Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling by array of human paediatric medulloblastoma samples and normal cerebellum to investigate the occurance of alternative splicing

ABSTRACT: Alternative pre-mRNA splicing critically contributes to the generation of protein variety in a tissue- and development-specific manner. Alterations in the normal pathways of alternative splicing (AS) have been associated with the growth and maintenance of several tumour types, and have been indicated as candidate bio-markers of tumour progression, metastasis and patient survival. In this study we applied genome-wide exon array technology to investigate AS events that may distinguish between human medulloblastoma and normal cerebellum. We initially investigated gene-level expression profiles to identify samples expressing gene signatures characteristic of previously described MB molecular subgroups. 3 medulloblastomas significantly over-expressed genes typically belonging to the Shh signalling pathway or associated with a granule cell progenitor status and were therefore classified as Shh-activated tumours (MB1). The remaining tumour samples were grouped together as medulloblastoma subset 2 (MB2). We then applied the Splicing Index algorithm and identified 1260 unique genes containing at least one candidate exon whose inclusion rate differed between different sample subgroups. Following the analysis of candidate event expression plots and gene structure annotation, we selected 14 examples of differential splicing of cassette exons and successfully validated 11 of them by semi-quantitative RT-PCR in a selection of the initial sample-set and subsequently in an independent set of 10 normal cerebellum and 20 medulloblastoma samples. Through the analysis of AS pathway in in vitro cultures of cerebellar granule cell progenitors (the putative cell of origin of least a subset of medulloblastomas), we showed that medulloblastoma-associated AS patterns could be indicative of a normal cerebellar undifferentiated phenotype and suggested that activation of oncogenic pathways during the development of the cerebellum may lead to a failure of neuronal differentiation also through the disruption of AS programs.

ORGANISM(S): Homo sapiens

SUBMITTER: Jonathan Ham

PROVIDER: E-MTAB-292 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide analysis of alternative splicing in medulloblastoma identifies splicing patterns characteristic of normal cerebellar development.

Menghi Francesca F Jacques Thomas S TS Barenco Martino M Schwalbe Ed C EC Clifford Steven C SC Hubank Mike M Ham Jonathan J

Cancer research 20110119 6

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 ...[more]

PMID: 21248070

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Project description:Medulloblastoma encompasses a collection of clinically and molecularly diverse tumor subtypes that together comprise the most common malignant childhood brain tumor. These tumors are thought to arise within the cerebellum, with approximately 25% originating from granule neuron precursor cells (GNPCs) following aberrant activation of the Sonic Hedgehog pathway (hereafter, SHH-subtype). The pathological processes that drive heterogeneity among the other medulloblastoma subtypes are not known, hindering the development of much needed new therapies. Here, we provide evidence that a discrete subtype of medulloblastoma that contains activating mutations in the WNT pathway effector CTNNB1 (hereafter, WNT-subtype), arises outside the cerebellum from cells of the dorsal brainstem. We found that genes marking human WNT-subtype medulloblastomas are more frequently expressed in the lower rhombic lip (LRL) and embryonic dorsal brainstem than in the upper rhombic lip (URL) and developing cerebellum. Magnetic resonance imaging (MRI) and intra-operative reports showed that human WNT-subtype tumors infiltrate the dorsal brainstem, while SHH-subtype tumors are located within the cerebellar hemispheres. Activating mutations in Ctnnb1 had little impact on progenitor cell populations in the cerebellum, but caused the abnormal accumulation of cells on the embryonic dorsal brainstem that included aberrantly proliferating Zic1+ precursor cells. These lesions persisted in all mutant adult mice and in 15% of cases in which Tp53 was concurrently deleted, progressed to form medulloblastomas that recapitulated the anatomy and gene expression profiles of human WNT-subtype medulloblastoma. We provide the first evidence that subtypes of medulloblastoma have distinct cellular origins. Our data provide an explanation for the marked molecular and clinical differences between SHH and WNT-subtype medulloblastomas and have profound implications for future research and treatment of this important childhood cancer. A total of 16 samples are analyzed, repsresenting 4 experimental groups: Ctnnb1 medulloblastoma (3 samples); Ptch1 medulloblastoma (6 samples); embryonic dorsal brainstem (4 samples); and postnatal granule neuron precursor cells (3 samples). Every sample was prepared from a different mouse.

Project description:Deregulated developmental processes in the cerebellum cause medulloblastoma, the most common malignant tumor of the central nervous system. About 20-30% of cases are caused by mutations increasing the activity of the Sonic hedgehog (Shh) pathway, a critical mitogen in cerebellar development. The proto-oncogene Smoothened is a key transducer of the Shh pathway. Activating mutations in Smoothened that lead to constitutive activity of the Shh pathway have been identified in human medulloblastoma. To understand the molecular and cellular effects of Smoothened variants in normal development and medulloblastoma genesis, we generated the SmoA2 transgenic mouse model which expresses the transgene exclusively in granule neuron precursors. In this study, we demonstrate how two point mutations in a single molecule can produce starkly different phenotypes as seen in comparison to our previous model, ND2:SmoA1. The SmoA2 mice have severe aberrations in cerebellar development whereas the SmoA1 mice are largely normal during development. Medulloblastomas in the SmoA2 mice develop in the dysplastic cerebellar milieu. Intriguingly, despite disruptions in the stereotypic organization of the cerebellum, the SmoA2 mice do not exhibit any overt abnormalities in motor coordination. The differences in the global transcriptional profiles downstream of SmoA1 and SmoA2 further demonstrate the distinctiveness of the two oncogenic Smoothened mutations. The SmoA2 model serves as a unique spatiotemporal tool to investigate the functional significance of the reiterative cerebellar circuitry as well as to further understand Shh pathway mechanics in cerebellar development and oncogenesis. We previously generated a SmoA1 transgenic mouse medulloblastoma model, which expresses the SmoA1 transgene driven by the GNP-specific fragment of the promoter of ND2 transcription factor leading to constitutively active Shh signaling exclusively in the cerebellum. In this study, we characterize the ND2:SmoA2 transgenic mouse model with a similarly designed transgene expressing the SmoA2 mutation. To assess transcriptional changes downstream of SmoA1 and SmoA2, we evaluated global gene expression profiles of P5 SmoA1, SmoA2 and Wt age-matched cerebella. We chose this specific developmental stage because (1) the phenotypes of SmoA1 and SmoA2 are robust and distinct at P5; (2) at P5 GNPs undergo proliferation, migration and differentiation and therefore expression profiling could capture key differences in multiple processes.

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Dataset Information

Transcription profiling by array of human paediatric medulloblastoma samples and normal cerebellum to investigate the occurance of alternative splicing

Publications

Genome-wide analysis of alternative splicing in medulloblastoma identifies splicing patterns characteristic of normal cerebellar development.

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