RNA-seq of proteostasis regultors
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ABSTRACT:
PROVIDER: PRJEB36386 | ENA |
REPOSITORIES: ENA
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Project description:Imbalances in endoplasmic reticulum (ER) proteostasis are associated with etiologically-diverse degenerative diseases linked to excessive extracellular protein misfolding and aggregation. Reprogramming of the ER proteostasis environment through genetic activation of the Unfolded Protein Response (UPR)-associated transcription factor ATF6 attenuates secretion and extracellular aggregation of amyloidogenic proteins. Here, we employed a screening approach that included complementary arm-specific UPR reporters and medium-throughput transcriptional profiling to identify non-toxic small molecules that phenocopy the ATF6-mediated reprogramming of the ER proteostasis environment. Comprehensive transcriptome analysis was employed to validate the capacity of three prioritized compounds to remodel the ER proteostasis environment, and to assess the prefential activation of ATF6 transcriptional targets relative to targets of the IRE1/XBP1s and PERK arms of the UPR. HEK293T-Rex and HEK293-DAX cells were treated for 6 hr with vehicle (DMSO), 1 µM Tg, 10 mM TMP (in HEK293DAX), or 10 µM 132, 147 or 263 in biological triplicate at 37 ÌC
2016-07-21 | E-GEOD-84636 | biostudies-arrayexpress
Project description:Imbalances in endoplasmic reticulum (ER) proteostasis are associated with etiologically-diverse degenerative diseases linked to excessive extracellular protein misfolding and aggregation. Reprogramming of the ER proteostasis environment through genetic activation of the Unfolded Protein Response (UPR)-associated transcription factor ATF6 attenuates secretion and extracellular aggregation of amyloidogenic proteins. Here, we employed a screening approach that included complementary arm-specific UPR reporters and medium-throughput transcriptional profiling to identify non-toxic small molecules that phenocopy the ATF6-mediated reprogramming of the ER proteostasis environment. Comprehensive transcriptome analysis was employed to validate the capacity of three prioritized compounds to remodel the ER proteostasis environment, and to assess the prefential activation of ATF6 transcriptional targets relative to targets of the IRE1/XBP1s and PERK arms of the UPR.
2016-07-21 | GSE84636 | GEO
Project description:Small molecule proteostasis regulators that reprogram the ER to reduce extracellular protein aggregation
| PRJNA330689 | ENA
Project description:Gametogenesis involves active protein synthesis and heavily relies on proteostasis. How animals regulate germline proteostasis at the organismal level is poorly understood. Our recent work in C. elegans indicates that germline development requires coordinated activities between insulin/IGF-1 signaling and HSF-1, the transcriptional activator of many molecular chaperones in stress and physiological conditions. In this study, we show that HSF-1 is important for germline proteostasis at ambient temperature. Depletion of HSF-1 from germ cells impairs chaperone gene expression, causing protein degradation and aggregation and, consequently, declines in fecundity and gamete quality. Reduced insulin/IGF-1 signaling confers germ cells' tolerance to limited protein folding capacity and proteotoxic stress by lowering ribosome biogenesis and translation. Interestingly, regulation of germline proteostasis by insulin/IGF-1 signaling occurs non-cell-autonomously. Our data suggest that insulin/IGF-1 signaling controls the expression of the evolutionarily conserved intestinal peptide transporter PEPT-1 via its downstream transcription factor FOXO/DAF-16, therefore allowing dietary proteins to be incorporated into an amino acid pool that fuels ribosomal biogenesis and translation in the germline. We propose that this pathway plays a critical role in regulating germline protein synthesis, which must be at balance with HSF-1-dependent protein folding to achieve proteostasis in gametogenesis.
2024-05-20 | GSE256186 | GEO
Project description:Alzheimer’s, Parkinson’s or Huntington’s disease can be caused by mutations that enhance protein aggregation, but we still do not know enough about the molecular players of these pathways to develop treatments for these devastating diseases. Here, we screen for mutations that might enhance aggregation and to investigate the mechanisms that protect against dysregulated homeostasis. We report that the protein UNC-1 activates neurohormonal signalling from the sulfotransferase SSU-1 in ASJ sensory/endocrine neurons. This hormone targets the nuclear receptor NHR-1, which acts cell-autonomously in the muscles to protect against aggregation. A second nuclear receptor, DAF-12, functions oppositely to NHR-1 to maintain protein homeostasis. Transcriptomics analyses of unc-1 mutants revealed changes in the expression of genes involved in fat metabolism, suggesting for the first time that fat metabolism changes, controlled by neurohormonal signalling, contribute to protein homeostasis. Furthermore, the enzymes involved in the identified signalling pathway are potential targets for treating neurodegenerative diseases caused by disrupted protein homeostasis.
2022-12-12 | GSE220662 | GEO
Project description:The goal of this RNA-Seq analysis was to identify genes differentially expressed in a C. elegans strain overexpressing HSP-90 in the neurons compared to control (N2) animals. C. elegans overexpressing HSP-90 protein in the neurons activate transcellular chaperone signalling that enhances organismal proteostasis. This study aimed to identify components of the signalling pathway responsible for this effect.
2018-06-05 | GSE108005 | GEO
Project description:Our study elucidates the broad-spectrum effects of proteasome hyperactivation on the proteome, demonstrating its substantial influence on the proteostasis network. Through comprehensive analyses, we identified a significant reorganization of the transcriptome, enhanced mRNA processing, and increased translation activity. The study further reveals the hyperactivation's impact on intrinsically disordered proteins, lipid synthesis, and biogenesis, evidenced by major changes in lipid droplets and peroxisome proliferation. Notably, we uncovered protective phenotypes against oxidative stress, primarily mediated by Super Oxide Dismutases (SODs), indicating an elevated stress response readiness. Additionally, our research highlighted the hyperactive proteasome's selective targeting of vitellogenins, crucial for lipid metabolism and implicated in the aging process of C. elegans. Enhanced ERAD-dependent degradation was observed, facilitating the clearance of senescent VIT-2 protein aggregates and promoting healthier aging. The α3ΔN mutant significantly reduced the quantity of human alpha-1 antitrypsin (ATZ) aggregates and delayed their formation in a C. elegans model for ATZ disease, suggesting its potential as an ERAD enhancer. These findings propose proteasome hyperactivation as a promising strategy for treating aggregation-prone diseases, offering novel avenues for drug development and therapeutic interventions against neurodegeneration.
2024-05-01 | GSE259419 | GEO
Project description:Tissue-specific transcriptome profiling of Protein Aggregation in Caenorhabditis elegans
| PRJEB41493 | ENA
Project description:Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse nuclear speckles and is frequently translocated to the cytoplasm. SINE-deleted cells exhibit an activated unfolded protein response and PKR and markedly increased DNA damage and apoptosis caused by dysregulation of TDP-43 localization and formation of cytotoxic inclusions. TDP-43 binds stronger to Malat1 without the SINE and is likely ”hijacked” by cytoplasmic Malat1 to the cytoplasm, resulting in the depletion of nuclear TDP-43 and redistribution of TDP-43 binding to repetitive element transcripts and mRNAs encoding mitotic and nuclear-cytoplasmic regulators. The SINE promotes Malat1 nuclear retention by facilitating Malat1 binding to HNRNPK, a protein that drives RNA nuclear retention, potentially through direct interactions of the SINE with KHDRBS1 and TRA2A, which bind to HNRNPK. Losing these RNA-protein interactions due to the SINE deletion likely creates more available TDP-43 binding sites on Malat1 and subsequent TDP-43 aggregation. These results highlight the significance of lncRNA TEs in TDP-43 proteostasis with potential implications in both cancer and neurodegenerative diseases.
2019-12-03 | GSE141303 | GEO
Project description:In this project we asked how reducing the activity of the insulin/IGF signaling (IIS) cascade by knocking down the expression of daf-2, affects global protein SUMOylation of C. elegans. We found that among other proteins, IIS reduction lowers the SUMOylation of CAR-1, a protein that negatively regulates the activity of the worm’s notch receptor, GLP-1. Thus, the knockdown of car-1 hyper-activates GLP-1, shortens lifespan and exposes the worm to toxic protein aggregation (proteotoxicity). In contrast, the expression of a SUMOylation resistant CAR-1 (K185R) promotes longevity and protects model nematodes from proteotoxicity.
2018-06-06 | PXD010011 | Pride