DNA hybridization arrays permit global gene expression profiling to be done in a single experiment. The evolution and challenges of DNA hybridization arrays are reflected in the variety of experimental platforms, probe composition, hybridization/signal detection methods, and bioinformatic interpretation. In tumor biology, DNA hybridization arrays are being used for gene/gene pathway discovery, diagnosis, and therapeutic design. Similar applications are advancing our understanding of oral cancer cell biology.
Get full access to this article
View all access options for this article.
References
1.
Alevizos I, Mahdevappa M, Ohyama H, Zhang X, Kohno Y, Colevas D, et al. -2001-. Head and neck/oral cancer gene expression profiling assisted by laser capture microdissection and GeneChip analysis. Oncogene20:6196–6204.
2.
Aschary MP, Jaggernauth W, Gross E, Alfieri A, Klinger HP, Vikram B -2000-. Cell lines from the same cervical carcinoma but with different radiosensitivities exhibit different cDNA microarray patterns of gene expression. Cytogenet Cell Genet91:39–43.
3.
Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, et al. -2000-. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA97:262–267.
4.
Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS -2000-. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci USA97:12182–12186.
5.
Calaluce R, Kunkel MW, Watts GS, Schmelz M, Hao J, Barrera J, et al. -2001-. Lamin-5-mediated gene expression in human prostate carcinoma cells. Mol Carcinog30:119–129.
6.
Califano J, van der Riet P, Westra W, Nawroz H, Clayman G, Piantadosi S, et al. -1996-. Genetic progression model for head and neck cancer: implications for field cancerization. Cancer Res56:2488–2492.
7.
Califano A, Stolovitzky G, Tu Y -2000-. Analysis of gene expression microarrays for phenotype classification. Proc Int Conf Intell Syst Mol Biol8:75–85.
8.
Chang DD, Park NH, Denny CT, Nelson SF, Pe M -1998-. Characterization of transformation related genes in oral cancer cells. Oncogene16:1921–1930.
9.
Clark EA, Golub TR, Lander ES, Hynes RO -2000-. Genomic analysis of metastasis reveals an essential role for RhoC. Nature406:532–535.
10.
Coller HA, Grandori C, Tamayo P, Colbert T, Lander ES, Eisenman RN, et al. -2000-. Expression analysis with oligonucleotide microarrays reveals that Myc regulates genes involved in growth, cell cycle, signaling, and adhesion. Proc Natl Acad Sci USA97:3260–3265.
11.
DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, et al. -1996-. Use of a cDNA microarray to analyze gene expression patterns in human cancer. Nat Genet14:457–460.
12.
Duan Z, Feller AJ, Penson RT, Chabner BA, Seiden MV -1999-. Discovery of differentially expressed genes associated with paclitaxel resistance using cDNA array technology: analysis of interleukin -IL- 6, IL-8, and monocyte chemotactic protein 1 in the paclitaxel-resistant phenotype. Clin Cancer Res5:3445–3453.
13.
Edman CF, Raymond DE, Wu DJ, Tu E, Sosnowski RG, Butler WF, et al. -1997-. Electric field directed nucleic acid hybridization on microchips. Nucleic Acids Res25:4907–4914.
14.
Emmert-Buck MR, Strausberg RL, Krizman DB, Bonaldo MF, Bonner RF, Bostwick DG, et al. -2000-. Molecular profiling of clinical tissues specimens: feasibility and applications. J Mol Diagn2:60–66.
15.
Fend F, Raffeld M -2000-. Laser capture microdissection in pathology. J Clin Pathol53:666–672.
16.
Freeman WM, Robertson DJ, Vrana KE -2000-. Fundamentals of DNA hybridization arrays for gene expression analysis. BioTechniques29:1042–1055.
17.
Golub TR, Slonin DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov CP, et al. -1999-. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science286:531–537.
18.
Hanna E, Shrieve DC, Ratanatharathorn V, Xia X, Breau R, Suen J, et al. -2001-. A novel alternative approach for prediction of radiation response of squamous cell carcinoma of the head and neck. Cancer Res61:2376–2380.
19.
He YD, Friend SH -2001-. Microarrays—the 21st century divining rod? Nat Med7:658–659.
20.
Heller MJ, Forster AH, Tu E -2000-. Active microelectronic chip devices which utilize controlled electrophoretic fields for multiplex DNA hybridization and other genomic applications. Electrophoresis21:157–164.
21.
Hippo Y, Yashiro M, Ishii M, Taniguchi H, Tsutsumi S, Hirakawa K, et al. -2001-. Differential gene expression profiles of scirrhous gastric cancer cells with high metastatic potential to peritoneum or lymph nodes. Cancer Res61:889–895.
22.
Hughes TR, Marton MJ, Jones AR, Roberts CJ, Soughton R, Armour CD, et al. -2000-. Functional discovery via a compendium of expression profiles. Cell102:109–126.
23.
Khan J, Wei JS, Ringner M, Saal LH, Ladanyi M, Westermann F, et al. -2001-. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med7:673–679.
24.
Leethanakul C, Patel V, Gillespie J, Pallente M, Ensley JF, Koontongkaew S, et al. -2000-. Distinct pattern of expression of differentiation and growth-related genes in squamous cell carcinomas of the head and neck revealed by the use of laser capture microdissection and cDNA arrays. Oncogene19:3220–3224.
25.
Luo L, Salunga RC, Guo H, Bittner A, Joy KC, Galindo JE, et al. -1999-. Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat Med5:117–122.
26.
Manos EJ, Jones DA -2001-. Assessment of tumor necrosis factor receptor and Fas signaling pathways by transcriptional profiling. Cancer Res61:433–438.
27.
Mao L -1997-. Leukoplakia: molecular understanding of pre-malignant lesions and implications for clinical management. Mol Med3:442–448.
28.
Muller H, Bracken AP, Vernell R, Moroni MC, Christians F, Grassilli E, et al. -2000-. E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis. Genes Dev15:267–285.
29.
Nees M, Geoghegan JM, Hyman T, Frank S, Miller L, Woodworth CD -2001-. Papillomavirus type 16 oncogenes downregulate expression of interferon-responsive genes and upregulate proliferation-associated and NF-kappa b-responsive genes in cervical keratinocytes. J Virol75:4283–4296.
30.
Ohyama H, Zhang X, Kohno Y, Alevizos I, Posner M, Wong DT, et al. -2000-. Laser capture microdissection-generated target sample for high-density oligonucleotide array hybridization. Biotechniques29:530–536.
31.
Parkin DM, Pisani P, Fernlay J -1999-. Global cancer statistics. CA Cancer J Clin49:33–64.
32.
Rajeevan MS, Dimulescu IM, Unger ER, Vernon SD -1999-. Chemiluminescent analysis of gene expression on high-density filter arrays. J Histochem Cytochem47:337–342.
33.
Ricci MS, El-Deiry WS -2000-. Novel strategies for therapeutic design in molecular oncology using gene expression profiles. Curr Opin Mol Ther2:682–690.
34.
Sherlock G -2000-. Analysis of large-scale gene expression. Curr Opin Immunol12:201–205.
35.
Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, et al. -1999-. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA96:2907–2912.
36.
Todd R, Gutkind JS, Shillitoe EJ, Wong DT -2001-. Solid tumors: microarray analysis of oral cancers. In: Microarrays in cancer research. Wong DT, Todd R, Warrington J, editors. Natick, MA: Eaton Press -in press-.
37.
Toronen P, Kolehmainen M, Wong C, Castren E -1999-. Analysis of gene expression data using self-organizing maps. FEBS Lett451:142–146.
38.
Vikhanskaya F, Marchini S, Marabese M, Galliera E, Broggini M -2001-. p73a overexpression is associated with resistance to treatment with DNA-damaging agents in a human ovarian cancer cell line. Cancer Res61:935–938.
39.
Villaret DB, Wang T, Dillon D, Xu J, Sivam D, Cheever MA, et al. -2000-. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope110:374–381.
40.
Young RA -2000-. Biomedical discovery with DNA arrays. Cell102:9–15.
