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Genome-wide analysis of gene expression and alternative splicing in human medulloblastoma

Menghi, F.; (2010) Genome-wide analysis of gene expression and alternative splicing in human medulloblastoma. Doctoral thesis, UCL (University College London). Green open access

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Abstract

Medulloblastoma is a malignant embryonal tumour of the cerebellum which most commonly affects children. A subset of tumours is thought to arise from cerebellar granule cell precursors (GCPs) that fail to undergo normal neuronal development, following the hyper-activation of the Sonic hedgehog (Shh) signalling pathway. To identify candidate genes that might be important for medulloblastoma pathogenesis, I investigated patterns of gene expression and alternative splicing in 14 paediatric medulloblastoma and five normal cerebellar samples using Affymetrix Human Exon arrays. Statistical analysis of the gene expression data identified a group of medulloblastomas with a molecular signature of Shh pathway activation. These tumours showed higher expression levels of genes involved in spindle formation, cytokines, and cell cycle regulation. Further studies using an in vitro mouse GCP cell culture model, in which Shh is necessary for the maintenance of the progenitor state, showed that a selection of candidate genes was also over-expressed when GCPs were cultured in the presence of Shh, as compared to control cells, as well as in human medulloblastoma cell lines. Ongoing and future in vitro experiments will investigate the potential role of candidate genes in sustaining the growth of precursor and tumour cells. Exon-level analysis of gene expression showed that abnormal expression of different transcript variants is likely to occur in medulloblastoma. I selected several examples of differential exon usage and validated these using an independent set of normal and tumour specimens. Tumour-associated splicing alterations were highly consistent, enabling clear separation of normal and cancer samples and in some cases of different medulloblastoma molecular subgroups. Interestingly, Shh-treated GCPs recapitulated the splicing patterns observed in the tumour samples for six out of the eight genes analysed, suggesting that the preferential expression of specific transcript forms is regulated during normal cerebellar development. The possible relationship between inappropriate splicing and medulloblastoma pathogenesis will be the subject of future investigation.

Type:Thesis (Doctoral)
Title:Genome-wide analysis of gene expression and alternative splicing in human medulloblastoma
Open access status:An open access version is available from UCL Discovery
Language:English
UCL classification:UCL > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute of Child Health

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