title: Identification of novel candidate target genes in amplicons of Glioblastoma multiforme tumors detected by expression and CGH microarray profiling.
abstract: BACKGROUND
  Conventional cytogenetic and comparative genomic hybridization (CGH) studies in brain malignancies have shown that glioblastoma multiforme (GBM) is characterized by complex structural and numerical alterations. However, the limited resolution of these techniques has precluded the precise identification of detailed specific gene copy number alterations.
  
  
  RESULTS
  We performed a genome-wide survey of gene copy number changes in 20 primary GBMs by CGH on cDNA microarrays. A novel amplicon at 4p15, and previously uncharacterized amplicons at 13q32-34 and 1q32 were detected and are analyzed here. These amplicons contained amplified genes not previously reported. Other amplified regions containing well-known oncogenes in GBMs were also detected at 7p12 (EGFR), 7q21 (CDK6), 4q12 (PDGFRA), and 12q13-15 (MDM2 and CDK4). In order to identify the putative target genes of the amplifications, and to determine the changes in gene expression levels associated with copy number change events, we carried out parallel gene expression profiling analyses using the same cDNA microarrays. We detected overexpression of the novel amplified genes SLA/LP and STIM2 (4p15), and TNFSF13B and COL4A2 (13q32-34). Some of the candidate target genes of amplification (EGFR, CDK6, MDM2, CDK4, and TNFSF13B) were tested in an independent set of 111 primary GBMs by using FISH and immunohistological assays. The novel candidate 13q-amplification target TNFSF13B was amplified in 8% of the tumors, and showed protein expression in 20% of the GBMs.
  
  
  CONCLUSIONS
  This high-resolution analysis allowed us to propose novel candidate target genes such as STIM2 at 4p15, and TNFSF13B or COL4A2 at 13q32-34 that could potentially contribute to the pathogenesis of these tumors and which would require futher investigations. We showed that overexpression of the amplified genes could be attributable to gene dosage and speculate that deregulation of those genes could be important in the development and progression of GBM. Our findings highlight the important influence in GBM of signaling pathways such as the PI3K/AKT, consistent with the invasive features of this tumor.
authors.affiliation: Genetics Department, Hospital Virgen de la Salud, Avda, Barber 30, 45004-Toledo, Spain. yruano@sescam.jccm.es
authors.forename: Yolanda
authors.initials: Y
authors.lastname: Ruano
authors.forename: Manuela
authors.initials: M
authors.lastname: Mollejo
authors.forename: Teresa
authors.initials: T
authors.lastname: Ribalta
authors.forename: Concepción
authors.initials: C
authors.lastname: Fiaño
authors.forename: Francisca I
authors.initials: FI
authors.lastname: Camacho
authors.forename: Elena
authors.initials: E
authors.lastname: Gómez
authors.forename: Angel Rodríguez
authors.initials: AR
authors.lastname: de Lope
authors.forename: Jose-Luis
authors.initials: JL
authors.lastname: Hernández-Moneo
authors.forename: Pedro
authors.initials: P
authors.lastname: Martínez
authors.forename: Bárbara
authors.initials: B
authors.lastname: Meléndez
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001932:Brain Neoplasms / Q000235:genetics* / Q000378:metabolism; D002878:Chromosomes, Human, Pair 1 / Q000235:genetics; D002882:Chromosomes, Human, Pair 13 / Q000235:genetics; D002894:Chromosomes, Human, Pair 4 / Q000235:genetics; D066246:ErbB Receptors / Q000032:analysis / Q000235:genetics; D005260:Female; D005784:Gene Amplification / Q000235:genetics; D018628:Gene Dosage / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D052138:Genes, Neoplasm / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics; D005909:Glioblastoma / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D007150:Immunohistochemistry / Q000379:methods; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D008297:Male; D008875:Middle Aged; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D051736:Proto-Oncogene Proteins c-mdm2 / Q000032:analysis / Q000235:genetics
chemical_list: C497206:MDM2 protein, human; D051736:Proto-Oncogene Proteins c-mdm2; D066246:ErbB Receptors