Acute lymphoblastic leukemia (ALL) leads to the abnormally high proliferation of immature lymphocytes (lymphoblasts). ALL treatment includes immunosuppressive and cytostatic agents called thiopurines (6-thioguanine (6-TG), 6-mercaptopurine (6-MP) and azathioprine (AZA)). Nudix hydrolase 15 (encoded by NUDT15) plays an important role in their metabolism is, thus variations in NUDT15 modulate the toxicity of thiopurines.
We wanted to determine the frequencies of previously determined polymorphisms (rs61746486, rs45465203, rs61973267, rs116855232) in Slovenian population and investigate their usefulness as pharmacogenetic diagnostic markers by calculating their MAF value. We compared their frequencies between Slovenian and other populations and calculated whether they were in Hardy – Weinberg equilibrium in the investigated Slovenian population. We also identified other polymorphisms in the coding regions of NUDT15. We checked if the bioinformatic models predicted their involvement in the response to thiopurine treatment.
We isolated DNA from the blood of healthy individuals and checked its quality. We performed a polymerase chain reaction (PCR) and Sanger sequencing of exons 1 and 3, including the surrounding regions. We checked the frequency of these genetic polymorphisms in other populations using bioinformatics tools and evaluated their effect on NUDT15 protein product.
We determined that polymorphisms rs45465203 in rs61973267 may be useful as pharmacogenomic markers, due to the appropriate MAF value. The frequencies of rs45465203 and rs61973267 in the Slovenian population are lower than in the European and higher than in the East Asian and African populations. In contrast, rs61746486 and rs116855232 polymorphisms are more widespread in the Slovenian population than in other European populations, but the frequency of the rs116855232 polymorphism is significantly higher among Asians. We determined that all of the investigated polymorphisms are in Hardy-Weinberg equilibrium. We also found two additional polymorphisms rs79687000 and rs1249937565 in NUDT15, whose frequencies cannot be compared due to the lack of data on population genetics. Using predictive models, we found that rs45465203, rs79687000, rs124937565 and rs61973267 polymorphisms could potentially affect protein function. The use of the rs116855232 polymorphism in the diagnostic panel would, despite its low MAF value in the Slovenian population, make sense due to its involvement in the CPIC recommendations.
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