Single-cell transcriptomics of Pacific white shrimp hepatopancreas reveal immune and metabolic responses to AHPND causing Vibrio parahaemolyticus

Authors: ALDERSEY, JO - Orise Fellow; Abernathy, Jason; Lange, Miles; Garcia, Julio; Shoemaker, Craig; Beck, Benjamin

Submitted to: Frontiers in Immunology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/2/2026
Publication Date: 1/27/2026
Citation: Aldersey, J., Abernathy, J.W., Lange, M.D., Garcia, J.C., Shoemaker, C.A., Beck, B.H. 2026. Single-cell transcriptomics of Pacific white shrimp hepatopancreas reveal immune and metabolic responses to AHPND causing Vibrio parahaemolyticus. Frontiers in Immunology. 17(2026):1713369. https://doi.org/10.3389/fimmu.2026.1713369.
DOI: https://doi.org/10.3389/fimmu.2026.1713369

Interpretive Summary: The shrimp aquaculture industry is vulnerable to large losses due to acute hepatopancreatic necrosis disease (AHPND), caused by the bacterium Vibrio parahaemolyticus. The mechanism by which the pathogen causes disease, and the host immune response, is not completely understood. The shrimp hepatopancreas is a multi-functional organ with roles in digestion, immunity, molting and reproduction. Therefore, we set out to characterize the cells of the hepatopancreas and the host response to Vibrio parahaemolyticus infection at single-cell resolution. The hepatopancreas from three individual shrimp were processed to create a single-cell transcriptomic atlas. Then the hepatopancreas from three Vibrio parahaemolyticus infected and two mocked treated shrimp were sampled for infection study. Individual cells of the hepatopancreas were characterized and the gene expression response to AHPND-causing V. parahaemolyticus was examined. The gene expression profiles of over 25,000 individual cells of the hepatopancreas were determined and specific cell types identified. Gene expression changes in response to AHPND included the alteration of both metabolic and immune system processes, indicating the importance of these two biological systems and processes in response to the disease. The outcomes will now be used to inform future functional studies and provide insights toward novel preventative measures or treatments.

Technical Abstract: Background: The shrimp aquaculture industry is severely impacted by acute hepatopancreatic necrosis disease (AHPND) caused by the bacterium Vibrio parahaemolyticus. The hepatopancreas is a multi-functional organ with roles in digestion, immunity, molting and reproduction. The mechanism by which the pathogen causes disease, and the host immune response is not completely understood. Therefore, we set out to characterize the cells of the hepatopancreas and host response to bacterial infection at single-cell resolution. Methods: First, hepatopancreas from three healthy Pacific white shrimp (Litopenaeus vannamei) were sampled to produce a single-cell transcriptomic atlas. Then, the hepatopancreas from three V. parahaemolyticus infected and two mocked treated shrimp were sampled for infection study. Primary cell suspensions were produced, and single-cell libraries were generated using the 10x Genomics Chromium X controller with GEM-X 3’ gene expression reagents. Data were aligned with Cell Ranger to the shrimp reference genome ASM4276789v1. Seurat and clusterProfiler were used for downstream analyses. Results: The atlas consists of 11,006 quality cells that were grouped into nine clusters, and represent the hepatopancreas epithelial cells, myocytes and hemocytes. The infection study generated 16,368 quality cells which were grouped into nine clusters. Cells from the infected shrimp exhibited expression of immune related genes including pathogen recognition receptors, hemocyanin, trypsin, chymotrypsin, peritrophins and chitin-binding proteins. We also found that cells expressed factors that the PirA/B toxins present in infective V. parahaemolyticus may bind to such as fatty acid binding protein (fabp). In response to infection, energy metabolism (oxidative phosphorylation, glycolysis, gluconeogenesis) was altered in a cluster-dependent manner. Other metabolic pathways altered in response to infection included fatty acid metabolism and cysteine/methionine metabolism. Conclusions: We characterized the cells of the hepatopancreas and examined the transcriptomic response to a virulent isolate of V. parahaemolyticus causing AHPND. Cells exhibited both immune and metabolic responses, suggesting the role of these processes in the activation of signaling cascades toward immune responsiveness to the pathogen. The outcomes will inform future functional studies and provide insights toward novel preventative measures or treatments.