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Label free proteomics analysis of osteosarcoma cells differing with respect to expression of endocytic receptor uPARAP.

ABSTRACT: We have performed a proteomics comparison of endosomal fractions from cells positive and negative for the endocytic receptor uPARAP. Comparing the protein content of endosomes may reveal the identity of ligands taken up by uPARAP-mediated endocytosis.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Bos Taurus (bovine) Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Niels Behrendt

LAB HEAD: Niels Behrendt

PROVIDER: PXD031272 | Pride | 2022-06-23

REPOSITORIES: Pride

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Combining laser capture micro-dissection and proteomics reveals an active translation machinery controlling invadosome formation

Project description:We developed a method that combines laser micro-dissection and mass spectrometry, enabling the analysis of subcellular structures in their native state based on low amounts of input material. Using this combinatorial method, we showed that invadosomes contain specific components of the translational machinery, in addition to known marker proteins.

2018-10-19 | PXD009390 | Pride

Proteomic analysis of BioID experiments performed with Toxoplasma gondii MyoJ protein tagged with TurboID in tachyzoites

Project description:The aim of the project was to identify proteins of the basal complex of Toxoplasma gondii using MyoJ as bait

2022-11-01 | PXD035106 | Pride

Analyses of FBXL6 interaction with newly synthesized proteins.

Project description:HEK cells were grown in light media for two weeks. One day before experiments, cells were transfected with FBXL6-flag or B-gal (control). At t=0, cells were switched to heavy media for 3h and then Flag immunoprecipitation were performed. Pulled down protein were analyzed by mass spectrometry.

2023-09-25 | PXD037602 | Pride

Short-range interactions between fibrocytes and CD8+ T cells in COPD bronchial inflammatory response

Project description:The peri-bronchial zone of chronic obstructive pulmonary disease (COPD) is the site of extensive infiltration of immune cell, allowing persistent contacts between resident cells and immune cells. Tissue fibrocytes interaction with CD8+ T cells and its consequences were investigated. We show that fibrocytes and CD8+ T cells are found in vicinity in distal airways and that potential interactions are more frequent in tissues from COPD patients compared to those of control subjects. Increased proximity and clusterization between CD8+ T cells and fibrocytes are associated with altered lung function. Tissular CD8+ T cells from COPD patients promote fibrocyte chemotaxis via the CXCL8-CXCR1/2 axis. CD8+ T cells establish short-term interactions with fibrocytes, that trigger CD8+ T cell proliferation in a CD54- and CD86-dependent manner, pro-inflammatory cytokines production, CD8+ T cell cytotoxic activity and fibrocyte immunologic signaling. We defined a computational model describing these intercellular interactions and calibrated the parameters based on our experimental measurements. We showed the model’s ability to reproduce histological ex vivo characteristics, and observed major contributions of fibrocyte-mediated CD8+ T cell proliferation and fibrocyte death in COPD development. Using the model to test therapeutic scenarios, we predicted a recovery time of several years, and the failure of targeting independently chemotaxis or interacting processes. Altogether, our study reveals that local interactions between fibrocytes and CD8+ T cells can occur in vivo and could jeopardize the balance between protective immunity and chronic inflammation in bronchi of COPD patients.

2023-07-28 | PXD041402 | Pride

Loss of Rnd3/RhoE induces entosis in human hepatocellular carcinoma

Project description:Entosis is a process that leads to the formation of cell-in-cell structures commonly found in cancers. Here, we identified entosis in hepatocellular carcinoma and the loss of Rnd3 as an efficient inducer of this mechanism. We characterized the different stages and the molecular regulators of entosis induced after silencing of Rnd3. We demonstrated that this process is dependent on RhoA/ROCK pathway, but independent on E-cadherin. The proteomic analysis of entotic cells allowed us to identify LAMP-1 as a protein implicated not only in the degradation final stage of entosis, but also in the full mechanism. By analyzing entosis in human hepatocellular carcinoma samples, we found a relationship between the presence of entotic cells and the metastatic potential of tumors. Altogether, these data suggest the involvement of entosis in liver tumor progression and highlight a new perspective for the entosis analysis in medicine research as a novel therapeutic target.

2024-01-26 | PXD043640 | Pride

STN7 kinase-dependent Light-harvesting complex (LHC) protein phosphorylations in the moss Physcomitrium (Physcomitrella) patens

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2022-06-24 | PXD026183 | Pride

Excretory-secretory proteins released by Schistosoma mansoni-resistant, susceptible and naïve Biomphalaria glabrata

Project description:Schistosomiasis is one of the most socioeconomically harmful neglected tropical diseases in the world. It occurs following infection from parasites of the Schistosoma genus, such as Schistosoma mansoni, which must transition within a molluscan and mammalian host to survive. Previous chemical analyses of schistosome-molluscan interactions indicate that schistosomes orientate towards potential hosts partially through chemosensation, displaying a preference for naïve (uninfected) hosts. Recent advances in proteomic techniques enable sophisticated comparative analyses between infected and naïve snail host proteins. This study aimed to compare the snail-conditioned water (SCW) released by F1 resistant, infected and naïve Biomphalaria glabrata to identify potential attractants and deterrents.

2019-09-26 | PXD015129 | Pride

PROTEOMIC PROFILING OF EXTRACELLULAR VESICLES OBTAINED FROM Toxoplasma gondii AND TOXOPLASMA-INFECTED CELLS

Project description:Here, we purified T. gondii obtained from human foreskin fibroblast (HFF) infected cells and performed the first comprehensive proteomic profiling of the extracellular vesicles secreted by these parasites.

2017-06-26 | PXD004895 | Pride

Proteomic study of low-birth-weight nephropathy molecular pathogenesis in rats

Project description:We investigated the molecular pathogenesis of LBW rats obtained by intraperitoneal injection of dexamethasone into pregnant animals. Normal-birth-weight (NBW) rats were used as controls with seven animals per group. When the rats were four weeks old, the left kidneys were removed and used for comprehensive label-free proteomic studies

2022-02-15 | PXD018948 | Pride

Adaptation to pH and pH signaling in the phytopathogenic fungus Botrytis cinerea

Project description:The grey mould fungus Botrytis cinerea is capable of developing on a wide variety of host plants and different organs that differ greatly in their pH values. The strategy developed by this necrotrophic fungus is partly based on the acidification of the plant tissues via the secretion of several organic acids including oxalic acid. That’s why B.cinerea is considered as an “acidic” fungus. However, we have previously shown that it is also capable of alkalinizing its ambient environment during sunflower cotyledons or bean leaves infection and that the alkalinization is achieved by amino acids catabolism and ammonia secretion ( Billon-grand et al, 2012). This capacity to modulate the surrounding pH reveals also an ability to regulate the expression and the secretion of an arsenal of enzymes in order to produce virulence factors in accordance with the ambient pH and enzymes requirement for optimal activity. Expression of pH-regulated genes is controlled by the highly conserved signaling pathway Pal/Pac that leads to activation of the zinc finger transcription factor PACC under neutral or alkaline conditions. Investigations of the role of this pH regulator in the infectious process of B.cinerea are presented.

2021-09-13 | PXD004145 | Pride

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