Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential chromatin landscape in myxoid liposarcoma and Ewing sarcoma

ABSTRACT: A subgroup of sarcomas and leukemias is defined by characteristic FET (FUS, EWSR1, TAF15) fusion oncogenes. Myxoid liposarcoma (MLS) and Ewing sarcoma (EWS) are the most common entities characterized by the fusion oncogenes FUS-DDIT3 and EWSR1-FLI1, respectively. Here, we performed ATAC-Seq on the cell lines MLS 1765-92 and EWS TC-71 to characterize and compare their chromatin landscape.

ORGANISM(S): Homo sapiens

PROVIDER: GSE235218 | GEO | 2025/09/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of FET-oncoprotein-interacting proteins by immunoprecipitation and mass spectrometry analysis in sarcoma cell lines

Project description:The FET family of fusion oncogenes carry one of the three genes, FUS, EWSR1 or TAF15, as 5’‑partners juxtaposed to one of many different DNA binding transcription factor genes as 3’‑partners. FET fusion oncogenes are pathognomonic for many types of sarcoma and leukemia, such as FUS-DDIT3 in myxoid liposarcoma (MLS) and EWSR1-FLI1 in Ewing sarcoma (EWS). We used recombinant FET N-terminal domains in a pulldown screen to find interaction partners to the FET proteins and identified components of the SWI/SNF complex. The ~2 MDa SWI/SNF chromatin remodeling complex utilizes energy from ATP hydrolysis to remodel nucleosomes and expose DNA. We used immunoprecipitation followed by mass spectrometry or western blot analysis to extensively characterize the interaction between FET fusion oncoproteins and the SWI/SNF complex.

2019-03-13 | PXD012680 | Pride

Differences in gene expression between myxoid liposarcoma and Ewing sarcoma cell lines

Project description:FET fusion oncoproteins, containing the N-terminal of a FET protein (FUS, EWSR1 and TAF15) together with a DNA-binding transcription factor partner, are characteristic for around 20 different sarcomas and leukemias, including myxoid liposarcoma (MLS) and Ewing sarcoma (EWS). Many of these tumors have few other genetic abberrations. Using RNA-sequencing on MLS and EWS cell lines, we showed that gene expression patterns varied between FET sarcoma subtypes. Together with other data, the information from this experiment can help to determine the oncogenic mechanism in FET sarcomas and how a common oncogenic mechanism can give rise to different tumor types, explaining the tumor-type specificity of FET oncoproteins.

2025-09-22 | GSE248354 | GEO

Genes regulated by JAK1/2 inhibitor ruxolitinib and myxoid liposarcoma-specific fusion onccogene FUS-DDIT3 in HT1080 cells.

Project description:Sarcomas and leukemias that are characterized by FET (FUS, EWSR1, TAF15) fusion oncogenes consist of more than 20 entities. Myxoid liposarcoma, one of the most common FET sarcoma types, is defined by the FUS-DDIT3 or the less common EWSR1-DDIT3 fusion oncogene. Previously, JAK-STAT signaling have been connected to cancer stem cell properties and chemotherapy resistance in myxoid liposarcoma, but the role of FUS-DDIT3 is not known. Therefore, we treated HT1080 fibrosarcoma cells expression FUS-DDIT3 with JAK1/2 inhibitor ruxolitinib and performed RNA sequencing of treated and control cells. Additionally, we analyzed native HT1080 cells to be able to compare the induced gene expression changes due to FUS-DDIT3 expression with those induced by JAK-STAT pathway inhibition.

2022-01-14 | GSE149650 | GEO

FET fusion oncoprotein-regulated genes in HT1080 cell line

Project description:Some specific sarcomas and leukemias are defined by characteristic FET (FUS, EWSR1, TAF15) fusion oncogenes. Myxoid liposarcoma and Ewing sarcoma are the most common entities characterized by FUS-DDIT3 and EWSR1-FLI1, respectively. Here, we performed whole transcriptome analysis of HT1080 cells with either ectopic FUS-DDIT3 or ectopic EWSR1-FLI1 expression.

2019-03-12 | GSE125941 | GEO

Gene expression profiles associated with myxoid liposarcoma scaffold culture compared to monolayer growth and effect of fusion oncogene FUS-DDIT3

Project description:Myxoid liposarcoma (MLS) is the second most common type of liposarcoma and is characterized by the fusion oncogene FUS‐DDIT3 or the less common EWSR1‐DDIT3. FUS-DDIT3 is causative in tumor development, but the molecular function of FUS-DDIT3 remains largely unknown. In addition, the tumor microenvironment is important in MLS development. However, due to a lack of relevant experimental model systems, it has been challenging to examine the microenvironmental impact in MLS development. Therefore, we have developed an in vivo-like experimental model system utilizing cell-free scaffolds derived from myxoid liposarcoma patient-derived xenograft tumors that can be repopulated with tumor cells. To study the effect of FUS-DDIT3 expression in combination with the MLS microenvironment, we analyzed MLS cell lines as well as fibrosarcoma cells with and without ectopic FUS-DDIT3 expression cultured in scaffolds using cells cultured in monolayers as reference. We identified several gene networks and processes that are uniquely associated with FUS-DDIT3 expression as well as microenvironment. The use of in vivo-like experimental systems opens new possibilities to understand tumor development and develop treatments.

2023-12-31 | GSE230773 | GEO

Single-cell gene expression profiling of myxoid liposarcoma cell line 402-91

Project description:Myxoid liposarcoma (MLS) is a rare tumor type generally occuring in deep soft tissues. Genetically, it is characterized by the FUS-DDIT3 fusion oncogene with few additional mutations. MLS 402-91 is one of few existing MLS cell lines. The purpose of this dataset is to study the variation in gene expression in MLS at the single-cell level.

2025-09-22 | GSE248661 | GEO

Single-cell gene expression profiles associated with myxoid liposarcoma scaffold culture compared to xenograft and effect of fusion oncogene FUS-DDIT3

Project description:Myxoid liposarcoma (MLS) is the second most common type of liposarcoma and is characterized by the fusion oncogene FUS‐DDIT3 or the less common EWSR1‐DDIT3. While the presence of FUS-DDIT3 as a driver oncoprotein in most MLS cases has been confirmed, the exact molecular action behind the capacity of FUS-DDIT3 for transformation is still unclear and therefore creates a challenge in finding new treatments against this type of cancer. The importance of the microenvironment for tumor progression have long been accepted and might also influence the effect of the fusion oncoprotein. However, due to a lack of relevant experimental model systems, it has been challenging to examine the microenvironmental impact in myxoid liposarcoma development. Therefore, we have developed a new model system utilizing scaffolds derived from myxoid liposarcoma patient-derived xenograft tumors that are decellularized and then repopulated with sarcoma cell lines. This cell culture system mimics in vivo-like tumor cell growth conditions and induce transcriptional changes within the cells. In order to investigate the effect of the microenvironment as well as the fusion oncogene, we analyzed myxoid liposarcoma cell lines as well as fibrosarcoma cells with and without ectopic FUS-DDIT3 expression cultured in scaffolds and adherent two-dimensional growth conditions. We identified several gene networks and processes that are uniquely associated with FUS-DDIT3 expression and with the microenvironment, respectively. The development of patient-derived scaffolds opens up new possibilities to understand tumor development.

2023-12-31 | GSE191132 | GEO

Correlation between gene expression responses to FUS, EWS, and TAF15 reduction and the stress granule sequestering capacity

Project description:Analysis of differentially expressed genes after siRNA mediated knock-down of the FET-family of proteins; the FUS, EWS, and TAF15 proteins. The FET-proteins are thought to function as transcription factors, and this hypothesis is tested in the present study. Results provide important information of the genes which expression are controlled by the FET-family of proteins. Total RNA obtained HEK293-cells transfected with siRNA targeted against the FUS, EWS, or TAF15 mRNA, or a combination of all three of them. Control cells are transfected with an equal amount of unspecific siRNA without known targets.

2012-02-07 | E-GEOD-35578 | biostudies-arrayexpress

Gene expression profiling of myxoid liposarcomas (validation set INT-B)

Project description:FUS-CHOP and EWS-CHOP balanced translocations characterize myxoid liposarcoma which encompasses myxoid (ML) and round cell (RC) variants initially believed to be distinct diseases. Currently, myxoid and RC liposarcoma are regarded to represent the well differentiated and the poorly differentiated ends, respectively, within spectrum of myxoid liposarcoma where the fusion proteins blocking lipogenic differentiation play a role in tumor initiation while molecular determinants associated to progression to RC remain poorly understood. Activation of AKT pathway sustained by PIK3CA and PTEN mutations and growth factor receptor signalling such as RET and IGF1R have been recently correlated with the increasing of aggressiveness and RC. Aim of the present study is to elucidate molecular events involved in driving round cell progression analyzing two small series of MLS selected to be representative of the two end of the gamut: the pure myxoid (0% of RC component) and RC with high cellular component (≥80%).

2014-10-30 | GSE55465 | GEO

Gene expression profiling of myxoid liposarcomas (training set INT-A)

2014-10-30 | GSE55464 | GEO