Biallelic NF1 Inactivation and Widespread Loss of Heterozygosity in a Subset of Unclassified Fibromyxoid Mesenchymal Neoplasms

ABSTRACT The integration of next generation sequencing into clinical practice has revolutionized the diagnosis of soft tissue tumors, enabling the discovery of novel tumor entities. We encountered a group of unclassified fibromyxoid mesenchymal neoplasms harboring biallelic NF1 loss of function (LOF) mutations, lacking features of neurofibroma or neurofibromatosis. The tumors were investigated by immunohistochemistry (IHC), targeted DNA and RNA sequencing and DNA methylation profiling. All cases occurred in male patients aged 4–76 years (median, 53 years). Tumor sites included the thigh (2), pelvis (2), and retroperitoneum (1), with size range of 5.7–12.2 cm (median, 9.1 cm). The tumors were well‐demarcated with minimal infiltration of adjacent tissue and shared morphologic features. The stroma ranged from predominantly myxoid, fibromyxoid to mostly fibrous. Tumor cells were spindle with scant cytoplasm and ovoid nuclei with fine chromatin and inconspicuous nucleoli. Mitoses were rare (≤ 2/2 mm 2 ), and necrosis was absent. IHC findings were largely nonspecific, with variable CD34 staining and lack of neural markers expression. All cases harbored NF1 LOF, four were somatic, and one was germline, all with accompanying loss of heterozygosity (LOH), leading to biallelic inactivation. No other recurrent somatic alterations were identified. Tumor mutational burden was consistently low, while fraction of genome altered was high, ranging from 0.25 to 0.93 (median, 0.46). Allele‐specific copy number analysis showed widespread LOH in four of five cases (> 70%). The remaining case demonstrated a high but subthreshold LOH (38%). Targeted RNA sequencing, performed in four cases, was negative for fusions. Dimensionality reduction of DNA methylation placed four cases in a distinct cluster near well‐differentiated/dedifferentiated liposarcoma, while the remaining case was placed near malignant peripheral nerve sheath tumor. All patients underwent surgical resection. Two patients developed local recurrences and are alive with disease, while the remaining three had no evidence of disease. We describe an unclassified fibromyxoid mesenchymal neoplasm of uncertain malignant potential characterized by recurrent biallelic NF1 LOF and widespread genomic LOH.