Genitourinary mesenchymal neoplasms with tumor-defining genetic alterations: A clinicopathologic and molecular correlative study of 71 cases

Genitourinary mesenchymal neoplasms (GMNs) encompass diverse tumors with limited research on clinicopathologic and genetic characteristics across different organs and age groups. We investigated 71 GMNs with tumor-defining genetic alterations (GMN-TDGA), categorizing tumors into spindle, round, or epithelioid based on predominant patterns. Pediatric GMN-TDGAs primarily involved the kidney, with six congenital mesoblastic nephromas showing spindly histology, including three cellular variants with ETV6::NTRK3 fusion, two classical variants with EGFR exon 18–25 duplications, and one novel TFG::NTRK3-positive case. Four renal clear cell sarcomas exhibited spindly and round cell patterns, harboring BCOR exon 15 duplications (n = 3) or YWHAE rearrangement (n = 1). Two renal EWSR1::FLI1-positive Ewing sarcomas (EWS) and one vesical ALK-rearranged inflammatory myofibroblastic tumor (IMT) occurred in children. In adults, recurrent histotypes included vesical IMTs (n = 15: 14 ALK-rearranged/positive, 1 RET-rearranged), renal synovial sarcomas (SS, n = 13: 7 poorly differentiated, 5 monophasic, 1 biphasic), renal EWS (n = 4, including one unreported EWSR1::ERG-positive atypical variant), renal sclerosing epithelioid fibrosarcomas (SEF, n = 3, all with EWSR1::CREB3L1), renal and vesical TFE3-rearranged PEComas (n = 3, 1 malignant), renal and preputial CIC-rearranged sarcomas (CICRS, n = 3), and multi-organ NAB2::STAT6-positive solitary fibrous tumors (SFTs, n = 10). Event-free survival varied significantly across adult GMN-TDGAs (P < 0.001), with CICRS (100 %), SS (61.5 %), and EWS (50 %) showing higher event rates compared to SEF (33.3 %), PEComa (33.3 %), SFT (20 %), and IMT (0 %). Ultra-rare GMN-TDGAs included a PTCH1::GLI1-positive renal epithelioid mesenchymal neoplasm, a BRAF-deleted renal spindle cell tumor, and a MYOD1-mutated prostatic spindle cell rhabdomyosarcoma. Conclusively, molecular profiling highlights the histologic and genetic diversity of GMNs, supporting challenging diagnoses and informing personalized therapies.