Extensive Proteomic Approach to Assess Protein Alterations in Human Hepatoma Huh7 Cells Infected with West Nile Virus

West Nile Virus (WNV) is a significant global health threat, and the molecular mechanisms of its pathogenic activity in human hosts remain partially understood. This study applies an extensive proteomic approach combining "top-down" (2DE/MS) and "bottom-up" (LC-MS/MS) technologies to investigate protein changes in the Huh7 human hepatoma cellular model at 48 h post-infection with WNV. Our results demonstrate that WNV infection induces a massive downregulation of host proteins, particularly those involved in cell-cell adhesion and extracellular matrix (ECM) integrity (FN1, VTN, desmosome proteins and tight junctional proteins), which supports theories of blood-brain barrier disruption. Moreover, we highlighted a modulation of iron homeostasis (FTH1, IRP1, and IREB2) reflecting a "nutritional immunity" host response aimed at limiting host enzyme functions essential for virus replication. In particular, the top-down approach demonstrated a significant protein species modulation related to the unfolded protein response (UPR) (HSP90, HSPA8), as well as the hijacking of translation initiation factors (EIF1, eIF3 complex, and EIF4A1), which suggests viral strategies for immune evasion and efficient replication. Taken together, these findings offer a comprehensive overview of WNV-induced perturbations, revealing the quantitative modulation of proteins and potential post-translational signatures, thereby providing a robust foundation for identifying new antiviral drug targets and therapeutic strategies.