Research

Identification of novel candidate target genes in amplicons of Glioblastoma multiforme tumors detected by expression and CGH microarray profiling

Yolanda Ruano¹ , Manuela Mollejo² , Teresa Ribalta³ , Concepción Fiaño⁴ , Francisca I Camacho² , Elena Gómez⁵ , Angel Rodríguez de Lope⁶ , Jose-Luis Hernández-Moneo⁶ , Pedro Martínez¹ and Bárbara Meléndez¹

¹  Genetics Department, Hospital Virgen de la Salud, Avda. Barber 30, 45004-Toledo, Spain

²  Department of Pathology, Hospital Virgen de la Salud, Avda. Barber 30, 45004-Toledo, Spain

³  Department of Pathology, Hospital Clinic, Barcelona, C/Villarroel, 170, 08036-Barcelona, Spain

⁴  Department of Pathology, Complejo Hospitalario Xeral-Cies, C/Pizarro, 22, 36204-Vigo, Spain

⁵  Banco de Tumores, Spanish National Cancer Centre (CNIO), c/Melchor Fernéndez Almagro 6, 28029-Madrid, Spain

⁶  Neurosurgery, Hospital Virgen de la Salud, Avda. Barber 30, 45004-Toledo, Spain

author email corresponding author email

Molecular Cancer 2006, 5:39doi:10.1186/1476-4598-5-39

Published:	26 September 2006

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 containg 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.

Conclusion

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.