Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors

FGFR1 fusions as a novel molecular driver in rhabdomyosarcoma

The wide application of RNA sequencing in clinical practice has allowed the discovery of novel fusion genes, which have contributed to a refined molecular classification of rhabdomyosarcoma (RMS). Most fusions in RMS result in aberrant transcription factors, such as PAX3/7::FOXO1 in alveolar RMS (ARMS) and fusions involving VGLL2 or NCOA2 in infantile spindle cell RMS. However, recurrent fusions driving oncogenic kinase activation have not been reported in RMS. Triggered by an index case of an unclassified RMS (overlapping features between ARMS and sclerosing RMS) with a novel FGFR1::ANK1 fusion, we reviewed our molecular files for cases harboring FGFR1-related fusions. One additional case with an FGFR1::TACC1 fusion was identified in a tumor resembling embryonal RMS (ERMS) with anaplasia, but with no pathogenic variants in TP53 or DICER1 on germline testing. Both cases occurred in males, aged 7 and 24, and in the pelvis. The 2nd case also harbored additional alterations, including somatic TP53 and TET2 mutations. Two additional RMS cases (one unclassified, one ERMS) with FGFR1 overexpression but lacking FGFR1 fusions were identified by RNA sequencing. These two cases and the FGFR1::TACC1-positive case clustered together with the ERMS group by RNAseq. This is the first report of RMS harboring recurrent FGFR1 fusions. However, it remains unclear if FGFR1 fusions define a novel subset of RMS or alternatively, whether this alteration can sporadically drive the pathogenesis of known RMS subtypes, such as ERMS. Additional larger series with integrated genomic and epigenetic datasets are needed for better subclassification, as the resulting oncogenic kinase activation underscores the potential for targeted therapy.

Rhabdomyosarcoma xenotransplants in zebrafish embryos

Rhabdomyosarcomas (RMS) are the most common pediatric soft tissue sarcomas. High-risk and metastatic disease continues to be associated with very poor prognosis. RMS model systems that faithfully recapitulate the human disease and provide rapid, cost-efficient estimates of antitumor efficacy of candidate drugs are needed to facilitate drug development and personalized medicine approaches. Here, we present a new zebrafish-based xenotransplant model allowing for rapid and easily accessible drug screening using low numbers of viable tumor cells and relatively small amounts of water-soluble chemicals. Under optimized temperature conditions, embryonal RMS xenografts were established in zebrafish embryos at 3 h postfertilization (hpf). In proof-of-principle experiments, chemotherapy drugs with established clinical anti-RMS efficacy (vincristine, dactinomycin) and the mitogen-activated protein kinase kinase inhibitor trametinib were shown to significantly reduce the cross-sectional area of the tumors by 120 hpf. RMS xenograft models in zebrafish embryos henceforth could serve as a valuable addition to cell culture and mammalian models of RMS and represent a rapid and cost-effective solution for preclinical candidate drug testing.

Molecular analysis of 10 pleomorphic rhabdomyosarcomas reveals potential prognostic markers and druggable targets

Pleomorphic rhabdomyosarcoma (PRMS) is a rare and aggressive adult sarcoma with a median overall survival of less than 2 years. Most PRMS do not respond to conventional chemotherapy and/or radiation, and targeted therapies are nonexistent as few PRMS have undergone the molecular characterization necessary to identify therapeutic options. To date, complex structural and few recurrent regional copy alterations have been reported in the PRMS cases evaluated by cytogenetic and comparative genomic hybridization. Thus, there remains an urgent need for more comprehensive molecular profiling to both understand disease pathogenesis and to identify potentially actionable targets. Ten PRMS resection cases were retrieved from institutional archives and clinicopathologic demographics were recorded. All tumors were subjected to DNA-based targeted next-generation sequencing (NGS) of 340 cancer-related genes while a subset (six cases) underwent gene-expression profiling of 770 genes. Alterations identified by NGS included genes involved in cell cycle regulation (90%), the RAS/MAPK and AKT pathways (80%), telomere maintenance (40%), chromatin remodeling (40%), and DNA repair (20%), as well as the cAMP-signaling pathway (10%). Microsatellite instability was absent in all cases, and tumor mutational burden was predominantly low. Gene expression profiling revealed up-regulation of many of the same pathways, including the RTK/MAPK, AKT/PIK3CA/mTOR, Wnt, Hedgehog and JAK/STAT pathways. Survival analysis demonstrated patients with concurrent biallelic inactivation of CDKN2A and TP53 showed significantly shorter overall survival (median: 2 vs. 50 months). Our integrated molecular characterization identified not only potentially targetable alterations, but also prognostic markers for stratification of PRMS patients.