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Background Medulloblastoma is the most common malignant brain tumor of childhood. Improvements in clinical outcome require a better understanding of the genetic alterations to identify clinically significant biological factors and to stratify patients accordingly. In the present study, we applied cytogenetic characterization to guide the identification of biologically significant genes from gene expression microarray profiles of medulloblastoma.
Methods We analyzed 71 primary medulloblastomas for chromosomal copy number aberrations (CNAs) using comparative genomic hybridization (CGH). Among 64 tumors that we previously analyzed by gene expression microarrays, 27 were included in our CGH series. We analyzed clinical outcome with respect to CNAs and microarray results. We filtered microarray data using specific CNAs to detect differentially expressed candidate genes associated with survival.
Results The most frequent lesions detected in our series involved chromosome 17; loss of 16q, 10q, or 8p; and gain of 7q or 2p. Recurrent amplifications at 2p23-p24, 2q14, 7q34, and 12p13 were also observed. Gain of 8q is associated with worse overall survival (p = 0.0141), which is not entirely attributable to MYC amplification or overexpression. By applying CGH results to gene expression analysis of medulloblastoma, we identified three 8q-mapped genes that are associated with overall survival in the larger group of 64 patients (p < 0.05): eukaryotic translation elongation factor 1D (EEF1D), ribosomal protein L30 (RPL30), and ribosomal protein S20 (RPS20).
Conclusion The complementary use of CGH and expression profiles can facilitate the identification of clinically significant candidate genes involved in medulloblastoma growth. We demonstrate that gain of 8q and expression levels of three 8q-mapped candidate genes (EEF1D, RPL30, RPS20) are associated with adverse outcome in medulloblastoma.
© 2006 De Bortoli et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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VCU Radiation Oncology Publications
Multivariate Analysis of 8q Gain for Overall and Progression-Free Survival Controlled for Other Prognostic Variables. Multivariate analysis of significance was performed for 8q gain with respect to clinical variables that are widely accepted as prognostically significant: age relative to 3 years old and metastatic stage at diagnosis, and the degree of primary resection. These results confirm the prognostic significance of 8q gain for Overall and Progression-Free Survival (p = 0.013 and p = 0.003. respectively). Abbreviations: CGH8q, 8q gain; age_3, age relative to 3 years; resection, degree of resection; M_status, metastatic (Chang) stage; B, regression coefficient of the model; SE, standard error; df, degrees of freedom; Sig, significance (p value based on Wald statistics); Exp(B), exponential function of B.