Application of physicochemically modified silicon substrates as reverse-phase protein microarrays

Journal of Proteome Research

Volumn 8, Issue 3, 2009, Pages 1247-1254

  Nijdam, A Jasper ^a,b   Zianni, Michael R ^c   Herderick, Edward E ^d   Cheng, Mark M C ^a,e   Prosperi, Jenifer R ^a,f,g   Robertson, Fredika A ^a,f,i,j   Petricoin, Emanuel F ^h   Liotta, Lance A ^h   Ferrari, Mauro ^a,i,j,k  

^a OHIO STATE UNIVERSITY   (United States)

^b GEORGE WASHINGTON UNIVERSITY   (United States)

^c OHIO STATE UNIVERSITY   (United States)

^d eehscience LLC   (United States)

^e Wayne State University   (United States)

^f THE OHIO STATE UNIVERSITY COLLEGE OF MEDICINE   (United States)

^g UNIVERSITY OF CHICAGO   (United States)

^h GEORGE MASON UNIVERSITY   (United States)

ⁱ UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^j UNIVERSITY OF TEXAS MEDICAL BRANCH   (United States)

^k UNIVERSITY OF TEXAS   (United States)

more..

Author keywords

Nanotechnology; Protein microarrays; Proteomics; Silicon

Indexed keywords

ALBUMIN; MITOGEN ACTIVATED PROTEIN KINASE; PYROXYLIN; QUANTUM DOT; SILICON;

ARTICLE; AUTOFLUORESCENCE; BINDING AFFINITY; BIOTINYLATION; CONTROLLED STUDY; FLUORESCENCE; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN MICROARRAY;

ALBUMINS; CELL LINE, TUMOR; HUMANS; PROTEIN ARRAY ANALYSIS; SILICON; SURFACE PROPERTIES;

EID: 65249133991     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr800455y     Document Type: Article

References (35)

1. Liotta, L. A.; Espina, V.; Mehta, A. I.; Calvert, V.; Rosenblatt, K.; Geho, D.; Munson, P. J.; Young, L.; Wulfkuhle, J.; Petricoin, E. F. Protein microarrays: Meeting analytical challenges for clinical applications. Cancer Cell 2003, 3, 317-325.
2. Wulfkuhle, J. D.; Liotta, L. A.; Petricoin, E. F. Proteomic application for the early detection of cancer. Nat. Rev. Cancer 2003, 3, 267-275.
3. Lal, S. P.; Christopherson, I.; dos Remedios, C. G. Antibody arrays: an embryonic but rapidly growing technology. Drug Discovery Today 2002, 7 (Suppl. 18), S143-S149.
4. MacBeath, G. Protein microarrays and proteomics. Nat. Gen. Suppl. 2002, 32, 526-532.
5. Geho, D. H.; Espina, V.; Wulfkuhle, J. D.; Petricoin, E. F.; Liotta, L. A. Protein pathway analysis in clinical proteomics using protein microarrays. Drug Discovery Today: Technol. 2005, 2.4, 353-359.
6. Quackenbush, J. Microarray analysis and tumor classification. N. Eng. J. Med. 2006, 354, 2463-2472.
7. Wulfkuhle, J. D.; Edmiston, K. H.; Liotta, L. A.; Petricoin, E. F., III. Technology insight: pharmacoproteomics for cancer-promises of patient-tailored medicine using protein microarrays. Nat. Oncol. 2006, 3.5, 256-268.
8. Geho, D. H.; Liotta, L. A.; Petricoin, E. F., III.; Zhao, W.; Araujo, R. P. The amplified peptidome: the new treasure of candidate biomarkers. Curr.Opin. Chem. Biol. 2006, 10, 50-55.
9. Winters, M. E.; Mehta, A. I.; Petricoin, E. F.; Kohn, E. C.; Liotta, L. A. Supra-additive growth inhibition by a celecoxib analogue and carboxyamido-triazole is primarily mediated through apoptosis. Cancer Res 2005, 65, 3853-3860.
10. Emmert-Buck, M. R.; Bonner, R. F.; Smith, P. D.; Chuaqui, R. F.; Zhuang, Z.; Goldstein, S. R.; Weiss, R. A.; Liotta, L. A. Laser capture microdissection. Science 1996, 274, 998-1001.
11. Wulfkuhle, J. D.; Aquino, J. A.; Calvert, V. S.; Fishman, D. A.; Coukos, G.; Liotta, L. A.; Petricoin, E. F., III. Signa pathway profiling of ovarian cancer from human tissue specimens using reverse-phase protein microarrays. Proteomics 2003, 3, 2085-2090.
12. Herrmann, P. C.; Gillespie, J. W.; Charboneau, L.; Bichsel, V. E.; Paweletz, C. P.; Calvert, V. S.; Kohn, E. C.; Emmert-Buck, M. R.; Liotta, L. A.; Petricoin, E. F. Mitochondrial proteome: altered cytochrome c oxidase subunit levels in prostate cancer. Proteomics 2003, 3, 1801-1810.
13. Zha, H.; Raffeld, M.; Charboneau, L.; Pittaluga, S.; Kwak, L. W.; Petricoin, E. F., III.; Liotta, L. A.; Jaffe, E. S. Similarities of prosurvival signals in Bcl-2-2positive and Bcl-2-negative follicular lymphomas identified by reverse phase protein microarray. Lab. Invest. 2004, 84, 235-244.
14. Gulmann, C.; Espina, V.; Petricoin, E., III.; Longo, D. M.; Santi, M.; Knutsen, T.; Raffeld, M.; Jaffe, E. S.; Liotta, L. A.; Feldman, A. L. Proteomic analysis of apoptotic pathways reveals prognostic factors in follicular lymphoma. Clin. Cancer Res. 2005, 11.16, 5847-5855.
15. Wulfkuhle, J. D.; Aquino, J. A.; Calvert, V. S.; Fishman, D. A.; Coukos, G.; Liotta, L. A.; Petricoin, E. F., III. Signal pathway profiling of ovarian cancer from human tissue specimens using reverse-phase protein microarrays. Proteomics 2003, 3, 2085-2090.
16. Wulfkuhle, J. D.; Sgroi, D. C.; Krutzsch, H.; McLean, K.; McGarvey, K.; Knowlton, M.; Chen, S.; Shu, H.; Sahin, A.; Kurek, R.; Wall-wiener, D.; Merino, M. J.; Petricoin, E. F., III.; Zhao, Y.; Steeg, P. S. Proteomics of human breast ductal carcinoma in situ. Cancer Res. 2002, 62, 6740-6749.
17. Sheehan, K. M.; Calvert, V. S.; Kay, E. W.; Lu, Y.; Fishman, D.; Espina, V.; Aquino, J.; Speer, R.; Araujo, R.; Mills, G. B.; Liotta, L. A.; Petricoin, E. F.; Wulfkuhle, J. D. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol. Cell. Proteomics 2005, 4, 346-355.
18. Paweletz, C. P.; Charboneau, L.; Bichsel, V. E.; Simone, N. L.; Chen, T.; Gillespie, J. W.; Emmert-Buck, M. R.; Roth, M. J.; Petricoin, I. E.; Liotta, L. A. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invastion front. Oncogene 2001, 20, 1981-1989.
19. Gulmann, C.; Espina, V.; Petricoin, E., III.; Longo, D. L.; Santi, M.; Knutsen, T.; Raffeld, M.; Jaffe, E. S.; Liotta, L. A.; Feldman, A. L. Proteomic analysis of apoptotic pathways reveals prognostic factors in follicular lymphoma. Clin. Cancer Res. 2005, 11, 5847-5855.
20. Petricoin, E. F.; Bichsel, V. E.; Calvert, V. S.; Espina, V.; Winters, M.; Young, L.; Belluco, C.; Trock, B. J.; Lippman, M.; Fishman, D. A.; Sgroi, D. C.; Munson, P. J.; Esserman, L. J.; Liotta, L. A. Mapping molecular networks using proteomics: a vision for patient-tailored combination therapy. J. Clin. Oncol. 2005, 23, 3614-3621.
21. Alivisatos, P. The use of nanocrystals in biological detection. Nat. Biotechnol. 2004, 22.1, 47-52.
22. Alivisatos, A. P. Semiconductor clusters, nanocrystals and quantum dots. Science 1996, 271, 933-937.
23. Alivisatos, A. P. Perspectives on the physical chemistry of semiconductor nanocrystals. J. Phys. Chem. 1996, 100, 3226-13239.
24. Bruchez, M., Jr.; Moronne, M.; Chin, P.; Wiess, S.; Alivisatos, A. P. Semiconductor nanocrystals as fluorescent biological labels. Science 1998, 281, 2013-2016.
25. King, G.; Payne, S.; Walker, F.; Murray, G. I. A highly sensitive detection method for immunohistochemistry using biotinylated tyramine. J. Pathol. 1997, 183, 237-241.
26. Geho, D.; Lahar, N.; Gurnani, P.; Huebschman, M.; Herrmann, P.; Espina, V.; Shi, A.; Wulfkuhle, J.; Garner, H.; Petricoin, E., III.; Liotta, L. A.; Rosenblatt, K. P. Pegylated, Streptavidin-conjugated quantum dots are effective detection elements for reverse-phase protein microarrays. Bioconjugate Chem. 2005, 16, 559-566.
27. Nijdam, A. J.; Cheng, M. M. C.; Fedele, R.; Geho, D. H.; Herrmann, P.; Killian, K.; Espina, V.; Petricoin, E. F.; Liotta, L. A.; Ferrari, M. Physicochemically modified silicon as substrate for protein mi-croarrays. Biomaterials 2007, 28, 550-558.
28. Mezzasoma, L.; Bacarese-Hamilton, T.; Di Critina, M.; Rossi, R.; Bistoni, F.; Crisanti, A. Antigen microarrays for serodiagnosis of infectious diseases protein. Clin. Chem. 2002, 48.1, 121-130.
29. Duburcq, X.; Olivier, C.; Malingue, F.; Bouzidi, A.; Zhou, F.; Auriault, C.; Gras-Masse, H.; Melnyk, O. Peptide-protein microar-rays for the simultaneous detection of pathogen infections. Bioconjugate Chem. 2004, 15, 307-316.
30. Duburcq, X.; Olivier, C.; Desmet, R.; Halasa, M.; Carion, O.; Grandidier, B.; Heim, T.; Stiévenard, D.; Auriault, C.; Melnyk, O. Polypeptide semicarbazide glass slide microarrays: characterization and comparison with amine slides in serodetection studies. Bioconjugate Chem. 2004, 15, 317-325.
31. Jansen, H.; Gardeniers, H.; de Boer, M.; Elwenspoek, M.; Fluitman, J. A survey on the reactive ion etching of silicon in microtechnol-ogy. J. Micromech. Microeng. 1996, 6, 14.
32. Yakovleva, J.; Davidsson, R.; Lobanova, A.; Bengtsson, M.; Eremin, S.; Laurell, T.; Emneus, E. Microfluidic enzyme immunoassay using silicon microchip with immobilized antibodies and chemilumi-nescence detection. Anal. Chem. 2002, 74, 2994-3004.
33. Weetall, H. H. Covalent Coupling Methods for Inorganic Support Materials Methods in Enzymology. In Methods in Enzymology; Mosbach, K., Ed.; Academic Press: New York, 1976; Vol. 44, Chapter 10, pp 134-148.
34. Moy, V. T.; Florin, E. L.; Gaub, H. E. Adhesive forces between ligand and receptor measured by AFM. Colloids Surf., A 1994, 93, 343-348.
35. Hegde, P.; Qi, R.; Abernathy, K.; Gay, C.; Dharap, S.; Gaspard, R.,; Hughes, J. E.; Snesrud, E.; Lee, N.; Quackenbush, J. Aconcise guide for cDNA microarray analysis. BioTechniques 2000, 29.3, 548.