Cancer proteomics

Rajapakse JC, Duan KB, Yeo WK. Proteomic cancer classification with mass spectrometry data. Am J Pharmacogenomics 2005 5(5) 281—292. Review. 

Costa LT, Thalhammer S, Heckl WM (2004) Atomic force microscopy as a tool in nanobiology - part II force spectroscopy in genomics and proteomics. Cancer Genomics Proteomics 1 71-76... 

Hamler, R. L. Zhu, K. Buchanan, N. S. Kreunin, P. Kachman, M. T. Miller, F. R. Lubman, D. M. A two-dimensional liquid-phase separation method coupled with mass spectrometry for proteomic studies of breast cancer and biomarker identification. Proteomics 2004,4, 562-577. 

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

Proteomic analysis and identification of new hiomarkers and therapeutic targets for invasive ovarian cancer. Proteomics 2(1), 76-84. 

DeSouza, L., Diehl, G., Rodrigues, M.J., Guo, J., Romaschin, A.D., Colgan, T.J., Siu, K.W. (2005). Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J. Proteome Res. 4, 377-386. 

Sandhu, C., Connor, M., Kislinger, T., Slingerland, J., Emili, A. (2005). Global protein shotgun expression profiling of proliferating mcf-7 breast cancer cells. J. Proteome Res. 4,674—689. 

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. 

Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, MD 21702, USA... 

Alaiya AA et al. Cancer proteomics from identification of novel markers to creation of artificial learning models for tumor classification. Electrophoresis 2000 21 1210-1217. 

Celis JE et al. Proteomics and immuno-histochemistry define some of the steps involved in the squamous differentiation of the bladder transitional epithelium a novel strategy for identifying metaplastic lesions. Cancer Res 1999 59 3003-3009. 

Ostergaard M et al. Proteome profiling of bladder squamous cell carcinomas identification of markers that define their degree of differentiation. Cancer Res 1997 57 4111 117. 

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

Vercoutter-Edouart AS et al. Proteomic detection of changes in protein synthesis induced by fibroblast growth fac-tor-2 in MCF-7 human breast cancer cells. Exp Cell Res 2001 262 59-68. 

Voss Tet al. Correlation of clinical data with proteomics profiles in 24 patients with B-cell chronic lymphocytic leukemia. Int J Cancer 2001 91 180-186. 

Many diseases are characterized by the expression of specific proteins1 in some cases, malignant cells yield unique protein profiles when total cellular protein extracts are analyzed by proteomic methods such as two-dimensional gel electrophoresis or matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS).2 High-throughput proteomic studies may be useful to differentiate normal cells from cancer cells, to identify and define the use of biomarkers for specific cancers, and to characterize the clinical course of disease. Proteomics can also be used to isolate and characterize potential drug targets and to evaluate the efficacy of treatments. 

Hood BL, Darfler MM, Guiel TG, et al. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol. Cell. Proteomics 2005 4 1741-1753. 

Hwang SI, Thumar J, Lundgren DH, et al. Direct cancer tissue proteomics a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene 2006 26 65-76. 

Patel V, Hood BL, Mohnolo AA, et al. Proteomic analysis of laser-captured paraffin-embedded tissues a molecular portrait of head and neck cancer progression. Clin. Cancer Res. 2008 14 1002-1014. 

High-throughput proteomic methods hold great promise for the discovery of novel protein biomarkers that can be translated into practical interventions for the diagnosis, treatment, and prevention of disease. These approaches may also facilitate the development of therapeutic agents that are targeted to specific molecular alterations in diseases such as cancer. In many cases, malignant cells yield unique protein profiles when total protein extracts from such cells are analyzed by 2-D gel electrophoresis or mass spectrometry (MS) methods. Such proteomic studies have the potential to provide an important complement to the analysis of DNA and mRNA extracts from these tissues.1... 

In one study by Hood et al., 282 of 1153 identified proteins were identified by at least 2 unique tryptic peptides from FFPE prostate cancer (PCa) tissue.9 According to the gene ontology classification of the proteins identified, -65% of proteins were predicted to be intracellular proteins, while -50% of the total human proteome is predicted to be located in the intracellular compartment. Additionally, 20% of the proteins identified in the PCa tissue were classified as membrane proteins, which is significantly less than the predicted 40% for the human proteome. This relative disparity is not unexpected, considering the Liquid Tissue sample preparation kit lacks specific protocols for membrane protein extraction. The Liquid Tissue method has also been used for proteomics studies of a variety of FFPE tissue samples, including pancreatic tumors,28 squamous cell carcinoma,4 and oral human papillomavirus lesions.27... 

Cheung W, Darfler M, Alvarez H, et al. Apphcation of a global proteomic approach to archival precursor lesions deleted in malignant brain tumors 1 and tissue transglutaminase 2 are upregulated in pancreatic cancers. Pancreatology 2008 8 608-616. 

Ross JS, Fletcher JA, Bloom KJ, et al. Targeted therapy in breast cancer the HER-2/neu gene and protein. Mol. Cell. Proteomics 2004 3 379-398. 

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