RNA Seq of rhabdomyosarcoma cells with sgRNA targeting oncofusion interacting proteins
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE314949 | GEO | 2026/03/26
REPOSITORIES: GEO
Similar Datasets
Project description:PAX3-FOXO1 is a fusion transcription factor characteristic for the majority of alveolar rhabdomyosarcoma tumors. It is the main oncogenic driver and deregulates expression of PAX3 target genes. The PAX3-FOXO1 target gene signature was determined in the Rh4 alveolar rhabdomyosarcoma cell line.
2015-09-29 | GSE73483 | GEO
Project description:CHD4 is an ATPase able to use the energy from ATP to shift or remove nucleosomes from specific sites in the chromatin, thereby affecting accessability of gene regulatory elements. It is part of the NuRD complex. The effect of CHD4 on global gene expression was evaluated in Rh4 alveolar rhabdomyosarcoma cells.
2015-09-29 | GSE73480 | GEO
Project description:We identified and interactome for seven diffent rhabdomyosarcoma oncofusions. The proliferative effects of the loss of these proteins was tested by a CRISPR loss of function library screen in four rhabdomyosarcoma cell lines engineered to be driven by 4 different oncofusions.
2026-03-26 | GSE314907 | GEO
Project description:PAX3-FOXO1 is the commonly identified oncofusion gene found in rhabdomyosarcoma. However, other rare fusions are also seen. Here, we have knocked down PAX3-FOXO1 in a fusion-positive RMS cell line (RH4) with shRNA targeting the breakpoint and rescued cell growth with 7 fusions found in this cancer. RNA sequencing was then used to asess how each fusion alters transcription by comparing the RNA sequencing to a PAX3-FOXO1 knock down cell.
2026-03-26 | GSE250125 | GEO
Project description:We report the genome-wide maps of PAX3-FKHR binding sites. Chromatin immunoprecipitation was performed against PAX3-FKHR positive (Rh4) and PAX3-FKHR negative (RD) rhabdomyosarcoma cells with a monoclonal antibody (pFM2) specific for the fusion region of PAX3-FKHR. We obtained 4 million sequence tags for both input and ChIP DNA that aligned to the human genome. We identified 1,463 binding sites from ChIP-seq of Rh4 cells, none of which appeared from ChIP-seq of fusion negative RD cells. The PAX3-FKHR binding sites were found to associate with 1,072 genes in RMS cells. The data shows that PAX3-FKHR binds to the same sites as PAX3, at the enhancers for MYF5, FGFR4, and the MYOD core enhancer previously shown to be regulated by PAX3. Moreover, our dataset has the precision for rapid identification and validation of novel and specific sequences required for the enhancer activity of MYOD and FGFR4. The genome wide analysis reveals that the PAX3-FKHR sites are: 1) mostly distal to transcription start sites; 2) conserved; 3) enriched for PAX3 motifs; and 4) strongly associated with genes over-expressed in PAX3-FKHR positive RMS cells and tumors. There is little evidence in our dataset for PAX3-FKHR binding at the promoters. In one instance, we show two intronic enhancer elements for MET, rather than at the previously described promoter. The genome-wide analysis further illustrates a strong association between PAX3 and E-box motifs in these binding sites, suggestive of a common co-regulation for many target genes. The map of PAX3-FKHR binding sites provides new links for PAX3 and PAX3-FKHR functions and new targets for RMS therapy. Examination of PAX3-FKHR binding sites in translocation-positive rhabdomyosarcoma cells via ChIP-seq with an antibody specific for the fusion protein.
2010-08-17 | E-GEOD-19063 | biostudies-arrayexpress
Project description:We have recently reported the down-regulation of pannexin 1 (PANX1) levels in rhabdomyosarcoma (RMS) and that restoration of its expression inhibits the progression of embryonal (eRMS) and alveolar (aRMS) rhabdomyosarcoma in vitro and in vivo. While we have shown that this PANX1-mediated inhibition of RMS progression involves reduction of cell proliferation and migration, as well as induction of apoptosis, the underlining molecular mechanisms at play remained to be elucidated. In the present study, using RNA sequencing (RNA-seq) combined with DAVID analysis, we identified the PANX1 interactome in RMS cells and showed that the Gene Ontology (GO) terms such as apoptosis and migration, and KEGG pathways such as MAPK and Rap1 Signaling pathways were amongst the most highly enriched processes in Rh30 (aRMS) cells expressing ectopic PANX1. We then used a proximity-dependent labeling approach (BioID) to screen for the PANX1 interactors in RMS cells, which was complemented by co-immunoprecipitation (co-IP) coupled to high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) performed using Myc-PANX1-enriched subcellular fractions. STRING protein network analyses of the overlapping hits from these two approaches revealed a PANX1 interactome with plasma membrane and cytoskeleton associated proteins from which ACTB and AHNAK were further validated by co-IP using whole cell lysates followed by Western blotting analysis. Using this new and comprehensive information, we have generated the first online PANX1 transcriptome and interactome databases that allow searching, in a user-friendly manner, for PANX1-regulated genes and PANX1 interactors. Moreover, AHNAK knockdown in PANX1-expressing Rh18 (eRMS) and Rh30 (aRMS) significantly abrogated the PANX1-mediated reduction in cell viability and migration, as well as the PANX1-mediated sensitivity to anoikis. Using a combination of genome-wide unbiased approaches, this study is thus the first to identify the PANX1 transcriptome and interactome, providing the research community with online searchable databases to access the PANX1-regulated genes and PANX1 interacting partners. We have shown that PANX1 interacts with AHNAK and that this interaction is critical to the PANX1-mediated inhibition of RMS cell viability and migration, and induction of apoptosis; thus demonstrating how this new information can be used to identify key members of the PANX1 signaling pathway and their relevance to PANX1 function.
2020-01-30 | MSV000084867 | MassIVE
Project description:The goal of this study was to explore in detail how the chromatin remodeler and NuRD subunit CHD4 controls the oncogenic signature of the tumor driver and fusion protein PAX3-FOXO1 in fusion-positive rhabdomyosarcoma. To this aim, we defined the interactome of CHD4 by LC-MS, identified its location in the genome by ChIP-seq, assessed its influence on DNA accessibility by DNase I hypersensitivity assays, and determined its target genes by RNA-seq.
2020-08-11 | PXD015231 | Pride
Project description:Genomic and clinical analyses of major amplification events in alveolar rhabdomyosarcoma Affymetrix SNP 50K XbaI chips were used to anaylyze 57 alveolar rhabdomyosarcoma samples and selected cases were further analyzed using Affymetrix SNP 250K StyI chips
2010-10-16 | E-GEOD-24715 | biostudies-arrayexpress
Project description:In this study we identified genes regulated by MYCN in RH4 cells
2023-10-19 | GSE208423 | GEO
Project description:We report the genome-wide maps of PAX3-FKHR binding sites. Chromatin immunoprecipitation was performed against PAX3-FKHR positive (Rh4) and PAX3-FKHR negative (RD) rhabdomyosarcoma cells with a monoclonal antibody (pFM2) specific for the fusion region of PAX3-FKHR. We obtained 4 million sequence tags for both input and ChIP DNA that aligned to the human genome. We identified 1,463 binding sites from ChIP-seq of Rh4 cells, none of which appeared from ChIP-seq of fusion negative RD cells. The PAX3-FKHR binding sites were found to associate with 1,072 genes in RMS cells. The data shows that PAX3-FKHR binds to the same sites as PAX3, at the enhancers for MYF5, FGFR4, and the MYOD core enhancer previously shown to be regulated by PAX3. Moreover, our dataset has the precision for rapid identification and validation of novel and specific sequences required for the enhancer activity of MYOD and FGFR4. The genome wide analysis reveals that the PAX3-FKHR sites are: 1) mostly distal to transcription start sites; 2) conserved; 3) enriched for PAX3 motifs; and 4) strongly associated with genes over-expressed in PAX3-FKHR positive RMS cells and tumors. There is little evidence in our dataset for PAX3-FKHR binding at the promoters. In one instance, we show two intronic enhancer elements for MET, rather than at the previously described promoter. The genome-wide analysis further illustrates a strong association between PAX3 and E-box motifs in these binding sites, suggestive of a common co-regulation for many target genes. The map of PAX3-FKHR binding sites provides new links for PAX3 and PAX3-FKHR functions and new targets for RMS therapy.
2010-08-17 | GSE19063 | GEO