title: Expression analysis of pediatric solid tumor cell lines using oligonucleotide microarrays.
abstract: We identified patterns of differentially-expressed genes in cell lines derived from several pediatric solid tumors. Affymetrix Human Cancer G110 Arrays, carrying 1,700 cancer-associated genes, were applied to a panel of 11 cell lines originating from Ewing tumors (ETs), neuroblastomas, and malignant melanoma of soft parts. Hierarchical clustering clearly differentiated these 3 entities and revealed groups of 75, 102, and 36 gene probe-sets exhibiting tumor-type specific up-regulation in these cell lines, respectively. Whereas ET lines demonstrated increased expression of microtubule-associated protein tau (MAPT), protein phosphatase 1 regulatory subunit 1A (PPP1R1A), NIMA (never in mitosis gene a)-related kinase 2 (NEK2), and cyclin D1 (CCND1), neuroblastoma samples exhibited high expression of wingless-type mouse mammary tumor virus integration site family member 11 (WNT11), Drosophila frizzled homolog 2 (FZD2), and adenomatous polyposis coli (APC) which are involved in regulating free beta-catenin levels. These genes likely maintain tumor-specific characteristics and participate in key downstream regulatory mechanisms. We also correlated the expression levels of up-regulated genes in ETs with their chromosomal localization and compared these data to the comparative genomic hybridization profiles of the cell lines. We demonstrate that gains of genetic material contribute essentially to differential gene expression.
authors.affiliation: Gerhard-Domagk-Institute of Pathology, University of Muenster, D-48149 Muenster, Germany.
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Wai
authors.forename: Karl-Ludwig
authors.initials: KL
authors.lastname: Schaefer
authors.forename: Alexander
authors.initials: A
authors.lastname: Schramm
authors.forename: Eberhard
authors.initials: E
authors.lastname: Korsching
authors.forename: Frans
authors.initials: F
authors.lastname: Van Valen
authors.forename: Toshifumi
authors.initials: T
authors.lastname: Ozaki
authors.forename: Werner
authors.initials: W
authors.lastname: Boecker
authors.forename: Lothar
authors.initials: L
authors.lastname: Schweigerer
authors.forename: Barbara
authors.initials: B
authors.lastname: Dockhorn-Dworniczak
authors.forename: Christopher
authors.initials: C
authors.lastname: Poremba
mesh_terms: D002648:Child; D016000:Cluster Analysis; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008545:Melanoma / Q000235:genetics; D009369:Neoplasms / Q000235:genetics*; D009447:Neuroblastoma / Q000235:genetics; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D009841:Oligonucleotides / Q000737:chemistry*; D018075:RNA, Complementary / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012512:Sarcoma, Ewing / Q000235:genetics; D014407:Tumor Cells, Cultured; D015854:Up-Regulation
chemical_list: D009841:Oligonucleotides; D018075:RNA, Complementary