XRN1-dependent RNA homeostasis regulates hepatitis D virus

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Abstract

Hepatitis delta virus (HDV) infection causes the most severe form of viral hepatitis, yet the host mechanisms restricting HDV replication remain poorly understood. Although HDV infection activates the MDA5-LGP2 pathway and induces robust interferon (IFN) responses, these antiviral programs have limited impact on viral replication. Here we identify the 5’-3’ exoribonuclease XRN1 as a key regulator of HDV infection. Loss of XRN1 in hepatoma cells increased double-stranded RNA (dsRNA) levels and induced interferon-stimulated genes (ISGs), including MDA5 and MAVS, and limited HDV infection. XRN1 deficiency enhanced ADAR1-mediated RNA editing, revealing a dynamic interplay between endogenous dsRNA metabolism and antiviral sensing. Inhibition of type I IFN signaling restored MDA5 expression and rescued HDV replication in XRN1-deficient cells. To identify the downstream effectors responsible for this restriction, we combined transcriptomic profiling with functional siRNA screening and identified DUSP5 and SIRPA as previously unrecognized ISGs with anti-HDV activity. Together, our findings establish XRN1 as a gatekeeper of dsRNA homeostasis that controls HDV replication through innate immune activation and reveals host antiviral effectors that may provide therapeutic opportunities for chronic hepatitis D.

Activation of dsRNA sensing pathway following XRN1 depletion upregulates IFN production and IFN downstream pathways, leading to increases in host defenses to HDV infection. In addition XRN1 depletion increases ADAR1 expression, which increases L-HDAg levels and suppresses HDV replication. Image created in BioRender : https://BioRender.com/t73u45i

AUTHOR SUMMARY

Hepatitis D virus causes the most severe form of viral hepatitis, yet how our cells defend against this virus remains poorly understood. Although infection triggers strong immune responses, their effects on viral replication are limited. In this study, we identified XRN1, an enzyme involved in cellular RNA degradation, as an important regulator of hepatitis D virus infection. We found that loss of XRN1 causes the accumulation of double-stranded RNA, activates antiviral immune responses, and suppresses viral replication. We also observed increased RNA editing, highlighting the connection between RNA metabolism and antiviral immunity. Furthermore, we identified two previously unrecognized antiviral factors, DUSP5 and SIRPA, that contribute to controlling viral infection. Our findings reveal how cellular RNA degradation regulates antiviral defenses and suggest potential new approaches to treating chronic hepatitis D.

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  1. XRN1-dependent RNA homeostasis regulates hepatitis D virus https://www.biorxiv.org/content/10.64898/2026.11.01.763535v1

  2. XRN1-dependent RNA homeostasis regulates hepatitis D virus https://www.biorxiv.org/content/10.64898/2026.11.01.763535v1