Mitogen induced-nucleosomal response pathway and transcriptional programming in mammalian fibroblasts
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE183856 | GEO | 2021/09/13
REPOSITORIES: GEO
Similar Datasets
Project description:Pervasive phosphorylation of histone H3 at serine 10 (H3S10ph) by Aurora B/C plays an important role in mitosis; however, this mark has also been observed at specific genic promoters and enhancers in interphase, implicating mitosis-independent functions. Using the FUCCI cell cycle reporter, we found that 30% of the genome is persistently marked with H3S10ph in interphase mouse embryonic stem cells (ESCs). H3S10ph demarcates broad gene-rich euchromatic regions in G1 and shows remarkable correlation with domains of early DNA replication timing (RT). Consistent with mitosis-independent H3S10 kinase activity, this pattern was preserved in ESCs treated with hesperidin, a potent inhibitor of Aurora B/C. Disruption of H3S10ph by expression of non-phosphorylatable H3.3S10A results in ectopic spreading of H3K9me2 into adjacent H3S10ph-enriched euchromatic regions, mimicking the phenotype observed in Drosophila JIL-1 kinase mutants. Conversely, H3S10ph domains expand in interphase Glp-/- ESCs, revealing that H3S10ph expansion is restricted by H3K9me2. Strikingly, spreading of H3S10ph at RT transition regions (TTRs) is accompanied by aberrant strand-biased transcription initiation of genes and repetitive elements co-oriented with the replication fork, indicating that H3K9me2 plays a critical role in establishing repressive chromatin on the leading strand. Finally, we show that H3S10ph is also present in interphase murine embryonic fibroblasts (MEFs), but is restricted to intragenic regions of actively transcribing genes. Our study provides a detailed map of interphase H3S10ph in ESCs and MEFs, uncovering a previously unappreciated crosstalk between the opposing marks H3S10ph and H3K9me2, and a role for the latter in ensuring appropriate transcription at TTRs in ESCs.
2017-11-20 | GSE97947 | GEO
Project description:An innovative multikinase inhibitor (H89)-based antitumor immunotherapy in colorectal cancer (CRC) is presented. The study was designed to evaluate the effect of H89 on colon tumor growth and carcinogenesis through in vivo analyses. Syngeneic mouse models of CRC cancer in BALB/c mice and chemically colon tumorigenesis, reveals that H89 delays colon oncogenesis, related to a preventive effect, and prevents tumor growth, underlying an antitumor effect respectively. Using immunodeficient and monoclonal antibody-specific immunosuppression, we identified immune cell populations involved in the preventive (NK-cell dependent) and antitumor activity of H89 (T-cell dependent). Flow cytometry analysis showed that the antitumor effect of H89 was correlated with an increase in the tumor microenvironment of CD4+ Th1 cells and CD8+ cytotoxic T cells and a decrease of CD4+ Treg cells infiltration. Furthermore, qRT-PCR revealed that H89 can promote naïve CD4+ T cells differentiation into Th1, decreases Treg differentiation and increases ex vivo CD8+ T cell-mediated killing of cancer cells. An RNAseq profiling experiment showed that H89 induces an overexpression of genes involved in antitumor immune response, such as IL-15RA, whose inhibition counteracts the antitumor effect of H89. In conclusion, our findings identify H89 as a potential strategy for the prevention and treatment of CRC.
2022-03-03 | GSE197598 | GEO
Project description:The effects of demycarosyl-3D-M-NM-2-D-digitoxosyl-mithramycin SK (DIG-MSK; EC-8042), a novel analogue of the antitumor antibiotic mithramycin A, on gene transcription were examined in human A2780 ovarian carcinoma cells. DIG-MSK down-regulated a different set of genes depending on the drug concentration. Moreover, several genes were significantly up-regulated. These results are rationalized in terms of DIG-MSK competition with Sp1 transcription factor for binding to consensus C/G-rich tracts encompassed in gene promoters. Human A2780 ovarian carcinoma cells were treated with either 8 nM or 80 nM DIG-MSK for 24 h, and RNA was extracted from treated cells as well as from untreated (control) cells.
2014-08-13 | E-GEOD-46926 | biostudies-arrayexpress
Project description:The effects of demycarosyl-3D-β-D-digitoxosyl-mithramycin SK (DIG-MSK; EC-8042), a novel analogue of the antitumor antibiotic mithramycin A, on gene transcription were examined in human A2780 ovarian carcinoma cells. DIG-MSK down-regulated a different set of genes depending on the drug concentration. Moreover, several genes were significantly up-regulated. These results are rationalized in terms of DIG-MSK competition with Sp1 transcription factor for binding to consensus C/G-rich tracts encompassed in gene promoters.
2014-08-13 | GSE46926 | GEO
Project description:We have used peptide capture in conjunction with super-SILAC quantification to carry out an unbiased high-throughput analysis of the composition of protein complexes that bind to histone H3K9/S10 and H3K27/S28 methyl-phospho modifications. We compared binding profiles of nuclear proteins from MPC11 myeloma cells to peptides carrying the H3K9me3, H3K27me3, H3S10ph, H3S28ph and the double H3K9me3/S10ph and H3K27me3/S28ph modifications. The analysis was carried out using peptides corresponding to amino acids 1-20 and 18-38 and the unmodified peptides were also analysed to assess binding to the unmodified histone tail. In order to ensure that the proteins present in any of the "heavy" capture assay samples have corresponding peptides in the common "light" internal reference, we adapted the super-SILAC approach using a reference sample that was obtained by mixing the 8 pulldowns and the negative beads-only control. The method allows us to accurately quantify binding and directly compare levels of binding to peptides that carry a number of different methyl-phospho combinations. This makes it possible for use indeatiled bioinformatic analyses.
2016-05-04 | PXD001273 | Pride
Project description:The distal convoluted tubule (DCT) and the cortical collecting ducts (CCD) are portions of renal tubule that are partly responsible for maintaining the systemic concentrations of potassium, sodium, calcium and magnesium. Despite being structurally similar, DCT and CCD cells have different transport capabilities due to a variety of different membrane-associated transport proteins. However, DCT and CCD cells appear to be modulated via the same hormones. The objective of this study was assess the differential response of DCT and CCD cells to long-term exposure to the hormones vasopressin or angiotensin II, both of which modulate DCT and CCD cells differently. Mass spectrometry based quantitative proteomics was used to profile the differential proteome between DCT and CCD.
2017-12-15 | PXD005454 | Pride
Project description:Medullary sponge kidney (MSK) disease, a rare kidney malformation featuring recurrent renal stones and nephrocalcinosis, continues to be diagnosed using expensive and time-consuming clinical/instrumental tests (mainly urography). Currently, no molecular diagnostic biomarkers are available. To identify such we employed a proteomic-based research strategy utilizing urine from 22 patients with MSK and 22 patients affected by idiopathic calcium nephrolithiasis (ICN) as controls. Notably, two patients with ICN presented cysts. In the discovery phase, the urine of 11 MSK and 10 controls, were randomly selected, processed, and analyzed by mass spectrometry. Subsequently, several statistical algorithms were undertaken to select the most discriminative proteins between the two study groups. ELISA, performed on the entire patients’ cohort, was used to validate the proteomic results. After an initial statistical analysis, 249 and 396 proteins were identified exclusive for ICN and MSK, respectively. A Volcano plot and ROC analysis, performed to restrict the number of MSK-associated proteins, indicated that 328 and 44 proteins, respectively, were specific for MSK. Interestingly, 119 proteins were found to differentiate patients with cysts (all patients with MSK and the two ICN with renal cysts) from ICN without cysts. Eventually, 16 proteins were found to be common to three statistical methods with laminin subunit alpha 2 (LAMA-2) reaching the higher rank by a Support Vector Machine, a binary classification/prediction scheme. ELISA for LAMA-2 validated proteomic results. Thus, using high-throughput technology, our study identified a candidate MSK biomarker possibly employable in future for the early diagnosis of this disease.
2021-05-24 | PXD025744 | Pride
Project description:We have employed gene expression profiling in order to identify targets of transcriptional response to stress in resting mouse Swiss 3T3 fibroblasts, either untreated (control) or treated with anisomycin for 3 or 6 hours to induce the p38/MAP kinase pathway. In order determine transcriptional effects dependent on MSK1/2 kinase activity, H89 inhibitor was used in the study. Serum starved (72 h 0.2% FCS) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 3 h or 6h (in duplicates) either with or without 15-min pre-treatment with MSK1/2 inhibitor H89 (10 uM). Untreated, serum-starved cells were used as a control. RNA was collected and gene expression profiling using strand-specific RNA-seq was performed.
2014-08-12 | E-GEOD-58746 | biostudies-arrayexpress
Project description:No systematic method exists to derive inter-nucleosomal potentials between nucleosomes along a chromosome consistently across a given genome. Such potentials can yield information on nucleosomal ordering, thermal as well as mechanical properties of chromosomes. Thus, indirectly, they shed light on a possible mechanical genomic code along a chromosome. To develop a method yielding effective inter-nucleosomal potentials between nucleosomes, a generalized Lennard-Jones potential for the parameterization is developed based on nucleosomal positioning data. This approach eliminates some of the problems that the underlying nucleosomal positioning data have, rendering the extraction difficult on the individual nucleosomal level. Furthermore, patterns on which to base a classification along a chromosome appear on larger domains, such as hetero- and euchromatin. An intuitive selection strategy for the noisy optimization problem is employed to derive effective exponents for the generalized potential. The method is tested on the Candida albicans genome. Applying k-means clustering based on potential parameters and thermodynamic compressibilities, a genome-wide clustering of nucleosome sequences is obtained for C. albicans. This clustering shows that a chromosome beyond the classical dichotomic categories of hetero- and euchromatin is more feature-rich.
| S-EPMC9001623 | biostudies-literature
Project description:Protein phosphorylation plays a crucial role in propagating cellular responses to both internal and external cues. One of the most important kinases responsible for protein phosphorylation is protein kinase A (PKA). N-[2-p-bromocinnamylamino-ethyl]-5-isoquinolinesulphonamide (H89) is often used as a “PKA specific inhibitor” to study the involvement of PKA in signaling pathways. However, evidence from cell-free experiments suggested that H89 can also inhibit other kinases. In this experiment, previously-generated mouse collecting duct cell lines with and without PKA were treated with H89, followed by mass spectrometry-based phosphoproteomics to globally assess changes in phosphorylation.
2019-03-28 | PXD011167 | Pride