Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Disease Free

SUBMITTER: Declan Williams

LAB HEAD: Gerold Schmitt-Ulms

PROVIDER: PXD004685 | Pride | 2017-02-13

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	NMuMGTGFb_wt_versus_ZIP6-ko_ZIP6_interactome_TMT_6_7_8_9_0_1_C18_1.raw	Raw
	NMuMGTGFb_wt_versus_ZIP6-ko_ZIP6_interactome_TMT_6_7_8_9_0_1_C18_2.raw	Raw
	NMuMGTGFb_wt_versus_ZIP6-ko_ZIP6_interactome_TMT_6_7_8_9_0_1_C18_3.raw	Raw
	NMuMGTGFb_wt_versus_ZIP6-ko_ZIP6_interactome_TMT_6_7_8_9_0_1_C18_4.raw	Raw
	NMuMGTGFb_wt_versus_ZIP6-ko_ZIP6_interactome_TMT_6_7_8_9_0_1_C18_5.raw	Raw

Items per page:

1 - 5 of 16

Similar Datasets

Global quantitative proteomes of PrP-deficient mouse models

Project description: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.

2016-06-01 | PXD003398 | 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

RNA-seq from animals treated with RNAi against prp-8, prp-6, and prp-31

Project description:Transcriptome analysis of a population of control animals and RNAi-treated to partially inactivate genes that are homologs to human genes causing Retinitis Pigmentosa. RNA-seq analyses were performed at L3 larval stage in wild type, and smg-1(r861) mutants that have a defective Non-mediated decay pathway. RNA-seq experiments were also performed in adults glp-4(bn2) mutants that lack of germline. synchronized N2 and smg-1(r861) L1 larvae fed for 24 hours at 20 Â°C with the RNAi clones of prp-6, prp-8, prp-31 and gfp; and 5-day adult glp-4(bn2) worms grown at 25 Â°C and fed first, for 72 hours with OP50 and next, for 48 more hours with the RNAi clones of prp-8, prp-31 and gfp

2016-07-03 | E-GEOD-72952 | biostudies-arrayexpress

The prion protein contributes to epithelial-to-mesenchymal transition in the mouse NMuMG epithelial cell model

Project description:The physiological function of the prion protein (PrP) has remained elusive despite its widely recognized role in neurodegenerative diseases and sustained efforts to understand its molecular biology. On the basis of its evolutionary relationship to ZIP zinc transporters, protein-protein interactions it engages in, and the characteristics of a gastrulation arrest phenotype in a PrP-deficient model, we considered that PrP may contribute to the morphogenetic reprogramming of cells underlying epithelial-to-mesenchymal (EMT) transitions. We have conducted three global proteomics analyses to (1) identify proteins whose levels are changed during EMT in wild-type NMuMG cells; and determine proteins whose levels are affected by (2) stable knockdown or (3) transient knockdown of the prion protein relative to levels observed in wild-type NMuMG cells. We observed a highly significant correlation between proteins, which are changed during EMT or following PrP knockdown.

2015-07-10 | PXD001875 | 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 (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

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

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

Dissecting stages of human kidney development and Tumorigenesis with surface markers affords simple prospective Purification of nephron stem cells

Project description:When assembling a nephron during development a multipotent stem cell pool becomes restricted as differentiation ensues. A faulty differentiation arrest in this process leads to transformation and initiation of a Wilms' tumor. Mapping these transitions with respective surface markers affords accessibility to specific cell subpopulations. NCAM1 and CD133 have been previously suggested to mark human renal progenitor populations. Herein, using cell sorting, RNA sequencing, in vitro studies with serum-free media and in vivo xenotransplantation we demonstrate a sequential map that links human kidney development and tumorigenesis; In nephrogenesis, NCAM1+CD133- marks SIX2+ multipotent renal stem cells transiting to NCAM1+CD133+ differentiating segment-specific SIX2- epithelial progenitors and NCAM1-CD133+ differentiated nephron cells. In tumorigenesis, NCAM1+CD133- marks SIX2+ blastema that includes the ALDH1+ WT cancer stem/initiating cells, while NCAM1+CD133+ and NCAM1-CD133+ specifying early and late epithelial differentiation, are severely restricted in tumor initiation capacity and tumor self-renewal. Thus, negative selection for CD133 is required for defining NCAM1+ nephron stem cells in normal and malignant nephrogenesis. Human fetal kidney mRNA profiles of 3 cell populations (NCAM1+/CD133-, NCAM+/CD133+, NCAM-/CD133+) were generated by deep sequencing using Illumina HiSeq.

2016-04-01 | E-GEOD-78502 | biostudies-arrayexpress

Zeb1 and Snail1 engage miR-200f transcriptional and epigenetic regulation during EMT

Project description:Cell plasticity is emerging as a key regulator of tumor progression and metastasis. During carcinoma dissemination epithelial cells undergo epithelial to mesenchymal transition (EMT) processes characterized by the acquisition of migratory/invasive properties, while the reverse, mesenchymal to epithelial transition (MET) process, is also essential for metastasis outgrowth. Different transcription factors, called EMT-TFs, including Snail, bHLH and Zeb families are drivers of the EMT branch of epithelial plasticity, and can be post-transcriptionally downregulated by several miRNAs, as the miR-200 family. The specific or redundant role of different EMT-TFs and their functional interrelations are not fully understood. To study the interplay between different EMT-TFs, comprehensive gain and loss-of-function studies of Snail1, Snail2 and/or Zeb1 factors were performed in the prototypical MDCK cell model system. We here describe that Snail1 and Zeb1 are mutually required for EMT induction while continuous Snail1 and Snail2 expression, but not Zeb1, is needed for maintenance of the mesenchymal phenotype in MDCK cells. In this model system, EMT is coordinated by Snail1 and Zeb1 through transcriptional and epigenetic downregulation of the miR-200 family. Interestingly, Snail1 is involved in epigenetic CpG DNA methylation of the miR-200 loci, essential to maintain the mesenchymal phenotype. The present results thus define a novel functional interplay between Snail and Zeb EMT-TFs in miR200f regulation providing a molecular link to their previous involvement in the generation of EMT process in vivo. Expression analysis of MDCK over-expression EMT-TF Analysis of 7 overexpression MDCK cells each of them using biological rpelicates (MDCK-E47, Snail2, Snail1, Twist1, Tiwst2, Zeb1, Zeb2)

2014-09-09 | E-GEOD-61217 | biostudies-arrayexpress

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