Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cell cycle dependent NEK2 interactome

ABSTRACT: TurboID proximity labeling was used to evaluate cell cycle dependent NEK2 interactome

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Diploid Cell

DISEASE(S): Osteosarcoma

SUBMITTER: Selahattin Can Ozcan

LAB HEAD: Ceyda Acilan

PROVIDER: PXD068515 | Pride | 2026-01-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	KUTTAM_20211228_OMICS-2111_2021-53-TurboID-S_1.raw	Raw
	KUTTAM_20211228_OMICS-2111_2021-53-TurboID-S_2-1.raw	Raw
	KUTTAM_20211228_OMICS-2111_2021-53-TurboID-S_3-1.raw	Raw
	KUTTAM_20211228_OMICS-2111_2021-54-TurboID-G1_1.raw	Raw
	KUTTAM_20211228_OMICS-2111_2021-54-TurboID-G1_2-1.raw	Raw

Items per page:

1 - 5 of 58

Similar Datasets

PABPN1-protein Interactome

Project description:Identification of PABPN1 interacting proteins by proximity labeling with TurboID coupled with mass spectrometry.

2023-08-04 | PXD039864 | Pride

The analysis of human RAF1 proxisome

Project description:RAF1 is a crucial element of the MAPK/ERK signaling pathway. TurboID, an efficient promiscuous biotin ligase, enables the biotinylation of proteins in the vicinity, thus facilitating the study of complex cellular processes. In this study, we utilized TurboID fused to RAF1WT, RAF1K375M (kinase inactive) and RAF1CAT(catalytic domain, constitutively active) to investigate the intricate interaction network of RAF1 under various conditions.

2025-04-08 | PXD053389 | Pride

The deubiquitinase OTUD1 regulates immunoglobulin production and proteasome inhibitor sensitivity in multiple myeloma

Project description:Serum monoclonal immunoglobulin (Ig) is the main diagnostic factor for patients with multiple myeloma (MM), however its prognostic potential remains unclear. On a large MM patient cohort (n=4146), we observe no correlation between serum Ig levels and patient survival, while amount of intracellular Ig has a strong predictive effect. Focused CRISPR screen, transcriptional and proteomic analysis identify deubiquitinase OTUD1 as a critical mediator of Ig synthesis, proteasome inhibitor sensitivity and tumour burden in MM. Mechanistically, OTUD1 deubiquitinates peroxiredoxin 4 (PRDX4), protecting it from endoplasmic reticulum (ER)-associated degradation. In turn, PRDX4 facilitates the synthesis of Ig which coincides with the accumulation of unfolded proteins and higher ER stress. The elevated load on proteasome ultimately potentiates myeloma response to proteasome inhibitors providing a window for a rational therapy. Collectively, our findings support the significance of the Ig production machinery as a yet unappreciated biomarker and target in the combinatory treatment of MM patients.

2023-03-11 | PXD037309 | Pride

Application of TurboID-mediated proximity labeling and phosphoproteomics for mapping a GSK3 kinase signaling network in Arabidopsis

Project description:Transient protein-protein interactions (PPIs), such as those between posttranslational modifying enzymes and their substrates, play key roles in cellular regulation, but are difficult to identify. Here we demonstrate the application of enzyme-catalyzed proximity labeling (PL), using the engineered promiscuous biotin ligase TurboID, as a sensitive method for characterizing PPIs in signaling networks. We show that TurboID fused with the GSK3-like kinase BIN2 or a PP2A phosphatase biotinylate their known substrate, the BZR1 transcription factor, with high specifically and efficiency. We optimized the protocol of biotin labeling and affinity purification in transgenic Arabidopsis expressing a BIN2-TurboID fusion protein. Subsequent quantitative mass spectrometry (MS) analysis identified about three hundred proteins biotinylated by BIN2-TurboID more efficiently than the YFP-TurboID control. These include a significant subset of previously proven BIN2 interactors and a large number of new BIN2 interactors that uncover a broad BIN2 signaling network. Our study illustrates that PL-MS using TurboID is a powerful tool for mapping signaling networks in plants, and reveals broad roles of this GSK3-like kinase in cellular signaling and regulation.

2023-05-10 | PXD017085 | Pride

Identification of the Drosophila centriolar satellite proximity interactome by direct and indirect biotin proximity labeling

Project description:In this set of experiments we identified the main scaffolding component of centriolar satellites, PCM1 or Cmb in Drosophila as a proximity interactor of the centriolar structural protein Sas4 by BioID in S2 cells and subsequently explored the Cmb proximity interactome by direct TurboID in S2 cells and indirect, GFP nanobody-targeted, TurboID in Drosophila testes.

2025-03-31 | PXD049372 | Pride

Identifying interactors of IRF1 and STAT1 during type I and type II interferon treatment using proximity-dependent labeling

Project description:Identifying interactors of IRF1 and STAT1 in bone marrow-derived macrophages during type I and type II interferon treatment using the proximity-dependent labeling approach TurboID followed by Mass Spectrometry

2024-03-12 | PXD040337 | Pride

LZTR1 is a Melanoma Oncogene that Promotes Cell Growth and Inhibits Apoptosis Under Stress

Project description:LZTR1 is known to act as a tumor suppressor in glioma, acting as an adaptor protein for Cullin 3 (CUL3) ubiquitin ligase. However, we demonstrated that LZTR1 is amplified in acral melanomas, and is required for melanoma cell proliferation and anchorage-independent growth. To understand the molecular mechanisms by which LZTR1 amplification promotes melanomas, we carried out proximity biotinylation by TurboID and co-immunoprecipitation assays. We identified LZTR1 proximal proteins associated not only with ubiquitination and autophagy, but also with de-ubiquitination, focal adhesion, stress response, and actin cytoskeleton. LZTR1 is not “just” an adaptor protein for Cullin 3 (CUL3) ubiquitin ligase complex but is a hub for additional molecular functions such as de-ubiquitination and actin organization that confer context-dependent tumor promoting activity. Downregulation of LZTR1 is therefore a novel cell death mechanism that can be targeted for melanoma therapy.

2025-10-13 | PXD054157 | Pride

Promixity labling and Affinity purification of TRIAD3A interactome

Project description:To identify cargo content involved in TRIAD3A-mediated selective autophagy, we expressed TRIAD3A fused to an engineered biotin ligase (TurboID) by viral transduction in mouse brain excitatory neurons (AAV-CAMKII-TRIAD3A-V5-TurboID). After treatment with biotin substrate, brain was harvested and biotinylated proteins were identified by liquid chromatography-tandem mass spectrometry

2024-06-14 | PXD053114 | Pride

Development of a proximity labeling vector to identify protein-protein interactions in human stem cells

Project description:Development a novel system employing TurboID-fusion proteins within an integrative and inducible expression vector to investigate the interactome during stem cell differentiation. Cells expressing U2AF2 (iU2) or GFP (iGFP) fused with TurboID in undifferentiated (D0) or mesoderm differentiated (D1) were analyzed to identified the interactome and detect changes under differentiation process.

2025-01-07 | PXD056299 | Pride

An improved TurboID-based proximity labeling pipeline in C. elegans by biochemical depletion of endogenously biotinylated carboxylases

Project description:To review an improved proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes, the interactome of a presynaptic active zone protein, ELKS-1, was analyzed as proof of principle. A significant constraint on the sensitivity of TurboID-based proximity labeling is the presence of abundant, endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a co-factor. We developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry, by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography (IMAC).

2022-09-12 | PXD034639 | 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