Proteomic insights into antiviral immunity: Comparative analysis of diploid, triploid, and allotetraploid cells reveals ploidy-specific defense mechanisms against SVCV infection

While triploid fish (3 n = 150) exhibited superior antiviral capability relative to both diploid (2 n = 100) and allotetraploid (4 n = 200) progenitors, the molecular basis for this enhanced resistance remained poorly characterized. This study explored the proteomic responses of caudal fin cells from red crucian carp (2 n), triploid hybrids (3 n), and allotetraploid fish (4 n) post spring viremia of carp virus (SVCV) challenge, focusing on how polyploidy affected cellular defense. Through comparative proteomic analysis, distinct molecular strategies emerged across different ploidy levels. Triploid (3 n) and allotetraploid (4 n) cells exhibited a greater number of differentially expressed proteins (DEPs) than diploid (2 n) cells, likely due to increased genomic content and gene dosage effects. Functional enrichment analysis highlighted that 3 n cells had significant metabolic adaptability, with up-regulated pathways including the tricarboxylic acid (TCA) cycle and proteolysis, both essential for strong antiviral responses. In contrast, 2 n and 4 n cells exhibited reduced activity in metabolic pathways, suggesting a shift in energy allocation from metabolism to immune function. Combinatorial analysis of transcriptomic and proteomic landscapes revealed a concerted regulation of differentially expressed extracellular matrix (ECM) components in 3 n and 4 n cells, with proteins such as COL6A, FN1, and LAMB1 playing key roles in the antiviral response. Notably, the increased expression of LAMB1 in 3 n cells, combined with down-regulation of FLNA and MYL9, pointed to a distinctive balance between structural support and intracellular signaling. Functional validation confirmed the proviral role of MYL9, as its overexpression significantly enhanced SVCV replication and viral gene expression in vitro. These results outlined a detailed framework for understanding how genomic complexity shapes antiviral defense and emphasized the role of metabolic and structural reprogramming in immune protection.