Ewing samples and EWS-FLI-1 inhibited Ewing cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE7007 | GEO | 2007/02/14
SECONDARY ACCESSION(S): PRJNA99237
REPOSITORIES: GEO
Similar Datasets
Project description:The cellular origin of Ewing tumor (ET), a tumor of bone or soft tissues characterized by specific fusions between EWS and ETS genes, is highly debated. Through gene expression analysis comparing ETs with a variety of normal tissues, we show that the profiles of different EWS-FLI1-silenced Ewing cell lines converge toward that of mesenchymal stem cells (MSC). Moreover, upon EWS-FLI1 silencing, two different Ewing cell lines can differentiate along the adipogenic lineage when incubated in appropriate differentiation cocktails. In addition, Ewing cells can also differentiate along the osteogenic lineage upon long-term inhibition of EWS-FLI1. These in silico and experimental data strongly suggest that the inhibition of EWS-FLI1 may allow Ewing cells to recover the phenotype of their MSC progenitor. Experiment Overall Design: Ewing tumors and EWS-FLI-1 inhibited cell lines were profiled on Affymetrix U133A (GPL96) arrays.
2008-06-15 | E-GEOD-7007 | biostudies-arrayexpress
Project description:We show that EWS-FLI1, an aberrant transcription factor responsible for the pathogenesis of Ewing sarcoma, reprograms gene regulatory circuits by directly inducing or directly repressing enhancers. At GGAA repeats, which lack regulatory potential in other cell types and are not evolutionarily conserved, EWS- FLI1 multimers potently induce chromatin opening, recruit p300 and WDR5, and create de novo enhancers. GGAA repeat enhancers can loop to physically interact with target promoters, as demonstrated by chromosome conformation capture assays. Conversely, EWS-FLI1 inactivates conserved enhancers containing canonical ETS motifs by displacing wild-type ETS transcription factors and abrogating p300 recruitment. ChIP-seq for of 4 histone modifications (H3K27ac, H3K4me1, H3K4me3 and H3K27me3), FLI1, p300, WDR5, ELF1 and GABPA in primary Ewing sarcomas, Ewing sarcoma cell lines (A673 and SKMNC cells), and mesenchymal stem cells (MSC). EWS-FLI1 was knocked down in Ewing sarcoma cell lines with lentiviral shRNAs (shFLI1 and shGFP control). EWS-FLI1 was expressed in MSCs with lentiviral expression vectors (pLIV EWSFLI1 or pLIV empty vector control). * Raw data not provided for the MSC and Primary Ewing sarcoma samples. *
2014-10-30 | E-GEOD-61944 | biostudies-arrayexpress
Project description:We show that EWS-FLI1, an aberrant transcription factor responsible for the pathogenesis of Ewing sarcoma, reprograms gene regulatory circuits by directly inducing or directly repressing enhancers. At GGAA repeats, which lack regulatory potential in other cell types and are not evolutionarily conserved, EWS- FLI1 multimers potently induce chromatin opening, recruit p300 and WDR5, and create de novo enhancers. GGAA repeat enhancers can loop to physically interact with target promoters, as demonstrated by chromosome conformation capture assays. Conversely, EWS-FLI1 inactivates conserved enhancers containing canonical ETS motifs by displacing wild-type ETS transcription factors and abrogating p300 recruitment. Mesenchymal stem cells (MSCs) and a Ewing sarcoma cell line (SKNMC) were analyzed by ATAC-seq. EWS-FLI1 was expressed in MSCs using a lentiviral vector (pLIV EWSFLI1 or pLIV empty vector control). * Raw data not provided for the MSC samples. *
2014-10-30 | E-GEOD-61951 | biostudies-arrayexpress
Project description:Ewing sarcoma (EwS) is an adolescent and young adult sarcoma characterized by chromosome translocations between members of the FET family of RNA binding proteins and members of the ETS family of transcription factors, the most frequent fusion being EWS-FLI1. EWS-FLI1 acts as a pioneer factor, creating de novo enhancers and activating genes located in the vicinity of EWS-FLI1-bound microsatellite sequences. recent results from our lab indicate that EWS-FLI1, which activates transcription through binding to the DNA at specific sites, can generate fully novel, unconventional transcription units in regions of the genome that are fully quiescent in normal cells (manuscript in preparation). The hypothesis of the project is that the open reading frames (ORFs) of these transcripts may encode peptides presented at the cell surface by HLA class I molecules and hence be recognized as non-self by the immune system. The aim of this study is to detect Ewing-specific neo-peptides/proteins using proteomics approach.
2022-05-12 | PXD027309 | Pride
Project description:We show that EWS-FLI1, an aberrant transcription factor responsible for the pathogenesis of Ewing sarcoma, reprograms gene regulatory circuits by directly inducing or directly repressing enhancers. At GGAA repeats, which lack regulatory potential in other cell types and are not evolutionarily conserved, EWS- FLI1 multimers potently induce chromatin opening, recruit p300 and WDR5, and create de novo enhancers. GGAA repeat enhancers can loop to physically interact with target promoters, as demonstrated by chromosome conformation capture assays. Conversely, EWS-FLI1 inactivates conserved enhancers containing canonical ETS motifs by displacing wild-type ETS transcription factors and abrogating p300 recruitment. Ewing sarcoma cell lines (A673 and SKNMC) were analyzed by RNA-seq. EWS-FLI1 was depleted by infection with lentiviral shRNAs (shFLI1 and shGFP control).
2014-10-30 | E-GEOD-61950 | biostudies-arrayexpress
Project description:Pediatric cancers frequently harbor sentinel mutations involving transcription factors (TFs) that dysregulate normal development. A recurrent mechanism involves the ability of mutant TFs to co-opt cell lineage-specific, activating TFs to promote cancer growth. Ewing sarcoma, the second most common pediatric bone cancer, is defined by the presence of a 11;22 chromosomal translocation fusing the N-terminus of the EWS protein with the C-terminal DNA binding domain of an ETS (E26 Transformation Specific) TF family member, most commonly (85-90% of cases), FLI1. The EWS/FLI fusion exhibits the neomorphic ability to pioneer de novo enhancers at repeating 5’-GGAA-3’ motifs in the cell-of-origin, which has not been identified. To date, efforts to elucidate the key mechanisms by which EWS/FLI promotes oncogenesis have prioritized identifying the genes that are profoundly activated by EWS/FLI and highly expressed in Ewing sarcoma compared to other cancers, with particular focus on transcription factors capable of altering cell state. However, it is not known whether, globally, these genes constitute the most critical drivers of Ewing sarcoma cell growth. Here, we describe the results of an unbiased deletion screen revealing that the wild-type repressive ETS family TF, ETV6 (ETS Variant 6, or TEL), is a novel and most critical TF dependency specific to Ewing sarcoma. We demonstrate that the repressive activity of ETV6 constrains EWS/FLI gene activation at GGAA repeat enhancers to promote Ewing sarcoma cell growth.
2022-10-05 | GSE211852 | GEO
Project description:Pediatric cancers frequently harbor sentinel mutations involving transcription factors (TFs) that dysregulate normal development. A recurrent mechanism involves the ability of mutant TFs to co-opt cell lineage-specific, activating TFs to promote cancer growth. Ewing sarcoma, the second most common pediatric bone cancer, is defined by the presence of a 11;22 chromosomal translocation fusing the N-terminus of the EWS protein with the C-terminal DNA binding domain of an ETS (E26 Transformation Specific) TF family member, most commonly (85-90% of cases), FLI1. The EWS/FLI fusion exhibits the neomorphic ability to pioneer de novo enhancers at repeating 5’-GGAA-3’ motifs in the cell-of-origin, which has not been identified. To date, efforts to elucidate the key mechanisms by which EWS/FLI promotes oncogenesis have prioritized identifying the genes that are profoundly activated by EWS/FLI and highly expressed in Ewing sarcoma compared to other cancers, with particular focus on transcription factors capable of altering cell state. However, it is not known whether, globally, these genes constitute the most critical drivers of Ewing sarcoma cell growth. Here, we describe the results of an unbiased deletion screen revealing that the wild-type repressive ETS family TF, ETV6 (ETS Variant 6, or TEL), is a novel and most critical TF dependency specific to Ewing sarcoma. We demonstrate that the repressive activity of ETV6 constrains EWS/FLI gene activation at GGAA repeat enhancers to promote Ewing sarcoma cell growth.
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Project description:Pediatric cancers frequently harbor sentinel mutations involving transcription factors (TFs) that dysregulate normal development. A recurrent mechanism involves the ability of mutant TFs to co-opt cell lineage-specific, activating TFs to promote cancer growth. Ewing sarcoma, the second most common pediatric bone cancer, is defined by the presence of a 11;22 chromosomal translocation fusing the N-terminus of the EWS protein with the C-terminal DNA binding domain of an ETS (E26 Transformation Specific) TF family member, most commonly (85-90% of cases), FLI1. The EWS/FLI fusion exhibits the neomorphic ability to pioneer de novo enhancers at repeating 5’-GGAA-3’ motifs in the cell-of-origin, which has not been identified. To date, efforts to elucidate the key mechanisms by which EWS/FLI promotes oncogenesis have prioritized identifying the genes that are profoundly activated by EWS/FLI and highly expressed in Ewing sarcoma compared to other cancers, with particular focus on transcription factors capable of altering cell state. However, it is not known whether, globally, these genes constitute the most critical drivers of Ewing sarcoma cell growth. Here, we describe the results of an unbiased deletion screen revealing that the wild-type repressive ETS family TF, ETV6 (ETS Variant 6, or TEL), is a novel and most critical TF dependency specific to Ewing sarcoma. We demonstrate that the repressive activity of ETV6 constrains EWS/FLI gene activation at GGAA repeat enhancers to promote Ewing sarcoma cell growth.
2022-10-05 | GSE181552 | GEO
Project description:Pediatric cancers frequently harbor sentinel mutations involving transcription factors (TFs) that dysregulate normal development. A recurrent mechanism involves the ability of mutant TFs to co-opt cell lineage-specific, activating TFs to promote cancer growth. Ewing sarcoma, the second most common pediatric bone cancer, is defined by the presence of a 11;22 chromosomal translocation fusing the N-terminus of the EWS protein with the C-terminal DNA binding domain of an ETS (E26 Transformation Specific) TF family member, most commonly (85-90% of cases), FLI1. The EWS/FLI fusion exhibits the neomorphic ability to pioneer de novo enhancers at repeating 5’-GGAA-3’ motifs in the cell-of-origin, which has not been identified. To date, efforts to elucidate the key mechanisms by which EWS/FLI promotes oncogenesis have prioritized identifying the genes that are profoundly activated by EWS/FLI and highly expressed in Ewing sarcoma compared to other cancers, with particular focus on transcription factors capable of altering cell state. However, it is not known whether, globally, these genes constitute the most critical drivers of Ewing sarcoma cell growth. Here, we describe the results of an unbiased deletion screen revealing that the wild-type repressive ETS family TF, ETV6 (ETS Variant 6, or TEL), is a novel and most critical TF dependency specific to Ewing sarcoma. We demonstrate that the repressive activity of ETV6 constrains EWS/FLI gene activation at GGAA repeat enhancers to promote Ewing sarcoma cell growth.
2022-10-05 | GSE181551 | GEO
Project description:Pediatric cancers frequently harbor sentinel mutations involving transcription factors (TFs) that dysregulate normal development. A recurrent mechanism involves the ability of mutant TFs to co-opt cell lineage-specific, activating TFs to promote cancer growth. Ewing sarcoma, the second most common pediatric bone cancer, is defined by the presence of a 11;22 chromosomal translocation fusing the N-terminus of the EWS protein with the C-terminal DNA binding domain of an ETS (E26 Transformation Specific) TF family member, most commonly (85-90% of cases), FLI1. The EWS/FLI fusion exhibits the neomorphic ability to pioneer de novo enhancers at repeating 5’-GGAA-3’ motifs in the cell-of-origin, which has not been identified. To date, efforts to elucidate the key mechanisms by which EWS/FLI promotes oncogenesis have prioritized identifying the genes that are profoundly activated by EWS/FLI and highly expressed in Ewing sarcoma compared to other cancers, with particular focus on transcription factors capable of altering cell state. However, it is not known whether, globally, these genes constitute the most critical drivers of Ewing sarcoma cell growth. Here, we describe the results of an unbiased deletion screen revealing that the wild-type repressive ETS family TF, ETV6 (ETS Variant 6, or TEL), is a novel and most critical TF dependency specific to Ewing sarcoma. We demonstrate that the repressive activity of ETV6 constrains EWS/FLI gene activation at GGAA repeat enhancers to promote Ewing sarcoma cell growth.
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