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Proteome adaptations of AC16 cells different oxygen exposure

ABSTRACT: To simulate in vitro different oxidative stress exposures, AC16 cells were cultured either under physioxia (5% oxygen) or normoxia (21% oxygen), and were consequently harvested either under physioxia or normoxia.

INSTRUMENT(S): maXis

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Tamara Tomin

LAB HEAD: Ruth Birner-Gruenberger

PROVIDER: PXD023620 | Pride | 2021-09-10

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	SPhumanCr-2019.fasta	Fasta
	TT_20200630_N2_BB1_01_16178.baf	Other
	TT_20200630_N3_BC1_01_16196.baf	Other
	TT_20200630_N4_BD1_01_16214.baf	Other
	TT_20200630_PN1_BA6_01_16168.baf	Other

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1 - 5 of 15

Publications

Mass Spectrometry-Based Redox and Protein Profiling of Failing Human Hearts.

Tomin Tamara T Schittmayer Matthias M Sedej Simon S Bugger Heiko H Gollmer Johannes J Honeder Sophie S Darnhofer Barbara B Liesinger Laura L Zuckermann Andreas A Rainer Peter P PP Birner-Gruenberger Ruth R

International journal of molecular sciences 20210211 4

Oxidative stress contributes to detrimental functional decline of the myocardium, leading to the impairment of the antioxidative defense, dysregulation of redox signaling, and protein damage. In order to precisely dissect the changes of the myocardial redox state correlated with oxidative stress and heart failure, we subjected left-ventricular tissue specimens collected from control or failing human hearts to comprehensive mass spectrometry-based redox and quantitative proteomics, as well as glu ...[more]

PMID: 33670142

Similar Datasets

Mass spectrometry-based redox and protein profiling reveals distinct protein expression and oxidation patterns in failing human hearts

Project description:Oxidative stress plays a key role in development and progression of cardiovascular diseases and it is correlated with left ventricular dysfunction and heart failure (HF). Oxidative environments lead to the formation of intra- and intermolecular disulfide bonds, as well as to plethora of other reversible and irreversible oxidative amino acid modifications, affecting the functionality of the proteins. Here we report that heart failure due to ischemic cardiomyopathy (ICM) or dilated cardiomyopathy (DCM) is correlated with increase in oxidative stress compared to non-failing control hearts, manifested through decreased GSH/GSSG ratio in failing heart tissue samples and adaptations of cardiac redox proteome which occur in correlation with two different heart pathologies.

2021-09-09 | PXD021261 | Pride

In-cell isotope-coded labeling and LC-MS/MS analysis probe warfarin inhibition mechanism

Project description:Warfarin targets human vitamin K epoxide reductase (hVKOR), a redox enzyme in the membrane of endoplasmic reticulum (ER), to prevent the formation of blood clots. Although warfarin has been a popular medication since 1954, its mechanism of action is still unclear. A fundamental issue is the controversial orientation of transmembrane helices (TM) in hVKOR. Stable isotope-coded reagents were usedto label VKOR in free, mutated, and warfarin-binding states directly in the cellular environment, followed by LC-MS/MS bottom-up approach to investigate the warfarin binding mechanism.

2017-03-30 | PXD003774 | Pride

The catalytic mechanism of vitamin K epoxide reduction in a cellular environment

Project description:Vitamin K epoxide reductases (VKOR) constitute a major family of integral membrane thiol oxidoreductases. In humans, VKOR sustains blood coagulation and bone mineralization through the vitamin K cycle. Previous chemical models assumed that the catalysis of human VKOR (hVKOR) starts from a fully reduced active site. This state, however, constitutes only a minor cellular fraction (5.6%). Thus, how hVKOR catalysis is carried out in the cellular environment remains largely unknown. Here we use quantitative mass spectrometry (MS) and electrophoretic mobility analysis to show that KO forms a covalent complex with a cysteine mutant mimicking hVKOR in a partially oxidized state. Trapping of this covalent reaction intermediate suggests that the partially oxidized state is catalytically active in cells. To investigate this activity, we analyze the correlation between the cellular activity and the cellular cysteine status of hVKOR. We find that the partially oxidized hVKOR has a considerably lower activity than hVKOR with a fully reduced active site. Although there are more partially oxidized hVKOR than fully reduced hVKOR in cells, these two reactive states contribute about equally to the overall hVKOR activity, and hVKOR catalysis can initiate from either of these states. Overall, the combination of MS quantification and biochemical analyses reveal the catalytic mechanism of this integral membrane enzyme in a cellular environment.

2020-12-03 | PXD020676 | Pride

Blockade of ROS production inhibits oncogenic signaling in acute myeloid leukemia and amplifies response to precision therapies

Project description:Mutations in the type III receptor tyrosine kinase FLT3 are frequent in patients with acute myeloid leukemia (AML) and are associated with a poor prognosis. AML is characterized by the overproduction of reactive oxygen species (ROS), which can induce cysteine oxidation in redox-sensitive signaling proteins. Here, we sought to characterize the specific pathways affected by ROS in AML by assessing oncogenic signaling in primary AML samples. The oxidation or phosphorylation of signaling proteins that mediate growth and proliferation was increased in samples from patient subtypes with FLT3 mutations. These samples also showed increases in the oxidation of proteins in the ROS-producing Rac/NADPH oxidase-2 (NOX2) complex. Inhibition of NOX2 increased the apoptosis of FLT3-mutant AML cells in response to FLT3 inhibitors. NOX2 inhibition also reduced the phosphorylation and cysteine oxidation of FLT3 in patient-derived xenograft mouse models, suggesting that decreased oxidative stress reduces the oncogenic signaling of FLT3. In mice grafted with FLT3 mutant AML cells, treatment with a NOX2 inhibitor reduced the number of circulating cancer cells, and combining FLT3 and NOX2 inhibitors increased survival to a greater extent than either treatment alone. Together, these data raise the possibility that combining NOX2 and FLT3 inhibitors could improve the treatment of FLT3 mutant AML.

2023-05-03 | PXD032104 | Pride

Combining redox proteomics with proximity labeling to monitor localized cysteine oxidation

Project description:Reactive oxygen species (ROS) can modulate protein function through cysteine oxidation. Identifying targets of ROS can provide insight into uncharacterized ROS-regulated pathways. Several redox-proteomic workflows, such as OxICAT, exist to identify sites of cysteine oxidation. However, determining ROS targets localized within subcellular compartments and ROS hotspots remains challenging with existing workflows. Here, we present a chemoproteomic platform, PL-OxICAT, which combines proximity labeling (PL) with OxICAT to monitor localized cysteine oxidation events. We show that TurboID-based PL-OxICAT can monitor cysteine oxidation events within subcellular compartments such as the mitochondrial matrix and intermembrane space. Furthermore, we use APEX-based PL-OxICAT to monitor oxidation events within ROS hotspots by using endogenous ROS as the source of peroxide for APEX activation. Together, these platforms further hone our ability to monitor cysteine oxidation events within specific subcellular locations and ROS hotspots and provide a deeper understanding of the protein targets of endogenous and exogenous ROS.

2024-05-21 | PXD034118 | Pride

Monitoring global protein thiol-oxidation and protein S-mycothiolation in Corynebacterium diphtheriae under hypochlorite stress

Project description:Mycothiol (AcCys-GlcN-Ins, MSH) is the major thiol-redox buffer in Actinomycetes, including Mycobacterium and Corynebacterium species. Protein S-mycothiolation controls the activities of several redox enzymes that function in detoxification of ROS and methionine sulfoxides, including the thiol peroxidase Tpx, the mycothiol peroxidase Mpx and the methionine sulfoxide reductase MsrA. Here we investigated the level of protein S-mycothiolation in Corynebacterium diphtheriae DSM43989 under oxidative stress as well as its NaOCl stress response.

2017-07-17 | PXD003321 | Pride

Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress

Project description:Mycothiol (AcCys-GlcN-Ins, MSH) is the major thiol-redox buffer in Actinomycetes, including Mycobacterium and Corynebacterium species. ). Protein S-mycothiolation controls the activities of several redox enzymes that function in detoxification of ROS and methionine sulfoxides, including the thiol peroxidase Tpx, the mycothiol peroxidase Mpx and the methionine sulfoxide reductase MsrA. Here we investigated the level of protein S-mycothiolation in Mycobacterium smegmatis under oxidative stress as well as its NaOCl stress response.

2017-06-30 | PXD003303 | Pride

SARS_CoV-2 substrate profiling in HEK-293 cell proteomes

Project description:To profile the human substrate degradome of the SARS-CoV-2 main viral protease by exposingnative proteome extracts from human embryonic kidney (HEK-293) cells (N = 3) to 3CLpro cleavage. Then, N Terminal Amine Labeling of Substates (TAILS) was used to identify the substrates. Here, heavy [+34] isotope dimethyl labeling is performed at the whole protein level in the 3CLpro-exposed samples, and the P1' side of substrates substrates was revealed by comparing to the samples exposed to inactive mutant labeled with ligh [+28 Da] dimethyl.

2021-11-03 | PXD026797 | Pride

SARS_CoV-2 substrate profiling in interferon-treated BEAS-2B cell proteomes

Project description:To profile the human substrate degradome of the SARS-CoV-2 main viral protease and to investigate whether 3CLpro cleavage of cellular substrates dampens host antiviral responses induced by type I interferons, we treated BEAS-2B cells with interferon-alpha (N = 3), interferon-beta (N = 3), or vehicle (N = 3), retrieve and exposed native proteome extracts from human embryonic kidney to 3CLpro cleavage. Then, N Terminal Amine Labeling of Substates (TAILS) was used to identify the substrates. Here, heavy [+34] isotope dimethyl labeling is performed at the whole protein level in the 3CLpro-exposed samples, and the P1' side of substrates substrates was revealed by comparing to the samples exposed to inactive mutant labeled with ligh [+28 Da] dimethyl.

2021-11-03 | PXD026815 | Pride

Transcription profiling of human chondrocytes from patients with osteosarcoma or osteomyelitis, cultured in either 1% or 20% oxygen for one or four days

Project description:Cartilage was taken from the femoral condyle and tibial plateau from eight patients, cut into small pieces and digested overnight with Collagenase Type 2. The resultant chondrocytes were put through a cell strainer, pelleted and resuspended in fresh media and cultured for one week in 20% oxygen. The culture was split into five sub-cultures, one of which was immediately frozen; the remainder were allowed to recover overnight. Cells were subsequently grown at either 1% oxygen (hypoxia simulation) or 20% oxygen (normoxia simulation) for either one or four days before RNA extraction. Labelled RNA was then hybridised to Affymetrix Human U133 plus 2.0 arrays.

2008-04-01 | E-MIMR-644 | biostudies-arrayexpress

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