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Subcellular fractionation in Ramos B-cells

ABSTRACT: In order to increase the proteome coverage, a subfractionation strategy has been performed to obtain proteins belonging to four different cellular compartments (i.e., cytoplasm (CYT), membrane (MB), organelle (ORG), and nucleus (NUC)). Experiments have been done in triplicate.

INSTRUMENT(S): LTQ Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Cell Suspension Culture

DISEASE(S): Lymphoma

SUBMITTER: Paula Díez

LAB HEAD: Manuel Fuentes

PROVIDER: PXD003939 | Pride | 2022-02-14

REPOSITORIES: Pride

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Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model.

Landeira-Viñuela Alicia A Díez Paula P Juanes-Velasco Pablo P Lécrevisse Quentin Q Orfao Alberto A De Las Rivas Javier J Fuentes Manuel M

Biomolecules 20211126 12

Human Proteome Project (HPP) presents a systematic characterization of the protein landscape under different conditions using several complementary-omic techniques (LC-MS/MS proteomics, affinity proteomics, transcriptomics, etc.). In the present study, using a B-cell lymphoma cell line as a model, comprehensive integration of RNA-Seq transcriptomics, MS/MS, and antibody-based affinity proteomics (combined with size-exclusion chromatography) (SEC-MAP) were performed to uncover correlations that c ...[more]

PMID: 34944421

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The value of subcellular fractionation for protein identification in a B-cell line (Ramos)

Project description:Integrated in the Chromosomic-centric Human Proteome Project (C-HPP), a lymphocytic B-cell line (Ramos) was selected as a model of B-cells. We performed a subfractionation strategy (in triplicate) for the extraction of proteins from 4 different fractions (cytoplasm, CYT; organella, ORG; membrane, MB; nucleus, NUC).

2015-08-04 | PXD001933 | Pride

Design and development of nanoproteomics strategies for biomarker identification in cerebrospinal fluid of leptomeningeal disease, using as model lymphoma non-Hodgkin B.

Project description:The early diagnosis of leptomeningeal disease is a challenge because it is an asymptomatic pathology in the early stages. Hence, it is highly relevant to identify a panel of biomarkers to help in the diagnosis and/or prognostic. For this purpose, we have explored a multipronged proteomics approaches, in cerebrospinal fluid, to determine a potential panel of biomarkers in cerebrospinal fluid. Thus, a systematic and exhaustive characterization of more than 347 CSF samples have been performed by an integrated LC-MS/MS (n 20) and functional proteomics (n 347) analysis to establish protein profiles which has been useful to develop a panel of biomarkers validated by in silico approaches.

2022-02-17 | PXD026016 | Pride

Comprehensive and systematic characterization of novel nanodrug conjugate based on multi-functionalized magnetic iron-nanoparticles conjugated with cisplatin derivative: From the chemistry to the animal model

Project description:Nanodrugs need a completely characterization by both chemically and biological point of view. As nanoparticles have evolved as multi-functional systems combining different custom anchorages, their pharmacological involvements require more comprehensive analysis. In this work, we present the design and synthesis of novel iron-NPs conjugated with a cisplatin derivate and their biological evaluation by quantitative proteomics approches. To decipher detailed insights related to the NP interactions with environment (as protein corona) and pharmacodynamics functionalities of the nanodrugs conjugates, LC-MS/MS analysis was perform to stablish protein profile. Biocompatibility and animal model provided complete insights of the potential of multifunctional iron NPs.

2022-08-12 | PXD026615 | Pride

Human Cdc14A is phosphorylated by Cdk1 at early mitosis

Project description:Cdc14 enzymes compose a family of highly conserved phosphatases that are present in a wide range of organisms, including yeast and humans, and that preferentially reverse the phosphorylation of Cyclin-Dependent Kinase (Cdk) substrates. The budding yeast Cdc14 orthologue has essential functions in the control of late mitosis and cytokinesis. In mammals, however, the two Cdc14 homologues, Cdc14A and Cdc14B, do not play a prominent role in controlling late mitotic events, suggesting that some Cdc14 functions are not conserved across species. Moreover, in yeast, Cdc14 is regulated by changes in its subcellular location and by phosphorylation events. In contrast, little is known about the regulation of human Cdc14 phosphatases. Here, we have studied how the human Cdc14A orthologue is regulated during the cell cycle. We found that Cdc14A is phosphorylated on Ser411, Ser453 and Ser549 by Cdk1 early in mitosis and becomes dephosphorylated during late mitotic stages. Interestingly, in vivo and in vitro experiments revealed that, unlike in yeast, Cdk1-mediated phosphorylation of human Cdc14A did not control its catalytic activity but likely modulated its interaction with other proteins in early mitosis. These findings point to differences in Cdk1-mediated mechanisms of regulation between human and yeast Cdc14 orthologues.

2018-08-13 | PXD009481 | Pride

Protein synthesis during myoblast differentiation

Project description:Mole (MSR) and fractional (FSR) synthesis rates of proteins during C2C12 myoblast differentiation were investigated. Myoblast cultures supplemented with D2O during 0-24 h or 72-96 h of differentiation were analysed by LC-MS/MS to calculate protein FSR and MSR after samples were spiked with yeast alcohol dehydrogenase (ADH1).

2020-10-22 | PXD021125 | Pride

Proteomic Analysis of the Lake Trout (Salvelinus namaycush) Heart and Blood: the beginning of a comprehensive lake trout protein database

Project description:Lake trout (Salvelinus namaycush) are a top-predator species in the Laurentian Great Lakes that are often used as bioindicators of chemical stressors in the ecosystem. Although many studies are done using these fish to determine concentrations of stressors like legacy persistent, bioaccumulative and toxic chemicals, there are currently no proteomic studies on the biological effects these stressors have on the ecosystem. This lack of proteomic studies on Great Lakes lake trout is because there is currently no complete, comprehensive protein database for this species. In this research, we aimed to use proteomic methods and established protein databases from NCBI and UniProtKB to identify potential proteins in the lake trout species. The current study utilized heart tissue and blood from two separate lake trout. Our previous published work on the lake trout liver revealed 4,194 potential protein hits in the NCBI databases and 3,811 potential protein hits in the UniProtKB databases. In the current study, using the NCBI databases we identified 838 potential protein hits for the heart and 580 potential protein hits for the blood of the first lake trout (biological replicate 1). In the second lake trout (biological replicate 2), using the NCBI databases we identified 1,180 potential protein hits for the heart and 561 potential protein hits for the blood. Similar results were obtained using the UniProtKB databases. This study builds on our previous work by continuing to build the first comprehensive lake trout protein database. Through this investigation, we are also able to make observations as to protein homology through evolutionary relationships.

2021-12-30 | PXD023970 | Pride

Effects of Caloric Restriction with Protein Supplementation on Plasma Protein Profiles in Middle-Aged Women with Metabolic Syndrome – A Preliminary Open Study

Project description:Clinical studies have demonstrated that higher protein intake based on caloric restriction (CR) alleviates metabolic abnormalities. However, no study has examined the effects of plasma protein profiles on caloric restriction with protein supplementation (CRPS) in metabolic syndrome (MetS). Therefore, using a proteomic perspective, this pilot study investigated whether CRPS ameliorated metabolic abnormalities associated with MetS in middle-aged women. Methods: Plasma samples of middle-aged women with MetS in CR and CRPS groups for 12-week intervention were obtained and their protein profiles were analysed. Briefly, blood samples from qualified participants were drawn before and after the dietary treatment. Anthropometric, clinical, and biochemical variables were measured and correlated with plasma proteomics. Results: In results, we found that body mass index, total body fat, and fasting blood glucose decreased significantly after the interventions but were not different between the CR and CRPS groups. After liquid chromatography–tandem mass spectrometry analysis, the relative plasma levels of A2M, C4BPA, C1RL, C6, C8G, and PROS were significantly different between the CRPS and CR groups. These proteins are involved in inflammation, the immune system, and coagulation responses. Moreover, blood low-density lipoprotein cholesterol levels were significantly and positively correlated with C6 plasma levels in both groups. Conclusions: These findings suggest that CRPS improves inflammatory responses in middle-aged women with MetS. Specific plasma protein expression (i.e. A2M, C4BPA, C1RL, C6, C8G, and PROS) associated with the complement system was highly correlated with FBG, BLs, and body fat.

2019-11-13 | PXD012213 | Pride

Geographical origin and antigenicity of venom. Intraspecies proteomic and immunological analysis of Naja mossambica venom.

Project description:The main objective of the project is to find the reason why antivenoms commonly used in treatments of Naja mossambica bites are not effective in Eswatini and Mozambique, whereas they exhibit normal activity in other countries of southern Africa. The main hypothesis here assumes that intra-species differences in protein composition of venoms from different part of the continent are the main cause of observed diversity in antivenom efficacy. In the course of the project, there is also a plan to identify the specific toxins that differ analyzed venoms in reactivity towards antivenom immunoglobulins.

2024-03-15 | PXD043647 | Pride

Reanalysis of Pandey lab's draft of the human proteome

Project description:The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides was lacking. To this end, Akhilesh Pandey's lab reported a draft map of the human proteome based on high resolution Fourier transform mass spectrometry-based proteomics technology, which included an in-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells ( http://dx.doi.org/10.1038/nature13302 ). The profiling resulted in identification of proteins encoded by greater than 17,000 genes accounting for ~84% of the total annotated protein-coding genes in humans. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) complements available human genome and transcriptome data to accelerate biomedical research in health and disease. Pandey's lab and collaborators request that those considering use of this primary dataset for commercial purposes contact pandey@jhmi.edu. The full details of this study can be found in the PRIDE database: www.ebi.ac.uk/pride/archive/projects/PXD000561/. This ArrayExpress entry represents a top level summary of the metadata only which formed the basis of the reanalysis performed by Joyti Choudhary's team ( jc4@sanger.ac.uk ), results of which are presented in the Expression Atlas at EMBL-EBI : http://www.ebi.ac.uk/gxa/experiments/E-PROT-1.

2015-03-10 | E-PROT-1 | biostudies-arrayexpress

HDX-MS Analysis of CD47 Conformational Dynamics

Project description:CD47 is the only 5-transmembrane (5-TM) spanning receptor of the immune system. Its extracellular domain (ECD) is a cell surface ‘marker of self’ that binds SIRPα and inhibits macrophage phagocytosis, and cancer immuno-therapy approaches in clinical trials are focused on blocking CD47/SIRPα interaction. Using hydrogen-deuterium exchange we show that CD47’s ECLR architecture, comprised of two extracellular loops and the SWF loop, creates a molecular environment stabilizing the ECD for presentation on the cell surface.

2021-07-15 | PXD026458 | Pride

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