Summary
Antibody arrays represent one of the high-throughput techniques enabling detection of multiple proteins simultaneously. One of the main advantages of the technology over other proteomic approaches resides on that the identities of the measured proteins are known at front of the experimental design or can be readily characterized, facilitating a biological interpretation of the obtained results. This chapter overviews the technical issues of the main antibody array formats as well as various applications using serum specimens in the context of neoplastic diseases. Clinical applications of antibody arrays vary from biomarker discovery for diagnosis, prognosis, and drug response to characterization of s protein pathways and modification changes associated with disease development and progression. As a high-throughput tool addressing protein levels and post-translational modifications, it improves the functional characterization of molecular bases for cancer. Furthermore, the identification and validation of protein expression patterns characteristic of cancer progression and tumor subtypes may enable tailored therapeutic intervention and improvement in the clinical management of cancer patients. Technical requirements such as lower sample volume, antibody concentration, format versatility, and high reproducibility support their increasing impact in cancer research.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Haab BB, Dunham MJ, Brown PO. (2001). Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2(2): research 0004.1–0004.13.
Chan SM, Ermann J, Su L, Fathman CG, Utz PJ. (2004). Protein microarrays for multiplex analysis of signal transduction pathways. Nat Med. 10, 1390–6.
Sanchez-Carbayo M. (2006). Antibody arrays: technical considerations and clinical applications in cancer. Clin Chem. 52, 1651–9.
Barry R, Diggle T, Terrett J, Soloviev M. (2003). Competitive assay formats for high-throughput affinity arrays. J Biomol Screen. 8, 257–63.
Pang S, Smith J, Onley D, Reeve J, Walker M, Foy C. (2005). A comparability study of the emerging protein array platforms with established ELISA procedures. J Immunol Meth. 302, 1–13.
Lash GE, Scaife PJ, Innes BA, Otun HA, Robson SC, Searle RF, Bulmer JN. (2006). Comparison of three multiplex cytokine analysis systems: Luminex, SearchLight and FAST Quant. J Immunol Meth. 309, 205–8.
de Jager W, Rijkers GT. (2006). Solid-phase and bead-based cytokine immunoassay: a comparison. Methods 38, 294–303.
Waterboer T, Sehr P, Pawlita M. (2006). Suppression of non-specific binding in serological Luminex assays. J Immunol Methods. 309, 200–4.
Kingsmore SF. (2006). Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat Rev Drug Discov. 5, 310–21.
Wang X, Yu J, Sreekumar A, Varambally S, Shen R, Giacherio D, Mehra R, Montie JE, Pienta KJ, Sanda MG, Kantoff PW, Rubin MA, Wei JT, Ghosh D, Chinnaiyan AM. (2005). Autoantibody signatures in prostate cancer.NEngl J Med. 353, 1224–35.
Anderson KS, LaBaer J. (2005). The sentinel within: exploiting the immune system for cancer biomarkers. J Proteome Res. 4, 1123–33.
Petricoin EF III, Bichsel VE, Calvert VS, Espina V, Winters M, Young L, Belluco C, Trock BJ, Lippman M, Fishman DA, Sgroi DC, Munson PJ, Esserman LJ, Liotta LA. (2005). Mapping molecular networks using proteomics: a vision for patient-tailored combination therapy. J Clin Oncol. 23, 3614–21.
Angenendt P, Glokler J, Murphy D, Lehrach H, Cahill DJ. (2002). Toward optimized antibody microarrays: a comparison of current microarray support materials. Anal Biochem. 309, 253–60.
Espina V, Woodhouse EC, Wulfkuhle J, Asmussen HD, Petricoin EF III, Liotta LA. (2004). Protein microarray detection strategies: focus on direct detection technologies. J Immunol Methods. 290, 121–33.
Levit-Binnun N, Lindner AB, Zik O, Eshhar Z, Moses E. (2003). Quantitative detection of protein arrays. Anal Chem. 75, 1436–41.
Pawlak B, Gordon R. (2005). Density estimation for positron emission tomography. Technol Cancer Res Treat. 4, 131–42.
Schweitzer B, Roberts S, Grimwade B, Shao W, Wang M, Fu Q, Shu Q, Laroche I, Zhou Z, Tchernev VT, Christiansen J, Velleca M, Kingsmore SF. (2002). Multiplexed protein profiling on microarrays by rolling-circle amplification. Nat Biotechnol. 20, 359–65.
Pasternack RF, Collings PJ. (1995). Resonance light scattering: a new technique for studying chromophore aggregation. Science. 269, 935–9.
Stich N, Gandhum A, Matyushin V, Raats J, Mayer C, Alguel Y, Schalkhammer T. (2002). Phage display antibody-based proteomic device using resonance-enhanced detection. J Nanosci Nanotechnol. 2, 375–81.
Lindskog M, Rockberg J, Uhlen M, Sterky F. (2005). Selection of protein epitopes for antibody production. Biotechniques. 38, 723–7.
Miller JC, Zhou H, Kwekel J, Cavallo R, Burke J, Butler EB, Teh BS, Haab BB. (2003). Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics. 3, 56–63.
Zhou H, Bouwman K, Schotanus M, Verweij C, Marrero JA, Dillon D, Costa J, Lizardi P, Haab BB. (2004). Two-color, rolling-circle amplification on antibody microarrays for sensitive, multiplexed serum-protein measurements. Genome Biol. 5, R28.
Shao W, Zhou Z, Laroche I, Lu H, Zong Q, Patel DD, Kingsmore S, Piccoli SP. (2003). Optimization of rolling-circle amplified protein microarrays for multiplexed protein profiling. J Biomed Biotechnol. 5, 299–307.
Sanchez-Carbayo M, Socci ND, Lozano JJ, Haab BB, Cordon-Cardo C. (2006). Profiling bladder cancer using targeted antibody arrays. Am J Pathol. 168, 93–103.
Saviranta P, Okon R, Brinker A, Warashina M, Eppinger J, Geierstanger BH. (2004). Evaluating sandwich immunoassays in microarray format in terms of the ambient analyte regime. Clin Chem. 50, 1907–20.
Huang R, Lin Y, Shi Q, Flowers L, Ramachandran S, Horowitz IR, Parthasarathy S, Huang RP. (2004). Enhanced protein profiling arrays with ELISA-based amplification for high-throughput molecular changes of tumor patients′ plasma. Clin Cancer Res. 10, 598–609.
Varnum SM, Woodbury RL, Zangar RC. (2004). A protein microarray ELISA for screening biological fluids. Methods Mol Biol. 264, 161–72.
Gembitsky DS, Lawlor K, Jacovina A, Yaneva M, Tempst P. (2004). A prototype antibody microarray platform to monitor changes in protein tyrosine phosphorylation. Mol Cell Proteomics. 3, 1102–18.
Janzi M, Odling J, Pan-Hammarstrom Q, Sundberg M, Lundeberg J, Uhlen M, Hammarstrom L, Nilsson P. (2005). Serum microarrays for large scale screening of protein levels. Mol Cell Proteomics. 4, 1942–7.
MacBeath G, Schreiber SL. (2000). Printing proteins as microarrays for highthroughput function determination. Science. 289, 1760–3.
Knezevic V, Leethanakul C, Bichsel VE, Worth JM, Prabhu VV, Gutkind JS, Liotta LA, Munson PJ, Petricoin EF 3rd, Krizman DB. (2001). Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics. 1, 1271–8.
Arenkov P, Kukhtin A, Gemmell A, Voloshchuk S, Chupeeva V, Mirzabekov A. (2000). Protein microchips: use for immunoassay and enzymatic reactions. Anal Biochem. 278, 123–31
Rai AJ, Gelfand CA, Haywood BC, Warunek DJ, Yi J, Schuchard MD, Mehigh RJ, Cockrill SL, Scott GB, Tammen H, Schulz-Knappe P, Speicher DW, Vitzthum F, Haab BB, Siest G, Chan DW. (2005). HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics. 5, 3262–77.
States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, Hanash SM. (2006). Challenges in deriving high-confidence protein identifications from Dissecting Cancer Serum data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol. 24, 333–8.
Uhlen M, Bjorling E, Agaton C, Szigyarto CA, Amini B, Andersen E, Andersson AC, Angelidou P, Asplund A, Asplund C, Berglund L, Bergstrom K, Brumer H, Cerjan D, Ekstrom M, Elobeid A, Eriksson C, Fagerberg L, Falk R, Fall J, Forsberg M, Bjorklund MG, Gumbel K, Halimi A, Hallin I, Hamsten C, Hansson M, Hedhammar M, Hercules G, Kampf C, Larsson K, Lindskog M, Lodewyckx W, Lund J, Lundeberg J, Magnusson K, Malm E, Nilsson P, Odling J, Oksvold P, Olsson I, Oster E, Ottosson J, Paavilainen L, Persson A, Rimini R, Rockberg J, Runeson M, Sivertsson A, Skollermo A, Steen J, Stenvall M, Sterky F, Stromberg S, Sundberg M, Tegel H, Tourle S, Wahlund E, Walden A, Wan J, Wernerus H, Westberg J, Wester K, Wrethagen U, Xu LL, Hober S, Ponten F. (2005). A human protein atlas for normal and cancer tissues based on antibody Proteomics. Mol Cell Proteomics. 4, 1920–32.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Sanchez-Carbayo, M. (2008). Dissecting Cancer Serum Protein Profiles Using Antibody Arrays. In: Vlahou, A. (eds) Clinical Proteomics. Methods in Molecular Biology™, vol 428. Humana Press. https://doi.org/10.1007/978-1-59745-117-8_15
Download citation
DOI: https://doi.org/10.1007/978-1-59745-117-8_15
Publisher Name: Humana Press
Print ISBN: 978-1-58829-837-9
Online ISBN: 978-1-59745-117-8
eBook Packages: Springer Protocols