Figure 4: Transcriptional changes induced by PZ in HLCs have universally conserved elements related to oxidative stress.

(a) Principal component analysis of expression data measured by Affymetrix microarray along the first principal component (PC1) and second principal component (PC2) axes. HLCs were treated with 100 μM PZ, represented by black outline, or with DMSO as control. Biological replicates of distinct origin and treatment type contribute to the dominant clusters. A shift in PC2 is seen for all HLCs with PZ treatment compared to their controls. (b) Heatmap visualizing expression levels of genes that undergo the largest PZ-induced changes in HLCs from HT and NHT groups. Top differentially expressed genes were identified for HT-HLCs and for NHT-HLCs and 24 probes corresponding to the union of these two gene lists are depicted. For each HLC, Δ indicates individual log2 fold-changes (log FC) relative to respective control. Each column corresponds to one of three biological replicates for each HLC line. (c) Heatmap of expression of genes in HLCs corresponding to a hepatocyte drug-induced oxidative stress (OS) signature derived from rat liver. Gene names in red are those for which an induction of expression is expected from original rat liver data. (d) GSEA enrichment plots for upregulated genes from OS signature (OS up) in HT-HLCs (i–iii) and NHT-HLCs (iv-v). For each HLC, all genes from expression dataset were rank-ordered according to their fold change between PZ- and control samples. Genes from the ‘OS up’ gene set are indicated by black bars and their rank in rank-ordered expression set suggests a strong bias for their upregulation in PZ-treated samples, reflected by the running enrichment score (ES) that peaks to the left of the plot. The normalized enrichment score (NES) and p-value of significance of enrichment are indicated for each plot.