Transcriptional profiling of Marek’s disease virus genes during cytolytic and latent infection

Differential Virus-Specific IFN-Gamma Producing T Cell Responses to Marek's Disease Virus in Chickens With B19 and B21 MHC Haplotypes

Marek’s disease virus (MDV), the etiologic agent for Marek’s disease (MD), causes a deadly lymphoproliferative disease in chickens. Causes of the well-documented association between genetically defined lines of chicken and resistance to MD remain unknown. Here, the frequencies of IFN-gamma producing pp38 and MEQ-specific T cell responses were determined in line N (B21 haplotype; MD-resistant) and line P2a (B19 haplotype, MD-susceptible) chickens after infection with vaccine and/or virulent (RB1B) strains of MDV using both standard ex vivo and cultured chIFN-gamma ELISPOT assays. Notably, MDV infection of naïve and vaccinated MD-resistant chickens induced higher frequencies of IFN-gamma producing MDV-specific T cell responses using the cultured and ex vivo ELISPOT assay, respectively. Remarkably, vaccination did not induce or boost MEQ-specific effector T cells in the susceptible chickens, while it boosted both pp38-and MEQ-specific response in resistant line. Taken together, our results revealed that there is a direct association between the magnitude of T cell responses to pp38 and MEQ of MDV antigens and resistance to the disease.

The Marek's Disease Virus Unique Gene MDV082 Is Dispensable for Virus Replication but Contributes to a Rapid Disease Onset

Marek's disease virus (MDV) is a highly oncogenic alphaherpesvirus of chickens that causes lymphomas in various organs. Most MDV genes are conserved among herpesviruses, while others are unique to MDV and may contribute to pathogenesis and/or tumor formation. High transcript levels of the MDV-specific genes MDV082, RLORF11, and SORF6 were recently detected in lytically infected cells; however, it remained elusive if the respective proteins are expressed and if they play a role in MDV pathogenesis. In this study, we first addressed if these proteins are expressed by inserting FLAG tags at their N or C termini. We could demonstrate that among the three genes tested, MDV082 is the only gene that encodes a protein and is expressed very late in MDV plaques in vitro. To investigate the role of this novel MDV082 protein in MDV pathogenesis, we generated a recombinant virus that lacks expression of the MDV082 protein. Our data revealed that the MDV082 protein contributes to the rapid onset of Marek's disease but is not essential for virus replication, spread, and tumor formation. Taken together, this study sheds light on the expression of MDV-specific genes and unravels the role of the late protein MDV082 in MDV pathogenesis. IMPORTANCE MDV is a highly oncogenic alphaherpesvirus that causes Marek's disease in chickens. The virus causes immense economic losses in the poultry industry due to the high morbidity and mortality, but also the cost of the vaccination. MDV encodes over 100 genes that are involved in various processes of the viral life cycle. Functional characterization of MDV genes is an essential step toward understanding the complex virus life cycle and MDV pathogenesis. Here, we have identified a novel protein encoded by MDV082 and two potential noncoding RNAs (RLORF11 and SORF6). The novel MDV082 protein is not needed for efficient MDV replication and tumor formation. However, our data demonstrate that the MDV082 protein is involved in the rapid onset of Marek's disease.

Gut microbiota is associated with protection against Marek's disease virus infection in chickens

Marek's Disease Virus (MDV) infects chickens via respiratory route and causes lymphomas in internal organs including gastrointestinal tract. MDV infection causes a shift in the gut microbiota composition. However, interactions between the gut microbiota and immune responses against MDV infection are not well understood. Therefore, the current study was performed to understand the effect of the gut microbiota on Marek's disease (MD) pathogenesis. The findings showed that depletion of gut microbiota increased the severity of MD in infected chickens. In addition, an increase in the transcription of interferon (IFN)-α, IFN-β and IFN-γ in the bursa of Fabricius at 4 days post-infection (dpi) was observed in the gut microbiota depleted chickens. The observations in this study shed more light on the association between the gut microbiota and MDV infection in chickens. More research is needed to explore the mechanisms of involvement of the gut microbiota in immunity against MD in chickens.

Differential expression of type I interferon mRNA and protein levels induced by virulent Marek's disease virus infection in chickens

Marek's disease virus (MDV), an α-herpesvirus targeting avian species, causes fatal Marek's disease (MD) in chickens. The host interferon (IFN) responses play a key role in resisting viral infection. However, host IFN responses following MDV infection in the chicken central immune organs (thymus and bursa of Fabricius), which contain numerous MDV target cells, is poorly understood. In this study, we performed animal experiments in specific pathogen-free chickens infected with two virulent MDV strains (BS/15 and Md5) or without infection as negative controls. Specifically, the type I IFN (IFN-α and IFN-β) transcriptional and proteomic expression levels at 7, 10, 14, 17, and 21 days post infection (dpi) were detected and analyzed. Our results indicated that the mRNA and protein expression levels of IFN-α and IFN-β in the thymus and bursa of Fabricius were mainly downregulated in cytolytic infection (such as 10 dpi) and reactivation (such as 17 dpi) stages, but not the latent (such as 14 dpi) stage of MDV infection, which was determined by comprehensively analyzing the MDV viral load and immune organ damage caused by MDV infection. These data suggest that MDV could inhibit the expression of host type I IFNs, which may be involved in the MDV-induced host immunosuppression and contribute to the immune escape of MDV from host immunity. Furthermore, we found that the downregulated expression of the host type I IFNs induced by BS/15 and Md5 infection was significantly different, which we speculated may be related to the diverse virulence and pathogenicity of MDV strains. In conclusion, our study demonstrated that MDV mostly inhibited the expression of type I IFNs in infected hosts, which may be associated to its pathogenesis.

The Transcriptional Landscape of Marek's Disease Virus in Primary Chicken B Cells Reveals Novel Splice Variants and Genes

Marek's disease virus (MDV) is an oncogenic alphaherpesvirus that infects chickens and poses a serious threat to poultry health. In infected animals, MDV efficiently replicates in B cells in various lymphoid organs. Despite many years of research, the viral transcriptome in primary target cells of MDV remained unknown. In this study, we uncovered the transcriptional landscape of the very virulent RB1B strain and the attenuated CVI988/Rispens vaccine strain in primary chicken B cells using high-throughput RNA-sequencing. Our data confirmed the expression of known genes, but also identified a novel spliced MDV gene in the unique short region of the genome. Furthermore, de novo transcriptome assembly revealed extensive splicing of viral genes resulting in coding and non-coding RNA transcripts. A novel splicing isoform of MDV UL15 could also be confirmed by mass spectrometry and RT-PCR. In addition, we could demonstrate that the associated transcriptional motifs are highly conserved and closely resembled those of the host transcriptional machinery. Taken together, our data allow a comprehensive re-annotation of the MDV genome with novel genes and splice variants that could be targeted in further research on MDV replication and tumorigenesis.

Evaluation of the transcriptional status of host cytokines and viral genes in the trachea of vaccinated and non-vaccinated chickens after challenge with the infectious laryngotracheitis virus

Infectious laryngotracheitis is a highly contagious disease of chickens responsible for significant economic losses for the poultry industry worldwide. The disease is caused by Gallid herpesvirus-1 (GaHV-1) commonly known as the infectious laryngotracheitis virus. Although characterized by their potential to regain virulence, chicken embryo origin (CEO) vaccines are the most effective vaccines against laryngotracheitis as they significantly reduce the replication of challenge virus in the trachea and conjunctiva. Knowledge on the nature of protective immunity elicited by CEO vaccines is very limited. Therefore, elucidating the origin of the immune responses elicited by CEO vaccination is relevant for development of safer control strategies. In this study the transcription levels of key host immune genes (IFN-γ, IFN-β, IL-1β, IL-6, IL-8, IL-18) and viral genes (ICP4, ICP27, UL46, UL49), as well as viral genome loads in trachea were quantified at 6 and 12 hours post-challenge of CEO vaccinated and non-vaccinated chickens. Immediately after challenge a significant increase in IFN-γ gene expression was followed by a significant reduction in viral replication. In contrast to the rapid induction of IFN-γ, expression of the pro-inflammatory cytokines (IL-1β, IL-6, IL-8) and type I IFN β was either slightly reduced or remained at basal levels. These suggest that the former cytokines may not play important roles during immediate early responses induced by ILTV challenge in either vaccinated or non-vaccinated chickens. Overall, these results suggest that the rapid expression of IFN-γ may induce pathways of antiviral responses necessary for blocking early virus replication.

Differential expression of Toll-like receptor genes in lymphoid tissues between Marek's disease virus-infected and noninfected chickens

Toll-like receptors (TLR) are trans-membrane sensors recognizing invading microbes. Toll-like receptors play a central role in initiating immune responses against several pathogens. In this study, we investigated the response of TLR and downstream genes to Marek's disease virus (MDV) infection. Forty 1-d-old chicks were randomly divided into 2 groups, with 20 chicks infected with MDV and 20 chicks mock-infected. Four chickens were euthanized respectively from infected and age-matched noninfected groups at 4, 7, 14, 21, and 28 d postinfection (dpi). Bursas, spleens, and thymuses were removed. The differential expression of TLR genes, including TLR3, TLR5, TLR7, TLR15, and TLR21, and downstream genes of TLR7, including MyD88, TRAF3, TRAF6, IFNA, IFNB, and IL6, in lymphoid tissues of MDV-infected and noninfected chickens was determined by real-time PCR. The results showed that the change of TLR genes was different in 3 lymphoid tissues. Expression of TLR7 and MyD88 was upregulated at 14 dpi and downregulated at 28 dpi in MDV-infected compared with noninfected spleens. The TRAF6 and IFNB were upregulated, and TRAF3, IFNA, and IL6 genes showed increasing trends in MDV-infected compared with noninfected spleens at 14 dpi. The expression of TLR3 and TLR15 genes was downregulated in MDV-infected compared with noninfected spleens at 28 dpi. The results indicated that TLR7 and its downstream genes were a response to MDV infection at 14 dpi. However, the function of TLR was impaired when the infection entered the tumor transformation phase. In bursas, TLR3 and TLR15 genes were upregulated at 7 and 4 dpi, respectively. It indicated that TLR3 and TLR15 might be involved in response to MDV infection in bursa at early phases. However, no differential expression of TLR genes was observed between MDV-infected and noninfected thymuses, which indicated that the thymus had little response to MDV infection mediated by TLR.

Immune responses against Marek's disease virus

It is more than a century since Marek's disease (MD) was first reported in chickens and since then there have been concerted efforts to better understand this disease, its causative agent and various approaches for control of this disease. Recently, there have been several outbreaks of the disease in various regions, due to the evolving nature of MD virus (MDV), which necessitates the implementation of improved prophylactic approaches. It is therefore essential to better understand the interactions between chickens and the virus. The chicken immune system is directly involved in controlling the entry and the spread of the virus. It employs two distinct but interrelated mechanisms to tackle viral invasion. Innate defense mechanisms comprise secretion of soluble factors as well as cells such as macrophages and natural killer cells as the first line of defense. These innate responses provide the adaptive arm of the immune system including antibody- and cell-mediated immune responses to be tailored more specifically against MDV. In addition to the immune system, genetic and epigenetic mechanisms contribute to the outcome of MDV infection in chickens. This review discusses our current understanding of immune responses elicited against MDV and genetic factors that contribute to the nature of the response.

Poultry genome sequences: progress and outstanding challenges

The first build of the chicken genome sequence appeared in March, 2004 - the first genome sequence of any animal agriculture species. That sequence was done primarily by whole genome shotgun Sanger sequencing, along with the use of an extensive BAC contig-based physical map to assemble the sequence contigs and scaffolds and align them to the known chicken chromosomes and linkage groups. Subsequent sequencing and mapping efforts have improved upon that first build, and efforts continue in search of missing and/or unassembled sequence, primarily on the smaller microchromosomes and the sex chromosomes. In the past year, a draft turkey genome sequence of similar quality has been obtained at a much lower cost primarily due to the development of 'next-generation' sequencing techniques. However, assembly and alignment of the sequence contigs and scaffolds still depended on a detailed BAC contig map of the turkey genome that also utilized comparison to the existing chicken sequence. These 2 land fowl (Galliformes) genomes show a remarkable level of similarity, despite an estimated 30-40 million years of separate evolution since their last common ancestor. Among the advantages offered by these sequences are routine re-sequencing of commercial and research lines to identify the genetic correlates of phenotypic change (for example, selective sweeps), a much improved understanding of poultry diversity and linkage disequilibrium, and access to high-density SNP typing and association analysis, detailed transcriptomic and proteomic studies, and the use of genome-wide marker- assisted selection to enhance genetic gain in commercial stocks.

Transcriptional profiling of host gene expression in chicken embryo lung cells infected with laryngotracheitis virus

Background

Infection by infectious laryngotracheitis virus (ILTV; gallid herpesvirus 1) causes acute respiratory diseases in chickens often with high mortality. To better understand host-ILTV interactions at the host transcriptional level, a microarray analysis was performed using 4 × 44 K Agilent chicken custom oligo microarrays.

Results

Microarrays were hybridized using the two color hybridization method with total RNA extracted from ILTV infected chicken embryo lung cells at 0, 1, 3, 5, and 7 days post infection (dpi). Results showed that 789 genes were differentially expressed in response to ILTV infection that include genes involved in the immune system (cytokines, chemokines, MHC, and NF-κB), cell cycle regulation (cyclin B2, CDK1, and CKI3), matrix metalloproteinases (MMPs) and cellular metabolism. Differential expression for 20 out of 789 genes were confirmed by quantitative reverse transcription-PCR (qRT-PCR). A bioinformatics tool (Ingenuity Pathway Analysis) used to analyze biological functions and pathways on the group of 789 differentially expressed genes revealed that 21 possible gene networks with intermolecular connections among 275 functionally identified genes. These 275 genes were classified into a number of functional groups that included cancer, genetic disorder, cellular growth and proliferation, and cell death.

Conclusion

The results of this study provide comprehensive knowledge on global gene expression, and biological functionalities of differentially expressed genes in chicken embryo lung cells in response to ILTV infections.

Facilitating functional annotation of chicken microarray data

Background

Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO). However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information.

Results

We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM) tool to help researchers to quickly retrieve corresponding functional information for their dataset.

Conclusion

Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and will be updated on regular basis.

Host responses in the bursa of Fabricius of chickens infected with virulent Marek's disease virus

The bursa of Fabricius serves as an important tissue in the process of Marek's disease virus (MDV) pathogenesis, since B cells of the bursa harbor the cytolytic phase of MDV replication cycle. In the present study, host responses associated with MDV infection in the bursa of Fabricius of chickens were investigated. The expression of MDV phosphoprotein (pp)38 antigen, MDV glycoprotein (gB) and MDV viral interleukin (vIL)-8 transcripts was at the highest at 4 days post-infection (d.p.i.) and then showed a declining trend. On the contrary, the expression of meq (MDV EcoRI Q) gene as well as the viral genome load increased gradually until day 14 post-infection. The changes in viral parameters were associated with significantly higher infiltration of macrophages and T cell subsets, particularly CD4+ T cells into the bursa of Fabricius. Of the genes examined, the expression of interferon (IFN)-alpha, IFN-gamma genes and inducible nitric oxide synthase (iNOS) was significantly up-regulated in response to MDV infection in the bursa of Fabricius. The results suggest a role for these cells and cytokines in MDV-induced responses in the bursa of Fabricius.

Comparative analysis of viral gene expression programs during poxvirus infection: a transcriptional map of the vaccinia and monkeypox genomes

BACKGROUND

Poxviruses engage in a complex and intricate dialogue with host cells as part of their strategy for replication. However, relatively little molecular detail is available with which to understand the mechanisms behind this dialogue.

METHODOLOGY/PRINCIPAL FINDINGS

We designed a specialized microarray that contains probes specific to all predicted ORFs in the Monkeypox Zaire (MPXV) and Vaccinia Western Reserve (VACV) genomes, as well as >18,000 human genes, and used this tool to characterize MPXV and VACV gene expression responses in vitro during the course of primary infection of human monocytes, primary human fibroblasts and HeLa cells. The two viral transcriptomes show distinct features of temporal regulation and species-specific gene expression, and provide an early foundation for understanding global gene expression responses during poxvirus infection.

CONCLUSIONS/SIGNIFICANCE

The results provide a temporal map of the transcriptome of each virus during infection, enabling us to compare viral gene expression across species, and classify expression patterns of previously uncharacterized ORFs.