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Gene Expression Profiling with DNA Microarrays

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Biomarkers in Breast Cancer

Part of the book series: Cancer Drug Discovery and Development ((CDD&D))

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Abstract

DNA microarrays are small solid supports on the surface of which DNA probes for thousands of genes have been orderly arrayed. Hybridization of labeled RNA from tissues or tumors allows evaluation of the relative amount of any specific mRNA present in the samples, depicting its gene expression profile. During development and progression of breast cancers, specific genetic programs are activated, which can be assayed on DNA microarrays. Studies performed so far show that the gene expression profile of a tumor defines its biology, its invasive and metastatic potential, and its responsiveness to treatments. Classification of breast cancer by expression profiling appears a very powerful approach, outperforming all commonly used methods of classification. However, much work has to be done before microarray will give robust information for clinical decisions and become routine practice.

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References

  1. White KP, Rifkin SA, Hurban P, Hogness DS. Microarray analysis of Drosophila development during metamorphosis. Science 1999;286:2179–2184.

    Article  PubMed  CAS  Google Scholar 

  2. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. The transcriptional program of sporulation in budding yeast. Science 1998;282:699–705. Erratum in: Science 1998;282:1421.

    Article  PubMed  CAS  Google Scholar 

  3. Lockhart DJ, IWinzeler EA. Genomics, gene expression and DNA arrays. Nature 2000;405:827–836.

    Article  PubMed  CAS  Google Scholar 

  4. Young RA. Biomedical discovery with DNA arrays. Cell 2000;102:9–15.

    Article  PubMed  CAS  Google Scholar 

  5. Phimister B, ed. The chipping forecast. Nat Genet 1999;21(Suppl):1–60.

    Google Scholar 

  6. Hughes TR, Shoemaker DD. DNA microarrays for expression profiling. Curr Opin Chem Biol 2001;5:21–25.

    Article  PubMed  CAS  Google Scholar 

  7. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression pattern with a complementary DNA microarray. Science 1995;270:467–470.

    Article  PubMed  CAS  Google Scholar 

  8. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 1991;251:767–773.

    Article  PubMed  CAS  Google Scholar 

  9. Blanchard AP, Kaiser RJ, Hood LE. High-density oligonucleotide arrays. Biosens Bioelectr 1996;6/7:687–690.

    Article  Google Scholar 

  10. Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM. High-fidelity mRNA amplification for expression profiling. Nat Biotechnol 2000;18:457–459.

    Article  PubMed  CAS  Google Scholar 

  11. Sotiriou C, Powles TJ, Dowsett M, et al. Gene expression profiles derived from fine needle aspiration correlate with response to systemic chemotherapy in breast cancer. Breast Cancer Res 2002;4:R3(1–8).

    Article  Google Scholar 

  12. Ma XJ, Salunga R, Tuggle JT, et al. Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci USA 2003;100:5974–5979.

    Article  PubMed  CAS  Google Scholar 

  13. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003;100:9440–9445.

    Article  PubMed  CAS  Google Scholar 

  14. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998;95:14863–14868.

    Article  PubMed  CAS  Google Scholar 

  15. Perou CM, Jeffrey SS, van de Rijn M, et al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA 1999;96:9212–9217.

    Article  PubMed  CAS  Google Scholar 

  16. Perou CM, Sorlie T, Eisen MB, et al. Molecular portraits of human breast tumours. Nature 2000;406:747–752.

    Article  PubMed  CAS  Google Scholar 

  17. Liu ET. Classification of cancers by expression profiling. Curr Opin Genet Dev 2003;13:97–103.

    Article  PubMed  CAS  Google Scholar 

  18. Desai KV, Xiao N, Wang W, et al. Initiating oncogenic event determines gene-expression patterns of human breast cancer models. Proc Natl Acad Sci USA 2002;99:6967–6972.

    Article  PubMed  CAS  Google Scholar 

  19. Shan L, He M, Yu M, Qiu C, Lee NH, Liu ET, Snyderwine EG. cDNA microarray profiling of rat mammary gland carcinomas induced by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine and 7,12-dimethylbenz[a] anthracene. Carcinogenesis 2002;23:1561–1568.

    Article  PubMed  CAS  Google Scholar 

  20. Pollack JR, Sorlie T, Perou CM, et al. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 2002;99:12963–12968.

    Article  PubMed  CAS  Google Scholar 

  21. Hyman E, Kauraniemi P, Hautaniemi S, et al. Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res 2002;62:6240–6245.

    PubMed  CAS  Google Scholar 

  22. van’t Veer LJ, Dai H, van de Vijver MJ, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002;415:530–536.

    Article  Google Scholar 

  23. Pusztai L, Ayers M, Stec J, et al. Gene expression profiles obtained from fine-needle aspirations of breast cancer reliably identify routine prognostic markers and reveal large-scale molecular differences between estrogen-negative and estrogen-positive tumors. Clin Cancer Res 2003;9:2406–2415.

    PubMed  CAS  Google Scholar 

  24. Sorbello V, Fuso L, Sfiligoi C, et al. Quantitative real-time RT-PCR analysis of eight novel estrogen-regulated genes in breast cancer. Int J Biol Markers 2003;18:123–129.

    PubMed  CAS  Google Scholar 

  25. Dressman MA, Baras A, Malinowski R, et al. Gene expression profiling detects gene amplification and differentiates tumor types in breast cancer. Cancer Res 2003;63:2194–2199.

    PubMed  CAS  Google Scholar 

  26. Kumar-Sinha C, Ignatoski KW, Lippman ME, Ethier SP, Chinnaiyan AM. Transcriptome analysis of HER2 reveals a molecular connection to fatty acid synthesis. Cancer Res 2003;63:132–139.

    PubMed  CAS  Google Scholar 

  27. Hedenfalk I, Duggan D, Chen Y, et al. Gene-expression profiles in hereditary breast cancer. N Engl J Med 2001;344:539–548.

    Article  PubMed  CAS  Google Scholar 

  28. Hedenfalk I, Ringner M, Ben-Dor A, et al. Molecular classification of familial non-BRCA1/BRCA2 breast cancer. Proc Natl Acad Sci USA 2003;100:2532–2537.

    Article  PubMed  CAS  Google Scholar 

  29. Sorlie T, Perou CM, Tibshirani R, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001;98:10869–10874.

    Article  PubMed  CAS  Google Scholar 

  30. van de Vijver MJ, He YD, van’t Veer LJ, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002;347:1999–2009.

    Article  PubMed  Google Scholar 

  31. van’t Veer LJ, Dai H, van de Vijver MJ, et al. Expression profiling predicts outcome in breast cancer. Breast Cancer Res 2002;5:57–58.

    Article  Google Scholar 

  32. Omoto Y, Hayashi S. A study of estrogen signaling using DNA microarray in human breast cancer. Breast Cancer 2002;9:308–311.

    Article  PubMed  Google Scholar 

  33. Inoue A, Yoshida N, Omoto Y, et al. Development of cDNA microarray for expression profiling of estrogen-responsive genes. J Mol Endocrinol 2002;29:175–192.

    Article  PubMed  CAS  Google Scholar 

  34. Bouras T, Southey MC, Chang AC, et al. Stanniocalcin 2 is an estrogen-responsive gene coexpressed with the estrogen receptor in human breast cancer. Cancer Res 2002;62:1289–1295.

    PubMed  CAS  Google Scholar 

  35. Levenson AS, Kliakhandler IL, Svoboda KM, et al. Molecular classification of selective oestrogen receptor modulators on the basis of gene expression profiles of breast cancer cells expressing oestrogen receptor alpha. Br J Cancer 2002;87:449–456.

    Article  PubMed  CAS  Google Scholar 

  36. Cicatiello L, Scafoglio C, Altucci L, et al. A genomic view of estrogen actions in human breast cancer cells by expression profiling of the hormone responsive transcriptome. J Mol Endocrinol 2004;32:719–795.

    Article  PubMed  CAS  Google Scholar 

  37. Assersohn L, Gangi L, Zhao Y, et al. The feasibility of using fine needle aspiration from primary breast cancers for cDNA microarray analyses. Clin Cancer Res 2002;8:794–801.

    PubMed  CAS  Google Scholar 

  38. Kim H, Zhao B, Snesrud EC, Haas BJ, Town CD, Quackenbush J. Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses. BioTechniques 2002;33:924–930.

    PubMed  CAS  Google Scholar 

  39. Puskas LG, Zvara A, Hackler L Jr, Micsik T, van Hummelen P. Production of bulk amounts of universal RNA for DNA microarrays. BioTechniques 2002;33:898–900, 902, 904.

    PubMed  CAS  Google Scholar 

  40. Dudley AM, Aach J, Steffen MA, Church GM. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc Natl Acad Sci USA 2002;99:7554–7559.

    Article  PubMed  CAS  Google Scholar 

  41. Lee PD, Sladek R, Greenwood CM, Hudson TJ. Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Res 2002;12:292–297.

    Article  PubMed  CAS  Google Scholar 

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© 2006 Humana Press Inc., Totowa, NJ

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De Bortoli, M., Biglia, N. (2006). Gene Expression Profiling with DNA Microarrays. In: Gasparini, G., Hayes, D.F. (eds) Biomarkers in Breast Cancer. Cancer Drug Discovery and Development. Humana Press. https://doi.org/10.1385/1-59259-915-X:047

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