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Genome-Wide Analysis of Alternative Splicing in Medulloblastoma Identifies Splicing Patterns Characteristic of Normal Cerebellar Development

Lookup NU author(s): Dr Ed Schwalbe, Professor Steven CliffordORCiD


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Alternative splicing is an important mechanism for the generation of protein diversity at a post-transcriptional level. Modifications in the splicing patterns of several genes have been shown to contribute to the malignant transformation of different tissue types. In this study, we used the Affymetrix Exon arrays to investigate patterns of differential splicing between pediatric medulloblastomas and normal cerebellum on a genome-wide scale. Of the 1,262 genes identified as potentially generating tumor-associated splice forms, we selected 14 examples of differential splicing of known cassette exons and successfully validated 11 of them by reverse transcriptase PCR. The pattern of differential splicing of three validated events was characteristic for the molecular subset of sonic hedgehog (Shh)-driven medulloblastomas, suggesting that their unique gene signature includes the expression of distinctive transcript variants. Generally, we observed that tumor and normal fetal cerebellar samples shared significantly lower exon inclusion rates than normal adult cerebellum. We investigated whether tumor-associated splice forms were expressed in primary cultures of Shh-dependent mouse cerebellar granule cell precursors (GCP) and found that Shh caused a decrease in the cassette exon inclusion rate of five of the seven tested genes. Furthermore, we observed a significant increase in exon inclusion between postnatal days 7 and 14 of mouse cerebellar development, at the time when GCPs mature into postmitotic neurons. We conclude that inappropriate splicing frequently occurs in human medulloblastomas and may be linked to the activation of developmental signaling pathways and a failure of cerebellar precursor cells to differentiate. Cancer Res; 71(6); 2045-55. (C) 2011 AACR.

Publication metadata

Author(s): Menghi F, Jacques TS, Barenco M, Schwalbe EC, Clifford SC, Hubank M, Ham J

Publication type: Article

Publication status: Published

Journal: Cancer Research

Year: 2011

Volume: 71

Issue: 6

Pages: 2045-2055

Print publication date: 19/01/2011

ISSN (print): 0008-5472

ISSN (electronic): 1538-7445

Publisher: American Association for Cancer Research


DOI: 10.1158/0008-5472.CAN-10-2519


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Funder referenceFunder name
Annabel McEnery Children's Cancer Fund
Great Ormond Street Hospital Children's Charity
Katie Trust
Medical Research Council
Olivia Hodson Cancer Fund
Samantha Dickson Brain Tumour Trust
057700Wellcome Trust