Cross-Cell line transcriptome profiling reveals host-Virus interactions in monkeypox virus infection

The monkeypox virus (MPXV), a re-emerging <i>Orthopoxvirus</i>, has triggered unprecedented global outbreaks, with over 130,000 confirmed cases reported by January 2025. Despite its escalating public health threat, the molecular mechanisms governing MPXV-host interactions remain inadequately characterized. In this study, we systematically explored the impact of MPXV Clade IIb infection on the host transcriptome across diverse cell lines, unveiling both conserved and cell-type-specific transcriptomic changes. Our analysis revealed significant disruptions in pathways associated with immune response, cell cycle regulation, metabolism, protein synthesis, and epigenetic modification. Additionally, we evaluated two widely used mRNA sequencing methodologies for MPXV transcriptome profiling, demonstrating that ribosomal RNA depletion offers a more comprehensive representation of viral mRNA compared to poly(A) tail enrichment. Through cross-cell-line comparisons and temporal transcriptomic analysis in A549 cells, we identified stage-specific regulation of MPXV gene expression. Leveraging the temporal host transcriptome profiles, we predicted and validated potential therapeutic targets, demonstrating that inhibitors targeting the mTOR pathway and growth factor receptors effectively inhibit MPXV infection. Collectively, these findings provide critical insights into the intricate interplay between MPXV and its host, offering a foundation for developing antiviral strategies and advancing our understanding of mpox pathogenesis.