RNA-sequencing reveals ECM-remodeling and tumorigenesis in Pacific mackerel with Puffy Snout Syndrome

Puffy Snout Syndrome (PSS) is an emerging, high-mortality condition of captive scombrids characterized by collagenous craniofacial overgrowth and tissue remodeling. Despite its prevalence in aquaculture, the molecular mechanisms underlying PSS remain unknown. Here, we performed mRNA and small RNA sequencing on facial tissues from wild-caught healthy, asymptomatic captive, and symptomatic captive Pacific mackerel (Scomber japonicus) to characterize transcriptional and post-transcriptional changes associated with the syndrome. Principal component analysis revealed strong separation between captive and wild groups, with symptomatic fish exhibiting the most pronounced transcriptional divergence. Across comparisons, 2293 genes were differentially expressed, with symptomatic fish showing enrichment of cancer-associated pathways (e.g., Wnt signaling, extracellular matrix-receptor interactions) and immune processes including leukocyte activation and MAPK signaling. Asymptomatic fish also exhibited cancer-related and proliferative gene signatures, suggesting early molecular changes precede visible pathology. Key Wnt ligands (wnt9b, wnt3a, wnt10a) were overexpressed in captive groups, while immune effectors (ccl20a.4, perforin-1) were downregulated in symptomatic fish, indicating concurrent proliferative activation and immune suppression. MicroRNA profiling identified differential expression of tumor-suppressive gmo-let-7h-2, immune-regulatory ola-miR-223, and stress-responsive tni-miR-212, with predicted targets enriched for extracellular matrix organization, cytokine signaling, and neuronal processes. This study provides the first transcriptomic and miRNA evidence linking neoplastic signaling, immune dysregulation, and extracellular matrix remodeling to PSS. The detection of cancer-like molecular signatures in asymptomatic fish highlights potential for early diagnosis and monitoring. These findings establish a molecular framework for investigating PSS etiology, inform biomarker development, and underscore the need to evaluate environmental and infectious triggers in scombrid aquaculture.