Transcriptomic insights into the immune responses of the lung and muscle of non-healthy harbor porpoises (Phocoena phocoena)

Non-healthy harbor porpoises showed a distinct host-pathogen defense reaction in the lung, suggesting similarities to immune responses of humans suffering from lung diseases, which may be conserved along the mammalian lineage despite vastly different habitats. However, the lung transcriptomes did not indicate a Th2 immune response which is typically activated upon parasitic insults. Severely infected harbor porpoises may be overwhelmed or weakened by prolonged parasitic exposure and immune activation, possibly affecting simultaneous pathogenic clearance and tissue repair. The muscles of non-healthy harbor porpoises exhibited enhanced stress signaling and tightly regulated tissue degradation/regeneration, potentially reflecting a chronic inflammation state. Higher expression of hypoxia- and oxidative stress-associated transcripts in the muscle were consistent with hypoxia-induced transcriptional patterns and suggest a systemic pathological challenge. The <i>de novo</i> assembly identified significantly dysregulated non-coding RNAs in the lung and muscle which may be associated with regulatory processes. Several transcripts of the <i>de novo</i> assembly remained unidentified, thus their putative function needs to be elucidated. In marine mammals, the understanding of molecular immune responses still remains incomplete. This is the first study to describe the lung transcriptome of wild harbor porpoises in regard to pathophysiology. These insights contribute to the understanding of the interaction between anthropogenic impacts, infectious diseases and molecular immune responses in cetaceans, thus supporting cetacean health assessments and conservation efforts.