E-GEOD-9385 - Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon arrays

Status
Submitted on 18 October 2007, released on 28 January 2008, last updated on 27 March 2012
Organism
Homo sapiens
Samples (55)
Array (1)
Protocols (6)
Description
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
Experiment type
transcription profiling by array 
Contacts
Pim French <p.french@erasmusmc.nl>, Elza Duijm, Ivar Siccama, Johan M Kros, Justine Peeters, Martin J van den Bent, Peter A Sillevis Smitt, Peter van der Spek, Pim J French, Sebastiaan Horsman, Theo M Luider
Citation
Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays. French PJ, Peeters J, Horsman S, Duijm E, Siccama I, van den Bent MJ, Luider TM, Kros JM, van der Spek P, Sillevis Smitt PA.
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