Integrated transcriptomic and proteomic analyses reveal immune activation and suppressed oxidative phosphorylation modules in chronic neck injection-site lesions of finishing pigs.

Abstract

Routine intramuscular neck injections, including vaccination, are frequently associated with persistent injection-site lesions (ISLs) in finishing pigs, leading to carcass trimming and economic loss. Here, we performed paired transcriptomic and TMT-based proteomic profiling of chronic neck ISLs and matched grossly normal neck muscle from the same animals. Grossly, lesions were palpable nodules with cavitary changes and turbid contents. Histology showed chronic inflammation with focal myofiber degeneration/necrosis and fibrous encapsulation. Integrative analysis identified 130 overlapping features with concordance between transcript and protein fold-changes. Enrichment analysis indicated a distinct split: upregulated features involved innate immune and phagosome-related pathways, whereas downregulated features were dominated by mitochondrial oxidative phosphorylation modules in bulk tissue. These data support a bulk immunometabolic signature of sustained inflammatory programs alongside suppressed oxidative phosphorylation in chronic ISLs, which may inform mitigation strategies under field conditions.