Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics analysis of expi293 conditioned media purified with immobilized metal affinity chromatography

ABSTRACT: Isthmin-1 (ISM1) is a recently described adipokine with insulin-like properties, reported to regulate hyperglycemia and liver steatosis. However, contrary to earlier studies, we demonstrate that highly purified ISM1 does not stimulate AKT phosphorylation in 3T3-F442A pre-adipocytes. Instead, this activity is attributed to co-purifying factors. Using proteomic mass spectrometry, we analyzed the ISM1-free sample that exhibits activity on AKT phosphorylation in 3T3-F442A cells and identified the growth factors PDGF-AA and/or GDF15 as the likely contributors to this effect.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell

SUBMITTER: Wenxue Li

LAB HEAD: Yansheng Liu

PROVIDER: PXD062353 | Pride | 2025-04-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20231121_Tongqing_F1_150min.raw	Raw
	20231121_Tongqing_F3_15min.raw	Raw
	20240403_152420_tongqing_2gel_150min_20231128_Report.tsv	Tabular

Items per page:

1 - 3 of 3

Similar Datasets

DIA-MS Detect the Dephosphorylation of Tau by Phosphorylation Targeting Chimera (PhosTAC)

Project description:Microtubule-associated protein tau is essential for microtubule assembly and stabilization. Hyperphosphorylation of the microtubule-associated protein tau plays an important pathological role in the development of Alzheimer’s disease and other tauopathies, one of the greatest unmet demands in the clinic. In vivo studies using kinase inhibitors suggest that reducing tau phosphorylation levels has therapeutic potential; however, such approaches invariably showed limited benefits. We sought to develop our recently demonstrated Phosphorylation Targeting Chimera (PhosTAC) technology to specifically induce tau dephosphorylation. Herein, we use PhosTACs to recruit tau to PP2A, a native tau phosphatase. PhosTACs induced the formation of a stable ternary complex, leading to a rapid, efficient, and sustained dephosphorylation of tau, which also correlated the enhanced down regulation of tau. Mass spectrometry data validated that PhosTACs downregulated multiple phosphorylation sites of tau. We believe that PhosTACs present advantages over current strategies to modulate tau phosphorylation and represent a new avenue for disease-modifying therapies for tauopathies.

2023-03-16 | PXD037459 | Pride

Proteomic analysis of the physiological E3 ubiquitin ligase responsible for PIN1 degradation

Project description:Induced oncoproteins degradation provides an attractive anti-cancer modality. Activation of anaphase-promoting complex (APC/CCDH1) prevents cell cycle entry by targeting crucial mitotic proteins for degradation. Phosphorylation of its co-activator CDH1 modulates the E3 ligase activity, but little is known about its regulation after phosphorylation and how to effectively harness APC/CCDH1 activity to treat cancer. Notably, Proline-directed phosphorylation is regulated by PIN1-catalyzed cis-trans prolyl isomerization to drive tumor malignancy. However, the mechanisms controlling its protein turnover remain elusive. Through proteomic screens, we identify a reciprocal antagonism of PIN1-APC/CCDH1 mediated by domain-oriented phosphorylation-dependent dual interactions as a fundamental mechanism governing mitotic protein stability and cell cycle entry.

2024-02-28 | PXD046325 | Pride

An Optogenetic-Phosphoproteomic Approach Links Akt Activation to Dynamic Temporal Changes in Signaling in Endothelial Cells

Project description:The serine/threonine kinase Akt is a central node in cell signaling. While aberrant Akt activation underlies the development of a variety of human diseases, how different patterns of Akt-dependent phosphorylation dictates downstream signaling and phenotypic outcomes remains largely enigmatic. Herein, we performed a systems-level analysis that integrates method advances of optogenetics, mass spectrometry-based phosphoproteomics, and bioinformatics to elucidate how different Akt intensity, durability, and pattern of stimulation activated temporal phosphorylation profiles in vascular endothelial cells. Through the analysis of ~35,000 phosphorylation sites across multiple conditions precisely controlled by light stimulation, we identified a series of signaling circuits that define the sequential downstream cascade of Akt activation and interrogated how Akt signaling cross-talks with growth factor signaling in endothelial cells. Furthermore, our results categorized substrates of kinases that are preferably activated by oscillating, transient, and sustained Akt signals. We validated a list of Akt motif-carrying phosphosites that covaried with Akt phosphorylation across experimental conditions as potential Akt substrates and presented the entire dataset a rich resource for future studies on Akt signaling and dynamics.

2023-06-27 | PXD034957 | Pride

LSD1 knockdown in 3T3-L1 preadipocytes

Project description:Obesity is often associated with a low-grade systemic inflammation state that contributes to the development of insulin resistance and atherosclerotic complications. This is usually coupled with increased macrophage infiltration in the adipose tissue and a defect in adipocyte differentiation that results in accumulation of hypertrophic fat cells characterized by a deregulated pattern of adipokine expression. Here we show that knockdown of histone demethylase lsd1 in 3T3-L1 preadipocytes results in defective adipogenesis and derepression of an inflammatory program in these cells. The dataset consists of four sample groups: [1] 3T3-L1 preadipocytes (passage 19) transfected with a control scrambled siRNA at 24h after transfection (siC.24h), [2] 3T3-L1 preadipocytes (p.19) transfected with a siRNA directed against LSD1 at 24h after transfection (siLsd1.24h), [3] 3T3-L1 preadipocytes (p.21) transfected with a control scrambled siRNA at 48h after transfection (siC.48h), and [4] 3T3-L1 preadipocytes (p.21) transfected with a siRNA directed against LSD1 at 48h after transfection (siLsd1.48h). The 24h sample groups (siC.24h and siLsd1.24h) consist of two biological replicate samples; the 48h sample groups (siC.48h and siLsd1.48h) consist of three biological replicate samples. Each sample was hybridized to a separate array, for a total of ten arrays.

2013-12-31 | E-GEOD-25423 | biostudies-arrayexpress

Protein expression in isogenic cancer cell line models of 1q aneuploidy

Project description:Investigating differential protein expression between 1q trisomy and 1q disomy cancer cell lines in isogenic backgrounds

2023-06-15 | PXD037956 | Pride

Mass spectrometry analysis of METTL3 phosphorylation in extracellular growth factor signaling

Project description:A fundamental facet of cell signaling is the conversion of extracellular signals into adaptive transcriptional responses. The role of RNA modifications in this process is poorly understood. We found that epidermal growth factor (EGF) promotes ERK-dependent phosphorylation of the m6A writer enzyme METTL3 at serine-43. Serine-43 phosphorylation increased METTL3-mediated methylation of the small nuclear RNA 7SK. Here we performed of phosphorylation mass spectrometry based on Data independent acquisition (DIA) of Hela cells stimulated with EGF in the absence or presence of the inhibitor U0126. Additionally, we validated known interactions between the 7SK-associated protein LARP7. Our findings establish a novel function for the m6A modification in converting growth-factor signaling events to a transcriptional elongation regulatory response via an RNA-methylation-dependent switch mediated by ERK signaling.

2023-06-27 | PXD036344 | Pride

Proteomic profile of extracellular vesicles released by breast cancer cells

Project description:The objective of the experiment was to compare the proteomic profile of extracellular vesicles released by breast cancer cells in basal untreated condition (C1, C2, etc) or treated with the adipokine leptin (L1, L2 etc).

2023-03-11 | PXD037266 | Pride

Transcriptional response to stress in serum deprived mouse fibroblasts

Project description:We have employed gene expression profiling in order to identify targets of transcriptional response to stress in mouse Swiss 3T3 fibroblasts, where we induced p38/MAP kinase pathway using anisomycin. Serum starved (72 h) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 1, 3, and 6 h (in triplicates). Untreated, serum-starved cells were used as a control. RNA was collected and gene expression profiling using mouse Agilent expression array (4x44k) was performed.

2014-08-12 | E-GEOD-55554 | biostudies-arrayexpress

LRG1 is an adipokine that promotes insulin sensitivity and suppresses inflammation

Project description:While dysregulation of adipocyte endocrine function plays a central role in obesity and its complications, the vast majority of adipokines remain uncharacterized. We employed bio-orthogonal non-canonical amino acid tagging (BONCAT) and mass spectrometry to comprehensively characterize the secretome of murine visceral and subcutaneous white and interscapular brown adipocytes. Over 600 proteins were identified, the majority of which showed cell type-specific enrichment. We here describe a metabolic role for leucine-rich α-2 glycoprotein 1 (LRG1) as an obesity-regulated adipokine secreted by mature adipocytes. LRG1 overexpression significantly improved glucose homeostasis in diet-induced and genetically obese mice. This was associated with markedly reduced white adipose tissue macrophage accumulation and systemic inflammation. Mechanistically, we found LRG1 binds cytochrome c in circulation to dampen its pro-inflammatory effect. These data support a new role for LRG1 as an insulin sensitizer with therapeutic potential given its immunomodulatory function at the nexus of obesity, inflammation, and associated pathology.

2022-11-21 | PXD035318 | Pride

Effects of supernatants of USP2 knockdown HL-60 cells and mock transfected HL60 cells on differentiated 3T3-L1 cells

Project description:Ubiquitin specifc protease (USP) 2 modulates various cellular responces including carcinogenesis, spermatogenesis, and glucose metabolism. So far, we established USP2 knockdown HL-60 cells to explore roles of USP2 in macrophages. In this experiment, we investigated whether USP2 knockdown HL-60 cells more prominently modulate function of adipocytes compared with control cells. USP2 knock down(KD) HL-60 cells and mock vector-transfected mock control cells were differentiated into macrophage-like cells in the presence of 30nM of phorbol 12-myristate 13-acetate for 5 days. Subseqently, supernatants of the USP2 KD cells and control cells were added to differentiated 3T3-L1 cells for 3 and 6 hrs. Total RNA was isolated from the supernatant-treated 3T3-L1 cells, and subjected to microarray analysis. Duplicate samples were prepared for each cell and time point.

2013-08-27 | E-GEOD-43313 | biostudies-arrayexpress

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