Muskara Andrew, Parthasarathy Prarthana B, Oyarbide Usua, Ma Yifeng, Ganguly Shinjini, Imamura Jarrell, Liao Ross, Rubin Brian P, Macaskill Aidan, Murphy Erin S, Anderson Peter M, Gryder Berkley E, Scott Jacob G, Zahler Stacey G, Mian Omar Y
Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, Ohio, USA.
Division of Pediatric Hematology, Oncology & Blood & Marrow Transplantation, Cleveland Clinic Children's, Cleveland, Ohio, USA.
Pediatr Blood Cancer. 2025 Sep;72(9):e31864. doi: 10.1002/pbc.31864. Epub 2025 Jun 26.
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.
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.
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.
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.
横纹肌肉瘤（RMS）是儿童期最常见的软组织肉瘤。历史上基于组织学进行分类，分子谱分析的进展使得能够进一步细分，从而改善了风险分层。尽管分子谱分析增进了我们对疾病进展和风险的理解，但RMS中治疗耐药性的分子演变仍未得到充分表征。对高危、复发性RMS患者进行转录组分析，目的是揭示RMS治疗失败的生物学见解。
获取来自复发性RMS患者的福尔马林固定、石蜡包埋（FFPE）组织样本，这些患者在诊断和复发时均有存档样本。确认组织学亚型和PAX3/7::FOXO1融合状态。使用高通量基因组学（HTG）全转录组面板对FFPE组织样本进行转录组分析。
我们确定了11例复发性RMS患者，他们在多模式治疗后的诊断和复发时均有FFPE组织样本存档。所有患者均被分层为高危，其中5例为PAX3/7::FOXO1融合阳性RMS（FP-RMS），6例为PAX3/7::FOXO1融合阴性RMS（FN-RMS）。转录组分析显示，FP-RMS患者在治疗前富集了与肌生成相关的通路和与肌源性分化相关的标志物，而FN-RMS患者在治疗后富集。在FP-RMS和FN-RMS样本中均观察到治疗后炎症反应通路的富集。
通过基于探针的转录组面板对RMS患者治疗前后匹配的组织样本进行表征，我们报告复发性RMS遵循融合状态依赖性的进化轨迹，其特征是肌生成相关基因、肌源性分化标志物和炎症反应通路的差异表达。
