Emerging protein array technologies for proteomics

Expert Review of Proteomics

Volumn 10, Issue 1, 2013, Pages 65-75

  Lee, Jung Rok ^a   Magee, Dewey Mitchell ^b   Gaster, Richard Samuel ^a   Labaer, Joshua ^a   Wang, Shan X ^a  

^a Stanford University   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

Author keywords

giant magnetoresistive sensors; magnetic immunoassays; molecular detection; protein array; protein interactions; self assembling assays

Indexed keywords

MAGNETIC NANOPARTICLE; NUCLEIC ACID;

ANTIBODY RESPONSE; CROSS REACTION; GENE EXPRESSION; MAGNETIC FIELD; NANOSENSOR; NUCLEAR MAGNETIC RESONANCE; PROTEIN EXPRESSION; PROTEIN IMMOBILIZATION; PROTEIN MICROARRAY; PROTEOMICS; REVIEW; SCREENING; SENSOR;

ANIMALS; HUMANS; MAGNETS; NANOTECHNOLOGY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN ARRAY ANALYSIS; PROTEOMICS;

EID: 84874049999     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/epr.12.67     Document Type: Review

References (73)

1. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235), 467-470 (1995).
2. Golub TR, Slonim DK, Tamayo P et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286(5439), 531-537 (1999).
3. Alizadeh AA, Eisen MB, Davis RE et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403(6769), 503-511 (2000).
4. Van't Veer LJ, Dai HY, Van De Vijver MJ et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415(6871), 530-536 (2002).
5. Hamburg MA, Collins FS. The path to personalized medicine. N. Engl. J. Med. 363(4), 301-304 (2010).
6. Kingsmore SF. Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat. Rev. Drug Discov. 5(4), 310-320 (2006).
7. Mitchell P. A perspective on protein microarrays. Nat. Biotechnol. 20(3), 225-229 (2002).
8. Stoevesandt O, Taussig MJ, He M. Protein microarrays: high-throughput tools for proteomics. Expert Rev. Proteomics 6(2), 145-157 (2009).
9. Uetz P, Giot L, Cagney G et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403(6770), 623-627 (2000).
10. 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).
11. MacBeath G. Protein microarrays and proteomics. Nat. Genet. 32, 526-532 (2002).
12. Zhu H, Snyder M. Protein chip technology. Curr. Opin. Chem. Biol. 7(1), 55-63 (2003).
13. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98(8), 4569-4574 (2001).
14. Hanash S. Disease proteomics. Nature 422(6928), 226-232 (2003).
15. Nielsen UB, Geierstanger BH. Multiplexed sandwich assays in microarray format. J. Immunol. Methods 290(1-2), 107-120 (2004).
16. Liotta LA, Espina V, Mehta AI et al. Protein microarrays: meeting analytical challenges for clinical applications. Cancer Cell 3(4), 317-325 (2003).
17. Ramachandran N, Hainsworth E, Bhullar B et al. Self-assembling protein microarrays. Science 305(5680), 86-90 (2004).
18. Tibes R, Qiu Y, Lu Y et al. Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells. Mol. Cancer Ther. 5(10), 2512-2521 (2006).
19. Liotta LA, Kohn EC. The microenvironment of the tumour-host interface. Nature 411(6835), 375-379 (2001).
20. 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 20(16), 1981-1989 (2001).
21. Gaster RS, Hall DA, Nielsen CH et al. Matrix-insensitive protein assays push the limits of biosensors in medicine. Nat. Med. 15(11), 1327-1332 (2009).
22. Keshishian H, Addona T, Burgess M et al. Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell Proteomics 8(10), 2339-2349 (2009).
23. Kirby R, Cho EJ, Gehrke B et al. Aptamerbased sensor arrays for the detection and quantitation of proteins. Anal. Chem. 76(14), 4066-4075 (2004).
24. Mairal T, Ozalp VC, Lozano Sánchez P, Mir M, Katakis I, O'Sullivan CK. Aptamers: molecular tools for analytical applications. Anal. Bioanal. Chem. 390(4), 989-1007 (2008).
25. Nimmagadda SV, Aavula SM, Biradhar N et al. Recombinant diabody-based immunocapture enzyme-linked immunosorbent assay for quantification of rabies virus glycoprotein. Clin. Vaccine Immunol. 17(8), 1261-1268 (2010).
26. Eriksson S, Vehniäinen M, Jansén T et al. Dual-label time-resolved immunofluorometric assay of free and total prostatespecific antigen based on recombinant Fab fragments. Clin. Chem. 46(5), 658-666 (2000).
27. Peluso P, Wilson DS, Do D et al. Optimizing antibody immobilization strategies for the construction of protein microarrays. Anal. Biochem. 312(2), 113-124 (2003).
28. Wang X, Yu J, Sreekumar A et al. Autoantibody signatures in prostate cancer. N. Engl. J. Med. 353(12), 1224-1235 (2005).
29. Robinson WH, DiGennaro C, Hueber W et al. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat. Med. 8(3), 295-301 (2002).
30. Sheehan KM, Calvert VS, Kay EW et al. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol. Cell Proteomics 4(4), 346-355 (2005).
31. Rusmini F, Zhong Z, Feijen J. Protein immobilization strategies for protein biochips. Biomacromolecules 8(6), 1775-1789 (2007).
32. Elbert DL, Hubbell JA. Surface treatments of polymers for biocompatibility. Annu. Rev. Mater. Sci. 26, 365-394 (1996).
33. Graves HC. The effect of surface charge on non-specific binding of rabbit immunoglobulin G in solid-phase immunoassays. J. Immunol. Methods 111(2), 157-166 (1988).
34. Chen H, Yuan L, Song W, Wu ZK, Li D. Biocompatible polymer materials: Role of protein-surface interactions. Prog. Polym. Sci. 33(11), 1059-1087 (2008).
35. Kusnezow W, Jacob A, Walijew A, Diehl F, Hoheisel JD. Antibody microarrays: an evaluation of production parameters. Proteomics 3(3), 254-264 (2003).
36. Osterfeld SJ, Yu H, Gaster RS et al. Multiplex protein assays based on real-time magnetic nanotag sensing. Proc. Natl Acad. Sci. USA 105(52), 20637-20640 (2008).
37. Yakovleva J, Davidsson R, Lobanova A et al. Microfluidic enzyme immunoassay using silicon microchip with immobilized antibodies and chemiluminescence detection. Anal. Chem. 74(13), 2994-3004 (2002).
38. Staros JV, Wright RW, Swingle DM. Enhancement by N- hydroxysulfosuccinimide of water-soluble carbodiimidemediated coupling reactions. Anal. Biochem. 156(1), 220-222 (1986).
39. Grabarek Z, Gergely J. Zero-length crosslinking procedure with the use of active esters. Anal. Biochem. 185(1), 131-135 (1990).
40. Bain CD, Troughton EB, Tao YT, Evall J, Whitesides GM, Nuzzo RG. Formation of monolayer films by the spontaneous assembly of organic thiols from solution onto gold. J. Am. Chem. Soc. 111(1), 321-335 (1989).
41. Oh SJ, Hong BJ, Choi KY, Park JW. Surface modification for DNA and protein microarrays. OMICS 10(3), 327-343 (2006).
42. Carlsson J, Drevin H, Axén R. Protein thiolation and reversible protein-protein conjugation. N-succinimidyl 3-(2-pyridyldithio) propionate, a new heterobifunctional reagent. Biochem. J. 173(3), 723-737 (1978).
43. Karyakin AA, Presnova GV, Rubtsova MY, Egorov AM. Oriented immobilization of antibodies onto the gold surfaces via their native thiol groups. Anal. Chem. 72(16), 3805-3811 (2000).
44. McDevitt MR, Chattopadhyay D, Kappel BJ et al. Tumor targeting with antibodyfunctionalized, radiolabeled carbon nanotubes. J. Nucl. Med. 48(7), 1180-1189 (2007).
45. Liu Z, Tabakman SM, Chen Z, Dai H. Preparation of carbon nanotube bioconjugates for biomedical applications. Nat. Protoc. 4(9), 1372-1382 (2009).
46. Vogt RF Jr, Phillips DL, Henderson LO, Whitfield W, Spierto FW. Quantitative differences among various proteins as blocking agents for ELISA microtiter plates. J. Immunol. Methods 101(1), 43-50 (1987).
47. Pruslin FH, To SE, Winston R, Rodman TC. Caveats and suggestions for the ELISA. J. Immunol. Methods 137(1), 27-35 (1991).
48. Hoffman WL, Jump AA. Inhibition of the streptavidin-biotin interaction by milk. Anal. Biochem. 181(2), 318-320 (1989).
49. Kötitz R, Matz H, Trahms L et al. SQUID based remanence measurements for immunoassays. IEEE Trans. Appl. Supercon. 7(2), 3678-3681 (1997).
50. Chemla YR, Grossman HL, Poon Y et al. Ultrasensitive magnetic biosensor for homogeneous immunoassay. Proc. Natl Acad. Sci. USA 97(26), 14268-14272 (2000).
51. Enpuku K, Soejima K, Nishimoto T et al. Quantitative evaluation of magnetic immunoassay with remanence measurement. Supercond. Sci. Tech. 19(5), S257-S260 (2006).
52. Baselt DR, Lee GU, Natesan M, Metzger SW, Sheehan PE, Colton RJ. A biosensor based on magnetoresistance technology. Biosens. Bioelectron. 13(7-8), 731-739 (1998).
53. Moodera JS, Kinder LR, Wong TM, Meservey R. Large magnetoresistance at room temperature in ferromagnetic thin film tunnel junctions. Phys. Rev. Lett. 74(16), 3273-3276 (1995).
54. Shen W, Schrag BD, Carter MJ, Xiao G. Quantitative detection of DNA labeled with magnetic nanoparticles using arrays of MgO-based magnetic tunnel junction sensors. Appl. Phys. Lett. 93(3), 033903 (2008).
55. Mao S, Linville E, Nowak J et al. Tunneling magnetoresistive heads beyond Gb/in2. IEEE Trans. Magn. 40(1), 307-312 (2004).
56. Aytur TS, Beatty PR, Boser B, Anwar M, Ishikawa T. An immunoassay platform based on CMOS Hall sensors. Presented at: Solid-State Sensor, Actuator and Microsystems Workshop, Hilton Head Island, SC, USA, 126-129 (2002).
57. Besse PA, Boero G, Demierre M, Pott V, Popovic R. Detection of a single magnetic microbead using a miniaturized silicon Hall sensor. Appl. Phys. Lett. 80(22), 4199-4201 (2002).
58. Perez JM, Josephson L, O'Loughlin T, Högemann D, Weissleder R. Magnetic relaxation switches capable of sensing molecular interactions. Nat. Biotechnol. 20(8), 816-820 (2002).
59. Lee H, Sun E, Ham D, Weissleder R. Chip-NMR biosensor for detection and molecular analysis of cells. Nat. Med. 14(8), 869-874 (2008).
60. Carr C, Matlachov AN, Sandin H, Espy MA, Kraus RH. Magnetic sensors for bioassay: HTS SQUIDs or GMRs? IEEE Trans. Appl. Supercon. 17(2), 808-811 (2007).
61. Han SJ, Xu L, Wilson RJ, Wang SX. A novel zero-drift detection method for highly sensitive GMR biochips. IEEE Trans. Magn. 42(10), 3560-3562 (2006).
62. de Boer BM, Kahlman JA, Jansen TP, Duric H, Veen J. An integrated and sensitive detection platform for magnetoresistive biosensors. Biosens. Bioelectron. 22(9-10), 2366-2370 (2007).
63. Gaster RS, Xu L, Han SJ et al. Quantification of protein interactions and solution transport using high-density GMR sensor arrays. Nat. Nanotechnol. 6(5), 314-320 (2011).
64. Hall DA, Gaster RS, Lin T et al. GMR biosensor arrays: A system perspective. Biosens. Bioelectron. 25(9), 2051-2057 (2010).
65. Harris LA, Goff JD, Carmichael AY et al. Magnetite nanoparticle dispersions stabilized with triblock copolymers. Chem. Mater. 15(6), 1367-1377 (2003).
66. Edelstein RL, Tamanaha CR, Sheehan PE et al. The BARC biosensor applied to the detection of biological warfare agents. Biosens. Bioelectron. 14(10-11), 805-813 (2000).
67. Gaster RS, Hall DA, Wang SX. Autoassembly protein arrays for analyzing antibody cross-reactivity. Nano Lett. 11(7), 2579-2583 (2011).
68. Gaster RS, Hall DA, Wang SX. nanoLAB: an ultraportable, handheld diagnostic laboratory for global health. Lab Chip 11(5), 950-956 (2011).
69. Ramachandran N, Raphael JV, Hainsworth E et al. Next-generation high-density self-assembling functional protein arrays. Nat. Methods 5(6), 535-538 (2008).
70. 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. 77(11), 4877-4886 (2009).
71. Graham DL, Ferreira HA, Feliciano N, Freitas PP, Clarke LA, Amaral MD. Magnetic field-assisted DNA hybridisation and simultaneous detection using micron-sized spin-valve sensors and magnetic nanoparticles. Sensor Actuat. B-Chem. 107(2), 936-944 (2005).
72. Dittmer WU, de Kievit P, Prins MW, Vissers JL, Mersch ME, Martens MF. Sensitive and rapid immunoassay for parathyroid hormone using magnetic particle labels and magnetic actuation. J. Immunol. Methods 338(1-2), 40-46 (2008).
73. Aytur T, Foley J, Anwar M, Boser B, Harris E, Beatty PR. A novel magnetic bead bioassay platform using a microchipbased sensor for infectious disease diagnosis. J. Immunol. Methods 314(1-2), 21-29 (2006).