Regulation of alpha1,3galactosyltransferase expression in pig endothelial cells. Implications for xenotransplantation

Allelic variation of the porcine alpha-1,3-galactosyltransferase 1 (GGTA1) gene

The alpha-1,3-galactosyltransferase 1 enzyme (GGTA1) produces the alpha-Gal epitopes, responsible for pig-to-human hyperacute xenograft rejection. Recently, efforts have been directed at inactivating the porcine GGTA1 gene in order to reduce hyperacute rejection. As very little is known about the genetic variability of this key gene among pig breeds, we investigated the variation in its nucleotide sequence, by amplification of the entire coding region with the use of polymerase chain reaction followed by DNA sequencing. Eight commercial pig populations were analysed and 17 single nucleotide polymorphisms (SNPs) were detected: 11 in intronic regions and 6 in the 3' untranslated region (UTR). No SNPs change the encoded protein; however, 8 of these SNPs may alter the transcriptional regulation and pre-mRNA splicing of GGTA1.

Advances in swine transcriptomics

The past five years have seen a tremendous rise in porcine transcriptomic data. Available porcine Expressed Sequence Tags (ESTs) have expanded greatly, with over 623,000 ESTs deposited in Genbank. ESTs have been used to expand the pig-human comparative maps, but such data has also been used in many ways to understand pig gene expression. Several methods have been used to identify genes differentially expressed (DE) in specific tissues or cell types under different treatments. These include open screening methods such as suppression subtractive hybridization, differential display, serial analysis of gene expression, and EST sequence frequency, as well as closed methods that measure expression of a defined set of sequences such as hybridization to membrane arrays and microarrays. The use of microarrays to begin large-scale transcriptome analysis has been recently reported, using either specialized or broad-coverage arrays. This review covers published results using the above techniques in the pig, as well as unpublished data provided by the research community, and reports on unpublished Affymetrix data from our group. Published and unpublished bioinformatics efforts are discussed, including recent work by our group to integrate two broad-coverage microarray platforms. We conclude by predicting experiments that will become possible with new anticipated tools and data, including the porcine genome sequence. We emphasize that the need for bioinformatics infrastructure to efficiently store and analyze the expanding amounts of gene expression data is critical, and that this deficit has emerged as a limiting factor for acceleration of genomic understanding in the pig.

Approach for defining endogenous reference genes in gene expression experiments

The quantification of gene expression by real-time polymerase chain reaction (PCR) has revolutionized the field of gene expression analysis. Due to its sensitivity and flexibility it is becoming the method of choice for many investigators. However, good normalization protocols still have to be implemented to facilitate data exchange and comparison. We have designed primers for 10 unrelated genes and developed a simple protocol to detect genes with stable expression that are suitable for use as endogenous reference genes for further use in the normalization of gene expression data obtained by real-time PCR. Using this protocol, we were able to identify human proteosome subunit Y as a reliable endogenous reference gene for human umbilical vein endothelial cells treated for up to 18 h with TNFalpha, IL-4, or IFNgamma and for B cells isolated from healthy controls and patients suffering from IgA nephropathy. Other optional endogenous reference genes that can be considered are phosphomannomutase (PPMM) and actin for endothelial cells and glyceraldehyde-3-phosphate dehydrogenase and PPMM for B cells.