Proteome changes of fibroblasts and endothelial cells upon incubation with human cytomegalovirus dense bodies
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Cell Culture, Fibroblast
SUBMITTER: 
Jia-Xuan Chen
LAB HEAD: Bodo Plachter
PROVIDER: PXD039032 | Pride | 2023-07-24
REPOSITORIES: Pride
Similar Datasets
Project description:BCR-ABL positive acute lymphoblastic leukemia (ALL) cell survival is strongly dependent on the IRE1α-XBP1 branch of the Unfolded Protein Response (UPR). In the study at hand, we have focused on exploring the link between BCR-ABL1 and IRE1α to better understand whether a simultaneous pharmacological inhibition of both pathways could represent a beneficial therapeutic strategy in Philadelphia positive (Ph+) ALL. Therefore, the effect on the phosphoproteome of two inhibitors (MKC-8866 and Nilotinib) as well as a combination of both compounds was analysed in this study.
2020-09-21 | PXD012024 | Pride
Project description:We used tyrosine phosphorylation profiling by anti-pTyr-antibody mediated enrichment and subsequent analysis by mass spectrometry in order to determine the changes in early signalling after mast cell activation. Mast cells were stimulated with varying concentrations of antigen for one minute and the differences between optimal (20 ng/ml) and supra-optimal (2000 ng/ml) antigen mast cell activation were analysed by nanoLC-MS/MS.
2018-08-17 | PXD009318 | Pride
Project description:MS-based proteomics study of the interstitial fluid of breast cancer of mice lacking or overexpressing cathepsin B
2016-03-31 | PXD002585 | Pride
Project description:Regulatory T (Treg) cells are important regulators of the immune system and have versatile functions for the homeostasis and repair of tissues. They express the forkhead box transcription factor Foxp3 as a lineage-defining protein. In mature Treg cells, the Foxp3 core promoter is unmethylated indicating that this area could harbor a transcription factor complex to initiate or repress gene expression, respectively. We used an unbiased method to identify Foxp3-promoter-binding transcription factors (TFs) by inverted chromatin immunoprecipitation (IP) followed by quantitative mass spectrometry. We identified several candidate factors which showed Foxp3-promoter suppressive capacity, one of which was T-cell factor 1 (Tcf1). Using viral overexpression and CRISPR/Cas knockout studies, we identified Tcf1 as a repressor of Foxp3 expression in primary conventional CD4 T cells (Tconv). In Tcf1-deficient animals, increased levels of Foxp3intermediateCD25negative T cells were identified in secondary lymphoid tissues, implicating that Tcf1 protects Foxp3-negative T cells from inadvertent Foxp3 expression.
2020-05-26 | PXD018764 | Pride
Project description:Single cell transcriptomic analyses (scRNAseq) of hepatocytes and liver endothelial cells (L-EC) have revolutionized the understanding of the spatial architecture of liver structure and function. The spatial alignment of L-EC and hepatocytes is pivotal for liver function in health and disease given that L-EC act as instructive gatekeeper of nearby hepatocytes including the maintenance of liver metabolic zonation in a Wnt-dependent manner. Advancing liver biology beyond the ’transcript-centric’ view of scRNAseq analyses is presently restricted by the limited resolution of proteomics and genome-wide techniques to analyse post-translational modifications. Here, by combining spatial cell sorting methodology with transcriptomic and quantitative proteomic/phospho-proteomic analyses, we established the first functionally and spatially-resolved proteome landscape of the liver endothelium, yielding deep mechanistic insight into zonated vascular signalling mechanisms. Phosphorylation of receptor tyrosine kinases (RTK) was detected preferentially in the central vein area resulting in an atypical enrichment of tyrosine phosphorylation. Prototypic biological validation of the identified strong phosphorylation gradient of the vascular RTK Tie1 by blockade resulted in the rapid peri-central dysregulation of the L-EC transcriptome. Notably, the expression of Wnt9b in L-EC was discovered as Tie receptor controlled with reciprocal regulation by FoxO1 and STAT3 transcription factors. Genetic inactivation of Tie1 in L-EC or antibody blockade resulted in reduced liver regeneration following partial hepatectomy with reduced Wnt ligand and Wnt target gene expression, including Axin2, Sox9, Tbx3 and Lgr5. Taken together, the study has yielded unparalleled insight into the spatial organization of L EC signalling and discovered a vascular Tie-Wnt signalling axis as regulator of liver function. The employed spatial sorting technique followed by phospho-proteomic analysis may be employed as a universally adaptable strategy for the spatial phosphoproteomic analysis of scRNAseq data-defined relevant cellular (sub)-populations.
2021-05-21 | PXD020805 | Pride
Project description:Dimethyl labeling was integrated into the microfluidic pipeline to allow for precise relative quantification of the trace samples at the nanogram level, and the new pipeline was applied to evaluating cancer cell lines and cancer tissue samples.
2023-03-24 | PXD036982 | Pride
Project description:Beta-lactones have recently been introduced as the first selective ClpP inhibitors that attenuate virulence of both sensitive Staphylococcus aureus and multiresistant strains (MRSA). Although previous knockout studies showed that ClpP is essential for S. aureus alpha-toxin production a link between beta-lactone inhibition and molecular virulence mechanisms has been lacking so far. We here perform a chemical-proteomic approach to elucidate anti-virulence pathways. First, we demonstrate by gel-free activity-based protein profiling that ClpP is the predominant target of beta-lactones. Only a few off-targets were discovered, which, unlike ClpP, were not involved in the reduction of alpha-toxin expression. Second, in-depth mechanistic insight was provided by a full proteomic comparison between lactone treated and untreated S. aureus cells. Quantitative mass spectrometric analysis revealed a strong up-regulation of Rot and a corresponding down-regulation of alpha-toxin, providing the first direct connection between the lactone-dependent phenotype and a corresponding cellular mechanism. By building up a quantitative virulence regulation network, we visualize the impact of ClpP inhibition in a systems biology context. Interestingly, a lack of in vitro Rot degradation by either ClpXP or ClpCP calls for an indirect mode of action that may involve ClpX-mediated RNA signaling and feed-back circuits.
2017-02-08 | PXD004680 | Pride
Project description:To combat methicillin-resistant Staphylococcus aureus (MRSA) infections novel drugs addressing unprecedented and resistance-free targets are desperately needed. From a screen of human kinase inhibitors, we find that the anti-cancer drug sorafenib effectively kills MRSA strains. By dissection of the sorafenib scaffold and systematic synthesis of 72 analogs, we identify a potent compound – PK150 – exhibiting a minimal inhibitory concentration of 300 nM against several MRSA strains. The antibiotic induced rapid killing of S. aureus, including challenging persisters, and eradicated established biofilms. PK150 holds promising therapeutic potential as it did not induce in vitro resistance and exhibited good oral bioavailability and in vivo efficacy in a mouse infection model. Mode of action analysis by chemical proteomics revealed several targets including stimulation of protein secretion by signal peptidase IB (SpsB). Enhanced levels of extracellular proteins and resulting imbalances in secreted autolysin levels of PK150-treated bacteria support this target hypothesis. The associated antibiotic effects, especially the lack of resistance development, likely stem from the polypharmacology attribute of the compound. PK150 is therefore the founding member of a new class of highly active antibiotics.
2022-01-19 | PXD008070 | Pride
Project description:The human cytomegalovirus (HCMV) genome was sequenced 20 years ago. However, like other complex viruses, our understanding of its protein coding potential is far from complete. Here, we use ribosome profiling and transcript analysis to experimentally define the HCMV translation products and follow their temporal expression. We identified several hundred previously unidentified open reading frames and confirmed a fraction by mass spectrometry. We found that regulated use of alternative transcript start sites plays a broad role in enabling tight temporal control of HCMV protein expression and allowing multiple distinct polypeptides to be generated from a single genomic locus. Our results reveal an unanticipated complexity to the HCMV coding capacity and illustrate the role of regulated changes in transcript start sites in generating this complexity. Ribosome profiling and mRNA-seq from 3 time points (5hr, 24hr, 72hr) along HCMV infection. The supplementary file 'GSE41605_merlin_final_orfs.bed.gz' includes the 751 ORFs of HCMV that were identified in this study.
2012-10-17 | E-GEOD-41605 | biostudies-arrayexpress
Project description:Nelfinavir has broad anti-cancer activity precilincally as a single agent and in combination. Clinically, it is particularly effective in the therapy of proteasome inhibitor-refractory multiple myeloma. The broad anti-cancer mechanism of action of nelfinavir implies that it may interfere with very fundamental aspects of cancer cell biology. We combined proteome-wide affinity-purification with genome-wide CRISPR/Cas9-based screening to identify protein partners interacting with nelfinavir alongside with candidate genetic contributors affecting nelfinavir cytotoxicity. We show that nelfinavir has multiple binding partners embedded in organellar lipid-rich membranes. By binding to these, nelfinavir affects the composition and fluidity of lipid-rich membranes, which subsequently disrupts downstream membrane-related processes, such as lipid metabolism, glucose processing, mitochondrial respiration, vesicular transport and ABCB1-mediated drug efflux. Targeting membrane fluidity by FDA-approved drug nelfinavir is a potent mechanism to achieve anti-cancer activity and is in particular suitable for the treatment of proteasome inhibitor-refractory multiple myeloma.
2021-11-02 | PXD023260 | Pride