Skip to main content

Protein Microarrays: Overview, Applications and Challenges

  • Chapter
  • First Online:
Genomics and Proteomics for Clinical Discovery and Development

Abstract

Microarrays technology represents a new tool to address high-throughput biological studies. Various types of protein microarrays based on the application, format and content find use in basic research, drug and biomarker discovery, as well as for the characterization of proteins. In this chapter, we discuss advantages and limitations of protein microarrays, their features and recent applications. We also consider the different methods to build protein microarrays and the recent advances in cell free protein expression systems to construct in situ protein microarrays. Finally, we describe four types of self-assembled protein microarrays: PISA (protein array to protein Array); DAPA (DNA to Protein Array); PuCa (in situ puromycin array) and NAPPA (Nucleic Acids Programmable Protein Arrays) and the recent applications of this latter in situ protein array.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Anderson KS, Ramachandran N, Wong J, et al. Application of protein microarrays for multiplexed detection of antibodies to tumor antigens in breast cancer. J Proteome Res. 2008;7:1490–9. doi:10.1021/pr700804c.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Anderson KS, Sibani S, Wallstrom G, et al. Protein microarray signature of autoantibody biomarkers for the early detection of breast cancer. J Proteome Res. 2011a;10:85–96. doi:10.1021/pr100686b.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Anderson KS, Wong J, D'Souza G, Riemer AB, Lorch J, Haddad R, Pai SI, Longtine J, McClean M, LaBaer J, Kelsey KT, Posner M. Serum antibodies to the HPV16 proteome as biomarkers for head and neck cancer. Br J Cancer. 2011b;104(12):1896–905.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Angenendt P, Kreutzberger J, Glokler J, Hoheisel JD. Generation of high density protein microarrays by cell-free in situ expression of unpurified PCR products. Mol Cell Proteomics. 2006;5:1658–66. T600024-MCP200 [pii]. doi:10.1074/mcp.T600024-MCP200.

  • Belov L, Huang P, Barber N, et al. Identification of repertoires of surface antigens on leukemias using an antibody microarray. Proteomics. 2003;3:2147–54. doi:10.1002/pmic.200300599.

    Article  CAS  PubMed  Google Scholar 

  • Bertone P, Snyder M. Advances in functional protein microarray technology. FEBS J. 2005;272:5400–11. doi:10.1111/j.1742-4658.2005.04970.x.

    Article  CAS  PubMed  Google Scholar 

  • Borrebaeck CAK, Wingren C. Design of high-density antibody microarrays for disease proteomics: key technological issues. J Proteomics. 2009;72:928–35.

    Article  CAS  PubMed  Google Scholar 

  • Carlsson A, Wuttge DM, Ingvarsson J, et al. Serum protein profiling of systemic lupus erythematosus and systemic sclerosis using recombinant antibody microarrays. Mol Cell Proteomics. 2011;10:M110.005033.

    Article  PubMed Central  PubMed  Google Scholar 

  • Casado-Vela J, González-González M, Matarraz S, et al. Protein arrays: recent achievements and their application to study the human proteome. Curr Prot. 2013;10:83–97.

    Article  CAS  Google Scholar 

  • Dahan S, Chevet E, Liu JF, Dominguez M. Antibody-based proteomics: from bench to bedside. Proteomics Clin Appl. 2007;1:922–33. doi:10.1002/prca.200700153.

    Article  CAS  PubMed  Google Scholar 

  • Dasilva N, Diez P, Matarraz S, et al. Biomarker discovery by novel sensors based on nanoproteomics approaches. Sensors (Basel). 2012;12:2284–308. doi:10.3390/s120202284.

    Article  CAS  Google Scholar 

  • Ekins R, Chu F. Multianalyte microspot immunoassay. The microanalytical “compact disk” of the future. Ann Biol Clin. 1992;50:337–53.

    CAS  Google Scholar 

  • Ekins R, Chu F, Biggart E. Multispot, multianalyte, immunoassay. Ann Biol Clin. 1990;48:655–66.

    CAS  Google Scholar 

  • Ellington AA, Kullo IJ, Bailey KR, Klee GG. Antibody-based protein multiplex platforms: technical and operational challenges. Clin Chem. 2010;56:186–93. doi:10.1373/clinchem.2009.127514.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gallagher RI, Silvestri A, Petricoin 3rd EF, et al. Reverse phase protein microarrays: fluorometric and colorimetric detection. Methods Mol Biol. 2011;723:275–301. doi:10.1007/978-1-61779-043-0_18.

    Article  CAS  PubMed  Google Scholar 

  • Gao WM, Kuick R, Orchekowski RP, et al. Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis. BMC Cancer. 2005;5:110. 1471-2407-5-110 [pii]. doi:10.1186/1471-2407-5-110.

  • Ghevaria N, Visser M, Hoffmann R. Quality control for a large-scale study using protein arrays and protein beads to measure immune response in serum and plasma. Proteomics. 2012;12:2802–7. doi:10.1002/pmic.201200082.

    Article  CAS  PubMed  Google Scholar 

  • Gibson DS, Qiu J, Mendoza EA, et al. Circulating and synovial antibody profiling of juvenile arthritis patients by nucleic acid programmable protein arrays. Arthritis Res Ther. 2012;14:R77. doi:10.1186/ar3800.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Glokler J, Angenendt P. Protein and antibody microarray technology. J Chromatogr B Analyt Technol Biomed Life Sci. 2003;797:229–40. S1570023203006962 [pii].

    Google Scholar 

  • Gonzalez-Gonzalez M, Jara-Acevedo R, Matarraz S, et al. Nanotechniques in proteomics: protein microarrays and novel detection platforms. Eur J Pharm Sci. 2012;45:499–506. doi:10.1016/j.ejps.2011.07.009.

    Article  CAS  PubMed  Google Scholar 

  • Gutmann O, Kuehlewein R, Reinbold S, Niekrawietz R, Steinert CP, de Heij B, Zengerle R, Daub M. Fast and reliable protein microarray production by a new drop-in-drop technique. Lab Chip. 2005;5(6):675–81. Epub 2005 Apr 27.

    Article  CAS  PubMed  Google Scholar 

  • Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 1999;19:1720–30.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Hanash S. Disease proteomics. Nature. 2003;422:226–32. doi:10.1038/nature01514.

    Article  CAS  PubMed  Google Scholar 

  • Hanash SM, Pitteri SJ, Faca VM. Mining the plasma proteome for cancer biomarkers. Nature. 2008;452:571–9. nature06916 [pii]. doi:10.1038/nature06916.

  • He M, Stoevesandt O, Palmer EA, et al. Printing protein arrays from DNA arrays. Nat Methods. 2008;5:175–7. doi:10.1038/nmeth.1178.

    Article  CAS  PubMed  Google Scholar 

  • Huang RP, Huang R, Fan Y, Lin Y. Simultaneous detection of multiple cytokines from conditioned media and patient’s sera by an antibody-based protein array system. Anal Biochem. 2001;294:55–62. S0003-2697(01)95156-5 [pii]. doi:10.1006/abio.2001.5156

  • Hunt I. From gene to protein: a review of new and enabling technologies for multi-parallel protein expression. Protein Expr Purif. 2005;40(1):1–22.

    Article  CAS  PubMed  Google Scholar 

  • Kellar KL, Kalwar RR, Dubois KA, et al. Multiplexed fluorescent bead-based immunoassays for quantitation of human cytokines in serum and culture supernatants. Cytometry. 2001;45:27–36. doi:10.1002/1097-0320(20010901)45:1<27::AID-CYTO1141>3.0.CO;2-I [pii].

  • Kellar KL, Mahmutovic AJ, Bandyopadhyay K. Multiplexed microsphere-based flow cytometric immunoassays. Curr Protoc Cytom. 2006;Chapter 13:Unit13 1. doi:10.1002/0471142956.cy1301s35.

  • Kigawa T, Yabuki T, Yoshida Y, Tsutsui M, Ito Y, Shibata T, Yokoyama S. Cell-free production and stable-isotope label-ing of milligram quantities of proteins. FEBS Lett. 1999;442(1):15–9.

    Article  CAS  PubMed  Google Scholar 

  • Kusnezow W, Jacob A, Walijew A, Diehl F, Hoheisel JD. Antibody microarrays: an evaluation of production parameters. Proteomics. 2003;3(3):254–64.

    Article  CAS  PubMed  Google Scholar 

  • LaBaer J, Ramachandran N. Protein microarrays as tools for functional proteomics. Curr Opin Chem Biol. 2005;9:14–9.

    Article  CAS  PubMed  Google Scholar 

  • Larsson K, Wester K, Nilsson P, et al. Multiplexed PrEST immunization for high-throughput affinity proteomics. J Immunol Methods. 2006;315:110–20. doi:10.1016/j.jim.2006.07.014.

    Article  CAS  PubMed  Google Scholar 

  • Manzano-Roman R, Diaz-Martin V, Gonzalez-Gonzalez M, et al. Self-assembled protein arrays from an Ornithodoros moubata salivary gland expression library. J Proteome Res. 2012;11:5972–82. doi:10.1021/pr300696h.

    CAS  PubMed  Google Scholar 

  • Matarraz S, Gonzalez-Gonzalez M, Jara M, et al. New technologies in cancer. Protein microarrays for biomarker discovery. Clin Transl Oncol. 2011;13:156–61.

    Article  CAS  PubMed  Google Scholar 

  • McQuain MK, Seale K, Peek J, Levy S, Haselton FR, McQuain MK, Seale K, Peek J, Levy S. Effects of relative humidity and buffer additives on the contact printing of microarrays by quill pins. Anal Biochem. 2003;320(2):281–91.

    Article  CAS  PubMed  Google Scholar 

  • Merbl Y, Kirschner MW. Protein microarrays for genome-wide posttranslational modification analysis. Wiley Interdiscip Rev Biol Med. 2011;3:347–56. doi:10.1002/wsbm.120.

    Article  CAS  Google Scholar 

  • Miersch S, et al. Serological autoantibody profiling of type 1 diabetes by protein arrays. J Proteomics. 2013;94:486–96.

    Article  CAS  PubMed  Google Scholar 

  • Mijakovic I, Macek B. Impact of phosphoproteomics on studies of bacterial physiology. FEMS Microbiol Rev. 2012;36(4):877–92.

    Article  CAS  PubMed  Google Scholar 

  • Molero C, Rodríguez-Escudero I, Alemán A, et al. Addressing the effects of Salmonella internalization in host cell signaling on a reverse-phase protein array. Proteomics. 2009;9:3652–65.

    Article  CAS  PubMed  Google Scholar 

  • Montor WR, Huang J, Hu Y, et al. Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays. Infect Immun. 2009;77:4877–86. doi:10.1128/IAI.00698-09.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Paweletz CP, Charboneau L, Bichsel VE, et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene. 2001;20:1981–9. doi:10.1038/sj.onc.1204265.

    Article  CAS  PubMed  Google Scholar 

  • Plotkin JB, Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet. 2011;12(1):32–42.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Poetz O, Ostendorp R, Brocks B, et al. Protein microarrays for antibody profiling: specificity and affinity determination on a chip. Proteomics. 2005;5:2402–11. doi:10.1002/pmic.200401299.

    Article  CAS  PubMed  Google Scholar 

  • Ramachandran N, Raphael JV, Hainsworth E, et al. Next-generation high-density self-assembling functional protein arrays. Nat Methods. 2008a;5:535–8. doi:10.1038/nmeth.1210.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ramachandran N, Srivastava S, Labaer J. Applications of protein microarrays for biomarker discovery. Proteomics Clin Appl. 2008b;2:1444–59. doi:10.1002/prca.200800032.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rusmini F, Zhong Z, Feijen J. Protein immobilization strategies for protein biochips. Biomacromolecules. 2007;8:1775–89. doi:10.1021/bm061197b.

    Article  CAS  PubMed  Google Scholar 

  • Schwenk JM, Lindberg J, Sundberg M, et al. Determination of binding specificities in highly multiplexed bead-based assays for antibody proteomics. Mol Cell Proteomics. 2007;6:125–32. T600035-MCP200 [pii]. doi:10.1074/mcp.T600035-MCP200.

  • Schwenk JM, Gry M, Rimini R, et al. Antibody suspension bead arrays within serum proteomics. J Proteome Res. 2008;7:3168–79. doi:10.1021/pr700890b.

    Article  CAS  PubMed  Google Scholar 

  • Spurrier B, Ramalingam S, Nishizuka S. Reverse-phase protein lysate microarrays for cell signaling analysis. Nat Protoc. 2008;3:1796–808. nprot.2008.179 [pii]. doi:10.1038/nprot.2008.179.

  • Sreekumar A, Nyati MK, Varambally S, et al. Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res. 2001;61:7585–93.

    CAS  PubMed  Google Scholar 

  • Stoevesandt O, Taussig MJ. Affinity reagent resources for human proteome detection: initiatives and perspectives. Proteomics. 2007;7:2738–50. doi:10.1002/pmic.200700155.

    Article  CAS  PubMed  Google Scholar 

  • Tannapfel A, Anhalt K, Hausermann P, et al. Identification of novel proteins associated with hepatocellular carcinomas using protein microarrays. J Pathol. 2003;201:238–49. doi:10.1002/path.1420.

    Article  CAS  PubMed  Google Scholar 

  • Tao SC, Zhu H. Protein chip fabrication by capture of nascent polypeptides. Nat Biotechnol. 2006;24:1253–4. nbt1249 [pii]. doi:10.1038/nbt1249.

  • Templin MF, Stoll D, Schrenk M, et al. Protein microarray technology. Drug Discov Today. 2002;7:815–22.

    Article  CAS  PubMed  Google Scholar 

  • Thanawastien A, Montor WR, Labaer J, et al. Vibrio cholerae proteome-wide screen for immunostimulatory proteins identifies phosphatidylserine decarboxylase as a novel Toll-like receptor 4 agonist. PLoS Pathog. 2009;5:e1000556. doi:10.1371/journal.ppat.1000556.

    Article  PubMed Central  PubMed  Google Scholar 

  • Theilacker N, Roller EE, Barbee KD, et al. Multiplexed protein analysis using encoded antibody-conjugated microbeads. J R Soc Interface. 2011;8:1104–13. rsif.2010.0594 [pii]. doi:10.1098/rsif.2010.0594.

  • Wong J, Sibani S, Lokko NN, et al. Rapid detection of antibodies in sera using multiplexed self-assembling bead arrays. J Immunol Methods. 2009;350:171–82. doi:10.1016/j.jim.2009.08.013.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yu X, Schneiderhan-Marra N, Joos TO. Protein microarrays and personalized medicine. Ann Biol Clin (Paris). 2011;69:17–29. doi:10.1684/abc.2010.0512.

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Joshua LaBaer MD, Ph.D. or Manuel Fuentes Ph.D. .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Lourido, L. et al. (2014). Protein Microarrays: Overview, Applications and Challenges. In: Marko-Varga, G. (eds) Genomics and Proteomics for Clinical Discovery and Development. Translational Bioinformatics, vol 6. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9202-8_8

Download citation

Publish with us

Policies and ethics