Human Milk Oligosaccharide Interactions in Mouse Macrophage
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos, Orbitrap Fusion
ORGANISM(S): Mus Musculus (mouse)
TISSUE(S): Embryo, Macrophage Cell Line, Macrophage
SUBMITTER: 
Jacob Wozniak
LAB HEAD: Christopher G. Parker
PROVIDER: PXD035729 | Pride | 2022-10-13
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| HMO_TMT-13_Fusion_1.raw | Raw | |||
| HMO_TMT-13_Fusion_2.raw | Raw | |||
| HMO_TMT-13_wLumosColAdjust_06.27.22.pdResult | Other | |||
| JW_HMO_TMT-10_Fusion_1_20220609165812.raw | Raw | |||
| JW_HMO_TMT-10_Fusion_2.raw | Raw |
Items per page: 5 1 - 5 of 13 |
Similar Datasets
Project description:SLC15A4 is an endolysosome-resident transporter intimately linked with autoinflammation and autoimmunity. Specifically, SLC15A4 is critical for Toll-like receptor (TLR) 7-9 as well as the nucleotide-binding oligomerization domain-containing protein (NOD) signaling in several immune cell subsets. Notably, SLC15A4 is essential for the development of systemic lupus erythematosus in murine models and is associated with autoimmune conditions in humans. Despite its therapeutic potential, to our knowledge no chemical probes have been developed that target SLC15A4. Here, we use an integrated chemical proteomics approach to develop a suite of chemical tools, including first-in-class functional inhibitors, for SLC15A4. We demonstrate SLC15A4 inhibitors described herein suppress endolysosomal TLR and NOD functions in a variety of human and mouse immune cells, furnish evidence of their ability to suppress inflammation in vivo and in clinical settings, and provide insights into their mechanism of action. Our findings establish SLC15A4 as a druggable target for the treatment of autoimmune/autoinflammatory conditions.
2023-11-29 | PXD045715 | Pride
Project description:practipractical access to the portimines and analogs thereof simplified the development of photoaffinity analogs, which were used in chemical proteomic experiments to identify a primary target of portimine A as the 60S ribosomal export protein NMD3cal access to the portimines and analogs thereof simplified the development of photoaffinity analogs, which were used in chemical proteomic experiments to identify a primary target of portimine A as the 60S ribosomal export protein NMD3
2023-07-12 | PXD041911 | Pride
Project description:Dialkyldiazirines have emerged as a photoaffinity probe of choice for interactome mapping in live cell experiments. Upon irradiation, ‘linear’ dialkyldiazirines produce dialkylcarbenes, which are susceptible to both intramolecular reactions and unimolecular elimination processes, as well as diazoalkanes, which also participate in intermolecular labeling. Cyclobutylidene has a nonclassical bonding structure and is stable enough to be captured in bimolecular reactions. Cyclobutanediazirines have more recently been studied as photoaffinity probes based on cyclobutylidene, but the mechanism, especially with respect to the role of putative diazo intermediates, was not fully understood. Here, we show that photolysis (365 nm) of cyclobutanediazirines can produce cyclobutylidene intermediates as evidenced by formation of their expected bimolecular and unimolecular products, including methylenecyclopropane derivatives. Unlike linear diazirines, cyclobutanediazirine photolysis in the presence of tetramethylethylene produces a [2+1] cycloaddition adduct. By contrast, linear diazirines produce diazo compounds upon low temperature photolysis in THF, whereas diazo compounds are not detected in similar photolyses of cyclobutanediazirines. Diazocyclobutane, prepared by independent synthesis, is labile, reactive toward water, and capable of protein alkylation. The rate of diazocyclobutane decomposition is not affected by 365 nm light, suggesting that the photochemical conversion of diazocyclobutane to cyclobutylidene is not an important pathway. Finally, chemical proteomic studies revealed that a likely consequence of this primary conversion to a highly reactive carbene is a marked decrease in labeling by cyclobutanediazirine-based probes relative to linear diazirine counterparts both at the individual protein and proteome-wide levels. Collectively, these observations are consistent with a mechanistic picture for cyclobutanediazirine photolysis that involves carbene chemistry with minimal formation of diazo intermediates, and contrasts with the photolyses of linear diazirines where alkylation by diazo intermediates plays a more significant role.
2024-10-13 | PXD052768 | Pride
Project description:Usnic acid is a natural product with versatile biological activities against various organisms. We here utilize a chemical proteomic strategy to gain insights into its target scope in bacterial and human cells. First, we excluded DNA binding as a major reason for its antibacterial activity and second commenced with target profiling which unravelled several metal cofactor-dependent enzymes in both species. This is in line with the metal complexation activities of usnic acid and suggests a polypharmacological mode of action. Interestingly, our synthetic studies revealed a selectivity switch at usnic acid which maintains antibacterial activity but lacks strong cytotoxic effects.
2024-08-10 | PXD049013 | Pride
Project description:Salinipostin A (Sal A) is a bicyclic phosphotriester natural product isolated from the marine bacterium Salinospora sp. that exhibits potent antimalarial activity. However, the direct targets and mechanisms by which it exerts its effects are poorly understood. Here, we use semi-synthesis to generate a Sal A-derived activity-based probe, enabling the identification of its targets in the human malaria parasite Plasmodium falciparum. All of the identified proteins contain an / serine hydrolase domain and several have been reported as essential for growth of the parasite. One of the essential targets is an uncharacterized protein (PF3D7_1038900, referred to as PfMAGLLP) that displays a high degree of homology to human monoacylglycerol lipase (MAGL). Recombinant expression of this protein confirms that it processes lipid esters as well as a bona fide MAGL acylglyceride substrate. PfMAGLLP is potently inhibited by Sal A, as well as by human MAGL inhibitors and by the anti-obesity drug Orlistat that disrupts lipid metabolism and induces a similar death phenotype in parasites as Sal A. Resistance selection studies with Sal A yielded parasites that showed only a mild reduction in sensitivity. Multiple whole-genome sequenced Sal A-selected clones displayed nonsynonymous mutations in a gene coding for a putative PRELI domain-containing protein (PF3D7_1324400) related to a mitochondrial protein linked to multidrug resistance in Toxoplasma gondii. Together, these data suggest that the antimalarial activity of Sal A results from inhibition of multiple essential serine hydrolases, leading to disruption of lipid metabolism pathways. The combination of the non-essentiality of many of these serine hydrolases in humans and the lack of parasite resistance pathways to fully overcome inhibitor treatment suggest that this class of enzymes represent promising targets for development of next-generation antimalarial agents.
2020-01-24 | PXD016835 | Pride
Project description:This study aimed to characterise the protein that a novel compound binds to, thus promoting its ability to inhibit BAK apoptotic activity.
2019-10-11 | PXD013129 | Pride
Project description:During mammalian development DNA methylation patterns need to be reset in primordial germ cells (PGC) and preimplantation embryos. However, many retro-transposons and imprinted genes are resistant to such global epigenetic reprogramming via hitherto undefined mechanisms. Here, we report that some of these sequences are immune to widespread erasure of DNA methylation in the mouse embryonic stem cells (mESCs) lacking de novo DNA methyltransferases. Persistence of DNA methylation at these loci in mESCs depends on the histone H3K9 methyltransferase Setdb1, as deletion of Setdb1 results in reduction of H3K9me3 and DNA methylation levels concomitant with an increase in 5-hydroxymethylation (5hmC). In addition, depletion of H3K9 methyltransferase G9a leads to genome-wide reduction of DNA methylation but to a lesser extent at the above sequences. Taken together, these data reveal that Setdb1 ensures the fidelity of DNA methylation at specific loci in mESCs, which may reflect mechanisms functioning in vivo during key developmental stages. Examination of genome-wide DNA hydroxy-methylation status in 3 cell types.
2014-06-03 | E-GEOD-47892 | biostudies-arrayexpress
Project description:We herein report a photo-oxidation driven proximity labeling strategy to profile mitochondrial proteome by light dependence in living cells with high spatiotemporal resolution. Taking advantage of organelle-localizable organic photoactivated probe generating reactive species and nucleophilic substrate for proximal proteins oxidation and trapping, mitochondrial proteins were selectively labeled by spatially limited reactions in native environment. Integration of photo-oxidation driven proximity labeling and quantitative proteomics facilitated the plotting of mitochondrial proteome in which up to 310 mitochondrial proteins were identified with the specificity of 64% in HeLa cells. Furthermore, mitochondrial proteome dynamics was deciphered in drug resistant Huh7 and LPS stimulated HMC3 cells which were hard-to-transfect. A number of differential proteins were quantified which were intimately linked to critical processes and provided insights into the related molecular mechanisms of drug resistance and neuroinflammation in the perspective of mitochondria.
2023-03-11 | PXD036630 | Pride
Project description:We previously demonstrated that inactivation of the replication checkpoint via a mec1 mutation led to chromosome breakage at replication forks initiated from virtually all origins of replication, after transient exposure to hydroxyurea (HU), an inhibitor of ribonucleotide reductase. Furthermore, we have shown that chromosomes break at replication forks that have suffered single-stranded DNA (ssDNA) formation. Here we sought to determine whether all replication forks containing ssDNA gaps have equal probability of producing double strand breaks (DSBs) when cells attempt to recover from HU exposure. We devised a new methodology, Break-Seq, that combines our previously described DSB labeling with NextGen sequencing to map chromosome breaks with improved sensitivity and resolution. We show that DSBs preferentially occur at genes transcriptionally induced by HU. Notably, different subsets of the HU-induced genes produced DSBs in MEC1 and mec1 cells as replication forks traversed greater distance in MEC1 cells than in mec1 cells during the recovery from HU. Specifically, while MEC1 cells exhibited chromosome breakage at stress-response transcription factors, mec1 cells predominantly suffered chromosome breakage at transporter genes, many of which are the substrates of the said transcription factors. We propose that HU-induced chromosome fragility arises at higher frequency near HU-induced genes as a result of destabilized replication forks encountering transcription factor binding and/or the act of transcription. Our model provides an explanation for a long-standing problem in chromosome biology: why different replication inhibitors produce different spectra of chromosome breakage? We propose that different inhibitors elicit different transcription responses as well as destabilize replication forks, and, when the two processes collide, ssDNA at the replication fork suffers further strand breakage, causing DSBs. We queried the yeast genome for DSBs after cells were treated with 200 mM hydroxyurea during S phase. Samples were collected from 1) cells synchronized in G1 phase by alpha factor; 2) cells released from G1 into medium containing 200 mM hydroxyurea for 1 h; 3) cells recovering in fresh medium without hydroxyurea for 1 h after the 1 h exposure to HU. These samples are referred to as G1, HU 1h, and R 1h, respectively. The strains from which the samples were collected are indicated following the time point, e.g. G1_MEC1 or R 1h_mec1. The experiment with mec1 was done twice (Experiments A and B) and that with MEC1 was done once (Experiment C). In addition, a control experiment of in vitro digestion with BamHI using the G1_mec1 sample (G1_BamHI) was performed.
2015-01-12 | E-GEOD-58808 | biostudies-arrayexpress
Project description:Chemical proteomics enables the global assessment of small molecule-protein interactions in native biological systems and has emerged as a versatile approach for ligand discovery. The range of small molecules explored by chemical proteomics has, however, been limited. Here, we describe a diversity-oriented synthesis (DOS)-inspired library of stereochemically-defined compounds bearing diazirine and alkyne units for UV light-induced covalent modification and click chemistry enrichment of interacting proteins, respectively. We find that these ‘photo-stereoprobes’ interact in a stereoselective manner with hundreds of proteins from various structural and functional classes in human cells and demonstrate that these interactions can form the basis for high-throughput screening-compatible nanoBRET assays. Integrated phenotypic analysis and chemical proteomics identified photo-stereoprobes that modulate autophagy by engaging the mitochondrial serine protease CLPP. Our findings show the utility of photo-stereoprobes for expanding the ligandable proteome, furnishing target engagement assays, and discovering and characterizing bioactive small molecules by cell-based screening.
2024-05-31 | PXD050096 | Pride