Genome-Wide Analysis in Swine Associates Corneal Graft Rejection with Donor-Recipient Mismatches in Three Novel Histocompatibility Regions and One Locus Homologous to the Mouse H-3 Locus

Abstract

In rodents, immune responses to minor histocompatibility antigens are the most important drivers of corneal graft rejection. However, this has not been confirmed in humans or in a large animal model and the genetic loci are poorly characterised, even in mice. The gene sequence data now available for a range of relevant species permits the use of genome-wide association (GWA) techniques to identify minor antigens associated with transplant rejection. We have used this technique in a pre-clinical model of corneal transplantation in semi-inbred NIH minipigs and Babraham swine to search for novel minor histocompatibility loci and to determine whether rodent findings have wider applicability. DNA from a cohort of MHC-matched and MHC-mismatched donors and recipients was analysed for single nucleotide polymorphisms (SNPs). The level of SNP homozygosity for each line was assessed. Genome-wide analysis of the association of SNP disparities with rejection was performed using log-likelihood ratios. Four genomic blocks containing four or more SNPs significantly linked to rejection were identified (on chromosomes 1, 4, 6 and 9), none at the location of the MHC. One block of 36 SNPs spanned a region that exhibits conservation of synteny with the mouse H-3 histocompatibility locus and contains the pig homologue of the mouse Zfp106 gene, which encodes peptide epitopes known to mediate corneal graft rejection. The other three regions are novel minor histocompatibility loci. The results suggest that rejection can be predicted from SNP analysis prior to transplant in this model and that a similar GWA analysis is merited in humans.

The major histocompatibility complex homozygous inbred Babraham pig as a resource for veterinary and translational medicine

“…This study shows that the inbred Babraham pigs are functionally MHC homozygous. Taken together with the high level of inbreeding as measured by SNPs over the entire genome, this confirms the Babraham pig as a very valuable model for swine and human disease research, as well in wider biomedical applications. This value can only increase as our ability to edit mammalian genomes and produce gene‐edited animals improves.…”

“…Furthermore, having a defined MHC allows one to predict tolerance and associated clinical interventions. For instance, the power of the inbred Babraham pig model has recently been shown in a genome‐wide analysis which identified minor histocompatibility antigens involved in corneal transplant rejection . This work was only possible using individuals with a controlled genetic background and a defined MHC region in order to facilitate matching and mismatching of histocompatibility loci.…”

“…During the period from this 1999 study until 2016, there were approximately 15 generations and recovery from a bottleneck of nine sows and three boars with the current population originating from five sows and one boar (animal records from The Pirbright Institute). At this point, single nucleotide polymorphism (SNP) analysis using the Illumina PorcineSNP60 chip suggested approximately 85% homozygosity across the Babraham genome, based on 59 852 genotyped SNPs . Other animals with the same level of inbreeding and homozygosity are not available for large veterinary species.…”

“…The SNP chip analysis by Nicholls et al indicated complete homozygosity across the MHC region of chromosome 7. However, measuring MHC variation using commercial SNP assays is not always accurate as much of the variation over polymorphic loci falls below the minimum minor allele frequency to be included in the assay.…”

“…At this point, single nucleotide polymorphism (SNP) analysis using the Illumina PorcineSNP60 chip suggested approximately 85% homozygosity across the Babraham genome, based on 59 852 genotyped SNPs. 10 Other animals with the same level of inbreeding and homozygosity are not available for large veterinary species.…”