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DNA Hybridization Arrays for Gene Expression Analysis of Human Oral Cancer

¹ Laboratory of Oral & Maxillofacial Surgery, Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA 02115, and Massachusetts General Hospital, 1 Fruit Street, Boston, MA 02114; and
² Laboratory of Molecular Pathology, Division of Oral Pathology, Department of Oral Medicine and Diagnostic Sciences, Harvard School of Dental Medicine, Boston, MA 02115;

View larger version (58K): [in a new window]   Figure 1. Array platforms. (A) Macroarrays use nucleic acid probes deposited on membrane filters. Samples are usually radioactively labeled and hybridized in parallel. Detection is performed either through autoradiography or phosphorimaging. (B) Microarrays are formated on glass or plastic. Fluorescently labeled control and experimental samples are hybridized to the array in a competitive manner. Detection is performed by means of a fluorescent scanner. (C) High-density oligonucleotide arrays use photolithographically synthesized probes on a silicon matrix. Due to the limited length and specificity of the probes, a mismatch pair is added to determine specific hybridization. (D) Microelectronic arrays are an emerging technology that uses an electric field generated by individually controllable electrodes to immobilize probes and to control target hybridization. Washing is accomplished by reversing the electric fields. (Reproduced with permission from Freeman et al., 2000)

View larger version (119K): [in a new window]   Figure 2. Laser-capture microdissection. (Panel A) Oral cancers commonly present as white or red-white mucosal lesions. They can be exophytic, endophytic, or a combination of the two. (Panel B) While advanced oral cancers can be several centimeters in size, many oral cancers present as lesions that are millimeters in diameter and are frequently overlooked. (Panel C) Like other cancers, oral cancers have heterogeneous cell populations in addition to the malignant epithelium (ME): connective tissues/fibroblasts (CT), vascular epithelium (VE), and acute/chronic inflammatory infiltrate (INFL). (Panel D) Laser-capture microdissection allows for the isolation and transfer of malignant oral epithelium (inset) for DNA, RNA, and protein studies. (Reproduced with permission from Todd et al., 2001)

View larger version (85K): [in a new window]   Figure 3. Computational tools to display gene expression profile data of five-paired cases of oral cancer. (A) Scatter plot identifies outlying genes between normal and malignant oral keratinocytes. (B) Hierarchical cluster analysis done on intensity values standardized by dividing by root mean square. Cosine correlation of similarity coefficient and complete linkage clustering classified the samples as shown. Normal ‘A’; Tumor ‘B’. (C) Self-organizing map (SOM) group expressed genes into co-expressed clusters (GeneCluster). (D) Principal component analysis (PCA) identifies the most significant expression patterns in all the genes examined. (E, F) Screen shoot of GeneSpring displays of selected gene expression (E, ß-actin; F, GRO1), comparing normal and tumor oral keratinocyte expression. Note that expression of ß-actin is relatively similar between normal and tumor specimens as well as between samples. GRO1, on the other hand, is dramatically overexpressed in malignant oral keratinocytes.