Browse
Submit Data
Databases
API
Help

Dataset Information

326 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Global quantitative proteomes of PrP-deficient mouse models

ABSTRACT: A popular method for studying the function of a given protein is to generate and characterize a suitable model deficient for its expression. Most researchers select mouse models for this purpose and investigate proteins of interest in the tissue they are most associated with. For the prion protein (PrP), best known for its role in several invariably fatal neurodegenerative diseases of humans and animals, a natural choice, therefore, would be to undertake such studies with mouse brain samples. We recently documented the surprising observation that PrP deficiency caused a loss or enhancement of NCAM1 polysialylation, dependent on the cell model used. To identify possible causes for this disparity, we set out to systematically investigate the consequence of PrP deficiency on the global proteome in brain tissue and in four distinct cell models. Here we report that PrP deficiency has no discernible impact on the global brain proteome but causes robust but surprisingly divergent changes to the global proteomes of cell models. Our data suggest that careful investigations in cell models, rather than mouse tissue, are the way forward for elucidating the molecular function of PrP.

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Ectodermal Cell, Brain, Skeletal Muscle Myoblast, Cell Culture, Mammary Gland Epithelial Cell, Neuroblast

DISEASE(S): Prion Disease,Alzheimer's Disease

SUBMITTER: Gerold Schmitt-Ulms

LAB HEAD: Gerold Schmitt-Ulms

PROVIDER: PXD003398 | Pride | 2016-06-01

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

mouse brain prion protein interactome

Project description:In vertebrates, the prion protein (PrP, gene name Prnp) is expressed in diverse cell types and tissues, especially in the brain. In the adult brain, PrP contributes to homeostasis. Here, proteins expressed in the adult mouse brain which coimmunoprecipitated with PrP via the Fab antibody D18 were identified by comparison to PrP-specific immunoprecipitates from Prnp knockout brain.

2021-11-02 | PXD024870 | Pride

CRISPR-Cas9-based knockout of the prion protein and its effect on the proteome

Project description:The molecular function of the cellular prion protein (PrPC) and the mechanism by which it may contribute to neurotoxicity in prion diseases and Alzheimer’s disease (AD) are only partially understood. Mouse neuroblastoma Neuro2a cells and, more recently, C2C12 myocytes and myotubes have emerged as popular models for investigating the cellular biology of PrP. Mouse epithelial NMuMG cells might become attractive models for studying the possible involvement of PrP in a morphogenetic program underlying epithelial-to-mesenchymal transitions. Here we describe the generation of PrP knockout clones from these cell lines using CRISPR-Cas9 knockout technology. More specifically, knockout clones were generated with two separate gRNAs targeting recognition sites on opposite strands within the first hundred nucleotides of the Prnp coding sequence. Several PrP knockout clones were isolated and genomic insertions and deletions near the CRISPR-target sites were characterized. Subsequently, deep quantitative global proteome analyses that recorded the relative abundance of > 3000 proteins were undertaken to begin to characterize the molecular consequences of PrP deficiency. The levels of ~120 proteins were shown to reproducibly correlate with the presence or absence of PrP, with most of these proteins as belonging to extracellular components, cell junctions or the cytoskeleton.

2014-11-19 | PXD001301 | Pride

The prion protein interactome in four mouse cell lines of distinct lineages

Project description:At times, it can be difficult to discern if a lack of overlap in reported interactions for a protein-of-interest reflects differences in methodology or biology. A case in point is the prion protein (PrP) which is best known for its central role in prion disorders. Despite having over two dozen interactors reported, there is little consensus regarding their importance for understanding the biology of PrP. In such instances, systematic analyses of protein-protein networks across diverse paradigms can provide valuable insights. Here, we interrogated the PrP interactome in four distinct mouse cell lines. Analyses made use of identical affinity capture reagents and sample processing workflows. To enable the discrimination of specific from non-specific binders, negative controls were generated from PrP knockout lines of the respective cell models, and the relative levels of peptides were quantified with the help of isobaric labels. The study uncovered 26 proteins, which reside in proximity to PrP. All of these proteins are predicted to have access to the outer face of the plasma membrane, and approximately half of them were not reported to interact with PrP before. Strikingly, although several proteins exhibited profound co-enrichment with PrP in a given model, except for Ncam1, no protein was highly enriched in all four PrP-specific interactome datasets.

2018-05-24 | PXD008781 | Pride

The Prion Protein (PrP) is involved in translation via RNA granule-like mRNPs, a connection which is impaired during neurodegenerative diseases

Project description:Cytoplasmic RNA granules have emerged as important elements of posttranscriptional and translational regulation. Stress, germinal and neuronal granules contain RNA-binding proteins capable of self-assembly due to prion-like domains. Hyperassembly mediated by these prion-like domains causes several neurodegenerative diseases. Here, we report a subset of the mammalian prion protein (PrP), also prone to self-assembly, propagation and to cause devastating diseases, is a component of naturally occurring messenger ribonucleoproteins (mRNPs) in adult mouse brains. Biomolecules co-purified with PrP revealed a multitude of diverse RNA granule associated proteins and mRNAs encoding members of the translation machinery, indicating a role in a specialized translation process. Importantly, PrP mutations linked to Creutzfeldt-Jakob disease (CJD) or fatal familial insomnia (FFI) severely impaired recovery of mRNPs from preclinical mice, possibly representing a very early pathological process. Thus, mutant PrP may cause dysfunction in RNA regulation, thereby joining the constantly expanding ranks of disease associated RNP granule proteins. The file Enrichment_analysis.xlsx contains mRNAs (FDR < 0.01) co-purified with PrP in both WT sample pools as identified by DESeq2 and the respective gene counts and log2 fold changes for CJD and FFI PrP:IP sample pools. RIP-Seq analysis of mRNAs co-purified with PrP from murine brain cytoplasmic fractions in wild-type (WT), CJD and FFI mice. Each RIP-Seq and control (input) library represents a pool of 12 to 16 co-immunoprecipitation samples out of 3 to 4 mice. To control for post-homogenization artifacts, we conducted an experiment in which we prepared homogenates from WT and PrP-KO (Prnp-/-) mice of different genetic backgrounds (C57BL/6 and 129S4) and identified SNPs in RIP-Seq and control libraries to finally identify specifically co-purified mRNAs.

2015-11-01 | E-GEOD-57233 | biostudies-arrayexpress

Somatostatin-interacting human brain proteins

Project description:Somatostatin (SST) is a cyclic peptide that is understood to inhibit the release of hormones and neurotransmitters from a variety of cells by binding to one of five canonical G protein-coupled SST receptors (SSTR1 to SSTR5). Recently, SST was observed to also interact with the amyloid beta (Aβ) peptide and affect its aggregation kinetics, raising the question which other brain proteins it can bind to. Here we report on an SST interactome analysis that made use of human brain extracts as biological source material and incorporated advanced mass spectrometry workflows for the relative quantitation of binders.

2019-04-04 | PXD010885 | Pride

Histone deacetylation-dependent and -independent transcriptional dysregulation in early-onset polyglutamine disease

Project description:Transcriptional dysregulation is an important early feature of polyglutamine diseases. One of its proposed causes is defective neuronal histone acetylation, but important aspects of this hypothesis, such as the precise genomic topography of acetylation deficits and the relationship between transcriptional and acetylation alterations at the whole-genome level, remain unknown. The new techniques for the mapping of histone posttranslational modifications at genomic scale enable such global analyses and are challenging important assumptions concerning the role of specific histone modifications in gene expression. We examined here the genome-wide correlation of histone acetylation and gene expression defects in a mouse model of early-onset Huntington’s disease. Our analyses identified hundreds of loci that were hypoacetylated for H3K9,14 and H4K12 in the chromatin of these mice. Surprisingly, few genes with altered transcript levels in mutant mice showed significant changes in these acetylation marks and vice versa. Our screen, however, identified a subset of genes in which H3K9,14 deacetylation and transcriptional dysregulation concur. Genes in this group were consistently affected in different brain areas, mouse models and tissue from patients, which suggests a role in the etiology of this pathology. Overall, the combination of histone acetylation and gene expression screenings demonstrates that histone deacetylation and transcriptional dysregulation are two early, largely independent, manifestations of polyglutamine disease and suggests that additional epigenetic marks or mechanisms are required for explaining the full range of transcriptional alterations associated with this disorder. Examination of 2 different histone modifications in the hippocampus of wild-type and HD mice (PrP-htt-N171-82Q (Schilling et al., 1999)). Samples were obtained from 10 week old mice.

2013-06-20 | E-GEOD-44854 | biostudies-arrayexpress

SIRT1 deficiency in microglia contributes to cognitive decline in aging and neurodegeneration via epigenetic regulation of IL-1beta

Project description:Aging is the predominant risk factor for neurodegenerative diseases. One key phenotype as brain ages is the aberrant innate immune response characterized by proinflammation. However, the molecular mechanisms underlying aging-associated proinflammation are poorly defined. Whether chronic inflammation plays a causal role in cognitive decline in aging and neurodegeneration has not been established. Here we established a mechanistic link between chronic inflammation and aging microglia, and demonstrated a causal role of aging microglia in neurodegenerative cognitive deficits. Expression of microglial SIRT1 reduces with the aging of microglia. Genetic reduction of microglial SIRT1 elevates IL-1Î² selectively, and exacerbates cognitive deficits in aging and in transgenic mouse models of frontotemporal dementia (FTD). Interestingly, the selective activation of IL-1Î² transcription by SIRT1 deficiency is likely mediated through hypomethylating the proximal promoter of IL-1Î². Consistent with our findings in mice, selective hypomethylation of IL-1Î² at two CpG sites are found in normal aging humans and demented patients with tauopathy. Our findings reveal a novel epigenetic mechanism in aging microglia that contributes to cognitive deficits in neurodegenerative diseases. Study of changes related to alterations of SIRT1 levels in microglia of young and aged animals and in models of neurodegenerative dementia

2014-10-01 | E-GEOD-56452 | biostudies-arrayexpress

Comparative interactome analyses of wild-type and P301L MAPT in two human neuronal cell lines

Project description:Protein interactions of the tau protein are of interest in efforts to decipher the mechanisms of cell death in Alzheimer Disease (AD), a subset of frontotemporal dementias (FTD) and other tauopathies. We recently reported on extensive interactions of tau with the ribonucleoproteome and chaperones. A confounder of this prior work was that it probed steady-state interactions of plasmid-encoded four-repeat (4R) tau in dividing cells. Since then, we genome-edited a genomic safe harbor locus in two human neuronal cell lines, namely IMR-32 and ReNcell VM, creating inducible EGFP tagged wild-type and P301L tau models. We expressed balanced levels of 3R- and 4R-tau and interrogated tau protein interactions at specific times following its induction. In addition to its association with the ribonucleoproteome, tau was observed to interact in these models with proteins that escaped prior investigations.

2019-11-13 | PXD010040 | Pride

Interactomes of neural cell adhesion molecule 1 and the metal ion transporter ZIP6 in mouse NMuMG epithelial cells with transforming growth factor beta 1-induced fibroblastoid morphology

Project description:The prion protein (PrP) evolved from the subbranch of ZIP metal ion transporters comprising ZIPs 5, 6 and 10, raising the prospect that the study of these ZIPs may reveal insights relevant for understanding PrP function. PrP and ZIP6 are required for the execution of a cellular program known as epithelial-to-mesenchymal transition (EMT). Polysialylation of neural cell adhesion molecule 1 (NCAM1) during EMT is also controlled by PrP. Here we report the ZIP6 interactome and ZIP6-dependent NCAM1 interactome in a mouse cell EMT model.

2017-02-13 | PXD004685 | Pride

The effects of aging vs. alpha7 nAChR subunit deficiency on the mouse brain transcriptome

Project description:Aging is accompanied by expression changes in multiple genes and the brain is one of the tissues most vulnerable to aging. Since the alpha7 nicotinic acetylcholine receptor (nAChR) subunit has been associated with neurodevelopmental disorders and cognitive decline during aging, we hypothesized that its absence might affect gene expression profiles in aged brains. To study whether transcriptional changes occur due to aging, alpha7 deficiency or both, we analyzed whole brain transcriptomes of young (8 week) and aged (2 year) alpha7 deficient and wild-type control mice, using Mouse Genome 430 2.0 microarray. Highly significant expression changes were detected in 47 and 1543 genes (after Bonferroni and FDR correction) in the brains of aged mice compared to young mice, regardless of their genotype. These included genes involved in immune system function and ribosome structure, as well as genes that were previously demonstrated as differentially expressed in aging human brains. Genotype-dependent changes were detected in only 3 genes, Chrna7 which encodes the alpha7 nAChR subunit, and two closely linked genes, likely due to a mouse background effect. Expression changes dependent on age-genotype interaction were detected in 207 genes (with a low significance threshold). Age-dependent differential expression levels were approved in all nine genes that were chosen for validation by real-time RT-PCR. Our results suggest that the robust effect of aging on brain transcription clearly overcomes the almost negligible effect of alpha7 nAChR subunit deletion, and that germline deficiency of this subunit has a minor effect on brain expression profile in aged mice. Total of 20 samples. 10 from young adult mice (8 weeks) and 10 from aged mice (2 years). In each age group, 5 were wild-type control mice and 5 alpha7 nAChR subunit defecient mice

2011-01-01 | E-GEOD-20411 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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