Novel motif of variable number of tandem repeats in TPMT promoter region and evolutionary association of variable number of tandem repeats with TPMT*3 alleles

Abstract

Aim: SNPs in the gene for TPMT exemplify one of the most successful translations of pharmacogenomics into clinical practice. This study explains the correlation between common SNPs and variable number of tandem repeats (VNTR) in promoter of the gene. Materials & methods: We determined VNTR polymorphisms, as well as TPMT*2 and TPMT*3 SNPs and TPMT activity in Slovenian and Italian individuals and lymphoblastoid cell lines. Results: We observed a previously unreported VNTR allele, AB7C, in a TPMT*3A heterozygous individual. VNTRs with two (AB2C) and three or more (ABnC, n ≥ 3) B motifs were statistically significant in complete linkage disequilibrium (D′ = 1, r² = 1, p < 0.0001) with the TPMT*3C and TPMT*3A alleles, respectively. Conclusion: The study provides insights into the stepwise evolution of TPMT*3 alleles from *3C to *3A, with increasing number of B motifs in the VNTR region.

Graphical abstract

Keywords::

• acute lymphoblastic leukemia
• genetic polymorphisms
• inflammatory bowel disease
• linkage disequilibrium
• lymphoblastoid cell lines
• thiopurine S-methyltransferase
• TPMT activity
• TPMT
• variable number of tandem repeats
• VNTR

Author's contributions

D Urbančič, I Mlinarič-Raščan and N Karas Kuželički designed research. D Urbančič and A Šmid performed research. D Urbančič analyzed data. I Mlinarič-Raščan, G Stocco and G Decorti contributed reagents/clinical samples/analysis tools. D Urbančič, A Šmid and N Karas Kuželički wrote the paper.

Acknowledgements

The authors wish to thank all participants who entered the study cohorts and clinical coordinators, M Rabusin and M Bramuzzo from the Institute for Maternal and Child Health IRCCS and BG Trieste for overseeing the recruitment of ALL and IBD patients. We would like to thank D Gurwitz from the Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv and A Metspalu from The Estonian Genome Center, University of Tartu for providing in vitro LCL model. We thank R Franca from the Institute for Maternal and Child Health IRCCS Burlo Garofolo Trieste for technical assistance and coordinating ALL repository, and M Lucafò from the Department of Medical, Surgical and Health Sciences, University of Trieste for coordinating IBD repository. The authors thank P Ferkov from the Faculty of Pharmacy, University of Ljubljana, D Selvestrel and O Montecchini from the Developmental and Reproductive Sciences, University of Trieste for technical assistance, and M Milek for providing useful information on TPMT in Slovene population. We would like to thank TJ Bevec for the proof reading of this manuscript.

Financial & competing interests disclosure

This work was supported by the Slovenian Research Agency (J3-6792, P1-0208, MR34512). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical disclosure

The authors state that, ‘the study has been approved by Local and National Medical Ethics Committees and has followed the principles outlined in the Declaration of Helsinki for all human experimental investigations. Written informed consent has been obtained from all participating subjects. The experiments comply with the current laws of the Republic of Slovenia and the Italian Republic’.

Additional information

Funding

This work was supported by the Slovenian Research Agency (J3-6792, P1-0208, MR34512). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript