Hum Mol Genet. 2013 Oct 1;22(19):4007-20. doi: 10.1093/hmg/ddt240. Epub 2013 May 29.
2-chloro-2-fluoro-deoxy-9-D-arabinofuranosyladenine (Clofarabine), a purine nucleoside analog, is used in the treatment of hematologic malignancies and as induction therapy for stem cell transplantation. The discovery of pharmacogenomic markers associated with chemotherapeutic efficacy and toxicity would greatly benefit the utility of this drug. Our objective was to identify genetic and epigenetic variants associated with clofarabine toxicity using an unbiased, whole genome approach. To this end, we employed International HapMap lymphoblastoid cell lines (190 LCLs) of European (CEU) or African (YRI) ancestry with known genetic information to evaluate cellular sensitivity to clofarabine. We measured modified cytosine levels to ascertain the contribution of genetic and epigenetic factors influencing clofarabine-mediated cytotoxicity. Association studies revealed 182 single nucleotide polymorphisms (SNPs) and 143 modified cytosines associated with cytotoxicity in both populations at the threshold P ≤ 0.0001. Correlation between cytotoxicity and baseline gene expression revealed 234 genes at P ≤ 3.98 × 10(-6). Six genes were implicated as: (i) their expression was directly correlated to cytotoxicity, (ii) they had a targeting SNP associated with cytotoxicity, and (iii) they had local modified cytosines associated with gene expression and cytotoxicity. We identified a set of three SNPs and three CpG sites targeting these six genes explaining 43.1% of the observed variation in phenotype. siRNA knockdown of the top three genes (SETBP1, BAG3, KLHL6) in LCLs revealed altered susceptibility to clofarabine, confirming relevance. As clofarabine's toxicity profile includes acute kidney injury, we examined the effect of siRNA knockdown in HEK293 cells. siSETBP1 led to a significant change in HEK293 cell susceptibility to clofarabine.
2-氯-2-氟-脱氧-9-D-阿拉伯呋喃基腺嘌呤（氯法拉滨），一种嘌呤核苷类似物，用于治疗血液系统恶性肿瘤和作为干细胞移植的诱导治疗。发现与化疗疗效和毒性相关的药物基因组标志物将极大地促进该药的应用。我们的目的是使用无偏倚的全基因组方法，确定与氯法拉滨毒性相关的遗传和表观遗传变异。为此，我们使用具有已知遗传信息的欧洲（CEU）或非洲（YRI）血统的国际人类基因组单体型图淋巴母细胞系（190 个 LCL）来评估细胞对氯法拉滨的敏感性。我们测量了修饰后的胞嘧啶水平，以确定影响氯法拉滨介导的细胞毒性的遗传和表观遗传因素的贡献。关联研究在两个群体中揭示了 182 个单核苷酸多态性（SNP）和 143 个修饰的胞嘧啶，与毒性相关，在阈值 P ≤ 0.0001 时达到关联。与细胞毒性相关的基因表达的相关性揭示了 234 个基因，在 P ≤ 3.98 × 10（-6）时达到关联。有 6 个基因被牵连：（i）它们的表达与细胞毒性直接相关，（ii）它们有一个与细胞毒性相关的靶向 SNP，（iii）它们有与基因表达和细胞毒性相关的局部修饰的胞嘧啶。我们确定了一组三个 SNP 和三个靶向这六个基因的 CpG 位点，解释了表型中观察到的变异的 43.1%。LCL 中六个基因的前三个基因（SETBP1、BAG3、KLHL6）的 siRNA 敲低显示出对氯法拉滨的易感性改变，证实了其相关性。由于氯法拉滨的毒性谱包括急性肾损伤，我们检查了 siRNA 敲低在 HEK293 细胞中的影响。siSETBP1 导致 HEK293 细胞对氯法拉滨的敏感性发生显著变化。
