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Human LMO2 binding protein LC-MSMS in U87MG(Glioblastoma cell)

ABSTRACT: To identify the binding partner of LMO2 for explanation of STAT3 signal-related protein in human glioblastoma

INSTRUMENT(S): LCQ Classic

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Brain Glioblastoma Multiforme

SUBMITTER: Sang-Hun Choi

LAB HEAD: Hyunggee Kim

PROVIDER: PXD028254 | Pride | 2022-08-11

REPOSITORIES: Pride

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			Action	DRS
	1.mgf	Mgf
	10.mgf	Mgf
	10_1.mht	Other
	10_2.mht	Other
	10_3.mht	Other

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1 - 5 of 72

Publications

Cytoplasmic LMO2-LDB1 Complex Activates STAT3 Signaling through Interaction with gp130-JAK in Glioma Stem Cells.

Park Cheol Gyu CG Choi Sang-Hun SH Lee Seon Yong SY Eun Kiyoung K Park Min Gi MG Jang Junseok J Jeong Hyeon Ju HJ Kim Seong Jin SJ Jeong Sohee S Lee Kanghun K Kim Hyunggee H

Cells 20220626 13

The oncogenic role of nuclear LIM domain only 2 (LMO2) as a transcriptional regulator is well established, but its function in the cytoplasm is largely unknown. Here, we identified LMO2 as a cytoplasmic activator for signal transducer and activator of transcription 3 (STAT3) signaling in glioma stem cells (GSCs) through biochemical and bioinformatics analyses. LMO2 increases STAT3 phosphorylation by interacting with glycoprotein 130 (gp130) and Janus kinases (JAKs). LMO2-driven activation of STA ...[more]

PMID: 35805116

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Identification of human dendricitc cell responses to microfilaria of B. malayi

Project description:Human dendritic cells were unexposed or exposed to the microfilaria of B. malayi for 48hrs. The cells were washed, protein extracted, processed and analyzed by mass spectrometry.

2016-07-12 | PXD004522 | Pride

chicken deubiquitinases in Salmonella infection

Project description:We infected HD11 macrophages with Salmonella Typhimurium, followed by chemical proteomic analysis of deubiquitinases by using ubiquitin-specific active-site probe.

2018-10-24 | PXD002594 | Pride

Tbeta4 identification CaCo2 cells

Project description:The paper describes new experiments about thymosin beta 4 nuclear translocation using different in vitro cellular stress in CaCo2 cell line adding new details regarding the role of this peptide during adaptive and defensive response. To this purpose, CaCo2 cells were submitted to different stress treatments, including serum starvation, DMSO and Butyrate treatment. The expression of Tβ4 was studied in culture cells before and after stress treatment in the cytosolic and nuclear fractions, with the use of different apporaches: immunohistochemistry with anti-Tβ4 antibody; mass-spectrometry characterization and quantification, and mRNA analysis.

2020-06-29 | PXD012161 | Pride

Human salivary basic proline-rich proteins

Project description:Human basic proline-rich proteins and basic glycosylated proline-rich proteins are the most complex family of human adult salivary proteins, secreted only by the parotid gland, expressed by the polymorphic PRB1-4 genes. This study reports the results obtained for their characterization in our laboratory utilizing integrated top-down and bottom-up HPLC-ESI-MS and MS/MS platform. The family include 11 parent peptides/proteins and more than 6 parent glycosylated proteins. Despite the complexity, on the basis of their primary structure they result the product of the duplication of three repeats and we propose that they can be classified in two main groups, the first including the peptides called P-E, P-Ko, IB-6, Ps-1, Ps-2, P-H, P-F, P-J, and P-D, the second including the peptides called IB-1, II-2 and the glycosylated basic proline-rich proteins codified by PRB3 and PRB4 genes. A third minor hybrid group includes the proteins called IB-8a Con1- and Con1+. Some of the proteins of the family (IB-1, II-2 and P-J) are almost always detectable in adult human saliva, while the others are expressed with different frequencies according to the phenotype. Various isoforms are detectable in the adult saliva and three of them, until now not reported (P-H S1→A, P-Ko P36→S, P-Ko A41→S), were characterized by MS/MS fragmentation.

2018-08-08 | PXD009813 | Pride

RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1

Project description:Notch signaling is an evolutionarily conserved signal transduction pathway that is essential for metazoan development. At the molecular level, the key components of the Notch pathway are the NOTCH-family receptors, the ligands of the DSL (Delta, Serrate, Lag-2) family and the transcription factor CSL [CBF1/RBPJ, Su(H), Lag-1]. Upon ligand binding, the NOTCH Intra-Cellular Domain (NOTCH ICD) translocates into the nucleus and forms a complex with RBPJ to activate the transcription of target genes. In the absence of NOTCH ICD, RBPJ acts as a transcriptional repressor. Using a proteomic approach, we identified L3MBTL3 as a novel interactor of RBPJ. We discovered that L3MBTL3 competes with NOTCH ICD for binding to RBPJ. In the absence of NOTCH ICD, RBPJ recruits L3MBTL3 and its co-factor KDM1A [lysine (K)-specific demethylase 1A] to the promoters/enhancers of Notch target genes to promote H3K4me2 demethylation and transcriptional repression. In three distinct cell contexts in which Notch signaling governs cell fate, i.e., mature T-cells as well as brain and breast tumor cells, the loss of L3MBTL3 results in the de-repression of Notch target genes. Finally, the genetic analyses of the homologs of RBPJ and L3MBTL3 in Drosophila melanogaster and Caenorhabditis elegans demonstrate that the functional link between RBPJ/Su(H)/lag-1 and L3MBTL3/dL(3)mbt/lin-61 is evolutionarily conserved, thus identifying L3MBTL3 as a universal modulator of Notch signaling in metazoans.

2017-10-17 | PXD004196 | Pride

Transcriptomic Responses of Synechocystis sp. PCC 6803 Encapsulated in Silica Gel

Project description:Global gene expression of Synechocystis sp. PCC 6803 encapsulated in silica gel was examined by microarray analysis. Cultures were encapsulated in gels derived from aqueous precursors and gels derived from alkoxide precursors and incubated under constant light for 24 hours prior to RNA extraction. Cultures suspended in liquid media were also exposed to 500 mM salt stress and incubated under identical conditions, for comparison purposes. The expression of 414 genes was significantly altered by encapsulation in aqueous-derived gels (fold change >/= 1.5 and P-value < 0.01), the expression of 1143 genes were significantly altered by encapsulation in alkoxide derived gels, and only 243 genes were common to both encapsulation chemistries. Additional qRT-PCR analyses of four select genes; ggpS, cpcG2, slr5055, and sll5057, confirmed microarray results. These results illustrate that encapsulation stress is quite different than salt stress in terms of gene expression response. Furthermore, a number of hypothetical and unknown proteins associated with encapsulation and alcohol stress have been identified, with implications for improving encapsulation protocols and rationally engineering microorganisms for direct biofuel production. 16 samples; 4 biological replicates each of 4 treatments

2012-04-23 | E-GEOD-37482 | biostudies-arrayexpress

Substitutional Analysis on Influenza PeB Binding

Project description:In search for peptides with higher or special binding affinity and for further understanding of the mode of action, a full substitutional analysis of peptide PeB using microarrays was performed. Thus, 152 PeB mutant variants were generated. In each of them, the full-length sequence was preserved except for only one amino acid from the eight loop-forming amino acids of the original PeB peptide (ARDFYDYDVFYYAMD) which was substituted with the 19 remaining natural amino acids. To assess binding, influenza material was labeled with a protein reacting fluorophore. Microarray-based substitutional analysis of peptide PeB was performed using a PepStarÂ® peptide library spotted on glass slides by JPT Peptide Technologies. The slides were used without additional treatment. For the labeling of proteins with a fluorescent dye, Dyomics DY-634 (Î»ex = 635 nm, Î»em = 654 nm, Fluoro-spin 634 Kit (emp Biotech) was used, according to the manufacturerÂ´s instructions. The following materials were labeled: NewYork H3N2, Aichi H3N2, Victoria H3N2 and California H1N1. Labeled analytes were incubated several hours or overnight at indicated concentrations using Femtotip buffer (FTP)30 (20 mM Tris, 30% glycerol, 3% polyvinylpyrrolidon 90, 0.1% Tween 20, pH 8.4) for dilution. The slides were washed twice in FTP and twice in ultrapure water and subsequently dried under a stream of nitrogen. Experiments were performed in triplicates using glycans (2,3'-/2,6'-sialyllactose) and proteins (Anti-H1/Anti-H3 antibodies, fetuin) as positive and negative controls.

2016-02-27 | E-GEOD-78700 | biostudies-arrayexpress

RNAseq Expression data for mouse liver, Phenobarbital exposed livers and resulting liver tumours.

Project description:Through the analysis of mouse liver tumours promoted by distinct routes (DEN exposure alone, DEN exposure plus non-genotoxic insult with phenobarbital and non-alcoholic fatty liver disease); we report that the cancer associated hyper-methylated CGI events in mice are also predicated by silent promoters that are enriched for both the DNA modification 5-hydroxymethylcytosine (5hmC) and the histone modification H3K27me3 in normal liver. During cancer progression these CGIs undergo hypo-hydroxymethylation, prior to subsequent hyper-methylation; whilst retaining H3K27me3. A similar loss of promoter-core 5hmC is observed in Tet1 deficient mouse livers indicating that reduced Tet1 binding at CGIs may be responsible for the epigenetic dysregulation observed during hepatocarcinogenesis. Consistent with this reduced Tet1 protein levels are observed in mouse liver tumour lesions. As in human, DNA methylation changes at CGIs do not appear to be direct drivers of hepatocellular carcinoma progression in mice. Instead dynamic changes in H3K27me3 promoter deposition are strongly associated with tumour-specific activation and repression of transcription. Our data suggests that loss of promoter associated 5hmC in diverse liver tumours licences DNA methylation reprogramming at silent CGIs during cancer progression. We carry out paired end , strand specific RNAseq prior to sequencing on Illumina Hiseq 2500 to report on the transcriptional landscape in replicate control mouse livers (n=2), 12 week Phenobarbital exposed livers (n=2)and resulting (35 week PB) liver tumours (n=3).

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Deubiquitinase Vulnerabilities Identified through Activity Based Protein Profiling in Non-Small Cell Lung Cancer

Project description:To aid in the prioritization of deubiquitinases (DUBs) as anticancer targets, we developed an approach combining activity-based protein profiling (ABPP) with mass spectrometry in both non-small cell lung cancer (NSCLC) tumor tissues and cell lines along with analysis of available RNA interference and CRISPR screens. We identified 67 DUBs in NSCLC tissues, 17 of which were overexpressed in adenocarcinoma or squamous cell histologies, and 12 scoring as affecting lung cancer cell viability in RNAi or CRISPR screens. We used the CSN5 inhibitor, which targets COPS5/ CSN5, as a tool to understand the biological significance of one of these 12 DUBs, COPS6, in lung cancer. Our study provides a powerful resource to interrogate the role of DUB signaling biology and nominates druggable targets for the treatment of lung cancer subtypes.

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