Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantitative proteomic analysis of SUMOylation in renal cortical collecting duct cells after aldosterone stimulation

ABSTRACT: SILAC was employed to investigate the effect of aldosterone stimulation on SUMOylation of cortical collecting duct (mpkCCD) cells.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Epithelial Cell

SUBMITTER: Qi Wu

LAB HEAD: Robert A. Fenton

PROVIDER: PXD013363 | Pride | 2019-10-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	CCD-S1-A.pdResult	Other
	CCD-S1-B.pdResult	Other
	CCD-S1-C.pdResult	Other
	CCD-S1-D.pdResult	Other
	CCD-S1-GluCKGG-FT-A.raw	Raw

Items per page:

1 - 5 of 185

Publications

SUMOylation Landscape of Renal Cortical Collecting Duct Cells.

Wu Qi Q Aroankins Takwa S TS Cheng Lei L Fenton Robert A RA

Journal of proteome research 20190918 10

Protein post-translational modification by the small ubiquitin-like modifier (SUMO) is a mechanism that allows a diverse response of cells to stress. Five SUMO family members, SUMO1-5, are expressed in mammals. We hypothesized that because kidney epithelial cells are often subject to stresses arising from various physiological conditions, multiple proteins in the kidney will be SUMOylated. Here, we profiled SUMO1- and SUMO2-modified proteins in a polarized epithelial cell model of the renal cort ...[more]

PMID: 31502464

Similar Datasets

SUMOylation proteomic analysis of renal cortical collecting duct cells

Project description:We profiled SUMO1 and SUMO2 modified proteins in cortical collecting duct (mpkCCD) as a precursor to targeted approaches to assess SUMO function. SUMO levels in cells following heat shock and treatment with deSUMOylation inhibitors were assessed.

2019-10-07 | PXD013346 | Pride

SUMOylation proteomic analysis of renal distal convoluted tubule cells

Project description:We profiled SUMO1 and SUMO2 modified proteins in distal convoluted tubule (mpkDCT) as a precursor to targeted approaches to assess SUMO function. SUMO levels in cells following heat shock and treatment with deSUMOylation inhibitors were assessed.

2021-11-25 | PXD028507 | Pride

Identification of SUMO sites by LC-MSMS

Project description:We developed a novel method for the identification of SUMO sites by expression of His-tagged SUMO mutants and affinity purification of SUMOylated proteins, followed by trypsin digestion and immunocapture of peptides containing diglycine signature tags. Lab Head: Dr Pascale Cossart, pascale.cossart@pasteur.fr Institut Pasteur Unité des Interactions Bactéries-Cellules, Inserm U604, INRA USC2020 25 rue du Dr. Roux 75015 Paris France

2014-07-29 | PXD000459 | Pride

Proteomic Analysis of Protein Methylation in the Yeast Saccharomyces cerevisiae

Project description:Protein methylation catalyzed by SAM-dependent methyltransferase represents a major PTM involved in important biological processes. Because methylation can occur on nitrogen, oxygen and sulfur centers and multiple methylation states exist on the nitrogen centers, methylproteome remains poorly documented. Here we present the methylation by isotope labeled SAM (MILS) strategy for a highly-confident analysis of the methylproteome of the SAM-auxotrophic Saccharomyces cerevisiae based on the online multidimensional μHPLC/MS/MS technology. We identified 117 methylated proteins, containing 182 methylation events associated with 174 methylation sites. About 90% of these methylation events were previously unknown. Our results indicated, 1) over 6% of the yeast proteome are methylated, 2) the amino acid residue preference of protein methylation follows the order Lys >> Arg > Asp > Glu ≈ Gln ≈ Asp > His > Cys, 3) the methylation state on nitrogen center is largely exclusive, and 4) the methylated proteins are located mainly in nucleus/ribosome associated with translation/transcription and DNA/RNA processing. Our dataset is the most comprehensive methylproteome known-to-date of all living organisms, and should significantly contribute to the field of protein methylation and related research.

2020-01-27 | PXD000606 | Pride

Identification of heat stress-targets of translational control by large scale analysis of Arabidopsis trancriptome and translatome.

Project description:Heat stress is one of the most prominent and deleterious environmental threads affecting plant growth and development. Upon high temperatures, plants launch specialized gene expression programs that promote stress protection and survival. These programs involve global and specific changes at the transcriptional and translational levels. However the coordination of these processes and their specific role in the establishment of the heat stress response is not fully elucidated. In this report, we have carried out a genome-wide analysis to simultaneously monitor the individual changes in the transcriptional and translational mRNA levels of Arabidopsis thaliana seedlings after the exposure to a heat shock stress. Our results demonstrated that, superimposed to transcription, translation exerts a wide but dual regulation of gene expression. For the majority of mRNAs, translation is severely repressed, causing a decreased of 50% of the association of the bulk of mRNAs to polysomes. However, some relevant mRNAs involved in different aspects of homeostasis maintenance follow a differential pattern of translation. Analysis of the sequence of the differentially translated mRNAs unravels that some features, like the 5M-BM-4UTR G+C content and the cDNA length, may take part in the discrimination mechanisms for mRNA polysome loading. Among the differential translated genes stand out master regulators of the stress response, highlighting the main role of translation in the early establishment of physiological response of plants to elevated temperatures. In total 8 ATH1 Affymetrix GeneChips were hybridized with all combinations of two factors: total mRNA/polysome-bound-RNA; 22M-BM-:C/38M-BM-:C. Two biological replicates per sample type were performed.

2014-01-22 | E-GEOD-44053 | biostudies-arrayexpress

Tumor cells express and maintain HMGB1 in the reduced isoform to enhance CXCR4-mediated migration

Project description:During inflammation and tissue regeneration, the alarmin High Mobility Group Box 1 (HMGB1), in its reduced isoform, enhances the activity of the chemokine CXCL12, forming a heterocomplex that acts via the chemokine receptor CXCR4. Despite the established roles of both HMGB1 and CXCL12 in tumor progression and metastatic spread to distal sites, the role of the CXCL12/HMGB1 heterocomplex in cancer has never been investigated. By employing a newly established mass spectrometry protocol that allows an unambiguous distinction between reduced (red HMGB1) and oxidized (ox HMGB1) HMGB1 isoforms in cell lysates, we demonstrate that human epithelial cells derived from breast (MCF-7 and MDA-MB-231) and prostate (PC-3) cancer predominantly express red-HMGB1, while primary CD3+ T lymphocytes from peripheral blood express both HMGB1 isoforms. All these cancer cells release HMGB1 in the extracellular microenvironment together with varying concentrations of thioredoxin and thioredoxin reductase. The CXCL12/HMGB1 heterocomplex enhances, via CXCR4, the directional migration and invasiveness of cancer cells characterized by high metastatic potential that possess a fully active thioredoxin system, contributing to maintain red-HMGB1. On the contrary, cancer cells with low metastatic potential, lack thioredoxin reductase, promptly uptake CXCL12 and fail to respond to the heterocomplex. Our study demonstrates that the responsiveness of cancer cells to the CXCL12/HMGB1 heterocomplex, resulting in enhanced cell migration and invasiveness, depends on the maintenance of HMGB1 in its reduced isoform, and suggests disruption of the heterocomplex as a potential therapeutic target to inhibit invasion and metastatic spread in cancer therapies.

2024-05-02 | PXD048091 | Pride

Hi-C of human acute leukemias and healthy donors

Project description:Hi-C of 17 primary samples obtained from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). As healthy controls, Hi-C of CD34+ HSPCs from 3 healthy donors were used. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011051 (dataset).

2023-08-31 | E-MTAB-13122 | biostudies-arrayexpress

Comparative proteomic analysis of kidney distal convoluted tubule and cortical collecting duct cells following long-term hormonal stimulation

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

Interferon restores replication fork stability and cell viability in BRCA-defective cells via ISG15

Project description:DNA replication and repair defects or genotoxic treatments trigger interferon (IFN)-mediated inflammatory responses. However, whether and how IFN signaling in turn impacts the DNA replication process has remained elusive. Here we show that basal levels of the IFN-stimulated gene 15, ISG15, and its conjugation (ISGylation) are essential to protect nascent DNA from degradation. Moreover, IFN treatment restores replication fork stability in BRCA1/2-deficient cells, which strictly depends on topoisomerase-1, and rescues lethality of BRCA2-deficient mouse embryonic stem cells. Although IFN activates hundreds of genes, these effects are specifically mediated by ISG15 and ISGylation, as their inactivation suppresses the impact of IFN on DNA replication. ISG15 depletion significantly reduces cell proliferation rates in human BRCA1-mutated triple-negative, whereas its upregulation results in increased resistance to the chemotherapeutic drug cisplatin in mouse BRCA2-deficient breast cancer cells, respectively. Accordingly, cells carrying BRCA1/2 defects consistently show increased ISG15 levels, which we propose as a novel, in-built mechanism of drug resistance linked to BRCAness.

2023-10-09 | PXD045154 | Pride

USP22 controls necroptosis by regulating receptor interacting protein kinase 3 ubiquitination

Project description:Dynamic control of ubiquitination by deubiquitinating enzymes is essential for almost all biological processes. Ubiquitin-specific peptidase 22 (USP22) is part of the SAGA complex and catalyzes the removal of monoubiquitination from histone H2B, thereby regulating gene transcription. However, novel roles for USP22 have recently emerged, such as tumor development and cell death. Apart from apoptosis, the relevance of USP22 in other programmed cell death pathways still remains unclear. Here, we describe a novel role for USP22 in controlling necroptotic cell death in a variety of tumor cell lines. Loss of USP22 expression significantly delays TNF/Smac mimetic/zVAD.fmk (TBZ)-induced necroptosis, without affecting TNF-mediated NF-B activation or extrinsic apoptosis. Mass-spectrometric ubiquitin remnant profiling identified lysine 518 of Receptor-interacting protein kinase 3 (RIPK3) as USP22-dependent ubiquitination target during necroptosis induction. Mutation of K518 in RIPK3 reduced necroptosisassociated RIPK3 ubiquitination and amplified necrosome formation and necroptotic cell death. In conclusion, we identify a novel role of USP22 in necroptosis and further elucidate the relevance of ubiquitination as crucial regulator of necroptotic cell death.

2021-05-03 | PXD020909 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data