Comparative transcriptome reveals the effect of IFITM1 on differential resistance to duck hepatitis A virus genotype 3 in Pekin ducks

Effects of age on differential resistance to duck hepatitis A virus genotype 3 in Pekin ducks by 16 S and transcriptomics

Duck hepatitis A virus genotype 3 (DHAV-3) is the major cause of viral hepatitis in ducks in Asia. Previous studies have shown that ducklings younger than 21 days are more susceptible to DHAV-3. To elucidate the mechanism by which age affects the differential susceptibility of Pekin ducks to DHAV-3, intestinal (n = 520), liver (n = 40) and blood (n = 260) samples were collected from control and DHAV-3-infected ducks at 7, 10, 14, and 21 days of age. Comparisons of plasma markers, mortality rates, and intestinal histopathological data showed that the resistance of Pekin ducks to DHAV-3 varied with age. 16 S sequencing revealed that the ileal microbial composition was influenced by age, and this correlation was greater than that recorded for caecal microbes. Candidatus Arthromitus, Bacteroides, Corynebacterium, Enterococcus, Romboutsia, and Streptococcus were the differntially abundant microbes in the ileum at the genus level after DHAV-3 infection and were significantly correlated with 7 differentially expressed genes (DEGs) in 7- and 21-day-old ducklings. 3 immunity-related pathways were significantly different between 7- and 21-day-old ducklings, especially for IFIH1-mediated induction of the interferon-alpha/beta pathway, which induces differential production of CD8(+) T cells and was influenced by a combination of differentially abundant microbiota and DEGs. We found that microbes in the ileum changed regularly with age. The intestinal microbiota was associated with the expression of genes in the liver through IFIH1-mediated induction of the interferon-alpha/beta pathway, which may partially explain why younger ducklings were more susceptible to DHAV-3 infection.

Whole-transcriptome sequencing revealed the role of noncoding RNAs in susceptibility and resistance of Pekin ducks to DHAV-3

As the most prevalent pathogen of duck viral hepatitis (DVH), duck hepatitis A virus genotype 3 (DHAV-3) has caused huge economic losses to the duck industry in China. Herein, we obtained whole-transcriptome sequencing data of susceptible (S) and resistant (R) Pekin duckling samples at 0 h, 12 h, and 24 h after DHAV-3 infection. We found that DHAV-3 infection induces 5,396 differentially expressed genes (DEGs), 85 differentially expressed miRNAs (DEMs), and 727 differentially expressed lncRNAs (DELs) at 24 hpi in S vs. R ducks, those upregulated genes were enriched in inflammation and cell communications pathways and downregulated genes were related to metabolic processes. Upregulated genes showed high connectivity with the miR-33, miR-193, and miR-11591, and downregulated genes were mainly regulated by miR-2954, miR-125, and miR-146b. With the construction of lncRNA-miRNA-mRNA axis, we further identified a few aberrantly expressed lncRNAs (e.g., MSTRG.36194.1, MSTRG.50601.1, MSTRG.34328.7, and MSTRG.29445.1) that regulate expression of hub genes (e.g., THBD, CLIC2, IL8, ACOX2, GPHN, SMLR1, and HAO1) by sponging those highly connected miRNAs. Altogether, our findings defined a dual role of ncRNAs in immune and metabolic regulation during DHAV-3 infection, suggesting potential new targets for treating DHAV-3 infected ducks.

Plasma lipidome reveals susceptibility and resistance of Pekin ducks to DHAV-3

Duck hepatitis A virus genotype 3 (DHAV-3) is the most popular pathogen of duck viral hepatitis (DVH) and has led to a huge economic threat to the Asian duck industry. In this work, we investigated the differences in the LC-MS/MS-based dynamic lipid profiles between susceptible and resistant Pekin duck lines with DHAV-3 infection. We found that the plasma lipidome of the two duck lines was characterized differently in expression levels of lipids during the infection, such as decreased levels of glycerolipids and increased levels of cholesteryl esters and glycerophospholipids in susceptible ducks compared with resistant ducks. By integrating lipidomics and transcriptomics analysis, we showed that the altered homeostasis of lipids was potentially regulated by a variety of differentially expressed genes including CHPT1, PI4K2A, and OSBP2 between the two duck lines, which could account for liver dysfunction, apoptosis, and illness upon DHAV-3 infection. Using the least absolute shrinkage and selection operator (LASSO) approach, we determined a total of 25 infection-related lipids that were able to distinguish between the infection states of susceptible and resistant ducks. This study provides molecular clues for elucidating the pathogenesis and therapeutic strategies of DHAV-3 infection in ducklings, which has implication for the development of resistance breeding.