Novel KDM1A inhibitors induce differentiation and apoptosis of glioma stem cells via unfolded protein response (UPR) pathway
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE84603 | GEO | 2017/09/06
SECONDARY ACCESSION(S): PRJNA330614
REPOSITORIES: GEO
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Project description:We are currently studying how these information-carrying oligosaccharides are involved in cellular stress responses, particularly in human genetic diseases called Congenital Disorders Of Glycosylation in which oligosaccharide assembly is defective. We are interested in endoplasmic stress responses/unfolded protein responses. ER glycans and ER lectins are intimately involved in the folding of ER proteins. Therefore, ER lectins and ER glycosyltransferases may be controlled by these stress responses, to produce and/or recognize key glycans in the stress response. Our model system is the human dermal fibroblast. We have successfully calibrated the ER stress responses in these cells by determining the magnitudes of various stress effects (such as chaperone transcription) with different forms of ER stress. We are also completing a study in which activation the signaling molecules Ire1 and ATF6 are also calibrated. We prepared multiple identical aliquots of RNA from cells stressed under several of these calibrated conditions. Endoplasmic reticulum (ER) stress and the unfolded protein response (UPR): Study of the role of ER stress in the expression of genes for ER transferases and lectins that participate in ER folding and quality control using human skin fibroblasts. The UPR response in these cells has been calibrated using various readouts in response to different stresses: 1) 40 nM L-azetidine-2-carboxylate (AZC) 1 hour, 2) 0.2 mg/ml castanospermine, 24 hours, 3) 2 mM Dithiothreitol (DTT), 20 minutes, 4) 100nm Thapsigargin (TG), 30 minutes, 5) 5 ug/ml tunicamycin, 5 hours, 6) untreated control cells
2011-02-17 | E-GEOD-27349 | biostudies-arrayexpress
Project description:We are currently studying how these information-carrying oligosaccharides are involved in cellular stress responses, particularly in human genetic diseases called Congenital Disorders Of Glycosylation in which oligosaccharide assembly is defective. We are interested in endoplasmic stress responses/unfolded protein responses. ER glycans and ER lectins are intimately involved in the folding of ER proteins. Therefore, ER lectins and ER glycosyltransferases may be controlled by these stress responses, to produce and/or recognize key glycans in the stress response. Our model system is the human dermal fibroblast. We have successfully calibrated the ER stress responses in these cells by determining the magnitudes of various stress effects (such as chaperone transcription) with different forms of ER stress. We are also completing a study in which activation the signaling molecules Ire1 and ATF6 are also calibrated. We prepared multiple identical aliquots of RNA from cells stressed under several of these calibrated conditions.
2011-02-17 | GSE27349 | GEO
Project description:Unfolded protein response (UPR) and endoplasmic reticulum (ER) stress in acromegaly
| PRJNA643979 | ENA
Project description:Acromegaly is a growth hormone (GH) excess pathological condition in humans and is associated with somatic disfigurement and a wide variety of systemic manifestations such as arthritis, neuropathies, carpal tunnel syndrome, reproductive disorders, metabolic disorders, and gastrointestinal complications. Studying the effect of growth hormone (GH) excess at the cellular level could help in understanding the underlying causes of acromegaly complications. In our previous publications, we have shown that excess GH increases DNA damage and impairs DNA repair pathways in somatic cells. In addition, we revealed that excessive GH reduces the number of stem cells and causes premature aging. Exaggerated growth is one of the main features of acromegaly and therefore, in this research, we have focused on protein production and biogenesis in acromegaly and whether excess GH is associated with unfolded protein response (UPR) and endoplasmic reticulum (ER) stress. Acromegaly-associated abnormal growth can be caused by hypertrophy or hyperplasia. Using pathway enrichment analysis of RNA seq data from our Zebrafish Acromegaly Model and Flow Cytometry Analysis, here we show a progressive increase in hepatocyte cell size and enrichment of hypertrophy pathways in the muscle and liver. That was associated with a progressive enrichment of protein production pathways and ribosome biogenesis. Moreover, using GSEA (Gene Set Enrichment Analysis) of acromegaly RNA seq data, here we show that endoplasmic reticulum (ER) stress is an accompanying feature of acromegaly disease. Our model exhibited endoplasmic reticulum (ER) stress in various organs, especially in the brain.
2021-03-04 | GSE153755 | GEO
Project description:We examined the transcriptional changes modulated by lysine-specific histone demethylase 1 (KDM1A/LSD1) by perfroming global transcriptome analysis. MDA-MB-231 cancer stem cells (CSCs) were transduced with control shRNA or KDM1A shRNA lentiviral particles and the RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that differentially expressed genes were enriched in biological processes of regulation of organismal processes, cell migration, cell motility, cell proliferation and cell differentiation. In terms of molecular function, the differentially expressed genes were enriched in growth factor activity, cytokine activity, and cytokine receptor binding. Importantly, GSEA results demonstrated that KDM1A regulated genes showed a negative correlation with the gene sets of IL6-JAK-STAT3 signaling and epithelial mesenchymal transition (EMT) pathways.
2023-07-13 | GSE154382 | GEO
Project description:The purpose of this study was to chacterise the effect of KDM1A knocking down on genome-wide gene expression in human NSCLC cells in vivo. Affymetrix human transcriptome array 2.0 was used to profile the transcriptome of xenograft tumors derived from PC9 cells stably expressing either ShRNA KDM1A or ShRNA control. These cells were subcutanously injected into the right axillary of the mouse, and allowd to grow for 5 weeks to form xenograft tumors. Although KDM1A is up-regulated in NSCLC, but key genes and pathways regulated by KDM1A was not well-understood in NSCLC. Using this approach, we have shown that KDM1A repressed or activated a distinctive set of pathways and key target genes in vivo. This first comprehesive study of transciptome profile upon KDM1A koncking-down in vivo highlights the distinctive pathways regulated by KDM1A during NSCLC tumorigenesis, and it will help to identify new therapeutic targets for NSCLC treatment. Xenograft tumors derived from two cell lines: PC9 cells stably expressing ShRNA KDM1A or ShRNA control. We extracted total RNA from 3 independent xenograft tumors per cell line.
2016-07-27 | E-GEOD-71358 | biostudies-arrayexpress
Project description:KDM1A requires an adaptor protein with specific DNA-binding activity to recognize chromatin sequence. We constructed HepG2 cells stably overexpressing KDM1A-Flag tag using lentivirus. We performed Co-IP with Flag-gel and we used LC-MS to determine the immunoprecipitates of KDM1A.
2023-05-19 | PXD043284 | iProX
Project description:2C embryos were generated from Kdm1a FL/Fl Zp3Cre females mated to wild type males for RNA-seq analysis using the Nugen Ovation RNA-seq system V2 3 replicates of maternal Kdm1a mutant 2C embryos were collected for RNA-seq , compared to wt 2C embryos and wt oocyte samples from Macfarlan TS et al, Nature 2012 (GEO acession GSE33923)
2015-03-10 | E-GEOD-66547 | biostudies-arrayexpress
Project description:We set out to determine the role of the IRE1/XBP1 pathway, the most ancient and highly conserved endoplasmic reticulum (ER) stress-sensing pathway of the unfolded protein response (UPR), in Schmid metaphyseal chondrodysplasia (MCDS). RNA derived from hypertrophic zones microdissected from growth plates of wildtype mice, mice lacking XBP1 activity in chondrocytes (Xbp1Cart?Ex2), mice carrying a COL10A1 pN617K mutation (ColXN617K), and compound mutants (C/X) was analyzed by whole genome microarray analysis. 1633 probes were differentially expressed between ColXN617K and wildtype, 215 probes were differentially expressed between Xbp1Cart?Ex2 and wildtype, and 1337 probes were differentially expressed between C/X and wildtype. 885 probes were differentially expressed between ColXN617K and wildtype but not Xbp1Cart?Ex2 and wildtype or C/X and wildtype, thus representing the XBP1-dependent response to hypertrophic chondrocyte ER stress. 688 probes were differentially expressed between ColXN617K and wildtype and between C/X and wildtype but not Xbp1Cart?Ex2 and wildtype, thus representing the XBP1-independent response to hypertrophic chondrocyte ER stress. Results were validated by qPCR. Entire growth plate hypertrophic zones were microdissected from one tibia from each of three 2-week old wildtype mice, three 2-week old mice carrying a COL10A1 p.N617K mutation (ColXN617K), three 2-week old mice lacking XBP1 activity in chondrocytes (Xbp1Cart?Ex2), and three 2-week old mice resulting from a cross between ColXN617K and Xbp1Cart?Ex2 (C/X).
2015-08-21 | E-GEOD-72261 | biostudies-arrayexpress
Project description:Stress pathways monitor intracellular systems and deploy a range of regulatory mechanisms in response to stress. One of the best-characterized pathways, the unfolded protein response (UPR), is responsible for maintaining endoplasmic reticulum (ER) homeostasis. The highly conserved Ire1 branch regulates hundreds of gene targets by activating a UPR specific transcription factor. To understand how the UPR manages ER stress, a novel genetic approach was applied to reveal how the system corrects disequilibria. The data show that UPR can address a wide range of dysfunctions that is otherwise lethal if not for its intervention. Transcriptional profiling of stress alleviated cells shows that the program can be modulated, not just in signal amplitude, but also through differential target gene expression depending on the stress. The breadth of the functions mitigated by the UPR further supports its role as a major mechanism maintaining systems robustness. Genes expression from early log phase of ALG5, LHS1, and SCJ1 knockout cell and untreated and DTT-treated WT cells. RNA was prepared from independent triplicate samples.
2011-11-23 | E-GEOD-33844 | biostudies-arrayexpress