Investigation Title Transcription profiling of mouse model of glioma reveals cancer stem cells are enriched in the side-population cells Comment[Submitted Name] Cancer Stem Cells Are Enriched In The Side-Population Cells In A Mouse Model Of Glioma Experimental Design unknown_experiment_design_type transcription profiling by array Experimental Design Term Source REF EFO Comment[SecondaryAccession] GSE13490 Comment[ArrayExpressReleaseDate] 2009-01-13 Comment[AEMIAMESCORE] 3 Comment[ArrayExpressAccession] E-GEOD-13490 Comment[MAGETAB TimeStamp_Version] 2010-07-30 10:47:39 Last Changed Rev: 13058 Experimental Factor Name Experimental Factor Type Experimental Factor Term Source REF Person Last Name Yun Person First Name Kyuson Person Mid Initials Person Email kyuson.yun@jax.org Person Phone Person Fax Person Address The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, USA Person Affiliation The Jackson Laboratory Person Roles submitter Person Roles Term Source REF The MGED Ontology Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2009-01-13 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Experiment Description The recent identification of cancer stem cells (CSCs) in multiple human cancers provides a new inroad to understanding tumorigenesis at the cellular level. CSCs are defined by their characteristics of self-renewal, multipotentiality, and tumor initiation upon transplantation. By testing for these defining characteristics, we provide evidence for the existence of CSCs in a transgenic mouse model of glioma, S100ß-verbB;Trp53. In this glioma model, CSCs are enriched in the side-population (SP) cells. These SP cells have enhanced tumor-initiating capacity, self-renewal, and multipotentiality compared to non-SP cells from the same tumors. Furthermore, gene expression analysis comparing FACS-sorted cancer SP cells to non-SP cancer cells and normal neural SP cells identified 45 candidate genes that are differentially expressed in glioma stem cells. We validated the expression of two genes from this list (S100a4 and S100a6) in primary mouse gliomas and human glioma samples. Analyses of xenografted human GBM (glioblatoma multiforme) cell lines and primary human glioma tissues show that S100A4 and S100A6 are expressed in a small subset of cancer cells and that their abundance is positively correlated to tumor grade. In conclusion, this study shows that CSCs exist in a mouse glioma model, suggesting that this model can be used to study the molecular and cellular characteristics of CSCs in vivo and to further test the cancer stem cell hypothesis. Experiment Overall Design: This study features two factors, injected cell origin (either tumorsphere or neurosphere) and FACS cell population (either side population or non-side population cells). There were two different tumorspheres, labeled 3447 and 4346 that were isolated from brain tumors in S100beta-verbB;p53-/- or S100beta-verbB;p53+/- mice. The tumorspheres were injected separately into the brains of NOD.Cg-PrkdcIl2rg/SzJ mice to generate biological triplicates of each primary tumor. Tumorspheres were isolated and cultured before FACS sorting to obtain side population and non-side population cells. As a control, untransformed neurospheres from three independent S100beta-verbB;p53-/- or S100beta-verbB;p53+/- mice were isolated, cultured, and FACS sorted to obtain side population and non-side population cells. Side population and non-side population cells cultured from three mice injected with the 3447 cultured tumorspheres were assayed for gene expression (six samples). Side-population stem cells cultured from three mice injected with the 4346 cultured tumorspheres were assayed for gene expression (three samples). Side-population and non-side population cells cultured from three mice injected with the neurospheres were assayed for gene expression (six samples). Protocol Name P-G13490-2 P-G13490-3 P-G13490-1 P-AFFY-6 Affymetrix:Protocol:ExpressionStat Protocol Type nucleic_acid_extraction nucleic_acid_extraction labeling feature_extraction bioassay_data_transformation Protocol Description Total RNA was isolated from FAC-sorted cells using the RNeasy Micro Kit (Qiagen, Inc.) according to the manufacturer’s instructions. Total RNA was isolated from FAC-sorted cells using the RNeasy Micro Kit (Qiagen, Inc.) according to the manufacturers instructions. Ovation Pico kit from NuGEN Title: Affymetrix CEL analysis. Description: Title: Affymetrix CHP Analysis (ExpressionStat). Description: Protocol Parameters Protocol Hardware Protocol Software MicroArraySuite 5.0 MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF The MGED Ontology SDRF File E-GEOD-13490.sdrf.txt Term Source Name NCBI Taxonomy The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File http://www.ncbi.nlm.nih.gov/Taxonomy/ http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version