Cross-species comparison of gene expression between human and porcine tissue, using single microarray platform--preliminary results.

INTRODUCTION: Xenotransplantation is a potential solution for inadequate supply of donor organs. Pigs are considered the ideal donor for kidney transplantation to human recipients, therefore it is important to understand the gene regulation in the porcine organs. Oligonucleotide array technology has been utilized largely for human, mouse and rat gene expression studies only. Its use with porcine genes has not been reported. We investigated the possibility of studying gene regulation in porcine kidney with a human GeneChip microarray platform.
METHODS: To assess the feasibility of using a single microarrray platform for comparison of expressing data across different species (human and pig), we compared the gene expression profiles of human brain, human kidney and pig kidney using the Affymetrix U-133 A human GeneChip, which contains probes for 22,283 genes. Kidney biopsies from pigs and humans, with normal histology, were used to obtain RNA for porcine and human samples, while a commercially available adult whole cortex total RNA sample (Clontech) was used for the human sample. We assessed the intensity ratio for housekeeping and tissue specific genes. To examine the potential for non-specific binding to create false positive errors in our data, we compared the expression profiles in our experiments to a number of public databases.
RESULTS: There were approximately the same number of genes expressed at higher levels in the pig kidney as in the human kidney and human brain. The major differences in gene expression were found for genes with tissue specific patterns of expression. Eighty genes were increased in human brain vs. human and pig kidney samples. Two hundred and eighty genes were increased in human and pig kidney vs. human brain samples. Of the top 25 genes increased in pig kidney compared with human brain, we were able to cross-reference 18 genes to the Unigene and SAGE public databases. We confirmed the expected higher levels of expression in the kidney in 18 genes. Of the top 25 genes increased in human brain vs. pig kidney, we were able to cross-reference 20 genes to the Unigene and SAGE databases and confirm the expected higher expression levels in brain in 17 genes with three inconclusive genes.
CONCLUSION: This low level of false positive findings, at this preliminary stage, supports the concept of using human GeneChip microarray platform to compare gene expression profiles between pig and human tissues in the absence of a porcine microarray platform. Our study opens a new avenue into the analysis of porcine genes relevant to xenotransplantation.