Dual RNA-seq analysis of gene co-expression and immune response mechanisms in chickens infected by Eimeria tenella

Abstract: Coccidiosis caused by Eimeria parasites is a worldwide problem, affecting chickens and leading to great losses in the poultry industry. Current vaccines are costly and non-optimal, and the parasite has developed resistance to the anticoccidials in use. To be able to develop more efficient and cost-effective vaccines, further research into the immune response in poultry is needed. Here, we have analyzed immune chickens undergoing a secondary E. tenella infection using dual RNA-seq, as well as compared the immune response of the immune chickens to that of naïve chickens. Samples were taken from caecal tissue where the parasites replicate at six timepoints between 0 and 10 days post infection. The reads were put through a bioinformatic pipeline for preprocessing, mapping, counting and differential expression analysis. Using this we found 69 differentially expressed chicken genes (DEGs) in the secondary infections.The results show that DEGs are mainly found 1 and 2 days post infection (dpi), and a large proportion are interferon (IFN) stimulated genes. Compared to samples from naïve chickens, the immune chickens also expressed fewer cytokines and chemokines and the responses are lower at late time points (4 and 10 dpi). There are also lower counts of parasites in the immune chickens. These results show that immune chickens have a much faster response to E. tenellacompared to that of naïve chickens, and that there is a clear IFN-signature. We hypothesize that IFN-mediated inhibition of parasite replication is an important effector mechanism in protective immunity to Eimeria infection.