Antibody micoarrays: The crucial impact of mass transport on assay kinetics and sensitivity

Expert Review of Molecular Diagnostics

Volumn 6, Issue 1, 2006, Pages 111-124

  Kusnezow, Wlad ^a   Syagailo, Yana V ^a   Goychuk, Igor ^b   Hoheisel, Jörg D ^a   Wild, David G ^c  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b UNIVERSITY OF AUGSBURG   (Germany)

^c ConvaTec ^*  (United Kingdom)

Author keywords

Affinity; Ambient analyte theory; Antibody microarrays; Diffusion; Kinetics; Mass transport; Protein expression profiling; Proteomics; Sensitivity; Surface chemistry; Two compartment model

Indexed keywords

ASSAY; HUMAN; IMMUNOASSAY; KINETICS; MICROARRAY ANALYSIS; REVIEW; SENSITIVITY ANALYSIS; SOLID; IMMUNOLOGY; METHODOLOGY; PHYSICAL CHEMISTRY; PROTEIN MICROARRAY; SENSITIVITY AND SPECIFICITY; STANDARD;

ANTIBODY;

ANTIBODIES; CHEMISTRY, PHYSICAL; HUMANS; IMMUNOASSAY; KINETICS; PROTEIN ARRAY ANALYSIS; SENSITIVITY AND SPECIFICITY;

EID: 33644842828     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/14737159.6.1.111     Document Type: Review

References (76)

1. Kusnezow W, Syagailo YV, Rueffer S et al. Kinetics of antigen binding to antibody microarray: strong limitation by mass transport to the surface. Proteomics 6(5), (2005) (In Press). Describes the first experimental quantitative evaluation of a mass transport-limited microspot reaction. The modified two-compartment model was used here for this goal.
2. Klenin KV, Kusnezow W, Langowski J. Kinetics of protein binding in solid-phase immunoassays: theory. J. Chem. Phys. 122(21), 214715 (2005). Presents a comprehensive kinetic model for conventional as well as microspot immunoassays. It is the theoretical first report on the issue of mass transport-dependent reactions of protein-antibody microspots. It is of particular interest from the physics perspective.
3. Chan V, Graves DJ, McKenzie SE. The biophysics of DNA hybridization with immobilized oligonucleotide probes. Biophys. J. 69(6), 2243-2255 (1995). One of the main fundamentals of the DNA microarray biophysics, also of interest for the protein field.
4. Ekins RP. Ligand assays: from electrophoresis to miniaturized microarrays. Clin. Chem. 44(9), 2015-2030 (1998). Fundamental publication for protein and DNA microarray fields. Presents the principles of the ambient analyte theory as well as some retrospectives into the immunoassay history.
5. Erickson D, Li D, Krull UJ. Modeling of DNA hybridization kinetics for spatially resolved biochips. Anal. Biochem. 317(2), 186-200 (2003).
6. Gadgil C, Yeckel A, Derby JJ, Hu W. A diffusion-reaction model for DNA microarray assays. J. Biotechnol. 114(1-2), 31-45 (2004).
7. Livshits MA, Mirzabekov AD. Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleotides. Biophys. J. 71(5), 2795-2801 (1996).
8. Bhanot G, Louzoun Y, Zhu J, DeLisi C. The importance of thermodynamic equilibrium for high-throughput gene expression arrays. Biophys. J. 84(1), 124-135 (2003).
9. Kusnezow W, Hoheisel JD. Solid supports for microarray immunoassays. J. Mol. Recognit. 16(4), 165-176 (2003).
10. Kusnezow W, Hoheisel JD. Antibody microarrays: promises and problems. Biotechniques Suppl. 14-23 (2002).
11. Harry JL, Wilkins MR, Herbert BR, Packer NH, Gooley AA, Williams KL. Proteomics: capacity versus utility. Electrophoresis 21(6), 1071-1081 (2000).
12. Miklos GL, Maleszka R. Protein functions and biological contexts. Proteomics 1(2), 169-178 (2001).
13. Kusnezow W, Jacob A, Walijew A, Diehl F, Hoheisel JD. Antibody microarrays: an evaluation of production parameters. Proteomics 3(3), 254-264 (2003).
14. Angenendt P, Glokler J, Sobek J, Lehrach H, Cahill DJ. Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications. J. Chromatogr. A 1009(1-2), 97-104 (2003).
15. Angenendt P, Glokler J, Murphy D, Lehrach H, Cahill DJ. Toward optimized antibody microarrays: a comparison of current microarray support materials. Anal. Biochem. 309(2), 253-260 (2002).
16. Brueggemeier SB, Kron SJ, Palecek S. Use of protein-acrylamide co-polymer hydrogels for measuring protein concentration and activity. Anal. Biochem. 329(2), 180-189 (2004).
17. Miller JC, Zhou H, Kwekel J et al. Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics 3(1), 56-63 (2003).
18. Stillman BA, Tonkinson JL. FAST slides: a novel surface for microarrays. Biotechniques 29(3), 630-635 (2000).
19. Yeo DS, Panicker RC, Tan LP, Yao SQ. Strategies for immobilization of biomolecules in a microarray. Comb. Chem. High Throughput Screen. 7(3), 213-221 (2004).
20. Haab BB, Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2(2), RESEARCH0004 (2001).
21. Haab BB. Antibody arrays in cancer research. Mol. Cell. Proteomics 4(4), 377-383 (2005).
22. Schweitzer B, Roberts S, Grimwade B et al. Multiplexed protein profiling on microarrays by rolling-circle amplification. Nature Biotechnol. 20(4), 359-365 (2002).
23. Bacarese-Hamilton T, Ardizzoni A, Gray J, Crisanti A. Protein arrays for serodiagnosis of disease. Methods Mol. Biol. 264, 271-283 (2004).
24. Saviranta P, Okon R, Brinker A, Warashina M, Eppinger J, Geierstanger BH. Evaluating sandwich immunoassays in microarray format in terms of the ambient analyte regime. Clin. Chem. 50(10), 1907-1920 (2004).
25. Wingren C, Steinhauer C, Ingvarsson J, Persson E, Larsson K, Borrebaeck CA. Microarrays based on affinity-tagged single-chain Fv antibodies: sensitive detection of analyte in complex proteomes. Proteomics 5(5), 1281-1291 (2005).
26. Sreekumar A, Nyati MK, Varambally S et al. Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res. 61(20), 7585-7593 (2001).
27. Knezevic V, Leethanakul C, Bichsel VE et al. Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics 1(10), 1271-1278 (2001).
28. MacBeath G. Protein microarrays and proteomics. Nature Genet. 32(Suppl.), 526-532 (2002).
29. Kusnezow W, Pulli T, Witt O, Hoheisel JD. Solid support for protein microarrays and related devices. In: Protein microarrays. Schena M (Ed.), Jones and Bartlett Publishers, Sudbury, UK 247-284 (2004).
30. Sreekumar A, Chinnaiyan AM. Using protein microarrays to study cancer. Biotechniques Suppl. 46-53 (2002).
31. Shao W, Zhou Z, Laroche I et al. Optimization of rolling-circle amplified protein microarrays for multiplexed protein profiling. J. Biomed. Biotechnol. 2003(5), 299-307 (2003).
32. Zhou H, Bouwman K, Schotanus M et al. Two-color, rolling-circle amplification on antibody microarrays for sensitive, multiplexed serum-protein measurements. Genome Biol. 5(4), R28 (2004).
33. Sukhanov S, Delafontaine P. Protein chip-based microarray profiling of oxidized low density lipoprotein-treated cells. Proteomics 5(5), 1274-1280 (2005).
34. Hudelist G, Pacher-Zavisin M, Singer CF et al. Use of high-throughput protein array for profiling of differentially expressed proteins in normal and malignant breast tissue. Breast Cancer Res. Treat. 86(3), 281-291 (2004).
35. Pawlak M, Schick E, Bopp MA, Schneider MJ, Oroszlan P, Ehrat M. Zeptosens' protein microarrays: a novel high performance microarray platform for low abundance protein analysis. Proteomics 2(4), 383-393 (2002).
36. Levicky R, Horgan A. Physicochemical perspectives on DNA microarray and biosensor technologies. Trends Biotechnol. 23(3), 143-149 (2005). Successful and comprehensive review on DNA microarray biophysics.
37. Scriba J, Tögl A, Kirchner R. Nanopumpen verbessern die microarray-inkubation. Transkript LABORWELT Nr. III, 12-14 (2002).
38. Adey NB, Lei M, Howard MT et al. Gains in sensitivity with a device that mixes microarray hybridization solution in a 25-microm-thick chamber. Anal. Chem. 74(24), 6413-6417 (2002).
39. Belleville E, Dufva M, Aamand J, Bruun L, Christensen CB. Quantitative assessment of factors affecting the sensitivity of a competitive immunomicroarray for pesticide detection. Biotechniques 35(5), 1044-1051 (2003).
40. Xu Y, Bao G. A filtration-based protein microarray technique. Anal. Chem. 75(20), 5345-5351 (2003).
41. Sapsford KE, Liron Z, Shubin YS, Ligler FS. Kinetics of antigen binding to arrays of antibodies in different sized spots. Anal. Chem. 73(22), 5518-5524 (2001).
42. Berg OG, von Hippel PH. Diffusion-controlled macromolecular interactions. Ann. Rev. Biophys. Chem. 14, 131-160 (1985). Simple and clear description of diffusional processes in biologic systems.
43. Schuck P, Minton AP. Analysis of mass transport-limited binding kinetics in evanescent wave biosensors. Anal. Biochem. 240(2), 262-272 (1996). First theoretical presentation of the two-compartment model, in an uncomplicated and convincing style suitable for nonphysicists.
44. Schuck P. Kinetics of ligand binding to receptor immobilized in a polymer matrix, as detected with an evanescent wave biosensor. I. A computer simulation of the influence of mass transport. Biophys. J. 70(3), 1230-1249 (1996).
45. Goldstein B, Coombs D, He X, Pineda AR, Wofsy C. The influence of transport on the kinetics of binding to surface receptors: application to cells and BIAcore. J. Mol. Recognit. 12(5), 293-299 (1999).
46. Halperin A, Buhot A, Zhulina EB. Sensitivity, specificity, and the hybridization isotherms of DNA chips. Biophys. J. 86(2), 718-730 (2004).
47. Sekar MM, Bloch W, St John PM. Comparative study of sequence-dependent hybridization kinetics in solution and on microspheres. Nucleic Acids Res. 33(1), 366-375 (2005).
48. Schuck A, Minton AP. Kinetic analysis of biosensor data: elementary test for self-consistency. Trends Biochem Sci. 21, 458-460 (1996).
49. Stenberg M, Nygren H. A diffusion-limited reaction theory for a solid-phase immunoassay. J. Theor. Biol. 113(3), 589-597 (1985). Diffusion-limited reaction theory for conventional immunoassays used for some theoretical considerations. Describes the biophysical fundamentals for conventional immunoassays.
50. Stenberg M, Werthen M, Theander S, Nygren H. A diffusion limited reaction theory for a microtiter plate assay. J. Immunol. Methods 112(1), 23-29 (1988).
51. Hlady W, Buijs J. Protein adsorption on solid surfaces. Curr. Opin. Biotechnol. 7(1), 72-77 (1996).
52. Huang NP, Michel R, Voros J et al. Poly(L-lysine)-g-poly(ethylene glycol) layers on metal oxide surfaces: surface-analytical characterization and resistance to serum and fibrinogen adsorption. Langmuir 17, 489-498 (2001).
53. Tengvall P, Lundstrom I, Liedberg B. Protein adsorption studies on model organic surfaces: an ellipsometric and infrared spectroscopic approach. Biomaterials 19(4-5), 407-422 (1998).
54. Zhang F, Kanq ET, Neoh KG et al. Surface modification of stainless steel by grafting of poly(ethylene glycol) for reduction in protein adsorption. Biomaterials 22, 1541-1548 (2001).
55. Krishnan A, Siedlecki CA, Vogler EA. Mixology of protein solutions and the Vroman effect. Langmuir 20(12), 5071-5078 (2004).
56. Pardue HL. The inseparable triad: analytical sensitivity, measurement uncertainty, and quantitative resolution. Clin. Chem. 43(10), 1831-1837 (1997).
57. Ekins R, Edwards P. On the meaning of 'sensitivity'. Clin. Chem. 43(10), 1824-1831 (1997).
58. Ekins R, Edwards P. On the meaning of 'sensitivity': a rejoinder. Clin. Chem. 44(8 Pt 1), 1773-1778 (1998).
59. Wang D, Gou SY, Axelrod D. Reaction rate enhancement by surface diffusion of adsorbates. Biophys. Chem. 43(2), 117-137 (1992).
60. Axelrod D, Wang MD. Reduction-of-dimensionality kinetics at reaction-limited cell surface receptors. Biophys. J. 66(3 Pt 1), 588-600 (1994).
61. Lee Y, Lee EK, Cho YW et al. ProteoChip: a highly sensitive protein microarray prepared by a novel method of protein immobilization for application of protein-protein interaction studies. Proteomics 3(12), 2289-2304 (2003).
62. Guilleaume B, Buness A, Schmidt C et al. Systematic comparison of surface coatings for protein microarrays. Proteomics 5(18), 4705-4712 (2005).
63. Seong SY. Microimmunoassay using a protein chip: optimizing conditions for protein immobilization. Clin. Diagn. Lab. Immunol. 9(4), 927-930 (2002).
64. Steinhauer C, Ressine A, Marko-Varga G, Laurell T, Borrebaeck CA, Wingren C. Biocompatibility of surfaces for antibody microarrays: design of macroporous silicon substrates. Anal. Biochem. 341(2), 204-213 (2005).
65. Zhu H, Snyder M. Protein chip technology. Curr. Opin. Chem. Biol. 7(1), 55-63 (2003).
66. Joos TO, Stoll D, Templin MF. Miniaturised multiplexed immunoassays. Curr. Opin. Chem. Biol. 6(1), 76-80 (2002).
67. Espina V, Mehta AI, Winters ME et al. Protein microarrays: molecular profiling technologies for clinical specimens. Proteomics 3(11), 2091-2100 (2003).
68. Silzel JW, Cercek B, Dodson C, Tsay T, Obremski RJ. Mass-sensing, multianalyte microarray immunoassay with imaging detection. Clin. Chem. 44(9), 2036-2043 (1998).
69. Angenendt P, Glokler J, Konthur Z, Lehrach H, Cahill DJ. 3D protein microarrays: performing multiplex immunoassays on a single chip. Anal. Chem. 75(17), 4368-4372 (2003).
70. Cretich M, Pirri G, Damin F, Solinas I, Chiari M. A new polymeric coating for protein microarrays. Anal. Biochem. 332(1), 67-74 (2004).
71. Kersten B, Feilner T, Kramer A et al. Generation of Arabidopsis protein chips for antibody and serum screening. Plant. Mol. Biol. 52(5), 999-1010 (2003).
72. Ressine A, Ekstrom S, Marko-Varga G, Laurell T. Macro-/nanoporous silicon as a support for high-performance protein microarrays. Anal. Chem. 75(24), 6968-6974 (2003).
73. Avseenko NV, Morozova TYa, Ataullakhanov FI, Morozov VN. Immobilization of proteins in immunochemical microarrays fabricated by electrospray deposition. Anal. Chem. 73(24), 6047-6052 (2001).
74. Li Y, Reichert WM. Adapting cDNA microarray format to cytokine detection protein microarray. Langmuir 19(5), 1557-1566 (2002).
75. Joos TO, Schrenk M, Hopfl P et al. A microarray enzyme-linked immunosorbent assay for autoimmune diagnostics. Electrophoresis 21(13), 2641-2650 (2000).
76. Pavlickova P, Knappik A, Kambhampati D, Ortigao F, Hug H. Microarray of recombinant antibodies using a streptavidin sensor surface self-assembled onto a gold layer. Biotechniques 34(1), 124-130 (2003).