NKX3.1 immunohistochemistry and methylome profiling in mesenchymal chondrosarcoma: additional diagnostic value for a well-defined disease?

Mesenchymal chondrosarcoma (MCS) is a rare and highly aggressive tumour of soft tissue and bone that is defined by an underlying and highly specific fusion transcript involving HEY1 and NCOA2. Histologically, the tumours show a biphasic appearance consisting of an undifferen-tiated blue and round cell component as well as islands of highly differentiated cartilage. Particularly in core needle biopsies, the chondromatous component can be missed and the non-specific morphology and immunophenotype of the round cell component can cause diagnostic chal-lenges. We applied NKX3.1 immunohistochemistry which was recently reported as a highly specific marker as well as methylome and copy number profiling to a set of 45 well characterised MCS cases to evaluate their potential diag-nostic value. Methylome profiling revealed a highly distinct cluster for MCS. Notably, the findings were reproducible also when analysing the round cell and cartilaginous component separately. Furthermore, four outliers were identified by methylome profiling for which the diagnosis had to be revised. NKX3.1 immunohistochemistry showed positivity in 36% of tumours, the majority of which was rather focal and weak. Taken together, NKX3.1 expression showed a low sensi-tivity but a high specificity in our analysis. Methylome profiling on the other hand represents a sensitive, specific and reliable tool to support the diagnosis of MCS, partic-ularly if only the round cell component is obtained in a biopsy and the diagnosis is not suspected. Furthermore, it can aid in confirming the diagnosis in case RNA sequencing for the HEY1::NCOA2 fusion transcript is not available.

Automated summary

Mesenchymal chondrosarcoma (MCS) is a rare and highly aggressive tumor defined by a fusion transcript involving HEY1 and NCOA2. Diagnosis of MCS can be challenging, especially in core needle biopsies. This study evaluated the diagnostic value of NKX3.1 immunohistochemistry and methylome profiling in 45 well-characterized MCS cases. Methylome profiling revealed a distinct cluster for MCS and showed potential to aid in diagnosis, even when analyzing separate components. NKX3.1 immunohistochemistry had low sensitivity but high specificity. Overall, methylome profiling is a reliable tool for supporting MCS diagnosis.