TAF15::NR4A3 gene fusion identifies a morphologically distinct subset of extraskeletal myxoid chondrosarcoma mimicking myoepithelial tumors

A large-scale method to measure the absolute stoichiometries of protein Poly-ADP-Ribosylation

Poly-ADP-ribosylation (PARylation) is a reversible posttranslational modification that occurs in higher eukaryotes. While thousands of PARylated substrates have been identified, the specific biological functions of most PARylated proteins remain elusive. PARylation stoichiometry is a critical parameter to assess the potential functions of a PARylated protein. Here, we developed a large-scale strategy to measure the absolute stoichiometries of protein PARylation. By integrating mild cell lysis, boronate enrichment and carefully designed titration experiments, we were able to determine the PARylation stoichiometries for a total of 235 proteins. This approach enables the capture of all PARylation events on various amino acid acceptors. We revealed that PARylation occupancy spans over three orders of magnitude. However, most PARylation events occur at low stoichiometric values (median 0.578%). Notably, we observed that high stoichiometry PARylation (>1%) predominantly targets proteins involved in transcription regulation and chromatin remodeling. Thus, our study provides a systems-scale, quantitative view of PARylation stoichiometries under genotoxic conditions, which serves as invaluable resources for future functional studies of this important protein posttranslational modification.

Reappraisal of soft tissue myoepithelial tumors by DNA methylation profiling reveals an epigenetically distinct group of mostly fusion-driven neoplasms

Soft tissue myoepithelial tumors (METs) are diagnostically challenging tumors that require careful histologic and immunohistochemical characterization for accurate classification. Nearly half of METs show recurrent EWSR1 or FUS gene rearrangements with a diverse set of fusion partners. The diversity of fusion partners and lack of known driver abnormalities in many cases raises the question of whether METs represent a uniformly distinct tumor entity. To address this question, we performed careful histopathologic and molecular analysis, including DNA methylation profiling (DNA-MP) and fusion testing, on a cohort of 30 institutionally diagnosed METs from 29 patients. On histologic and immunophenotypic evaluation, 22 of 30 tumors diagnosed as MET fulfilled strict histologic and immunophenotypic criteria. Among those failing to meet criteria, most were reclassified as another tumor entity by DNA-MP. Seven tumors meeting criteria grouped with another sarcoma reference type by DNA-MP, with confirmation of the characteristic driver abnormality of that tumor in selected cases. The remaining tumors histologically "consistent" with METs (n = 15) formed a distinct epigenetic cluster, independent of other reference entities. Recurrent gene fusions were identified in 11 of 15 tumors in this epigenetically distinct group, including EWSR1::KLF15 (n = 4), EWSR1::PBX3 (n = 2), and EWSR1::POU5F1 (n = 1) rearrangements. Clinicopathologic correlation suggests that EWSR1::KLF15 tumors are enriched in pediatric patients with aggressive histology. Our work shows that at least a subset of METs falls within an epigenetically distinct but heterogenous group. Furthermore, DNA-MP provides a useful adjunct to other molecular testing to help distinguish METs from histologic mimics.

Non-myxoid solid variant of extraskeletal myxoid chondrosarcoma: An underrecognized subtype

INTRODUCTION

Extraskeletal myxoid chondrosarcoma (EMC) is a rare sarcoma defined by NR4A3 gene rearrangements, typically featuring uniform cells with eosinophilic cytoplasm and mild atypia, arranged in cords or clusters within a chondromyxoid stroma. A cellular variant, characterized by increased cellular density and a solid growth pattern, has been recognized.

METHODS

We encountered three cases of round cell sarcomas, diagnosed as EMC based on NR4A3 or NR4A2 rearrangements. To identify additional pure solid EMC cases, we performed a retrospective review of our institutional files spanning 22 years, focusing on cases labeled as "myxoid chondrosarcoma" with "cellular" features. Histologic slides and clinical data were reviewed.

RESULTS

In addition to the three study cases, 43 cases of EMC with cellular features were identified, none of which exhibited the exclusive round-to-spindle cell morphology seen in the study cases. The three unique cases involved two females and one male (ages 42-62) with tumors in the proximal extremities and trunk. The tumors (3.5-10 cm) were well-circumscribed and densely cellular. One tumor exhibited a biphasic pattern with distinct round and spindle cell areas, whereas the other two were composed purely of round/epithelioid cells. High-grade nuclear atypia and brisk mitotic activity (9-13 per 10 HPFs) were observed, with necrosis identified in one case. Next-generation sequencing revealed TCF12::NR4A3, EWSR1::NR4A3, and EWSR1::NR4A2 fusions. Two patients developed metastases (lymph nodes and lungs), whereas one remained disease-free at last follow-up.

CONCLUSION

We describe a round cell subtype of EMC, distinct from the traditional cellular variant, characterized by a sheet-like proliferation of large, uniform round-to-epithelioid cells and the absence of chondromyxoid stroma. This potentially underrecognized subtype requires molecular testing for accurate diagnosis. Moreover, the presence of NR4A2 fusions, although rare, suggests that the absence of NR4A3 rearrangements does not entirely exclude EMC.

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. Although 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 with 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 >50-fold increased expression in EMC compared with other tumors. Using RNA chromogenic in situ hybridization, we observed strong and diffuse expression of CHRNA6 in 25 cases of EMC, including both EWSR1-rearranged and TAF15-rearranged variants. All examined cases of histologic mimics were negative for CHRNA6 overexpression; however, limited CHRNA6 expression, not reaching a threshold of >5 puncta or 1 aggregate of chromogen in >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 chromogenic in situ hybridization is a potentially useful ancillary histologic tool for the diagnosis of EMC.