Browse
Submit Data
Databases
API
Help

Dataset Information

678 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ubiquitin remnant analysis in melanoma post inhibition of Usp9x

ABSTRACT: Assay the ubiquitinated protein remmants post depletion or inhibition of the deubiquitinase Usp9x in melanoma cells.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

DISEASE(S): Melanoma

SUBMITTER: Luke Peterson

LAB HEAD: Luke Peterson

PROVIDER: PXD005417 | Pride | 2017-02-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Usp9x regulates Ets-1 ubiquitination and stability to control NRAS expression and tumorigenicity in melanoma.

Potu Harish H Peterson Luke F LF Kandarpa Malathi M Pal Anupama A Sun Hanshi H Durham Alison A Harms Paul W PW Hollenhorst Peter C PC Eskiocak Ugur U Talpaz Moshe M Donato Nicholas J NJ

Nature communications 20170215

ETS transcription factors are commonly deregulated in cancer by chromosomal translocation, overexpression or post-translational modification to induce gene expression programs essential in tumorigenicity. Targeted destruction of these proteins may have therapeutic impact. Here we report that Ets-1 destruction is regulated by the deubiquitinating enzyme, Usp9x, and has major impact on the tumorigenic program of metastatic melanoma. Ets-1 deubiquitination blocks its proteasomal destruction and enh ...[more]

PMID: 28198367

Similar Datasets

cow MFGM LC-MS/MS - Evaluation of six sample preparation procedures for qualitative and quantitative proteomics analysis of milk fat globule membrane

Project description:Pasteurized whole cow milk (Grade A) was purchased from the supermarket. Whole cow milk was centrifuged at 3 000 g at 4°C for 30 min and the fat layer was recovered. The recovered fat was washed with PBS for 20 min at 37°C, and the resuspened mixture was centrifuged again to obtain the milk fat. The wash procedure was repeated three times. Finally, milk fat was washed with MilliQ water to recover the fat globules. Milk fat globules were solubilized with a SDS solution (100 mM Tris-HCl, pH 7.4, 100 mM DTT and 4% SDS) and then incubated in 95°C water bath for 10 min. The mixtures were centrifuged at 14 000 g for 15 min, and the protein samples were collected. S-Trap, FASP, in-gel, and traditional Chl/MeOH, as well as modified chloroform/methanol (Chl/MeOH) or acetone precipitation followed by in-solution digestion without clean-up of tryptic peptides methods were applied to characterization cow MFGM proteome.

2018-10-19 | PXD009288 | Pride

Proteomic response of Deinococcus radiodurans to short-term real microgravity during parabolic flight

Project description:As plans for future space exploration are becoming more ambitious, a better understanding of all factors affecting humans, plants, and microorganisms in space is necessary. Microgravity is an important variable in outer space and understanding the short- and long- term effects of microgravity on cellular processes will be important to minimize its negative effects on the physiology of any organism. Gravitational force has had an important role in the development of life on Earth, and short- and long-term changes in perceived gravitational force can induce notable changes within cells. Deinococcus radiodurans is the gram-positive bacterium that is best known for its extreme resistance to UV-C and gamma radiation, oxidation stress and desiccation, which has led to increased interest in this species in the context of astrobiology. The present study aimed to elucidate the short-term proteomic response of this species to real microgravity during parabolic flight. Overnight cultures were subjected to microgravity during a single parabola, and metabolic activity quenched using methanol. Proteins were extracted and subsequently measured using HPLC ESI MS/MS. Results indicated multiple affected processes in the cell envelope of D. radiodurans, such as increased peptidoglycan synthesis and altered S-layer activities. Energy metabolism upregulation and increased activity of DNA repair pathways could indicate increased endogenous ROS production that contributes to the stress response. The present study shows that the D. radiodurans proteome reacts to real microgravity within seconds. Differential expression patterns in response to microgravity show similarities to previously reported stress responses, thus the present results could be used as basis for future research aiming to better understand the complex regulatory processes underpinning stress management in D. radiodurans.

2022-02-17 | PXD027236 | Pride

Amblyomma sculptum sialotranscriptome and proteome

Project description:Ticks are obligate blood feeding ectoparasites that transmit a wide variety of pathogenic organisms to their vertebrate hosts. The tick Amblyomma sculptum is vector of Rickettsia rickettsii, the causative agent of Rock Mountain spotted fever, the most lethal rickettsiosis that affects humans. It is known that the transmission of pathogens by ticks is mainly associated with the physiology of the feeding process. Pathogens that are acquired with the blood meal must first colonize the tick gut and later the salivary glands (SG). Then, to be transmitted during a subsequent blood feeding, pathogens must reach the saliva. Tick saliva contains a complex mixture of bioactive molecules with anti-clotting, anti-platelet aggregation, vasodilatory, anti-inflammatory, and immunomodulatory properties to counteract both the host hemostasis and defense mechanisms, which besides facilitating tick feeding, may also benefits survival and establishment of pathogens in the host. In the current study, we compared the sialotranscriptome of unfed A. sculptum ticks and fed for 72 hours on rabbits using RNA-seq. The total of reads obtained were mapped in 9,560 coding sequences (CDSs) distributed in six major functional classes. Genes encoding secreted proteins, including lipocalins, mucins, protease inhibitors, glycine rich, metalloprotease, and 8.9 kDa superfamily were mostly upregulated by blood feeding. Selected genes were analyzed by RT-qPCR and all of them presented the same transcriptional profile regulation observed in RNA-seq, corroborating the transcriptional findings of this study. Finally, we mapped 116 proteins secreted in tick saliva by mass spectrometry-based proteomic analysis. Identified proteins should be functionally characterized and might be potential targets to develop vaccines for tick control and/or blocking of R. rickettsii transmission as well as pharmacological bioproducts with anti-hemostatic, anti-inflammatory and anti-bacterial activities.

2021-03-07 | PXD006143 | Pride

Metaprotemic analysis of groundwaters from a coal tar-contaminated aquifer in South Glens Falls, NY: MW37, Gel Slice

Project description:Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here we used environmental metaproteomics to obtain information about the identity and activity of subsurface microbial populations in coal-tar-contaminated groundwater. The present study reports metaproteomic data showing high representation of Candidatus Methylomirabilis oxyfera in our study site’s subsurface microbial community. In addition, eight of the nine proteins of the n-damo pathway were identified—indicating that n-damo is an active process occurring in situ in this habitat.

2022-02-22 | PXD001035 | Pride

Metaprotemic analysis of groundwaters from a coal tar-contaminated aquifer in South Glens Falls, NY: MW37, Shotgun 2

2022-02-22 | PXD001037 | Pride

Metaprotemic analysis of groundwaters from a coal tar-contaminated aquifer in South Glens Falls, NY: MW37, Shotgun 1

2022-02-22 | PXD001036 | Pride

Quantitative phosphoproteomics of drought-stressed Arabidopsis thaliana Col-0 wild type as well as mutants of Clade E and Clade A (Highly ABA-Induced 1) protein phosphatase 2Cs.

Project description:I-Traq based quantitative phosphoproteomics was used to examine changes in phosphopeptide abundance over longer term drought (low water potential) treatments. Samples were analyzed from unstressed seedlings grown on agar plates and from seedlings of the same age that had been transferred to low water potential (-1.2 MPa) for 96 h on PEG-infused agar plates. The genotypes analyzed were wild type Col-0 and two phosphatases mutants. One was a double mutant of two Clade E protein phosphatase 2Cs (Salk_011589 which lacks activity of AT3G05640 and Salk_048861 which lacks activity of AT5G27930). The other was a mutant (hai1-2) of the Clade A protein phosphatase 2C Highly ABA-Induced 1 (HAI1): Salk_108282 which lacks activity of AT5G59220). Our characterization of hai1-2 as well as detailed description of growth conditions and stress treatments has been reported in Bhaskara et al. (Plant Physiology 160:379-395, 2012). Characterization of the Clade E protein phosphatase 2Cs have not been previously reported and we have designated these as Clade E Growth Regulating PP2Cs (EGRs) based on characterization in our laboratory. The double mutant used for phosphoproteomic analysis has been designated egr1-1egr2-1. Three biological replicates were performed and microarray analysis of gene expression was performed on samples collected from the same experiments. The gene expression data sets have been deposited in Gene Expression Onmibus (GEO) under accession numbers GSE35258 (hai1-2 data) and GSE71237 (egr1-1egr2-1 data).

2017-01-17 | PXD004869 | Pride

working day and night: plastid casein kinase 2 catalyses phosphorylation of target proteins with diverse functions in light and dark-adapted plastids

Project description:Casein kinase 2 is a ubiquitous protein kinase that has puzzled researchers for several decades because of its pleiotropic activity. Here we set out to identify the _in vivo_ targets of plastid casein kinase 2 (pCK2) in _Arabidopsis thaliana_. Survey phosphoproteome analyses were combined with targeted analyses with wildtype and _pck2_ knockdown mutants to identify potential pCK2 targets by their decreased phosphorylation state in the mutant. To validate potential substrates, we complemented the _pck2_ knockdown line with TAP-tagged pCK2 and found it to restore growth parameters as well as many -but not all- of the putative pCK2-dependent phosphorylation events. We further performed a targeted analysis at the end-of-night to increase the specificity of target protein identification. This analysis confirmed light-independent phosphorylation of some pCK2 target proteins. Based on the aforementioned data, we define a set of _in vivo_ pCK2-targets that span different chloroplast functions such as metabolism, transcription, translation and photosynthesis. The pleiotropy of CK2 functions is also manifested by altered state transition kinetics during short-term-acclimation and significant alterations in the mutant metabolism supporting its crosstalk with photosynthetic regulation. Thus, our data expand our understanding on chloroplast phosphorylation networks and provide novel insights into kinase crosstalk in the biogenic regulation of chloroplast functions.

2021-07-19 | PXD014930 | Pride

Aspartate residues far from the active site drive O-GlcNAc transferase substrate selection

Project description:Here we use protein microarray technology and proteome-wide glycosylation profiling to show that conserved aspartate residues in the tetratricopeptide repeat (TPR) lumen of OGT drive substrate selection. Changing these residues to alanines alters substrate selectivity and unexpectedly increases rates of protein glycosylation. Our findings support a model where sites of glycosylation for many OGT substrates are determined by TPR domain contacts to substrate side chains five to fifteen residues Cterminal to the glycosite. In addition to guiding design of inhibitors that target OGT’s TPR domain, this information will inform efforts to engineer substrates to explore biological functions.

2019-07-26 | PXD014731 | Pride

Spectral histopathology supported laser capture microdissection and quantitative proteome analysis of diffuse malignant mesothelioma

Project description:FTIR based spectral histopathology was used for label-free classification of tumor tissue sections. The regions of interest were identified and annotated with high spatial resolution. The spatial information was used for automated laser capture microdissection of relevant tissue areas. Subsequently, the collected tissue samples were analyzed using quantitative proteomics. This novel approach for precise sample collection in clinical studies was applied to differentiate epitheloid and sarcomatoid subtypes of diffuse malignant mesothelioma.

2017-03-31 | PXD004818 | 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