{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Steven Wink"],"study_type":["transcription profiling by array"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-54256"],"description":["Drug-induced liver injury (DILI) is an important clinical problem. Here we used a genomics approach to establish the critical drug-induced toxicity pathways that act in synergy with the pro-inflammatory cytokine tumor necrosis factor M-oM-^AM-! (TNFM-oM-^AM-!) to cause cell death of liver HepG2 cells. Transcriptomics of the cell injury stress response pathways initiated by two hepatoxicants, diclofenac and carbamazepine, revealed the endoplasmic reticulum (ER) stress/translational initiation signaling and Nrf2 antioxidant signaling as two major affected pathways, which was similar to that observed for the majority of ~80 DILI compounds in primary human hepatocytes. The ER stress was primarily related to PERK and ATF4 activation and subsequent expression of CHOP, which was all independent of TNFM-NM-1 signaling. Identical ATF4 dependent transcriptional programs were observed in primary human hepatocytes as well as primary precision cut human liver slices. Targeted RNA interference studies revealed that while ER stress signaling through IRE1M-NM-1 and ATF6 acted cytoprotective, activation of the ER stress protein kinase PERK and subsequent expression of CHOP was pivotal for the onset of drug/TNF-induced apoptosis. While inhibition of the Nrf2-dependent adaptive oxidative stress response enhanced the drug/TNF cytotoxicity, Nrf2 signaling did not affect CHOP expression. Both hepatotoxic drugs enhanced expression of the translational initiation factor EIF4A1, which was essential for CHOP expression and drug/TNFM-oM-^AM-!-mediated cell killing. Our data support a model in which enhanced drug-induced translation initiates PERK-mediated CHOP signaling in an EIF4A1 dependent manner, thereby sensitizing towards caspase-8-dependent TNF induced apoptosis. 4 biological  replicates of Diclofenac and 6 biological replicates of vehicle.  46 hours after isolation, cells were exposed to either 300 M-BM-5M DCF or the solvent DMSO for 24 hours."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - Forty-six hours after isolation, hepatocytes were exposed to either 300 M-5M DCF or the solvent DMSO.","Hybridization - hybridized to the Affymetrix Mouse Genome 430 2.0 GeneChip arrays, according to the manufacturerM-bM-^@M-^Ys instructions.","Growth Protocol - Primary mouse hepatocytes were isolated from 8-10 weeks old male C57BL/6 mice by a modified two-step collagenase perfusion technique (collagenase type IV, Sigma-Aldrich, Zwijndrecht, The Netherlands), as described by van Kesteren et al. (2011). In short, hepatocytes suspensions with at least 80% viability were seeded onto plates coated with collagen gel and after attachment overlayed with a second layer of collagen gel, to form a sandwich configuration. Cells were kept in serum-free medium and the culture medium was changed daily until exposures were performed.","Scaning - After hybridization the array chips were washed and stained with a Genechip Fluidics Station 450 and scanned using the Affymetrix gene chip scanner 3000.","Nucleic Acid Extraction - RNA was extracted using TRIzol (Invitrogen) and purified using a RNeasy mini kit (Qiagen), both according to the manufacturerM-bM-^@M-^Ys protocol.","Labeling - Labeled RNA was prepared using the Affymetrix gene chip 3M-bM-^@M-^YIVT express kit"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Bram Herpers","Giulia Benedetti","Marjo de Graauw","Lisa Fredriksson","Mirjam Luijten","John Meerman","Steven Wink","Bob van de Water","Hans de Bont","Geny Groothuis","Erik Danen","Mackenzie Hadi"],"data_protocol":["Data Transformation - Affymetrix CEL files were each checked on quality, including RNA degradation control, correlation and clustering. All quality checks were within acceptable limits, according to Affymetrix standards. After quality control the files were normalized with the Multichip Average (RMA) procedure (Irizarry et al., 2003), using the custom chip description files (CDFs) as described by de Leeuw et al. (2008). Of the hybrid probe-set definitions included in the custom annotation, only the 16,331 probe sets selected according to Dai et al. (2005) and the 4,648 Affymetrix probe sets corresponding to an Entrez Gene ID were used for further analysis, giving a total of 20,979 probe sets. Principal Component Analysis (PCA) was used to rule out effects of the experimental variables. For detecting significantly regulated genes, the microarray analysis of variance (MAANOVA) package in R was used (R version 2.9.2, www.r-project.org). For the analyses on significantly regulated genes per compound between treated and control samples, an F1-test was used. Gene-specific P-values were corrected with a Benjamini- Hochberg false discovery rate (FDR) with a cut-off at 0.05 (Benjamini and Hochberg, 1995). ID_REF =  VALUE = log2 RMA signal"],"additional_accession":[]},"is_claimable":false,"name":"Expression data from primary mouse hepatocytes treated with Diclofenac","description":"Drug-induced liver injury (DILI) is an important clinical problem. Here we used a genomics approach to establish the critical drug-induced toxicity pathways that act in synergy with the pro-inflammatory cytokine tumor necrosis factor M-oM-^AM-! (TNFM-oM-^AM-!) to cause cell death of liver HepG2 cells. Transcriptomics of the cell injury stress response pathways initiated by two hepatoxicants, diclofenac and carbamazepine, revealed the endoplasmic reticulum (ER) stress/translational initiation signaling and Nrf2 antioxidant signaling as two major affected pathways, which was similar to that observed for the majority of ~80 DILI compounds in primary human hepatocytes. The ER stress was primarily related to PERK and ATF4 activation and subsequent expression of CHOP, which was all independent of TNFM-NM-1 signaling. Identical ATF4 dependent transcriptional programs were observed in primary human hepatocytes as well as primary precision cut human liver slices. Targeted RNA interference studies revealed that while ER stress signaling through IRE1M-NM-1 and ATF6 acted cytoprotective, activation of the ER stress protein kinase PERK and subsequent expression of CHOP was pivotal for the onset of drug/TNF-induced apoptosis. While inhibition of the Nrf2-dependent adaptive oxidative stress response enhanced the drug/TNF cytotoxicity, Nrf2 signaling did not affect CHOP expression. Both hepatotoxic drugs enhanced expression of the translational initiation factor EIF4A1, which was essential for CHOP expression and drug/TNFM-oM-^AM-!-mediated cell killing. Our data support a model in which enhanced drug-induced translation initiates PERK-mediated CHOP signaling in an EIF4A1 dependent manner, thereby sensitizing towards caspase-8-dependent TNF induced apoptosis. 4 biological  replicates of Diclofenac and 6 biological replicates of vehicle.  46 hours after isolation, cells were exposed to either 300 M-BM-5M DCF or the solvent DMSO for 24 hours.","dates":{"release":"2014-01-22T00:00:00Z","modification":"2023-09-07T07:19:35.981Z","creation":"2022-03-14T12:41:05.361Z"},"accession":"E-GEOD-54256","cross_references":{"GEO":["GSE54256"],"EFO":["EFO_0002768"]}}