Target Discovery and Validation Reviews and Protocols

17
Protein Arrays
A Versatile Toolbox for Target Identification and Monitoring
of Patient Immune Responses
Lina Cekaite, Eivind Hovig, and Mouldy Sioud
Summary
Functional proteomics is a promising technique for the rational identification of novel
therapeutic targets and biological markers. The studies of protein–protein interactions have
been gained from the development of high-throughput technologies such as the yeast twohybrid
system, protein arrays, phage display, and systematic analysis of interaction maps for
the prediction of protein functions. Because antibodies are used extensively as diagnostic and
clinical tools, the characterization of their antigen specificity is of prime importance. Indeed,
screening protein arrays with sera from patients with either cancer or autoimmune diseases
would facilitate the identification of autoantibody signatures that can be used for diagnosis
and/or prognosis of patients. The usefulness of multiplexed measurements lies not only in the
ability to screen many individual marker candidates but also in evaluating the use of multiple
markers in combination. Here, we review the advantage of protein and serum screening of
peptides and cDNA repertoires displayed on phages as well as the fabrication of protein
microarrays for probing immune responses in patients.
Key Words: Autoimmunity; cancer; phage display; protein microarray.
1. Introduction
1.1. Yeast and Phage Technologies as High-Throughput
Proteomics Toolbox
Protein–protein interactions play pivotal roles in various aspects of the structural
and functional organization of the cell. Today, the identification of proteins
that interact with a protein of interest is a focus of the rapidly growing field of
proteomics.
From: Methods in Molecular Biology, vol. 360, Target Discovery and Validation Reviews and Protocols
Volume I, Emerging Strategies for Targets and Biomarker Discovery
Edited by: M. Sioud © Humana Press Inc., Totowa, NJ
335