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EXPLORING THE NEUROBLASTOMA EPIGENOME: PERSPECTIVES FOR THE DISCOVERY OF PROGNOSISTIC BIOMARKERS
M. Ongenaert, A. Decock, J. Vandesompele, F. Speleman
Center for Medical Genetics, Ghent University, Ghent, Belgium (email@example.com)
Neuroblastoma (NB) is a childhood tumor originating from sympathetic nervous system cells. Although recently new insights into genes involved in NB have emerged, the molecular basis of neuroblastoma development and progression still remains poorly understood. The best-characterized genetic alterations include amplification of the proto-oncogene MYCN, ALK activating mutations or amplification, gain of chromosome arm 17q and losses of 1p, 3p, and 11q. Epigenetic alterations have been described as well: caspase-8 (CASP8) and RAS-association domain family 1 isoform A (RASSF1A) DNA-methylation are important events for the development and progression of neuroblastoma. In total, there are about 75 genes described as epigenetically affected in NB cell lines and/or NB primary samples.
Most of these methylation markers are found using ‘candidate gene’ approaches and the methylation frequencies are usually very low. In order to find novel methylation markers that can be used for improved prognosis, we applied a whole-genome methylation screen. This technique relies on capturing with the MBD2 protein, containing a methyl-binding domain (MBD), with a very high affinity towards methylated genomic regions. In an initial phase, MBD2-seq was performed on 8 NB cell lines (where we also had micro-array data of, before and after treatment with DAC). As these results are promising, we will explore the complete methylomes of 45 primary NB tumors.
Based on an integrative analysis (re-expression results, expression micro-arrays, MBD2-sequencing on cell lines), 48 MSP (Methylation Specific PCR) assays were tested on 89 primary neuroblastoma patients of different risk categories. The results of this validation study demonstrate the power of epigenetic biomarkers as several assays are informative for prognosis and survival.