Spatial Transcriptomics Reveals Region-Specific Host Responses in Amoebic Gill Disease of Atlantic Salmon
- 1University of Glasgow
Abstract
Amoebic gill disease (AGD), caused by the parasite Neoparamoeba perurans, is a major welfare and economic burden for the Atlantic salmon aquaculture industry. However, the spatial organisation of immune functions within the gill, the site of infection, remains poorly resolved. Here, we present the first spatial transcriptomic atlas of the Atlantic salmon gill affected by AGD, generated using 10x Genomics Visium on four AGD-positive fish, confirmed by gill scoring and quantitative PCR for parasite load. As no uninfected gills were included, this study maps the anatomical and immunological organisation of AGD-affected gills rather than defining AGD-specific pathology. Unsupervised clustering of spatial gene expression resolved distinct transcriptional domains that grouped into four principal anatomical compartments of the gill, including (i) epithelial and lamellar regions defined by keratin and osmoregulatory gene expression, (ii) gill arch regions enriched for connective tissue and smooth muscle markers, (iii) an erythroid-associated vascular cluster, and (iv) a skeletal muscle cluster with signatures of glycolysis and oxidative phosphorylation. Across these domains, we identified a spatially organised and diffused immune landscape, with pattern recognition receptors, antimicrobial effectors and chemokines concentrated at the filament surface, and immunoglobulin light chain transcripts consistent with B lymphocyte activity enriched toward the gill arch. Integration of the spatial data with a published single-nucleus reference atlas using reference-based deconvolution resolved the cellular identity underlying these domains and revealed frequent co-localisation of immune and structural cell types, suggesting regulated cell to cell communication within the gill-associated lymphoid tissue. Overall, our results show that the Atlantic salmon gill is not a transcriptionally uniform surface but a regionally specialised organ, with immune functions distributed across, and specialised within, distinct anatomical compartments
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BibTeX
@misc{liu2026spatial,
title = {{Spatial Transcriptomics Reveals Region-Specific Host Responses in Amoebic Gill Disease of Atlantic Salmon}},
author = {Y. W. Liu and B. Cheaib and A. Bacigalupo and B. Robertson and M. Sinton and J. Quintana and G. Thomson and V. Morrison and C. Nixon and E. Krol and S. Martin and H. Rodger and A. C. West and R. Bickerdike and F. Egan and N. Ruane and M. Barrett and M. Llewellyn},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.09.756816},
url = {https://www.biorxiv.org/content/10.64898/2026.10.09.756816v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Spatial Transcriptomics Reveals Region-Specific Host Responses in Amoebic Gill Disease of Atlantic Salmon
AU - Y. W. Liu
AU - B. Cheaib
AU - A. Bacigalupo
AU - B. Robertson
AU - M. Sinton
AU - J. Quintana
AU - G. Thomson
AU - V. Morrison
AU - C. Nixon
AU - E. Krol
AU - S. Martin
AU - H. Rodger
AU - A. C. West
AU - R. Bickerdike
AU - F. Egan
AU - N. Ruane
AU - M. Barrett
AU - M. Llewellyn
PY - 2026
DA - 2026/10/09
PB - bioRxiv
DO - 10.64898/2026.10.09.756816
UR - https://www.biorxiv.org/content/10.64898/2026.10.09.756816v1
AB - Amoebic gill disease (AGD), caused by the parasite Neoparamoeba perurans, is a major welfare and economic burden for the Atlantic salmon aquaculture industry. However, the spatial organisation of immune functions within the gill, the site of infection, remains poorly resolved. Here, we present the first spatial transcriptomic atlas of the Atlantic salmon gill affected by AGD, generated using 10x Genomics Visium on four AGD-positive fish, confirmed by gill scoring and quantitative PCR for parasite load. As no uninfected gills were included, this study maps the anatomical and immunological organisation of AGD-affected gills rather than defining AGD-specific pathology. Unsupervised clustering of spatial gene expression resolved distinct transcriptional domains that grouped into four principal anatomical compartments of the gill, including (i) epithelial and lamellar regions defined by keratin and osmoregulatory gene expression, (ii) gill arch regions enriched for connective tissue and smooth muscle markers, (iii) an erythroid-associated vascular cluster, and (iv) a skeletal muscle cluster with signatures of glycolysis and oxidative phosphorylation. Across these domains, we identified a spatially organised and diffused immune landscape, with pattern recognition receptors, antimicrobial effectors and chemokines concentrated at the filament surface, and immunoglobulin light chain transcripts consistent with B lymphocyte activity enriched toward the gill arch. Integration of the spatial data with a published single-nucleus reference atlas using reference-based deconvolution resolved the cellular identity underlying these domains and revealed frequent co-localisation of immune and structural cell types, suggesting regulated cell to cell communication within the gill-associated lymphoid tissue. Overall, our results show that the Atlantic salmon gill is not a transcriptionally uniform surface but a regionally specialised organ, with immune functions distributed across, and specialised within, distinct anatomical compartments
ER -