Gene expression data of serially sorted primary AML patient blasts prior and after treatment with the DNMT inhibitor decitabine (DAC). Gene expression data of serially sorted primary AML patient blasts prior and after treatment with the DNMT inhibitor decitabine (DAC)

DNMT inhibitors (DNMTi) are finally approved for AML/MDS, also based on their activity in patients with high-risk cytogenetics (often monosomal karyotype) such as -5/del(5q) or -7/del(7q), often - but not always - harboring TP53-mutations. Several studies provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes. We hypothesized that transcriptional repression on monosomal gene loci may be preferentially reversed by DNMTi. Using an unbiased RNA-seq approach we aimed to identify preferentially regulated genes in cells monoallelic for chromosome 7q. We validated these findings in serially sorted primary AML patient blasts at day 0 and day 8 of DNMTi treatment (within the DECIDER trial). Overall design: Affymetrix HTA 2.0 expression arrays were performed in technical triplicates (duplicates for samples 02_d8, 04_d0, 17_d0 and 17_d8), on primary AML blast of 14 patients at day 0 and day 8 of decitabine treatment

DNMT抑制剂（DNMT inhibitor, DNMTi）最终获批用于急性髓系白血病（Acute Myeloid Leukemia, AML）/骨髓增生异常综合征（Myelodysplastic Syndromes, MDS），其获批依据还包括其在携带高危细胞遗传学特征（常为单体核型（monosomal karyotype），如-5/del(5q)或-7/del(7q)）患者中的抗肿瘤活性；此类患者通常（但并非始终）携带TP53突变（TP53-mutation）。
多项研究已证实，包括抑癌基因在内的单等位基因位点存在异常高甲基化修饰与基因沉默现象。
我们提出研究假说：单等位基因位点的转录抑制可被DNMTi优先逆转。本研究采用无偏倚RNA测序（RNA-seq）策略，旨在鉴定7号染色体长臂（7q）单等位基因状态下的优先调控基因。
我们在DECIDER试验（DECIDER trial）框架内，对14例原发性AML患者的原始白血病母细胞在DNMTi治疗第0天和第8天进行连续分选，并以此验证了上述实验发现。
总体实验设计：针对14例患者在地西他滨（decitabine）治疗第0天和第8天采集的原始AML母细胞，采用Affymetrix HTA 2.0表达芯片开展检测；其中样本02_d8、04_d0、17_d0及17_d8采用双技术重复，其余样本采用三技术重复。