TY - JOUR
T1 - Gene expression alterations over large chromosomal regions in cancers include multiple genes unrelated to malignant progression
AU - Masayesva, Brett G.
AU - Ha, Patrick
AU - Garrett-Mayer, Elizabeth
AU - Pilkington, Thomas
AU - Mao, Rong
AU - Pevsner, Jonathan
AU - Speed, Traci
AU - Benoit, Nicole
AU - Moon, Chul So
AU - Sidransky, David
AU - Westra, William H.
AU - Califano, Joseph
PY - 2004/6/8
Y1 - 2004/6/8
N2 - 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.
AB - 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.
KW - Allelic imbalance
KW - Chromosomal mapping
KW - Comparative genomic hybridization
KW - Head and neck squamous cell carcinoma
KW - Microarrays
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U2 - 10.1073/pnas.0400027101
DO - 10.1073/pnas.0400027101
M3 - Article
C2 - 15155901
AN - SCOPUS:2942588529
SN - 0027-8424
VL - 101
SP - 8715
EP - 8720
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 23
ER -