Transcriptomic Profiling of Relapsed Rhabdomyosarcoma: Pre‐ and Post‐Treatment Tissue Analysis Reveals Molecular Characteristics of Treatment Failure

ABSTRACT Background Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood. Historically classified based on histology, advances in molecular profiling have allowed further sub‐classification, which has improved risk stratification. Although molecular profiling has improved our understanding of disease progression and risk, the molecular evolution of therapy resistance in RMS remains poorly characterized. Transcriptomic profiling of patients with high‐risk, relapsed RMS was undertaken with the goal of uncovering insights into the biology of RMS treatment failure. Procedure Formalin‐fixed, paraffin‐embedded (FFPE) tissue samples from patients with relapsed RMS who had samples archived at diagnosis and relapse were obtained. Histologic subtype and PAX3/7::FOXO1 fusion status were confirmed. Transcriptomic profiling of the FFPE tissue samples was performed using the high‐throughput genomics (HTG) whole transcriptome panel. Results We identified 11 patients with relapsed RMS who had FFPE tissue samples archived at diagnosis and relapse following multimodality therapy. All patients were stratified as high risk, including five with PAX3/7::FOXO1 fusion‐positive RMS (FP‐RMS) and six with PAX3/7::FOXO1 fusion‐negative RMS (FN‐RMS). The transcriptomic analysis revealed that the myogenesis pathway and markers associated with myogenic differentiation were enriched pre‐treatment in patients with FP‐RMS and enriched post‐treatment in patients with FN‐RMS. Post‐treatment enrichment of the inflammatory response pathway was observed in both FP‐RMS and FN‐RMS samples. Conclusions Using a probe‐based transcriptome panel to characterize matched pre‐ and post‐treatment tissue samples from patients with RMS, we report that relapsed RMS follows a fusion status‐dependent evolutionary trajectory, marked by differential expression of myogenesis‐associated genes, myogenic differentiation markers, and inflammatory response pathways.