Transcriptome analysis of mRNA and long non-coding RNA profiles in the brains of CVA10-infected suckling mice

Hand, foot, and mouth disease (HFMD) caused by Coxsackievirus A10 (CVA10) remains an important public health concern. Although most infections are self-limiting, severe cases may develop neurological complications, including acute flaccid paralysis and aseptic meningitis. However, host transcriptional responses to CVA10 infection within the central nervous system (CNS) remain poorly understood. Here, we established a CVA10-infected ICR suckling mouse model and performed transcriptomic profiling of brain tissues using RNA-seq, followed by RT-qPCR validation. A total of 243 differentially expressed mRNAs and 776 differentially expressed lncRNAs were identified in the brains of CVA10-infected mice. Interferon-stimulated genes (ISGs) such as Ifit1 exhibited significant dysregulation in CVA10-infected brain tissue. Integrated GO and KEGG functional enrichment analyses revealed that these genes were significantly associated with innate immune and inflammatory responses, particularly interferon-related signaling pathways. Protein-protein interaction network analysis identified ten immune-related hub genes, including Irf7, Rsad2, Isg15, Stat1, Ifih1, Ifit1, Ifit3, Oasl2, Rtp4 and Usp18. RT-qPCR validation showed overall agreement with RNA-seq findings, supporting the reliability of the transcriptomic analysis. Long non coding RNAs can extensively regulate these immune-related genes in both directions. These results offer a foundation for further investigation of the molecular basis of CVA10-related neurological disease, and for exploring candidate biomarkers and molecular targets.