Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

BioID proximity labelling of MAP4K4 interactors in DAOY medulloblastoma cells

ABSTRACT: Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) is Ser/Thr protein kinase highly expressed in medulloblastoma (MB) patient samples which promotes cell migration and invasiveness downstream of growth factor receptors. Although MAP4K4 implication in the control of the membrane protrusions at the leading edge of cells during migration and invasion in MB is established, its downstream effectors governing and mediating this process in MB have not been identified. In this study we explored the proteomic neighborhood of MAP4K4 in MB cells and to identify candidate potentially affecting its activity and pro-migratory functions. Towards this aim, we expressed BioID fused versions of MAP4K4 (N- and C-terminal) in DAOY cells under presence of biotin. In the control setup, we expressed the BioID enzyme alone. After Streptavidin purification of biotinylated proteins, we performed mass spectrometry and quantified relative abundances compared to control conditions.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Immortal Human Cell Line Cell

DISEASE(S): Medulloblastoma

SUBMITTER: Martin Baumgartner

LAB HEAD: Martin Baumgartner

PROVIDER: PXD031870 | Pride | 2022-08-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20190523_12139_DAOY_BioID_CTRL_1.raw	Raw
	20190523_12139_DAOY_BioID_CTRL_1_FTHCD__F276632_.mgf	Mgf
	20190523_12139_DAOY_BioID_CTRL_1_FTHCD__F276632_.mzid.gz	Mzid
	20190523_12139_DAOY_BioID_CTRL_2.raw	Raw
	20190523_12139_DAOY_BioID_CTRL_2_FTHCD__F276628_.mgf	Mgf

Items per page:

1 - 5 of 29

Similar Datasets

BioID proximity labelling of MAP4K4 interactors in HEK-293T cells

Project description:Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) is Ser/Thr protein kinase highly expressed in medulloblastoma (MB) patient samples which promotes cell migration and invasiveness downstream of growth factor receptors. Although MAP4K4 implication in the control of the membrane protrusions at the leading edge of cells during migration and invasion in MB is established, its downstream effectors governing and mediating this process in MB have not been identified. In this study we explored the proteomic neighborhood of MAP4K4 in MB cells and to identify candidate potentially affecting its activity and pro-migratory functions. Towards this aim, we expressed BioID fused versions of MAP4K4(N- and C-terminal) in HEK-293T cells under presence of biotin. In the control setup, we expressed the BioID enzyme alone. After Streptavidin purification of biotinylated proteins, we performed mass spectrometry and quantified relative abundances compared to control conditions.

2022-08-04 | PXD031863 | Pride

Identifying global and mtCU independent MICU1 interactome utilizing BioID2 based proximity labeling and screening

Project description:MICU1 is a Ca2+-binding protein that regulates the mitochondrial Ca2+ uniporter channel (mtCU ) and mitochondrial Ca2+ (mCa2+) uptake. MICU1 knockout mice display perinatal lethality and disorganized mitochondrial architecture. These phenotypes are distinct from other mtCU loss-of-function models and thus are not explained by changes in mCa2+ content. Utilizing multiple proteomic approaches, we found that MICU1 localized to mitochondrial complexes lacking MCU, suggesting that MICU1 has cellular functions independent of mCa2+ uptake. The overall aim of the current project is to identify the global and mtCU independent MICU1 interactome to characterize the MCU independent functions of the MICU1.

2024-01-26 | PXD028462 | Pride

Bone morphogenetic protein-7 is a MYC target with pro-survival functions in childhood medulloblastoma

Project description:Medulloblastoma (MB) is the most common malignant brain tumor in children, among whom overexpression or amplification of MYC oncogenes has been associated with poor clinical outcome. Although the MYC functions during normal development and oncogenesis in various systems have been extensively investigated, the transcriptional targets mediating MYC effects in MB are still elusive. Their identification and roles during MB onset and progression are important and will ultimately suggest novel potential therapeutic targets. cDNA microarray analysis was used to compare the effects of overexpressing and silencing MYC on the transcriptome of a MB-derived cell line. We identified 209 genes with potential relevance to MYC-dependent cellular responses in MB. Among the MYC-responsive genes, we found members of the bone morphogenetic protein (BMP) signaling pathway, which plays a crucial role during the development of the cerebellum. In particular, the cytokine gene BMP7 was identified as a direct target of MYC in MB cells. Similar to the effect induced by BMP7 silencing by siRNA, the use of a small-molecule inhibitor of the BMP/SMAD signaling pathway reduced cell viability in a panel of MB cells. Altogether, our findings indicate that high MYC levels drive BMP7 expression in MB to induce pro-survival and pro-proliferative cellular pathways. This observation suggests that targeting the BMP/SMAD pathway may be a new therapeutic concept for the treatment of childhood MB. 6 samples (3 replicates for each sample): wild-type MB cell line, empty vector-transfected control cell line, 2 c-MYC-overexpressing clones, 1 clone upon c-MYC silencing, 1 silencing control cell line.

2011-05-16 | E-GEOD-22139 | biostudies-arrayexpress

Comprehensive analysis of the host-virus interactome of SARS-CoV-2

Project description:Host-virus protein-protein interaction is the key component of SARS-CoV-2 life cycle, which can be targeted for therapeutic intervention. Thus, we conducted a comprehensive interactome study between the virus and host cell using tandem affinity purification (TAP) and BioID2 labeling strategies. In addition, we compared the interactomes of two key SARS-CoV-2 encoded viral proteins, NSP1 and N protein, to the interactomes of their counterparts in other human coronaviruses.

2021-06-29 | PXD023209 | Pride

BioID samples ARS2/ARS2c1/ARS2c2

Project description:BioID data. LC-MS/MS. Hek293T cell line. Biotinylation

2022-04-04 | PXD026453 | Pride

Nitric oxide synthase interactome

Project description:Identify the proteins interacting with human nitric oxide synthases

2023-06-01 | PXD040726 | Pride

Transcriptional response to stress in serum deprived mouse fibroblasts in the presence of MSK1/2 inhibitor.

Project description:We have employed gene expression profiling in order to identify targets of transcriptional response to stress in resting mouse Swiss 3T3 fibroblasts, either untreated (control) or treated with anisomycin for 3 or 6 hours to induce the p38/MAP kinase pathway.Â In order determine transcriptional effects dependent on MSK1/2 kinase activity, H89 inhibitor was used in the study. Serum starved (72 h 0.2% FCS) mouse 3T3 cells were treated with anisomycin (188.5 nM) for 3 h or 6h (in duplicates) either with or without 15-min pre-treatment with MSK1/2 inhibitor H89 (10 uM). Untreated, serum-starved cells were used as a control. RNA was collected and gene expression profiling using strand-specific RNA-seq was performed.

2014-08-12 | E-GEOD-58746 | biostudies-arrayexpress

The hGID GID4 E3 ubiquitin ligase complex targets ARHGAP11A to regulate cell migration

Project description:The human GID (hGID) complex is a key E3 ligase regulating multiple cellular processes, including cell cycle progression and metabolic activity. However, the biological functions controlled by hGID remain poorly investigated. Here, we show that the hGID substrate receptor GID4 regulates cell migration and growth. Biochemical and cellular assays combined with proximity-dependent biotinylation (BioID2) uncovered that GID4 targets ARHGAP11A for degradation. Knockdown of GID4 or inhibition of the GID4 substrate binding pocket impairs motility and directed cell movement, whereas abrogation of ARHGAP11A significantly rescues this cell migration defect. GID4 inhibits cell migration by degrading ARHGAP11A thereby preventing its accumulation at the cell periphery where it turns off RhoA activity. Moreover, our BioID2-GID4 screens revealed a variety of substrate profiles beyond Pro/N-degron motifs with functions in microtubule binding, cytoskeletal dynamics and other biological processes. Overall, we identified cellular functions and a wide range of physiological hGID degradation substrates, which paves the way for deciphering molecular pathways regulated by hGID E3 ligase activity through its GID4 substrate receptor.

2024-09-24 | PXD054003 | Pride

A Conserved Nuclear Membrane Protein As an Essential Component of Plant Nuclear Lamina Is Required for Proper Genome Organization and Activity

Project description:Plant conserved nuclear membrane protein PNET2 was identified to associate with nucleoskeleton protein CRWN and KAKU4, nucleosome histone H2. As an essential component of nuclear lamina, PNET2 is required for global transcriptional reprogramming and chromasomal packing, thus to control plant survival.

2023-03-11 | PXD026924 | Pride

The OTUD6B-LIN28B-MYC axis determines cell cycle progression in multiple myeloma

Project description:Deubiquitylases (DUBs) remove ubiquitin from proteins. In the context of cancer, their inhibition can induce the degradation of oncoproteins, that may otherwise be “undruggable”. Multiple myeloma (MM) is the second most common hematological malignancy with poor outcome and high sensitivity towards ubiquitin-proteasome-system (UPS) inhibitory therapies. However, the role of DUBs in MM pathophysiology and therapy has remained elusive. Starting from genetic screening for DUB dependencies in MM, we here identify OTUD6B as a central vulnerability in MM that drives the G1/S cell cycle transition by means of deubiquitylating and stabilizing LIN28B subsequent to LIN28B phosphorylation. LIN28B regulates miRNA biogenesis and exerts high expression in embryonic stem cells that becomes re-established in certain tumors, including MM. Binding of LIN28B at G1/S activates OTUD6B, which otherwise remains in a catalytically inactive state. As a consequence, stabilized LIN28B drives MYC expression via inhibition of let7 microRNAs, which in turn allows for a rapid transition of MM cells from G1 to S phase. Analyses of primary MM patient samples reveal a positive correlation of OTUDB6B expression with poor outcome, high MYC expression and MYC target gene induction, suggesting that high MYC levels in MM result from an activation of the OTUD6B-LIN28B nexus. Together, we here specify phosphorylation and cell cycle-dependent substrate binding as a means by which OTUD6B becomes activated to drive the G1/S transition via the LIN28B-MYC axis and nominate OTUD6B and LIN28B as actionable vulnerabilities in MM.

2022-10-12 | PXD027480 | 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