Imbalance between innate antiviral and pro-inflammatory immune responses may contribute to different outcomes involving low- and highly pathogenic avian influenza H5N3 infections in chickens

Comparative Analysis of Different Inbred Chicken Lines Highlights How a Hereditary Inflammatory State Affects Susceptibility to Avian Influenza Virus

Evidence suggests that susceptibility to avian influenza A virus in chickens is influenced by host genetics, but the mechanisms are poorly understood. A previous study demonstrated that inbred line 0 chickens are more resistant to low-pathogenicity avian influenza (LPAI) infection than line CB.12 birds based on viral shedding, but the resistance was not associated with higher AIV-specific IFNγ responses or antibody titres. In this study, we investigated the proportions and cytotoxic capacity of T-cell subpopulations in the spleen and the early immune responses in the respiratory tract, analysing the innate immune transcriptome of lung-derived macrophages following in vitro stimulation with LPAI H7N1 or the TLR7 agonist R848. The more susceptible C.B12 line had a higher proportion of CD8αβ+ γδ and CD4+CD8αα+ αVβ1 T cells, and a significantly higher proportion of the CD8αβ+ γδ and CD8αβ+ αVβ1 T cells expressed CD107a, a surrogate marker of degranulation. Lung macrophages isolated from line C.B12 birds expressed higher levels of the negative regulator genes TRIM29 and IL17REL, whereas macrophages from line 0 birds expressed higher levels of antiviral genes including IRF10 and IRG1. After stimulation with R848, the macrophages from line 0 birds mounted a higher response compared to line C.B12 cells. Together, the higher proportion of unconventional T cells, the higher level of cytotoxic cell degranulation ex vivo and post-stimulation and the lower levels of antiviral gene expression suggest a potential role of immunopathology in mediating susceptibility in C.B12 birds.

Comparative Investigation of Gene Regulatory Processes Underlying Avian Influenza Viruses in Chicken and Duck

Simple Summary

Avian influenza poses a great risk to gallinaceous poultry, while mallard ducks can withstand most virus strains. To date, the mechanisms underlying the susceptibility of chicken and the effective immune response of duck have not been completely understood. In this study, our aim is to investigate the transcriptional gene regulation governing the expression of important avian-influenza-induced genes and to reveal the master regulators stimulating an effective immune response after virus infection in ducks while dysfunctioning in chicken.

Abstract

The avian influenza virus (AIV) mainly affects birds and not only causes animals’ deaths, but also poses a great risk of zoonotically infecting humans. While ducks and wild waterfowl are seen as a natural reservoir for AIVs and can withstand most virus strains, chicken mostly succumb to infection with high pathogenic avian influenza (HPAI). To date, the mechanisms underlying the susceptibility of chicken and the effective immune response of duck have not been completely unraveled. In this study, we investigate the transcriptional gene regulation underlying disease progression in chicken and duck after AIV infection. For this purpose, we use a publicly available RNA-sequencing dataset from chicken and ducks infected with low-pathogenic avian influenza (LPAI) H5N2 and HPAI H5N1 (lung and ileum tissues, 1 and 3 days post-infection). Unlike previous studies, we performed a promoter analysis based on orthologous genes to detect important transcription factors (TFs) and their cooperation, based on which we apply a systems biology approach to identify common and species-specific master regulators. We found master regulators such as EGR1, FOS, and SP1, specifically for chicken and ETS1 and SMAD3/4, specifically for duck, which could be responsible for the duck’s effective and the chicken’s ineffective immune response.

Transcriptomic analysis of the liver in aged laying hens with different intensity of brown eggshell color

OBJECTIVE

Eggshell color is an important indicator of egg quality for consumers, especially for brown eggs. Various factors related to laying hens and their environment affect brown eggshell coloration. However, there have been no studies investigating hepatic functions of laying hens with variable intensity of brown eggshell color. Therefore, this study was aimed to identify potential factors affecting brown eggshell coloration in aged laying hens at the hepatic transcriptomic level.

METHODS

Five hundred 92-wk-old Hy-line Brown laying hens were screened to select laying hens with different intensity of brown eggshell color based on eggshell color fans. Based on eggshell color scores, hens with dark brown eggshells (DBE; eggshell color fan score = 14.8) and hens with light brown eggshells (LBE; eggshell color fan score = 9.7) were finally selected for the liver sampling. We performed RNA-seq analysis using the liver samples through the paired-end sequencing libraries. Differentially expressed genes (DEGs) profiling was carried out to identify their biological meaning by bioinformatics.

RESULTS

A total of 290 DEGs were identified with 196 being up-regulated and 94 being down-regulated in DBE groups as compared to LBE groups. The Kyoto encyclopedia of genes and genomes (KEGG) analysis revealed that these DEGs belong to several biological pathways including herpes simplex infection (toll-like receptor 3 [TLR3], cyclin-dependent kinase 1, etc.) and influenza A (TLR3, radical S-adenosyl methionine domain containing 2, myxovirus [influenza virus] resistance 1, etc.). Genes related to stress response (ceremide kinase like) and nutrient metabolism (phosphoenolpyruvate carboxy-kinase 1, methylmalonic aciduria [cobalamin deficiency] cblB type, glycine receptor alpha 2, solute carrier family 7 member 11, etc.) were also identified to be differentially expressed.

CONCLUSION

The current results provide new insights regarding hepatic molecular functions related to different intensity of brown eggshell color in aged laying hens. These insights will contribute to future studies aiming to optimize brown eggshell coloration in aged laying hens.

Deep proteome profiling reveals novel pathways associated with pro-inflammatory and alcohol-induced microglial activation phenotypes

Microglia, the resident immune cells of the brain, can exhibit a broad range of activation phenotypes, many of which have been implicated in several diseases and disorders of the central nervous system including those related to alcohol abuse. Given the complexity of global-scale molecular changes that define microglial activation, accurate phenotypic classification in the context of alcohol exposure is still lacking. We employed an optimized method for deep, quantitative proteome profiling of primary microglia in order to characterize their response to acute exposure to alcohol (ethanol) as well as the pro-inflammatory driver and TLR4 agonist, LPS. From this analysis, 5,062 total proteins were identified where 4,857 and 4,928 of those proteins were quantifiable by label-free quantitation in ethanol and LPS treatment groups, respectively. This study highlights the subtle, yet significant proteomic changes that occur in ethanol-treated microglia, which do not align with the robust pro-inflammatory phenotype induced by TLR4 activation. Specifically, our results indicate inhibition of several upstream regulators associated with inflammation, opposing effects on pathways such as phagocytosis upon comparison to TLR4-mediated pro-inflammatory phenotype, and a potential metabolic shift associated with increased expression of proteins related to OXPHOS and lipid homeostasis. Data are available via ProteomeXchange with identifier PXD14466. SIGNIFICANCE: Alcohol abuse has a significant impact on the central nervous system, which includes the pathophysiological mechanisms resulting from glial cell activation. Microglia, in particular, are the resident immune cells of the brain and exhibit a broad range of activation phenotypes. The molecular changes that drive microglial activation phenotype are complex and have yet to be fully characterized in the context of alcohol exposure. Our study highlights the first and most comprehensive characterization of alcohol-induced proteomic changes in primary microglia to date and has shed light on novel immune-related and metabolic pathways that are altered due to alcohol exposure. The results from this study provide an important foundation for future work aimed to understand the complexity of alcohol-induced microglial activation in vivo and other translational models of acute and chronic alcohol exposure.

Gene expression profiles of the small intestine of village chickens from an Ascaridia galli infested environment

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The transcriptome of chickens from parasite infested environment was sequenced.

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Different genes were reported between A. galli infected and non-infected chickens.

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Upregulated immune and inflammatory response genes are associated with fighting parasites.

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T cell receptor signalling and arachidonic acid metabolism pathways were impacted.

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Different segments of the intestines differed in gene expression and associated pathways.

Nematodes of the genus Ascaridia are known to infect many species of birds and result in fatal diseases. A. galli damages the intestinal mucosa of chickens leading to blood loss, secondary infection and occasionally the obstruction of small intestines due to high worm burden. This study investigated the gene expression profiles in chickens from two different provinces of South Africa naturally exposed to A. galli infestations and tested either positive or negative for the parasite. The study further investigated gene expression profiles of the A. galli infected duodenum, jejunum and ileum tissues of the small intestines. The A. galli positive intestines displayed hypertrophy of the intestinal villi with accumulation of inflammatory cells and necrosis of the crypts of Lieberkühn glands, lesions that were absent in the uninfected intestines. Total RNA isolated from small intestines of infected and non-infected intestines was sequenced using Illumina HiSeq technology to generate up to 23,856,130 reads. Between any two-way comparisons of the intestines, 277 and 190 transcripts were significantly expressed in Limpopo and KwaZulu-Natal (KZN) chickens, respectively. Gene ontology analysis of the differentially expressed genes (DEGs) revealed an enrichment of genes reported to function in the immune response, defense response, inflammatory response and cell signalling genes. T cell receptor signalling pathways and arachidonic acid metabolism pathways were among the most significantly impacted pathways. Overall, the study provided insights into adaptative mechanisms for chickens extensively raised in parasite infected environments.

Creating Disease Resistant Chickens: A Viable Solution to Avian Influenza?

Influenza A virus (IAV) represents an ongoing threat to human and animal health worldwide. The generation of IAV-resistant chickens through genetic modification and/or selective breeding may help prevent viral spread. The feasibility of creating genetically modified birds has already been demonstrated with the insertion of transgenes that target IAV into the genomes of chickens. This approach has been met with some success in minimising the spread of IAV but has limitations in terms of its ability to prevent the emergence of disease. An alternate approach is the use of genetic engineering to improve host resistance by targeting the antiviral immune responses of poultry to IAV. Harnessing such resistance mechanisms in a “genetic restoration” approach may hold the greatest promise yet for generating disease resistant chickens. Continuing to identify genes associated with natural resistance in poultry provides the opportunity to identify new targets for genetic modification and/or selective breeding. However, as with any new technology, economic, societal, and legislative barriers will need to be overcome before we are likely to see commercialisation of genetically modified birds.