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Updated: Aug 14, 2025

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
Head and Neck Mesenchymal Tumors with Kinase Fusions: A Report of 15 Cases With Emphasis on Wide Anatomic
Bin Xu1, Albert J H Suurmeijer2, Narasimhan P Agaram1
1Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.
Abstract:
Mesenchymal tumors harboring various kinase fusions were recently recognized as emerging entities mainly in the soft tissues. We herein investigate the clinicopathologic and molecular characteristics of head and neck mesenchymal tumors harboring kinase fusions. The study cohort included 15 patients with a median age of 13 years (ranging from congenital to 63 y). The kinase genes involved in descending order were NTRK1 (n=6), NTRK3 (n=5), BRAF (n=2), and 1 each with MET, and RET. The anatomic locations were broad involving all tissue planes, including skin (n=4), intraosseous (n=4), major salivary glands (n=2), sinonasal tract (n=2), soft tissue of face or neck (n=2), and oral cavity (n=1). The histologic spectrum ranged from benign to high grade, in descending order including tumors resembling malignant peripheral nerve sheath tumor (MPNST)-like, fibrosarcoma (infantile or adult-type), lipofibromatosis-like neural tumor (LPFNT), inflammatory myofibroblastic tumor-like, and a novel phenotype resembling myxoma. Perivascular hyalinization/stromal keloid-like collagen bands and staghorn vasculature were common features in MPNST-like and LPFNT-like tumors. Two tumors (1 each with NTRK1 or BRAF rearrangement) were classified as high grade. By immunohistochemistry, S100 and CD34 positivity was noted in 71% and 60%, frequently in MPNST-like and LPFNT-like phenotypes. Pan-TRK was a sensitive marker for NTRK-translocated tumors but was negative in tumor with other kinase fusions. One patient with a high-grade tumor developed distant metastasis. Molecular testing for various kinase fusions should be considered for S100+/CD34+ spindle cell neoplasms with perivascular hyalinization and staghorn vessels, as pan-TRK positivity is seen only in NTRK fusions.
Insights
Head and neck mesenchymal tumors with kinase fusions, particularly NTRK gene fusions, are emerging entities. Molecular testing is crucial for diagnosing these rare tumors, especially S100+/CD34+ spindle cell neoplasms.
Area of Science:
- Oncology
- Molecular Pathology
- Genetics
Background:
- Mesenchymal tumors with kinase fusions are increasingly recognized, primarily in soft tissues.
- This study focuses on the clinicopathologic and molecular features of head and neck mesenchymal tumors harboring kinase fusions.
Observation:
- The cohort comprised 15 patients (median age 13 years) with kinase genes including NTRK1, NTRK3, BRAF, MET, and RET.
- Tumors occurred in diverse head and neck locations and exhibited a wide histologic spectrum, from benign to high-grade.
- Common features included perivascular hyalinization and staghorn vasculature, particularly in MPNST-like and LPFNT-like tumors.
Findings:
- NTRK fusions were the most common (NTRK1: 6, NTRK3: 5).
- Histologic subtypes included MPNST-like, fibrosarcoma, LPFNT-like, and inflammatory myofibroblastic tumor-like.
- Pan-TRK immunohistochemistry was sensitive for NTRK fusions but negative for other kinase fusions.
Implications:
- Molecular testing for kinase fusions is recommended for S100+/CD34+ spindle cell neoplasms with specific histologic features.
- Accurate diagnosis of these rare tumors is essential for appropriate management and understanding their behavior.
- Identifying kinase fusions aids in targeted therapy selection and predicting patient outcomes.
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