Epigenetic profiling of biphenotypic sinonasal sarcoma across fusion variants and high-grade transformation

Biphenotypic sinonasal sarcoma (BSS) is a rare mesenchymal neoplasm characterized by dual neural and myogenic differentiation, recurrent PAX3 gene rearrangements, and low-grade morphology. High-grade transformation has been described, posing significant diagnostic challenges due to overlap among sinonasal tumors. DNA methylation profiling has emerged as a powerful diagnostic tool for sinonasal neoplasms, although BSS was not included in previous cohorts. In this study, we investigated the DNA methylation profile of BSS and its relationship with fusion type and high-grade transformation. Fourteen BSS samples were retrospectively collected from four academic institutions. All cases underwent genome-wide methylation profiling using the Illumina Infinium MethylationEPIC array, and available clinical, radiological, histopathologic, and immunohistochemical data were reviewed. RNA sequencing was performed when sufficient material was available. Methylation profiles were analyzed using t-distributed stochastic neighbor embedding (t-SNE) and compared with a reference cohort of sinonasal tumors. The median patient age was 52.7 years, with a female predominance (M:F ratio 1:2.25). The most common fusion was PAX3::MAML3 (6/12, 50.0%), followed by PAX3::FOXO1 and other rare rearrangements, including PAX3::NCOA2, PAX3::YAP1, and FUS::POU2AF3, detected in one case each (1/12, 8.3%). Most importantly, all BSS samples formed a cohesive epigenetic group upon dimensionality reduction, clearly separated from other sinonasal tumors. No specific clustering was seen among different fusion types or tumor grade. Our findings support that BSS represents a unique and molecularly distinct sinonasal sarcoma with a characteristic DNA methylation signature, independent of gene fusion partners or histologic progression, providing a valuable tool for the classification of challenging cases.