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Integrated Chromosome 19 Transcriptomic and Proteomic Datasets Derived from Six Glioma-Derived Cancer Stem Cell Lines

Lichti, Cheryl; Liu, Huiling; Shavkunov, A.S.; Mostovenko, Elisabet; Sulman, E.P.; Ezhilarasan, R.; Wang, Q; Kroes, Roger; Moskal, J.C. and Fenyö, David, et al. (2014) In Journal of Proteome Research 13(1). p.191-199
Abstract
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... (More)
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 viral 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. (Less)
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keywords
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
in
Journal of Proteome Research
volume
13
issue
1
pages
191 - 199
publisher
The American Chemical Society
external identifiers
  • wos:000329472700020
  • scopus:84891794331
ISSN
1535-3893
DOI
10.1021/pr400786s
language
English
LU publication?
yes
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7658da26-12ca-4e8e-b61d-8c988e39c2ed (old id 4193449)
date added to LUP
2014-01-07 10:58:12
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2017-07-23 03:06:50
@article{7658da26-12ca-4e8e-b61d-8c988e39c2ed,
  abstract     = {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 viral integration site 1 (AAVS1) in GSC11 in response to oncolytic adenovirus treatment was demonstrated. Taken together, our<br/><br>
results may indicate new roles for chromosome 19, beyond the 1p/19q codeletion, in the future of personalized medicine for glioma patients.},
  author       = {Lichti, Cheryl and Liu, Huiling and Shavkunov, A.S. and Mostovenko, Elisabet and Sulman, E.P. and Ezhilarasan, R. and Wang, Q and Kroes, Roger and Moskal, J.C. and Fenyö, David and Oksuz, B.A. and Conrad, Charles A. and Lang, Fredrick F. and Berven, Frode S. and Végvári, Ákos and Rezeli, Melinda and Marko-Varga, György and Hober, Sofia and Nilsson, Carol L.},
  issn         = {1535-3893},
  keyword      = {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},
  language     = {eng},
  number       = {1},
  pages        = {191--199},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {Integrated Chromosome 19 Transcriptomic and Proteomic Datasets Derived from Six Glioma-Derived Cancer Stem Cell Lines},
  url          = {http://dx.doi.org/10.1021/pr400786s},
  volume       = {13},
  year         = {2014},
}