Mimotopes and proteome analyses using human genomic and cDNA epitope phage display

In the post‐genomic era, validation of candidate gene targets frequentlyrequires protein‐based strategies. Phage display is a powerful tool to defineprotein‐protein interactions by generating peptide binders against targetantigens. Epitope phage display libraries have the potential to enrich codingexon sequences from human genomic loci. We evaluated genomic and cDNA phagedisplay strategies to identify genes in the 5q31 Interleukin gene clusterand to enrich cell surface receptor tyrosine kinase genes from a breast cancer cDNAlibrary. A genomic display library containing 2x10 6 clones withexon‐sized inserts was selected with antibodies specific for human Interleukin‐4(IL‐4) and Interleukin‐13. The library was enriched significantly after twoselection rounds and DNA sequencing revealed unique clones. One clone matcheda cognate IL‐4 epitope; however, the majority of clone insert sequences correspondedto E. coli genomic DNA. These bacterial sequences act as ‘mimotopes’(mimetic sequences of the true epitope), correspond to open reading frames,generate displayed peptides, and compete for binding during phage selection.The specificity of these mimotopes for IL‐4 was confirmed by competition ELISA.Other E. coli mimotopes were generated using additional antibodies.Mimotopes for a receptor tyrosine kinase gene were also selected using a breastcancer SKBR‐3 cDNA phage display library, screened against an anti‐erbB2 monoclonalantibody. Identification of mimotopes in genomic and cDNA phage librariesis essential for phage display‐based protein validation assays and two‐hybridphage approaches that examine protein‐protein interactions. The predominanceof E. coli mimotopes suggests that the E. coli genome may beuseful to generate peptide diversity biased towards protein coding sequences. Abbreviations used: IL, interleukin; ELISA, enzyme linked immunoabsorbantassay; PBS, phospho‐buffered saline; cfu, colony forming units. Copyright© 2002 John Wiley & Sons, Ltd.