Transcriptomic analysis identifies candidate genes and functional networks controlling the response of porcine...

It is difficult to obtain phenotypic data on disease susceptibility directly from swine in an industry setting. The magnitude of the proliferative response of peripheral blood mononuclear cells (PBMC) to the T cell mitogen concanavalin A (Con A) has long been used as an indirect measure of the responsiveness of the immune system to antigenic stimulation. This trait is known to exhibit moderate heritability in swine, but little is known about the identity of the genes that control the response. In this study, we carried out a time-course microarray experiment to measure gene expression at 3 different stages (3, 20, and 68 h) poststimulation of PBMC with Con A. A total of 46, 452, and 418 differentially expressed (DifEx) genes were identified at each time point, respectively. Expression changes for a subset of these genes were subsequently confirmed by real-time PCR. Functional annotation analyses of the microarray results successfully identified sets of genes involved in processes associated with multiple aspects of cell division, such as DNA and protein synthesis, and control of mitosis. However, the discovery of genes that controlled the response of PBMC to mitogen was limited with this approach, because the drastic changes in the transcriptional program necessitated by cells undergoing division masked changes in smaller immune response gene sets. Pathway and network analyses that focused on immune cells proved to be a more effective strategy for the identification of genes that coordinate aspects of the mitogenic response that are specific to PBMC. The cytokine gene IL15 was shown to be central to the highest scoring network at 20 h and affect the expression of 16 other DifEx genes, including some genes known to regulate T cell activation, such as IL7R, JUN, TNFRSF9, and ZAP70. The IL15 gene maps to a previously identified QTL interval for immune responsiveness to Con A on SSC 8, which also contains the related IL2 gene. At 68 h, a distinct downregulation of major histocompatibility complex class II antigen presentation genes was observed. Overall, the gene expression profile of the Con A-stimulated porcine PBMC points to a Th(1) bias in immune activation. Further work is required to determine whether polymorphisms linked to genes identified in this study affect this immune response trait in pig populations and whether the trait itself correlates with decreased susceptibility to intracellular pathogens in swine.