Allele-specific expression of CD4+ T cells in response to Marek’s disease virus infection

Authors: BAI, HAO - University Of Maryland; HE, YANGHUA - University Of Maryland; DING, YI - University Of Maryland; CARRILLO, JOSE - University Of Maryland; SELVARAJ, RAMESH - The Ohio State University; Zhang, Huanmin; CHEN, JILAN - Chinese Academy Of Agricultural Sciences; SONG, JIUZHOU - University Of Maryland

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2019
Publication Date: 9/17/2019
Citation: Bai, H., He, Y., Ding, Y., Carrillo, J.A., Selvaraj, R.K., Zhang, H., Chen, J., Song, J. 2019. Allele-specific expression of CD4+ T cells in response to Marek’s disease virus infection. Genes. 10(9):718. https://doi.org/10.3390/genes10090718.
DOI: https://doi.org/10.3390/genes10090718

Interpretive Summary: All diploid organisms have two members at each gene position, known as alleles at each genetic locus in science. Studies show so far that the two members do not necessarily always express themselves equally and the unequal expression of one member over the other is often differentially associated with cellular functionalities. This study systematically examined gene member expression in chicken in response to an avian herpesvirus exposure, known as Marek’s disease virus challenge, and identified over a hundred genes with unequal member expression between two genetically divergent cross flocks. The identified genes genetic polymorphisms would be instrumental in genetic improvement for Marek’s disease resistance by selection.

Technical Abstract: Marek’s disease (MD) is a T cell lymphoma disease induced by Marek’s disease virus (MDV), a highly oncogenic a 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.