朝着基于药物基因组学的结核病（TB）治疗迈进：肯尼亚混合族群中感染结核分枝杆菌的乙酰转移酶-2 基因型。
Towards pharmacogenomics-guided tuberculosis (TB) therapy: N-acetyltransferase-2 genotypes among TB-infected Kenyans of mixed ethnicity.
机构信息
Centre for Respiratory Disease Research, Kenya Medical Research Institute, Nairobi, Kenya.
Department of Medical Microbiology & Immunology, Faculty of Health Sciences, University of Nairobi, Nairobi, Kenya.
出版信息
BMC Med Genomics. 2024 Jan 6;17(1):14. doi: 10.1186/s12920-023-01788-1.
BACKGROUND
Though persons of African descent have one of the widest genetic variability, genetic polymorphisms of drug-metabolising enzymes such as N-Acetyltransferase-2 (NAT2) are understudied. This study aimed to identify prevalent NAT2 single nucleotide polymorphisms (SNPs) and infer their potential effects on enzyme function among Kenyan volunteers with tuberculosis (TB) infection. Genotypic distribution at each SNP and non-random association of alleles were evaluated by testing for Hardy-Weinberg Equilibrium (HWE) and Linkage Disequilibrium (LD).
METHODS
We isolated genomic DNA from cryopreserved Peripheral Blood Mononuclear Cells of 79 volunteers. We amplified the protein-coding region of the NAT2 gene by polymerase chain reaction (PCR) and sequenced PCR products using the Sanger sequencing method. Sequencing reads were mapped and aligned to the NAT2 reference using the Geneious software (Auckland, New Zealand). Statistical analyses were performed using RStudio version 4.3.2 (2023.09.1 + 494).
RESULTS
The most frequent haplotype was the wild type NAT24 (37%). Five genetic variants: 282C > T (NAT213), 341 T > C (NAT25), 803A > G (NAT212), 590G > A (NAT26) and 481C > T (NAT211) were observed with allele frequencies of 29%, 18%, 6%, 6%, and 4% respectively. According to the bimodal distribution of acetylation activity, the predicted phenotype was 76% rapid (mainly consisting of the wildtype NAT24 and the NAT213A variant). A higher proportion of rapid acetylators were female, 72% vs 28% male (p = 0.022, odds ratio [OR] 3.48, 95% confidence interval [CI] 1.21 to 10.48). All variants were in HWE. NAT2 341 T > C was in strong complete LD with the 590G > A variant (D' = 1.0, r = - 0.39) but not complete LD with the 282C > T variant (D' = 0.94, r = - 0.54).
CONCLUSION
The rapid acetylation haplotypes predominated. Despite the LD observed, none of the SNPs could be termed tag SNP. This study adds to the genetic characterisation data of African populations at NAT2, which may be useful for developing relevant pharmacogenomic tools for TB therapy. To support optimised, pharmacogenomics-guided TB therapy, we recommend genotype-phenotype studies, including studies designed to explore gender-associated differences.
背景
尽管非裔人群具有最广泛的遗传变异性之一，但药物代谢酶如 N-乙酰基转移酶-2（NAT2）的遗传多态性研究较少。本研究旨在确定肯尼亚结核病（TB）感染者中常见的 NAT2 单核苷酸多态性（SNP），并推断其对酶功能的潜在影响。通过检测 Hardy-Weinberg 平衡（HWE）和连锁不平衡（LD），评估每个 SNP 的基因型分布和等位基因的非随机关联。
方法
我们从 79 名志愿者的冷冻外周血单核细胞中分离基因组 DNA。我们通过聚合酶链反应（PCR）扩增 NAT2 基因的蛋白编码区，并使用 Sanger 测序方法对 PCR 产物进行测序。使用 Geneious 软件（新西兰奥克兰）将测序读数映射并与 NAT2 参考序列进行比对。使用 RStudio 版本 4.3.2（2023.09.1+494）进行统计分析。
结果
最常见的单倍型是野生型 NAT24（37%）。观察到 5 种遗传变异：282C>T（NAT213）、341T>C（NAT25）、803A>G（NAT212）、590G>A（NAT26）和 481C>T（NAT211），等位基因频率分别为 29%、18%、6%、6%和 4%。根据乙酰化活性的双峰分布，预测表型为 76%快速（主要由野生型 NAT24 和 NAT213A 变异组成）。快速乙酰化者中女性比例较高，为 72%，男性为 28%（p=0.022，优势比[OR]3.48，95%置信区间[CI]1.21 至 10.48）。所有变体均符合 HWE。NAT2 341T>C 与 590G>A 变体完全连锁不平衡（D'=1.0，r=-0.39），但与 282C>T 变体不完全连锁不平衡（D'=0.94，r=-0.54）。
结论
快速乙酰化单倍型占主导地位。尽管观察到了 LD，但没有一个 SNP 可以被称为标记 SNP。本研究增加了非洲人群 NAT2 的遗传特征数据，这可能有助于为结核病治疗开发相关的药物基因组学工具。为支持优化的、基于药物基因组学的结核病治疗，我们建议进行基因-表型研究，包括旨在探索性别相关差异的研究。
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