Transcriptomics of Fish Immune Responses

Transcriptomics—the large-scale study of RNA transcripts—has transformed understanding of how teleost fish detect, respond to and recover from pathogenic challenge. By profiling gene expression in immune organs such as head kidney, spleen, intestine and gill, researchers can delineate innate and adaptive responses at unprecedented resolution. High-throughput RNA sequencing identifies differentially expressed genes (DEGs) and reveals activation of pattern recognition receptors, cytokine networks and signalling cascades such as Toll-like receptor and NF-κB pathways. Integrative analyses, including pathway enrichment and gene-coexpression networks, have uncovered conserved defence modules across diverse species as well as lineage-specific innovations. This body of work has global significance for aquaculture health, vaccine design and selective breeding for disease resistance. Emerging studies also link host transcriptomes with microbiome dynamics, nutrition and environmental stressors, pointing to a holistic view of fish immunity that bridges molecular detail with practical applications in sustainable fisheries and ecosystem management.

Research from Nature Portfolio

A de novo transcriptome assembly of grass carp intestine following Aeromonas hydrophila infection revealed 315 up-regulated and 234 down-regulated genes associated with inflammatory responses. Gene Ontology enrichment highlighted terms in cytokine activity and leukocyte migration, while pathway analysis implicated complement cascades and cell-adhesion molecules. A time-course qPCR validation demonstrated stage-specific modulation of key inflammatory mediators, shedding light on the kinetics of mucosal defence. This work provides a tissue-specific atlas of host–pathogen interaction and underscores the importance of intestinal inflammation in early bacterial clearance.

Transcriptomics of Fish Immune Responses publication trend

The graph below shows the total number of articles in transcriptomics of fish immune responses across all publications each year (not limited to Nature Index journals).

Technical terms

Transcriptomics: genome-wide characterisation of all RNA molecules in a cell or tissue.

RNA-Seq: high-throughput sequencing of complementary DNA to quantify and discover transcripts.

Differentially expressed genes (DEGs): genes showing statistically significant expression changes between experimental conditions.

Gene Ontology (GO) enrichment: statistical assessment of overrepresented functional categories within a gene set.

KEGG pathway: a collection of manually curated metabolic and signalling pathways for interpreting gene functions.

Toll-like receptor: a family of innate immune receptors that recognise conserved microbial molecules to trigger host defence.

NF-κB pathway: a principal transcriptional cascade regulating inflammation, cell survival and immune responses.

References

1. Differentially expressed genes in head kidney of Pelteobagrus fulvidraco following Vibrio cholerae challenge. Frontiers in Immunology (2023).
2. Identification and Functional Analysis of Ras-Related Associated with Diabetes Gene (rrad) in Edwardsiella piscicida-Resistant Individuals of Japanese Flounder (Paralichthys olivaceus). International Journal of Molecular Sciences (2024).
3. Transcriptome, intestinal microbiome and histomorphology profiling of differences in the response of Chinese sea bass (Lateolabrax maculatus) to Aeromonas hydrophila infection. Frontiers in Microbiology (2023).
4. A transcriptome analysis focusing on inflammation-related genes of grass carp intestines following infection with Aeromonas hydrophila. Scientific Reports (2017).