title: Gene expression alterations over large chromosomal regions in cancers include multiple genes unrelated to malignant progression.
abstract: In solid tumors, the relationship between DNA copy number and global expression over large chromosomal regions has not been systematically explored. We used a 12,626-gene expression array analysis of head and neck squamous cell carcinoma and normal oral mucosa and annotated gene expression levels to specific chromosomal loci. Expression alterations correlated with reported data using comparative genomic hybridization. When genes with significant differences in expression between normal and malignant lesions, as defined by significance analysis of microarrays (SAM), were compared to nonsignificant genes, similar chromosomal patterns of alteration in expression were noted. Individual tumors underwent microsatellite analysis and chi(2) analysis of expression at 3p and 22q. Significant 3p underexpression and 22q overexpression were found in all primary tumors with 3p and 22q allelic imbalance, respectively, whereas no tumor without allelic imbalance on these chromosomal arms demonstrated expression differences. Loss and gain of chromosomal material in solid cancers can alter gene expression over large chromosomal regions, including multiple genes unrelated to malignant progression.
authors.affiliation: Department of Otolaryngology-Head and Neck Surgery, Head and Neck Cancer Research Division, Johns Hopkins Medical Institutions, 720 Rutland Avenue, Baltimore, MD 21205, USA.
authors.forename: Brett G
authors.initials: BG
authors.lastname: Masayesva
authors.forename: Patrick
authors.initials: P
authors.lastname: Ha
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Garrett-Mayer
authors.forename: Thomas
authors.initials: T
authors.lastname: Pilkington
authors.forename: Rong
authors.initials: R
authors.lastname: Mao
authors.forename: Jonathan
authors.initials: J
authors.lastname: Pevsner
authors.forename: Traci
authors.initials: T
authors.lastname: Speed
authors.forename: Nicole
authors.initials: N
authors.lastname: Benoit
authors.forename: Chul-So
authors.initials: CS
authors.lastname: Moon
authors.forename: David
authors.initials: D
authors.lastname: Sidransky
authors.forename: William H
authors.initials: WH
authors.lastname: Westra
authors.forename: Joseph
authors.initials: J
authors.lastname: Califano
mesh_terms: D022981:Allelic Imbalance; D016022:Case-Control Studies; D002877:Chromosomes, Human / Q000235:genetics*; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D002893:Chromosomes, Human, Pair 3 / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics; D018628:Gene Dosage; D015870:Gene Expression; D020869:Gene Expression Profiling; D006258:Head and Neck Neoplasms / Q000209:etiology / Q000235:genetics; D006801:Humans; D009369:Neoplasms / Q000209:etiology / Q000235:genetics*
chemical_list: D004273:DNA, Neoplasm