Skip to main content
SpringerLink
Log in

Planar Antibody Arrays for Biomarkers in Nephritis

  • Reference work entry
  • First Online:
Biomarkers in Kidney Disease

  • 1383 Accesses

Abstract

Affinity proteomics, represented by planar antibody arrays, is an established methodology for high-throughput disease proteomics. The technology can be used to generate multiplexed protein expression profiles of even crude proteomes. The antibodies are deposited one by one in an ordered pattern, an array, onto a planar, solid support, where they will act as specific catcher molecules. Next, the sample is added, and any specifically bound proteins are detected and quantify using mainly fluorescence as sensing technology. The observed binding pattern is then converted into a high-resolution protein expression map, or protein atlas, outlining the composition of the sample at the molecular level. Using state-of-the-art bioinformatics, candidate biomarker signatures are identified. Hence, the technology platforms provide unique opportunities for, e.g., biomarker discovery, disease diagnostics, monitoring, and evidence-based therapy selection, setting the stage for personalized medicine. Nephritis is inflammation of the kidney, a focal or diffuse proliferative or destructive disease, for which new panels of high-performing, blood-based biomarkers could have a clinical impact. In this chapter, we will describe the design and development of planar antibody microarrays for biomarker discovery and illustrate their use for delineating disease-associated biomarkers in nephritis.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 449.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 549.99
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

Abbreviations

GPS:

Global proteome survey

scFv:

Single-chain fragment variable

SLE:

Systemic lupus erythematosus

TXP:

Triple-X Proteomics

References

  • Alhamdani MS, Youns M, Buchholz M, Gress TM, Beckers MC, Marechal D, Bauer A, Schroder C, Hoheisel JD. Immunoassay-based proteome profiling of 24 pancreatic cancer cell lines. J Proteomics. 2012;75(12):3747–59.

    Article  CAS  PubMed  Google Scholar 

  • Arntz Y, Seelig JD, Lang HP, Zhang J, Hunziker P, Ramseyer JP, Meyer E, Hegner M, Gerber C. Label-free protein assay based on a nanomechanical cantilever array. Nanotechnology. 2003;14:86–90.

    Article  CAS  Google Scholar 

  • Backmann N, Zahnd C, Huber F, Bietsch A, Pluckthun A, Lang HP, Guntherodt HJ, Hegner M, Gerber C. A label-free immunosensor array using single-chain antibody fragments. Proc Natl Acad Sci U S A. 2005;102(41):14587–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Belov L, De La Vega O, Dos Remedios CG, Mulligan SP, Christopherson RI. Immunophenotyping of leukemias using a cluster of differentiation antibody microarray. Cancer Res. 2001;61(11):4483–9.

    CAS  PubMed  Google Scholar 

  • Belov L, Huang P, Barber N, Mulligan SP, Christopherson RI. Identification of repertoires of surface antigens on leukemias using an antibody microarray. Proteomics. 2003;3(11):2147–54.

    Article  CAS  PubMed  Google Scholar 

  • Berthet-Duroure N, Leïchlé T, Pourciel J-B, Martin C, Bausells J, Lora-Tamayo E, Perez-Murano F, François J, Trévisiol E, Nicu L. Interaction of biomolecules sequentially deposited at the same location using a microcantilever-based spotter. Biomed Microdevices. 2008;10(4):479–87.

    Article  PubMed  Google Scholar 

  • Borrebaeck CA, Wingren C. High-throughput proteomics using antibody microarrays: an update. Expert Rev Mol Diagn. 2007;7(5):673–86.

    Article  CAS  PubMed  Google Scholar 

  • Borrebaeck CA, Wingren C. Design of high-density antibody microarrays for disease proteomics: key technological issues. J Proteomics. 2009a;72(6):928–35.

    Article  CAS  PubMed  Google Scholar 

  • Borrebaeck CA, Wingren C. Transferring proteomic discoveries into clinical practice. Exp Rev Proteomics. 2009b;6(1):11–3.

    Article  Google Scholar 

  • Borrebaeck CK, Wingren C. Recombinant antibodies for the generation of antibody arrays. In: KORF U, editor. Protein microarrays. New York: Humana Press; 2011.

    Google Scholar 

  • Bruckbauer A, Zhou D, Kang D-J, Korchev YE, Abell C, Klenerman D. An addressable antibody nanoarray produced on a nanostructured surface. J Am Chem Soc. 2004;126(21):6508–9.

    Article  CAS  PubMed  Google Scholar 

  • Campbell CJ, O’looney N, Chong Kwan M, Robb JS, Ross AJ, Beattie JS, Petrik J, Ghazal P. Cell interaction microarray for blood phenotyping. Anal Chem. 2006;78(6):1930–8.

    Article  CAS  PubMed  Google Scholar 

  • Carlsson A, Wuttge DM, Ingvarsson J, Bengtsson AA, Sturfelt G, Borrebaeck CA, Wingren C. Serum protein profiling of systemic lupus erythematosus and systemic sclerosis using recombinant antibody microarrays. Mol Cell Proteomics. 2011;10(5): M110 005033.

    Google Scholar 

  • Cordero OJ, De Chiara L, Lemos-Gonzalez Y, Paez De La Cadena M, Rodriguez-Berrocal FJ. How the measurements of a few serum markers can be combined to enhance their clinical values in the management of cancer. Anticancer Res. 2008;28(4C):2333–41.

    PubMed  Google Scholar 

  • D’cruz DP, Khamashta MA, Hughes GR. Systemic lupus erythematosus. Lancet. 2007;369(9561):587–96.

    Article  PubMed  Google Scholar 

  • Dexlin L, Ingvarsson J, Jönsson M, Ellmark P, Frendeus B, Borrebaeck CA, Wingren C. Membrane protein profiling of intact cells using recombinant antibody microarrays. J Proteome Res. 2006;7(1):319–27.

    Article  Google Scholar 

  • Ekins RP. Ligand assays: from electrophoresis to miniaturized microarrays. Clin Chem. 1998;44(9):2015–30.

    CAS  PubMed  Google Scholar 

  • Ellmark P, Ghatnekar-Nilsson S, Meister A, Heinzelmann H, Montelius L, Wingren C, Borrebaeck CA. Attovial-based antibody nanoarrays. Proteomics. 2009;9(24):5406–13.

    Article  CAS  PubMed  Google Scholar 

  • Ghatnekar-Nilsson S, Dexlin L, Wingren C, Montelius L, Borrebaeck CA. Design of atto-vial based recombinant antibody arrays combined with a planar wave-guide detection system. Proteomics. 2007;7(4):540–7.

    Article  CAS  PubMed  Google Scholar 

  • Griffiths B, Mosca M, Gordon C. Assessment of patients with systemic lupus erythematosus and the use of lupus disease activity indices. Best Pract Res Clin Rheumatol. 2005;19(5):685–708.

    Article  PubMed  Google Scholar 

  • Haab BB. Methods and applications of antibody microarrays in cancer research. Proteomics. 2003;3(11):2116–22.

    Article  CAS  PubMed  Google Scholar 

  • Haab BB. Antibody arrays in cancer research. Mol Cell Proteomics. 2005;4(4):377–83.

    Article  CAS  PubMed  Google Scholar 

  • Haab BB. Applications of antibody array platforms. Curr Opin Biotechnol. 2006;17(4):415–21.

    Article  CAS  PubMed  Google Scholar 

  • Haab, BB., Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2001;2(2):RESEARCH0004.

    Google Scholar 

  • Hanash S. Disease proteomics. Nature. 2003;422(6928):226–32.

    Article  CAS  PubMed  Google Scholar 

  • Hanash SM, Pitteri SJ, Faca VM. Mining the plasma proteome for cancer biomarkers. Nature. 2008;452(7187):571–9.

    Article  CAS  PubMed  Google Scholar 

  • Hartmann M, Roeraade J, Stoll D, Templin MF, Joos TO. Protein microarrays for diagnostic assays. Anal Bioanal Chem. 2009;393(5):1407–16.

    Article  CAS  PubMed  Google Scholar 

  • He M, Stoevesandt O, Palmer EA, Khan F, Ericsson O, Taussig MJ. Printing protein arrays from DNA arrays. Nat Methods. 2008a;5(2):175–7.

    Article  CAS  PubMed  Google Scholar 

  • He M, Stoevesandt O, Taussig MJ. In situ synthesis of protein arrays. Curr Opin Biotechnol. 2008b;19(1):4–9.

    Article  CAS  PubMed  Google Scholar 

  • He M, Taussig MJ. Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method). Nucleic Acids Res. 2001;29(15):E73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Herbst R, Liu Z, Jallal B, Yao Y. Biomarkers for systemic lupus erythematosus. Int J Rheum Dis. 2012;15(5):433–44.

    Article  CAS  PubMed  Google Scholar 

  • Hoff JD, Cheng LJ, Meyhofer E, Guo LJ, Hunt AJ. Nanoscale protein patterning by imprint lithography. Nano Lett. 2004;4(5):853–7.

    Article  CAS  Google Scholar 

  • Hoheisel JD, Alhamdani MSS, Schröder C. Affinity-based microarrays for proteomic analysis of cancer tissues. Proteomics Clin App. 2013;7(1-2):8–15.

    Article  CAS  Google Scholar 

  • Hutcheson J, Ye Y, Han J, Arriens C, Saxena R, Li QZ, Mohan C, Wu T. Resistin as a potential marker of renal disease in lupus nephritis. Clin Exp Immunol. 2015;179(3):435–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ingvarsson J, Larsson A, Sjoholm AG, Truedsson L, Jansson B, Borrebaeck CA, Wingren C. Design of recombinant antibody microarrays for serum protein profiling: targeting of complement proteins. J Proteome Res. 2007;6(9):3527–36.

    Article  CAS  PubMed  Google Scholar 

  • Irvine EJ, Hernandez-Santana A, Faulds K, Graham D. Fabricating protein immunoassay arrays on nitrocellulose using dip-pen lithography techniques. Analyst. 2011;136(14):2925–30.

    Article  CAS  PubMed  Google Scholar 

  • Jang J-W, Smetana A, Stiles P. Multi-ink pattern generation by dip-pen nanolithography®. Scanning. 2010;32(1):24–9.

    CAS  PubMed  Google Scholar 

  • Kingsmore SF. Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat Rev Drug Discov. 2006;5(4):310–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kusnezow W, Banzon V, Schroder C, Schaal R, Hoheisel JD, Ruffer S, Luft P, Duschl A, Syagailo YV. Antibody microarray-based profiling of complex specimens: systematic evaluation of labeling strategies. Proteomics. 2007;7(11):1786–99.

    Article  CAS  PubMed  Google Scholar 

  • Lee K-B, Park S-J, Mirkin CA, Smith JC, Mrksich M. Protein nanoarrays generated by Dip-Pen nanolithography. Science. 2002;295(5560):1702–5.

    Article  CAS  PubMed  Google Scholar 

  • Lee K, Lee S, Yu H, Kang SH. Ultra-sensitive detection of tumor necrosis factor-alpha on gold nano-patterned protein chip formed via E-beam nanolithography by total internal reflection fluorescence microscopy. J Nanosci Nanotechnol. 2010;10(5):3228–31.

    Article  CAS  PubMed  Google Scholar 

  • Liu Cc MS, Kao A, Js N, Jm A. Cell-bound complement biomarkers for systemic lupus erythematosus: from benchtop to bedside. Rheum Dis Clin North Am. 2010;36(1):161–72. x.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lynch M, Mosher C, Huff J, Nettikadan S, Johnson J, Henderson E. Functional protein nanoarrays for biomarker profiling. Proteomics. 2004;4(6):1695–702.

    Article  CAS  PubMed  Google Scholar 

  • Macbeath G. Protein microarrays and proteomics. Nat Genet. 2002;32(Suppl):526–32.

    Article  CAS  PubMed  Google Scholar 

  • Macbeath G, Schreiber SL. Printing proteins as microarrays for high-throughput function determination. Science. 2000;289(5485):1760–3.

    CAS  PubMed  Google Scholar 

  • Meister A, Liley M, Brugger J, Pugin R, Heinzelmann H. Nanodispenser for attoliter volume deposition using atomic force microscopy probes modified by focused-ion-beam milling. Appl Phys Lett. 2004;85(25):6260–2.

    Article  CAS  Google Scholar 

  • Merrill Jt BJ. The role of biomarkers in the assessment of lupus. Best Pract Res Clin Rheumatol. 2005;19(5):709–26.

    Article  PubMed  Google Scholar 

  • Mischak H, Apwiler R, Banks RE, Conaway M, Coon J, Dominiczak A, Ehrich JH, Fliser D, Girolami M, Hermjakob H, Hochstrasser D, Jankowski J, Julian BA, Kolch W, Massy ZA, Neusuess C, Novak J, Peter K, Rossing K, Schanstra JP, Semmes OJ, Theodorescu D, Thongboonkerd V, Weissinger EM, Van Eyk JE, Yamamoto T. Clinical proteomics: a need to define the field and begin to set adequate standards. Clin Proteomics. 2007;1:148–56.

    Article  CAS  Google Scholar 

  • Mok CC. Biomarkers for lupus nephritis: a critical appraisal. J Biomed Biotechnol. 2010;2010:638413.

    Article  PubMed  PubMed Central  Google Scholar 

  • Neiman M, Hedberg JJ, Donnes PR, Schuppe-Koistinen I, Hanschke S, Schindler R, Uhlen M, Schwenk JM, Nilsson P. Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment. J Proteome Res. 2011;10(11):4925–34.

    Article  CAS  PubMed  Google Scholar 

  • Nettikadan S, Radke K, Johnson J, Xu J, Lynch M, Mosher C, Henderson E. Detection and quantification of protein biomarkers from fewer than 10 cells. Mol Cell Proteomics. 2006;5(5):895–901.

    Article  CAS  PubMed  Google Scholar 

  • Olsson N, Carlsson P, James P, Hansson K, Waldemarson S, Malmstrom P, Ferno M, Ryden L, Wingren C, Borrebaeck CA. Grading breast cancer tissues using molecular portraits. Mol Cell Proteomics. 2013;12(12):3612–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Petersson L, Berthet Duroure N, Auger A, Dexlin-Mellby L, Borrebaeck CA, Ait Ikhlef A, Wingren C. Generation of miniaturized planar recombinant antibody arrays using a microcantilever-based printer. Nanotechnol. 2014a;25(27):275104.

    Article  Google Scholar 

  • Petersson L, Coen M, Amro N, Truedsson L, Borrebaeck CA, Wingren C. Miniaturization of multiplexed planar recombinant antibody arrays for serum protein profiling. Bioanalysis. 2014b;6(9):1175–85.

    Article  CAS  PubMed  Google Scholar 

  • Petersson L, Dexlin-Mellby L, Bengtsson AA, Sturfelt G, Borrebaeck CA, Wingren C. Multiplexing of miniaturized planar antibody arrays for serum protein profiling--a biomarker discovery in SLE nephritis. Lab Chip. 2014c;14(11):1931–42.

    Article  CAS  PubMed  Google Scholar 

  • Poetz O, Hoeppe S, Templin MF, Stoll D, Joos TO. Proteome wide screening using peptide affinity capture. Proteomics. 2009;9(6):1518–23.

    Article  CAS  PubMed  Google Scholar 

  • Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau AY, Walter JC, Labaer J. Self-assembling protein microarrays. Science. 2004;305(5680):86–90.

    Article  CAS  PubMed  Google Scholar 

  • Ramachandran N, Raphael JV, Hainsworth E, Demirkan G, Fuentes MG, Rolfs A, Hu Y, Labaer J. Next-generation high-density self-assembling functional protein arrays. Nat Methods. 2008;5(6):535–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rovin BH, Birmingham DJ, Nagaraja HN, Yu CY, Hebert LA. Biomarker discovery in human SLE nephritis. Bull NYU Hosp Jt Dis. 2007;65(3):187–93.

    PubMed  Google Scholar 

  • Manzi S. Lupus update: perspective and clinical pearls. Cleve Clin J Med. 2009;76(2):137–42.

    Article  PubMed  Google Scholar 

  • Sanchez-Carbayo M. Antibody array-based technologies for cancer protein profiling and functional proteomic analyses using serum and tissue specimens. Tumor Biol. 2010;31(2):103–12.

    Article  CAS  Google Scholar 

  • Söderlind E, Strandberg L, Jirholt P, Kobayashi N, Alexeiva V, Aberg A-M, Nilsson A, Jansson B, Ohlin M, Wingren C, Danielsson L, Carlsson R, Borrebaeck CA. Recombining germline-derived CDR sequences for creating diverse single-framework antibody libraries. Nat Biotechnol. 2000;18(8):852–6.

    Article  PubMed  Google Scholar 

  • Tran PL, Gamboa JR, You DJ, Yoon JY. FRET detection of Octamer-4 on a protein nanoarray made by size-dependent self-assembly. Anal Bioanal Chem. 2010;398(2):759–68.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wacker R, Niemeyer CM. DDI-microFIA--A readily configurable microarray-fluorescence immunoassay based on DNA-directed immobilization of proteins. Chembiochem. 2004;5(4):453–9.

    Article  CAS  PubMed  Google Scholar 

  • Wacker R, Schroder H, Niemeyer CM. Performance of antibody microarrays fabricated by either DNA-directed immobilization, direct spotting, or streptavidin-biotin attachment: a comparative study. Anal Biochem. 2004;330(2):281–7.

    Article  CAS  PubMed  Google Scholar 

  • Wingren C, Borrebaeck C. Antibody microarrays – current status and key technological advances. OMICS. 2006;10(3):411–27.

    Article  CAS  PubMed  Google Scholar 

  • Wingren C, Borrebaeck CA. Progress in miniaturization of protein arrays--a step closer to high-density nanoarrays. Drug Discov Today. 2007;12(19–20):813–9.

    Article  CAS  PubMed  Google Scholar 

  • Wingren C, Borrebaeck CA. Antibody microarray analysis of directly labelled complex proteomes. Curr Opin Biotechnol. 2008;19(1):55–61.

    Article  CAS  PubMed  Google Scholar 

  • Wingren C, Borrebaeck CA. Antibody-based microarrays. Methods Mol Biol. 2009;509:57–84.

    Article  CAS  PubMed  Google Scholar 

  • Wingren C, Ingvarsson J, Dexlin L, Szul D, Borrebaeck CA. Design of recombinant antibody microarrays for complex proteome analysis: choice of sample labeling-tag and solid support. Proteomics. 2007;7(17):3055–65.

    Article  CAS  PubMed  Google Scholar 

  • Wingren C, James P, Borrebaeck CA. Strategy for surveying the proteome using affinity proteomics and mass spectrometry. Proteomics. 2009;9(6):1511–7.

    Article  CAS  PubMed  Google Scholar 

  • Wingren C, Sandström A, Segersvärd R, Carlsson A, Andersson R, Löhr M, Borrebaeck CA. Identification of serum biomarker signatures associated with pancreatic cancer. Cancer Res. 2012;72(10):2481–90.

    Article  CAS  PubMed  Google Scholar 

  • Wu T, Du Y, Han J, Singh S, Xie C, Guo Y, Zhou XJ, Ahn C, Saxena R, Mohan C. Urinary angiostatin--a novel putative marker of renal pathology chronicity in lupus nephritis. Mol Cell Proteomics. 2013;12(5):1170–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zheng G, Patolsky F, Cui Y, Wang WU, Lieber CM. Multiplexed electrical detection of cancer markers with nanowire sensor arrays. Nat Biotechnol. 2005;23(10):1294–301.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Immunotechnology and CREATE Health, Lund University, Medicon Village, SE-223 81, Lund, Sweden

    Christer Wingren

Authors
  1. Christer Wingren
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Christer Wingren .

Editor information

Editors and Affiliations

  1. DeptofBiomedlSci,FacltyofSci&Technology, University of Westminster , London, United Kingdom

    Vinood B. Patel

  2. Department of Nutrition and Dietetics,Division of Diabetes and Nutritional Sciences, Faculty of Life Science and Medicine, King’s College London, London, United Kingdom

    Victor R. Preedy

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media Dordrecht

About this entry

Cite this entry

Wingren, C. (2016). Planar Antibody Arrays for Biomarkers in Nephritis. In: Patel, V., Preedy, V. (eds) Biomarkers in Kidney Disease. Biomarkers in Disease: Methods, Discoveries and Applications. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7699-9_52

Download citation

Publish with us

Policies and ethics

Search

Navigation