Cancer proteomics cell lines

Proteomic Mapping and Clustering of Multiple Samples—Application to Ovarian Cancer Cell Lines... 

Xiang, R., Shi, Y., Dillon, D.A., Negin, B., Horvath, C., Wilkins, J.A. (2004). 2D LC/MS analysis of membrane proteins from breast cancer cell lines MCF7 and BT474. J. Proteome Res. 3, 1278-1283. 

Ornstein DK et al. Proteomic analysis of laser capture microdissected human prostate cancer and in vitro prostate cell lines. Electrophoresis 2000 21 2235-2242. 

Nishizuka, S., Charboneau, L., Young, L., Major, S., Reinhold, W.C., Waltham, M., Kouros-Mehr, H., Bussey, K.J., Lee, J.K., Espina, V., Munson, RJ., Petricoin, E., Liotta, L.A., and Weinstein, J.N., Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays, Proc. Natl. Acad. Sci. USA, 24, 14229-14234, 2003. 

Mendes, K.N., et al. (2007) Analysis of signaling pathways in 90 cancer cell lines by protein lysate array. /Proteome Res. 6, 2753-67. 

The term proteome means the total protein complement of a genome, and pro-teomics means the analysis for proteome. The combination of two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) is a proteomic method of high-throughput analysis of protein expression. By using this 2-DE and MS, proteomic studies have identified many proteins that may be involved in the pathogenic mechanism of cancers. These studies analyzed cancer cell lines, as well as cancer tissues or serum from patients. 

In this study, a machine learning model system was developed to classify cell line chemosensitivity exclusively based on proteomic profiling. Using reverse-phase protein lysate microarrays, protein expression levels were measured by 52 antibodies in a panel of 60 human cancer cell (NCI-60) lines. The model system combined several well-known algorithms, including Random forests, Relief, and the nearest neighbor methods, to construct the protein expression-based chemosensitivity classifiers. 

Mian S, Ball G, Hornbuckle J, et al. A prototype methodology combining surface-enhanced laser desorption/ionization protein chip technology and artificial neural network algorithms to predict the chemoresponsiveness of breast cancer cell lines exposed to Paclitaxel and Doxorubicin under in vitro conditions. Proteomics 2003 3(9) 1725-1737. 

Using the isoTOP-ABPP method, the soluble proteome of the breast cancer cell line MCF7 was interrogated and, of the 800 probe-labeled cysteines, 10% were found to be hyper-reactive (/ io i < 2). A database search further revealed that hyper-reactive cysteines were over-represented in functional residues (active site... 

The use of proteomics in prostate cancer, the most common cancer in men, was reviewed [94]. In vitro studies on prostate cell lines provided positive proof-of-principle results in the identification of novel biomarker when proteomics was utilized to query prostate tissue specimens. 2D-PAGE followed by MS was used to investigate protein profiles in voided urine after prostatic massage in patients with prostate cancer or with benign prostatic hyperplasia [95]. In this study, a potential novel cancer biomarker, calgranulin B/MRP-14, was identified. In another study, agarose 2D-gel... 

Most functional proteomic studies have been performed in cancer cell lines, that is, after exposition to toxicants, RNA inhibition, differentiation agents, viral transfection, and so on. These studies covered several aspects of mutagenesis, tumor promotion, and progression. In the recent years, it has been shown that repeated analysis of the proteome at different tumor stages also deliver distinct patterns and thus a functional picture of disease progression at the molecular level. 

Skvortsov S, Sarg B, Loeffler-Ragg J, Skvortsova I, Lindner H, Werner Ott H, et al. Different proteome pattern of epidermal growth factor receptor-positive colorectal cancer cell lines that are responsive and nonresponsive to C225 antibody treatment. Mol Cancer Ther 2004 3(12) 1551-1558. 

Toward the above objectives, and also that of developing new methods for proteomic investigation, this laboratory has undertaken the identification of proteins whose abundances or primary structures are modified in drug-resistant strains of the human breast cancer cell line MCF-7. The parental cell line and several strains selected by exposure to different anti-cancer drugs were provided by K. H. Cowan (Eppley Cancer Center, University of Nebraska), P. Gutierrez and D. D. Ross, (Greenebaum Cancer Center, University of Maryland), and J. A. Moscow, (Department of Pediatrics, University of Kentucky). 

Bernardi, L. R., Biunno, f (2005). Protein profile changes in the human breast cancer cell line MCF-7 in response to SELIL gene induction. Proteomics 5, 2433-2442. 

Nagaraj N, Wisniewski JR, Geiger T et al (2011) Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 7 548... 

Li, N., Guo, R., Li, W., Shao, J., Li, S., Zhao, K., et al. (2005). A proteomic investigation into a human gastric cancer cell line BGC823 treated with diallyl trisulfide. Carcinogenesis. 

The identification of enzymes selectively expressed by tumor cells and tissues may provide a rich source of new biomarkers and targets for the diagnosis and treatment of cancer. In one such effort, the activity, subcellular distribution, and glycosylation state of members from the SH superfamily of enzymes was quantitatively profiled across a panel of human cancer cell lines [20]. The SHs represent one of the largest and most diverse enzyme classes in higher eukaryotic proteomes, consisting of proteases, lipases, esterases,... 

A. Sommer, Comparison of proteomic and genomic analyses of the human breast cancer cell line T47D and the antiestrogen-resistant derivative T47D-r, Mol. Cell. Proteomics 2004, 3, 43-55. 

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