Transcriptomics

Dataset Information

27

Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon arrays


ABSTRACT: Aberrant splice variants are involved in the initiation and/or progression of glial brain tumors. We therefore set out to identify splice variants that are differentially expressed between histological subgroups of gliomas. Splice variants were identified using a novel platform that profiles the expression of virtually all known and predicted exons present in the human genome. Exon-level expression profiling was performed on 26 glioblastomas, 22 oligodendrogliomas and 6 control brain samples. Our results demonstrate that Human Exon arrays can identify subgroups of gliomas based on their histological appearance and genetic aberrations. We next used our expression data to identify differentially expressed splice variants. In two independent approaches, we identified 49 and up to 459 exons that are differentially spliced between glioblastomas and oligodendrogliomas a subset of which (47% and 33%) were confirmed by RT-PCR. In addition, exon-level expression profiling also identified >700 novel exons. Expression of ~67% of these candidate novel exons was confirmed by RT-PCR. Our results indicate that exon-level expression profiling can be used to molecularly classify brain tumor subgroups, can identify differentially regulated splice variants and can identify novel exons. The splice variants identified by exon-level expression profiling may help to detect the genetic changes that cause or maintain gliomas and may serve as novel treatment targets. Keywords: cell type comparison 6 adult non diseased brain, 26 glioblastomas, 21 oligodendrogliomas

ORGANISM(S): Homo sapiens  

SUBMITTER: Sebastiaan Horsman   Justine Peeters  Pim French  Ivar Siccama  Johan M Kros  Pim J French  Peter A Sillevis Smitt  Theo M Luider  Martin J van den Bent  Peter van der Spek  Elza Duijm 

PROVIDER: E-GEOD-9385 | ArrayExpress | 2008-01-28

SECONDARY ACCESSION(S): GSE9385PRJNA103101

REPOSITORIES: GEO, ArrayExpress

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Publications

Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays.

French Pim J PJ   Peeters Justine J   Horsman Sebastiaan S   Duijm Elza E   Siccama Ivar I   van den Bent Martin J MJ   Luider Theo M TM   Kros Johan M JM   van der Spek Peter P   Sillevis Smitt Peter A PA  

Cancer research 20070601 12


Aberrant splice variants are involved in the initiation and/or progression of glial brain tumors. We therefore set out to identify splice variants that are differentially expressed between histologic subgroups of gliomas. Splice variants were identified using a novel platform that profiles the expression of virtually all known and predicted exons present in the human genome. Exon-level expression profiling was done on 26 glioblastomas, 22 oligodendrogliomas, and 6 control brain samples. Our resu  ...[more]

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