Inhibition of RNA splicing is a novel therapeutic strategy for disruption of nuclear replicating viruses

Abstract

RNA splicing is a fundamental feature of eukaryotic gene expression that is co-opted by many nuclear-replicating viruses to produce viral transcripts. Recent clinical development of spliceosome-targeting therapeutics has demonstrated that splicing can be safely modulated in vivo, raising the possibility that viral dependence on host RNA processing may represent an exploitable antiviral vulnerability. Here, we show that pharmacologic inhibition of cellular RNA splicing preferentially suppresses the expression of spliced viral transcripts and profoundly impairs replication of multiple splicing-dependent viruses. In human adenovirus, low-dose inhibition of the spliceosome using mechanistically distinct chemical inhibitors, or genetic depletion of SF3B1, disrupted splicing of complex late viral transcripts while largely sparing simple early transcripts. This resulted in impaired viral DNA replication, reduced late protein accumulation, and multi-log decreases in infectious progeny production. Splicing inhibitors similarly impaired RNA splicing and viral replication of DNA virus Herpes Simplex virus 1 and RNA virus influenza A, which both rely on host-dependent RNA processing strategies. In contrast, cytoplasmic RNA viruses lacking spliceosome dependence were unaffected, supporting an on-target mechanism. Together, these findings identify viral RNA processing complexity as a determinant of antiviral sensitivity and establish host spliceosome dependence as a shared and targetable vulnerability across diverse viral families.