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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from human OC+BAP+ double positive versus OC-BAP- double negative cells

ABSTRACT: Subpopulation of circulating monocyte/macrophage lineage cells show a calcifying ability in vivo and in vitro. These cells may contribute to intimal calcification within atherosclerotic lesions and may have pathophysiological clinical and therapeutic implication in vascular disorders. Such cells express Osteocalcin (OC) and Bone Alkaline Phosphatase (BAP). We analysed the expression profile of human OC+BAP+ cells versus OC-BAP- cells We compared three biological repilcates of OC+BAP+ versus OC-BAP- (each population coming from the same donor), each of the three coming from different healthy non diabetic donors.

ORGANISM(S): Homo sapiens

SUBMITTER: Nicol Poncina

PROVIDER: E-GEOD-47060 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from human OC+BAP+ double positive versus OC-BAP- double negative cells

Project description:Subpopulation of circulating monocyte/macrophage lineage cells show a calcifying ability in vivo and in vitro. These cells may contribute to intimal calcification within atherosclerotic lesions and may have pathophysiological clinical and therapeutic implication in vascular disorders. Such cells express Osteocalcin (OC) and Bone Alkaline Phosphatase (BAP). We analysed the expression profile of human OC+BAP+ cells versus OC-BAP- cells

2013-05-17 | GSE47060 | GEO

Characterization of biofilm associated protein (Bap) in Staphylococcus xylosus

Project description:The biofilm associated protein (Bap) is recognised as the essential component for biofilm formation in Staphylococcus aureus V329 and other species. Although Bap orthologs are also present in most S. xylosus strains, their contribution to biofilm formation has not yet been determined. In this study, different experimental approaches were used to elucidate the effect of Bap on biofilm formation in S. xylosus and the motif structure of two biofilm-forming S. xylosus strains TMW 2.1023 and TMW 2.1523 was compared to Bap of S. aureus V329. We found that despite an identical structural arrangement into four regions, Bap from S. xylosus differs in key factors to Bap of S. aureus i.e. isoelectric point of aggregation prone Region B, protein homology and type of repeats. Disruption of bap had no effect on aggregation behavior of selected S. xylosus strains and a significant reduction in biofilm was only observed for one strain (TMW 2.1523) under neutral conditions. Further we could not observe any typical characteristics of a S. aureus Bap positive phenotype such as functional impairment by calcium addition and rough colony morphology on CRA. A predominant role of Bap in cell aggregation and biofilm formation as reported for S. aureus V329 was not observed. We therefore suggest that biofilm formation follows different, multifactorial mechanisms, and cannot be referred to as the primary function of Bap in S. xylosus.

2022-01-20 | PXD029728 | Pride

Oral Benzo[a]pyrene in Cyp1a1/1b1(-/-) Double-Knockout Mice: Microarray Analysis During Squamous Cell Carcinoma Formation in Preputial Gland Duct

Project description:Benzo[a]pyrene (BaP) is a prototypical polycyclic aromatic hydrocarbon (PAH) found in combustion processes. Cytochrome P450 1A1 and 1B1 enzymes (CYP1A1, CYP1B1) and other enzymes can activate PAHs to reactive oxygenated intermediates involved in mutagenesis and tumor initiation; also, CYP1 enzymes can detoxify PAHs. Cyp1(+/+) wild-type (WT) and Cyp1b1(-/-) knockout mice receiving oral BaP (12.5 mg/kg/day) remain healthy for >12 months. In contrast, we found that global knockout of the Cyp1a1 gene (1a1KO) results in proximal small intestine (PSI) adenocarcinoma within 8 to 12 weeks on this BaP regimen; striking compensatory increases in PSI CYP1B1 likely participate in initiation of adenocarcinoma in 1a1KO mice. Cyp1a1/1b1(-/-) double-knockout (DKO) mice on this BaP regimen show no PSI adenocarcinoma, but instead preputial gland duct (PGD) squamous cell carcinoma (SCC) occurs by 12 weeks. Herein we compare microarray expression of PGD genes in WT, 1a1KO and DKO mice at zero, 4, 8, 12, and 16 weeks of oral BaP; about four dozen genes up- or down-regulated during the most critical time-points were further verified by qRT-PCR. In DKO mice, CYP3A59 was unequivocally identified as the BaP-inducible and BaP-metabolizing best candidate responsible for initiation of BaP-induced SCC. Striking increases or decreases were found in 26 cancer-related genes plus eight Serpin genes in DKO, but not in 1a1KO or WT, mice on this BaP regimen; of the 26, eight were RAS-related oncogenes. The mechanism by which cancer-related genes are responsible for SCC tumor progression in the PGD remains to be elucidated. The tissue being tested is preputial gland duct of mice. Three genotypes (WT, Cyp1a1 KO and Cyp1a1/1b1 DKO) were compared with one another, at zero, 4, 8, 12 and 16 weeks of oral BaP. The five time-points within each genotype were also compared.

2012-09-06 | E-GEOD-40633 | biostudies-arrayexpress

Toxicogenomics and phenotypic characterization of adult male zebrafish liver treated with benzo-[A]-pyrene (BAP)

Project description:We performed microarray-based expression profiling on liver of male zebrafish exposed to 5, 50, and 500 µg/L of benzo-[A]-pyrene (BAP) for 24 and 96 hours, to identify global transcriptional programs and biological pathways involved in BAP-induced adaptive responses under in vivo environment. We analyzed 34 arrays of BAP-treated adult male zebrafish liver and 15 arrays of control fish.

2012-01-01 | E-GEOD-30035 | biostudies-arrayexpress

Development of a method for quantitative analysis of in vivo interactions of pluripotency transcription factors Sox2, Oct4, Nanog by mass spectrometry

Project description:Protein-protein proximity of core pluripotency transcription factors plays an important role during cell reprogramming. Pluripotent embryonic stem (ES) cell identity is controlled by a trio of transcription factors: Sox2, Oct4, and Nanog. These proteins often bind to closely localized genomic sites. The precise mode by which Sox2, Oct4, and Nanog interact with DNA is likely to make a crucial contribution to their function. Here, a detailed protocol for in vivo detection and quantitative analysis of protein-protein proximity of Sox2 and Oct4 using Proximity Utilizing Biotinylation (PUB) method based on the use of the BAP/BirA (target/enzyme) system is described. The method includes design and cloning of DNA plasmid construct, transient transfection of HEK293T cells, Western blot analysis of nuclei fraction and LC-MS/MS analysis. Experiments with coexpression of BAP-X+BirA-Y (X, Y=Sox2, Oct4 and GFP as control) revealed strong biotinylation level of target proteins when X and Y were pluripotency transcription factors compared with control when X=GFP. Since mass spectrometry provides both high sensitivity and more accurate quantification of data a modified workflow was used, in which SDS-PAGE step was eliminated and His-tagged BAP-fused proteins from cell lysate were purified in 6M guanidine HCl buffer, washed, propionylated, digested directly on the Ni sepharose beads using trypsin and analysed on Q-TOF Impact II instrument. Using mass spectrometry allows making quantitative estimation of in vivo interaction of BAP-Sox2 and BirA-Oct4 which was demonstrated by measuring ratios of biotinylation levels of BAP fused either with Sox2 or GFP at different biotin pulse times. After vector preparation this protocol can be completed in seven working days.

2020-01-21 | PXD015756 | Pride

BAP and ADCK4 interactor proteomic data LC-MS/MS

Project description:Although identification of single gene mutations associated with SRNS have yielded insights into pathogenic mechanisms and localized its pathogenesis to glomerular podocytes, the disease mechanisms of SRNS remain obscure. ADCK4 mutations usually manifest as steroid-resistant nephrotic syndrome, and cause coenzyme Q10 (CoQ10) deficiency. We performed proteomic analysis to understand the function of ADCK4 via the identification of its interactome. We generated HEK293 cells that stably overexpressed C-terminal FLAG-tagged bacterial alkaline phosphatase (BAP; BAP-3xFLAG) and ADCK4 (ADCK4-3xFLAG). We confirmed that ADCK4-3xFLAG mostly localized to the mitochondria. Following affinity purification using anti-FLAG beads, protein eluates were analyzed using a liquid chromatograph coupled to a high-resolution mass spectrometer (LC-MS/MS). In total, 612 proteins were identified as interactors of ADCK4. Among them, the cytoplasmic proteins, including myosin (MYH10, MYH11, MYO1B, and MYO1C), filamin (FLNC), and kinase proteins (STK24, STK25, STK38 and ROCK1) were detected. In addition, the mitochondrial proteins, including ATP synthase subunit (ATP5L), cytochrome c oxidase subunit (COX6A1 and UQCRQ), and COQ5, were also identified as interactors.

2021-09-08 | PXD016147 | Pride

Human glioma cell line T98G: BAP-PCBP2 RIP vs. BAP-GFP RIP (Control)

Project description:RIP-Chip analysis of PCBP2 and identification of preferentially associated mRNAs. T98G cells were transfected transiently with BAP-tagged constructs. BAP-tagged proteins were biotinylated in vivo by the co-transfected hBirA enzyme. RNPs were recovered via precipitation with Steptavidin-sepharose beads. Finally, RNAs were purified and analyzed on microarrays. BAP-GFP as control was used in three independent sets of experiments.

2013-07-24 | GSE44048 | GEO

Transcription profiling of human hepatoma cell lines HepG2 and HepaRG using whole genome gene expression analysis before and after exposure to the GTX carcinogens AFB1 and BaP, and the NGTX carcinogens CsA, E2 and TCDD for 12 and 48 h

Project description:Direct comparison of the hepatoma cell lines HepG2 and HepaRG using whole genome gene expression analysis before and after exposure to the GTX carcinogens AFB1 and BaP and the NGTX carcinogens CsA, E2 and TCDD for 12 and 48 h.

2010-04-15 | E-MEXP-2458 | biostudies-arrayexpress

Human glioma cell line T98G: BAP-PCBP2 RIP vs. BAP-GFP RIP (Control)

2013-07-24 | E-GEOD-44048 | biostudies-arrayexpress