title: Gene dosage alterations revealed by cDNA microarray analysis in cervical cancer: identification of candidate amplified and overexpressed genes.
abstract: Cervical cancer (CC) cells exhibit complex karyotypic alterations, which is consistent with deregulation of numerous critical genes in its formation and progression. To characterize this karyotypic complexity at the molecular level, we used cDNA array comparative genomic hybridization (aCGH) to analyze 29 CC cases and identified a number of over represented and deleted genes. The aCGH analysis revealed at least 17 recurrent amplicons and six common regions of deletions. These regions contain several known tumor-associated genes, such as those involved in transcription, apoptosis, cytoskeletal remodeling, ion-transport, drug metabolism, and immune response. Using the fluorescence in situ hybridization (FISH) approach we demonstrated the presence of high-level amplifications at the 8q24.3, 11q22.2, and 20q13 regions in CC cell lines. To identify amplification-associated genes that correspond to focal amplicons, we examined one or more genes in each of the 17 amplicons by Affymetrix U133A expression arrays and semiquantitative reverse-transcription PCR (RT-PCR) in 31 CC tumors. This analysis exhibited frequent and robust upregulated expression in CC relative to normal cervix for genes EPHB2 (1p36), CDCA8 (1p34.3), AIM2 (1q22-23), RFC4, MUC4, and HRASLS (3q27-29), SKP2 (5p12-13), CENTD3 (5q31.3), PTK2, RECQL4 (8q24), MMP1 and MMP13 (11q22.2), AKT1 (14q32.3), ABCC3 (17q21-22), SMARCA4 (19p13.3) LIG1 (19q13.3), UBE2C (20q13.1), SMC1L1 (Xp11), KIF4A (Xq12), TMSNB (Xq22), and CSAG2 (Xq28). Thus, the gene dosage and expression profiles generated here have enabled the identification of focal amplicons characteristic for the CC genome and facilitated the validation of relevant genes in these amplicons. These data, thus, form an important step toward the identification of biologically relevant genes in CC pathogenesis. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.
authors.affiliation: Department of Pathology, Columbia University Medical Center, NY 10032, USA.
authors.forename: Gopeshwar
authors.initials: G
authors.lastname: Narayan
authors.forename: Veronique
authors.initials: V
authors.lastname: Bourdon
authors.forename: Seeta
authors.initials: S
authors.lastname: Chaganti
authors.forename: Hugo
authors.initials: H
authors.lastname: Arias-Pulido
authors.forename: Subhadra V
authors.initials: SV
authors.lastname: Nandula
authors.forename: Pulivarthi H
authors.initials: PH
authors.lastname: Rao
authors.forename: Lutz
authors.initials: L
authors.lastname: Gissmann
authors.forename: Matthias
authors.initials: M
authors.lastname: Dürst
authors.forename: Achim
authors.initials: A
authors.lastname: Schneider
authors.forename: Bhavana
authors.initials: B
authors.lastname: Pothuri
authors.forename: Mahesh
authors.initials: M
authors.lastname: Mansukhani
authors.forename: Katia
authors.initials: K
authors.lastname: Basso
authors.forename: R S K
authors.initials: RS
authors.lastname: Chaganti
authors.forename: Vundavalli V
authors.initials: VV
authors.lastname: Murty
mesh_terms: D045744:Cell Line, Tumor; D005260:Female; D005784:Gene Amplification; D018628:Gene Dosage; D015870:Gene Expression; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D002583:Uterine Cervical Neoplasms / Q000235:genetics*