Analysis of gene expression patterns by microarray hybridization in blood mononuclear cells of SLA-DRB1 defined Canadian Yorkshire pigs

Abstract

Background: The Swine Leukocyte Antigen (SLA) system encodes molecules for self-nonself discrimination and is associated with immune responses and disease resistance. Three lines of pigs defined by their SLA-DRB1 alleles were developed at the University of Guelph for xenotransplantation and immune response studies. The aim of this project was to explore the potential association between defined SLA-DRB1 alleles and gene transcriptional patterns of other immune-related genes in blood mononuclear cells.

Findings: Three SLA-DRB1 alleles were characterized using a RT-PCR-based sequencing method. The loci represented included a new allele, DRB1*04ns01. Next, microarray heterologous (bovine-porcine) hybridization together with qPCR were used to explore differential gene expression between SLA-DRB1-defined groups. Microarray analysis showed significant (p < 0.01) differential expression for 5 genes, mostly related to inflammation. Genes varied according to the comparison analyzed. Further testing with qPCR revealed the same trend of differential expression for 4 of the genes, although statistical significance was reached for only one.

Conclusion: A new SLA-DRB1 allele was characterized. A potential association was found between SLA-DRB1 alleles and inflammation-related genes. However, the influence of other genes cannot be ruled out. These preliminary findings agree with other studies linking MHC haplotypes and inflammation processes, including autoimmune disease. The study provides an initial view of the biological interactions between the SLA complex and other immune-related genes. Future studies will focus on characterization of SLA-haplotypes associated with these particular alleles and the dynamics of the immune response to antigenic challenges.

Figure 1

Nucleotide and protein sequence alignment of SLA-DRB1 alleles. Multiple sequence alignment for (a) nucleotide and (b) protein of published SLA-DRB1*0403 alleles (designated by their GenBank accession numbers) and *04ns01 (new allele). The black arrows mark (a) the point mutation and (b) the corresponding amino acid residue substitution.

Figure 2

Differential transcriptional activity detected by cDNA microarray hybridization and qPCR. Mean fold changes in transcript quantification obtained by cDNA microarray hybridization () and qPCR (□). a) Microarray (n = 2 per group) and qPCR (*0502, n = 9; *04ns01, n = 14) results for the comparison between SLA-DRB1*0502 and *04ns01. b) Microarray (n = 2 per group) and qPCR (*0502, n = 9; *0701, n = 6) results for the comparison between SLA-DRB1*0502 and *0701 alleles. c) Microarray (n = 2 per group) and qPCR (*0701, n = 6; *04ns01, n = 14) results for the comparison between SLA-DRB1*0701 and *04ns01.