Genome-wide binding of SUDHL4 DLBCL cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA487806 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Using ChIP-seq, we identified the genome-wide targets of BCL6 and LSD1 in lymphoma cells SUDHL4 and performed H3K4me1 ChIP-seq in cells treated with control siRNA or siRNA targeted to BCL6.
2018-12-13 | GSE119038 | GEO
Project description:Recently, the existence of extracellular miRNAs enclosed in exosomes has raised the possibility that they play an important role in cell-cell communication. To gain more insight into cell-cell communication via exosomal miRNAs, we investigated whether or not tumor cells exposed to hypoxia secrete exosomes which may affect angiogeneic activity. We used SUDHL4 cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from SUDHL4 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h were used for validation of angiogeneic activity, such as tube formation assay. The exosome secreted from SUDHL4 cells in hypoxic condition significantly enhanced tube formation by HUVECs when compared with exosome obtained from SUDHL4 cell in normoxic condition. To identify cellular and exosomal miRNAs universally responding to hypoxic condition, we assess the expression profiles of intercellular and extracellular miRNAs in SUDHL4 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA). SUDHL4 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturerM-bM-^@M-^Ys recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).
2013-12-03 | E-GEOD-45387 | biostudies-arrayexpress
Project description:Recently, the existence of extracellular miRNAs enclosed in exosomes has raised the possibility that they play an important role in cell-cell communication. To gain more insight into cell-cell communication via exosomal miRNAs, we investigated whether or not tumor cells exposed to hypoxia secrete exosomes which may affect angiogeneic activity. We used SUDHL4 cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from SUDHL4 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h were used for validation of angiogeneic activity, such as tube formation assay. The exosome secreted from SUDHL4 cells in hypoxic condition significantly enhanced tube formation by HUVECs when compared with exosome obtained from SUDHL4 cell in normoxic condition. To identify cellular and exosomal miRNAs universally responding to hypoxic condition, we assess the expression profiles of intercellular and extracellular miRNAs in SUDHL4 cells cultured in normoxia (20%) or hypoxia (1%) for 24 h using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA).
2013-12-03 | GSE45387 | GEO
Project description:Mapping of WT FOXO1 and M1L FOXO1 binding sites in SUDHL4 cells
| PRJNA601647 | ENA
Project description:Genome-wide maps of HHEX binding
| PRJNA615887 | ENA
Project description:Genome-wide binding of Lola in S2 cells
| PRJNA564244 | ENA
Project description:CC-122 is a next-generation cereblon E3 ligase modulating agent that has demonstrated promising clinical efficacy in relapsed or refractory diffuse large B‐cell lymphoma (R/R DLBCL) patients. Mechanistically, CC-122 induces the degradation of IKZF1/3, leading to T cell activation and robust cell-autonomous killing in DLBCL. Here, we report a genome-wide CRISPR/Cas9 positive selection screen for CC-122 in a DLBCL cell line SU-DHL-4 with follow-up mechanistic characterization in 6 DLBCL cell lines to identify genes regulating the response to CC-122. Top-ranked CC-122 resistance genes encode not only well-defined members or regulators of the CUL4-DDB1-RBX1-CRBN E3 ubiquitin ligase complex, but also key components of several signaling and transcriptional networks that have not previously been shown to modulate the response to other cereblon modulators. Ablation of CYLD, NFKBIA, TRAF2, or TRAF3 induces hyper-activation of the canonical and/or non-canonical NF-κB pathways and subsequently diminishes CC-122-induced apoptosis in 5 out of 6 DLBCL cell lines. Depletion of KCTD5, the substrate receptor of the CUL3-RBX1-KCTD5 ubiquitin ligase complex, promotes the stabilization of its cognate substrate, GNG5, resulting in CC-122 resistance in HT, SU-DHL-4, and WSU-DLCL2. Furthermore, knockout of AMBRA1 renders resistance to CC-122 in SU-DHL-4 and U-2932, whereas knockout of RFX7 leads to resistance specifically in SU-DHL-4. The ubiquitous and cell line-specific mechanisms of CC-122 resistance in DLBCL cell lines revealed in this work pinpoint genetic alternations that are potentially associated with clinical resistance in patients, and facilitate the development of biomarker strategies for patient stratification, which may improve clinical outcome of CC-122 for R/R DLBCL.
2020-10-01 | GSE158303 | GEO
Project description:CUDC-907 is a small-molecule dual-acting inhibitor of HDACs and PI3Ks, which effectively suppresses the growth and survival of MYC-altered DLBCL. To evaluate the effect of CUDC-907 on MYC-associated genes, two DLBCL cell lines were treated with CUDC-907, a total of 948 differentially regulated genes were identified. 24 genes from the CUDC-907–regulated 948-gene set present either in the "HALLMARK_MYC_TARGETS_V1” 200-gene set or in the “HALLMARK_MYC_TARGETS_V2” 58-gene set in the Molecular Signatures Database (MSigDB). We then computed the correlation coefficients (r) between gene expression levels and MYC protein levels across all samples in the TCGA DLBCL dataset. We found that mRNA expression changes induced by CUDC-907 in the two DLBCL cell lines are negatively correlated with correlation coefficients between expression levels and MYC protein level in the TCGA DLBCL dataset
2016-11-02 | GSE89339 | GEO