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Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE173185 | GEO | 2021/09/15

REPOSITORIES: GEO

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Identification of a Novel FUS/ETV4 Fusion and Comparative Analysis with Other Ewing Sarcoma Fusion Proteins.

Project description:Ewing sarcoma is a pediatric bone cancer defined by a chromosomal translocation fusing one of the FET family members to an ETS transcription factor. There have been seven reported chromosomal translocations, with the most recent reported over a decade ago. We now report a novel FET/ETS translocation involving FUS and ETV4 detected in a patient with Ewing sarcoma. Here, we characterized FUS/ETV4 by performing genomic localization and transcriptional regulatory studies on numerous FET/ETS fusions in a Ewing sarcoma cellular model. Through this comparative analysis, we demonstrate significant similarities across these fusions, and in doing so, validate FUS/ETV4 as a bona fide Ewing sarcoma translocation. This study presents the first genomic comparison of Ewing sarcoma-associated translocations and reveals that the FET/ETS fusions share highly similar, but not identical, genomic localization and transcriptional regulation patterns. These data strengthen the notion that FET/ETS fusions are key drivers of, and thus pathognomonic for, Ewing sarcoma. IMPLICATIONS: Identification and initial characterization of the novel Ewing sarcoma fusion, FUS/ETV4, expands the family of Ewing fusions and extends the diagnostic possibilities for this aggressive tumor of adolescents and young adults.

| S-EPMC8568690 | biostudies-literature

Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins [CUT&Tag]

Project description:The purpose of this study was to determine the genomic localization similarities and differences in the FET/ETS translocations that have been identified as drivers of Ewing sarcoma.

2021-09-15 | GSE173184 | GEO

Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins [RNA-seq]

Project description:The purpose of this study was to determine the transcriptional regulatory similarities and differences in the FET/ETS translocations that have been identified as drivers of Ewing sarcoma.

2021-09-15 | GSE173183 | GEO

Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins

Project description:Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins

| PRJNA724650 | ENA

Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins [CUT&Tag]

Project description:Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins [CUT&Tag]

| PRJNA724652 | ENA

Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins [RNA-seq]

Project description:Identification of a novel FUS/ETV4 fusion and comparative analysis with other Ewing sarcoma fusion proteins [RNA-seq]

| PRJNA724653 | ENA

DNA methylation profiling distinguishes Ewing-like sarcoma with EWSR1-NFATc2 fusion from Ewing sarcoma.

Project description:PURPOSE:Recent 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. METHODS:We 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. RESULTS:Unsupervised 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. CONCLUSION:In 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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Comparative evaluation of strategies for quantifying signaling pathway proteins in Ewing sarcoma.

Project description:Targeted therapies are increasingly being evaluated for patients with Ewing sarcoma (EWS). Optimal strategies for quantifying key signaling proteins in EWS remain unclear. We sought to quantify tumor expression of signaling pathway proteins in EWS using 3 methodologies. A total of 46 blocks of formalin-fixed paraffin-embedded tissue were obtained from 40 patients with EWS. Tumor was evaluated for the expression of proteins in the insulin-like growth factor type 1 receptor (IGF-1R), epithelial growth factor receptor (EGFR), and mTOR pathways using standard immunohistochemical analysis (IHC), automated quantitative analysis (AQUA) immunohistochemical analysis, and mass spectrometry quantification. The mean age at diagnosis was 14 years (range, 1 to 49 y). About 67.5% were male and 57.5% had localized disease. Samples displayed a wide range of expression by AQUA: mean (range) IGF-1R=10,702 (393 to 14,424); EGFR=2750 (672 to 9798); and phosphatase and tensin homolog (PTEN)=2250 (251 to 6557). Mean IGF-1R expression by AQUA did not differ between standard IHC expression categories (low IHC=11,255; medium IHC=11,070; high IHC=11,023; P=0.98). Mean PTEN expression by AQUA was higher in the medium and high IHC categories (low IHC=1229; medium IHC=2715; high IHC=2940; P=0.064). Only 2 samples expressed EGFR by standard IHC. Mass spectrometry trended toward correlation with standard IHC but did not yield interpretable results in the majority of samples. This study demonstrates that the relative quantification of signaling protein expression in EWS is dependent on the methodology used. Optimization and validation of these tools are necessary before clinical application for risk stratification of patients or measurement of biomarker expression.

| S-EPMC4148473 | biostudies-literature

Identification of a novel, recurrent MBTD1-CXorf67 fusion in low-grade endometrial stromal sarcoma

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-03-31 | E-GEOD-46285 | biostudies-arrayexpress

Novel PAX3-MAML3 Fusion in Biphenotypic Sinonasal Sarcoma

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-04-17 | E-GEOD-52323 | biostudies-arrayexpress