcinoma, it is imperative to improve our understanding of the tumorigenesis and the factors associated with increased risk. It is possible that therapeutic targets or protein markers can be identified that will ultimately facilitate improved patient survival.Proteomics technologies have been used for the identification of candidate markers for early cancer detection (3). The global analysis of protein expression complements genomics analyses. For example, proteomics analysis may provide further insight into post-translational mod...

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“…Refs. [11][12][13][14]. The PF2D uses chromatofocusing in the first dimension (separating proteins based on their pI) and reversed phase chromatography in the second dimension.…”

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confidence: 99%

Expanding the Subproteome of the Inner Mitochondria Using Protein Separation Technologies

McDonald

Sheng

Stanley

et al. 2006

Molecular & Cellular Proteomics

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Currently no single proteomics technology has sufficient analytical power to allow for the detection of an entire proteome of an organelle, cell, or tissue. One approach that can be used to expand proteome coverage is the use of multiple separation technologies especially if there is minimal overlap in the proteins observed by the different methods. Using the inner mitochondrial membrane subproteome as a model proteome, we compared for the first time the ability of three protein separation methods (twodimensional liquid chromatography using the ProteomeLab TM PF 2D Protein Fractionation System from Beckman Coulter, one-dimensional reversed phase high performance liquid chromatography, and two-dimensional gel electrophoresis) to determine the relative overlap in protein separation for these technologies. Data from these different methods indicated that a strikingly low number of proteins overlapped with less than 24% of proteins common between any two technologies and only 7% common among all three methods. Utilizing the three technologies allowed the creation of a composite database totaling 348 non-redundant proteins. 82% of these proteins had not been observed previously in proteomics studies of this subproteome, whereas 44% had not been identified in proteomics studies of intact mitochondria. Each protein separation method was found to successfully resolve a unique subset of proteins with the liquid chromatography methods being more suited for the analysis of transmembrane domain proteins and novel protein discovery. We also demonstrated that both the one-and two-dimensional LC allowed for the separation of the ␣-subunit of F 1 F 0 ATP synthase that differed due to a change in pI or hydrophobicity. The eukaryotic proteome is a compilation of proteins that represents the integration of numerous cellular processes that begin with the variable transcription of genes to mRNA. These products are then translated to proteins, which may in turn be potentially co-and/or post-translationally modified to produce an array of proteins (1, 2). Due to the large number of unique protein species produced coupled with differences in their relative abundance, there is as of yet no single proteomics technology that has the analytical capacity or sensitivity to realize the goal of complete proteome coverage. One strategy to maximize proteome coverage is to combine synergistic proteomics technologies, particularly if each technology reveals a unique subset of proteins. Using the inner mitochondrial membrane as a model subproteome, we compared the ability of three protein separation methods (two-dimensional LC (2-DLC 1 with the PF2D), one-dimensional reversed phase HPLC (1-DLC; reversed phase high performance liquid chromatography (RP-HPLC)), and two-dimensional gel electrophoresis (2-DE) to determine the relative overlap in protein separation for these technologies.2-DE, a classical proteomics technology that separates proteins based on their pI and molecular weight, has a practical dynamic range of 10 4 orders of magnitude (for r...

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Classification of Cancer Cell Lines Using an Automated Two-dimensional Liquid Mapping Method with Hierarchical Clustering Techniques

Cited by 23 publications

References 28 publications

The histone deacetylase inhibitor panobinostat demonstrates marked synergy with conventional chemotherapeutic agents in human ovarian cancer cell lines

The histone deacetylase inhibitor panobinostat demonstrates marked synergy with conventional chemotherapeutic agents in human ovarian cancer cell lines

Comparative Proteomics Analysis of Barrett Metaplasia and Esophageal Adenocarcinoma Using Two-dimensional Liquid Mass Mapping

Expanding the Subproteome of the Inner Mitochondria Using Protein Separation Technologies

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