title: Genomic imbalances in rhabdomyosarcoma cell lines affect expression of genes frequently altered in primary tumors: an approach to identify candidate genes involved in tumor development.
abstract: Rhabdomyosarcomas (RMS) are the most common pediatric soft tissue sarcomas. They resemble developing skeletal muscle and are histologically divided into two main subtypes; alveolar and embryonal RMS. Characteristic genomic aberrations, including the PAX3- and PAX7-FOXO1 fusion genes in alveolar cases, have led to increased understanding of their molecular biology. Here, we determined the effect of genomic copy number on gene expression levels through array comparative genomic hybridization (CGH) analysis of 13 RMS cell lines, confirmed by multiplex ligation-dependent probe amplification copy number analyses, combined with their corresponding expression profiles. Genes altered at the transcriptional level by genomic imbalances were identified and the effect on expression was proportional to the level of genomic imbalance. Extrapolating to a public expression profiling dataset for 132 primary RMS identified features common to the cell lines and primary samples and associations with subtypes and fusion gene status. Genes identified such as CDK4 and MYCN are known to be amplified, overexpressed, and involved in RMS tumorigenesis. Of the many genes identified, those with likely functional relevance included CENPF, DTL, MYC, EYA2, and FGFR1. Copy number and expression of FGFR1 was validated in additional primary material and found amplified in 6 out of 196 cases and overexpressed relative to skeletal muscle and myoblasts, with significantly higher expression levels in the embryonal compared with alveolar subtypes. This illustrates the ability to identify genes of potential significance in tumor development through combining genomic and transcriptomic profiles from representative cell lines with publicly available expression profiling data from primary tumors.
authors.affiliation: Molecular Cytogenetics Team, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK.
authors.forename: Edoardo
authors.initials: E
authors.lastname: Missiaglia
authors.forename: Joanna
authors.initials: J
authors.lastname: Selfe
authors.forename: Mohamed
authors.initials: M
authors.lastname: Hamdi
authors.forename: Daniel
authors.initials: D
authors.lastname: Williamson
authors.forename: Gerben
authors.initials: G
authors.lastname: Schaaf
authors.forename: Cheng
authors.initials: C
authors.lastname: Fang
authors.forename: Jan
authors.initials: J
authors.lastname: Koster
authors.forename: Brenda
authors.initials: B
authors.lastname: Summersgill
authors.forename: Boo
authors.initials: B
authors.lastname: Messahel
authors.forename: Rogier
authors.initials: R
authors.lastname: Versteeg
authors.forename: Kathy
authors.initials: K
authors.lastname: Pritchard-Jones
authors.forename: Marcel
authors.initials: M
authors.lastname: Kool
authors.forename: Janet
authors.initials: J
authors.lastname: Shipley
mesh_terms: D022981:Allelic Imbalance; D045744:Cell Line, Tumor; D002869:Chromosome Aberrations; D055028:Comparative Genomic Hybridization; D005260:Female; D018628:Gene Dosage; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D009363:Neoplasm Proteins / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D051496:Receptor, Fibroblast Growth Factor, Type 1 / Q000235:genetics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012208:Rhabdomyosarcoma / Q000235:genetics*; D018709:Statistics, Nonparametric
chemical_list: D009363:Neoplasm Proteins; C496348:FGFR1 protein, human; D051496:Receptor, Fibroblast Growth Factor, Type 1