Pharmacogenetic aspects of thiopurine methyltransferase in Maltese individuals.

Abstract

Thiopurine methyltransferase (TPMT) is an important enzyme for the metabolism of thiopurine drugs, and pharmacogenetic variability has been associated with serious adverse effects in treated patients. There is currently no information on TMPT gene variants in the Maltese population. The aims of this project were to (i) identify the frequencies of the clinically relevant alleles *2, *3B and *3C and (ii) screen the TPMT gene promoter for novel variants. DNA was obtained from patients suffering from Crohn's disease, and from anonymous random samples maintained at the Malta Biobank. Genotyping and promoter screening were carried out using PCR-RFLP, tetraprimer ARMS-PCR and Sanger sequencing. Assays were designed and optimized accordingly. Where necessary, bioinformatic tools were used for assay design and analysis of results. We identified the following allelic frequencies: TPMT*2: 0% (n=390) including both Crohn's and Biobank cord blood samples, TPMT*3B: (n=390) of which 41190 or 2.1 % of Crohn's patients' samples and 11200 or 0.5% Biobank cord blood samples, TPMT*3C: (n=856) of which 11172 or 0.6% of Crohn's patients' samples and 3/684 or 0.4% Biobank cord blood samples. Promoter sequencing (n=126 chromosomes) revealed 3 SNPs (4567T>A, 4621T>A, 4793A>T) and 5 different homozygous or heterozygous deletions of 17 or 34bp starting at different points between positions 4989-5023 (cumulative allelic frequency 36.9%, n=138)(NCBI Accession NG_012137.2). Two of these deletions were tandem repeats (VNTRs), while another deletion was in incomplete VNTR due to two mismatches. We also identified a hypervariable region terminating approximately 40bp upstream of the transcriptional start site (TSS) having multiple heterozygous SNPs that could not be electronically deconvoluted to indel variants.

TPMT pharmacogene allelic frequencies are comparable to international reported values. The identified promoter variability could potentially confer important transcriptional regulatory influences, especially due to its TSS proximity. Further molecular and clinical studies are required to investigate this.