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Series GSE83958 Query DataSets for GSE83958
Status Public on Dec 06, 2016
Title Integrative "-omics" analysis in primary human hepatocytes unravels persistent mechanisms of cyclosporine A-induced cholestasis (RNA)
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Cyclosporine A (CsA), is an endecapeptide with strong immunosuppressant activities and has contributed significantly towards clinical progress in organ transplantation. Furthermore, it has various toxic effects in the kidney and especially in the liver where it may induce cholestasis. The CsA drug-induced cholestasis (DIC) pathway includes important genes involved in the uptake, synthesis, conjugation and secretion of bile acids, which can be verified also in hepatic models in vitro. However, whether changes in CsA-induced cholestasis pathway induced in vitro are persistent thus presenting important biomarkers for repeated dose toxicity, has not yet been investigated. We therefore performed multiple -omics analyses, including whole genome analysis of DNA methylation, gene expression and microRNA expression in primary human hepatocytes (PHH) cultured in sandwich configuration, during and after terminating CsA treatment. For this, cells were exposed to a non-cytotoxic dose of 30 µM CsA daily for 3 and 5 days. To investigate the persistence of induced changes upon terminating the CsA exposure of 5 days, a subset of PHH was subjected to a washout period (WO-period) of three days. DNA methylation (using NimbleGen 2.1 deluxe promoter arrays), transcriptomic (using Affymetrix Human Genome U133 Plus 2.0 arrays) and microRNA (using Agilent Sureprint G3 Unrestricted Human miRNA V16 8 × 60 K microarrays) analyses were performed on days 3, 5 and 8. Identification of differentially methylated genes (DMGs), differentially expressed genes (DEGs), and differentially expressed microRNAs (DE-miRs) was performed using several R packages. DMGs, DEGs and DE-miRs were found after CsA treatment of PHH for 3 and 5 days as well after the WO-period. Interestingly, 828 persistent DEGs and 6 persistent DE-miRs, but no persistent DMGs, were found after the WO-period. These persistent DEGs and DE-miRs showed concordance for 22 genes (13 genes upregulated in gene expression and downregulated in microRNA expression; 9 genes downregulated in gene expression and upregulated in microRNA expression). Some of the persistent transcriptomic changes as well as DE-miRs could be successfully mapped onto the DIC pathway, while epigenetic changes not. Furthermore, 29 persistent DEGs in vitro showed changes in the same direction as observed in livers from cholestasis patients. None of those 29 DEGs were present in the DIC pathway or cholestasis adverse outcome pathway. We have for the first time demonstrated a persistent impact of gene expression and microRNA expression related to DIC after repeated dose administration of CsA in vitro.
Overall design 18 samples (3 time-points (3 days, 5 days and 8 days) with triplicates of control-samples (0.5% DMSO) and treatment-samples (30µM CsA))
Contributor(s) Wolters JE
Citation(s) 27989131
Submission date Jul 01, 2016
Last update date Mar 07, 2017
Contact name Jarno Wolters
Organization name Maastricht University
Department Toxicogenomics
Street address Universiteitssingel 40
City Maastricht
ZIP/Postal code PO BOX 616/ 6200MD
Country Netherlands
Platforms (1)
GPL17996 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array (custom CDF: HGU133Plus2_Hs_ENTREZG.cdf version 15.1.0)
Samples (18)
GSM2224474 ConDMSO_day3_rep1
GSM2224475 ConDMSO_day3_rep2
GSM2224476 ConDMSO_day3_rep3
This SubSeries is part of SuperSeries:
GSE84281 Integrative "-omics" analysis in primary human hepatocytes unravels persistent mechanisms of cyclosporine A-induced cholestasis
BioProject PRJNA327557

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE83958_RAW.tar 103.6 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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