Introduction

Extraskeletal osteosarcoma (ESOS) is a rare malignant mesenchymal tumor characterized by the production of osteoid or bone matrix in soft tissue without direct skeletal involvement. ESOS accounts for less than 1% of all soft tissue sarcomas and approximately 4% of all osteosarcomas. It commonly affects the extremities and trunk1. The treatment of ESOS is challenging due to its aggressive nature, rarity, and frequent presentation with metastases2. Despite new molecular therapeutic strategies, treatment modalities have not significantly changed for ESOS over decades1,2. To the best of our knowledge, we present the first worldwide reported case of ESOS with an NTRK fusion, successfully treated with larotrectinib, demonstrating excellent clinical benefit.

Patients characteristics

A 74-year-old man presented to a peripheral hospital with a painful, 7.9 × 7.1 × 6.6 cm mass on the left side of his neck. The lesion had been noticeable for only a few months and had just recently started to grow. MRI revealed an inoperable tumor localized in the parapharyngeal/paravertebral space.

Methods

Formalin-fixed and paraffin-processed tissue sections (4 μm) from tissue biopsy specimens were routinely stained with haematoxylin and eosin. IHC staining for pan-TRK expression was performed on the Benchmark Ultra platform (Ventana Medical Systems, Tucson, AZ) with iVIEW DAB Detection Kit (Ventana Medical Systems, Tucson, AZ), using a commercially available pan-TRK assay (rabbit monoclonal antibody, clone EPR17341, Assay, RTU, Roche, Ventana). Normal appendix and brain tissues were used as positive controls. In addition, IHC was performed for SATB2, MDM2, Pan-cytokeratin (CK), CK AE1/3, Desmin, H3.3, CD34, SMA and CD45 (LCA) see Table 1.

Table 1 List of used antibodies
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Genomic DNA and RNA were extracted from the FFPE block. Targeted RNA sequencing was performed using the Archer Fusion Plex Pan Solid Tumor v2 panel, along with a DNA-based targeted analysis utilizing the Ion Torrent Oncomine Comprehensive Assay Plus, according to the manufacturers’ protocols. The analysis was performed with ArcherDX Analysis software Version 7.1.0-14, and for the DNA Panel, the Thermo Fisher- IonReporter 5.18.

Both assays use proprietary, closed bio-informatics pipelines. Archer uses AMP PCR with a gene-specific primer (GSP) and an adapter primer, combined with molecular barcodes for error correction. Quality filters are applied automatically (e.g., minimum reads on target, minimum number of unique molecules per GSP). Oncomine uses targeted PCR where both primers are within the target. Filtering is based primarily on minimum read counts. In practice, further filtering is rarely needed due to a very low rate of false positives. Both platforms rely on their internal pipelines with default quality thresholds for single-nucleotide variant calling, which are part of the proprietary system.

This case report was conducted in full compliance with the ethical principles outlined in the 1964 Helsinki Declaration and its subsequent amendments. The participant gave full written informed consent. Institutional Review Board Approval was obtained (EK1232/2025).

Reporting summary

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.

Results

Histological examination of the core needle biopsy revealed mesenchymal tumor tissue. Focal osteoid deposition surrounding tumor cells in a lace-like pattern, as well as regions of necrosis, were also identified (Fig. 1a). The tumor was composed of round to oval cells with vesicular chromatin, occasional prominent nucleoli, and eosinophilic cytoplasm with indistinct cell borders (Fig. 1b). Multinucleated osteoclast-like giant cells and inflammatory cells were also present. The tumor demonstrated markedly increased mitotic activity, including atypical mitoses.

Fig. 1: Histological and molecular characteristics of the tumor.
Fig. 1: Histological and molecular characteristics of the tumor.
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a Overview of the core needle biopsy exhibiting different components (blue star—spindle cell tumor tissue, green star—lace-like osteoid formation, yellow star—tumor necrosis) (4× magnification); b spindle cell like tumor tissue with highly atypical tumor cells; c Pan-TRK immunohistochemistry showing focal weak to moderate positivity; d SATB2 immunohistochemistry showing strong positivity (b–d – 40× magnification); e molecular testing identified an ETV6::NTRK3 fusion (Archer).

IHC studies demonstrated a focal and partially weak staining reaction for pan-TRK (Fig. 1c), which can be used to screen for neurotrophic tyrosine receptor kinase (NTRK) fusions with high sensitivity and specificity3. Staining also revealed a strong nuclear expression of SATB2 (Fig. 1d). The IHC stains CD163 and MDM2 were expressed in some tumor cells. Pan-cytokeratin, cytokeratin AE1/3, Desmin, H3.3, CD34, and SMA were negative. CD45 (LCA) marked inflammatory cells and histiocytic cells.

Molecular testing identified an ETV6::NTRK3 fusion (Archer) (Fig. 1e) and mutations in the ARID1B, KMT2D, and SMARCA4 genes, all classified as likely pathogenic (https://varsome.com/variant/hg19/chr6-157527437-GC-G, https://varsome.com/variant/hg19/chr12-49435872-C-T, https://varsome.com/variant/hg19/chr19-11097268-TG-T) as well as a BRCA1 mutation classified as likely benign (https://varsome.com/variant/hg19/chr17-41244184-T-C). Additionally, the copy number variation (CNV) profile demonstrated loss (n < 1) of the genes OR4M2, HLA-B, CDKN2A, HLA-A, and MTAP, as well as gain (n > 5) of the genes PIK3CB, FGF3, CCND1, and FGF19. Based on the identified ETV6::NTRK3 fusion, treatment with larotrectinib, a selective NTRK1-3 inhibitor, was promptly initiated with the standard full dose of 2 × 100 mg/24 h. The therapy demonstrated remarkable clinical benefit within a short period.

The MRI and CT scans performed prior to treatment start revealed that the tumor was causing significant compression of the hypopharynx and infiltrating the paravertebral musculature (Fig. 2a, b). The tumor was deemed inoperable. Significant improvement was seen after just 3 weeks (Fig. 2d), and after 2 months, MRI revealed partial remission of the tumor (4.7 × 3.9 × 2.8 cm) (Fig. 2c). Subsequent MRI at 8 months after treatment initiation with larotrectinib showed further tumor shrinkage to 4.4 × 3.7 × 2.4 cm.

Fig. 2: Clinico-radiological correlation of the disease course.
Fig. 2: Clinico-radiological correlation of the disease course.
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a MRI of the tumor (coronal cut) before initiation of treatment with larotrectinib (tumor encircled). b Clinical picture of the patient’s neck before treatment initiation (tumor encircled). c MRI of the tumor (coronal cut) 2 months after treatment with larotrectinib (tumor encircled). d Clinical picture of the patient’s neck 3 weeks after treatment initiation (tumor encircled).

In the interim, the patient faced several significant health complications. Initially diagnosed with urothelial carcinoma of the bladder in 2019, he experienced a recurrence 5 years later, this time with neuroendocrine differentiation. This required three cycles of chemotherapy with carboplatin and etoposide, followed by a cystoprostatectomy in the same year. At the beginning of the neoadjuvant therapy with carboplatin and etoposide, the dose of larotrectinib was reduced to 100 mg once a day. Postoperatively, the therapy with larotrectinib was stopped for a month due to postoperative infection. After that, therapy with larotrectinib was resumed, and the dose remained unchanged. The patient did not exhibit any side effects in the context of the TRK inhibitor.

Use of larotrectinib was associated with continued success in our patient, resulting in a partial response (assessed using the “Response evaluation criteria in solid tumors”—RECIST 1.14), in the following month. Consequently, consolidative proton therapy was additionally administered 11 months after treatment initiation. One year after initiating treatment, the patient exhibited stable disease with excellent tolerability of the prescribed regimen.

Discussion

Molecular analysis has brought significant insights into the pathogenesis of sarcomas, revealing actionable genetic alterations that can influence therapeutic strategies. One such alteration is the NTRK fusion, a rare but clinically significant oncogenic driver found in various tumor types. NTRK fusions result from the joining of the kinase domain of NTRK1,2,3 genes with various partner genes. This fusion leads to ligand-independent dimerization and activation of TRK receptors, driving downstream signaling through the MAPK, PI3K/AKT, and PLCγ pathways. This oncogenic activation enhances proliferation, survival, and metastasis1,5,6.

NTRK fusions are common in certain tumors secretory breast carcinoma, mammary analog secretory carcinoma, and infantile fibrosarcoma7, but rare in bone tumors, especially osteosarcoma6,8. Authors found pan-TRK positivity in 19/354 cases, but RNA-based next-generation sequencing (NGS) detected no NTRK fusions9. Another study identified three NTRK fusions in 113 osteosarcoma cases, but these were non-functional10. Furthermore, there has been a report of a functional EML4:NTRK3 fusion in spindle cell sarcoma, responsive to larotrectinib11.

Patients with confirmed NTRK fusions independent of tumor type benefit from precision medicine approaches that offer substantial clinical responses, even in advanced or metastatic settings6,12. Key therapeutic agents include the selective TRK inhibitors larotrectinib and entrectinib, both approved for adult and pediatric patients with NTRK fusion-positive solid tumors regardless of tumor type. Both drugs have been shown to be effective, well-tolerated, with side effects primarily including fatigue, dizziness, and nausea13,14,15,16,17. Extensive screening and accurate detection of NTRK fusions are critical for identifying patients.

Given the tumor’s inoperability in our patient, pan-TRK immunohistochemistry was performed, revealing focal yet specific pan-TRK expression. Although NTRK fusions are not typically associated with ESOS, this unexpected finding prompted comprehensive molecular profiling. NTRK fusion analysis was conducted in accordance with the testing algorithm proposed by the ESMO Translational Research and Precision Medicine Working Group17. An RNA-based NGS assay was employed due to its high reliability and its proven superiority over FISH and RT-PCR, particularly in tumors that are not known to harbor recurrent NTRK fusions17.

While histology and immunophenotyping remain essential for diagnosing bone and soft tissue tumors, molecular techniques—including RNA and DNA sequencing for the detection of gene fusions, somatic structural variants, CNVs, and mutations, as well as methylome profiling—are becoming increasingly indispensable for accurate diagnosis, prognostication, and therapeutic stratification17,18. Emerging technologies such as nanopore sequencing and AI-driven image analysis hold promise for further accelerating and refining diagnostic workflows in these rare tumor types.

NTRK fusions are exceedingly rare in bone sarcomas, and to date, no functionally confirmed case of osteosarcoma or ESOS has been reported in the literature. To the best of our knowledge, this represents the first documented case of ESOS harboring a functional NTRK fusion successfully treated with larotrectinib. In conclusion, this case underscores the vital role of comprehensive molecular diagnostics in the management of soft tissue and bone sarcomas, demonstrating that even in tumor types not typically associated with actionable alterations, such testing can reveal clinically significant targets and enable personalized treatment strategies with meaningful therapeutic benefit.