Proteomes of wild-type and ubr4 KO HEK293T cells by label-free mass spectrometry
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Cell Culture, Kidney
SUBMITTER: 
Sara Hegazi
LAB HEAD: Hai-Ying Mary Cheng
PROVIDER: PXD020630 | Pride | 2022-03-24
REPOSITORIES: pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| MaxquantOutput.tar.gz | Other | |||
| SHegazi_KD1.raw | Raw | |||
| SHegazi_KD2.raw | Raw | |||
| SHegazi_KD3.raw | Raw | |||
| SHegazi_KD4.raw | Raw |
Items per page: 5 1 - 5 of 9 |
Similar Datasets
Project description:An important question for the use of the mouse as a model for studying human disease is the degree of functional conservation of genetic control pathways from human to mouse. The human and mouse placenta show structural similarities but there have been no systematic attempt to assess their molecular similarities or differences. We built a comprehensive database of protein and microarray data for the highly vascular exchange region micro-dissected from the human and mouse placenta near-term. Abnormalities in this region are associated with two of the most common and serious complications of human pregnancy, maternal preeclampsia (PE) and fetal intrauterine growth restriction (IUGR), each disorder affecting ~5% of all pregnancies. Over 7,000 orthologs were detected with 70% co-expressed and over 80% of genes known to cause placental phenotypes in mouse were co-expressed. These genes form a tight protein-protein interaction network with novel candidate genes likely to be important in placental structure and/or function. The entire data is available as a web-accessible database to guide the informed development of mouse models to study human disease This experiment is now fully represented in NCBI Peptidome database with accession PSE115; http://www.ncbi.nlm.nih.gov/peptidome/search/index.shtml?acc=PSE115 Microdissection of human villous trees and mouse placental labyrinth. Tissues were split for microarray and protein analysis. For protein analysis samples were first fractionated by differential sucrose gradients into mitochrondria, cytosol, microsomes and nuclei. Mitochrondira and neuclei were each extracted by two different methods for soluble and insoluble material. Each subcellular fraction for each tissue was analysed in quintuplet by 9 step 2 dimensional LC/MSMS. This generated a total of 270 mzXML files for each tissue.
2009-06-29 | E-GEOD-13299 | biostudies-arrayexpress
Project description:Campylobacter jejuni (C. jejuni) protein microarrays were used to identify immunogenic C. jejuni proteins that may be useful in the development of biomarkers, diagnostic assays, or subunit vaccines for humans or livestock. A native protein microarray with over 1400 individually purified GST-tagged C. jejuni proteins (86 % of the proteome), was constructed and screened for antibody titers present in test sera. The protein arrays were screened with antisera from rabbits inoculated with whole C. jejuni or various serotypes of E. coli or Salmonella, with antisera from mice infected with C. jejuni, and sera from healthy humans. Dual detection of GST signals was incorporated as a way of normalizing the variation of protein concentrations contributing to the antibody staining intensities.
2018-12-29 | E-MTAB-7535 | biostudies-arrayexpress
Project description:Analysis of the interactions between WDR44 and Rab11 utilizing HDX-MS
2023-02-22 | PXD032837 | Pride
Project description:Anthocyanins and flavonols are natural compounds that accumulate preferentially in grapevine flowers and fruits. They are among the most abundant flavonoids and play a very important role in grape and wine quality. In particular, they confer and stabilize colour and contribute to other organoleptic characteristics of the final product. Their complex profile in terms of concentration and relative abundance varies among cultivars and makes wine typicity. The synthesis of these compounds is mainly regulated at transcriptional level. Flavonoids accumulate at specific stages and in specific tissues during flower and berry development, as a consequence of the timely expression of the genes necessary for their synthesis. Although the general flavonoid pathway has been genetically and biochemically elucidated and the main determinants of colour have been identified, the molecular reasons of the fine variation among grape cultivars are still not completely understood. To shed light on this issue, extreme genotypes of a segregating population derived from the cross Syrah x Pinot Noir were characterized at transcriptional level. The transcriptome analysis along three berry developmental stages of these genotypes has allowed the identification of a large set of transcripts differentially modulated between the two groups. A population derived from M-bM-^@M-^XSyrahM-bM-^@M-^Y x M-bM-^@M-^XPinot NoirM-bM-^@M-^Y consisting of 170 F1 individuals plus the parental lines was characterized for the content of flavonols and anthocyanins in the skins of mature berries (38E-L; 18M-BM-0Brix). Based on the biochemical data, 4 high- and 4 low-flavonol producers (HFPs and LFPs: F1 16, F1 56, F1 63, F1 223 and F1 64, F1 256, F1 260, PN), two of which having also either very high or very low anthocyanin content (HAPs and LAPs: F1 63, F1 223 and F1 256, F1 260), were selected for gene expression analysis. A representative sample for each individual (one biological replicate) was collected at three berry developmental stages (hard green berry (33E-L, PV), veraison (35E-L, 50% coloured berries, VER) and maturity (38E-L, 18M-BM-0Brix, MAT)) during the 2007 season.
2014-08-13 | E-GEOD-42909 | biostudies-arrayexpress
Project description:MKRN3, whose deletion or loss-of-function mutations were genetically associated with human centeral precocious puberty (CPP). To identify the potential substrates for MKRN3, MKRN3 was transfected into HEK293T cells as bait, and its interacting proteins were identified by mass spectrum and functions were extensively studied.
2021-02-22 | PXD022346 | Pride
Project description:E. coli and many other bacterial species can alternate their cell cycle according to nutrient availability. As a result, they grow and divide very fast under optimal conditions or slow down the cell cycle when conditions deteriorate. This adaptability is underlined by mechanisms coordinating cell growth with duplication of genetic material and cell division. Several mechanisms regulating DNA replication process in E. coli have been described so far with biochemical details, nevertheless we still don’t fully understand the source of remarkable precision that bacterial cells coordinate their growth and chromosome replication with. To shed light on regulation of E. coli DNA replication at systemic level, we used affinity purification coupled with mass spectrometry (AP-MS) to characterize protein-protein interactions (PPIs) formed by key E. coli replication proteins, under disparate bacterial growth conditions and phases. We present the resulting dynamic replication protein interaction network (PIN) and highlight links between DNA replication and several cellular processes, like outer membrane synthesis, RNA degradation and modification or starvation response.
2022-03-03 | PXD030113 | Pride
Project description:We hypothesized that the transcriptome of primary cultures of morphologically normal ovarian surface epithelial cells could be altered by the presence of a heterozygous BRCA1 or BRCA2 mutation. We aimed to discover early events associated to ovarian carcinogenesis, which could represent putative targets for preventive strategies of this silent killer tumor. We identified the first molecular signature associated with French Canadian BRCA1 or BRCA2 founder mutations in morphologically normal ovarian epithelial cells. We discovered that wild-type and mutated BRCA2 allelic transcripts were expressed not only in morphologically normal but also in tumor cells from 8765delAG BRCA2 carriers. Further analysis of morphologically normal ovarian and tumor cells from C4446T BRCA1 carriers lead to the same observation. Our data support the idea that one single hit in BRCA1 or BRCA2 is sufficient to alter the transcriptome of phenotypically normal ovarian epithelial cell. The highest level of BRCA2 mutated allele transcript expression was measured in cells originating from the most aggressive ovarian tumor. The penetrance of the mutation and the aggressiveness of the related tumor could depend on a dosage effect of the mutated allele transcript. We studied the molecular profiles associated with 5 a priori classes of samples : 4 non-familial morphologically normal ovarian surface epithelium (NOSEs) : NM class, 2 BRCA1-mutated NOSEs : M1 class, 3 BRCA2-mutated NOSEs : M2 class, 3 BRCA1-mutated ovarian tumor cells (TOVs) : TM1 class and one BRCA2-mutated TOV :TM2 class. No technical replicates were included in this study. The following contrasts were computed : NM vs. M1, NM vs. M2, M1 vs. M2, M1 vs. TM1 and M (M1 union M2) vs. TM (TM1 union TM2).
2012-06-14 | E-GEOD-34928 | biostudies-arrayexpress
Project description:Drug Toxicity Signature Generation Center (DToxS) at the Icahn School of Medicine at Mount Sinai is an integral part of the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. A key aim of DToxS is to generate both proteomic and transcriptomic signatures that cab predict adverse effects, especially cardiotoxicity, of drugs approved by the Food and Drug Administration. Towards this goal, high throughput shot-gun proteomics experiments on 308 cell line/drug combinations (from four primary human cardiomyocyte cell lines purchased from PromoCell), 64 HeLa control lysates, and 9 auxiliary treatment samples have been conducted at the Center for Advanced Proteomics Research at Rutgers-New Jersey Medical School. The integrated proteomic and transcriptomic signatures have been used for computational network analysis to identify cellular signatures of cardiotoxicity that may predict drug-induced toxicity and possible mitigation of such toxicities by mixing different drugs. Both raw and processed proteomics data have been carefully controlled for quality and have been made publicly available via the PRoteomics IDEntifications (PRIDE) database. As such, this broad drug-stimulated proteomic dataset is valuable for the prediction drug toxicities and their mitigation. All data are available through CC BY 4.0 open license.
2020-03-02 | LDS-1575 | LINCS
Project description:Small heat shock proteins are chaperones that are essential in preserving the integrity of the cellular proteome during stress conditions. The human genome encodes ten small heat shock proteins (HspB1-HspB10), which often form polydisperse multimeric functional structures. Uniquely, HspB2 and HspB3 form a tetrameric complex with a well-defined 3:1 subunit ratio, suggesting that precise control of their expression is crucial for their function as chaperones. Indeed, disruption of the HspB2-HspB3 interaction and stoichiometry has been linked to myopathic disorders. To gain insight in the molecular mechanisms involved in such disorders, we studied the intracellular behavior of HspB2 and HspB3 at varying ratios. In this study, we show that expression of HspB2 alone results in the formation of liquid nuclear condensates, while co-expression of a small amount of HspB3 results in a diffuse distribution of HspB2 in the nucleus. In contrast, co-expression of HspB3 in equimolar amounts to HspB2 resulted in the formation of large aggregates in both the cytoplasm and the nucleus. The condensates as well as the aggregates can be dissolved by shifting the HspB2:HspB3 balance, indicating that these structures are reversible and able to dynamically exchange biomolecules with the environment. Both condensates and aggregates are expected to interact with, and potentially trap specific sets of proteins, which may be linked to associated pathologies. To identify these proteins and elucidate the composition of HspB2 condensates and aggregates, we performed proximity labelling using an engineered ascorbate peroxidase (APEX). We found a striking enrichment of disordered proteins in HspB2:HspB3 containing aggregates, as well as multiple autophagy factors, indicating that the cell is actively attempting to clear these aggregates. In contrast, very few proteins were specifically enriched in condensates, suggesting that most proteins interact only weakly and transiently with the liquid condensates.
2022-09-20 | PXD035040 | Pride
Project description:Oncogenic EZH2 is overexpressed and extensively involved in the pathophysiology of different cancers including extranodal natural killer/T-cell lymphoma (NKTL). However, the mechanisms regarding EZH2 upregulation is poorly understood, and it still remains untargetable in NKTL. In this study, we examine EZH2 protein turnover in NKTL and identify MELK kinase as a regulator of EZH2 ubiquitination and turnover. Using quantitative mass spectrometry (MS) analysis, we observed a MELK-mediated increase of EZH2 S220 phosphorylation along with a concomitant loss of EZH2 K222 ubiquitination, suggesting a phosphorylation-dependent regulation of EZH2 ubiquitination. MELK inhibition through both chemical and genetic means led to ubiquitination and destabilization of EZH2 protein. Importantly, we determine that MELK is upregulated in NKTL, and its expression correlates with EZH2 protein expression as determined by tissue microarray derived from NKTL patients. Interestingly, FOXM1, which connected MELK to EZH2 signaling in glioma, was not involved in mediating EZH2 ubiquitination. Furthermore, we identify USP36 as the deubiquitinating enzyme which deubiquitinates EZH2 at K222. These findings uncover an important role of MELK and USP36 in mediating EZH2 stability in NKTL. Moreover, MELK overexpression led to decreased sensitivity to Bortezomib treatment in NKTL based on deprivation of EZH2 ubiquitination. Therefore, modulation of EZH2 ubiquitination status by targeting MELK may be a new therapeutic strategy for NKTL patients with poor Bortezomib response.
2019-08-26 | PXD015008 | Pride