Pharmacogenomics of thiopurines: distribution of TPMT and NUDT15 polymorphisms in the Brazilian Amazon

NUDT15 and TPMT polymorphisms in three distinct native populations of the Brazilian Amazon

This is the first report of the distribution of TPMT and NUDT15 single nucleotide polymorphisms and metabolic phenotypes associated with cytotoxicity of thiopurine drugs, in indigenous groups of Brazilian Amazon: Munduruku, Paiter-Suruí and Yanomami. The minor allele frequency (MAF) of NUDT15 rs116855232 did not differ significantly across the groups; TPMT rs1800462 was absent, while rs1800460 and rs1142345 were in strong linkage disequilibrium, and 10- and 30-fold more common in Paiter-Suruí. Indeed, the MAFs in Paiter-Surui (0.193 and 0.188) are the largest report globally. The distribution of combined NUDT15/TPMT metabolic phenotypes differed significantly (p < 0.0001) and largely (Cramér´s V = 0.37) across cohorts. This has important pharmacogenetic implications: the Clinical Pharmacogenetics Implementation Consortium recommendations to reduce or consider reduction of thiopurine dose applies to 4.4% Yanomami, 5.6% Munduruku, versus 41% Paiter-Suruí. The proportion of Paiter-Suruí at risk of thiopurine intolerance is 3- to 4-fold higher than any other population worldwide.

The c.415C>T polymorphism in NUDT15 is more frequent than the polymorphisms in TPMT in Chilean patients who use thiopurine drugs

Azathioprine (AZA) and 6-mercaptopurine (6-MP) are drugs widely used in the treatment of autoimmune diseases. Among the enzymes involved in the metabolism of AZA and 6-MP are thiopurine methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15). The existence of single nucleotide polymorphisms in the genes that code for these enzymes could decreased enzymatic activity AND lead to severe myelosuppression. The most relevant polymorphism is NUDT15*3 (rs116855232), where the replacement of cytosine for thymine at position 415, which in turn leads to a loss of enzymatic activity. In a previous study, it was identified that together the polymorphisms in the TPMT gene reach an allelic frequency of 3.81%. There is no information regarding the rs116855232 polymorphism in the NUDT15 gene, so this corresponds to the objective of this report. Blood samples from Chilean adult patients with indications for the use of AZA or 6-MP for different pathologies and who had undergone a TPMT gene polymorphism study were retrospectively analyzed. A total of 253 blood samples were analyzed. Of the 253 patients, 47 presented the c.415C>T polymorphism in the NUDT15 gene, 3 being homozygous and 44 heterozygous. Four of the heterozygous patients for NUDT15 also had the *3A variant in the TPMT gene, also heterozygous. The allelic frequency of the minor T allele found (9.88%) was very similar to that found in patients of Asian origin, and much higher than that reported for the European Caucasian or Latin American population.

Population pharmacogenomics: an update on ethnogeographic differences and opportunities for precision public health

Both safety and efficacy of medical treatment can vary depending on the ethnogeographic background of the patient. One of the reasons underlying this variability is differences in pharmacogenetic polymorphisms in genes involved in drug disposition, as well as in drug targets. Knowledge and appreciation of these differences is thus essential to optimize population-stratified care. Here, we provide an extensive updated analysis of population pharmacogenomics in ten pharmacokinetic genes (CYP2D6, CYP2C19, DPYD, TPMT, NUDT15 and SLC22A1), drug targets (CFTR) and genes involved in drug hypersensitivity (HLA-A, HLA-B) or drug-induced acute hemolytic anemia (G6PD). Combined, polymorphisms in the analyzed genes affect the pharmacology, efficacy or safety of 141 different drugs and therapeutic regimens. The data reveal pronounced differences in the genetic landscape, complexity and variant frequencies between ethnogeographic groups. Reduced function alleles of CYP2D6, SLC22A1 and CFTR were most prevalent in individuals of European descent, whereas DPYD and TPMT deficiencies were most common in Sub-Saharan Africa. Oceanian populations showed the highest frequencies of CYP2C19 loss-of-function alleles while their inferred CYP2D6 activity was among the highest worldwide. Frequencies of HLA-B*15:02 and HLA-B*58:01 were highest across Asia, which has important implications for the risk of severe cutaneous adverse reactions upon treatment with carbamazepine and allopurinol. G6PD deficiencies were most frequent in Africa, the Middle East and Southeast Asia with pronounced differences in variant composition. These variability data provide an important resource to inform cost-effectiveness modeling and guide population-specific genotyping strategies with the goal of optimizing the implementation of precision public health.

Population impact of pharmacogenetic tests in admixed populations across the Americas

The current population of the Americas (~1 billion people) is highly heterogeneous as a result of five centuries of admixture between three major parental populations, namely Native Amerindians, Europeans, and subSaharan Africans. This heterogeneity has important pharmacogenetic (PGx) implications. The present study explores this issue with respect to the population impact of PGx tests listed in the CPIC and DWPG guidelines for the cancer chemotherapeutic agents fluoropyrimidines, irinotecan, and thiopurines. Population impact was assessed by the number of individuals needed to genotype (NNG) and to treat [NNT] in order to prevent one additional adverse effect. The 1000 Genomes Project database was accessed to obtain genotypes for the relevant PGx markers and to estimate individual proportions of Native, European, and African ancestry for six recently admixed populations across the Americas. The ancestry proportions were then employed to devise three sub-cohorts, denoted NAT, EUR, and AFR, in which one of the three major ancestral roots predominates largely (8 to 30-fold) over the other two. Minor allele frequency (MAF) of NUDT15 rs116855232, TPMT rs1800460, and UGT1A1 rs887829 differed significantly across the three sub-cohorts, whereas no difference was observed for TPMT rs1142345 and 1800462, and the four DPYD variants interrogated. The frequency of combined TPMT/NUDT and UGT1A1, but not DPD, metabolic phenotypes differed significantly among the sub-cohorts. The NNGs for the drug/sub-cohorts pairs, ranged from 12 (irinotecan/UGT1A1 in EUR) to 360 (fluoropyrimidines/DPYD in NAT). Differences in MAF of the interrogated variants and consequently in the distribution of metabolic phenotypes, plus the variable individual proportions of biogeographical ancestry concur to the 30-fold range of NNGs for the PGx tests, across the sub-cohorts. This large variation is likely to influence the perceived benefits and the clinical adoption of PGx screening for the chemotherapeutic agents investigated. This is of especial concern for fluoropyrimidines, in view of the large NNGs observed in the study sub-cohorts (NNG = 176-360) and confirmed in cancer patients from Brazil (NNG = 312).