Location: Endemic Poultry Viral Diseases Research
2018 Annual Report
Objectives
1. Enhance the chicken genomic resources to support genetic selection and other strategies to reduce Marek’s disease.
1.1. Enhance the chicken genetic map and its integration with the genome assembly.
1.2. Improve the annotation of the chicken genome.
2. Identify and characterize chicken genes and pathways that confer resistance to Marek’s disease or improve vaccinal efficacy.
2.1. Identify driver mutations associated with genetic resistance to Marek’s disease.
2.2. Characterize long-range enhancer-promoter interactions, especially for those involved in genetic resistance to Marek’s disease.
2.3. Validate genes and polymorphisms that confer Marek’s disease vaccine protective efficacy.
2.4. Identify non-coding RNA genes that confer genetic resistance to Marek’s disease and vaccinal protective efficacy.
Approach
Poultry is the primary meat consumed in the U.S. To achieve economic efficiency, birds are raised at very high density. Since these conditions promote the spread of infectious diseases, the industries rely heavily on biosecurity and vaccines for disease prevention and control. Control of Marek’s disease (MD), a T-cell lymphoma induced by the Marek’s disease virus (MDV), routinely ranks as a major disease concern to the industries. Since the 1960s, field strains of MDV have evolved to higher virulence. Consequently, there is a need to develop alternative and sustainable strategies to augment current MD control methods. We define two objectives to help achieve this goal. First, we continue to enhance and curate the East Lansing (EL) chicken genetic map, which provides the foundation for the chicken genome assembly and many of our molecular genetic studies. In addition, we will aid in the annotation of the chicken genome to allow more efficient understanding and the subsequent use of genomic variation. Second, we use and integrate various genomic approaches to (1) identify genetic and epigenetic variation associated with genetic resistance to MD or MD vaccinal efficiency, and (2) mutations associated with MD tumors.
If successful, this project will provide a number of products including (1) a more complete genetic map that will aid in improving the chicken genome assembly, and (2) candidate genes and pathways conferring MD resistance or vaccinal response for evaluation in commercial breeding lines. Ultimately, the poultry industries and U.S. consumers will benefit by the production of safe and economical products.
Progress Report
In collaboration with investigators at Washington University School of Medicine in St. Louis, Missouri, the current chicken reference assembly (galGal6) is being updated with genes associated with the immune system, especially the T cell receptor (TCR) locus. This improved assembly provides the basis and tools for understanding chicken biology including genetics and immunology of disease and disease resistance.
ARS researchers validated that importance of somatic mutations beyond Marek’s disease virus (MDV) infection in the formation of T cell tumors associated with Marek’s disease. Specifically, ~80% of the tumors had either mutations in key regions or low expression of Ikaros, which is the master regulator of lymphocyte development. Interestingly, there was also an association of aberrant TCR expression in tumors with Ikaros mutations. This information provides fundamental biological information on how MDV infection in combination with alterations in the chicken generate promoter MDV-induced tumors.
It has been well-documented that variation in genetic resistance to infectious diseases is not only attributable to differences in the amino acid composition of proteins but also to variation in gene expression. Current studies are examining both the gene and non-coding RNA profiles of birds that are resistant or susceptible to MD in response to challenge with MDV or MD vaccines. This information will lead to advancing our understanding of the genetic and epigenetic mechanisms conferring MD resistance and vaccine protective efficacy.
To investigate the expression pattern of MDV genes in the skin and spleen tissues of infected birds, RNA (gene) profiling was conducted at 10, 20, and 30 days after infection. The results revealed many MDV genes were differentially expressed in the skin of infected birds compared to the spleen. This result is noteworthy as the skin is the only place where infectious virions are produced. The generation of recombinant MDVs lacking these genes is in underway, which should help to characterize and determine the specific roles of each viral gene. This study provides the groundwork for development of mutant recombinant viruses as vaccine against the evolving and highly pathogenic strains of MDV.
The role of B cells in MD vaccines was investigated. Chicks were initially depleted of B cells, vaccinated, and challenged one week later after adoptive transfer of lymphocytes from control birds. The initial results indicate that B cells do not play a critical role in the vaccine-mediated protection as MD vaccinated birds in the absence of B cells were fully protected. Also, non-vaccinated and MDV challenged birds with depleted B cells, however, exhibited reduced disease symptoms when compared similar birds with an intact B cell population. The data sheds light on the mechanism of vaccine protection and design of future recombinant vaccines with improved protective features.
Accomplishments
1. Both low expression or mutations in the Ikaros gene drive Marek’s disease virus (MDV)-induced transformation in chicken. Understanding the biological mechanism for MDV to induce T cell lymphomas is critical for future control using vaccines or genetic resistance. To address this question, ARS researchers at East Lansing, Michigan, in collaboration with investigators at Purdue University in West Lafayette, Indiana, and University of California in Davis, California, DNA- and RNA-sequenced tumors to identify causal mutations. It was determined that the majority of tumors had either low expression or mutations in key regions of Ikaros, which is the master regulator for immune cell development. This information will aid future efforts to select birds for superior disease resistance to Marek’s disease (MD) and improved MD vaccines. As chicken is the primary meat consumed in the U.S., this will benefit consumers and society by reducing the amount of feed and waste produced, and increasing health and well-being of reared birds.
Review Publications
Li, X., Chen, W., Zhang, H., Li, A., Shu, D., Li, H., Dai, Z., Yan, Y., Zhang, X., Lin, W., Ma, J., Xie, Q. 2017. Naturally occurring frame-shift mutations in the tvb receptor gene are responsible for decreased susceptibility to subgroups B, D, and E. Journal of Virology. 92(8):e01770-17. https://doi.org/10.1128/JVI.01770-17.
Webb, A.E., Youngworth, I.A., Kaya, M., Gitter, C.L., O’Hare, E.A., May, B.P., Cheng, H.H., Delany, M.E. 2018. Narrowing the wingless-2 mutation to a 227 Kb candidate region on chicken chromosome 12. Poultry Science. 97(6):1872–1880. https://dx.doi.org/10.3382/ps/pey073.
Chen, W., Liu, Y., Li, A., Li, X., Li, H., Dai, Z., Yan, Y., Zhang, X., Shu, D., Zhang, H., Lin, W., Ma, J., Xie, Q. 2017. A premature stop codon within the tvb receptor gene results in decreased susceptibility to infection by avian leukosis virus subgroups B, D, and E. Oncotarget. 8(62):105942-105956.
Xie, Q., Chang, S., Dong, K., Dunn, J.R., Song, J., Zhang, H. 2017. Genomic fariation between genetic lines of white leghorns differed in resistance to Marek’s disease. Journal of Clinical Epigenetics. 3:29. https://doi.org/10.21767/2472-1158.100063.
Zhang, X., Yan, Y., Lei, X., Li, A., Zhang, H., Dai, Z., Li, X., Chen, W., Lin, W., Chen, F., Ma, J., Xie, Q. 2018. Identification of aberrantly expressed circRNAs in subgroup J avian leucosis virus induced tumor livers by RNA sequencing. Oncotarget. 2018:1-13.
Dong, K., Chang, S., Xie, Q., Black Pyrkosz, A.A., Zhang, H. 2017. Comparative transcriptomics of genetically divergent lines of chickens in response to Marek’s disease virus challenge at cytolytic phase. PLoS One. 12(6):e0178923. https://doi.org/10.1371/journal.pone.0178923.
Lin, W., Xu, Z., Yan, Y., Zhang, H., Li, H., Chen, W., Chen, F., Xie, Q. 2018. Avian leukosis virus subgroup J attenuates type I interferon production through blocking IkB phosphorylation. Frontiers in Microbiology. 9(1089):1-13. https://doi.org/10.3389/fmicb.2018.01089.
Wang, D., Sun, S., Heidari, M. 2018. Marek’s disease vaccine activates chicken macrophages. Journal of Veterinary Science. 19(3):375-383. https://doi.org/10.4142/jvs.2018.19.3.375.
