KDM5B occupancy profiling by CUT&Tag from murine BMDMs untreated (UT) or stimulated with LPS
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE212808 | GEO | 2023/05/10
REPOSITORIES: GEO
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Project description:KDM5B occupancy profiling by CUT&Tag from murine BMDMs untreated (UT) or stimulated with LPS
| PRJNA877366 | ENA
Project description:Bone marrow was extracted from mice that are COP1-wt Rosa26-CreERT2 or COP1-floxed Rosa26-CreERT2 BMDMs were obtained by culturing bone marrow precursors in media containing 20% of supernatant from L929 cells. At day 4 of differentiation 4-OHT was added at 1uM to induce deletion of COP1 in BMDMs derived from COP1-floxed mice. At day 7 of differentiation, BMDMs were treated with 100 ng/ml of LPS or not. BMDMs were directly harvested in lysis buffer (from Qiagen RNeasy mini kit) at different time points (0h, 2.5h, 2.5h, 4h, 6h, 9h and 13h) following LPS stimulation. Three BMDMs preparations per group: G1: BMDMs from COP1-wt mice (expressing the wt allele of COP1) CRE positive. G2: BMDMs from COP1-floxed mice (expressing the floxed allele of COP1) CRE positive
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Project description:Purpose: The purpose of this study was to compare the BMDMs transcriptome in the control LPS and LPS plus BHB group in order to identify the critical pathway that contributed to the inhibiton of BHB on M1 polarization. Methods: 1× 106 BMDMs were pre-treated with PBS or BHB for 1 hours before LPS administration. Four hours later, BMDMs were harvested for RNA preparation. Results: Among 16650 mapped genes, 7325 differentially expressed genes were identified, including 244 LPS inducible BHB down regulated named class A and 537 LPS repressed BHB up regulated genes named class B. The genes in class A were mainly TLR4 and TNF signaling pathway, while genes in class B were associated with negative regulation of transcription and NF-KB signaling. The GSEA showed that BHB have the similar profiles chnage on BMDMs with TSA. Conclusions: Our study revealed that BHB down regulated TLR4 and NF-KB pathway related genes to inhibited M1 polarization, and BHB have a similar effect on BMDMs with TSA through comparing the genetic changes of two substance caused in cells.
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Project description:Here we show that the RNA-binding protein CPEB4 sustains the expression of anti-inflammatory factors in LPS-stimulated BMDMs, by binding to the corresponding mRNAs and promoting their stabilization. in macrophages.
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Project description:ES cell pluripotency is thought to be regulated in part by H3K4 methylation. However, it is unclear how H3K4 demethylation contributes to ES cell function and participates in iPS cell reprogramming. Here, we show that KDM5B, which demethylates H3K4, is important for ES cell differentiation, and presents a barrier to the reprogramming process. Depletion of Kdm5b leads to an extension in the self-renewal of ES cells in the absence of LIF. Transcriptome analysis revealed the persistent expression of pluripotency-genes and underexpression of developmental genes during differentiation in the absence of Kdm5b, suggesting that KDM5B plays a key role in cellular fate changes. We also observed accelerated reprogramming of differentiated cells in the absence of Kdm5b, demonstrating that KDM5B is a barrier to the reprogramming process. Expression analysis revealed that mesenchymal master regulators associated with epithelial-to-mesenchymal transition (EMT) are downregulated during reprogramming in the absence of Kdm5b. Moreover, global analysis of H3K4me3/2 revealed that enhancers of fibroblast genes are rapidly deactivated in the absence of Kdm5b, and genes associated with EMT lose H3K4me3/2 during the early reprogramming process. These findings provide functional insight into the role for KDM5B in regulating ES cell differentiation and as a barrier to the reprogramming process. ChIP-Seq for H3K4me3 and H3K4me2 in murine shLuc and shKdm5b 4TF-MEFs (tetO-Pou5f1,-Sox2,-Klf4,-c-Myc) at 48h.
2013-10-14 | E-GEOD-47123 | biostudies-arrayexpress
Project description:ES cell pluripotency is thought to be regulated in part by H3K4 methylation. However, it is unclear how H3K4 demethylation contributes to ES cell function and participates in iPS cell reprogramming. Here, we show that KDM5B, which demethylates H3K4, is important for ES cell differentiation, and presents a barrier to the reprogramming process. Depletion of Kdm5b leads to an extension in the self-renewal of ES cells in the absence of LIF. Transcriptome analysis revealed the persistent expression of pluripotency-genes and underexpression of developmental genes during differentiation in the absence of Kdm5b, suggesting that KDM5B plays a key role in cellular fate changes. We also observed accelerated reprogramming of differentiated cells in the absence of Kdm5b, demonstrating that KDM5B is a barrier to the reprogramming process. Expression analysis revealed that mesenchymal master regulators associated with epithelial-to-mesenchymal transition (EMT) are downregulated during reprogramming in the absence of Kdm5b. Moreover, global analysis of H3K4me3/2 revealed that enhancers of fibroblast genes are rapidly deactivated in the absence of Kdm5b, and genes associated with EMT lose H3K4me3/2 during the early reprogramming process. These findings provide functional insight into the role for KDM5B in regulating ES cell differentiation and as a barrier to the reprogramming process. RNA-Seq of undifferentiated and embryoid body (EB) differentiated murine shLuc and shKdm5b ES cells
2013-10-14 | E-GEOD-47124 | biostudies-arrayexpress
Project description:Gene expression in bone marrow-derived macrophages (BMDMs) from WT and mice lacking the transcriptional repressor Kruppel-like factor 3 (KLF3). We cultured BMDMs from bone marrow for 7-10 days then treated cells with 100 ng/mL lipopolysaccharide (LPS) or vehicle (PBS) for 0 h or 8 h, followed by RNA extraction. We aimed to investigate deregulated genes and pathways in macrophages lacking KLF3, during the inflammatory response to endotoxin (LPS).
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Project description:Purpose: Advanced melanoma patients have poor prognosis. Although immune checkpoint blockade has revolutionized treatment for melanoma patients, majority of patients do not respond. The goal of this research is to evaluate whether epigenetic therapy targeting KDM5B could overcome resistance to immunotherapy. Methods:RNA-Seq analysis of KDM5B KO mouse melanoma cell lines compared to control cells to evaluate whether KDM5B depletion induces activation of retroelements, which subsequently activates type I interferon responses. Mouse studies were conducted to evaluate whether anti-tumor immunity induced by KDM5B loss could overcome immunotherapy resistance. Results: We identified that KDM5B depletion derepress retroelement expression, which subsequently activates type I interferon response and enhances anti-tumor immunity. Loss of KDM5B could overcome resistance to anti-PD-1 immunotherapy. Conclusions: Our work characterized ablation of histone demethylase KDM5B in melanoma augments anti-tumor immunity through Upregulation of retroelements.
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Project description:Purpose: Advanced melanoma patients have poor prognosis. Although immune checkpoint blockade has revolutionized treatment for melanoma patients, majority of patients do not respond. The goal of this research is to evaluate whether epigenetic therapy targeting KDM5B could overcome resistance to immunotherapy. Methods:RNA-Seq analysis of KDM5B KO mouse melanoma cell lines compared to control cells to evaluate whether KDM5B depletion induces activation of retroelements, which subsequently activates type I interferon responses. Mouse studies were conducted to evaluate whether anti-tumor immunity induced by KDM5B loss could overcome immunotherapy resistance. Results: We identified that KDM5B depletion derepress retroelement expression, which subsequently activates type I interferon response and enhances anti-tumor immunity. Loss of KDM5B could overcome resistance to anti-PD-1 immunotherapy. Conclusions: Our work characterized ablation of histone demethylase KDM5B in melanoma augments anti-tumor immunity through Upregulation of retroelements.
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Project description:Bone marrow was harvested from Rosa26CreER; Stk40+/+ (WT; n = 3) and Rosa26CreER; Stk40loxp/loxp (Stk40 KO; n = 3) mice and differentiated for 6 days in the presence of 100 nM 4-OHT to generate WT and Stk40 KO bone-marrow derived macrophages (BMDMs). 2. On day 7 following differentiation BMDMs were treated with 100 ng x ml-1 LPS and harvested at 0 hrs, 6 hrs, 16 hrs, and 32 hrs following LPS exposure. 3. The cells were snap-frozen at the time of harvest. RNA was extracted using the Qiagen RNeasy mini kit as per manufacturer’s protocol including the on-column DNase digestion. Groups: There are cells from 3 mice x 2 genotypes x 4 time points G1: WT 0 hr LPS G2: WT 6 hr LPS G3: WT 16 hr LPS G4: WT 32 hr LPS G5: Stk40 KO 0 hr LPS G6: Stk40 KO 6 hr LPS G7: Stk40 KO 16 hr LPS G8: Stk40 KO 32 hr LPS
2018-12-28 | GSE124410 | GEO