Dataset on transcriptomic profiling of cholestatic liver injury induced by food additives and a cosmetic ingredient

The provided dataset describes the differential gene expression profile of human hepatoma HepaRG cells cultured in monolayer configuration upon treatment with chemical compounds with cholestatic potential, including food additives sunset yellow and tartrazine and cosmetic ingredient triclosan, while being exposed to a highly concentrated bile acid mixture. Whole genome microarray Affymetrix Human U133 plus 2.0 was used to obtain the raw data followed by normalization, summarization and background adjustments by means of Robust Multichip Average Express software. Raw data of the different conditions were included as .CEL files in the Gene Expression Omnibus with accession number GSE169072. These data may serve as the basis for further refinement studies to establish an adequate transcriptomic signature of chemical-induced cholestasis fit-for-purpose in screening the cholestatic liability of different types of chemical compounds.


Specifications
Bioinformatics, hepatology and toxicology. Specific subject area Cholestatic liver injury Type of data Raw Data How data were acquired Affymetrix GeneChip Human Genome U133 plus 2.0 array (ThermoFisher, Belgium) Ingenuity Pathway Analysis (IPA) (Qiagen, Belgium) Transcriptome Analysis Console (TAC) (ThermoFisher, Belgium) Data format Raw (.CEL), normalized and analyzed Parameters for data collection Cryopreserved differentiated human hepatoma HepaRG cells (Biopredic International, France) were cultured according to the manufacturer's instructions (Biopredic International, France). HepaRG cells were exposed to 13 mM acetaminophen (APAP), 10 mM sunset yellow (SUN), 50 mM tartrazine (TART) and 0.050 mM triclosan (TRI). Simultaneously, HepaRG cells were co-exposed to a bile acid (BA) mixture, which is 50 × concentrated and consists of 5 BAs, including 66 μM glycochenodeoxycholic acid, 20 μM deoxycholic acid, 19.5 μM chenodeoxycholic acid, 19 μM glycodeoxycholic acid, and 17.5 μM glycocholic acid. Both the 50 × concentrated BA mixture and the tested compounds were included in the cell culture medium of HepaRG cells from day 7 after seeding. HepaRG were routinely exposed for 72 h with daily renewal of the cell culture medium, including the 50 × concentrated BA mixture and tested chemicals.

Value of the Data
• This data reflects a genome-wide gene expression signature of non-pharmaceuticals, including food additives and a cosmetic ingredient, with a presumed cholestatic liability. • The data may assist further research in the development of in vitro tools applicable for assessing the cholestatic liability of both pharmaceutical as non-pharmaceutical compounds, while identifying novel mechanisms underlying chemical-induced cholestasis. • The data supports possible follow-up experiments that refine the established transcriptomic signature of cholestasis, as foundation for an improved technique that accurately predicts different types of chemical-induced cholestasis.

Data Description
A total of 3 different batches of HepaRG cells were exposed to 3 non-pharmaceutical compounds, namely the food additives SUN (10 mM) and TART (50 mM) and cosmetic ingredient TRI (0.050 mM), which were believed to bear a cholestatic risk [ 2 , 3 ], in the presence of a 50 × concentrated BA mixture ( i.e. datasets SUNSET + BA 1-3; TART + BA 1-3 and TRI + BA 1-3). Next to these cholestatic compounds, the non-cholestatic hepatotoxic compound APAP was included in the transcriptomic analysis to verify the specificity of the obtained profile of cholestatic liver injury. HepaRG cells were exposed to the cytotoxic concentration that achieves 50% viability (IC 50 ) of APAP, being 13 mM, in the presence of the 50 × concentrated BA mixture ( i.e. datasets APAP + BA 1-3). HepaRG cells were also solely exposed to the 50 × concentrated BA mixture to identify BA-induced transcriptional changes ( i.e. datasets BA 1-3). The control consisted of Hep-aRG cells solely exposed to the vehicle ( i.e. datasets CTL 1-3). After 72 h of exposure, HepaRG cells were sampled, and RNA was isolated. Transcriptomic data were obtained using Affymetrix Human Genome U133 plus 2.0 which, in turn, were processed by the software program Robust Multichip Average (RMA) Express [4] . Gene expression analysis was performed with Transcriptome Analysis Console Software (version 4.0.025, Applied Biosystems) and Ingenuity Pathway Analysis (version 62089861, Qiagen) [5] with a cut-off fold change of ≤−1.5 and ≥1.5, and False Discovery Rate p -value < 0.05 calculated via ANOVA and Benjamini-Hochberg correction. Transcriptomic data generated by the different conditions were visualized by presenting the absolute number of significantly modulated genes ( Fig. 1 ) and volcano plots ( Fig. 2 ). The top 30 differentially expressed genes of each condition were presented in Table 1 . Potentially interesting canonical pathways related to cholestasis were introduced in Fig. 3 and compared to previously published datasets in HepaRG cells treated with the cholestatic drugs, atazanavir (ATA, 60 μM), cyclosporin A (CsA, 20 μM) and nefazodone (NEFA, 30 μM) in the presence of a 50 × concentrated BA mixture [6] .

Experimental Design, Materials and Methods
Cryopreserved differentiated HepaRG cells, including the required culturing reagents, were all purchased from Biopredic International, France. HepaRG cells were thawed and seeded in basal hepatic medium enriched with HepaRG Thawing/Plating/General Purpose Medium Supplement with antibiotics following manufacturer's instructions. HepaRG cells were seeded onto 24 well plates at a concentration of 0.48 × 10 6 cells/well coated with rat tail collagen (0.1 mg/ml) (Corning, Sigma Aldrich, Belgium). Afterwards, the HepaRG cells were allowed to attach for about 24 h and subsequently refreshed every 2, 3 days with basal hepatic medium enriched with Maintenance/Metabolism Medium Supplement with antibiotics. After 7 days of cultivation, Hep-aRG cells were exposed to APAP (13 mM), SUN (10 mM), TART (50 mM) and TRI (0.050 mM) (Sigma Aldrich, Belgium) with a 50 × concentrated BA mixture ( i.e. 66 μM glycochenodeoxycholic acid, 20 μM deoxycholic acid, 19.5 μM chenodeoxycholic acid, 19 μM glycodeoxycholic acid, and 17.5 μM glycocholic acid (Sigma Aldrich, Belgium)) added to the cell culture medium. Stock solutions from TRI and the BAs were made in DMSO. The final incubation solutions were prepared ex tempore by diluting the stock solution with basal hepatic cell medium enriched with Serum-free Induction Medium Supplement with antibiotics (Biopredic International, France). Final solutions of APAP, SUN and TART were directly prepared in the induction serum-free medium. All conditions contained a final DMSO concentration of 0.25% v/v. HepaRG cells were exposed for 72 h to the tested compounds and the BA mixture. Afterwards, cell culture medium was aspirated, and cells were lysed by means of a lysis buffer (lysis solution with 1/100 β-mercaptoethanol, Qiagen, Belgium). Total RNA extraction was performed with the RNeasy Mini Kit (Qiagen, Belgium) according to manufacturer's instructions. Subsequently, purity and quantification of the acquired and isolated RNA were determined via spectrophotometric analysis by means of a NanoDrop® ND-100 Spectrophotometer (ThermoFisher Scientific, Belgium). A cut-off ratio of [1.8-2.1] for the absorption at 260/280 nm was respected during the purity assessment.

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this article.