Dual Host and Pathogen RNA-Seq Analysis Unravels Chicken Genes Potentially Involved in Resistance to Highly Pathogenic Avian Influenza Virus Infection

Abstract

Highly pathogenic avian influenza viruses (HPAIVs) cause severe systemic disease and high mortality rates in chickens, leading to a huge economic impact in the poultry sector. However, some chickens are resistant to the disease. This study aimed at evaluating the mechanisms behind HPAIV disease resistance. Chickens of different breeds were challenged with H7N1 HPAIV or clade 2.3.4.4b H5N8 HPAIV, euthanized at 3 days post-inoculation (dpi), and classified as resistant or susceptible depending on the following criteria: chickens that presented i) clinical signs, ii) histopathological lesions, and iii) presence of HPAIV antigen in tissues were classified as susceptible, while chickens lacking all these criteria were classified as resistant. Once classified, we performed RNA-Seq from lung and spleen samples in order to compare the transcriptomic signatures between resistant and susceptible chickens. We identified minor transcriptomic changes in resistant chickens in contrast with huge alterations observed in susceptible chickens. Interestingly, six differentially expressed genes were downregulated in resistant birds and upregulated in susceptible birds. Some of these genes belong to the NF-kappa B and/or mitogen-activated protein kinase signaling pathways. Among these six genes, the serine protease-encoding gene PLAU was of particular interest, being the most significantly downregulated gene in resistant chickens. Expression levels of this protease were further validated by RT-qPCR in a larger number of experimentally infected chickens. Furthermore, HPAIV quasi-species populations were constructed using 3 dpi oral swabs. No substantial changes were found in the viral segments that interact with the innate immune response and with the host cell receptors, reinforcing the role of the immune system of the host in the clinical outcome. Altogether, our results suggest that an early inactivation of important host genes could prevent an exaggerated immune response and/or viral replication, conferring resistance to HPAIV in chickens.

Silent Infection of Highly Pathogenic Avian Influenza Virus (H5N1) Clade 2.3.4.4b in a Commercial Chicken Broiler Flock in Italy

“…A systemic review and meta-analysis of the virus shedding of avian influenza viruses [ 8 ] considered different explanatory variables for the viral shedding of AIVs in poultry species such as pathotype (HPAI/LPAI), shedding route, virus origin, inoculation route, age and chicken categories; it is reported that low viral shedding in chicken can be due to the avian host from which the virus originated. Moreover, some avian genes involved in resistance to clade 2.3.4.4b H5N8 HPAIV in commercial broilers (Ross 308 Broiler) and six local Spanish chicken breeds have recently been experimentally investigated [ 12 ] and PLAU, VCAM, TNFRSF1-1A and PGF gene expression, which are mainly involved in inflammation response, resulted downregulated in resistant chickens.…”

Regulation of mRNA and miRNA in the response to Salmonella enterica serovar Enteritidis infection in chicken cecum

“…The expression of TLR1A in the cecum tissue was significantly up-regulated on 7-days post infection with SE of White Leghorn Layer in our previous research [ 11 ]. The research that performed RNA-Seq from lung and spleen samples suggested that an early inactivation of important host genes could prevent an exaggerated immune response and/or viral replication, conferring resistance to HPAIV in chickens [ 12 ]. In addition, transcriptomic analysis revealed that more severe disease in line W chicken was associated with significant up-regulation of pathways involved in inflammation, cytoskeletal regulation by Rho GTPases, and Wnt signaling in the bursa, etc.…”

Primary goose kidney tubular epithelial cells for goose astrovirus genotype 2 infection: establishment and RNA sequencing analysis

“…Hence, renal tubular epithelial ( RTE ) cells are a promising option for GAstV-2 proliferation and pathogenesis analysis. RNA sequencing ( RNA-seq ), a powerful approach that can provide precise measurements for transcriptome profiling, can reveal dynamic changes in host gene expression during pathogen infections, including various viral infections ( Ma et al, 2021 ; Pan et al, 2022 ; Perlas et al, 2021 ). Therefore, in the current study, we isolated goose primary RTE ( GRTE ) cells from goose embryos and investigated GAstV-2 growth characteristics in GRTE cells and GAstV-2–GRTE cell interactions through RNA-seq.…”