Characterization of the inosine triphosphatase (ITPA) gene: Haplotype structure, haplotype-phenotype correlation and promoter function

Inosine triphosphatase (ITPA) cleaves phosphate residues from inosine triphosphate (ITP) and deoxy ITP (dITP), thereby recovering inosine monophosphate, which is a substrate for further purine nucleotide pathways. Deficient ITPA activity leads to intracellular accumulation of ITP/dITP and would, under thiopurine therapy, lead to accumulation of unusual thio-inosine metabolites (thio-ITP) with the potential for adverse metabolic effects. ITPA is a promising candidate for a more comprehensive understanding of thiopurine pharmacogenetics. We therefore studied the haplotype structure, haplotype-phenotype association, and promoter function of ITPA in a Western European population. ITPA haplotyping was performed based on haplotype tagging SNPs (selected from HapMap data) in healthy 130 controls. Haplotypes were reconstructed, and the haplotype-phenotype association was assessed by haplotype trend regression. A 1.5 kb upstream region and stepwise deletions thereof were tested for promoter activity in reporter gene assays in HcpG2 and CCRF-CEM cells. Transcription factor binding (Sp1, Sp3)to the proximal promoter region was studied by chromatin immunoprecipitation. Among haplotypes with a frequency greater than 0.01, we did not find any new low-activity haplotypes besides those carrying 94C>A or IVS2 + 21A>C variants. Two promoter SNPs had no influence on promoter activity. An approximately 200 bp sized GC-rich proximal promoter region was sufficient to fully drive reporter gene activity. Chromatin immunoprecipitation showed binding of Sp I and Sp3 transcription factors to this region. Only the two haplotypes carrying 94C>A or IVS2 + 21A>C were associated with reduced enzyme activity. The gene promoter is associated with a CpG island and driven by Sp-family transcription factors. There was no evidence for functional promoter SNPs, and it is suggested that only SNPs within the very proximal promoter region (approximately 200 bp) have the potential to be functionally significant.