Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines

Cheryl F. Lichti, Huiling Liu, Alexander S. Shavkunov, Ekaterina Mostovenko, Erik P. Sulman, Ravesanker Ezhilarasan, Qianghu Wang, Roger A. Kroes, Joseph C. Moskal, David Fenyö, Betül Akgöl Oksuz, Charles A. Conrad, Frederick F. Lang, Frode S. Berven, Ákos Végvári, Melinda Rezeli, György Marko-Varga, Sophia Hober, Carol L. Nilsson

Research output: Contribution to journalArticle

17 Scopus citations

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 results may indicate new roles for chromosome 19, beyond the 1p/19q codeletion, in the future of personalized medicine for glioma patients.

Original languageEnglish (US)
Pages (from-to)191-199
Number of pages9
JournalJournal of Proteome Research
Volume13
Issue number1
DOIs
StatePublished - Jan 3 2014

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Keywords

  • bioinformatics
  • cancer proteomics
  • chromosome 19
  • Chromosome-centric Human Proteome Project
  • glioma
  • glioma stem cells
  • mass spectrometry
  • mRNA
  • neurocan core protein
  • oncolytic virus
  • proteins
  • RNA-Seq
  • symplekin

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

Lichti, C. F., Liu, H., Shavkunov, A. S., Mostovenko, E., Sulman, E. P., Ezhilarasan, R., Wang, Q., Kroes, R. A., Moskal, J. C., Fenyö, D., Oksuz, B. A., Conrad, C. A., Lang, F. F., Berven, F. S., Végvári, Á., Rezeli, M., Marko-Varga, G., Hober, S., & Nilsson, C. L. (2014). Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines. Journal of Proteome Research, 13(1), 191-199. https://doi.org/10.1021/pr400786s