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Open AccessArticle

Allele-Specific Expression of CD4+ T Cells in Response to Marek’s Disease Virus Infection

1
Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
2
Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
3
Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
4
USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
5
Department of Animal Sciences, The Ohio State University, Wooster, OH 44691, USA
6
Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, HI 96822, USA
*
Author to whom correspondence should be addressed.
Genes 2019, 10(9), 718; https://doi.org/10.3390/genes10090718
Received: 24 July 2019 / Revised: 9 September 2019 / Accepted: 10 September 2019 / Published: 17 September 2019
(This article belongs to the Section Animal Genetics and Genomics)
Marek’s disease (MD) is a T cell lymphoma disease induced by Marek’s disease virus (MDV), a highly oncogenic α herpesvirus primarily affecting chickens. MD is a chronic infectious disease that threatens the poultry industry. However, the mechanisms of genetic resistance for MD are complex and not completely understood. In this study, to identify high-confidence candidate genes of MD genetic resistance, high throughput sequencing (RNA-seq) was used to obtain transcriptomic data of CD4+ T cells isolated from MDV-infected and non-infected groups of two reciprocal crosses of individuals mating by two highly inbred chicken lines (63 MD-resistant and 72 MD-susceptible). After RNA-seq analysis with two biological replicates in each group, we identified 61 and 123 single nucleotide polymorphisms (SNPs) (false discovery rate (FDR) < 0.05) annotated in 39 and 132 genes in intercrosses 63 × 72 and 72 × 63, respectively, which exhibited allele-specific expression (ASE) in response to MDV infection. Similarly, we identified 62 and 79 SNPs annotated in 66 and 96 genes in infected and non-infected groups, respectively. We identified 534 and 1543 differentially expressed genes (DEGs) (FDR < 0.05) related to MDV infection in intercrosses 63 × 72 and 72 × 63, respectively. We also identified 328 and 20 DEGs in infected and non-infected groups, respectively. The qRT-PCR using seven DEGs further verified our results of RNA-seq analysis. The qRT-PCR of 11 important ASE genes was performed for gene functional validation in CD4+ T cells and tumors. Combining the analyses, six genes (MCL1, SLC43A2, PDE3B, ADAM33, BLB1, and DMB2), especially MCL1, were highlighted as the candidate genes with the potential to be involved in MDV infection. Gene-set enrichment analysis revealed that many ASE genes are linked to T cell activation, T cell receptor (TCR), B cell receptor (BCR), ERK/MAPK, and PI3K/AKT-mTOR signaling pathways, which play potentially important roles in MDV infection. Our approach underlines the importance of comprehensive functional studies for gaining valuable biological insight into the genetic factors behind MD and other complex traits, and our findings provide additional insights into the mechanisms of MD and disease resistance breeding in poultry. View Full-Text
Keywords: Marek’s disease virus; CD4+ T cells; allele-specific expression; differential expression; genetic resistance Marek’s disease virus; CD4+ T cells; allele-specific expression; differential expression; genetic resistance
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Bai, H.; He, Y.; Ding, Y.; Carrillo, J.A.; Selvaraj, R.K.; Zhang, H.; Chen, J.; Song, J. Allele-Specific Expression of CD4+ T Cells in Response to Marek’s Disease Virus Infection. Genes 2019, 10, 718.

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