XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells

Emerging data suggest that induction of viral mimicry responses through activation of double-stranded RNA (dsRNA) sensors in cancer cells is a promising therapeutic strategy. One approach to induce viral mimicry is to target molecular regulators of dsRNA sensing pathways. Here, we show that the exoribonuclease XRN1 is a negative regulator of the dsRNA sensor protein kinase R (PKR) in cancer cells with high interferon-stimulated gene (ISG) expression. XRN1 deletion causes PKR pathway activation and consequent cancer cell lethality. Disruption of interferon signaling with the JAK1/2 inhibitor ruxolitinib can decrease cellular PKR levels and rescue sensitivity to XRN1 deletion. Conversely, interferon-b stimulation can increase PKR levels and induce sensitivity to XRN1 inactivation. Lastly, XRN1 deletion causes accumulation of endogenous complementary sense/anti-sense RNAs, which may represent candidate PKR ligands. Our data demonstrate how XRN1 regulates PKR, and how this interaction creates a vulnerability in cancer cells with an activated interferon cell state. Overall design: To determine the RNA transcripts that are regulated by XRN1 in human cancer cell lines, we performed strand-specific RNA sequencing on rRNA-depleted samples from control, XRN1 knockout, PKR knockout, or XRN1/PKR double knockout HCC366 cells and control or XRN1 knockout NCI-H1650 cells. To understand the gene expression changes induced with each condition, we performed standard differential gene expression analysis between samples within each cancer cell line. To identify candidate double-stranded RNA transcripts that may stimulate PKR activation after XRN1 deletion, we developed a novel computational pipeline with which we found that XRN1 deletion causes increased accumulation of complementary sense and anti-sense RNA transcript pairs.