NTRK-rearranged spindle cell neoplasms are ubiquitous tumors of myofibroblastic lineage with a distinct methylation class

NTRK gene fusions have been described in a wide variety of central nervous system (CNS) and soft tissue tumors, including the provisional tumor type "spindle cell neoplasm, NTRK-rearranged" (SCN-NTRK), added to the 2020 World Health Organization Classification of Soft Tissue Tumors. Because of histopathological and molecular overlaps with other soft tissue entities, controversy remains concerning the lineage and terminology of SCN-NTRK.This study included 16 mesenchymal tumors displaying kinase gene fusions (NTRK fusions and one MET fusion) initially diagnosed as infantile fibrosarcomas (IFS), SCN-NTRK, and adult-type fibrosarcomas from the soft tissue, viscera and CNS. We used immunohistochemistry, DNA methylation profiling, whole RNA-sequencing and ultrastructural analysis to characterize them. Unsupervised t-distributed stochastic neighbor embedding analysis showed that 11 cases (2 CNS tumors and 9 extra-CNS) formed a unique and new methylation cluster, while all tumors but one, initially diagnosed as IFS, clustered in a distinct methylation class. All the tumors except one formed a single cluster within the hierarchical clustering of whole RNA-sequencing data. Tumors from the novel methylation class co-expressed CD34 and S100, had variable histopathological grades and frequently displayed a CDKN2A deletion. Ultrastructural analyses evidenced a myofibroblastic differentiation.Our findings confirm that SCN-NTRK share similar features in adults and children and in all locations combine an infiltrative pattern, distinct epigenetic and transcriptomic profiles, and ultrastructural evidence of a myofibroblastic lineage. Further studies may support the use of new terminology to better describe their myofibroblastic nature.