Integration of Whole-Genome Sequencing Analysis with Unique Patient-Derived Models Reveals Clinically Relevant Drug...

Precision medicine is a likely future for all cancer treatment but may have its greatest impact on less common, high-mortality, and molecularly heterogeneous cancers. TFCP2-rearranged rhabdomyosarcoma (RMS) is a rare, aggressive cancer with poor survival due to the lack of effective therapies and relevant models to facilitate research. In this study, we establish the first matched patient-derived xenograft and cell line model for TFCP2-rearranged intraosseous RMS, coupled with comprehensive multiomic and functional analyses, to discover and preclinically validate novel actionable molecular targets for this malignancy. Sequencing analyses of matched patient tumor and xenograft material revealed alterations in gene networks associated with the oncogenic, potentially targetable PI3K/AKT pathway. Preclinical assessments revealed that targeting the pathway with a small-molecule PI3K/mTOR inhibitor dactolisib presents a promising treatment approach for this rare cancer, decreasing cancer cell viability in vitro and significantly reducing tumor growth in vivo. Parallel identification of the codeletion of adjacent genes cyclin-dependent kinase inhibitor 2A and methylthioadenosine phosphorylase in these tumors led us to further explore protein arginine methyltransferase 5 inhibition as a potential therapeutic approach. Strikingly, combined inhibition of protein arginine methyltransferase 5 and PI3K/mTOR signaling synergistically enhanced antitumor response and significantly improved survival in vivo. This study highlights the importance of new patient-derived models for the elucidation of the biology of rare cancers and identification of new therapeutic entry points, with clear implications for the future treatment of TFCP2-rearranged intraosseous RMS.