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.

Anaplastic lymphoma kinase status in rhabdomyosarcomas

“…This finding is consistent with that of a previous report in which rhabdomyosarcoma cell lines were found not to harbor DNA copy number gain at the 2p23 locus, where the ALK gene is located. 39 Similarly, ALK was not found to be a differentially amplified gene when genomic imbalances were compared between primary rhabdomyosarcoma tissues and normal muscle. 39 Our finding of a low incidence of increased ALK copy number in rhabdomyosarcoma was in contrast with the results of a recent large study by van Gaal et al 23 In their study, the absolute ALK copy number increased (44 copies in 410% of cells) in 88% of alveolar rhabdomyosarcomas and 52% of embryonal tumors, and a selective ALK gain (average ALK/LAF41.5) was seen in 45% of alveolar tumors and 61% of embryonal cases.…”

Blocking the FGF/FGFR system as a ⿿two-compartment⿿ antiangiogenic/antitumor approach in cancer therapy

“…Recent studies have demonstrated focal FGFR1 amplification in non-small cell lung carcinoma cells in 3% of lung adenocarcinomas and 21% of squamous cell carcinomas [60,61]. FGFR1 amplifications have been observed also in oral squamous carcinomas [62] and are found at a low incidence in ovarian cancer [63], bladder cancer [58] and rhabodomyosarcoma [64]. As to FGFR2, approximately 10% of gastric cancers show FGFR2 amplification, which is associated with poor prognosis in diffuse-type cancers [65].…”

Activation of the hedgehog pathway confers a poor prognosis in embryonal and fusion gene-negative alveolar rhabdomyosarcoma

“…The expression profiling of the two data sets was quality evaluated as described previously in Missiaglia et al (2009) and Williamson et al (2010) and normalized by the gcRMA function, which is a modified Robust Multiarray Average that takes into account probe sequence information for the background adjustment. Microarray analysis was performed by HGU133plus2 arrays (cohort 1) or by U133A expression arrays (cohort 2).…”