Single cell transcriptomics of Atlantic salmon (Salmo salar L.) liver reveals cellular heterogeneity and immunological responses to challenge by Aeromonas salmonicida

The liver is a multitasking organ with essential functions for vertebrate health spanning metabolism and immunity. To explore the multifaceted role played by liver cells in response to bacterial infection in fishes, we generated a transcriptomic atlas of nuclei isolated from the liver of Atlantic salmon (Salmo salar L.), contrasting control fish with those challenged with a pathogenic strain of Aeromonas salmonici. We found a dominant hepatocyte population that radically remodels its transcriptome following infection to activate the acute phase response and other defense functions, while repressing routine functions such as metabolism. In addition, we discover numerous cell specific responses to infection within the immune cell compartments, and identify many novel cell-specific marker genes to empower future studies of this organ in fishes. Twenty Atlantic salmon were anaesthetized and given an intraperitoneal injection of either PBS (n=10), or the pathogenic Hooke strain of A. salmonicida (n=10). Sampling was performed 24 h post-injection and control (n=2) and infected (n=2) fish were selected based on immune response validated with qPCR. Single nucleus libraries were constructed according using the 10x Genomics Chromium platform.