Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The proteome of B cell maturation identifies PDCD4 as limiting the response of marginal zone B cells

ABSTRACT: During B cell maturation, transitional and mature B cells acquire cell-intrinsic features that determine their ability to exit quiescence and mount effective immune responses. We used high-resolution mass spectrometry to quantify the proteome of B cell subsets from the mouse spleen and map the differential expression of environmental sensing, transcription- and translation initiation-factors that define cellular identity and function. By comparing transcriptome and proteome, we identified mRNAs linked to B cell activation and differentiation that are expressed without detectable protein. These "poised" mRNAs might enable rapid protein production through increased translation or protein stability. In addition, we found that the translational repressor PDCD4 restrains the response of marginal zone B cells to a T-independent antigen. Our molecular characterization of B cell maturation is a valuable resource to further explore the mechanisms underpinning the specialised functions of B cell subsets.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Spleen, B Cell

SUBMITTER: Andrew Howden

LAB HEAD: Martin Turner

PROVIDER: PXD027054 | Pride | 2023-06-21

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	AH-10-1.raw	Raw
	AH-10-2.raw	Raw
	AH-10-3.raw	Raw
	AH-10-4.raw	Raw
	AH-10-5.raw	Raw

Items per page:

1 - 5 of 132

Similar Datasets

The proteome of B cell maturation identifies PDCD4 as limiting the response of marginal zone B cells – B cell subsets. Includes Fasta file.

Project description:During B cell maturation, transitional and mature B cells acquire cell-intrinsic features that determine their ability to exit quiescence and mount effective immune responses. We used high-resolution mass spectrometry to quantify the proteome of B cell subsets from the mouse spleen and map the differential expression of environmental sensing, transcription- and translation initiation-factors that define cellular identity and function. By comparing transcriptome and proteome, we identified mRNAs linked to B cell activation and differentiation that are expressed without detectable protein. These "poised" mRNAs might enable rapid protein production through increased translation or protein stability. In addition, we found that the translational repressor PDCD4 restrains the response of marginal zone B cells to a T-independent antigen. Our molecular characterization of B cell maturation is a valuable resource to further explore the mechanisms underpinning the specialised functions of B cell subsets.

2023-06-29 | PXD043349 | Pride

The proteome of B cell maturation identifies PDCD4 as limiting the response of marginal zone B cells – WT and PDCD4 KO MZ B cells. Includes Fasta file

2023-06-29 | PXD043351 | Pride

The proteome of B cell maturation identifies PDCD4 as limiting the response of marginal zone B cells – marginal zone B cells WT and PDCD4 KO

2023-06-21 | PXD037563 | Pride

Concomitant deletion of Shp-1 and Shp-2 in T cells fails to improve anticancer responses

Project description:Anticancer T cells acquire a dysfunctional state characterized by poor effector function and expression of inhibitory receptors, such as programmed cell death protein 1 (PD-1). Blockade of PD-1 signalling leads to T cell reinvigoration and is increasingly applied as an effective anticancer treatment. Recent work challenged the commonly held view that the phosphatase Src homology 2 (SH2) domain–containing phosphatase (SHP)-2 is essential for the molecular cascade downstream PD-1, suggesting functional redundancy with the homologous phosphatase SHP-1. Therefore, we investigated the effect of concomitant SHP-1 and 2 deletion in T cells by knocking out these phosphatases under the CD4cre promoter. In vivo results not only indicate that Shp-1/2 deletion is insufficient to ameliorate tumour control, but also that it impairs the therapeutic effects of anti-PD1 treatment, affecting tumour-infiltrating CD8+ T cells. Notably, acute deletion of Shp-1/2 in effector T cells also fails to improve tumour control. In vitro results show that Shp-1/2-deleted CD8+ T cells exhibit impaired expansion due to a survival defect and proteomics analysis reveals substantial alterations in their proteome, including in apoptosis-related pathways. This data indicates that concomitant ablation of SHP-1/2 in polyclonal T cells fails to improve their anticancer properties, implying that caution shall be taken when considering their inhibition for immunotherapeutic approaches.

2022-09-29 | PXD034897 | Pride

Phosphatidylinositol-3-kinase p110 delta differentially restrains and directs naïve versus effector CD8+ T cell transcriptional programs Phosphatidylinositol-3-kinase p110 delta differentially restrains and directs naïve versus effector CD8+ T cell transcriptional programs

Project description:Phosphatidylinositol-3-kinase p110 delta (PI3Kp110δ) is pivotal for CD8+ T cell immune responses. To inform how PI3Kp110δ regulates CD8+ T cells, the current study focuses on PI3Kp110δ controlled transcriptional programs and reveals how PI3Kp110δ selectively induces and represses expression of key genes that create a cytotoxic T cell (CTL). The data identify differences in PI3Kp110δ regulated transcriptional programs between naïve and cytotoxic T cells including differential control of cytolytic effector molecules, costimulatory receptors and the critical inhibitory receptors CTLA4 and SLAMF6. However, common to both naïve and effector cells is PI3Kp110δ control of the production of chemokines and cytokines that orchestrate communication between the adaptive and innate immune system. The study provides a comprehensive resource for understanding how PI3Kp110δ uses multiple mechanisms dependent on Protein Kinase B/AKT, FOXO1 dependent and independent mechanisms and mitogen-activated protein kinases (MAPK) to direct CD8+ T cell fate.

2021-06-14 | PXD025046 | Pride

Gene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer (copy number data)

Project description:Hypothesis: Non-small cell lung cancer (NSCLC) is characterized by a multitude of genetic aberrations with unknown clinical impact. In this study, we aimed to identify gene copy number changes that correlate with clinical outcome in NSCLC. To maximize the chance to identify clinically relevant events, we applied a strategy involving two prognostically extreme patient groups. Results: Genetic aberrations were strongly associated with tumor histology. In adenocarcinoma (n=50), gene copy number gains on chromosome 8q21-q24.3 (177 genes) were more frequent in long-term survivors. In squamous cell carcinoma (n=28), gains on chromosome 14q23.1-24.3 (133 genes) were associated with shorter survival, whereas losses in a neighboring region, 14q31.1-32.33 (110 genes), correlated with favorable outcome. In accordance with copy number gains and losses, mRNA expression levels of corresponding genes were increased or decreased, respectively. Conclusion: Comprehensive tumor profiling permits the integration of genomic, histologic and clinical data. We identified gene copy number gains and losses, with corresponding changes in mRNA levels, that were associated with prognosis in adenocarcinoma and squamous cell carcinoma of the lung. Short-term (<20 months; n=53) and long-term survivors (>58 months;n=47) were selected from a clinically well-characterized NSCLC patient cohort with available fresh-frozen tumor specimens. The samples were analyzed using high-resolution SNP-array technology. The molecular data was combined with information on clinical parameters.

2011-11-01 | E-GEOD-28572 | biostudies-arrayexpress

Genome-wide analysis of siRNA accumulation in Arabidopsis treated with bacteria

Project description:To identify endogenous siRNAs in response to bacterial pathogen at a whole genome level, we performed small RNA profiling on Pseudomonas syringae-challenged Arabidopsis and obtained more than 24.6 million (M) reads with more than 3.8 M unique small RNAs that perfectly matched Arabidopsis genome. We found some new miRNAs and some miRNA induced by pathogen infection. We also identified more than 20K unique siRNAs from the NAT mRNAs and 22K siRNAs from the introns or intron-exon junction of the NATs. Sequencing of small RNAs from Arabidopsis infected by control and 3 bacterias in 6h and 14h.

2010-07-23 | E-GEOD-19694 | biostudies-arrayexpress

Gene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer

Project description:This SuperSeries is composed of the following subset Series: GSE28571: Gene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer (expression data) GSE28572: Gene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer (copy number data) Refer to individual Series

2011-11-01 | E-GEOD-28582 | biostudies-arrayexpress

Liver zonation patterns and cell size variability in isolated human hepatocytes

Project description:Human hepatocytes differ in gene expression and function across the hexagonal lobules of the tissue microarchitecture, a phenomenon referred to as liver zonation. Hepatocytes also display intra-lobular differences in cell size, but to what extent zonal expression and function correlate with cell size in isolated human hepatocytes is not entirely clear. Here, we first used our accumulated experience of nearly 100 hepatocyte isolations to assess the impact of donor background and process parameters on hepatocyte quality. We observed substantial inter-batch variability in cell size distributions and a tendency for overall cell size to affect the outcome of hepatocyte isolation and cryopreservation. We further separated cells into different size fractions and analyzed them with label-free quantitative proteomics. This showed that protein abundances in different hepatocyte size fractions recapitulated the in vivo expression patterns of well-known zonal markers. We also found that proteins with sequential enrichment across fractions largely represented biological processes with known zonal specificity. This was confirmed by differences in the metabolic activity of zonated CYP enzymes. Altogether, our results show that hepatocyte size corresponds to zonal origin, and that our size fractionation approach can be used to study zone-specific liver functions in vitro.

2021-01-26 | PXD013142 | Pride

RNA helicase EIF4A1-mediated translation is essential for the GC response

Project description:EIF4A1 and cofactors EIF4B and EIF4H have been well characterised in cancers, including B cell malignancies, for their ability to promote the translation of oncogenes with structured 5’ untranslated regions. However, very little is known of their roles in non-malignant cells. Using mouse models to delete Eif4a1, Eif4b or Eif4h in B cells we show that EIF4A1, but not EIF4B or EIF4H, is essential for B cell development and the germinal centre response. Following B cell activation in vitro, EIF4A1 facilitates an increased rate of protein synthesis, MYC expression and expression of cell cycle regulators. However, EIF4A1-deficient cells remain viable whereas inhibition of EIF4A1 and EIF4A2 by Hippuristanol treatment induces cell death.

2023-11-09 | PXD046710 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data