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Integrated Chromosome 19 Transcriptomic and Proteomic Data Sets Derived from Glioma Cancer Stem-Cell Lines
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2014 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 13, no 1, 191-199 p.Article in journal (Refereed) Published
Abstract [en]

One subproject within the global Chromosome 19 Consortium is to define chromosome 19 gene and protein expression in glioma-derived cancer stem cells (GSCs). Chromosome 19 is notoriously linked to glioma by 1p/19q codeletions, and clinical tests are established to detect that specific aberration. GSCs are tumor-initiating cells and are hypothesized to provide a repository of cells in tumors that can self-replicate and be refractory to radiation and chemotherapeutic agents developed for the treatment of tumors. In this pilot study, we performed RNA-Seq, label-free quantitative protein measurements in six GSC lines, and targeted transcriptomic analysis using a chromosome 19-specific microarray in an additional six GSC lines. The data have been deposited to the ProteomeXchange with identifier PXD000563. Here we present insights into differences in GSC gene and protein expression, including the identification of proteins listed as having no or low evidence at the protein level in the Human Protein Atlas, as correlated to chromosome 19 and GSC subtype. Furthermore, the upregulation of proteins downstream of adenovirus-associated integration site 1 (AAVS1) in GSC11 in response to oncolytic adenovirus treatment was demonstrated. Taken together, our results may indicate new roles for chromosome 19, beyond the 1p/19q codeletion, in the future of personalized medicine for glioma patients.

Place, publisher, year, edition, pages
2014. Vol. 13, no 1, 191-199 p.
Keyword [en]
Chromosome-centric Human Proteome Project, proteins, mRNA, RNA-Seq, mass spectrometry, bioinformatics, glioma, glioma stem cells, cancer proteomics, chromosome 19, oncolytic virus, neurocan core protein, symplekin
National Category
Biochemistry and Molecular Biology
URN: urn:nbn:se:kth:diva-141314DOI: 10.1021/pr400786sISI: 000329472700020ScopusID: 2-s2.0-84891794331OAI: diva2:696640

QC 20140214

Available from: 2014-02-14 Created: 2014-02-13 Last updated: 2014-02-14Bibliographically approved

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Hober, Sophia
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Protein Technology
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