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Series GSE17618 Query DataSets for GSE17618
Status Public on Dec 01, 2011
Title Inflammatory gene profiling of Ewing sarcoma family of tumors (set A)
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Purpose: Unlike in most adult-onset cancers, an association between typical paediatric neoplasms and inflammatory triggers is rare. We studied whether immune system related genes are activated and have prognostic significance in Ewing sarcoma family of tumours (ESFT). Experimental design: Data-analysis was performed on gene expression profiles of 44 ESFT patient, 11 ESFT cell line, and 18 normal muscle tissue samples. 238 inflammation related genes were selected based on literature and a macrophage gene expression signature was derived from SymAtlas. Differential expression of the genes was analysed by t-test and survival analysis was performed according to gene expression.
Results: Inflammatory genes are activated in ESFT patient samples, as 38 of 238 (16%) inflammatory genes were significantly upregulated (p<0.001) when compared to ESFT cell lines. This inflammatory gene activation was characterized by significant enrichment of macrophage related gene expression with 58 of 299 (19%) of these genes being upregulated (p<0.001). By combining expression data from ESFT patients, cell lines and muscle tissue samples we were able to identify a total of 32 presumptive inflammatory genes that characterize and distinguish tumour site in vivo from surrounding normal tissues. High expression of C5 correlated with better event free (p=0.01) and overall survival (p=0.004) in dose dependent manner. C5 and its receptor C5aR1 expression was verified at protein level by immunohistochemistry on tumor tissue microarray. Also, high expression of JAK1 correlated with favourable overall survival (p=0.04) and high expression of IL8, derived presumably from infiltrating immune cells, resulted in poor overall survival in Ewing sarcoma (p=0.04). Conclusions: Immune system related gene activation is observed in ESFT patient samples and several prognostically significant inflammatory genes (C5, JAK1 and IL8) for ESFT were identified.
 
Overall design 44 Ewing sarcoma family of tumor patient and 11 cell line samples were analysed for their gene expression.
 
Contributor(s) Savola S, Klami A, Myllykangas S, Manara C, Scotlandi K, Picci P, Knuutila S, Vakkila J
Citation(s) 22084725
Submission date Aug 12, 2009
Last update date Mar 25, 2019
Contact name Suvi Savola
URL http://www.helsinki.fi/cmg
Organization name University of Helsinki
Department Pathology
Lab Laboratory of Cytomolecular Genetics
Street address Haartmaninkatu 3
City Helsinki
ZIP/Postal code 00014
Country Finland
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (55)
GSM439886 Ewing sarcoma patient sample R194 (set A)
GSM439887 Ewing sarcoma patient sample R196 (set A)
GSM439888 Ewing sarcoma patient sample R29 (set A)
This SubSeries is part of SuperSeries:
GSE17679 Inflammatory gene profiling of Ewing sarcoma family of tumors
Relations
BioProject PRJNA123367

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE17618_RAW.tar 241.5 Mb (http)(custom) TAR (of CEL)
GSE17618_Survival_data_Savola.txt.gz 652 b (ftp)(http) TXT
Processed data included within Sample table
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