Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Secretome & Cellular Proteome Analysis of Human Glioma LN229

ABSTRACT: Experimentalists most frequently rely upon reductionist methods to isolate and analyze discrete signaling compartments - including subcellular domains, organelles and protein-protein interactions. Amongst the systems-biology community, there is a growing need to integrate multiple datasets to resolve complex cellular networks. Provided is procedural framework to discover collaborative signaling networks across multiple proteomic experiments.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Glial Cell, Brain, Cell Culture

DISEASE(S): Brain Cancer

SUBMITTER: Vincent Chen

LAB HEAD: Vincent Chen, PhD

PROVIDER: PXD024001 | Pride | 2022-03-18

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Idnetification of chicken embryo muscular and liver proteins

Project description:Aim of the projects to identified proteins responsible for inducing regenerative processes in adult animals.

2020-05-27 | PXD015146 | Pride

pH stress in Desulfovibrio vulgaris Hildenborough

Project description:Using data from microarray experiments, we investigated the effects of excess NaCl on D. vulgaris. Keywords: stress response, time course Comparison of cells treated with pH10 pH to untreated cells at times of 0,120,240,30,60 min.

2007-08-31 | E-GEOD-8197 | biostudies-arrayexpress

Multi-omics analyses reveal that HIV-1 alters CD4 T cell immunometabolism to fuel virus replication

Project description:Human Immunodeficiency Virus type-1 (HIV-1)-infected individuals show metabolic alterations of CD4 T cells through unclear mechanisms with undefined consequences. We analyzed the transcriptome of CD4 T cells from HIV-1 patients and revealed that elevated oxidative phosphorylation (OXPHOS) pathway is associated with poor outcomes. Inhibition of OXPHOS by the FDA-approved drug metformin, which targets mitochondrial respiratory chain complex I, suppresses HIV-1 replication in human CD4 T cells and humanized mice. In patients, HIV-1 peak viremia positively correlates with the expression of NLRX1, a mitochondrial innate immune receptor. Quantitative proteomics and metabolic analyses reveal that NLRX1 enhances OXPHOS and glycolysis during HIV-1-infection of CD4 T cells to promote viral replication. At the mechanistic level, HIV infection induces the association of NLRX1 with the mitochondrial protein, FASTKD5, to promote the expression of mitochondrial respiratory complex components. This study uncovers the OXPHOS pathway in CD4 T cells as a target for HIV-1 therapy.

2022-02-16 | PXD023565 | Pride

Human HepG2 ITRAQ LC-MS/MS - Integrated proteomic and transcriptomic analysis revealslong noncoding RNA HOTAIR promotes hepatocellular carcinoma cell proliferation by regulating opioid growth factor receptor (OGFr)

Project description:Long non-coding RNA HOX transcript antisense RNA (HOTAIR) is involved in human tumorigenesis and dysregulated in hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying HOTAIR functions in HCC are not well understood. Here, an integrated RNA sequencing transcriptomic and quantitative proteomic analysis were employed to systematically explore the regulatory role of HOTAIR in HCC. A total of 673 transcripts and 298 proteins were identified to be dysregulated after HOTAIR inhibition. Bioinformatics studies indicated that the differentially expressed genes (DEGs) and proteins (DEPs) are involved in many biological processes, especially cancer-related signalling pathways.

2017-11-24 | PXD006554 | Pride

Transcription profiling of E. coli BW25113 fhlAL/pCA24N-FhlA133 vs fhlA/pCA24N-FhlA in modified-complex 20 mM formate at 37A?C

Project description:Variant FhlA133 (Q11H, L14V, Y177F, K245R, M288K, and I342F) had eight- fold higher hydrogen production than FhlA wild-type under 30 min of anaerobic incubation in modified-complex 20 mM formate at 37ÂºC. The mechanism by which the FhlA133 mutations increase hydrogen production is by increasing the transcription of all of the genes activated by the native FhlA (FHL complex). Experiment Overall Design: Strains: E. coli BW25113 fhlA/pCA24N-FhlA wild-type and E. coli BW25113 fhlA/pCA24N-FhlA133 (Q11H, L14V, Y177F, K245R, M288K, and I342F). Experiment Overall Design: Medium: Modified-complex 20 mM formate Experiment Overall Design: 1 mL of overnight culture in modified - complex 20 mM formate + Cm 30 Âµg/mL was inoculated in 9 mL of fresh modified - complex 20 mM formate + Cm 30 Âµg/mL and incubated anaerobically at 37oC in 27 mL glass vials. Experiment Overall Design: Time: 30 minutes Experiment Overall Design: Cell type: Suspension

2009-12-19 | E-GEOD-13902 | biostudies-arrayexpress

Proteomic profiling of HT1080 fibrosarcoma cells of mesenchymal or amoeboid migratory phenotype

Project description:Amoeboid and mesenchymal migration of cancer cells both contribute to metastatic spreading of tumors. To characterize proteome changes underlying the different migratory modes, we performed mass spectrometry profiling of HT1080 fibrosarcoma cells undergoing mesenchymal-amoeboid transition induced by either doxycycline-inducible constitutively active RhoA or dasatinib treatment. Cells were kept in three-dimensional collagen gels with or without induction for 48 hours, lysed and processed for mass spectrometry analysis. In case of the inducible RhoA system, we also performed parallel two-dimensional experiments with cells on top of a dense layer of collagen (it was not feasible with dasatinib treatment).

2020-04-23 | PXD010425 | Pride

The Yin and Yang of GDF15: a secreted biomarker of eribulin response in breast cancer cells, yet required for survival of drug tolerant persister (DTP) cells

Project description:Drug tolerant persister (DTP) cells enter into a reversible slow-cycling state after cancer drug treatment. These cells are the living proof of response to a drug, and an interesting experimental subject for biomarker discovery. Here, we performed proteomic characterization of the breast cancer (BC) DTP cell secretome after eribulin treatment. First, we showed that eribulin induces a specific secretome in DTP cells as compared to other microtubule targeting agents. Then, we selected and functionally validated growth differentiation factor 15 (GDF15) as a protein significantly over-secreted upon eribulin treatment. Interestingly, GDF15 expression is low/absent in cells that are sensitive to eribulin, strongly upregulated during the response to the drug, and downregulated when stable resistance is ultimately established. Proteomic results were confirmed in 3D-cell culture models using BC cells lines and PDXs, as well as in a TNBC in vivo model. Unexpectedly, despite its biomarker potential for eribulin response, we found that GDF15 is also paradoxically required for survival of DTP cells, although once full resistance to eribulin is established, GDF15 expression largely disappears. Direct participation of GDF15 and its receptor GFRAL in eribulin-induction of DTPs was established by the enhanced cell killing of DTPs by eribulin seen under GDF15 and GFRAL loss of function conditions. These results pointed to a potential benefit of simultaneous targeting of GDF15/GFRAL and eribulin, and indeed we showed that combination therapy of eribulin plus an anti-GDF15 antibody kills BC-DTP cells. Our results suggest that targeting GDF15 may help eradicate DTP cells and block the onset of acquired eribulin resistance, and possibly other cytotoxic drugs. Overall, the combination of cytotoxic agents with targeted agents aimed specifically at DTP cells could be an effective therapeutic approach for metastatic breast cancer patients.

2023-01-09 | PXD034037 | Pride

Cell-based characterization of caspase-3 cleavage sites by LATE and HYATNE

Project description:Proteins' N-termini contain information about their biochemical properties and functions, and they can undergo co- or post-translational modifications, as well as be processed by proteases. To expand the coverage of the N-terminome, we have developed LATE (LysN Amino Terminal Enrichment), a method that uses selective chemical derivatization of α-amines to isolate the N-terminal peptides. We applied LATE in combination with other N-terminomic method to study caspase-3 mediated proteolysis both in vitro and during apoptosis in cells. This enable us to identify many unreported caspase-3 cleavages, including some that cannot be identified by other methods. Furthermore, we find direct evidence that some of the caspase-3 generated neo-N-termini can be further modified by Nt-acetylation. This provides a global picture of the caspase-3 degradome and uncovers previously unrecognised functional crosstalk between post-translational Nt-acetylation and caspase proteolysis pathways.

2023-06-27 | PXD036648 | Pride

Transcriptome analysis of human astrocytes upon FGF1 stimulation

Project description:In a previous study performed in our laboratory, the level of FGF1 RNA was found to be increased in remyelinated multiple sclerosis lesions compared to control brain (unpublished observation). Astrocytes play a key role in multiple sclerosis lesion formation. To shed light on potential FGF1-mediated functions in multiple sclerosis, the impact of FGF1 on astrocytes was investigated.

2015-04-10 | E-MTAB-2485 | biostudies-arrayexpress

Shotgun Proteomics and Quantitative Pathway Analysis Study of the Mechanisms of Action of Dehydroeffusol, a Bioactive Phyto-chemical in Medulla Junci with Anti-cancer Activity

Project description:Dehydroeffusol (DHE) is a rare compound of phenanthrene class isolated from Medulla Junci used in Traditional Chinese herbal medicines. Initial biological evaluation of this compound reveals in vitro and in vivo anticancer ac-tivities. We performed a shotgun proteomic analysis using Orbitrap liquid chromatography-tandem mass spectrometry to investigate the changes in the protein profiles in cancer cells upon DHE treatment. DHE affected cancer-associated signaling pathways, including NF-B, β-catenin and endoplasmic reticulum stress. Through quantitative pathway and key-node analysis of the proteomics data, activating transcription factor 2 (ATF-2) and c-Jun kinase (JNK) were found to be the key components in DHE’s modulated biological pathways. Furthermore, based on the pathway analysis as well as chemical similarity, DHE is predicted to be a phytoestrogen. Our predictions derived from proteomic, bio-informatic and chemoinformatic analyses were validated with individual cell-based experiments. In addition to elucidating the major mechanisms of action of DHE, our study demonstrates an effective workflow for identifying the mechanisms of action of bioactive compounds through shotgun proteomic analysis.

2018-06-05 | PXD009389 | 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