Multiscale omic assessment of EWSR1-NFATc2 fusion positive sarcomas to identify conserved fusion breakpoint and activation of the mTOR pathway.

Abstract

e23536 Background: EWSR1-NFATc2 ( E-N) fusion positive sarcomas are rare cancers historically categorized as Ewing sarcomas. Emerging evidence suggests unique molecular characteristics and chemotherapy sensitivities in these cancers. Here we present the largest cohort of genomically profiled E-N fusion positive sarcomas and evaluate their breakpoints and putative pathway alterations. Methods: Comprehensive genomic profiling of 1,024 EWSR1 fusion positive sarcomas, including 14 E-N fusions, was obtained through the Foundation Medicine research database (FMI). Additional data from the Gene Expression Omnibus, the Genomics of Drug Sensitivity in Cancer (GDSC), and The Cancer Genome Atlas (TCGA) datasets were used. Descriptive statistics, principle component analysis, differential expression, and pathway analysis were used as appropriate. Results: E-N fusions identified in the FMI database demonstrated consistent breakpoints located between exon 2 and 3 on NFATc2; consistent with previous reports suggesting that the primary transactivation domain and regulatory domains of NFATc2 are conserved in the EWRS1-NFATc2 fusion. Cluster analysis demonstrated separate E-N fusion positive sarcoma grouping than other EWRS1 sarcomas, while identifying an enrichment of mTOR pathway variants in E-N fusion positive samples (p = 0.05). Gene expression data from E-N identified a significant activation of the mTOR pathway in E-N positive sarcomas compared to either EWSR1-ETS (p = 0.002) or CIC-DUX4 positive sarcomas (p < 0.001). In the GDSC database, NFATc2-High lines exhibited activation of the mTOR pathway (p < 0.0001) and were more sensitive to the mTOR inhibitor rapamycin (p = 0.0006). Pan-cancer analysis of 33 non-overlapping TCGA datasets, elevated NFATc2 mRNA expression was significantly associated with activated RICTOR and mTOR signaling (p < 0.0001). Elevated NFATc2 correlated with higher tumor grade and poorer progression-free survival and overall survival. Conclusions: Taken together, the data presented here suggests that E-N fusion positive sarcomas represent a distinct molecularly entity in comparison to traditional Ewing sarcomas. Conserved action of NFATc2 may correlate to mTOR over activation.