CHRNA6 RNA in situ hybridization is a useful tool for the diagnosis of extraskeletal myxoid chondrosarcoma

Extraskeletal myxoid chondrosarcoma (EMC) is an uncommon mesenchymal neoplasm characteristically composed of uniform-appearing round to spindle-shaped cells with eosinophilic cytoplasm and abundant myxoid extracellular matrix. While the majority of cases harbor a pathognomonic t(9;22) translocation that fuses EWSR1 with the orphan nuclear receptor NR4A3, there are less common variants that partner NR4A3 with TAF15, TCF12, or TFG. By immunohistochemistry, EMC has features of both cartilaginous and neuroendocrine differentiation, as evidenced by inconsistent expression of S100 protein and synaptophysin or INSM1, respectively, in a subset of cases. Given the limitations of available immunohistochemical stains for the diagnosis of EMC, we analyzed genome-wide gene expression microarray data to identify candidate biomarkers based on differential expression in EMC in comparison to other mesenchymal neoplasms. This analysis pointed to CHRNA6 as the gene with the highest relative expression in EMC (96-fold; P = 8.2×10-26), and the only gene with more than 50-fold increased expression in EMC compared to other tumors. Using RNA chromogenic in situ hybridization (CISH), we observed strong and diffuse expression of CHRNA6 in 25 cases of EMC, including both EWSR1- and TAF15-rearranged variants. All examined cases of histological mimics were negative for CHRNA6 overexpression; however, limited CHRNA6 expression, not reaching a threshold of greater than 5 puncta or one aggregate of chromogen in more than 25% of cells, was observed in 69 of 685 mimics (10.1%), spanning an array of mesenchymal tumors. Taken together, these findings suggest that, with careful interpretation and the use of appropriate thresholds, CHRNA6 RNA CISH is a potentially useful ancillary histological tool for the diagnosis of EMC.