The genetic and epigenetic cartography of multiple myeloma

项目摘要 遗传学和基因表达的研究已经彻底改变了我们对浆细胞恶性肿瘤的认识 多发性骨髓瘤因此，骨髓瘤分子亚型已被确定，高- 风险疾病现在优先考虑患者进行风险适应疗法。然而，目前的分子标记无法识别超过 40%的高危患者在诊断后两年内复发或死亡。高风险骨髓瘤的例子是 一种增殖基因表达亚型，含有通常在标准风险中发现的遗传改变， 亚型因此，这种高危骨髓瘤不能用潜在的遗传事件来解释， 表观遗传成分表观遗传修饰如DNA甲基化（DNAm）调节基因表达 并提供了对肿瘤抑制基因和癌基因活性的机制性认识。重要的是，DNA m被维持 通过细胞分裂，并且可以传播癌性表型。我们在老鼠身上的研究显示， 浆细胞分化过程中DNAm的重塑，以及DNA甲基转移酶活性的破坏 促进浆细胞增殖。然而，关于DNAm在高危骨髓瘤中的作用的数据有限， 增殖亚型我们推测，DNAm的失调导致了细胞不受控制的增殖， 高危骨髓瘤。这将通过计算分析的体细胞遗传变异， 全基因组测序、来自RNA-seq的基因表达和来自全基因组的DNAm数据 对CoMMpass试验（NCT 01454297）的392份标本进行亚硫酸氢盐测序。在目标1中，我们将确定 骨髓瘤亚型的DNAm程序由体细胞改变和基因表达定义。在此为 重点将是阐明高风险增殖性疾病的表观遗传程序。在目标2中，我们将确定 DNAm程序预后不良的结果，并与复发标本中观察到的变化进行对比。 与增殖亚型、预后结局和复发重编程相关的DNA m基因座 骨髓瘤将被优先用于使用基于CRISPR的位点特异性表观遗传编辑的询问。结果 这些目标将有助于解决侵袭性骨髓瘤中DNA m失调的功能后果， 提供多发性骨髓瘤患者预后的分子图谱。从这项工作的见解将 优先考虑针对高危多发性骨髓瘤的后续转化和机制研究。

Project Summary Genetic and gene expression studies have revolutionized our understanding of the plasma cell malignancy multiple myeloma. As a result, myeloma molecular subtypes have been defined, and genetic markers of high- risk disease now prioritize patients for risk-adapted therapies. Yet current molecular markers fail to identify over 40% of high-risk patients who relapse or die within two years of diagnosis. High-risk myeloma is exemplified by a proliferation gene expression subtype that contains genetic alterations normally found in standard-risk subtypes. Therefore, this high-risk myeloma is not explained by underlying genetic events suggesting an epigenetic component. Epigenetic modifications such as DNA methylation (DNAm) regulate gene expression and provide mechanistic insight into tumor suppressor and oncogene activity. Importantly, DNAm is maintained through cell division and can propagate cancerous phenotypes. Our studies in mice have shown a dramatic remodeling of DNAm during plasma cell differentiation, and that disruption of DNA methyltransferase activity promotes plasma cell proliferation. Yet there is limited data on the role of DNAm in high-risk myeloma and the proliferation subtype. We hypothesize that dysregulation of DNAm contributes to uncontrolled proliferation in high-risk myeloma. This will be investigated through computational analyses of somatic genetic alterations from whole genome sequencing, gene expression from RNA-seq, and DNAm data derived from whole genome bisulfite sequencing on 392 specimens from the CoMMpass trial (NCT01454297). In aim 1, we will determine the DNAm program of myeloma subtypes defined by both somatic alterations and gene expression. Here, a focus will be to elucidate the epigenetic program of high-risk proliferative disease. In aim 2, we will identify the DNAm program prognostic of poor outcome and contrast that with changes observed in relapsed specimens. DNAm loci associated with the proliferative subtype, prognostic of outcome, and reprogrammed in relapse myeloma will be prioritized for interrogation using CRISPR-based site-specific epigenetic editing. Results from these aims will help resolve the functional consequences of dysregulated DNAm in aggressive myeloma and provide a molecular map of multiple myeloma in the context of patient outcomes. Insights from this work will prioritize avenues for follow-up translational and mechanistic studies to target high-risk multiple myeloma.