Pharmacogenomics of Ara-C in AML

描述（由申请人提供）：急性髓性白血病（AML）是第二种最常见的儿童白血病，在所有主要儿童癌症中预后最差。核苷类似物阿糖胞苷（ara-C）是用于治疗AML的最有效和最广泛使用的化疗剂。然而，其治疗反应、耐药性的发展和严重毒性的广泛患者间差异仍然是有效阿糖胞苷化疗的主要障碍。阿糖胞苷药代动力学（PK）和药效学（PD）基因表达和/或活性的患者间差异可能导致阿糖胞苷治疗结果的变异性。在本申请的最后一个资助期内，我们评估了阿糖胞苷代谢途径中的12个PK基因，并确定了可以解释阿糖胞苷临床应答变异性的很大一部分的遗传多态性，并且可能与AML患者中目前使用的风险分层因素具有相似的生物学相关性。我们发现，PK基因的遗传变异可以解释11%的预后变异（无事件生存期，EFS），在解释了6个公认的预后因素后，累积解释了18%的EFS变异。为了更全面地了解阿糖胞苷治疗结果变异性的机制，我们现在建议研究阿糖胞苷药效学反应中涉及的基因，不幸的是，迄今为止还没有得到很好的研究。我们开发了一种新的统计方法，PROMISE（PROjection Onto the Most Interesting Statistical Evidence），通过识别具有生物学意义的与多个药理学和临床终点相关的遗传特征，极大地提高了我们进行重要药物基因组学发现的能力。作为第一步，我们将使用PROMISE来鉴定与体外白血病原始细胞对阿糖胞苷敏感性以及AML患者的多种临床结局相关的诊断性白血病原始细胞基因表达特征（目的1）。在候选ara-C PD基因的功能验证之后，我们将鉴定并验证来自多个独立队列的AML患者中ara-C PD基因多态性的临床和预后意义（目的2）。由于表观遗传机制如DNA甲基化已被认为影响AML中的基因表达，我们还将评估DNA甲基化在调节ara-C PK和PD基因表达中的作用，以及在影响接受ara-C治疗的AML患者的临床结局中的作用（目的3）。最后，我们将在AML患者的独立队列中确定并验证药物遗传学和药物表观遗传学标记物，这些标记物在确定治疗强度的风险分配综合系统中补充了目前已知的预后因素。了解遗传和表观遗传因素在介导阿糖胞苷反应中的相互作用及其与当前预后特征的整合，将为提高我们预测AML治疗结果的准确性提供机会，并允许更有针对性的风险分层治疗方法-这是对当前策略的重大进步。

DESCRIPTION (provided by applicant): Acute myeloid leukemia (AML) is the second most common form of childhood leukemia and has the worst prognosis of all major childhood cancers. The nucleoside analog, Cytarabine (ara-C), is the most effective and widely used chemotherapeutic agent used to treat AML. However, wide inter-patient variation in its treatment response, development of resistance, and severe toxicity remain major hurdles to effective ara-C chemotherapy. Inter-patient variation in expression and/or activity of ara-C pharmacokinetic (PK) and pharmacodynamic (PD) genes is likely to contribute to the variability observed in ara-C treatment outcomes. During the last funding period of this application, we evaluated 12 PK genes in ara-C metabolic pathway and identified genetic polymorphisms that could explain a substantial portion of the variability in ara-C clinical response and could be of similar prognosti relevance as currently used risk stratification factors in AML patients. We found that genetic variation in PK genes may explain 11% of variation in prognosis (event-free survival, EFS) after accounting for 6 well established prognostic factors that cumulatively explain 18% of variation in EFS. To more fully understand the mechanisms contributing to variability in ara-C treatment outcomes, we now propose to study genes involved in ara-C pharmacodynamic response, which unfortunately have not been well studied so far. We have developed a novel statistical method, PROMISE (PRojection Onto the Most Interesting Statistical Evidence), which dramatically increases our power to make important pharmacogenomic discoveries by identifying genetic features with a biologically meaningful pattern of associations with multiple pharmacologic and clinical endpoints. As a first step, we will use PROMISE to identify diagnostic leukemic blast gene expression signatures associated with in vitro leukemic blast sensitivity to ara-C as well as multiple clinical outcomes in AML patients (Aim 1). Following functional validation of candidate ara-C PD genes, we will identify and validate the clinical and prognostic significance of polymorphisms in ara-C PD genes in AML patients from multiple independent cohorts (Aim 2). Since epigenetic mechanisms such as DNA methylation have been suggested to influence gene expression in AML, we shall also evaluate DNA methylation for its role in regulating expression of ara-C PK and PD genes, and in influencing clinical outcomes in AML patients treated with ara-C (Aim 3). Finally, we will identify, and validate in independent cohorts of AML patients, the pharmacogenetic and pharmacoepigenetic markers that supplement currently known prognostic factors in an integrated system of risk assignment for purposes of determining treatment intensity. Understanding the interplay of genetic and epigenetic factors in mediating ara-C response and their integration into current prognostic features would present an opportunity to increase our accuracy in forecasting therapeutic outcomes in AML and allow more tailored, risk-stratified treatment approaches - a major advancement over current strategy.