Integrative proteomics and lipidomics reveals dual roles for lipid droplets in the host cell antiviral response

Lipid droplets (LDs), once viewed as inert lipid storage sites, are now recognised as dynamic organelles central to cellular signalling and immunity. This study presents a dual-omics approach, integrating proteomics and lipidomics, to investigate LDs in the host antiviral response. In vivo and in vitro RNA viral infection models demonstrate that LDs rapidly remodel both their proteome and lipidome. The antiviral proteins RIG-I, MDA5, STAT1, STAT2, and viperin are specifically recruited to virus-induced LDs. Simultaneously, the LD lipidome shifts toward enrichment in long-chain polyunsaturated fatty acids and bioactive phospholipids, likely enhancing membrane dynamics and protein recruitment. Correlation analysis of matched proteomic and lipidomic datasets revealed extensive lipid–protein co-regulation on LDs and identified distinct correlation networks in which immune and antiviral proteins preferentially aligned with neutral lipid species. Enzymes involved in lipid metabolism and post-translational modifications are also upregulated, suggesting a mechanistic link between lipid remodeling and protein localisation. Functional assays utilizing artificial LDs revealed that arachidonic-acid and eicosapentaenoic-acid suppress viral replication and enhance type I and III interferon responses. These findings position LDs as key immunometabolic platforms in early antiviral defence. Dual proteomics–lipidomics demonstrates that virus-induced lipid droplets rapidly recruit antiviral proteins and remodel lipids. These lipid–protein networks form signalling hubs, while specific long chain fatty acids enhance interferon responses and restrict viral replication.