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Koelsche, Christian; Kriegsmann, Mark; Kommoss, Felix K. F.; Stichel, Damian; Kriegsmann, Katharina; Vokuhl, Christian; Grünewald, Thomas G. P.; Romero-Perez, Laura; Kirchner, Thomas; de Alava, Enrique; Diaz-Martin, Juan; Hartmann, Wolfgang; Baumhoer, Daniel; Antonescu, Cristina R.; Szuhai, Karoly; Flucke, Uta; Dirksen, Uta; Pfister, Stefan M.; Jones, David T. W.; Mechtersheimer, Gunhild and Deimling, Andreas von (2019): DNA methylation profiling distinguishes Ewing-like sarcoma with EWSR1-NFATc2 fusion from Ewing sarcoma. In: Journal of Cancer Research and Clinical Oncology, Vol. 145, No. 5: pp. 1273-1281

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Abstract

PurposeRecent studies revealed divergent gene expression patterns in Ewing sarcoma (EwS) with canonical EWSR1-ETS gene fusions and undifferentiated round cell sarcomas (URCS) with EWSR1 rearrangements fused to the non-ETS gene NFATc2. Thus, the question arises whether the latter tumors really belong to EwS.MethodsWe collected five cases matching the group of URCS with EWSR1-NFATc2 fusion and performed DNA methylation and copy number profiling. Results were compared to methylation data of 30 EwS with various EWSR1-ETS fusions and one EwS with FUS-ERG fusion, 16 URCS with CIC rearrangement and 10 URCS with BCOR alteration and a total of 81 EWSR1-associated soft tissue sarcomas including 7 angiomatoid fibrous histiocytomas, 7 clear cell sarcomas of the soft tissue, 28 desmoplastic small round cell tumors, 10 extraskeletal myxoid chondrosarcomas and 29 myxoid liposarcomas.ResultsUnsupervised hierarchical clustering and t-distributed stochastic neighbor embedding analysis of DNA methylation data revealed a homogeneous methylation cluster for URCS with EWSR1-NFATc2 fusion, which clearly segregated from EwS and the other subtypes. Copy number profiles of EWSR1-NFATc2 cases showed recurrent losses on chromosome 9q and segmental gains on 20q13 and 22q12 involving the EWSR1 and NFATc2 loci, respectively.ConclusionIn summary, URCS with EWSR1-NFATc2 fusion share a distinct DNA methylation signature and carry characteristic copy number alterations, which emphasizes that these sarcomas should be considered separately from EwS.

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