Detecting function variation in immune cell types and their implications on genetic resistance to Marek’s Disease

Authors: VELEZ-IRIZARRY, DEBORAH - Orise Fellow; CHENG, HANS - Retired ARS Employee; Hearn, Cari

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/8/2025
Publication Date: 1/29/2025
Citation: Velez-Irizarry, D., Cheng, H.H., Hearn, C.J. 2025. Detecting function variation in immune cell types and their implications on genetic resistance to Marek’s Disease. Scientific Reports. 2025(15):3689. https://doi.org/10.1038/s41598-025-86174-w.
DOI: https://doi.org/10.1038/s41598-025-86174-w

Interpretive Summary: Marek's disease virus (MDV) is a highly contagious virus that causes disease in the form of tumors in chickens known as Marek’s Disease (MD). Genetically resistant and susceptible chicken lines have been utilized to study how the chicken immune system either controls or fails to control the infection. This information is valuable for improving breeding and vaccine development strategies. In our study, we looked at the immune systems of three types of chickens: Line 6 (L6), which is highly resistant to MD, Line 7 (L7), which is very susceptible to MD, and a first-generation (F1) cross between L6 and L7. We used single-cell RNA sequencing, which measures the gene expression of every captured immune cell, to study the immune systems of these three lines during infection. By analyzing these datasets together, we found new populations of immune cells that had not previously been described in the chicken based on their gene expression patterns. We also identified specific gene expression signatures unique to immune cell activation states in response to infection in resistant and susceptible birds. This gave us new information about how MD resistance might work by how their immune cells respond to infection. Finally, we used the F1 to examine how the genetic traits of the resistant L6 and susceptible L7 can alter gene expression in response to infection in the different immune cell types based on the disparity in expression of parental alleles. This study helps us better understand the immune cell types in chickens and how they respond to MDV infection in genetically resistant and susceptible birds, which could help us develop new strategies to prevent MD.

Technical Abstract: Marek’s disease (MD) is a highly contagious alphaherpesvirus infection ubiquitous in the poultry industry. Marek’s disease virus (MDV) causes the lymphoproliferative MD and genetically resistant Line 6(3) and susceptible Line 7(2) have been instrumental to research on the avian immune system response to MDV infection. In this study we characterized molecular signatures unique to splenic immune cell types across different genetic backgrounds 6 days after infection with MDV. Using three populations, resistant Line 6(3) (L6), susceptible Line 7(2) (L7) and a first-generation (F1) cross between L6xL7 we evaluate the immune cell type transcriptome within cells with active viral replication and responding cell types using single cell RNA sequencing. We found cytotoxic T cells and natural killer cells had the highest viral load compared to other immune cell types and show immune cell type signatures that can be used to identify activated states of avian immune cells. Using the F1 cross we quantified allele specific expression (ASE) of biallelic SNPs and found biased expression of parental alleles that were specific to immune cell subtypes. SNPs with ASE can be functionally linked to causative polymorphisms that alter the transcription of nearby genes. We identified 22 SNPs with ASE in response to MDV infection in F1; these SNPs were in gene rich regions surrounding 59 genes. SNPs with ASE mapped to genes with critical functions in immune response including genes known to promote viral replication. These results show that potential functional variants associated with susceptibility to MD may have a bigger impact in a subset of immune cell types, and by characterizing the transcriptomes of these subtypes we can unravel molecular signatures unique to activated avian immune cells and evaluate their contributions to genomic resistance to MD.