Time-series transcriptome analysis identified differentially expressed genes in broiler chicken infected with mixed Eimeria species

Abstract

Coccidiosis caused by the Eimeria species is a highly problematic disease in the chicken industry. Here, we used RNA sequencing to observe the time-dependent host responses of Eimeria-infected chickens to examine the genes and biological functions associated with immunity to the parasite. Transcriptome analysis was performed at three time points: 4, 7, and 21 days post-infection (dpi). Based on the changes in gene expression patterns, we defined three groups of genes that showed differential expression. This enabled us to capture evidence of endoplasmic reticulum stress at the initial stage of Eimeria infection. Furthermore, we found that innate immune responses against the parasite were activated at the first exposure; they then showed gradual normalization. Although the cytokine-cytokine receptor interaction pathway was significantly operative at 4 dpi, its downregulation led to an anti-inflammatory effect. Additionally, the construction of gene co-expression networks enabled identification of immunoregulation hub genes and critical pattern recognition receptors after Eimeria infection. Our results provide a detailed understanding of the host-pathogen interaction between chicken and Eimeria. The clusters of genes defined in this study can be utilized to improve chickens for coccidiosis control.

Transcriptomic analysis of LMH cells in response to the overexpression of a protein of Eimeria tenella encoded by the locus ETH_00028350

“…Previous studies showed that cytokine-cytokine receptor interaction pathway was associated with Eimeria infection ( 29 , 36 ). Of the DEGs enriched in this pathway, IL22RA1, IL1R2 and IL20RA are implicated in immune or inflammatory responses ( 37 – 39 ).…”

“…Previous studies showed that T. gondii infection could modulate host cell apoptosis through ER stress ( 26 – 28 ). Notably, ER stress is also associated with E. tenella infection ( 29 ). The DEGs enriched in protein processing in the endoplasmic reticulum pathway included HSPA2, HSPA8, HSP90AA1 and HSPH1, which are the immune-related genes ( 30 ).…”

Major histocompatibility complex genes exhibit a potential immunological role in mixed Eimeria-infected broiler cecum analyzed using RNA sequencing

“…To uncover candidate genes and biological pathways underlying the immune response to disease, researchers have investigated changes in gene expression [11][12][13]. RNA sequencing technology has enabled comprehensive examinations of gene expression across the genome.…”

“…Numerous studies have examined chicken coccidiosis to develop antibiotic alternatives [14,15] and effective anticoccidial vaccines [16,17], and identified candidate genes associated with immune function [11,18]. Previously, our research team identified chronological changes in gene expression patterns throughout the genome in the cecum of broilers affected by coccidiosis, thereby elucidating key responses and pathways [11].…”

“…Numerous studies have examined chicken coccidiosis to develop antibiotic alternatives [14,15] and effective anticoccidial vaccines [16,17], and identified candidate genes associated with immune function [11,18]. Previously, our research team identified chronological changes in gene expression patterns throughout the genome in the cecum of broilers affected by coccidiosis, thereby elucidating key responses and pathways [11]. Building upon these past findings, the present study aims to extend our understanding by investigating the gene expression profiles of chromosome 16, encompassing MHC genes, using an updated reference genome.…”