Longitudinal tracking of myelodysplatic syndrome patients using next generation sequencing provides a predictive measure for azacitidine response and acute myeloid leukemia progression

Hypomethylating agents such as azacitidine (AZA) are commonly used to treat myelodysplastic syndrome as a frontline therapy. Although its survival benefits are well documented, the underlying genetics and clonal dynamics upon AZA treatment have not been systematically examined using serial samples. In this study, we performed targeted serial sequencing on 285 bone marrow samples from 95 MDS patients treated with AZA. Genes involved in DNA methylation, spliceosome, and chromatin modification were the most frequently mutated. When assessing the mutation dynamics with clinical measures, we found significant VAF reduction in responders compared to non-responders. Multivariate analyses revealed that mutation burden in different genes and biological pathways have distinct impact on AZA response, leukemia progression, and overall survival. Most notably, mutations in activated signaling pathway genes are associated with AML progression. In addition, we could not detect decreased allelic burden in activated signaling pathway genes even in responders. Patients with SRSF2 mutations tended to respond to AZA. Mutations in tumor suppressors and myeloid transcription factors were adverse prognostic factors in overall survival. Interestingly, mutations in DNA methylation pathway genes were not an independent prognostic factor for any of the three measures. Our study shows that longitudinal tracking of MDS patients using next generation sequencing can be used to improve criteria for AZA response and for early detection of AML progression.

以阿扎胞苷（azacitidine, AZA）为代表的低甲基化剂（hypomethylating agents）常作为一线疗法用于治疗骨髓增生异常综合征（myelodysplastic syndrome, MDS）。尽管其生存获益已有充分文献记载，但阿扎胞苷治疗后的潜在遗传学特征与克隆动态尚未通过系列样本得到系统性研究。本研究对95名接受阿扎胞苷治疗的骨髓增生异常综合征患者的285份骨髓样本开展了靶向系列测序。涉及DNA甲基化、剪接体（spliceosome）与染色质修饰的基因是最常见的突变基因。在结合临床指标评估突变动态时，我们发现应答者的变异等位基因频率（variant allele frequency, VAF）较无应答者出现显著降低。多变量分析显示，不同基因与生物学通路的突变负荷对阿扎胞苷应答、白血病进展与总生存期具有截然不同的影响。最值得注意的是，激活信号通路基因的突变与急性髓系白血病（acute myeloid leukemia, AML）进展相关。此外，即便在应答者中，我们也未检测到激活信号通路基因的等位基因负荷出现下降。携带SRSF2突变的患者往往对阿扎胞苷产生应答。肿瘤抑制基因与髓系转录因子的突变为总生存期的不良预后因素。有趣的是，DNA甲基化通路基因的突变并非上述三项临床结局的独立预后因素。本研究表明，通过下一代测序（next-generation sequencing, NGS）对骨髓增生异常综合征患者进行纵向追踪，可用于优化阿扎胞苷应答的评估标准，并实现急性髓系白血病进展的早期检测。