Pharmacogenomics of Ara-C in AML

描述(申请人提供)：急性髓系白血病(AML)是儿童白血病的第二种最常见的形式，是所有主要儿童癌症中预后最差的。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药物。然而，其治疗反应、耐药性的形成和严重毒性的患者间差异很大，仍然是有效进行Ara-C化疗的主要障碍。患者间Ara-C药代动力学(PK)和药效学(PD)基因表达和/或活性的差异可能是导致Ara-C治疗结果差异的原因之一。在这项应用的最后一次资助期间，我们评估了Ara-C代谢途径中的12个PK基因，并确定了可以解释Ara-C临床反应的很大一部分变异性的基因多态，并可能与目前在AML患者中使用的危险分层因素具有类似的预后相关性。我们发现，在解释了6个公认的预后因素后，PK基因的遗传变异可以解释11%的预后变异(无事件生存，EFS)，累积起来可以解释18%的EFS变异。为了更全面地了解导致Ara-C治疗结果差异的机制，我们现在建议研究涉及Ara-C药效反应的基因，遗憾的是，到目前为止还没有得到很好的研究。我们开发了一种新的统计学方法Promise(投影到最有趣的统计证据上)，通过识别与多个药理学和临床终点相关的具有生物学意义的模式的遗传特征，极大地增强了我们进行重要药物基因组发现的能力。作为第一步，我们将使用Promise来确定与体外白血病原始细胞对Ara-C的敏感性以及AML患者的多种临床结果相关的诊断白血病原始细胞基因表达特征(目标1)。在对候选的Ara-C PD基因进行功能验证后，我们将从多个独立队列中鉴定和验证Ara-C PD基因多态性在AML患者中的临床和预后意义(AIM 2)。由于表观遗传学机制，如DNA甲基化已被认为影响AML的基因表达，我们还将评估DNA甲基化在调节Ara-C PK和PD基因表达以及影响Ara-C治疗AML患者临床结果方面的作用(AIM 3)。最后，我们将在AML患者的独立队列中识别和验证药物遗传学和药物表观遗传学标记物，这些标记物在一个综合的风险分配系统中补充目前已知的预后因素，以确定治疗强度。了解遗传和表观遗传因素在调节Ara-C反应中的相互作用及其与当前预后特征的整合将为我们提供一个机会，提高我们预测急性髓细胞白血病治疗结果的准确性，并允许更多定制的、风险分层的治疗方法--这是相对于当前策略的一个重大进步。

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.