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

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Malignant Cell, Cell Culture

DISEASE(S): Colon Cancer

SUBMITTER: Thomas Kucharski

LAB HEAD: Duane Compton

PROVIDER: PXD058821 | Pride | 2025-02-18

REPOSITORIES: pride

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Similar Datasets

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

Project description: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.

2025-02-18 | PXD058823 | Pride

Matrisome Proteomics Reveals Novel Mediators of Muscle Remodeling with Aerobic Exercise Training

Project description:Skeletal muscle has a unique ability to remodel in response to stimuli such as contraction and aerobic exercise training. Phenotypic changes in muscle that occur with training such as a switch to a more oxidative fiber type, and increased capillary density contribute to the well-known health benefits of aerobic exercise. The muscle matrisome likely plays an important role in muscle remodeling with exercise. However, due to technical limitations in studying muscle ECM proteins, which are highly insoluble, little is known about the muscle matrisome and how it contributes to muscle remodeling. Here, we utilized two-fraction methodology to extract muscle proteins, combined with multiplexed tandem mass tag proteomic technology to identify 161 unique ECM proteins in mouse skeletal muscle. In addition, we demonstrate that aerobic exercise training induces remodeling of a significant proportion of the muscle matrisome. We performed follow-up experiments to validate exercise-regulated ECM targets in a separate cohort of mice using Western blotting and immunofluorescence imaging. Our data demonstrate that changes in several key ECM targets are strongly associated with muscle remodeling processes such as increased capillary density in mice. We also identify LOXL1 as a novel muscle ECM target associated with aerobic capacity in humans. In addition, publically available data and databases were used for in silico modeling to determine the likely cellular sources of exercise-induced ECM remodeling targets and identify ECM interaction networks. This work greatly enhances our understanding of ECM content and function in skeletal muscle and demonstrates an important role for ECM remodeling in the adaptive response to exercise.

2024-07-30 | PXD053003 | 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

Compositional Proteomics: The Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags

Project description:Mass spectrometry (MS) has become an accessible tool for whole proteome quantitation with the ability to characterize protein expression across thousands of proteins within a single experiment. A subset of MS quantification methods (e.g., SILAC and label-free) monitor the relative intensity of intact peptides, where thousands of measurements can be made from a single mass spectrum. An alternative approach, isobaric labeling, enables precise quantification of multiple samples simultaneously through unique and sample specific mass reporter ions. Consequently, in a single scan, the quantitative signal comes from a limited number of spectral features (≤11). The signal observed for these features is constrained by automatic gain control, forcing codependence of concurrent signals. The study of constrained outcomes primarily belongs to the field of compositional data analysis. We show experimentally that isobaric tag proteomics data are inherently compositional and highlight the implications for data analysis and interpretation. We present a new statistical model and accompanying software, which improves estimation accuracy and the ability to detect changes in protein abundance. Finally, we demonstrate a unique compositional effect on proteins with infinite changes. We conclude that many infinite changes will appear small and that the magnitude of these estimates is highly dependent on experimental design.

2018-03-27 | PXD008259 | 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

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

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

Quantitative proteomics in G1 cells reveals the insulin receptor adaptor IRS2 as an APC/CCdh1 substrate

Project description:The anaphase promoting complex/cyclosome (APC/C) is a ubiquitin ligase that controls progression through the eukaryotic cell cycle by targeting key substrates for degradation through the ubiquitin proteasome pathway. During G1, the APC/C works in concert with its co-activator Cdh1 to recognize and ubiquitinate specific substrates during this phase of the cell cycle. While many APC/CCdh1 substrates play a role cell cycle regulation, others are involved in distinct cellular processes, indicating that diverse biological pathways are subject to APC/C-mediated control. To identify novel pathways and substrates regulated by APC/CCdh1, we conducted an unbiased proteomic screen in G1-arrested RPE1 cells acutely treated with small molecule APC/C inhibitors. Combining these results with degron prediction analysis, we discovered a range of putative APC/C substrates. We validated IRS2, a key adaptor protein involved in signaling downstream of the insulin and IGF1 receptors, as a novel direct APC/CCdh1 target. We demonstrate that genetic deletion of IRS2 reduces the expression of proteins involved in cell division and functionally impairs the spindle assembly checkpoint. Together, these findings reveal a novel connection between the insulin/IGF1 signaling network and the cell cycle regulatory machinery.

2020-06-22 | PXD018329 | 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

Proteome profiling of exponentially growing and heat-shock treated UBC4 and UBC5 deletion strains of S. cerevisiae

Project description:The Ubiquitin Proteasome System (UPS) governs numerous cellular processes by modulating protein stability and activity via the conjugation of the small molecule ubiquitin, either as a single chain or as linkages with distinct functions. Dysregulation of the UPS has been associated with many diseases, including neurodegenerative and neurodevelopmental diseases, as well as cancer. Ubiquitin conjugating enzymes (E2s) are important players of the UPS which work together with ubiquitin ligases (E3s) to promote substrate ubiquitylation. In this study, we conduct a comparative proteome-wide abundance profiling of S. cerevisiae cells during exponential growth phase with and without heat shock treatment. We focus on cells with deletions of the two highly homologous E2s, UBC4 or UBC5, and use isobaric tag-based quantitative mass spectrometry to elucidate variations and similarities in their proteome profiles. Our analysis revealed that Ubc4 has a much stronger effect on the proteome compared to Ubc5, particularly in exponentially growing cells. In contrast, the effect of Ubc5 on the proteome only becomes evident after heat shock, and even then, it remains minor compared to Ubc4. Furthermore, we identified proteins increasing in absence of each enzyme, which may represent their candidate substrates, potentially contributing to a better understanding of their cellular role.

2024-10-18 | PXD056103 | Pride

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