Peters Eric J, Kraja Aldi T, Lin Shiow J, Yen-Revollo Jane L, Marsh Sharon, Province Michael A, McLeod Howard L
Schools of Pharmacy and Medicine, University of North Carolina, Chapel Hill, North Carolina, USA.
Pharmacogenet Genomics. 2009 May;19(5):399-401. doi: 10.1097/FPC.0b013e328329fdec.
Identifying relevant cytotoxicity genes using an ex-vivo lymphoblastoid cell line (LCLs) model has distinct advantages for pharmacogenomic discovery studies of cancer chemotherapy, including standardized treatment conditions, availability of large numbers of samples, and publicly available genotypic data. However, there is little proof of principal data to confirm the promise of this approach. One of the known targets of 5-fluorouracil (5-FU) treatment is thymidylate synthase (TYMS). We hypothesized that genetic variants in TYMS would alter cytotoxicity because of 5-FU treatment using a LCL model system. LCLs from the Centre d'Etude du Polymorphisme Humain (CEPH) pedigrees (N=427) were treated with eight concentrations of 5-FU for 72 h, and cytotoxicity was determined using an Alamar Blue assay. For a subset of the 30 International Haplotype Mapping project (HapMap) trios, genotype data for 46 single-nucleotide polymorphism (SNP) variants encompassing the TYMS gene were downloaded from the HapMap website. Using a mixed models approach, each SNP was tested for association to 5-FU cytotoxicity in the subset of HapMap trios. Putatively associated SNPs (P<0.01), were then genotyped in the remaining LCLs in the CEPH pedigrees and tested for association. Two intronic SNPs in TYMS (rs2847153 and rs2853533) were significantly associated (P<0.01) with 5-FU cytotoxicity in the HapMap subset using the mixed models approach. After genotyping these SNPs in the full CEPH pedigrees, the associations with cytotoxicity showed a more reliable significance (P<0.0005), as a result of the increase in sample size. These results highlight the importance of the TYMS gene variants in response to 5-FU treatment. Furthermore, they provide additional biological validation of the relevance of LCLs as a model for pharmacogenomic gene discovery in cancer chemotherapy.
利用体外淋巴母细胞系（LCLs）模型鉴定相关细胞毒性基因，对于癌症化疗的药物基因组学发现研究具有明显优势，包括标准化的治疗条件、大量样本的可获得性以及公开可用的基因型数据。然而，几乎没有主要数据证据来证实这种方法的前景。5-氟尿嘧啶（5-FU）治疗的已知靶点之一是胸苷酸合成酶（TYMS）。我们假设，使用LCL模型系统，TYMS中的基因变异会因5-FU治疗而改变细胞毒性。来自人类多态性研究中心（CEPH）家系（N = 427）的LCLs用八种浓度的5-FU处理72小时，并使用阿拉玛蓝测定法测定细胞毒性。对于30个国际单倍型图谱计划（HapMap）三联体的一个子集，从HapMap网站下载了涵盖TYMS基因的46个单核苷酸多态性（SNP）变异的基因型数据。使用混合模型方法，在HapMap三联体子集中测试每个SNP与5-FU细胞毒性的关联。然后，在CEPH家系的其余LCLs中对推定相关的SNP（P < 0.01）进行基因分型并测试其关联性。使用混合模型方法，TYMS中的两个内含子SNP（rs2847153和rs2853533）在HapMap子集中与5-FU细胞毒性显著相关（P < 0.01）。在完整的CEPH家系中对这些SNP进行基因分型后，由于样本量增加，与细胞毒性的关联显示出更可靠的显著性（P < 0.0005）。这些结果突出了TYMS基因变异在对5-FU治疗反应中的重要性。此外，它们为LCLs作为癌症化疗药物基因组学基因发现模型的相关性提供了额外的生物学验证。
