Systems-Level Analysis of HPAI H5N1 Infection in Ducks: Integrating Transcriptomic, Proteomic, and Phosphoproteomic Data

Ducks, once considered mere reservoirs, now serve as both victims and amplifiers of persistent highly pathogenic avian influenza (HPAI) virus cycles in wild populations. The molecular pathogenesis of HPAI is shaped by complex, dysregulated molecular networks, necessitating a systems biology approach that integrates computational modeling of host-pathogen interactions. Despite recent advances, a comprehensive understanding of the signaling pathways, molecular mechanisms, and hub genes driving HPAI H5N1 pathogenesis in avian hosts remains incomplete. This study addresses this gap by employing an integrated multi-omics strategy-combining transcriptomic, proteomic, and phosphoproteomic analyses-to map the signaling networks and key host factors involved in HPAI H5N1 infection in duck lung tissue. Our network analysis revealed activation of RIG-I-like receptor, toll-like receptor, NOD-like receptor, NF-κB, and JAK/STAT signaling pathways. Phosphoproteomic profiling independently confirmed the activation of these pathways, supporting the integrated network findings. Key regulatory hub genes identified include <i>STAT1</i>, <i>DDX58 (RIG-I)</i>, <i>MYD88</i>, <i>NFKBIA</i>, <i>NFKB1</i>, <i>IRF7</i>, <i>SOCS3</i>, <i>ACTB</i>, <i>TLR4</i>, <i>TLR7</i>, <i>IL-6</i>, <i>CASP1</i>, <i>and CASP8</i>, which form a central hub in duck antiviral immunity. Some of these genes may represent promising targets for therapeutic or vaccine development against avian influenza. Collectively, this work delineates the critical signaling pathways and hub genes underlying HPAI H5N1 pathogenesis in ducks through comprehensive multi-omics integration.