Molecular Signatures of Zika Virus Infection: Insights into Host Transcriptomic and microRNA Responses in Human Cell Models

Abstract

Zika virus (ZIKV) is a mosquito-borne <em>Flavivirus</em> capable of causing severe neurological complications, including congenital Zika syndrome (CZS) in newborns and Guillain-Barré syndrome (GBS) in adults. Although incidence has declined following the 2015–2016 epidemic in the Americas, ZIKV continues to circulate at low levels and poses a persistent health concern, particularly in regions where <em>Aedes</em> mosquito vectors are endemic or expanding due to climate change. <br/> While the clinical consequences of ZIKV infection are well recognized, the underlying molecular mechanisms driving impact on host development remain poorly understood. Given the emerging roles of microRNAs (miRNAs) and extracellular vesicles (EVs) in gene regulation and intercellular communication, this study primarily investigated how ZIKV modulates host miRNA and mRNA expression in biologically relevant human cell models. <br/> Transcriptomic and miRNA profiling were conducted in long-term neuroepithelial-like stem cells (lt-NES^®), representing early neural development. In parallel, gene expression changes were analysed in HaCaT keratinocytes, which model the skin epithelium as the likely initial site of viral entry. Cells were infected with ZIKV strains from the African (Uganda) and Asian (French Polynesia) lineages. The Asian strain is linked to microcephaly, whereas the neuroteratogenic potential of the African strain remains unclear. Host mRNA responses were assessed by microarray, and intracellular as well as EV-associated miRNAs were profiled by next-generation sequencing. Integrative analyses were conducted to identify regulatory networks and molecular signatures associated with infection. <br/> ZIKV infection resulted in widespread and strain-specific dysregulation of host transcripts and miRNAs. In lt-NES^® cells, infection altered genes and miRNAs involved in neurodevelopmental and oxidative stress pathways, with the African strain inducing stronger cytopathic effects and broader gene expression changes than the Asian strain. Key dysregulated miRNAs, including miR-205-5p, miR-4792, and miR-431-5p, were linked to neuronal differentiation, antiviral defence, and redox regulation. ZIKV infection induced oxidative stress, as indicated by Sestrin 2 (<em>SESN2</em>) upregulation and increased protein carbonylation. In HaCaT cells, a robust induction of interferon-stimulated genes was observed, including <em>BST2</em> (tetherin), which was modulated by fibroblast growth factor 7 (FGF7) treatment. <br/> These findings provide new insights into the molecular mechanisms of ZIKV pathogenesis, revealing transcriptional and post-transcriptional host responses across relevant human cell types. The identification of lineage-specific molecular profiles and regulatory networks enhances the understanding of ZIKV-induced neuropathology and provides candidate molecular signatures that could guide future biomarker discovery and the development of targeted antiviral strategies.