45 DNA Methylation Profiling of Mesenchymal Tumors with BCOR Genetic Alterations Reveals the Existence of Three Epigenetically Distinct Groups

Background BCOR alterations and the related YWHAE::NUTM2B fusion play a central role in the pathogenesis of multiple tumor types, namely small round cell sarcoma with BCOR genetic alterations (SBRCT BCOR, also including primitive myxoid mesenchymal tumor of infancy, PMMTI), clear cell sarcoma of the kidney (CCSK), high-grade endometrial stromal sarcoma (ESS HG), and ossifying fibromyxoid tumor (OFMT BCOR). While these neoplasms differ in their clinical features, they overlap considerably in their histomorphology and genetic background. To decipher their epigenetic relationship and compare them with morphological mimickers, we performed DNA methylation analysis on a large cohort of BCOR-rearranged mesenchymal tumors. Design DNA methylation data were obtained using Infinium Methylation Kits (Illumina). R software was used for dimensionality reduction analysis (UMAP). The study cohort consisted of SBRCT BCOR (n=19), PMMTI (n=12), CCSK (n=21), ESS HG (n=24), and OFMT BCOR (n=8) from institutional registries and publicly available datasets. For comparison, infantile fibrosarcoma, myoepithelial tumors, non-BCOR-rearranged OFMT, and other entities were used. Results Epigenetically, the tumors formed 3 distinct clusters (Figure 1). The first comprised all OFMT BCOR, 9 highly rearranged ESS HG, and 3 outliers from the SBRCT BCOR/PMMTI group. Most of these had a ZC3H7B::BCOR fusion, with amplification of MDM2 and/or loss of CDKN2A frequently seen in their CNV plots. The second cluster showed a spectrum from most (n=14) SBRCT BCOR on one side of the cluster to the rest of ESS HG on the other, with 1 PMMTI in between. The most common alterations in this cluster were BCOR::CCNB3 and YWHAE::NUTM2B. The third cluster contained all CCSKs and most PMMTIs, as well as 6 SBRCT BCOR. Similar to the second cluster, a continuum with CCSK on one side of the cluster to PMMTI on the other was observed. Internal tandem duplication (ITD) of BCOR was the most prevalent genetic alteration here. Conclusions Our study revealed that mesenchymal tumors with BCOR alterations and related rearrangements form three distinct epigenetic clusters. ESS HG splits into two separate clusters, one overlapping with OFMT BCOR, the other co-locating with SBRCT BCOR. Although PMMTI is grouped with SBRCT BCOR in the current WHO classification, it epigenetically seems closer to CCSK, with both tumor types commonly harboring BCOR ITD. The few discordant cases reflect the diagnostic challenge posed by these neoplasms