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Functional Proteomics in Oncology: A Focus on Antibody Array-Based Technologies

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An Omics Perspective on Cancer Research
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Abstract

Protein–protein interactions, post-translational modifications, and interaction between protein and DNA or RNA can all shift the activity of a protein from what would have been predicted by its level of transcription. Functional proteomics studies the interaction of proteins within their cellular environment to determine how a given protein accomplishes its specific cellular task. Accordingly, the promise of functional proteomics is that by chronicling the function of aberrant or over-expressed proteins, it will be possible to characterize the mechanism of the disease-sustaining proteins. The further understanding of the disease networks will lead to targeted cancer therapy and specific biomarkers for diagnosis, prognosis or therapeutic response prediction based on disease specific proteins. In the context of other proteomic technologies, targeted antibody arrays are strongly contributing for functional proteomics analyses. This chapter describes how such strategies reported to date that may assist in the diagnosis, surveillance, prognosis, and potentially for predictive and therapeutic purposes for patients affected with solid and haematological neoplasias.

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References

  • Anderson KS, Labaer J (2005) The sentinel within: exploiting the immune system for cancer biomarkers. J Proteome Res 4:1123–1133

    Article  CAS  PubMed  Google Scholar 

  • Angenendt P, Glokler J, Murphy D et al (2002) Toward optimized antibody microarrays: a comparison of current microarray support materials. Anal Biochem 309:253–260

    Article  CAS  PubMed  Google Scholar 

  • Azad NS, Rasool N, Annunziata CM et al (2006) Proteomics in clinical trials and practice: present uses and future promise. Mol Cell Proteomics 5:1819–1829

    Article  CAS  PubMed  Google Scholar 

  • Bartling B, Hofmann HS, Boettger T et al (2005) Comparative application of antibody and gene array for expression profiling in human squamous cell lung carcinoma. Lung Cancer 49:145–154

    Article  PubMed  Google Scholar 

  • Belov L, de la Vega O, dos Remedios CG et al (2001) Immunophenotyping of leukemia using a cluster of differentiation antibody microarray. Cancer Res 61:4483

    CAS  PubMed  Google Scholar 

  • Belov L, Mulligan SP, Barber N et al (2006) Classification of human leukemias and lymphomas using extensive immunophenotypes obtained by cell capture on an antibody microarray. Brit J Haem 135:184–197

    Article  CAS  Google Scholar 

  • Bock C, Coleman M, Collins B et al (2004) Photoaptamer arrays applied to multiplexed proteomic analysis. Proteomics 4:609–618

    Article  CAS  PubMed  Google Scholar 

  • Borrebaeck CA, Wingren C (2007) High-throughput proteomics using antibody microarrays: an update. Expert Rev Mol Diagn 7:673–686

    Article  CAS  PubMed  Google Scholar 

  • Celis JE, Gromov P, Cabezón T et al (2004) Proteomic characterization of the interstitial fluid perfusing the breast tumor microenvironment: a novel resource for biomarker and therapeutic target discovery. Mol Cell Proteomics 3:327–344

    Article  CAS  PubMed  Google Scholar 

  • Celis JE, Moreira JM, Cabezón T et al (2005) Identification of extracellular and intracellular signaling components of the mammary adipose tissue and its interstitial fluid in high risk breast cancer patients: toward dissecting the molecular circuitry of epithelial-adipocyte stromal c. Mol Cell Proteomics 4:492–522

    Article  CAS  PubMed  Google Scholar 

  • Chan SM, Ermann J, Su L et al (2004) Protein microarrays for multiplex analysis of signal transduction pathways. Nat Med 10:1390–1396

    Article  CAS  PubMed  Google Scholar 

  • Chen S, LaRoche T, Hamelinck D et al (2007) Multiplexed analysis of glycan variation on native proteins captured by antibody microarrays. Nat Methods 4:437–444

    Article  CAS  PubMed  Google Scholar 

  • De Jager W, Rijkers GT (2006) Solid-phase and bead-based cytokine immunoassay: a comparison. Methods 38:294–303

    Article  PubMed  Google Scholar 

  • Dotan N, Altstock RT, Schwarz M et al (2006) Anti-glycan antibodies as biomarkers for diagnosis and prognosis. Lupus 15:442–450

    Article  CAS  PubMed  Google Scholar 

  • Ek S, Andréasson U, Hober S et al (2006) From gene expression analysis to tissue microarrays – a rational approach to identify therapeutic and diagnostic targets in lymphoid malignancies. Mol Cell Proteomics 5:1072–1081

    Article  CAS  PubMed  Google Scholar 

  • Flores-Delgado G, Liu CW, Sposto R et al (2007) A limited screen for protein interactions reveals new roles for protein phosphatase 1 in cell cycle control and apoptosis. J Proteome Res 6:1165–1175

    Article  CAS  PubMed  Google Scholar 

  • Garcia BH II, Hargrave A, Morgan A et al (2007) Antibody microarray analysis of inflammatory mediator release by human leukemia T-cells and human non small cell lung cancer cells. J Biomol Tech 18:245–251

    PubMed  Google Scholar 

  • Gembitsky DS, Lawlor K, Jacovina A et al (2004) A prototype antibody microarray platform to monitor changes in protein tyrosine phosphorylation. Mol Cell Proteomics 3:1102–1118

    Article  CAS  PubMed  Google Scholar 

  • 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:RESEARCH0004.

    Google Scholar 

  • Huang R, Lin Y, Shi Q et al (2004) Enhanced protein profiling arrays with ELISA-based amplification for high-throughput molecular changes of tumor patients’ plasma. Clin Cancer Res 10:598–609

    Article  CAS  PubMed  Google Scholar 

  • Hudelist G, Pacher-Zavisin M, Singer CF et al (2004) Use of high-throughput protein array for profiling of differentially expressed proteins in normal and malignant breast tissue. Breast Cancer Res Treat 86:281–291

    Article  CAS  PubMed  Google Scholar 

  • Ivanov SS, Chung AS, Yuan ZL et al (2004) Antibodies immobilized as arrays to profile protein post-translational modifications in mammalian cells. Mol Cell Proteomics 3:788–795

    Article  CAS  PubMed  Google Scholar 

  • Kato K, Ishimuro T, Arima Y et al (2007) High-throughput immunophenotyping by surface plasmon resonance imaging. Anal Chem 79:8616–8623

    Article  CAS  PubMed  Google Scholar 

  • Kellner U, Steinert R, Seibert V et al (2004) Epithelial cell preparation for proteomic and transcriptomic analysis in human pancreatic tissue. Pathol Res Pract 200:155–163

    Article  CAS  PubMed  Google Scholar 

  • Kingsmore SF (2006) Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat Rev Drug Discov 5:310–321

    Article  CAS  PubMed  Google Scholar 

  • Kopf E, Zharhary D (2007) Antibody arrays – an emerging tool in cancer proteomics. Int J Biochem Cell Biol 39:1305–1317

    Article  CAS  PubMed  Google Scholar 

  • Lash GE, Scaife PJ, Innes BA et al (2006) Comparison of three multiplex cytokine analysis systems: Luminex, SearchLight and FAST Quant. J Immunol Meth 309:205–208

    Article  CAS  Google Scholar 

  • Li Y, Lee HJ, Corn RM (2007) Detection of protein biomarkers using RNA aptamer microarrays and enzymatically amplified surface plasmon resonance imaging. Anal Chem 79:1082–1088

    Article  CAS  PubMed  Google Scholar 

  • Lin Y, Huang R, Cao X et al (2003a) Detection of multiple cytokines by protein arrays from cell lysate and tissue lysate. Clin Chem Lab Med 41:139–145

    Article  CAS  PubMed  Google Scholar 

  • Lin Y, Huang R, Chen L et al (2004) Identification of interleukin-8 as estrogen receptor-regulated factor involved in breast cancer invasion and angiogenesis by protein arrays. Int J Cancer 109:507–515

    Article  CAS  PubMed  Google Scholar 

  • Lin Y, Huang R, Chen LP et al (2003b) Profiling of cytokine expression by biotin-labelled-based protein arrays. Proteomics 3:1750–1757

    Article  CAS  PubMed  Google Scholar 

  • Miller JC, Zhou H, Kwekel J et al (2003) Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics 3:56–63

    Article  CAS  PubMed  Google Scholar 

  • Nettikadan S, Radke K, Johnson J et al (2006) Detection and quantification of protein biomarkers from fewer than 10 cells. Mol Cell Proteomics 5:895–901

    Article  CAS  PubMed  Google Scholar 

  • Nielsen UB, Cardone MH, Sinskey AJ et al (2003) Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc Natl Acad Sci USA 100:9330–9335

    Article  PubMed  Google Scholar 

  • Nishizuka S, Charboneau L, Young L et al (2003) Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc Natl Acad Sci USA 100:14229–14234

    Article  CAS  PubMed  Google Scholar 

  • Petricoin EF 3rd, Bichsel VE, Calvert VS et al (2005) Mapping molecular networks using proteomics: a vision for patient-tailored combination therapy. J Clin Oncol 23:3614–3621

    Article  CAS  PubMed  Google Scholar 

  • Romeo MJ, Espina V, Lowenthal M et al (2005) CSF proteome: a protein repository for potential biomarker identification. Expert Rev Proteomics 2:57–70

    Article  CAS  PubMed  Google Scholar 

  • Sanchez-Carbayo M (2006) Antibody arrays: technical considerations and clinical applications in cancer. Clin Chem 52:1651–1659

    Article  CAS  PubMed  Google Scholar 

  • Sanchez-Carbayo M, Socci ND, Lozano JJ et al (2006) Profiling bladder cancer using targeted antibody arrays. Am J Pathol 168:93–103

    Article  CAS  PubMed  Google Scholar 

  • Saviranta P, Okon R, Brinker A et al (2004) Evaluating sandwich immunoassays in microarray format in terms of the ambient analyte regime. Clin Chem 50:1907–1920

    Article  CAS  PubMed  Google Scholar 

  • Schweitzer B, Roberts S, Grimwade B et al (2002) Multiplexed protein profiling on microarrays by rolling-circle amplification. Nat Biotechnol 20:359–365

    Article  CAS  PubMed  Google Scholar 

  • Shao W, Zhou Z, Laroche I et al (2003) Optimization of rolling- circle amplified protein microarrays for multiplexed protein profiling. J Biomed Biotechnol 5:299–307

    Article  Google Scholar 

  • Uhlén M, Björling E, Agaton C et al (2005) A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol Cell Proteomics 4:1920–1932

    Article  PubMed  Google Scholar 

  • Varnum SM, Woodbury RL, Zangar RC (2004) A protein microarray ELISA for screening biological fluids. Methods Mol Biol 264:161–172

    CAS  PubMed  Google Scholar 

  • Vazquez-Martin A, Colomer R, Menendez JA (2007) Protein array technology to detect HER2 (erbB-2)-induced ‘cytokine signature’ in breast cancer. Eur J Cancer 43:1117–1124

    Article  CAS  PubMed  Google Scholar 

  • Wang X, Yu J, Sreekumar A et al (2005) Autoantibody signatures in prostate cancer. N Engl J Med 353:1224–1235

    Article  CAS  PubMed  Google Scholar 

  • Waterboer T, Sehr P, Pawlita M (2006) Suppression of non-specific binding in serological Luminex assays. J Immunol Methods 309:200–204

    Article  CAS  PubMed  Google Scholar 

  • Yeretssian G, Lecocq M, Lebon G et al (2005) Competition on nitrocellulose-immobilized antibody arrays: from bacterial protein binding assay to protein profiling in breast cancer cells. Mol Cell Proteomics 4:605–617

    Article  CAS  PubMed  Google Scholar 

  • Zajac A, Song D, Qian W et al (2007) Protein microarrays and quantum dot probes for early cancer detection. Colloids Surf B Biointerfaces 58:309–314

    Article  CAS  PubMed  Google Scholar 

  • Zhou H, Bouwman K, Schotanus M et al (2004) Two-colour, rolling-circle amplification on antibody microarrays for sensitive, multiplexed serum-protein measurements. Genome Biol 5:R28

    Article  PubMed  Google Scholar 

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Correspondence to Marta Sanchez-Carbayo .

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Sanchez-Carbayo, M. (2010). Functional Proteomics in Oncology: A Focus on Antibody Array-Based Technologies. In: Cho, W. (eds) An Omics Perspective on Cancer Research. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-2675-0_6

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