Identify genes involved in ER stress in wheat using RNA sequencing
Ontology highlight
ABSTRACT:
ORGANISM(S): Triticum aestivum
PROVIDER: GSE128485 | GEO | 2019/05/15
REPOSITORIES: GEO
Similar Datasets
Project description:We used dithiothreitol (DTT) and tauroursodeoxycholic acid (TUDCA) to induce or suppress ER stress in wheat cells, respectively, with the aim to reveal the molecular background of ER stress responses using miRNA sequencing. After sequencing, we revealed a total of 1,939 miRNAs involved in the process of ER stress response, including 1,740 known miRNAs and 199 novel miRNAs.
2024-01-19 | GSE165109 | GEO
Project description:We used dithiothreitol (DTT) and tauroursodeoxycholic acid (TUDCA) to induce or suppress ER stress in wheat cells, respectively, with the aim to reveal the molecular background of ER stress responses using degradome sequencing. After combined analysis of high-throughput sequencing, a total of 12,453 miRNA-target pairs were verified by degradome sequencing, and among them, 7,484 genes were targeted by 1,233 miRNAs.
2024-01-19 | GSE165108 | GEO
Project description:Transcriptional profiling of ER stress condition comparing control (untreated), dithiothreitol (DTT) treated, or tunicamycin (TM) treated conditions on P. angusta DL1 strain.
2015-07-22 | GSE68528 | GEO
Project description:Cells respond to endoplasmic reticulum (ER) stress through activation of signaling pathways such as the Unfolded Protein Response (UPR) which improve the ER folding environment capacity upon changes in misfolded protein burden. Small molecules termed chemical chaperones can attenuate the UPR under stress conditions and improve folding and trafficking of specific mutant proteins. One such compound is the bile acid tauroursodeoxycholic acid (TUDCA). Despite promising results in multiple models of protein folding diseases, TUDCA’s mechanism of action remains unclear. To better define how TUDCA attenuate ER stress, we leveraged the genetically tractable budding yeast, S. cerevisiae. Consistent with properties described for TUDCA, we found it significantly improves growth of yeast subjected to ER stress caused by the N-glycosylation inhibitor tunicamycin (Tm) independently of activity of the UPR. In addition to other data, transcriptomics of strains treated with TUDCA link its ability to resuce Tm-induced stress with cell wall remodeling.
2024-11-13 | GSE186390 | GEO
Project description:Transcriptional profiling of ER stress condition comparing control (untreated), dithiothreitol (DTT) treated, or tunicamycin (TM) treated conditions on P. angusta DL1 strain. Six-condition experiment: normal condition vs. ER stress condition (TM 30, 60, 120min; DTT 30, 60, 120min) in P. angusta DL1 strain. Independently grown and harvested. Two replicates per array.
2015-07-22 | E-GEOD-68528 | biostudies-arrayexpress
Project description:We induced ER stress in Jurkat T-cells with dithiothreitol (DTT), which reduces the protein disulfide bonds and causes the accumulation of misfolded proteins in the ER lumen. For assessment of DTT effects on cells, we performed Affymetrix whole transcriptome gene expression analysis. The cells were treated for 6 hours with 2.5 mM Dithiothreitol (Sigma-Aldrich). Total RNA was isolated from DTT-treated (2 replicates) and control (2 replicates) Jurkat cells and hybridized to a gene expression arrays (GeneChip Gene 1.0 ST Array System; Affymetrix, Santa Clara, CA).
2017-04-15 | E-MTAB-5574 | biostudies-arrayexpress
Project description:Cholesterol efflux capacity dysfunction in macrophages is thought to be important in atherosclerosis. However, the molecular mechanism underlying this dysfunction remains unclear. Our previous analysis found that the increase of endoplasmic reticulum stress in macrophages during atherosclerotic plaque formation. Here we extended our analysis to ApoE-/- mice fed a high fat diet, some of which were treated with tauroursodeoxycholic acid (TUDCA) and collected the arteries of mice among these three groups (NFD, HFD and HFD+TUDCA) to perform the Bulk-RNA sequencing. There was significantly high expression of matrix metalloproteinase family (MMP9, MMP25, MMP8, MMP12, MMP13 and MMP3), CD68, inflammasome (IL1b, IL18bp, ifi44, ifi204 and Nlrp3), ER stress (Hspa5) and cholesterol transporters (ABCA1 and ABCG1) in the HFD group compared with the NFD group, however, TUDCA rescued the high expression of the above DEGs to different degrees. As shown by the expression levels of ifi204, Nlrp3, Il1b, and Il18, inflammasome activation was evident in the arteries of the HFD group compared to the NFD group. The ER stress inhibitor TUDCA not only decreased expression of the ER stress-related gene Hspa5 but also down-regulated inflammasome activation (as seen with the expression levels of ifi204, ifi44, NLRP3 and IL1b) in the artery of TUDCA treated mice compared with mice without drugs.
2024-03-05 | GSE260610 | GEO
Project description:The accumulation of unfolded proteins in the lumen of the endoplasmic reticulum (ER) causes stress and induces the unfolded protein response (UPR) which is characterised in part by the transcriptional induction of genes involved in assisting protein folding. Translational responses to ER stress have been less well described and here we report on a genome-wide analysis of translational regulation in the response to the ER stress-inducing agent dithiothreitol (DTT) in Saccharomyces cerevisiae. Although the observed polysome profiles were similar under control and ER stress conditions microarray analysis identified transcipt-specific translational regulation. Genes with functions in ribosomal biogenesis and assembly were translationally repressed under ER stress. In contrast mRNAs for known UPR genes, including the UPR transcription factor HAC1, the ER-oxidoreductase ERO1 and the ER-associated protein degradation (ERAD) gene DER1 were enriched in polysomal fractions under ER stress conditions. In addition, we show that splicing of HAC1 mRNA is required for efficient ribosomal loading and that Gcn2p is required for normal HAC1 splicing, so shedding light on the role of this protein kinase in the UPR pathway. Experiment Overall Design: Polyribosomes were extracted from S. cerevisiae cells treated with 2 mM DTT or water (control), and fractionated according to ribosome loading. Following RNA purification from these fractions, for each sub-polysomal and polysomal RNA sample, fractions from three independent extracts per treatment (DTT/control) were pooled.
2008-06-11 | E-GEOD-10091 | biostudies-arrayexpress
Project description:Myeloperoxidase (MPO), oxidative stress (OS), and endoplasmic reticulum (ER) stress are all increased in the lungs of neonatal rat pups raised in hyperoxia (HOX, >90% O2), an established model of bronchopulmonary dysplasia (BPD). However, the relationship between OS, MPO, and ER stress has not been examined in HOX rat pups. To determine the relationship between OS, MPO, and ER stress in BPD we treated Sprague-Dawley neonatal rat pups with Tunicamycin (Tun) or with HOX. Tun directly induces ER stress and simplifies neonatal lung alveolarization. Previously, we showed that HOX induces a cycle of destruction that we hypothesize through increased OS, MPO, and ER stress to induce BPD. To inhibit ER stress specifically, we used tauroursodeoxycholic acid (TUDCA), a molecular chaperone. To break the cycle of destruction and reduce OS and MPO we used N-acetyl-lysyltyrosylcysteine-amide (KYC), a systems pharmacology agent. Lung structure was studied morphometrically. ER stress was detected using immunofluorescence (IF), transcriptomic, proteomic, and electron microscopic analyses. Increased ER stress was observed in the lungs of HOX rat pups and also in human BPD lungs by IF. Morphometric and proteomic studies of rat lungs showed that Tun treatment decreased lung complexity and increased ER stress and BPD severity. The fact that TUDCA improved lung complexity in Tun-treated neonatal rat pups, and decreased BPD induced by HOX provides strong support for the idea that ER stress plays a causal role in BPD. Additional support comes from data showing TUDCA decreased lung myeloid cells and MPO levels in the lungs of both Tun- and HOX-treated neonatal rat pups. These data link OS and MPO to ER stress in the mechanisms mediating BPD. KYC's effective inhibition of ER stress in the lungs of Tun-treated rat pups provides additional support for the idea that MPO-induced ER stress plays a direct causal role in BPD. Thus, ER stress appears to expand our proposed cycle of destruction. Our results suggest ER stress evolves from OS and MPO to increase neonatal lung injury and impaired neonatal lung growth and development. The encouraging effect of TUDCA indicates chemical chaperone has the potential in treating BPD. Using multiomic data to investigate the role of endoplasmic reticulum stress in the development of BPD in rat model.
2022-08-11 | GSE197403 | GEO
Project description:SEPN1 is a type II protein of the endoplasmic reticulum (ER) whose loss of function gives rise to a collection of debilitating autosomal recessive myopathies gathered under the umbrella term of SEPN1-related myopathy (RM). At the moment, SEPN1-RM lacks an effective pharmacological treatment; thus, the medical management of the disease is only supportive. The potentially fatal diaphragmatic weakness leading to respiratory insufficiency in patients still ambulant is the main reason for medical concerns. Thus, studies on SEPN1-RM pathogenesis are necessary to implement a targeted pharmacological therapy aimed at relieving the general muscle weakness and the more worrisome diaphragmatic dysfunction. Here, we show a physical and functional interaction between SEPN1 and the ER stress mediator ERO1 alpha (henceforth, ERO1). Both SEPN1 and ERO1 are involved in the redox regulation of proteins into the ER, although in an opposite way SEPN1 imposes a less oxidant ER poise while ERO1 a more oxidant one, conceivable with a reductase function of SEPN1 and an oxidase one of ERO1. Furthermore, both are mainly localized in a region of the ER in close contact with mitochondria termed mitochondria-associated membranes (MAMs) and their loss impacts oppositely on the short-range MAMs, thereby impinging ER-mitochondria Ca2+ dynamics, OXPHOS, and bioenergetics. We find that ERO1 depletion restores the impaired short-range MAMs due to SEPN1 loss together with mitochondrial ATP. ERO1 knockout in a mouse background of SEPN1 loss blunts ER stress and the consequent Unfolded Protein Response (UPR) while it rescues the diaphragmatic weakness by improving ER/mitochondria contacts, calcium dynamics, and OXPHOS. Importantly, treatments of SEPN1 knock out mice with the chemical chaperone tauroursodeoxycholic acid (TUDCA) mimic the results of ERO1 loss improving calcium dynamics, OXPHOS, ER/mitochondria contacts, thereby rescuing diaphragmatic weakness as well. In addition, TUDCA-treated SEPN1-RM patients-derived myoblasts show a dynamic dose-dependent increase in ATP levels under ER stress conditions suggesting improved mitochondrial function. Thus, our findings point to the ERO1 axis in the pathogenesis of SEPN1-RM thereby impinging on MAMs and mitochondria bioenergetics and recall for the efficacy of a pharmacology therapy with ad hoc ER stress/ERO1 inhibitors for SEPN1-RM.
2024-02-14 | E-MTAB-12460 | biostudies-arrayexpress