EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA767691 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16134800_1.fastq.gz | Fastqsanger.gz | |||
| SRR16134800_2.fastq.gz | Fastqsanger.gz | |||
| SRR16134801_1.fastq.gz | Fastqsanger.gz | |||
| SRR16134801_2.fastq.gz | Fastqsanger.gz | |||
| SRR16134802_1.fastq.gz | Fastqsanger.gz |
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Project description:EWS-FLI-1 was silenced by an shRNA in A673 Ewing sarcoma cells and the resulting alterations in the secretome was analyzed by GeLC-MS/MS approach (six gel slices for each sample, luciferase shRNA-expressing cell secretome as control)
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Project description:Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. EWS/FLI binding is primarily associated with compartment activation, establishment of topologically-associated domain (TAD) boundaries, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators through three-dimensional reprogramming of chromatin.
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Project description:Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. EWS/FLI binding is primarily associated with compartment activation, establishment of topologically-associated domain (TAD) boundaries, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators through three-dimensional reprogramming of chromatin.
2022-08-15 | GSE185125 | GEO
Project description:Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. EWS/FLI binding is primarily associated with compartment activation, establishment of topologically-associated domain (TAD) boundaries, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators through three-dimensional reprogramming of chromatin.
2022-08-15 | GSE185130 | GEO
Project description:Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. EWS/FLI binding is primarily associated with compartment activation, establishment of topologically-associated domain (TAD) boundaries, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators through three-dimensional reprogramming of chromatin.
2022-08-15 | GSE185128 | GEO
Project description:Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. EWS/FLI binding is primarily associated with compartment activation, establishment of topologically-associated domain (TAD) boundaries, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators through three-dimensional reprogramming of chromatin.
2022-08-15 | GSE185127 | GEO
Project description:Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. EWS/FLI binding is primarily associated with compartment activation, establishment of topologically-associated domain (TAD) boundaries, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators through three-dimensional reprogramming of chromatin.
2022-08-15 | GSE185126 | GEO
Project description:The purpose of this study was to define the genome-wide functional relationship between LSD1 and EWS/FLI in Ewing sarcoma cells. We found EWS/FLI and LSD1 co-localize throughout the genome and that EWS/FLI induces a large change in the genomic distribution of LSD1, and that this also occurs for the LSD1 interacting partner, REST.
2020-05-12 | GSE144685 | 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 | 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.
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