Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome

Abstract

BackgroundNewcastle disease virus (NDV) is a threat to poultry production worldwide. A better understanding of mechanisms of resistance and susceptibility to this virus will improve measures for NDV prevention and control. Males and females from resistant Fayoumi and susceptible Leghorn lines were either challenged with a lentogenic strain of the virus or given a mock infection at 3 weeks of age. The lung transcriptomes generated by RNA-seq were studied using contrasts across the challenged and nonchallenged birds, the two lines, and three time points post-infection, and by using Weighted Gene Co-expression Network Analysis (WGNCA).ResultsGenetic line and sex had a large impact on the lung transcriptome. When contrasting the challenged and nonchallenged birds, few differentially expressed genes (DEG) were identified within each line at 2, 6, and 10 days post infection (dpi), except for the more resistant Fayoumi line at 10 dpi, for which several pathways were activated and inhibited at this time. The interaction of challenge and line at 10 dpi significantly impacted 131 genes (False Discovery Rate (FDR) <0.05), one of which was PPIB. Many DEG were identified between the Fayoumi and Leghorns. The number of DEG between the two lines in the challenged birds decreased over time, but increased over time in the nonchallenged birds. The nonchallenged Fayoumis at 10 dpi showed enrichment of immune type cells when compared to 2 dpi, suggesting important immune related development at this age. These changes between 10 and 2 dpi were not identified in the challenged Fayoumis. The energy allocated to host defense may have interrupted normal lung development. WGCNA identified important modules and driver genes within those modules that were associated with traits of interest, several of which had no known associated function.ConclusionsThe lines’ unique response to NDV offers insights into the potential means of their resistance and susceptibility. The lung transcriptome shows a unique response to lentogenic NDV compared to a previous study on the trachea of the same birds. It is important to analyze multiple tissues in order to best understand the chicken’s overall response to NDV challenge and improve strategies to combat this devastating disease.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4380-4) contains supplementary material, which is available to authorized users.

Novel Combined Tissue Transcriptome Analysis After Lentogenic Newcastle Disease Virus Challenge in Inbred Chicken Lines of Differential Resistance

“…As time progressed, the number of DEG decreased between the challenged and non-challenged birds in the trachea, suggesting the trachea was consistently active in host response and in recovery from the virus in both lines (Deist et al, 2017b). The transcriptomes of the lung and Harderian gland were more impacted by line than by the challenge (Deist et al, 2017a;Deist et al, 2018). The Leghorn lung appeared to be nonresponsive to the virus, whereas the Fayoumi lung produced a large number of DEG at 10 dpi when comparing the challenged to non-challenged birds (Deist et al, 2017a).…”

“…The numbers of differentially expressed genes (DEG) for the challenge by tissue interaction, within each line and dpi, are shown in Table 1. Large numbers of DEG were identified by the interaction between the lung and Harderian gland in the Fayoumis at 10 dpi (Table 1), and separately the large numbers of DEG in the Leghorns at 6 dpi ( Table 1) may have resulted from large numbers of DEG due to challenge within an individual tissue (Deist et al, 2017a;Deist et al, 2018). With the exception of the Fayoumis at 10 dpi and the Leghorns at 6 dpi, there were few DEG between the lung and Harderian gland.…”

“…Because the transcriptome is not stagnant, a more comprehensive physiological picture can be obtained by an integrative analysis of the transcriptomes of multiple tissues at multiple time points after a treatment. Previously, the trachea epithelial cells, lung, and Harderian gland of Fayoumis and Leghorns at 2, 6, and 10 days post-infection (dpi) with lentogenic NDV have been individually analyzed with RNA-seq (Deist et al, 2017a;Deist et al, 2017b;Deist et al, 2018). The three tissues had very distinct responses to NDV (Deist et al, 2017a;Deist et al, 2017b;Deist et al, 2018).…”

“…Previously, the trachea epithelial cells, lung, and Harderian gland of Fayoumis and Leghorns at 2, 6, and 10 days post-infection (dpi) with lentogenic NDV have been individually analyzed with RNA-seq (Deist et al, 2017a;Deist et al, 2017b;Deist et al, 2018). The three tissues had very distinct responses to NDV (Deist et al, 2017a;Deist et al, 2017b;Deist et al, 2018). Taking a systems biology approach and analyzing the three tissues together will provide a more comprehensive picture of how the whole animal responded to NDV.…”

Specific genes related to nucleopolyhedrovirus in Bombyx mori susceptible and near‐isogenic resistant strains through comparative transcriptome analysis

“…The 871 strain is susceptible to BmNPV infection, and the 871C strain is highly resistant. Here, we identified antiviral genes via weighted gene co‐expression network analysis (WGCNA), which has been used widely in disease research and to identify trait correlation genes (Chen et al ., ; Deist et al ., ; Huang et al ., ; Liu et al ., ; Wang et al ., ; ; Liu et al ., ). We identified a total of 2899 DEGs, including genes potentially related to BmNPV resistance in the 871C strains.…”