Knockdown of RNA editing proteins reshapes the HepaRG transcriptome and pharmacogene expression

The RNA-editing proteins ADAR and ADARB1 regulate gene expression through both editing-dependent and editing-independent mechanisms. RNA-Seq analysis of HepaRG cells after knocking down (KD) either protein caused widespread transcriptomic changes, including nearly 1,000 pharmacogenes that were either differentially expressed or alternatively spliced, with isoform switches observed in HNF4A and CYP2C9. These effects were editing-independent, and the two treatments primarily affected distinct gene sets, with ADAR KD having broader effects than ADARB1 KD. Because ADAR KD triggers a type I interferon response, we compared siADAR and IFNα treatments. Although both activated interferon signaling, their transcriptional profiles differed markedly. Despite this, 70% of siADAR-responsive genes were rescued by BX795, an inhibitor of the interferon pathway. Therefore, many of siADAR’s effects are likely due to the activation of immune pathways. Overall, our findings indicated that the ADARs maintain hepatic homeostasis and regulate numerous pharmacogenes, especially those involved in drug metabolism and disposition.