Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors

doi:10.1186/1471-2407-9-17

BMC Cancer
Volume 9

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Savola S
Klami A
Tripathi A
Niini T
Serra M
Picci P
Kaski S
Zambelli D
Scotlandi K
Knuutila S

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Savola S
Klami A
Tripathi A
Niini T
Serra M
Picci P
Kaski S
Zambelli D
Scotlandi K
Knuutila S
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Research article

Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors

Suvi Savola¹^,2 , Arto Klami³ , Abhishek Tripathi³ , Tarja Niini¹^,2 , Massimo Serra⁴ , Piero Picci⁴ , Samuel Kaski³ , Diana Zambelli⁴ , Katia Scotlandi⁴ and Sakari Knuutila¹^,2

¹Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki, Helsinki, Finland

²Helsinki University Central Hospital, Helsinki, Finland

³Department of Information and Computer Science, Helsinki University of Technology, Espoo, Finland

⁴Laboratorio di Ricerca Oncologica, Istituti Ortopedici Rizzoli, Bologna, Italy

author email corresponding author email

BMC Cancer 2009, 9:17doi:10.1186/1471-2407-9-17


Published:	14 January 2009

Abstract

Background

Ewing sarcoma family of tumors (ESFT), characterized by t(11;22)(q24;q12), is one of the most common tumors of bone in children and young adults. In addition to EWS/FLI1 gene fusion, copy number changes are known to be significant for the underlying neoplastic development of ESFT and for patient outcome. Our genome-wide high-resolution analysis aspired to pinpoint genomic regions of highest interest and possible target genes in these areas.

Methods

Array comparative genomic hybridization (CGH) and expression arrays were used to screen for copy number alterations and expression changes in ESFT patient samples. A total of 31 ESFT samples were analyzed by aCGH and in 16 patients DNA and RNA level data, created by expression arrays, was integrated. Time of the follow-up of these patients was 5–192 months. Clinical outcome was statistically evaluated by Kaplan-Meier/Logrank methods and RT-PCR was applied on 42 patient samples to study the gene of the highest interest.

Results

Copy number changes were detected in 87% of the cases. The most recurrent copy number changes were gains at 1q, 2, 8, and 12, and losses at 9p and 16q. Cumulative event free survival (ESFT) and overall survival (OS) were significantly better (P < 0.05) for primary tumors with three or less copy number changes than for tumors with higher number of copy number aberrations. In three samples copy number imbalances were detected in chromosomes 11 and 22 affecting the FLI1 and EWSR1 loci, suggesting that an unbalanced t(11;22) and subsequent duplication of the derivative chromosome harboring fusion gene is a common event in ESFT. Further, amplifications on chromosomes 20 and 22 seen in one patient sample suggest a novel translocation type between EWSR1 and an unidentified fusion partner at 20q. In total 20 novel ESFT associated putative oncogenes and tumor suppressor genes were found in the integration analysis of array CGH and expression data. Quantitative RT-PCR to study the expression levels of the most interesting gene, HDGF, confirmed that its expression was higher than in control samples. However, no association between HDGF expression and patient survival was observed.

Conclusion

We conclude that array CGH and integration analysis proved to be effective methods to identify chromosome regions and novel target genes involved in the tumorigenesis of ESFT.