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 Citations (Scopus)

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

Fingerprint

Chromosomes, Human, Pair 19
Neoplastic Stem Cells
Chromosomes
Stem cells
Glioma
Proteomics
Cell Line
Proteins
Tumors
Adenoviridae
Virus Integration
Gene Expression
Precision Medicine
Microarrays
Datasets
Atlases
Aberrations
Refractory materials
Medicine
Labels

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., ... 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

Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines. / Lichti, Cheryl F.; Liu, Huiling; Shavkunov, Alexander S.; Mostovenko, Ekaterina; Sulman, Erik P.; Ezhilarasan, Ravesanker; Wang, Qianghu; Kroes, Roger A.; Moskal, Joseph C.; Fenyö, David; Oksuz, Betül Akgöl; Conrad, Charles A.; Lang, Frederick F.; Berven, Frode S.; Végvári, Ákos; Rezeli, Melinda; Marko-Varga, György; Hober, Sophia; Nilsson, Carol L.

In: Journal of Proteome Research, Vol. 13, No. 1, 03.01.2014, p. 191-199.

Research output: Contribution to journalArticle

Lichti, CF, Liu, H, Shavkunov, AS, Mostovenko, E, Sulman, EP, Ezhilarasan, R, Wang, Q, Kroes, RA, Moskal, JC, Fenyö, D, Oksuz, BA, Conrad, CA, Lang, FF, Berven, FS, Végvári, Á, Rezeli, M, Marko-Varga, G, Hober, S & Nilsson, CL 2014, 'Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines', Journal of Proteome Research, vol. 13, no. 1, pp. 191-199. https://doi.org/10.1021/pr400786s
Lichti, Cheryl F. ; Liu, Huiling ; Shavkunov, Alexander S. ; Mostovenko, Ekaterina ; Sulman, Erik P. ; Ezhilarasan, Ravesanker ; Wang, Qianghu ; Kroes, Roger A. ; Moskal, Joseph C. ; Fenyö, David ; Oksuz, Betül Akgöl ; Conrad, Charles A. ; Lang, Frederick F. ; Berven, Frode S. ; Végvári, Ákos ; Rezeli, Melinda ; Marko-Varga, György ; Hober, Sophia ; Nilsson, Carol L. / Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines. In: Journal of Proteome Research. 2014 ; Vol. 13, No. 1. pp. 191-199.
@article{fc4ae0f388ea4d57b9bca0e75ea1ad85,
title = "Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines",
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.",
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",
author = "Lichti, {Cheryl F.} and Huiling Liu and Shavkunov, {Alexander S.} and Ekaterina Mostovenko and Sulman, {Erik P.} and Ravesanker Ezhilarasan and Qianghu Wang and Kroes, {Roger A.} and Moskal, {Joseph C.} and David Feny{\"o} and Oksuz, {Bet{\"u}l Akg{\"o}l} and Conrad, {Charles A.} and Lang, {Frederick F.} and Berven, {Frode S.} and {\'A}kos V{\'e}gv{\'a}ri and Melinda Rezeli and Gy{\"o}rgy Marko-Varga and Sophia Hober and Nilsson, {Carol L.}",
year = "2014",
month = "1",
day = "3",
doi = "10.1021/pr400786s",
language = "English (US)",
volume = "13",
pages = "191--199",
journal = "Journal of Proteome Research",
issn = "1535-3893",
publisher = "American Chemical Society",
number = "1",

}

TY - JOUR

T1 - Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines

AU - Lichti, Cheryl F.

AU - Liu, Huiling

AU - Shavkunov, Alexander S.

AU - Mostovenko, Ekaterina

AU - Sulman, Erik P.

AU - Ezhilarasan, Ravesanker

AU - Wang, Qianghu

AU - Kroes, Roger A.

AU - Moskal, Joseph C.

AU - Fenyö, David

AU - Oksuz, Betül Akgöl

AU - Conrad, Charles A.

AU - Lang, Frederick F.

AU - Berven, Frode S.

AU - Végvári, Ákos

AU - Rezeli, Melinda

AU - Marko-Varga, György

AU - Hober, Sophia

AU - Nilsson, Carol L.

PY - 2014/1/3

Y1 - 2014/1/3

N2 - 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.

AB - 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.

KW - bioinformatics

KW - cancer proteomics

KW - chromosome 19

KW - Chromosome-centric Human Proteome Project

KW - glioma

KW - glioma stem cells

KW - mass spectrometry

KW - mRNA

KW - neurocan core protein

KW - oncolytic virus

KW - proteins

KW - RNA-Seq

KW - symplekin

UR - http://www.scopus.com/inward/record.url?scp=84891794331&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84891794331&partnerID=8YFLogxK

U2 - 10.1021/pr400786s

DO - 10.1021/pr400786s

M3 - Article

C2 - 24266786

AN - SCOPUS:84891794331

VL - 13

SP - 191

EP - 199

JO - Journal of Proteome Research

JF - Journal of Proteome Research

SN - 1535-3893

IS - 1

ER -