The CLIP-CHIP™: A focused oligonucleotide microarray platform for transcriptome analysis of the complete human and murine cancer degradomes

The Cancer Degradome: Proteases and Cancer Biology

Volumn , Issue , 2008, Pages 17-35

  Kappelhoff, Reinhild ^a   Wilson, Claire H ^a   Overall, Christopher M ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 72749090432     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-69057-5_2     Document Type: Chapter

References (42)

1. Acuff H.B., Sinnamon M., Fingleton B., et al. (2006). Analysis of host-and tumor-derived proteinases using a custom dual species microarray reveals a protective role for stromal matrix metalloproteinase-12 in non-small cell lung cancer. Cancer Res. 6616:7968-7975.
2. Balbin M., Fueyo A., Tester A.M., et al. (2003). Loss of collagenase-2 confers increased skin tumor susceptibility to male mice. Nat. Genet. 35(3):252-257.
3. Barczak A., Rodriguez M.W., Hanspers K., et al. (2003). Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res. 13:1775-1785.
4. Barrett A.J., Rawlings N.D., and Woessner J.F. (1998). Handbook of proteolytic enzymes. San Diego: Academic Press.
5. Borgono C.A., and Diamandis E.P. (2004). The emerging roles of human tissue kallikreins in cancer. Nat. Rev. Cancer. 4(11):876-890.
6. Cheung V.G., Morley M., Aguilar F., et al. (1999). Making and reading microarrays. Nat. Genet. 21:15-19.
7. Churchill G.A. (2002). Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 32(Suppl):490-495.
8. Colebatch G., Trevaskis B., and Udvardi M. (2002). Functional genomics: Tools of the trade. New Phytol. 153:27-36.
9. Dean R.A., and Overall C.M. (2007). Proteomics discovery of metalloproteinase substrates in the cellular context by iTRAQ labeling reveals a diverse MMP-2 substrate degradome. Mol. Cell. Proteomics 6(4):611-623.
10. Dean R.A., Butler G.S., Hamma-Kourbali Y., et al. (2007). Identification of candidate angiogenic inhibitors processed by MMP-2 in cell based proteomic screens: Disruption of VEGF/HARP (Pleiotrophin) and VEGF/CTGF angiogenic inhibitory complexes by MMP-2 proteolysis. Mol. Cell. Biol. 27(24):8454-65.
11. Egeblad M., and Werb Z. (2002). New functions for the matrix metalloproteinases in cancer progression. Nat. Rev. Cancer. 2(3):161-174.
12. Glas A.M., Floore A., Delahaye L.J., et al. (2006). Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics 7:278.
13. Gupta G.P., Nguyen D.X., Chiang A.C., et al. (2007). Mediators of vascular remodelling co-opted for sequential steps in lung metastasis. Nature 446(7137):765-770.
14. Jones G.C., Corps A.N., Pennington C.J., et al. (2006). Expression profiling of metalloproteinases and tissue inhibitors of metalloproteinases in normal and degenerate human achilles tendon. Arthritis Rheum. 54(3):832-842.
15. Kappelhoff R., and Overall C.M. (2007). The CLIP-CHIP2 oligonucleotide microarray: Dedicated array for analysis of all protease, nonproteolytic homolog, and inhibitor gene transcripts in human and mouse. Curr. Protoc. Protein Sci. 49:21.19.1-21.19.16.
16. Li M., Chen D., Shiloh A., et al. (2002). Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization. Nature 416(6881):648-653.
17. Lockhart D.J., Dong H., Byrne M.C., et al. (1996). Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14:1675-1680.
18. Loez-Ot?n C., and Matrisian L.M. (2007). Emerging roles of proteases in tumour suppression. Nat. Rev. Cancer. 7(10):800-808.
19. Loez-Ot?n C., and Overall C.M. (2002). Protease degradomics: A new challenge for proteomics. Nat. Rev. Mol. Cell Biol. 3:509-519.
20. Maindonald J.H., Pittelkow Y.E., and Wilson S.R. (2003). Some considerations for the design of microarray experiments. Sci. Stat. 40:367-390.
21. McQuibban G.A., Gong J.H., Tam E.M., et al. (2000). Inflammation dampened by gelatinase A cleavage of monocyte chemoattractant protein-3. Science 289(5482):1202-1206.
22. McQuibban G.A., Butler G.S., Gong J.H., et al. (2001). Matrix metalloproteinase activity inactivates the CXC chemokine stromal cell-derived factor-1. J. Biol. Chem. 276(47):43503-43508.
23. Minn A.J., Gupta G.P., Siegel P.M., et al. (2005a). Genes that mediate breast cancer metastasis to lung. Nature 436(7050):518-524.
24. Minn A.J., Kang Y., Serganova I., et al. (2005b). Distinct organ-specific metastatic potential of individual breast cancer cells and primary tumors. J. Clin. Invest. 115(1):44-55.
25. Nuttall R.K., Pennington C.J., Taplin J., et al. (2003). Elevated membrane-type matrix metalloproteinases in gliomas revealed by profiling proteases and inhibitors in human cancer cells. Mol. Cancer Res. 1(5):333-345.
26. Overall C.M., and Kleifeld O. (2006). Validating matrix metalloproteinases as drug targets and anti-targets for cancer therapy. Nat. Rev. Cancer. 6:227-239.
27. Overall C.M., Tam E.M., Kappelhoff R., et al. (2004). Protease degradomics: Mass spectrometry discovery of protease substrates and the CLIP-CHIP2, a dedicated DNA microarray of all human proteases and inhibitors. Biol. Chem. 385(6):493-504.
28. Pedersen T.X., Pennington C.J., Almholt K., et al. (2005). Extracellular protease mRNAs are predominantly expressed in the stromal areas of microdissected mouse breast carcinomas. Carcinogenesis 26(7):1233-1240.
29. Petersen D., Chandramouli G.V.R., Geoghegan J., et al. (2005). Three microarray platforms: An analysis of their concordance in profiling gene expression. BMC Genomics 6:63.
30. Puente X.S., Sa?chez L.M., Overall C.M., et al. (2003). Human and mouse proteases: a comparative genomic approach. Nat. Rev. Genet. 4:544-558.
31. Rawlings N.D., Morton F.R., Kok C.Y., Kong J. & Barrett, A.J. (2008). MEROPS: the peptidase database. Nucleic Acids Res. 36: D320-325.
32. Schwartz D.R., Moin K., Yao B., et al. (2007). Hu/Mu ProtIn oligonucleotide microarray: Dualspecies array for profiling protease and protease inhibitor gene expression in tumors and their microenvironment. Mol. Cancer Res. 5(5):443-454.
33. Smyth G.K., Yang Y.H., and Speed T. (2003). Statistical issues in cDNA microarray data analysis. Methods Mol. Biol. 224:111-136.
34. Tester A.M., Cox J.H., Connor A.R., et al. (2007). LPS responsiveness and neutrophil chemotaxis in vivo require PMN MMP-8 activity. PLoS ONE 2(3):e312.
35. Vergote D., Butler G.S., Ooms M., Cox J.H., Silva C., Hollenberg M.D., Jhamandas J.H., Overall C.M., Power C. (2006). Proteolytic processing of SDF-1a reveals a change in receptor specificity mediating HIV-Associated neurodegeneration. Proc. Natl. Acad Sci U S A. 103(50): 19182-7.
36. Vant Veer L.J., Dai H., van de Vijver M.J., et al. (2002). Gene expression profiling predicts clinical outcome of breast cancer. Nature 415(6871):530-536.
37. Weigelt B., Hu Z., He X., et al. (2005). Molecular portraits and 70-gene prognosis signature are preserved throughout the metastatic process of breast cancer. Cancer Res. 65(20):9155-9158.
38. Yang Y.H., and Speed T. (2002). Design issues for cDNA microarray experiments. Nat. Rev. 3:579-5888.
39. Yang Y.H., and Thorne N.P. (2003). Normalization for two-color cDNA microarray data. In: D.R. Goldstein (ed.), Science and Statistics: A Festschrift for Terry Speed, IMS Lecture Notes-Monograph Series, Volume 40, pp. 403-418.
40. Yang Y.H., Buckley M.J., and Speed T.P. (2001). Analysis of cDNA microarray images. Brief. Bioinform. 2(4):341-349.
41. Yang Y.H., Dudoit S., Luu P., et al. (2002). Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30:e15.
42. Yauk C.L., Berndt M.L., Williams A., et al. (2004). Comprehensive comparison of six microarray technologies. Nucleic Acids Res. 32:1-7