Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

¬An Aurora kinase A-BOD1L1-PP2A B56 Axis promotes chromosome segregation fidelity

ABSTRACT: The goal of this experiment was to discover mediators of resistance to the MCAK agonist chemical UMK57. Naive SW620 cells were compared to cells exposed to UMK57 for 3 days, and then all cells were synchronized in mitosis. The cells were then harvested, frozen and sent for phosphoproteomic analysis. 3 independent biological repeats were performed over 3 consecutive weeks.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Malignant Cell, Cell Culture

DISEASE(S): Colon Cancer

SUBMITTER: Thomas Kucharski

LAB HEAD: Duane Compton

PROVIDER: PXD058823 | Pride | 2025-02-18

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	checksum.txt	Txt
	g04406.mzXML	Mzxml
	g04406.raw	Raw
	g04407.mzXML	Mzxml
	g04407.raw	Raw

Items per page:

1 - 5 of 27

Similar Datasets

Integrated multi-omics approach reveals the role of SPEG in skeletal muscle biology including its relationship with myospryn complex

Project description:We applied multi-omics approaches (interactomic, proteomic, phosphoproteomic, and transcriptomic analyses) to assess underlying molecular pathways impacted by SPEG using mouse skeletal muscle from 2-month-old WT (n=4) and Speg-CKO (n=3) mice.

2024-06-22 | PXD041692 | Pride

¬An Aurora kinase A-BOD1L1-PP2A B56 Axis promotes chromosome segregation fidelity

Project description:The objective of this experiment is to discover mediators of resistance to the MCAK agonist compound UMK57. In this experiment, SW620 cells treated with DMSO were compared to SW620 cells exposed to UMK57 for 3 days prior to mitotic synchronization and harvesting. The samples were then processed and analyzed for differences in total protein levels. The experiment was performed as 3 independent biological repeats on 3 consective weeks.

2025-02-18 | PXD058821 | Pride

Nicotine-induced protein expression profiling reveals mutually altered proteins across four human cell lines

Project description:Mass spectrometry-based proteomic strategies can profile the expression level of proteins in response to external stimuli. Nicotine affects diverse cellular pathways, however, the nicotine-induced alterations on the global proteome across human cell lines have not been fully elucidated. We measured perturbations in protein levels resulting from nicotine treatment in four cell lines - HEK, HeLa, PaSC, and SH-SY5Y- in a single experiment using tandem mass tags (TMT10-plex) and high-resolution mass spectrometry. We quantified 8590 proteins across all cell lines. Of these, nicotine increased the abundance of 31 proteins 1.5-fold or greater in all cell lines. Likewise, considering proteins with altered levels in at least 3 of the 4 cell lines, 64 were up-regulated, while 1 was down-regulated. Gene ontology analysis revealed that ~40% of these proteins were membrane-bound, and functioned in transmembrane signaling and receptor activity. We highlighted proteins, including APP, APLP2, LAPTM4B, and NCOA4, which were dysregulated by nicotine in all cell lines investigated and may have implications in downstream signaling pathways, particularly autophagy. Using the outlined methodology, studies in additional (including primary) cell lines will provide further evidence that alterations in the levels of these proteins are indeed a general response to nicotine and thereby merit further investigation.

2018-10-26 | PXD005361 | Pride

Structural basis of respiratory complexes adaptation to cold temperatures

Project description:In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain. Yet, the structural basis of respiratory complex adaptation to cold remains elusive. Herein we combined thermoregulatory physiology and cryo-EM to study endogenous respiratory supercomplexes exposed to different temperatures. A cold-induced conformation of CI:III2 (termed type 2) was identified with a ~25 rotation of CIII2 around its inter-dimer axis, shortening inter-complex Q exchange space, and exhibiting different catalytic states which favor electron transfer. Large-scale supercomplex simulations in lipid membrane reveal how unique lipid-protein arrangements stabilize type 2 complexes to enhance catalytic activity. Together, our cryo-EM studies, multiscale simulations and biochemical analyses unveil the mechanisms and dynamics of respiratory adaptation at the structural and energetic level.

2024-10-02 | PXD054042 | Pride

Enriching cysteine-containing peptides using a sulfhydryl-reactive alkylating reagent with a phosphonic acid group, and immobilized metal affinity chromatography

Project description:The reduction of disulfide bonds and their subsequent alkylation is commonplace in typical proteomics workflows. Here, we highlight a sulfhydryl-reactive alkylating reagent with a phosphonic acid group (iodoacetamido-LC-phosphonic acid, 6C-CysPAT) that facilitates the enrichment of cysteine-containing peptides for isobaric tag-based proteome abundance profiling. Specifically, we profile the proteome of SH-SY5Y cells following 24 hr treatments with two proteasome inhibitors (bortezomib and MG-132) in a TMTpro9-plex experiment. We acquired three datasets - 1) Cys-enriched, 2) Cys-depleted, and 3) non-depleted - and compared the peptides and proteins quantified in each dataset, with emphasis on Cys-containing peptides. The data show that enrichment using 6C-CysPAT quantified over 38,000 Cys-containing peptides in 5 hr with >90% specificity. In addition, our combined dataset provides the research community with a resource of over 9,900 protein abundance profiles that exhibit the effects of two different proteosome inhibitors. Overall, the seamless incorporation of alkylation by 6C-CysPAT into a current TMT-based workflow permits the enrichment of a Cys-containing peptide subproteome. The acquisition of this “Mini-Cys” dataset can be used to preview and assess the quality of a deep, fractionated dataset.

2023-12-28 | PXD038382 | Pride

MCL-1 Drives a Metabolic Dependency on Fatty Acid Oxidation in Cancer Independent of its Anti-Apoptotic Function

Project description:MCL-1 is an anti-apoptotic BCL-2 family protein essential to the survival of diverse cell types and is a major driver of cancer and chemoresistance. The unique oncogenic supremacy of MCL-1, as compared to its anti-apoptotic homologs, suggests that it has additional functions to complement apoptotic suppression. Here, we find that MCL-1-dependent hematologic cancer cells selectively rely on fatty acid oxidation (FAO) as a fuel source due to metabolic wiring enforced by MCL-1 itself. Importantly, this metabolic function is independent of anti-apoptotic activity, as demonstrated by metabolomic, proteomic, and genomic profiling of MCL-1-dependent leukemia cells lacking pro-apoptotic BAX and BAK. Genetic deletion of Mcl-1 results in selective downregulation of proteins within the FAO pathway, accompanied by cell death upon glucose deprivation despite apoptotic blockade. Our data reveal that MCL-1 drives a programmatic dependency on FAO in hematologic cancer cells, which can be effectively targeted by FAO inhibitors.

2022-10-03 | PXD031364 | Pride

PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems

Project description:The protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed-forward mechanism involving ubiquitin (Ub) phosphorylation (pUb), Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins to support recruitment of mitophagy receptors. The ubiquitin ligase substrate receptor FBXO7/PARK15 is mutated in an early-onset parkinsonian-pyramidal syndrome. Previous studies have proposed a role for FBXO7 in promoting Parkin-dependent mitophagy. Here, we systematically examine the involvement of FBXO7 in depolarization and mtUPR-dependent mitophagy in the well-established HeLa and induced-neurons cell systems. We find that FBXO7-/- cells have no demonstrable defect in: 1) kinetics of pUb accumulation, 2) pUb puncta on mitochondria by super-resolution imaging, 3) recruitment of Parkin and autophagy machinery to damaged mitochondria, 4) mitophagic flux, and 5) mitochondrial clearance as quantified by global proteomics. Moreover, global proteomics of neurogenesis in the absence of FBXO7 reveals no obvious alterations in mitochondria or other organelles. These results argue against a general role for FBXO7 in Parkin-dependent mitophagy and point to the need for additional studies to define how FBXO7 mutations promote parkinsonian-pyramidal syndrome.

2023-06-19 | PXD037797 | Pride

HEK293T cell degradome (pulse chase) analysis upon 12h Torin1 treatment. Related to Supplementary Table 3 from An et al (2020)

Project description:HEK293T Azidohomoalanine (AHA) Pulse Chase (degradome) experiment, were cells from various genetic background (WT, ATG7-/-, RB1CC1-/-) are treated or not with Torin1 for 12h. Samples are Biotin-click, and streptavidin enriched.

2020-04-30 | PXD017857 | Pride

HEK293 cell proteome remodeling upon Torin1 treatment or amino acid withdraw. Related to Supplementary Table 1 from An et al (2020)

Project description:HEK293 cells with two genotype (WT or ATCG5 KO), treated with Torin1 or amino acid withdraw. TMT 11 plex.

2020-07-12 | PXD017852 | Pride

HEK293T cell nuclear & cytosolic proteome remodelling upon amino acid withdrawal. Related to Supplementary Table 4 from An et al (2020)

Project description:HEK293T proteome cytosolic vs nuclear fractionation upon short (3h) amino acids withdrawal.

2020-04-30 | PXD017856 | Pride