New Cell lines Expanding the Diversity of Ewing Sarcoma Models
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PROVIDER: PRJNA1221571 | ENA |
REPOSITORIES: ENA
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Project description:New Cell lines Expanding the Diversity of Ewing Sarcoma Models - methylation
| PRJNA1220949 | ENA
Project description:New Cell lines Expanding the Diversity of Ewing Sarcoma Models – Affymetrix Data
| PRJNA1220738 | ENA
Project description:Ewings sarcoma (EwS) is a highly aggressive, malignant, solid tumor of childhood and adolescence. Most EwS develop in bone, while it originates from connective, adipose or muscle tissue less frequently. We report the establishment of new human EwS cell lines, all of which carry a t(11;22) (q24;q12) translocation generating the oncogenic transcription factor EWSR1::FLI1. Sequencing of the chimeric mRNAs indicated genomic DNA breakpoints localized in intron 8 of the EWSR1 gene and 3 different introns of translocation partner gene FLI1. While three EwS cell lines carry the EWSR1::FLI1 fusions of ex7/ex6 (type I) or ex7/ex5 (type II), the EWSR1::FLI1 fusion variant ex7/ex7 (type IV) is described for the first time in a continuous EwS model. The cell lines presented genomic, epigenomic and transcriptomic stability over a period of six months, though some variations in the chromosomal aberrations were observed in one cell line. Transcriptome and epigenome were stable over time and there was only little variation between the novel EwS cell lines. The TP53 mutational status seemed to have the biggest impact on drug sensitivity profiles. The new EwS models presented here may help to identify small molecule inhibitors that act directly on EWSR1::FLI1 fusion proteins or uncover other genetic vulnerabilities of the altered epigenome and transcriptome in EwS, which would contribute to a better understanding of Ewing sarcoma tumorigenesis.
2025-08-22 | GSE289061 | GEO
Project description:Ewings sarcoma (EwS) is a highly aggressive, malignant, solid tumor of childhood and adolescence. Most EwS develop in bone, while it originates from connective, adipose or muscle tissue less frequently. We report the establishment of new human EwS cell lines, all of which carry a t(11;22) (q24;q12) translocation generating the oncogenic transcription factor EWSR1::FLI1. Sequencing of the chimeric mRNAs indicated genomic DNA breakpoints localized in intron 8 of the EWSR1 gene and 3 different introns of translocation partner gene FLI1. While three EwS cell lines carry the EWSR1::FLI1 fusions of ex7/ex6 (type I) or ex7/ex5 (type II), the EWSR1::FLI1 fusion variant ex7/ex7 (type IV) is described for the first time in a continuous EwS model. The cell lines presented genomic, epigenomic and transcriptomic stability over a period of six months, though some variations in the chromosomal aberrations were observed in one cell line. Transcriptome and epigenome were stable over time and there was only little variation between the novel EwS cell lines. The TP53 mutational status seemed to have the biggest impact on drug sensitivity profiles. The new EwS models presented here may help to identify small molecule inhibitors that act directly on EWSR1::FLI1 fusion proteins or uncover other genetic vulnerabilities of the altered epigenome and transcriptome in EwS, which would contribute to a better understanding of Ewing sarcoma tumorigenesis.
2025-08-22 | GSE289060 | GEO
Project description:Ewings sarcoma (EwS) is a highly aggressive, malignant, solid tumor of childhood and adolescence. Most EwS develop in bone, while it originates from connective, adipose or muscle tissue less frequently. We report the establishment of new human EwS cell lines, all of which carry a t(11;22) (q24;q12) translocation generating the oncogenic transcription factor EWSR1::FLI1. Sequencing of the chimeric mRNAs indicated genomic DNA breakpoints localized in intron 8 of the EWSR1 gene and 3 different introns of translocation partner gene FLI1. While three EwS cell lines carry the EWSR1::FLI1 fusions of ex7/ex6 (type I) or ex7/ex5 (type II), the EWSR1::FLI1 fusion variant ex7/ex7 (type IV) is described for the first time in a continuous EwS model. The cell lines presented genomic, epigenomic and transcriptomic stability over a period of six months, though some variations in the chromosomal aberrations were observed in one cell line. The transcriptional variation within the novel EwS cell line panel might have been influenced by the EWSR1::FLI1 fusion type and TP53 mutations. Furthermore, the TP53 mutational status seemed to have the biggest impact on drug sensitivity profiles. The new EwS models presented here may help to identify small molecule inhibitors that act directly on EWSR1::FLI1 fusion proteins or uncover other genetic vulnerabilities of the altered epigenome and transcriptome in EwS, which would contribute to a better understanding of Ewing sarcoma tumorigenesis.
2025-08-22 | GSE289064 | GEO
Project description:Ewings sarcoma (EwS) is a highly aggressive, malignant, solid tumor of childhood and adolescence. Most EwS develop in bone, while it originates from connective, adipose or muscle tissue less frequently. We report the establishment of new human EwS cell lines, all of which carry a t(11;22) (q24;q12) translocation generating the oncogenic transcription factor EWSR1::FLI1. Sequencing of the chimeric mRNAs indicated genomic DNA breakpoints localized in intron 8 of the EWSR1 gene and 3 different introns of translocation partner gene FLI1. While three EwS cell lines carry the EWSR1::FLI1 fusions of ex7/ex6 (type I) or ex7/ex5 (type II), the EWSR1::FLI1 fusion variant ex7/ex7 (type IV) is described for the first time in a continuous EwS model. The cell lines presented genomic, epigenomic and transcriptomic stability over a period of six months, though some variations in the chromosomal aberrations were observed in one cell line. The transcriptional variation within the novel EwS cell line panel might have been influenced by the EWSR1::FLI1 fusion type and TP53 mutations. Furthermore, the TP53 mutational status seemed to have the biggest impact on drug sensitivity profiles. The new EwS models presented here may help to identify small molecule inhibitors that act directly on EWSR1::FLI1 fusion proteins or uncover other genetic vulnerabilities of the altered epigenome and transcriptome in EwS, which would contribute to a better understanding of Ewing sarcoma tumorigenesis.
2025-08-22 | GSE289062 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2025-08-22 | GSE289118 | GEO
Project description:Purpose: Our experimental results demonstrate an essential role for the lncRNA HOTAIR in Ewing sarcoma. We have repressed HOTAIR expression in three Ewing sarcoma cell lines and overexpressed HOTAIR, alone and with EWS-FLI1, in htert-immortalized human mesenchymal stem cells to evaluate its effects on gene expression in this cancer. Methods: RNA-Seq of Ewing sarcoma cell lines with HOTAIR represssed by GapmeR or treated with nonsilencing control, and hTERT-immortalized hMSCs with expression of control GFP, HOTAIR, or HOTAIR and EWS-FLI1, was used for gene expression analysis. Results: Defined gene expression signatures were defined as driven by HOTAIR in each cell line model, with a consensus set of gene identified in the Ewing sarcoma cell lines. Additionally, a set of genes regulated by HOTAIR independently of EWS-FLI1 was identified in the hTERT-hMSC models. Conclusions: HOTAIR expression regulates a set of genes critical to viability, cell adhesion, cell motility, and other markers of EMT and metastasis in Ewing sarcoma, independently of EWS-FLI1.
2018-01-24 | GSE109483 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE36857: Goldengate Methylation analysis: Ewing Sarcoma GSE36858: 5- AZA treatment of EWS cell lines Refer to individual Series
2012-09-01 | E-GEOD-36859 | biostudies-arrayexpress
Project description:Ewing sarcoma is an aggressive pediatric small round cell tumor that predominantly occurs in bone. Approximately 85% of Ewing sarcomas harbor the EWS/FLI fusion protein, which arises from a chromosomal translocation, t(11:22)(q24:q12). EWS/FLI interacts with numerous lineage-essential transcription factors to maintain mesenchymal progenitors in an undifferentiated state. We previously showed that EWS/FLI binds the osteogenic transcription factor RUNX2 and prevents osteoblast differentiation. In this study, we investigated the role of another Runt-domain protein, RUNX3, in Ewing sarcoma. RUNX3 participates in mesenchymal-derived bone formation and is a context dependent tumor suppressor and oncogene. RUNX3 was detected in all Ewing sarcoma cells examined, whereas RUNX2 was detected in only 73% of specimens. Like RUNX2, RUNX3 binds to EWS/FLI via its Runt domain. EWS/FLI prevented RUNX3 from activating the transcription of a RUNX-responsive reporter, p6OSE2. Stable suppression of RUNX3 expression in the Ewing sarcoma cell line A673 delayed colony growth in anchorage independent soft agar assays and reversed expression of EWS/FLI-responsive genes. These results demonstrate an important role for RUNX3 in Ewing sarcoma. RNA-seq to compare transcriptiome of control A673 ewing sarcoma cells stably expression a non-target or RUNX3 shRNA
2014-05-01 | E-GEOD-56900 | biostudies-arrayexpress