Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chickens

Lan, Xi; Wang, Yan; Tian, Kai; Ye, Fei; Yin, Huadong; Zhao, Xiaoling; Xu, Hengyong; Huang, Yong; Li, Haibo; Hsieh, John; Lamont, Susan J.; Zhu, Qing

doi:10.1038/srep46156

Cited by 21 publications

(17 citation statements)

References 69 publications

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“…While in cattle the GC content were 48.79% and 51.38%, respectively ( Fig 3D). The present results that are in accordance with those of previous studies [33][34][35].…”

Section: A Boxplot Of Average Expression Level Histogram Of Lengthssupporting

confidence: 94%

Whole-transcriptome analysis of heart in bovidae reveals regulatory pathways associated with high-altitude adaptation

Wang¹,

Chai²,

Zhong³

et al. 2019

Preprint

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Background: the yak (Bos grunniens) is one of the major livestock that can survive the extremely cold, harsh and oxygen-poor conditions and provide meat, milk and transportation for Tibetans living in the Qinghai-Tibetan Plateau, and there are some cattle migrate to yak habitat but cannot survive the extremely conditions well. However, the regulatory mechanisms that drive hypoxic adaptation of yak remain elusive. Results: Thus, we collected heart tissues from Leiwuqi (LWQ) yak and their relatives, the migration cattle in LWQ yak habitat (HAC) and low-altitude cattle (LAC), respectively, for RNA sequencing, 178 co-differentially expressed protein-coding transcripts (CETs) including 6 down-regulated and 172 up-regulated CETs were discovered in both LAC-vs-LWQY and LAC-vs-HAC comparison groups. There were 133, 11 and 3 lncRNA transcripts were specific expressed in LWQY, HAC, and LAC groups, respectively. 2 and 230 lncRNA transcripts differentially expressed in LAC-vs-LWQY and LAC-vs-HAC，respectively, but no lncRNA transcripts co-differentially expressed in those two comparison groups. Among the 58 miRNAs that were co-differentially expressed, 18 were up-regulated and 40 were down-regulated. In addition, 640 (501 up-regulated and 139 down-regulated) and 152 (152 up-regulated and 1 down-regulated) circRNAs showed differential expression in LAC-vs-LWQY and LAC-vs-HAC comparison groups, respectively, and 53 up-regulated co-differentially expressed circRNAs were shared. Multiply CETs which are the target genes for miRNAs/lncRNAs were significantly enriched in high-altitude adaptation related processes, for instance, T cell receptor signaling, VEGF signaling, and cAMP signaling. A competing endogenous RNA (ceRNA) network by integrating competing relationships among CETs, miRNAs, lncRNAs and circRNAs were constructed. Furthermore, we constructed a hypoxic adaptation related ceRNA network to identified that 8 miRNAs and 15 circRNAs were predicted to regulated MAPKAPK3, PXN, NFATC2, ATP7A, DIAPH1 and F2R genes. Conclusion: In conclusion, our data reinforce the view that the molecular network of high-altitude adaptation is composed of several protein-coding transcripts and non-coding transcripts that involved in multiply hypoxic adaptation regulatory pathways. The detailed mechanism for how this network crosstalk each other in heart of Bovidae are worthy of future research efforts.

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“…While in cattle the GC content were 48.79% and 51.38%, respectively ( Fig 3D). The present results that are in accordance with those of previous studies [33][34][35].…”

Section: A Boxplot Of Average Expression Level Histogram Of Lengthssupporting

confidence: 94%

Whole-transcriptome analysis of heart in bovidae reveals regulatory pathways associated with high-altitude adaptation

Wang¹,

Chai²,

Zhong³

et al. 2019

Preprint

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“…According to the RNA-seq technology, Lan combined four datasets: ALV gene expression, lncRNA, microRNA and mRNA to reveal pathology and inflammatory response mechanisms and the combined analysis revealed that the defenses gene family plays an important role in the immunosuppression caused by ALV-J [13]. The change of ALV-J injected DF-1 cells proteomic was detected by iTRAQ, and METAP2, PRDX1, ACTR3, ACTR5 may play vital roles in mechanism of ALV-J injection [14]. However, fewer studies have focused on the relationship of exosomes with ALV-J, what's more less the relationship between exosome proteins and RNA.…”

Section: Ivyspringmentioning

confidence: 99%

Exosomes Transmit Viral Genetic Information and Immune Signals may cause Immunosuppression and Immune Tolerance in ALV-J Infected HD11 cells

Wang

et al. 2020

Int. J. Biol. Sci.

Self Cite

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Avian leukosis virus (ALV) is oncogenic retrovirus that not only causes immunosuppression but also enhances the host's susceptibility to secondary infection. Exosomes play vital role in the signal transduction cascades that occur in response to viral infection. We want to explore the function of exosomes in the spread of ALV and the body's subsequent immunological response. RNA-sequencing and the isobaric tags for relative and absolute quantitation (iTRAQ) method were used to detect differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in exosomes secreted by macrophage cells in response to injection with ALV subgroup J (ALV-J). RNA-sequencing identified 513 DEGs in infected cells, with specific differential regulation in mRNA involved in tight junction signaling, TNF signaling, salmonella infection response, and immune response, among other important cellular processes. Differential regulation was observed in 843 lncRNAs, with particular enrichment in those lncRNA targets involved in Rap1 signaling, HTLV-I infection, tight junction signaling, and other signaling pathways. A total of 50 DEPs were identified in the infected cells by iTRAQ. The proteins enriched are involved in immune response, antigen processing, the formation of both MHC protein and myosin complexes, and transport. Combined analysis of the transcriptome and proteome revealed that there were 337 correlations between RNA and protein enrichment, five of which were significant. Pathways that were enriched on both the RNA and protein levels were involved in pathways in cancer, PI3K-Akt signaling pathway, Endocytosis, Epstein-Barr virus infection. These data show that exosomes are transmitters of intercellular signaling in response to viral infection. Exosomes can carry both viral nucleic acids and proteins, making it possible for exosomes to be involved in the viral infection of other cells and the transmission of immune signals between cells. Our sequencing results confirme previous studies on exosomes and further find exosomes may cause immunosuppression and immune tolerance.

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“…The shared significance and direction of effect between the analyses (NDV; heat + NDV), a lack of significance in the heat + NDV group, and a lack of significant haplotype by treatment interaction indicate the robustness of the action of IFI27L2 during viral challenge. Interferon alpha inducible protein 27 ( IFI27L2 ) has been previously shown to be upregulated in response to several viruses, including NDV [ 13 , 47 , 48 , 49 , 50 ]. The current study is the first record of association of IFI27L2 with antibody response and/or heat challenge.…”

Section: Resultsmentioning

confidence: 99%

Association of Candidate Genes with Response to Heat and Newcastle Disease Virus

Rowland

Saelao

Wang

et al. 2018

Genes

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Newcastle disease is considered the number one disease constraint to poultry production in low and middle-income countries, however poultry that is raised in resource-poor areas often experience multiple environmental challenges. Heat stress has a negative impact on production, and immune response to pathogens can be negatively modulated by heat stress. Candidate genes and regions chosen for this study were based on previously reported associations with response to immune stimulants, pathogens, or heat, including: TLR3, TLR7, MX, MHC-B (major histocompatibility complex, gene complex), IFI27L2, SLC5A1, HSPB1, HSPA2, HSPA8, IFRD1, IL18R1, IL1R1, AP2A2, and TOLLIP. Chickens of a commercial egg-laying line were infected with a lentogenic strain of NDV (Newcastle disease virus); half the birds were maintained at thermoneutral temperature and the other half were exposed to high ambient temperature before the NDV challenge and throughout the remainder of the study. Phenotypic responses to heat, to NDV, or to heat + NDV were measured. Selected SNPs (single nucleotide polymorphisms) within 14 target genes or regions were genotyped; and genotype effects on phenotypic responses to NDV or heat + NDV were tested in each individual treatment group and the combined groups. Seventeen significant haplotype effects, among seven genes and seven phenotypes, were detected for response to NDV or heat or NDV + heat. These findings identify specific genetic variants that are associated with response to heat and/or NDV which may be useful in the genetic improvement of chickens to perform favorably when faced with pathogens and heat stress.

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Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chickens

Cited by 21 publications

References 69 publications

Whole-transcriptome analysis of heart in bovidae reveals regulatory pathways associated with high-altitude adaptation

Whole-transcriptome analysis of heart in bovidae reveals regulatory pathways associated with high-altitude adaptation

Exosomes Transmit Viral Genetic Information and Immune Signals may cause Immunosuppression and Immune Tolerance in ALV-J Infected HD11 cells

Association of Candidate Genes with Response to Heat and Newcastle Disease Virus

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