Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Intact HepG2 CHKA target engagement with CETSA

ABSTRACT: To confirm UNC638 and UNC737 target engagement to CHKA in live cells.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hepatocyte

SUBMITTER: Tuomas Tolvanen

LAB HEAD: Daniel Martinez-Molina

PROVIDER: PXD057925 | Pride | 2025-01-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20220603_EXI281_TMT75.pdResult	Other
	20220603_EXI281_TMT75_.msf	Msf
	20220603_EXI281_TMT75_01.raw	Raw
	20220603_EXI281_TMT75_02.raw	Raw
	20220603_EXI281_TMT75_03.raw	Raw

Items per page:

1 - 5 of 35

Publications

Phenomics-Based Discovery of Novel Orthosteric Choline Kinase Inhibitors.

Bauer Ludwig G LG Ward Jennifer A JA Díaz-Sáez Laura L Sundström Yvonne Y Tolvanen Tuomas T Alarcón Barrera Juan Carlos JC Kostidis Sarantos S Rogers Catherine M CM Panagakou Ioanna I Singh Usha U Rothweiler Elisabeth M EM Gonzalez Orta Alejandro A Kaniskan H Ümit HÜ Hu Jianping J Jin Jian J Sievers Sonja S Waldmann Herbert H Giera Martin M Sundström Michael M Berg Louise L Huber Kilian V M KVM

Angewandte Chemie (International ed. in English) 20250113 7

Choline kinase alpha (CHKA) is a central mediator of cell metabolism linked to cancer and immune regulation. Cellular and clinical evaluation of CHKA has been hampered by challenges in the development of drug-like choline kinase inhibitors. Here, we identify CHKA as an unexpected off-target of histone methyltransferase inhibitors using an integrated phenomic approach. We confirm CHKA as a direct protein target of the aminoquinazolines UNC0638 and UNC0737 using a combination of chemoproteomic, bi ...[more]

PMID: 39740997

Similar Datasets

K562 lysate CHKA target engagement with CETSA

Project description:Studying the target enagement of UNC0638 and UNC737 in K562 cell lysate with CETSA.

2025-01-28 | PXD058045 | Pride

Control vs Elp3-deficient mouse myeloid progenitors 6-plex TMT LC-MSMS

Project description:6-plex TMT LC-MSMS quantification of proteins in myeloid progenitors (Lineage- Sca1- Kit+ cells) isolated from the bone marrow of 8-12 week old male and female control and Elp3-deficient (Elp3fl/fl vav-iCreT/+) mice. Biological triplicates of each genotype were analyzed, each consisting of 1.10e6 cells from pools of 12-14 control (Elp3fl/fl) or 26-38 (Elp3-deficient) male and female mice.

2021-01-26 | PXD010486 | Pride

Genome-wide mapping of immature erythrocyte transcribed chromosomal domains (F1-seq)

Project description:Transcriptional regulation is impacted by multiple layers of genome organization. Here, we identified and mapped out all the transcriptionally active chromosomal domains in the chicken immature erythrocyte genome, including the known Î²- and Î±-globin domains, by combining a powerful chromatin fractionation method with next generation DNA and RNA sequencing. To characterize transcriptionally active chromatin domains, we used two biological replicates. Each replicate set has one control SE fraction and one transcriptionally active chromatin fraction (F1)

2016-07-03 | E-GEOD-75849 | biostudies-arrayexpress

An oxygen-sensing network of RNA-binding proteins controls glycolysis via hypoxic translatome remodeling.

Project description:System-wide remodeling of protein synthesis is a keystone of cellular stress adaptation. Accumulating evidence suggests that changes in protein output (translatome) are controlled predominantly by translational mechanisms that restructure mRNA translation efficiencies (TEs), rather than simple fluctuations in mRNA expression. At the core of this phenomenon lies the key outstanding issue as to the drivers of such stimuli-induced translatome reprogramming, especially from an unbiased, systemic perspective. Oxygen deficiency (hypoxia) is frequently encountered in health and disease. In this study, we report the RNA-binding protein (RBP) nexus that governs oxygen-sensitive translatome reprogramming. Global MATRIX analysis produced an impartial, activity-based blueprint of dynamic RBP utilization, revealing hypoxia-augmented translational activities of HuR hnRNP A2/B1, PCBP1, PCBP2, and PTBP1. Translatome analysis by TMT-pSILAC of each aforementioned RBP revealed a synergistic network that effectuates oxygen-dependent translatome reorganization to enable hypoxic adaptation. Specifically, each RBP is tasked with activating a distinct portfolio of targets and cellular processes that synergistically contribute toward a comprehensive hypoxic response. Notably, the activation of glycolysis and hypoxic cell survival are critically dependent on this RBP network. The hypoxia-inducible factor 2α (HIF-2α) operates as the critical translation-regulating oxygen-sensor that collaborates with this RBP network to regulate mRNA TE and steady-state levels. These observations reveal an RBP/HIF-2α axis that restructures protein output in response to oxygen fluctuations. Conceptually, these findings demonstrate that stress-sensing RBP networks act as gatekeepers of mRNA utilization for global translational remodeling.

2020-07-02 | PXD011979 | Pride

Extracellular membrane vesicle-driven crosstalk between legume plants and rhizobia: the symbiosome space as protein trafficking interface

Project description:Prokaryotes and eukaryotes secrete extracellular membrane vesicles (MVs) into the extracellular milieu to preserve and transport elevated concentrations of a given cargo across long distances. MVs encapsulate metabolites, DNA, RNA, and proteins, whose abundance and composition fluctuate depending on environmental cues. Importantly, MVs are involved in eukaryote-to-prokaryote communication owing to their ability to navigate different ecological niches and exchange molecular cargoes between the two domains. Amongst the different bacterium-host relationships, rhizobium-legume symbiosis is one of the closest known to nature. A crucial developmental stage of symbiosis is the formation of N2-fixing root nodules, which are endocytosed rhizobia -called bacteroids- confined by the plant-derived membrane. The unrestricted interface between the two membranes is the symbiosome space. To date many molecular aspects of symbiosis have been extensively studied, but the possibility of interbacterial and interdomain molecule trafficking by MVs in the symbiosome space was not questioned yet. Here we unveil intensive MV trafficking within the symbiosome interface of several rhizobium-legume dual systems by developing a robust MV isolation procedure. We analyse the MVs-encased proteomes encountered in the symbiosome space of each bacterium-host partnership uncovering both conserved and differential traits of every symbiotic system. This study opens the gates for designing MV-based biotechnological tools suitable for sustainable agriculture.

2025-05-07 | PXD056185 | Pride

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation [HIT-Seq]

Project description:Histone modifications regulate chromatin-dependent processes, yet the mechanisms by which they contribute to specific outcomes remain unclear. H3K4me3 is a prominent histone mark that is associated with active genes and promotes transcription through interactions with effector proteins that include initiation factor TFIID. We demonstrate that H3K4me3-TAF3 interactions direct global TFIID recruitment to active genes, some of which are p53 targets. Further analyses show that (i) H3K4me3 enhances p53-dependent transcription by stimulating preinitiation complex (PIC) formation; (ii) H3K4me3, through TAF3 interactions, can act either independently or cooperatively with the TATA box to direct PIC formation and transcription; and (iii) H3K4me3-TAF3/TFIID interactions regulate gene-selective functions of p53 in response to genotoxic stress. Our findings indicate a mechanism by which H3K4me3 directs PIC assembly for the rapid induction of specific p53 target genes Examination of genome wide binding sites of TAF3 full length protein vs TAF3 PHD domain alone (Full vs PHD), with or without M880A mutation (WT vs mut) in mouse MEF cells using HITseq method (PNAS 2010, 107:3135-3140, PMID: 20133638)

2013-03-02 | E-GEOD-43540 | biostudies-arrayexpress

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-03-02 | E-GEOD-43542 | biostudies-arrayexpress

MonoMac6 (MM6) cells proteomics LC-MS/MS

Project description:MicroRNAs (miRs) are small non-coding RNAs, which control the expression of target genes by either translational repression or RNA degradation, known as canonical miR function. MiR-328 has a non-canonical function and can activate gene expression by antagonizing the activity of heterogeneous ribonuclear protein E2 (hnRNP E2). The global importance of such non-canonical miR function is not yet known. In order to achieve a better understanding of the non-canonical miR activity, a compartment specific tandem mass tag (TMT)-based proteomic analysis in differentiated MonoMac6 (MM6) cells was performed.

2019-11-27 | PXD013106 | Pride

Quantitative proteomic analysis of hypoxia induced primary kidney cells

Project description:Chronic kidney disease (CKD) is characterized by a slow and gradual loss of kidney function, with glomerular filtration loss over months or years, inevitably leading to end-stage renal disease. The renal failure resulting from this irreversible process derives from fibrotic lesions of each compartment of the kidney; glomerulosclerosis, vascular sclerosis, and tubulointerstitial fibrosis. Nevertheless, despite numerous research efforts, both the definitive mechanism underlying the progression from CKD to end stage renal disease and an effective treatment have remained elusive. In this study, We utilized TMT-multiplexed quantitative proteomics approaches to identify protein expression changes associated with chronic injury in primary cultured renal cells.

2021-01-19 | PXD019678 | Pride

Cotranslational signal independent SRP preloading during membrane targeting

Project description:Cotranslational targeting into the endoplasmic reticulum (ER) by the Signal Recognition Particle (SRP) is a key event determining polypeptide fate in eukaryotic cells. Here, we globally define the principles and mechanisms of SRP binding and ER targeting in vivo. Cotranslational targeting through SRP is the dominant route into the ER for all secretory proteins, regardless of targeting signal characteristics. Cytosolic SRP functions in a pioneer translation round that builds a membrane-resident mRNAs pool, explaining how low SRP levels suffice for the secretory load. SRP does not induce an elongation arrest; consequently, kinetic competition between targeting and translation elongation dictates which substrates are translocated post-translationally. Unexpectedly, SRP binds most secretory ribosomal complexes before targeting signals are synthesized. We show non-coding mRNA elements can promote signal-independent SRP pre-recruitment. Our study defines the complex kinetic interplay between elongation and determinants in the polypeptide and mRNA modulating SRP-substrate selection and membrane targeting in vivo. Ribosome profiling (RiboSeq) and RNA-seq of subcellular fractions of ribosomes. Soluble and membrane bound ribosomes are separated by centrifugation, and SRP-bound ribosomes are immunoprecipitated from the soluble fraction. Polysomes and monosomes are separated by sucrose gradient ultracentrifugation.

2016-08-03 | E-GEOD-74393 | 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