Assessing targetable NTRK1/2/3 fusions in mesenchymal tumors via whole-exome RNA sequencing.

backgroundNeurotrophic receptor tyrosine kinase (NTRK) 1/2/3 fusions, though rare, are highly sought in cancer diagnostics due to tyrosine kinase inhibitors' histology-agnostic approval based on significant efficacy across tumor types. In mesenchymal tumors, these fusions are identified in five typical NTRK-rearranged mesenchymal tumors (NMT): infantile fibrosarcomas, lipofibromatosis-like neural tumors, NTRK-rearranged spindle cell neoplasms, and minority subsets of ALK-negative inflammatory myofibroblastic tumors and quadruple wild-type gastrointestinal stromal tumors. However, their occurrence in other subtypes and actionability remain uncertain.

methodsThis retrospective study included adult and pediatric patients with mesenchymal FFPE (formalin-fixed, paraffin-embedded) tumor samples collected between January 2016 and March 2023. Eligible samples underwent whole-exome RNA sequencing (WERS) for mesenchymal tumor diagnosis or theranostic assessment. Results were reviewed by a multidisciplinary molecular board to assess technical, biological, and clinical relevance.

resultsAmong 3015 samples, primarily malignant, intermediate, and benign mesenchymal tumors, 111 (3.68%) harbored at least one bioinformatically detected NTRK fusion. Forty-three were biologically irrelevant due to absent kinase domains (group 1), and 11 were technical false positives (group 2). Of the 57 robustly identified cases (1.8%), 54 were typical NMT subtypes with canonical gene partners (group 3). Group 4 included three rare fusions in genetically complex sarcomas: MDM2/CDK4-amplified liposarcoma, MDM2/CDK4-amplified intimal sarcoma, and uterine leiomyosarcoma. These cases featured novel fusion partners, higher fusion counts, and comparable single nucleotide variants (SNVs) to group 3.

conclusionWERS reliably identifies actionable NTRK fusions, predominantly in five NMT subtypes, whereas NTRK fusions were rare and extremely rare in other sarcomas where their targetability remains unclear. Routine NTRK screening should prioritize tumors suspected of being NMT rather than being broadly applied.