Genetic expression profiling of parotid neoplasms by cDNA microarrays

Abstract

Differentially expressed genes in various benign and malignant salivary gland tumours were identified by use of cDNA microarrays containing 19,000 human expressed sequence tags. Samples were derived from 5 patients with pleomorphic adenoma, 4 with Warthin's tumour, one with clear cell carcinoma, and 2 with mucoepidermoid carcinoma. Tumours were classified by using a subset of 486 genes. Benign Warthin's tumour and pleomorphic adenoma showed very distinctive gene expression patterns. A total of 133 genes differentiated the single malignant clear cell carcinoma from non-tumour salivary glands (p < 0.01), whereas only 16 genes separated it from the highly related benign pleomorphic adenoma (p < 0.01). A total of 57 cDNAs were associated with mucoepidermoid carcinoma (p < 0.01). The results show gene expression alterations common to all tumours and unique to each benign and malignant tumour. The numerous Expressed Sequence Tags of unknown function we identified could also become useful as tumour markers and represent a set of novel tumour-associated genes.

Fig. 1

Clustering of 713 spotted cDNA probes corresponding to 486 Unigene clusters, selected by t test, that were differentially expressed in salivary gland tumours (p < 0.01, mean t test significant spots in bootstrap, 80.4; pFDR, 0.04). Rows, cDNA probes; columns, individual patient samples. Dark grey: probe over–expression; light grey: under–expression.

Fig. 2

Clones with expression patterns coherent to prominent tumour–associated genes, selected by using similarity search with Euclidean distances on variance normalized expression patterns.