Gene expression alterations over large chromosomal regions in cancers include multiple genes unrelated to malignant progression

Brett G. Masayesva, Patrick Ha, Elizabeth Garrett-Mayer, Thomas Pilkington, Rong Mao, Jonathan Pevsner, Traci Speed, Nicole Benoit, Chul So Moon, David Sidransky, William H. Westra, Joseph Califano

Research output: Contribution to journalArticle

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 χ2 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.

Original languageEnglish (US)
Pages (from-to)8715-8720
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume101
Issue number23
DOIs
StatePublished - Jun 8 2004

Keywords

  • Allelic imbalance
  • Chromosomal mapping
  • Comparative genomic hybridization
  • Head and neck squamous cell carcinoma
  • Microarrays

ASJC Scopus subject areas

  • General

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