Project description:This study consists of 24 genome-wide methylation profiles which have been generated from blood and saliva samples collected from ten volunteers in the Personal Genome Project UK. The Personal Genome Project UK aims to create publicly available genome, health and trait data, and these ten volunteers represent the pilot study (PGP-UK10) and the first three genome donation participants. These samples were bisulphite converted using the EZ DNA methylation kit (Zymo), using the alternative incubation conditions recommended for HumanMethylation450 BeadChip (Illumina). Genome-wide DNA methylation was then profiled using the HumanMethylation450 BeadChip (Illumina).
Project description:Nanostring miRNA Array on PGP human bipolar spindle neuron For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:Breast Cancer Resistance Protein (Bcrp) and P-glycoprotein (Pgp) are xenobiotic efflux transporters that limit permeability of their substrates in the gastrointestinal system and brain, and increase drug clearance in liver and kidney. Bcrp and Pgp are also known to transport different endogenous metabolites such as riboflavin, urate, sulfated steroids and glucocorticoids. However, a systemic approach to understand the endogenous substrates and function of these transporters is still lacking. We hypothesized that Bcrp and Pgp have important endogenous functions and play a crucial role in maintaining metabolomic homeostasis in the biological system. To understand the impact of Bcrp and Pgp on endogenous metabolome, we performed untargeted metabolomics of CSF and plasma of male Sprague Dawley (SD) rats (WT) and SD rats lacking both Bcrp and Pgp (double knock-out, dKO rats) (n= 8 per genotype). In addition, we performed genome-wide microarray analysis of brain frontal cortex, kidney and liver from the same animals to analyze changes in gene expression (n=5 per genotype). Our results indicate distinct differences in metabolites and gene expression between WT and dKO rats. Rank order based on both fold change (>1.5 or <0.67) and significance (p <0.05) identified 29 metabolites in CSF and 47 metabolites in plasma as most significantly altered between WT and dKO rats, which includes, among other biochemicals, known substrates of Bcrp e.g., riboflavin, urate, daidzein and its metabolites. Significantly altered metabolites in plasma as well as CSF showed signatures of altered fatty acid metabolism and oxidative stress, which was further supported by the pathway analysis of significantly altered genes. These findings may lead to new insights in understanding the endogenous function of Bcrp and Pgp transporters and identification of functional biomarkers of these transporters
Project description:A drug currently efficient for cerebral stroke therapy is Semax, a synthetic peptide bearing a fragment of ACTH (4â7) and the C-terminal tripeptide Pro-Gly-Pro (PGP) was included to ensure resistance to peptidases.The genome-wide expression changes induced by Semax and PGP in rat brain cortex tissues damaged by focal ischemia were studied using the genome-wide RatRef-12 Expression BeadChip (Illumina, USA), which contains 22,226 genes, according to NCBI. We compared the biochip data obtained at 3 h and 24 h after permanent middle cerebral artery occlusion (pMCAO) in each of the three groups (âischemia,â âischemia + Semax,â and âischemia + PGPâ). The transcriptome profiles were examined at 24 h vs. 3 h after pMCAO in rats that produced ischemic cortical injury and in rats with the same injury treated with Semax or PGP.
Project description:The ATP-binding cassette subfamily B member 1 (ABCB1), encoding a multidrug transporter P-glycoprotein, plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however, little information regarding Pgp at the zebrafish. In addition, to study the function of Pgp in the zebrafish brain in the aging process, we performed RNA-seq using brain tissue of WT and abcb4 knockout zebrafish at different ages, such as 2 months and 30 months.
Project description:To understand how nitric oxide is involved in reversal of resistance and investigate mechanisms of Pgp-dependent efflux and genes in involved in drug resistance.
Project description:Cross-linking mass-spectrometry (XL-MS) was applied to ABC transporter P-glycoprotein (Pgp) under quasi-intact natural lipid environment. Two experimental approaches were carried out using different cross-linkers: (i) on living cells, followed by membrane preparation and immunoprecipitation enrichment of Pgp, (ii) on-bead, subsequent to membrane preparation and immunoprecipitation. Pgp-containing complexes were enriched employing extracellular monoclonal anti-Pgp antibodies on magnetic beads, followed by on-bead enzymatic digestion and LC-MS/MS analysis.