title: Profiling and functional annotation of mRNA gene expression in pediatric rhabdomyosarcoma and Ewing's sarcoma.
abstract: Using Affymetrix oligonucleotide microarrays, we analyzed mRNA gene expression patterns of 12 primary pediatric rhabdomyosarcomas (RMS) and 11 Ewing's sarcomas (EWS), which belong to the small round blue cell tumors (SRBCTs). Diagnostic classification of these cancers is frequently complicated by the highly similar appearance in routine histology, and additional molecular markers could significantly improve tumor classification. A combination of three independent statistical approaches (t-test, SAM, k-nearest neighborhood analysis) resulted in 101 highly significant probe sets that clearly discriminate between EWS and RMS. We identified novel marker transcripts that have not been previously associated with either RMS or EWS yet, including CITED2, glypican 3 (GPC3), and cyclin D1 (CCND1). Expression levels for selected candidate genes were validated by quantitative real-time reverse-transcription PCR. Furthermore, to identify biologically meaningful trends, functional annotations were assigned to 946 genes differentially expressed between EWS and RMS (t-test). Genes involved in protein biosynthesis (n = 28) and complex assembly (n = 9), lipid metabolism (n = 23), energy generation (n = 22), and mRNA processing (n = 11) were expressed significantly higher in EWS. Thus, functional annotation of tumor-specific genes reveals detailed insights into tumor biology and differentiation-specific expression patterns and gives important clues related to the possible cellular origin of these pediatric tumors. Supplementary material for this article is available at the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7136/suppmat/index.html.
authors.affiliation: Deparment of Pediatric Oncology, Hematology and Immunology, University Children's Hospital, Heidelberg, Germany. claudia.baer@med.uni-heidelberg.de
authors.forename: Claudia
authors.initials: C
authors.lastname: Baer
authors.forename: Mattias
authors.initials: M
authors.lastname: Nees
authors.forename: Stephen
authors.initials: S
authors.lastname: Breit
authors.forename: Barbara
authors.initials: B
authors.lastname: Selle
authors.forename: Andreas E
authors.initials: AE
authors.lastname: Kulozik
authors.forename: Karl-Ludwig
authors.initials: KL
authors.lastname: Schaefer
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Braun
authors.forename: Daniel
authors.initials: D
authors.lastname: Wai
authors.forename: Christopher
authors.initials: C
authors.lastname: Poremba
mesh_terms: D014408:Biomarkers, Tumor; D002454:Cell Differentiation; D045744:Cell Line, Tumor; D002648:Child; D019938:Cyclin D1 / Q000096:biosynthesis; D017931:DNA Primers / Q000494:pharmacology; D004268:DNA-Binding Proteins / Q000096:biosynthesis; D018450:Disease Progression; D005347:Fibroblasts / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic; D005819:Genetic Markers; D053673:Glypicans; D019812:Heparan Sulfate Proteoglycans / Q000096:biosynthesis; D006801:Humans; D050356:Lipid Metabolism; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D018075:RNA, Complementary / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism*; D012097:Repressor Proteins / Q000096:biosynthesis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012208:Rhabdomyosarcoma / Q000235:genetics*; D012512:Sarcoma, Ewing / Q000235:genetics*; D015534:Trans-Activators / Q000096:biosynthesis
chemical_list: D014408:Biomarkers, Tumor; C486381:CITED2 protein, human; D017931:DNA Primers; D004268:DNA-Binding Proteins; D005819:Genetic Markers; D053673:Glypicans; D019812:Heparan Sulfate Proteoglycans; D018075:RNA, Complementary; D012333:RNA, Messenger; D012097:Repressor Proteins; D015534:Trans-Activators; D019938:Cyclin D1