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Molecular & Cellular Proteomics 5:43-52, 2006.
© 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

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Technology

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

Yanfei Wang, Rong Wu, Kathleen R. Cho^,¶, Kerby A. Shedden^||, Timothy J. Barder^** and David M. Lubman^,,¶,,

From the Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, Department of Surgery, The University of Michigan Medical Center, Ann Arbor, Michigan 48109-0654, Department of Pathology, The University of Michigan Medical Center, Ann Arbor, Michigan 48109-0602, ^|| Department of Statistics, The University of Michigan, Ann Arbor, Michigan 48109-1092, ^** Eprogen, Inc., Darien, Illinois 60561, and the ^¶ Comprehensive Cancer Center, The University of Michigan Medical Center, Ann Arbor, Michigan 48109-0942

A two-dimensional liquid mapping method was used to map the protein expression of eight ovarian serous carcinoma cell lines and three immortalized ovarian surface epithelial cell lines. Maps were produced using pI as the separation parameter in the first dimension and hydrophobicity based upon reversed-phase HPLC separation in the second dimension. The method can be reproducibly used to produce protein expression maps over a pH range from 4.0 to 8.5. A dynamic programming method was used to correct for minor shifts in peaks during the HPLC gradient between sample runs. The resulting corrected maps can then be compared using hierarchical clustering to produce dendrograms indicating the relationship between different cell lines. It was found that several of the ovarian surface epithelial cell lines clustered together, whereas specific groups of serous carcinoma cell lines clustered with each other. Although there is limited information on the current biology of these cell lines, it was shown that the protein expression of certain cell lines is closely related to each other. Other cell lines, including one ovarian clear cell carcinoma cell line, two endometrioid carcinoma cell lines, and three breast epithelial cell lines, were also mapped for comparison to show that their protein profiles cluster differently than the serous samples and to study how they cluster relative to each other. In addition, comparisons can be made between proteins differentially expressed between cell lines that may serve as markers of ovarian serous carcinomas. The automation of the method allows reproducible comparison of many samples, and the use of differential analysis limits the number of proteins that might require further analysis by mass spectrometry techniques.

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