Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48 hours post-infection through RNA-seq

Zhang, Xuelian; Cao, Chen; Liu, Yue; Qi, Haihui; Zhang, Wenjing; Hao, Chunxue; Chen, Haotian; Zhang, Qi; Zhang, Wenlong; Gao, Mingchun; Wang, Junwei; Ma, Bo

doi:10.1186/s13567-018-0545-7

Cited by 15 publications

(19 citation statements)

References 25 publications

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“…Similarly, pathway enrichment analysis for 7,717 DEGs of the transcriptome produced similar results. This pathway enrichment result is also consistent with another study that investigated the transcriptome of DHAV-3 infected ducklings at 48 hpi [9]. Previous reports have…”

Section: Discussionsupporting

confidence: 92%

Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

Fan

et al. 2019

Preprint

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Background: Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings is remain poorly understood. To elucidate the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in DHAV-3 infection in ducklings, we conducted global miRNA and mRNA expression profiling of duckling liver tissues infected with lethal DHAV-3 using high-throughput sequencing. Results: We found 156 differentially expressed miRNAs (DEMs) and 7717 differentially expressed miRNAs (DEGs) between mock-infected and DHAV-3-infected duckling livers. A total of 19,606 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of these DEMs and DEGs. Moreover, immune-related pathways including the cytokine-cytokine receptor interaction, apoptosis, Toll-like receptor, Jak-STAT, and RIG-I-like receptor signaling pathway were significantly enriched through analyzing functions of mRNAs in the network in response to DHAV-3 infection. Besides, apl-miR-32-5p, apl-miR-125-5p, apl-miR-128-3p, apl-miR-460-5p, and novel-m0012-3p were identified as potential regulators in the immune-related signaling pathways during the DHAV-3 infection. Conclusions: To our knowledge, this is the first report on integrated analysis of miRNA-seq and mRNA-seq in DHAV-3-infected ducklings. The results indicated the important roles of miRNAs in regulating immune response genes and revealed the immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver. Our findings may provide valuable information to further investigate the roles of miRNAs and their target genes in DHAV-3 replication and pathogenesis; additionally, they may offer clues for further understanding host-virus interactions.

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Section: Discussionsupporting

confidence: 92%

Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

Fan

et al. 2019

Preprint

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“…hpi [9]. Previous reports have shown that these pathways are involved in the host anti-virus processes [31][32][33][34].…”

Section: Discussionmentioning

confidence: 97%

“…DHAV-3 causes acute hepatitis and induces typical duckling liver lesions, which is characterized by petechial hemorrhages of the liver surface [8]. The results of detecting DHAV-3 loads in the liver exhibited that the virus could replicate rapidly in the liver [9]. In addition, the highest viral titer was detected in the liver among DHAV-3 infected organs in vivo [10].…”

mentioning

confidence: 99%

Integrated analysis of miRNA-seq and mRNA-seq reveals immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver

Fan

et al. 2019

Preprint

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KEYWORDSDuck hepatitis A virus type 3, miRNA-seq, mRNA-seq, miRNA-mRNA network, Innate immune response, Host-virus interactions 2 Abstract Background: Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings is remain poorly understood. To elucidate the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in DHAV-3 infection in ducklings, we conducted global miRNA and mRNA expression profiling of duckling liver tissues infected with lethal DHAV-3 using high-throughput sequencing. Results: We found 156 differentially expressed miRNAs (DEMs) and 7717 differentially expressed miRNAs (DEGs) between mock-infected and DHAV-3-infected duckling livers. A total of 19,606 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of these DEMs and DEGs. Moreover, immune-related pathways including the cytokine-cytokine receptor interaction, apoptosis, Toll-like receptor, Jak-STAT, and RIG-I-like receptor signaling pathway were significantly enriched through analyzing functions of mRNAs in the network in response to DHAV-3 infection. Besides, apl-miR-32-5p, apl-miR-125-5p, apl-miR-128-3p, apl-miR-460-5p, and novel-m0012-3p were identified as potential regulators in the immune-related signaling pathways during the DHAV-3 infection. Conclusions: To our knowledge, this is the first report on integrated analysis of miRNA-seq and mRNA-seq in DHAV-3-infected ducklings.The results indicated the important roles of miRNAs in regulating immune response genes and revealed the immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver.Our findings may provide valuable information to further investigate the roles of miRNAs and their target genes in DHAV-3 replication and pathogenesis; additionally, they may offer clues for further understanding host-virus interactions.

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“…Transcriptome analysis is a promising tool that can provide a comprehensive understanding of the molecular mechanisms involved in speci c biological processes and diseases [17]. Previous studies have described the transcriptome pro le of DHAV-, Reovirus-and DHBV-infection in ducks [18][19][20][21]. In the present study, transcriptome sequencing was employed to explore and compare the gene expression patterns of infection with different subtype DHAV-1 in duck pancreatic tissues, with the aim to compare different molecular events during DHAV-1s infection.…”

Section: Discussionmentioning

confidence: 99%

Differential metabolism -associated gene expression of duck pancreatic cells in response to two subtype s of duck hepatitis A virus type 1

Shi¹,

Chen

Huang³

et al. 2020

Preprint

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Background: Duck hepatitis A virus type 1 (DHAV-1) causes a highly contagious disease in domestic ducklings, which is traditionally characterized by lesions in the liver and rarely in the pancreas. However, several outbreaks of DHAV-1, which were characterized by yellow coloration and hemorrhage in pancreatic tissues, have occurred in China. Genomic sequencing indicated variation rates of 3.4-6.5% in the genome of the novel DHAV-1 compared with those of DHAV-1. The antigenic relationship between the novel DHAV-1 and DHAV-1 indicated large variation. Therefore, the novel DHAV-1 was named as DHAV-1 subtype (DHAV-1s). However, the mechanism involved in infection of DHAV-1s is still unclear. Results: In the present study, transcriptome analysis of duck pancreas infected with DHAV-1 and DHAV-1s was carried out. Following deep sequencing with Illumina-Solexa, a total of 53.9 Gb clean data were obtained from the cDNA library of the pancreas and a total of 29,597 unigenes with an average length of 993.43 bp were generated following de novo sequence assembly. The expression levels of D-3-phosphoglyceratedehydrogenase, phosphoserine aminotransferase, phosphoserine phosphatase, which are involved in glycine, serine and threonine metabolism pathway, were significantly downregulated in the DHAV-1s-infected group compared with those of the DHAV-1-infected group.Conclusion: These findings provide information regarding differential expression levels of metabolism-associated genes between the novel DHAV-1s and DHAV-1, indicating that intensive metabolism disorders may contribute to different phenotypes of DHAV-1-infection.

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Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48 hours post-infection through RNA-seq

Cited by 15 publications

References 25 publications

Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

Integrated analysis of miRNA-seq and mRNA-seq reveals immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver

Differential metabolism -associated gene expression of duck pancreatic cells in response to two subtype s of duck hepatitis A virus type 1

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