Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative analyses of the N-glycoproteomes in HCT116 cancer cells and their non-tumorigenic DNMT1/3b double knockout (DKO1) cells and insight into the Mannose-6-phosphate pathway

ABSTRACT: N-glycoproteomic analyses provide valuable resources for investigation of cancer mechanisms, biomarkers, and therapeutic targets. Here, we mapped and compared the site-specific N-glycoproteomes of colon cancer HCT116 cells and isogenic non-tumorigenic DNMT1/3b double knockout (DKO1) cells using Fbs1-GYR N-glycopeptide enrichment technology and trapped ion mobility spectrometry. Many significant changes in site-specific N-glycosylation were revealed, providing a molecular basis for further elucidation of the role of N-glycosylation in protein function. HCT116 cells display hypersialylation especially in cell surface membrane proteins. Both HCT116 and DKO1 show an abundance of paucimannose and 80% of paucimannose-rich proteins are annotated to reside in exosomes. The most striking N-glycosylation alteration was the degree of mannose-6-phosphate (M6P) modification. N-glycoproteomic analyses revealed that HCT116 display hyper-M6P modification, which was orthogonally validated by M6P immunodetection. Significant observed differences in N-glycosylation patterns of the major M6P receptor, CI-MPR in HCT116 and DKO1 may contribute to the hyper-M6P phenotype of HCT116 cells.

INSTRUMENT(S): timsTOF Pro 2

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

DISEASE(S): Colon Cancer

SUBMITTER: Minyong Chen

LAB HEAD: Minyong Chen

PROVIDER: PXD035301 | Pride | 2023-01-17

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Proteomic changes to immune and inflammatory processes underlie lung preservation using ex vivo cytokine adsorption

Project description:The field of graft preservation has made considerable strides in recent years improving outcomes related to solid organ restoration and regeneration. In lungs, the use of ex vivo lung perfusion (EVLP) in line with devices and treatments has shown promising results within preclinical and clinical studies with the potential to improve graft quality. The benefit of the therapy would be to render marginal and declined donor lungs suitable for transplantation, ultimately increasing the donor pool available for transplantation. Additionally, such therapies used in machine perfusion could also increase preservation time, facilitating logistical planning. Cytokine adsorption has been demonstrated as a potentially safe and effective therapy when applied to the EVLP circuit and post transplantation. The mechanism by which this treatment improves the donor lung on a molecular basis is not yet fully elucidated. We hypothesized that there were characteristic inflammatory and immunomodulatory differences between lungs treated with and without cytokine adsorption, reflecting in proteomic changes in gene ontology pathways and across inflammation-related proteins. In the current study we investigate the molecular mechanisms and signaling pathways of how cytokine adsorption impacts the lung function when used during EVLP and when used post transplantation as hemoperfusion in a porcine model. Lung tissue from EVLP and post lung transplantation were analyzed for their proteomic profile using mass spectrometry. The inflammatory and immune processes were compared between the treated and the non-treated groups to show the differences occurring between the forms of graft preservation.

2023-10-24 | PXD044413 | Pride

Comparative Proteomic Profiling of Variants SARS-CoV-2 Virus-Like-Particles (VLPs) Incubated Cells

Project description:The COVID-19 pandemic is arguably the most important global threat to humankind that the world has seen in the 21st century. Since the initial outbreak of SARS-CoV-2 in 2019, the virus genome is continuously mutating that may affect virus characteristics such as infectivity, transmission, and pathogenicity. We recently found that two consecutive amino acid mutations R203K and G204R in the nucleocapsid (N) protein, are linked with higher viral load and severity in COVID-19 patients. Here, we performed comparative total proteomic analysis of HEK293T (stably expressing ACE2/TMPRSS2) cell lines infected with wildtype (WT) VLP, KR-mutant (KR) VLP with two mutations R203K/G204R in the nucleocapsid protein, and two additional controls D614G-KR (containing both R203K/G204R and spike D614G mutations) and D614G (only spike D614G mutation). Our data reveal enhanced expression of immune response proteins in KR VLP infected cells.

2023-04-15 | PXD034557 | Pride

Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 disease specific mechanisms and vulnerabilities.

Project description:Coronaviruses constitute a constant threat as documented by the recent emergence of SARS-CoV-2 that has caused more than 2,5 million deaths worldwide. Despite this our understanding of coronaviruses and how they interact with their host is very limited. Here we describe a novel phage display library for the discovery of viral short linear interaction motifs (SLiMs) from RNA viruses that mediate binding to human host factors. We utilize this library to uncover the unique patterns of viral SLiMs mediating SARS-CoV-2 - host factor interactions. This established a specific interaction between the human G3BP1/2 proteins and an xFG peptide motif in the viral nucleocapside (N) protein that when disrupted reduce viral replication and infection. We show that the N protein through this xFG motif modulates the G3BP1/2 host interactome by competing with numerous cellular xFG containing proteins and inhibits G3BP1/2 mediated stress granule formation. Collectively our work outlines a strategy for system-wide understanding of viral-host factor interactions that provides both mechanistic insight and pinpoints therapeutically relevant interactions for development of novel antiviral strategies.

2021-10-29 | PXD025410 | Pride

The NSP3 protein of SARS-CoV-2 binds fragile X mental retardation proteins to disrupt UBAP2L binding

Project description:Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1 and FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have slightly attenuated replication in vitro and reduced levels of viral antigen in lungs during early stages of infection. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins and provides molecular insight to the possible underlying molecular defects in fragile X syndrome.

2023-12-28 | PXD047232 | Pride

Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation

Project description:Protein degradation, a major eukaryotic response to cellular signals, is subject to numerous layers of regulation. In yeast, the evolutionarily conserved GID E3 ligase mediates glucose-induced degradation of fructose-1,6-bisphosphatase (Fbp1) and other gluconeogenic enzymes. “GID” is a collection of E3 ligase complexes; a core scaffold, RING-type catalytic core and supramolecular module along with interchangeable substrate receptors select targets for ubiquitylation. However, knowledge of additional cellular factors directly regulating GID-type E3s remains rudimentary. Here, we structurally and biochemically characterize Gid12 as a modulator of the GID E3 ligase complex targeting Fbp1. Our collection of cryo-EM reconstructions shows that Gid12 forms an extensive interface sealing the substrate receptor Gid4 onto the scaffold, and remodeling the degron binding site. Gid12 also sterically blocks a recruited Fbp1 from the ubiquitylation active sites. Our analysis of the role of Gid12 establishes principles that may more generally underlie E3 ligase regulation.

2022-05-29 | PXD028579 | Pride

Hepatic palmitoyl-proteomes and acyl-protein thioesterase protein proximity networks link lipid modification and mitochondria

Project description:Elevated fatty acids are associated with insulin resistance. Fatty acids can reversibly modify proteins through a process known as S-palmitoylation. To test the hypothesis that depalmitoylation by acyl-protein thioesterases 1 and 2 (APT1 and APT2) in the liver regulates glucose metabolism, we generated liver-specific APT1 and/or APT2 knockout mice, fed them a high-fat diet (HFD), and then used acyl resin-assisted capture to isolate palmitoylated proteins from APT KO livers. We found that APT1 predominates over APT2 in the liver, primarily depalmitoylating mitochondrial proteins, including several proteins linked to glutamine metabolism. To corroborate these APT1 and APT2 substrates and identify other APT regulators, we determined the protein-protein proximity network of APT1 and APT2 by fusing each enzyme to the biotin ligase miniTurbo (mT). Expression of these APT-mT constructs in HepG2 cells, followed by purification of biotin-labeled proteins and mass spectrometry, revealed APT proximity networks encompassing mitochondrial proteins including the major translocases Tomm20 and Timm44. APT1 also interacted with Slc1a5 (ASCT2), the only glutamine transporter known to localize to mitochondria. HFD-fed male mice with dual but not single deletion of APT1 and APT2 from the liver had insulin resistance and fasting hyperglycemia. Elevated fasting glucose was also associated with increased glutamine-driven gluconeogenesis and decreased liver mass. These data suggest that APT1 and APT2 regulate hepatic glucose metabolism and insulin signaling in a functionally redundant manner. The identification of hepatic depalmitoylation substrates and protein-protein proximity networks for APT1 and APT2 establishes a framework for defining mechanisms underlying metabolic disease.

2023-11-05 | PXD041552 | Pride

Deep Proteome profiling reveals signatures of age and sex differences in paw skin and sciatic nerve of naïve mice

Project description:The age and sex of studied animals profoundly impacts experimental outcomes in animal-based biomedical research. However, most preclinical studies in mice use a wide-spanning age range from 4 to 14 weeks and do not assess study parameters in male and female mice in parallel. This raises concerns regarding reproducibility and neglect of potentially relevant age and sex differences. Furthermore, the molecular setup of tissues in dependence of age and sex is unknown in naïve mice precluding efficient translational research. Here, we first compared two different mass spectrometric acquisition methods – DDA- and DIA-PASEF – in order to maximize the depth of proteome quantitation. We then employed an optimized workflow of quantitative proteomics based on DIA-PASEF followed by DIA-NN data analysis, and revealed significant differences in mouse paw skin and sciatic nerve (SCN) when comparing (i) male and female mice, and, in parallel, (ii) adolescent mice (4 weeks) with adult mice (14 weeks).

2022-11-29 | PXD034476 | Pride

Wistar rat, lung, NanoLC-MS/MS

Project description:Wistar rats, male, treated with 500 mg/Kg/day of diacetyl by gavage, during 4 weeks

2018-04-18 | PXD004504 | Pride

RNA-seq of DCIS-pInducer21-SOX11 cells grown in 2D and 3D

Project description:Using the pINDUCER21 system, we modified DCIS.com cells so that SOX11 is expressed at much higher levels after induction with Doxycycline (Dox) than observed with the constitutive DCIS-SOX11 cells we have used to model DCIS progression. After Dox induction of pIND21-SOX11 cells, both SOX11 and CD24 expression are significantly increased ). Higher ALDH levels are detected in pIND21-SOX11 cells, suggesting that high levels of SOX11 promotes acquisition of features associated with distinct types of cancer stem cells.

2020-09-21 | E-MTAB-9108 | biostudies-arrayexpress

First identification of a large set of serine hydrolases by activity-based protein profiling in dibutyl phthalate-exposed zebrafish larvae

Project description:Despite the involvement of several serine hydrolases (SHs) in the metabolism of xenobiotics such as dibutyl phthalate (DBP), no study has focused on mapping this enzyme class in zebrafish, a model organism frequently used in ecotoxicology. Here, we survey and identify active SHs in zebrafish larvae and search for biological markers of SH type after exposition to DBP. Zebrafish were exposed to 0, 5, and 100 µg/L DBP from 4 to 120 h post-fertilization. A significant decrease in vitellogenin expression level of about 2-fold compared to the control was found in larvae exposed to 100 µg/L DBP for 120h. The first comprehensive profiling of active SHs in zebrafish proteome was achieved with an activity-based protein profiling (ABPP) approach. Among 49 SHs identified with high confidence, one was the carboxypeptidase ctsa overexpressed in larvae exposed to 100 µg/L DBP for 120h. To the best of our knowledge, this is the first time that a carboxypeptidase has been identified as deregulated following exposure to DBP. The overall results indicate that targeted proteomics approaches such as ABPP can therefore be an asset for understanding the mechanism of action related to xenobiotics in ecotoxicology.

2023-03-11 | PXD038229 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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