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Analysis of Protein Expression in Cell Microarrays: A Tool for Antibody-based Proteomics

Ann-Catrin Andersson, Sara Strömberg, Helena Bäckvall, Caroline Kampf, Mathias Uhlen, Kenneth Wester and Fredrik Pontén

Department of Genetics and Pathology, Rudbeck Laboratory, University Hospital, Uppsala, Sweden (A-CA,SS,HB,CK,KW,FP), and Department of Biotechnology, Royal Institute of Technology, Stockholm, Sweden (MU)

Correspondence to: Fredrik Pontén, Dept. of Genetics & Pathology, Rudbeck Laboratory C5:3, SE-751 85 Uppsala, Sweden. E-mail: fredrik.ponten{at}genpat.uu.se

Tissue microarray (TMA) technology provides a possibility to explore protein expression patterns in a multitude of normal and disease tissues in a high-throughput setting. Although TMAs have been used for analysis of tissue samples, robust methods for studying in vitro cultured cell lines and cell aspirates in a TMA format have been lacking. We have adopted a technique to homogeneously distribute cells in an agarose gel matrix, creating an artificial tissue. This enables simultaneous profiling of protein expression in suspension- and adherent-grown cell samples assembled in a microarray. In addition, the present study provides an optimized strategy for the basic laboratory steps to efficiently produce TMAs. Presented modifications resulted in an improved quality of specimens and a higher section yield compared with standard TMA production protocols. Sections from the generated cell TMAs were tested for immunohistochemical staining properties using 20 well-characterized antibodies. Comparison of immunoreactivity in cultured dispersed cells and corresponding cells in tissue samples showed congruent results for all tested antibodies. We conclude that a modified TMA technique, including cell samples, provides a valuable tool for high-throughput analysis of protein expression, and that this technique can be used for global approaches to explore the human proteome. (J Histochem Cytochem 54:1413–1423, 2006)

Key Words: immunohistochemistry • cell line • tissue microarray • affinity proteomics • antibody-based proteomics

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