Epigenetic biomarkers of response to Azacytidine in Myelodysplastic Syndromes

 描述（由申请人提供）：骨髓增生异常综合征（MDS）是一组异质性克隆性血液疾病，其特征为无效造血，可导致骨髓衰竭并进展为急性髓性白血病（AML）。异常的DNA超甲基化是这种疾病的特征，因此，DNA甲基转移酶抑制剂（DMTis）通常用于治疗MDS，代替已被证明对这种疾病无效的常规化疗。然而，即使使用DMTi疗法，也只有约三分之一的MDS患者实现导致生存益处的临床应答。此外，目前用于MDS的基于DMTi的方案需要至少6个月的治疗，然后才能认为患者对该疗法具有抗性。鉴于只有约30-40%的患者对这种治疗有反应，大多数患者将花费6个月接受他们不太可能有反应的治疗。因此，在诊断时识别区分敏感和耐药患者的分子差异至关重要，以便利用这些差异开发预测DMTi反应的分子生物标志物。这些生物标志物将使我们能够更准确地对这些患者进行风险分层，并防止对耐药患者进行不必要和无效的治疗。使用下一代测序技术，我们对一组患有慢性粒单核细胞白血病（CMML）（MDS/MPN重叠综合征）的患者进行了全基因组DNA甲基化，基因表达和突变分析，包括对DMTi地西他滨（DAC）敏感和耐药的患者。我们发现DMTi应答者和非应答者之间存在强大的表观遗传和基因表达差异。从这些差异中，我们能够开发一种表观遗传分类器，预测这些患者对地西他滨治疗的反应，准确率为87%。此外，使用RNA-seq，我们鉴定了与CMML中对DAC的原发性抗性相关的基因表达特征。基于这些数据，我们假设在对DMTi氮杂胞苷（AZA）敏感或耐药的MDS患者中可能发现相当的差异，并且这些差异也有可能用作反应的分子分类器的基础以及识别对药物的原发性耐药机制。我们建议在250例接受AZA治疗的MDS患者队列中进行全基因组研究DNA甲基化和表达研究，以确定预测MDS对该药物反应的DNA甲基化和表达生物标志物。从这些研究中，我们希望能够开发出临床上有用的生物标志物，这些生物标志物可以转化为可应用于分子诊断实验室的CLIA兼容技术。

 DESCRIPTION (provided by applicant): Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal blood disorders characterized by ineffective hematopoiesis that can lead to bone marrow failure and progression to acute myeloid leukemia (AML). Aberrant DNA hypermethylation is characteristic of this disorder and, as such, DNA methyltransferase inhibitors (DMTis) are often used to treat MDS in lieu of conventional chemotherapies that have proven to be ineffective for this disease. However, even with DMTi therapy, only about one third of MDS patients achieve a clinical response leading to a survival benefit. Moreover, current DMTi-based regimens for MDS require a minimum of 6 months of treatment before a patient can be deemed resistant to this therapy. Given that only ~30-40% of patients respond to this treatment, the majority of patients will spend 6 months receiving a therapy to which they are unlikely to respond. Therefore, the identification of molecular differences that distinguish between sensitive and resistant patients at the time of diagnosis is critical in order to harness these differences for the development of molecular biomarkers predictive of DMTi response. These biomarkers would allow us to more accurately risk-stratify these patients and prevent unwarranted and ineffective therapy for resistant patients. Using next-generation sequencing technology we performed genome-wide DNA methylation, gene expression and mutational analysis on a cohort of patients with chronic myelomonocytic leukemia (CMML), an MDS/MPN overlap syndrome, including both sensitive and resistant patients to the DMTi Decitabine (DAC). We found that robust epigenetic and gene expression differences exist between DMTi responders and non-responders. From these differences, we were able to develop an epigenetic classifier that predicts response to decitabine therapy in these patients with 87% accuracy. Moreover, using RNA-seq we identified a gene expression signature associated with primary resistance to DAC in CMML. Based on these data, we hypothesize that comparable differences are likely to be found in MDS patients who are either sensitive or resistant to the DMTi Azacytidine (AZA), and that these too have the potential to be used as the basis of a molecular classifier of response as well as to identify mechanisms of primary resistance to the drug. We propose to perform genome-wide studies DNA methylation and expression studies in a cohort of 250 MDS patients treated with AZA in order to identify DNA methylation and expression biomarkers predictive of response to this agent in MDS. From these studies, we expect to be able to develop clinically useful biomarkers that can be translated to CLIA-compatible technologies that can be applied in molecular diagnostics labs.