Quantitative real-time PCR analysis of degradome gene expression

The Cancer Degradome: Proteases and Cancer Biology

Volumn , Issue , 2008, Pages 49-65

  Pennington, Caroline J ^a   Nuttall, Robert K ^a   Sampieri Ramirez, Clara ^a   Wallard, Matthew ^a   Pilgrim, Simon ^a   Edwards, Dylan R ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 72749110556     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-69057-5_4     Document Type: Chapter

References (39)

1. Bhatia P., Taylor W. R., et al. (1994). Comparison of glyceraldehyde-3-phosphate dehydrogenase and 28S-ribosomal RNA gene expression as RNA loading controls for northern blot analysis of cell lines of varying malignant potential. Anal Biochem 216(1): 223-6.
2. Bustin S. A., and Nolan T. (2004). Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J Biomol Tech 15(3): 155-66.
3. Bustin S. A., Benes V., et al. (2005). Quantitative real-time RT-PCR-A perspective. J Mol Endocrinol 34(3): 597-601.
4. Curry J., McHale et al. (2002). Low efficiency of the Moloney murine leukemia virus reverse transcriptase during reverse transcription of rare t(8;21) fusion gene transcripts. Biotechniques 32(4): 768, 770, 772, 754-5.
5. Eisen M. B., Spellman P. T., et al. (1998). Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95(25): 14863-8.
6. Goldsworthy S. M., Goldsworthy T. L., et al. (1993). Variation in expression of genes used for normalization of Northern blots after induction of cell proliferation. Cell Prolif 26(6): 511-8.
7. Hamalainen H. K., Tubman J. C. et al. (2001). Identification and validation of endogenous reference genes for expression profiling of T helper cell differentiation by quantitative realtime RT-PCR. Anal Biochem 299(1): 63-70.
8. Jones G. C., Corps A. N., et al. (2006). Expression profiling of metalloproteinases and tissue inhibitors of metalloproteinases in normal and degenerate human achilles tendon. Arthritis Rheum 54(3): 832-42.
9. Karrer E. E., Lincoln J. E., et al. (1995). In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries. Proc Natl Acad Sci USA 92(9): 3814-8.
10. Morimoto A. M., Tan N., et al. (2004). Gene expression profiling of human colon xenograft tumors following treatment with SU11248, a multitargeted tyrosine kinase inhibitor. Oncogene 23(8): 1618-26.
11. Nolan T., Hands R. E., et al. (2006a). Quantification of mRNA using real-time RT-PCR. Nat Protoc 1(3): 1559-82.
12. Nolan T., Hands R. E., et al. (2006b). SPUD: a quantitative PCR assay for the detection of inhibitors in nucleic acid preparations. Anal Biochem 351(2): 308-10.
13. Nuttall R. K., Pennington C. 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): 333-45.
14. Nuttall R. K., Sampieri C. L., et al. (2004). Expression analysis of the entire MMP and TIMP gene families during mouse tissue development. FEBS Letters 563: 129-134.
15. Nuttall R. K., Silva C., et al. (2007). Metalloproteinases are enriched in microglia compared with leukocytes and they regulate cytokine levels in activated microglia. Glia 55(5): 516-26.
16. Overall C. M., Wrana J. L., et al. (1991). Transcriptional and post-transcriptional regulation of 72-kDa gelatinase/type IV collagenase by transforming growth factor-beta 1 in human fibroblasts. Comparisons with collagenase and tissue inhibitor of matrix metalloproteinase gene expression. J Biol Chem 266(21): 14064-71.
17. Overbergh L., Giulietti A., et al. (2003). The use of real-time reverse transcriptase PCR for the quantification of cytokine gene expression. J Biomol Tech 14(1): 33-43.
18. Paule M. R., and White R. J. (2000). Survey and summary: transcription by RNA polymerases I and III. Nucleic Acids Res 28(6): 1283-98.
19. Pedersen T. X., Pennington C. J., et al. (2005). Extracellular protease mRNAs are predominantly expressed in the stromal areas of microdissected mouse breast carcinomas. Carcinogenesis 26(7): 1233-40.
20. Porter S., Scott S. D., et al. (2004). Dysregulated expression of adamalysin-thrombospondin genes in human breast carcinoma. Clin Cancer Res 10(7): 2429-40.
21. Porter S., Span P. N., et al. (2006). ADAMTS8 and ADAMTS15 expression predicts survival in human breast carcinoma. Int J Cancer 118(5): 1241-7.
22. Riddick A. C. P., Shukla C. J., et al. (2005). Identification of degradome components associated with prostate cancer prostate cancer progression by expression analysis of human prostatic tissues. Br. J. Cancer 92: 2171-2180.
23. Rozen S., and Skaletsky H. (2000). Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-86.
24. Sambrook J., MacCullum P., Russell D. (2001). Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press.
25. Schmittgen T. D., and Zakrajsek B. A. (2000). Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR. J Biochem Biophys Methods 46(1-2): 69-81.
26. Schoor O., Weinschenk T., et al. (2003). Moderate degradation does not preclude microarray analysis of small amounts of RNA. Biotechniques 35(6): 1192-6, 1198-201.
27. Schroeder A., Mueller O., et al. (2006). The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 7: 3.
28. Solanas M., Moral R., et al. (2001). Unsuitability of using ribosomal RNA as loading control for Northern blot analyses related to the imbalance between messenger and ribosomal RNA content in rat mammary tumors. Anal Biochem 288(1): 99-102.
29. Sotiriou C., and Piccart M. J. (2007). Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care? Nat Rev Cancer 7(7): 545-53.
30. Stahlberg A., Hakansson J., et al. (2004a). Properties of the reverse transcription reaction in mRNA quantification. Clin Chem 50(3): 509-15.
31. Stahlberg A., Kubista M., et al. (2004b). Comparison of reverse transcriptases in gene expression analysis. Clin Chem 50(9): 1678-80.
32. Stangegaard M., Dufva I H., et al. (2006). Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA. Biotechniques 40(5): 649-57.
33. Vandesompele J., De Preter K., et al. (2002). Accurate normalization of real-time quantitative RTPCR data by geometric averaging of multiple internal control genes. Genome Biol 3(7): RESEARCH0034.
34. Wall S. J., and Edwards D. R. (2002). Quantitative reverse transcription-polymerase chain reaction (RT-PCR): a comparison of primer-dropping, competitive, and real-time RT-PCRs. Anal Biochem 300(2): 269-73.
35. Wallard M. J., Pennington C. J., et al. (2006). Comprehensive profiling and localisation of the matrix metalloproteinases in urothelial carcinoma. Br J Cancer 94(4): 569-77.
36. Wang X., and Seed B. (2003). A PCR primer bank for quantitative gene expression analysis. Nucleic Acids Res 31(24): e154.
37. Young D. A., Phillips B. W., et al. (2002). Identification of an initiator-like element essential for the expression of the tissue inhibitor of metalloproteinases-4 (Timp-4) gene. Biochem J 364 (Pt. 1): 89-99.
38. Zhang J., and Byrne C. D. (1999). Differential priming of RNA templates during cDNA synthesis markedly affects both accuracy and reproducibility of quantitative competitive reverse-transcriptase PCR. Biochem J 337 (Pt. 2): 231-41.
39. Zhong H., and Simons J. W. (1999). Direct comparison of GAPDH, beta-Actin, cyclophilin, and 28S rRNA as internal standards for quantifying RNA levels under hypoxia. Biochem Biophys Res Commun 259(3): 523-6