Proteomic profiling of PDI-deficient mouse liver
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Mus Musculus (mouse)
TISSUE(S): Liver
SUBMITTER: 
Fengwu Chen
LAB HEAD: Fengwu Chen
PROVIDER: PXD055737 | Pride | 2025-01-16
REPOSITORIES: pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 7721TQ_1.raw | Raw | |||
| 7721TQ_10.raw | Raw | |||
| 7721TQ_11.raw | Raw | |||
| 7721TQ_12.raw | Raw | |||
| 7721TQ_13.raw | Raw |
Items per page: 5 1 - 5 of 20 |
Similar Datasets
Project description:Cysteine redox states in MTP from PDI-deficient mouse liver were determined using differential cysteine alkylation and PRM-MS analysis.
2025-01-16 | PXD055650 | Pride
Project description:Suppressor of cytokine signaling 3 (SOCS3) down-regulates several signaling pathways in multiple cell types, and previous data suggest that SOCS3 may shut off cytokine activation at the early stages of liver regeneration. We developed hepatocyte-specific Socs3 knockout (Socs3 h-KO) mice to directly study the role of SOCS3 during liver regeneration after 2/3 partial hepatectomy (PH). Socs3 h-KO mice demonstrate marked enhancement of DNA replication and liver weight restoration after 2/3 PH in comparison with littermate controls. Without SOCS3, signal transducer and activator of transcription 3 (STAT3) phosphorylation is prolonged, and activation of the mitogenic kinases extracellular signal-regulated kinase 1/2 (ERK1/2) is enhanced after PH. In vitro, we show that SOCS3 deficiency enhances hepatocyte proliferation in association with enhanced STAT3 and ERK activation after epidermal growth factor (EGF) or interleukin 6 (IL-6) stimulation. Microarray analyses show that SOCS3 modulates a distinct set of genes after PH, which fall into diverse physiologic categories. Using a model of chemical-induced carcinogenesis, we found that Socs3 h-KO mice develop hepatocellular carcinoma (HCC) at an accelerated rate. By acting on cytokines and multiple proliferative pathways, SOCS3 modulates both physiologic and neoplastic proliferative processes in the liver, and may act as a tumor suppressor. Experiment Overall Design: Hepatocyte-specific excision of the Socs3 gene was achieved by breeding Socs3 fl/fl mice with mice expressing the Cre recombinase transgene under control of the albumin promoter (Alb-Cre+), yielding Socs3 h-KO mice. Socs3 fl/fl, Alb-Cre- littermates were used as controls for all experiments, and are henceforth referred to as littermates. All mice (C57BL/6) were free of Helicobacter species, housed in a specific pathogen free facility with 12-h light/dark cycles with free access to standard food and water. 2/3 PH and sham operations were performed as previously described (15, 50) (n=3-6 mice per genotype per time point). Liver remnants were weighed after removal of necrotic stumps and sutures, and compared to post-operative body weight. For HCC experiments, a single i.p. injection of DEN (5mg/kg, Sigma) was performed 12-14 d after birth. For short time points, a single injection of DEN (100mg/kg) (31) was given to 4 wk old mice. At indicated time points, mice were sacrificed by CO2 inhalation. All animal studies were carried out under approved IACUC protocols at the University of Washington.
2008-06-16 | E-GEOD-9549 | biostudies-arrayexpress
Project description:Multiple Sulfatase Deficiency (MSD) is a fatal, inherited lysosomal storage disorder characterised by reduced activities of all cellular sulfatases in patients. Sulfatases require a unique post-translational modification of an active site cysteine to formylglycine that is catalysed by the Formylglycine Generating Enzyme (FGE). FGE mutations leading to MSD affect the intracellular protein stability that determines residual enzyme activity and defines disease severity in MSD patients. Here, we show that Protein Disulfide Isomerase (PDI) plays a pivotal role in the recognition and quality control of MSD-causing FGE variants. Overexpression of PDI reduces the residual activity of unstable FGE variants, whereas inhibition of PDI function rescues the residual activity of sulfatases in MSD fibroblasts. Analysing a covalent complex consisting of PDI and a FGE variant by LC-MALDI mass spectrometry allowed to determine the molecular signature for FGE recognition by PDI. Our findings highlight the role of PDI as a disease modifier in MSD, which may be relevant also for other ER-associated protein folding pathologies.
2018-07-04 | PXD009758 | Pride
Project description:The liver plays a central role in whole-body lipid and glucose homeostasis. Increasing dietary fat intake results in increased hepatic fat deposition, which is associated with a risk for development of insulin resistance and type 2 diabetes. In this study, we demonstrate a role for the phosphate inorganic transporter 1 (PiT1/SLC20A1) in regulating metabolism. Specific knockout of Pit1 in hepatocytes significantly improved glucose tolerance and insulin sensitivity, enhanced insulin signalling, and decreased hepatic lipogenesis. We identified USP7 as a PiT1 binding partner and demonstrated that Pit1 deletion inhibited USP7/IRS1 dissociation upon insulin stimulation. This prevented IRS1 ubiquitination and its subsequent proteasomal degradation. As a consequence delayed insulin negative feedback loop and sustained insulin signalling were observed. Moreover, PiT1-deficient mice were protected against high fat diet-induced obesity and diabetes. Our findings indicate that PiT1 has potential as a therapeutic target in the context of metabolic syndrome, obesity, and diabetes.
2016-08-25 | E-MTAB-4989 | biostudies-arrayexpress
Project description:Cytokines of the interleukin 12 (IL-12) family are assembled combinatorially from shared alpha and beta subunits. A common theme is that human IL-12 family alpha subunits remain incompletely structured in isolation until they pair with a designate beta subunit. Accordingly, chaperones need to support and control specific assembly processes. Here, we site-specifically introduce photo-crosslinking amino acids into the IL-12 and IL-23 alpha subunits (IL-12alpha and IL-23alpha). This allows to stabilize transient chaperone:client complexes for mass spectrometry and reveals a large set of ER chaperones to interact with IL-12alpha and IL-23alpha. Among those, we focus on protein disulfide isomerase (PDI) family members and reveal IL-12 family subunits to be clients of several ill-characterized PDIs. We find that different PDIs show selectivity for different cysteines in IL-12alpha and IL-23alpha. Despite this, PDI binding generally stabilizes unassembled IL-12alpha and IL-23alpha against degradation. In contrast, alpha:beta assembly appears robust and only multiple simultaneous PDI depletions reduce IL-12 secretion. Our comprehensive analysis of the IL-12/IL-23 chaperone machinery reveals a hitherto uncharacterized role for several PDIs in this process. This extends our understanding of how cells accomplish the task of specific protein assembly reactions for signaling processes. Furthermore, our findings show that cytokine secretion can be modulated by targeting specific ER chaperones.
2022-11-28 | PXD036463 | Pride
Project description:Protein homeostasis is linked with aging and aging associated diseases. Oxidative protein folding occurs in the endoplasmic reticulum (ER) and produces H2O2 as a byproduct. The role of oxidative protein folding in human stem cells aging remains unknown. Here, we succeed to knockout protein disulfide isomerase (PDI), a key oxidoreductase for catalyzing oxidative protein folding, in human embryonic stem cells (hESCs) and human mesenchymal stem cells (hMSCs). Deletion of PDI does not affect the self-renewal of hESCs but significantly delays hMSCs senescence. Mechanistically, knockout of PDI slows down the rate of oxidative protein folding and decreases the leakage of ER-derived H2O2 into the nucleus, therefore alleviating oxidative stress and the secretory-associated senescence phenotype (SASP). Among the SASP-related genes, SERPINE1 is identified as a key driver for cell senescence. These findings establish a novel link between oxidative protein folding and aging. The previously unrecognized function of PDI in regulating cell senescence provides a potential target for aging and aging-related disease intervention.
2023-06-12 | PXD037244 | Pride
Project description:Microarray expression profiling has become a valuable tool in the evaluation of the genetic consequences of metabolic disease. Although 3â??-biased gene expression microarray platforms were the first generation to have widespread availability, newer platforms are gradually emerging that have more up-to-date content and/or higher cost efficiency. Deciphering the relative strengths and weaknesses of these various platforms for metabolic pathway level analyses can be daunting. We sought to determine the practical strengths and weaknesses of four leading commercially-available expression array platforms relative to biologic investigations, as well as assess the feasibility of cross-platform data integration for purposes of biochemical pathway analyses. METHODS: Liver RNA from B6.Alb/cre,Pdss2loxP/loxP mice having primary Coenzyme Q deficiency was extracted either at baseline or following treatment with an antioxidant/antihyperlipidemic agent, probucol. Target RNA samples were prepared and hybridized to Affymetrix 430 2.0, Affymetrix Gene 1.0 ST, Affymetrix Exon 1.0 ST, and Illumina Mouse WG-6 expression arrays. Probes on all platforms were re-mapped to coding sequences in the current version of the mouse genome. Data processing and statistical analysis were performed by R/Bioconductor functions, and pathway analyses were carried out by KEGG Atlas and GSEA. RESULTS: Expression measurements were generally consistent across platforms. However, intensive probe-level comparison suggested that differences in probe locations were a major source of inter-platform variance. In addition, genes expressed at low or intermediate levels had lower inter-platform reproducibility than highly expressed genes. All platforms showed similar patterns of differential expression between sample groups, with â??steroid biosynthesisâ?? consistently identified as the most down-regulated metabolic pathway by probucol treatment. CONCLUSIONS: This work offers a timely guide for metabolic disease investigators to enable informed end-user decisions regarding choice of expression microarray platform best-suited to specific research project goals. Successful cross-platform integration of biochemical pathway expression data is also demonstrated, especially for well-annotated and highly-expressed genes. However, integration of gene-level expression data is limited by individual platform probe design and the expression level of target genes. Cross-platform analyses of biochemical pathway data will require additional data processing and novel computational bioinformatics tools to address unique statistical challenges. 4 samples are analyzed on each of 4 different Mouse Microarray Expression platforms (Affymetrix Mo430 2.0, Affymetrix Gene, Affymetrix Exon 1.0 ST, and Illumina Whole Genome 6).
2010-06-24 | E-GEOD-18677 | biostudies-arrayexpress
Project description:The HGF/c-Met system is an essential inducer of hepatocyte growth and proliferation. Although a fundamental role for the HGF receptor c-Met has been demonstrated in acute liver regeneration its cell specific role in hepatocytes during chronic liver injury and fibrosis progression has not been determined yet. In order to better characterize the role of c-Met in hepatocytes we generated a hepatocyte-specific c-Met knockout mouse (c-MetM-bM-^HM-^Fhepa) using the Cre-loxP system and studied its relevance after bile-duct ligation. Two strategies for c-Met deletion in hepatocytes were tested. Early deletion during embryonic development was lethal, while post-natal Cre-expression was successful leading to the generation of viable c-MetM-bM-^HM-^Fhepa mice. Bile-duct ligation in these mice resulted in extensive necrosis and lower proliferation rates of hepatocytes. Gene array analysis of c-MetM-bM-^HM-^Fhepa mice revealed a significant reduction of anti-apoptotic genes in c-Met deleted hepatocytes. These findings could be functionally tested as c-MetM-bM-^HM-^Fhepa mice showed a stronger apoptotic response after bile-duct ligation and Jo-2 stimulation. This phenotype was associated with increased expression of pro-inflammatory cytokines (TNF-a and IL-6) and an enhanced recruitment of neutrophils. Activation of these mechanisms triggered a stronger pro-fibrogenic response as evidenced by increased TGF-b1, a-SMA, collagen-1a mRNA expression and enhanced collagen-fiber staining in c-MetM-bM-^HM-^Fhepa mice. For gene array analysis c-MetDhepa and c-MetloxP/loxP controls were stimulated for 2 hours with 2M-BM-5g recombinant mouse HGF.Three animals per group were treated in parallel, before and after i.p. injection of recombinant HGF or NaCl.
2009-02-18 | E-GEOD-13992 | biostudies-arrayexpress
Project description:Excessive glucose production in the liver is a key factor in the hyperglycemia observed in diabetes mellitus type 2. It is generally agreed to result from an increase in hepatic gluconeogenesis. Considerable attention has been devoted to the transcriptional regulation of key gluconeogenic enzymes, but much less is known about the regulation of amino-acid catabolism, which generates gluconeogenic substrates. Here, we highlight a novel role of LKB1 in this regulation. We show that mice with a hepatocyte-specific deletion of Lkb1 have higher levels of hepatic amino acid catabolism, driving gluconeogenesis. This effect was observed during both fasting and the postprandial period, identifying Lkb1 as a critical suppressor of postprandial hepatic gluconeogenesis. Hepatic Lkb1 deletion was associated with major changes in whole-body metabolism, leading to a lower lean body mass and, in the longer term, sarcopenia and cachexia, as a consequence of the diversion of amino acids to liver metabolism at the expense of muscle. Using genetic and pharmacological approaches, we identified the aminotransferases and specifically, Agxt as effectors of the suppressor function of Lkb1 in amino acid-driven gluconeogenesis. The present dataset is from the phosphoproteomic analysis of the refed mice in a study where a global quantitative analysis ( PXD013478 ) is also described in the same publication.
2020-12-01 | PXD019755 | Pride
Project description:Excessive glucose production in the liver is a key factor in the hyperglycemia observed in diabetes mellitus type 2. It is generally agreed to result from an increase in hepatic gluconeogenesis. Considerable attention has been devoted to the transcriptional regulation of key gluconeogenic enzymes, but much less is known about the regulation of amino-acid catabolism, which generates gluconeogenic substrates. Here, we highlight a novel role of LKB1 in this regulation. We show that mice with a hepatocyte-specific deletion of Lkb1 have higher levels of hepatic amino acid catabolism, driving gluconeogenesis. This effect was observed during both fasting and the postprandial period, identifying Lkb1 as a critical suppressor of postprandial hepatic gluconeogenesis. Hepatic Lkb1 deletion was associated with major changes in whole-body metabolism, leading to a lower lean body mass and, in the longer term, sarcopenia and cachexia, as a consequence of the diversion of amino acids to liver metabolism at the expense of muscle. Using genetic and pharmacological approaches, we identified the aminotransferases and specifically, Agxt as effectors of the suppressor function of Lkb1 in amino acid-driven gluconeogenesis. The present dataset is from the phosphoproteomic analysis of fasting mice in a study where a global quantitative analysis ( PXD013478 ) is also described in the same publication.
2020-12-01 | PXD019757 | Pride