177 Functional Annotation of an Array of Immune Cells and Various Tissues in the Chicken
Authors: Drechsler Yvonne , Ng Theros , Sparling Brandi , Hawkins R David 
Published: October 2023

Abstract
Infection and disease negatively affect performance, growth, and health in production animals and has major economic impacts on commercial poultry production. Regulatory elements control the expression of genes and consequently phenotype. Epigenetic modifications such as histone tail modifications and DNA methylation are not only key to the regulation of unique transcriptome patterns, these modifications are indispensable as genome annotators to uncover cell- and tissue-specific regulatory elements. The objectives of our current projects are to leverage transcriptomic and epigenomic methods to annotate transcripts, coding and noncoding, and cis-regulatory elements in the chicken genome, including promoters, enhancers and insulators. In addition, we are employing single-cell sequencing to characterize new or rare cell populations in tissues relevant to production and investigate underlying mechanisms of disease resistance to pathogens. The transcriptome of a number of important cells and tissues has been analyzed, including immune, intestinal and reproductive. The animal procedure was approved and conducted according to guidelines established by the Western University of Health Sciences, Pomona, California (WesternU) Institutional Animal Care and Use Committee. Cell and tissue collection, processing and bioinformatic analysis for transcriptome studies were performed as described in Overbey et al. (2021; Frontiers Genetics). Single-cell studies were performed as described in Sparling et al. (2022; Journal of Immunology) using the 10x Genomics platform. Results for the transcriptome studies show that in the immune cells, many DEGs were mostly involved in cellular processes relating to differentiation and cell metabolism as well as basic functions of immune cells such as cell adhesion and signal transduction. This was to be expected, as there was no explicit immunological stimulus involved. Nevertheless, it was notable that DEGs in the comparison between bursa and thymus that were upregulated in the thymus were related to T cell differentiation and maturation. On the other hand, genes differentially upregulated in B cell vs Bursa or Bursa vs Thymus, are mostly involved in B cell development and differentiation, or activation. Genes differentially regulated in B cells and monocytes are involved in specific functions of the cell types. In the intestinal tissues, we were able to correlate most of the differential expressed genes to metabolic processes related to nutrient digestion and absorption. Several genes in the distal part of the intestine were particularly implicated in vitamin metabolism. Genes involved in energy metabolism are also abundant in the cecum, which suggests that microbial contribution of energy production in the intestine is especially important. Finally, single cell studies on the chicken shell gland are ongoing, but we found differences in cellular populations and gene expression dependent on the chicken haplotype profiled and differences in expression of Ig-like receptors that need to be further explored.