Genome-wide comparison of differentially expressed genes in hepatoma cell lines with and without treatment of dimethyl dicarboxylate biphenyl. Genome-wide comparison of differentially expressed genes in hepatoma cell lines with and without treatment of dimethyl dicarboxylate biphenyl

Backgrounds/Aims: Dimethyl dicarboxylate biphenyl (DDB), a synthetic compound of Schizandrin C, is an adjuvant medicine to support the treatment of various hepatitis. Although it protects hepatocytes from different toxic chemicals, the principal pharmaco-biological mechanism of DDB is still unclear. This study aimed to identify genes changed by the DDB in hepatoma cell lines. Methods: Using Agilent SurePrint G3 Human GE 8X60K, V3 Microarrays, we analyzed the DDB-induced genes genome-widely in a hepatoblastoma (HB) cell line, HepG2, and two hepatocellular carcinomas (HCC), Hep3Band Huh7, after 48 hours of exposure to 0.1 mM DDB. We explored data using the software packages edgeR and limma and KEGG pathway analysis and re-confirmed with RT-PCR for several selected genes. Results: Hierarchical clustering, heatmap, and MDS plot analysis showed that HepG2 belonged to the different cluster from the HCC cell lines. When compared among the DDB-untreated control cells (con), number of genes expressed higher and lower (≥1.5 folds (≥.2 folds)) than the other was 5530 vs. 5250 (2916 vs. 2890) in the Hep3Bcon vs. HepG2con, 5931 vs. 5411 (3172 vs. 3197) in the Huh7con vs. HepG2con, and 4835 vs. 4962 (2483 vs. 2497) in the Huh7con vs. Hep3Bcon, respectively. In the comparison of the DDB-untreated and treated cells in each cell line, the up- and downregulated genes (≥1.5 folds (≥.2 folds)) were 328 vs. 696 (53 vs. 76) in HepG2, 226 vs. 250 (45 vs. 44) in Hep3B, and 250 vs. 229 (51 vs. 47) in Huh7, respectively. Only the CYP1A1 upregulation was significantly common to all three cells. Curiously, the metallothionein genes (MT1G, MT1L, MT2A, MT1E, MT1B, MT1HL1, MT1F, and MT1A) tended to be upregulated by DDB. We also noticed tenascin as a target gene regulating the attachment of cells to the extracellular matrix. Conclusions: HB and HCC have different properties regarding the gene expression in the baseline state. The different responses of each cell line to the DDB are inherent given the genomewide difference of gene expression. CYP1A1 and metallothionein are the target genes of DDB that are common to the three cell lines. Overall design: Dimethyl dicarboxylate biphenyl (DDB)-induced gene expression in three different human hepatoma cell lines, including HepG2, Hep3B, and Huh7, was compared after 48 h of culture with 0.1 mmol/L DDB between the DDB-treated and -untreated cell. Also, we compared gene expression between Control-HepG2 and Control-Hep3B, between Control-HepG2 and Control-Huh7, and between Control-Hep3B and Control-Huh7. DDB DMSO (7.6 g/L) was used as a control reagent.