Abstract 6218: NKX3.1 immunohistochemistry and methylome profiling in mesenchymal chondrosarcoma: additional diagnostic value for a well defined disease
Authors: Glauser Salome , Ameline Baptiste , Andrei Vanghelita , Harder Dorothee , Pauli Chantal , Trautmann Marcel , Hartmann Wolfgang , Baumhoer Daniel 
Published: April 2023

Abstract
Background: Mesenchymal chondrosarcoma (MCS) is a high-grade sarcoma characterized by a biphasic histological appearance. However, more often than not, only the poorly differentiated component is present on a biopsy, thus more entities enter the differential diagnosis. Since the small cell component is morphologically non-specific, the differential diagnoses are broad, such as Ewing sarcoma, rhabdomyosarcoma, poorly differentiated synovial sarcoma small cell carcinoma, lymphoma and also melanoma. Morevoer, although the HEY1::NCOA2 gene fusion is present in almost all MCS, some studies have shown alternative alterations in the absence of the HEY1::NCOA2 fusion, suggesting genomic heterogeneity in at least a small subset of MCS. Thus, new diagnostic aids would be helpful to confirm the diagnosis. While most of the immunohistochemical profile overlaps between these tumours, NKX3.1 was recently proposed as a useful diagnostic marker for MCS. Furthermore, studies using DNA-methylation profiling show that MCS forms a distinct methylation cluster. The aim of this study is to evaluate the utility of these new diagnostic tools.
Methods: Slides from 45 samples with MCS were stained with NKX3.1 antibody (EP356, Cell Marque, Roche) and were also investigated by methylome analysis (Mehylation Epic BeadChips, Illumina). Depending on tissue availability, the cases were subjected to HEY1::NCOA2 gene fusion testing.
Results: The methylation profile showed a distinct cluster for mesenchymal chondrosarcoma, in line with the previous studies. Moreover, these findings were reproduced even when submitting tissue solely from one component, either the cellular or the cartilaginous one. In addition, the copy number profile derived from the methylome analysis proves its utility in distinguishing MCS from its mimics. On the other hand, only 32.6% of cases were positive for NKX3.1. Four samples initially diagnosed as MCS were histologically re-evaluated due to an atypical methylome profile, a high amount of CNV and/or lack of validation of the gene fusion. Methylation profiling led to the re-classification of three cases, whereas the fourth sample could not be further classified.
Conclusions: We conclude that the methylation analysis, along with the copy number profile, are reliable tools in terms of diagnosing MCS. On the contrary, the immunomarker NKX3.1 shows contradicting results, proving itself as an unreliable marker in this setting.
Citation Format: Salome Glauser, Baptiste Ameline, Vanghelita Andrei, Dorothee Harder, Chantal Pauli, Marcel Trautmann, Wolfgang Hartmann, Daniel Baumhoer. NKX3.1 immunohistochemistry and methylome profiling in mesenchymal chondrosarcoma: additional diagnostic value for a well defined disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6218.