The anti-splicing drug SRPIN340 inhibits the human papillomavirus life cycle and reverses virus-mediated changes in the infected epithelium

Human papillomaviruses (HPV) infect epithelial causing benign lesions. However, the so- called “high risk” HPVs that infect the anogenital regions and the oropharynx can cause precancerous lesions with can progress to malignant tumours. Understanding the HPV life cycle is important to the discovery of novel antiviral therapies. HPV uses cellular splicing for production of the full suite of viral mRNAs. Members of the serine/arginine rich (SR) protein family can positively regulate splicing. SR protein activity and cellular location is regulated by kinases through phosphorylation of their serine-arginine domains. SR protein kinase 1 (SRPK1) phosphorylates SR proteins to licence their nuclear entry and can promote nuclear splicing in conjunction with another SR protein kinase, Clk1. SRPIN340 is an SRPK1 inhibitor that has been reported to inhibit replication of HCV, Sindbis virus and HIV. Using organotypic raft cultures supporting the HPV16 life cycle we show that SRPIN340 inhibits expression of the viral replication and transcription factor, E2. Drug-mediated loss of E2 is specifically associated with inhibition of late gene expression since early gene expression is unaffected. RNA sequencing revealed that SRPIN340 treatment resulted in a partial reversal of the gene expression changes induced by HPV16 infection. In particular, loss of epithelial barrier structure and immune function was restored. SRPIN340 treatment resulted in changes in alternative splicing of 935 RNAs and pathway analysis showed a predominance of changes to RNAs encoding proteins involved in chromatin conformation, DNA repair and RNA processing. SRPIN340 treatment was not associated with changes in proliferation or differentiation or non-specific toxicity to the host cells. Collectively, these results provide evidence that SRPK1 is a host factor that is essential for HPV16 replication and therefore, targeting this factor or the phosphorylation events it mediates could be considered as a therapeutic strategy for HPV16 infection.