Use of high density antibody arrays to validate and discover cancer serum biomarkers

Molecular Oncology

Volumn 1, Issue 3, 2007, Pages 313-320

  Loch, Christian M ^a   Ramirez, Arturo B ^a   Liu, Yan ^a   Sather, Cassandra L ^a   Delrow, Jeffrey J ^a   Scholler, Nathalie ^a   Garvik, Barbara M ^a   Urban, Nicole D ^a   McIntosh, Martin W ^a   Lampe, Paul D ^a  

^a USA   (United States)

Author keywords

Antibody microarray; Biomarker; Cancer; Ovarian; Serum

Indexed keywords

BIOLOGICAL MARKER; DNA ANTIBODY; MITOGEN ACTIVATED PROTEIN KINASE;

ARTICLE; CANCER CLASSIFICATION; CONTROLLED STUDY; DNA MICROARRAY; GENE FUNCTION; HUMAN; HUMAN TISSUE; OVARY CANCER; PRIORITY JOURNAL; REPRODUCIBILITY; RNA TRANSLATION; VALIDATION STUDY;

EID: 36549058160     PISSN: 15747891     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molonc.2007.08.004     Document Type: Article

References (45)

1. Aebersold R., Anderson L., Caprioli R., Druker B., Hartwell L., and Smith R. Perspective: a program to improve protein biomarker discovery for cancer. J. Proteome Res. 4 4 (2005) 1104-1109
2. Angenendt P., Glokler J., Murphy D., Lehrach H., and Cahill D.J. Toward optimized antibody microarrays: a comparison of current microarray support materials. Anal. Biochem. 309 2 (2002) 253-260
3. Bast Jr. R.C., Feeney M., Lazarus H., Nadler L.M., Colvin R.B., and Knapp R.C. Reactivity of a monoclonal antibody with human ovarian carcinoma. J. Clin. Invest. 68 5 (1981) 1331-1337
4. Bereczki E., Gonda S., Csont T., Korpos E., Zvara A., Ferdinandy P., and Santha M. Overexpression of biglycan in the heart of transgenic mice: an antibody microarray study. J. Proteome Res. 6 2 (2007) 854-861
5. Bi Q., Cen X., Wang W., Zhao X., Wang X., Shen T., and Zhu S. A protein microarray prepared with phage-displayed antibody clones. Biosens. Bioelectron 22 12 (2007) 3278-3282
6. Biade S., Marinucci M., Schick J., Roberts D., Workman G., Sage E.H., O'Dwyer P.J., Livolsi V.A., and Johnson S.W. Gene expression profiling of human ovarian tumours. Br.J. Cancer 95 8 (2006) 1092-1100
7. Birner P., Schindl M., Obermair A., Breitenecker G., and Oberhuber G. Expression of hypoxia-inducible factor 1alpha in epithelial ovarian tumors: its impact on prognosis and on response to chemotherapy. Clin. Cancer Res. 7 6 (2001) 1661-1668
8. Bratt T. Lipocalins and cancer. Biochim. Biophys. Acta 1482 1-2 (2000) 318-326
9. Chi J.T., Wang Z., Nuyten D.S., Rodriguez E.H., Schaner M.E., Salim A., Wang Y., Kristensen G.B., Helland A., Borresen-Dale A.L., et al. Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med. 3 3 (2006) e47
10. Davidson B., Zhang Z., Kleinberg L., Li M., Florenes V.A., Wang T.L., and Shih Ie M. Gene expression signatures differentiate ovarian/peritoneal serous carcinoma from diffuse malignant peritoneal mesothelioma. Clin. Cancer Res. 12 20 Pt 1 (2006) 5944-5950
11. Davis M.A., and Hanash S. High-throughput genomic technology in research and clinical management of breast cancer. Plasma-based proteomics in early detection and therapy. Breast Cancer Res. 8 6 (2006) 217
12. Frank D.E., and Carter W.G. Laminin 5 deposition regulates keratinocyte polarization and persistent migration. J. Cell Sci. 117 Pt 8 (2004) 1351-1363
13. Gu Q., Sivanandam T.M., and Kim C.A. Signal stability of Cy3 and Cy5 on antibody microarrays. Proteome Sci. 4 (2006) 21
14. Haab B.B., Dunham M.J., and Brown P.O. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2 2 (2001) research0004.1-0004.13
15. Han M.K., Hong M.Y., Lee D., Lee D.E., Noh G.Y., Lee J.H., Kim S.H., and Kim H.S. Expression profiling of proteins in L-threonine biosynthetic pathway of Escherichia coli by using antibody microarray. Proteomics 6 22 (2006) 5929-5940
16. Hanahan D., and Weinberg R.A. The hallmarks of cancer. Cell 100 1 (2000) 57-70
17. Hartwell L., Mankoff D., Paulovich A., Ramsey S., and Swisher E. Cancer biomarkers: a systems approach. Nat. Biotechnol. 24 8 (2006) 905-908
18. Hellstrom I., Raycraft J., Hayden-Ledbetter M., Ledbetter J.A., Schummer M., McIntosh M., Drescher C., Urban N., and Hellstrom K.E. The HE4 (WFDC2) protein is a biomarker for ovarian carcinoma. Cancer Res. 63 13 (2003) 3695-3700
19. Ko I.K., Kato K., and Iwata H. Antibody microarray for correlating cell phenotype with surface marker. Biomaterials 26 6 (2005) 687-696
20. Lau A.T., and Chiu J.F. The possible role of cytokeratin 8 in cadmium-induced adaptation and carcinogenesis. Cancer Res. 67 5 (2007) 2107-2113
21. Lim R., Ahmed N., Borregaard N., Riley C., Wafai R., Thompson E.W., Quinn M.A., and Rice G.E. Neutrophil gelatinase-associated lipocalin (NGAL) an early-screening biomarker for ovarian cancer: NGAL is associated with epidermal growth factor-induced epithelio-mesenchymal transition. Int. J. Cancer 120 11 (2007) 2426-2434
22. Liu J., Guo Q., Chen B., Yu Y., Lu H., and Li Y.Y. Cathepsin B and its interacting proteins, bikunin and TSRC1, correlate with TNF-induced apoptosis of ovarian cancer cells OV-90. FEBS Lett. 580 1 (2006) 245-250
23. MacBeath G., and Schreiber S.L. Printing proteins as microarrays for high throughput function determination. Science 289 5485 (2000) 1760-1763
24. McIntosh M.W., Drescher C., Karlan B., Scholler N., Urban N., Hellstrom K.E., and Hellstrom I. Combining CA 125 and SMR serum markers for diagnosis and early detection of ovarian carcinoma. Gynecol. Oncol. 95 1 (2004) 9-15
25. McIntosh M.W., Liu Y., Drescher C., Urban N., and Diamandis E.P. Validation and characterization of human kallikrein 11 as a serum marker for diagnosis of ovarian carcinoma. Clin. Cancer Res. 13 15 (2007) 4422-4428
26. Miller J.C., Zhou H., Kwekel J., Cavallo R., Burke J., Butler E.B., The B.S., and Haab B.B. Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics 3 1 (2003) 56-63
27. Mor G., Visintin I., Lai Y., Zhao H., Schwartz P., Rutherford T., Yue L., Bray-Ward P., and Ward D.C. Serum protein markers for early detection of ovarian cancer. Proc. Natl. Acad. Sci. U.S.A. 102 21 (2005) 7677-7682
28. Moubayed N., Weichenthal M., Harder J., Wandel E., Sticherling M., and Glaser R. Psoriasin (S100A7) is significantly up-regulated in human epithelial skin tumours. J. Cancer Res. Clin. Oncol. 133 4 (2007) 253-261
29. Orchekowski R., Hemelinck D., Li L., Gliwa E., vanBrocklin M., Marrero J.A., Vande Woude G.F., Feng Z., Brand R., and Haab B.B. Antibody microarray profiling reveals individual and combined serum proteins associated with pancreatic cancer. Cancer Res. 65 23 (2005) 11193-11202
30. Peluso P., Wilson D.S., Do D., Tran H., Venkatasubbaiah M., Quincy D., Heidecker B., Poindexter K., Tolani N., Phelan M., et al. Optimizing antibody immobilization strategies for the construction of protein microarrays. Anal. Biochem. 312 2 (2003) 113-124
31. Pepe M.S., Janes H., Longton G., Leisenring W., and Newcomb P. Limitations of the odds ratio in gauging the performance of a diagnostic, prognostic, or screening marker. Am. J. Epidemiol. 159 9 (2004) 882-890
32. Smyth G.K. Limma: linear models for microarray data. In: Gentleman R., Carey V., Dudoit S., Irizarry R., and Huber W. (Eds). Bioinformatics and Computational Biology Solutions using R and Bioconductor (2005), Springer, New York 397-420
33. Smyth G.K., and Speed T. Normalization of cDNA microarray data. Methods 31 4 (2003) 265-273
34. Sreekumar A., Nyati M.K., Varambally S., Barrette T.R., Ghosh D., Lawrence T.S., and Chinnaiyan A.M. Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res. 61 20 (2001) 7585-7593
35. States D.J., Omenn G.S., Blackwell T.W., Fermin D., Eng J., Speicher D.W., and Hanash S.M. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol. 24 3 (2006) 333-338
36. Steinhauer C., Wingren C., Khan F., He M., Taussig M.J., and Borrebaeck C.A. Improved affinity coupling for antibody microarrays: engineering of double-(His)6-tagged single framework recombinant antibody fragments. Proteomics 6 15 (2006) 4227-4234
37. Storey J.D. The positive false discovery rate: a Bayesian interpretation and the q-value. Ann. Statist. 31 (2003) 2013-2035
38. Storey J.D., Taylor J.E., and Siegmund D. Strong control, conservative point estimation, and simultaneous conservative consistency of false discovery rates: a unified approach. J. Roy. Statist. Soc. Ser. B. 66 (2004) 187-205
39. Subramanian A., Tamayo P., Mootha V.K., Mukherjee S., Ebert B.L., Gillette M.A., Paulovich A., Pomeroy S.L., Golub T.R., Lander E.S., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U.S.A. 102 43 (2005) 15545-15550
40. Treiber M., Schulz H.U., Landt O., Drenth J.P., Castellani C., Real F.X., Akar N., Ammann R.W., Bargetzi M., Bhatia E., et al. Keratin 8 sequence variants in patients with pancreatitis and pancreatic cancer. J. Mol. Med. 84 12 (2006) 1015-1022
41. Usui-Aoki K., Shimada K., and Koga H. A novel antibody microarray format using non-covalent antibody immobilization with chemiluminescent detection. Mol. Biosyst. 3 1 (2007) 36-42
42. Vitzthum F., Behrens F., Anderson N.L., and Shaw J.H. Proteomics: from basic research to diagnostic application. A review of requirements & needs. J. Proteome Res. 4 4 (2005) 1086-1097
43. Wacker R., Schroder H., and Niemeyer C.M. Performance of antibody microarrays fabricated by either DNA-directed immobilization, direct spotting, or streptavidin-biotin attachment: a comparative study. Anal. Biochem. 330 2 (2004) 281-287
44. Whiteaker J.R., Zhang H., Eng J.K., Fang R., Piening B.D., Feng L.C., Lorentzen T.D., Schoenherr R.M., Keane J.F., Holzman T., Fitzgibbon M., Lin C., Zhang H., Cooke K., Liu T., Camp II D.G., Anderson L., Watts J., Smith R.D., McIntosh M.W., and Paulovich A.G. Head-to-head comparison of serum fractionation techniques. J. Proteome Res. 6 2 (2007) 828-836
45. Witton C.J., Reeves J.R., Going J.J., Cooke T.G., and Bartlett J.M. Expression of the HER1-4 family of receptor tyrosine kinases in breast cancer. J. Pathol. 200 3 (2003) 290-297