Epigenomic markers of circulating cell-free DNA and treatment outcome in multiple myeloma

项目摘要 多发性骨髓瘤（MM）是一组异质性疾病，具有明显的骨髓依赖性，临床表现为： 特征、预后和对治疗的反应。尽管有最好的治疗方法，但MM通常无法治愈 并且患者最终将发展为复发性/难治性疾病。早期复发与不良的临床表现有关。 结果和总体生存率。目前还没有有效的标志物可以预测哪些患者会 早期复发。长期目标是更好地了解表观遗传学在治疗结果中的作用， MM和开发一种非侵入性的，临床上方便的方法来预测复发。的总体目标 本申请旨在评价循环中的5-羟甲基胞嘧啶（5 hmC）和5-甲基胞嘧啶（5 mC） 来自MM患者的无细胞DNA（cfDNA）作为预测处于早期复发高风险的患者的标记物， 诊断时间。已知更大的表观遗传异质性与更差的生存和复发相关。 我们提出，敏感和稳健的基于cfDNA的表观遗传标记可能提供更大的便利性， 除5 mC外，5 hmC的变化，丰富的 与5 mC相比，具有不同基因调节功能的稳定修饰胞嘧啶与癌症有关 发展和病理生物学。然而，由于技术的限制，以前的癌症研究 表观遗传学在很大程度上将修饰的胞嘧啶解释为仅为5 mC，并且没有研究评估了不同的细胞周期。 5 hmC和5 mC在MM治疗意义中的作用。为了填补目前的研究和技术空白， 考虑到开发MM微创血液检测的高影响，我们将利用高度 由我们的团队开发的灵敏和强大的技术，纳米密封序列（化学标记技术 与下一代测序集成），以准确测定cfDNA中的5 hmC和5 mC谱， 来自骨髓的CD 138+骨髓瘤“癌”细胞。中心假设是5 hmC/5 mC信号 诊断时cfDNA中的差异可以通过早期复发状态区分MM患者。在目标1中，我们将描述5 hmC， 来自约240名MM患者的cfDNA中的5 mC（12个月内复发[早期复发，n=120]对比>12个月[晚期复发，n=120]） 复发，n=120]开始初始治疗），以开发早期复发的综合预测指数。我们将 在约750例MM患者的两个独立复制群体中验证5 hmC/5 mC标志物。在目标2中， 将在来自具有配对血浆的患者的CD 138+骨髓瘤细胞的300个基因组DNA中分析5 hmC/5 mC cfDNA来确定基于骨髓的预测指数，其性能将与 cfDNA标记的数量。在目标3中，我们将研究在130个细胞中连续cfDNA中5 hmC/5 mC随时间的变化。 患者，以确定其治疗意义。这项研究非常重要，因为它是 预计将垂直推进对早期复发MM生物学基础的理解，并促进 发展一种新的模式，表观遗传监测（并最终，治疗），具有广泛的 在高风险患者的个性化管理中具有重要意义。

PROJECT SUMMARY Multiple myeloma (MM) is a heterogeneous group of disorders with distinct bone marrow dependence, clinical features, prognosis, and response to therapy. Despite the best available treatments, MM is generally incurable and patients will eventually develop relapsed/refractory disease. Early relapse is associated with poor clinical outcomes and overall survival. There are currently no effective markers that can predict which patients will have early relapse. The long-term goal is to better understand the role of epigenetics in treatment outcomes of MM and develop a non-invasive, clinically convenient approach for predicting relapse. The overall objective of this application is to evaluate 5-hydroxymethylcytosines (5hmC) and 5-methylcytosines (5mC) in circulating cell-free DNA (cfDNA) from MM patients as markers for predicting patients at high risk of early relapse at the time of diagnosis. It is known that greater epigenetic heterogeneity is linked with poorer survival and relapse. We propose that sensitive and robust cfDNA-based epigenetic markers may offer greater convenience and minimal invasiveness for predicting early relapse in MM. In addition to 5mC, changes in 5hmC, an abundant and stable modified cytosine with a distinct gene regulatory function from 5mC, have been implicated in cancer development and pathobiology. However, due to technological constraints, previous studies of cancer epigenetics have largely interpreted modified cytosines as 5mC only, and no study has evaluated the distinct roles of 5hmC and 5mC in the therapeutic significance for MM. To fill the current research and technical gaps and consider the high impact of developing a minimally invasive blood test for MM, we will utilize a highly sensitive and robust technique developed by our team, the nano-Seal-Seq (a chemical labeling technique integrated with the next-generation sequencing), to accurately determine 5hmC and 5mC profiles in cfDNA and CD138+ myeloma “cancer” cells from bone marrow. The central hypothesis is that the 5hmC/5mC signatures in cfDNA at diagnosis can distinguish MM patients by early relapse status. In Aim 1, we will profile 5hmC and 5mC in cfDNA from ~240 MM patients (relapse within 12 months [early relapse, n=120] vs. >12 months [late relapse, n=120] of starting initial therapy) to develop an integrated predictive index for early relapse. We will validate the 5hmC/5mC markers in two independent replication population of ~750 MM patients. In Aim 2, we will profile 5hmC/5mC in 300 genomic DNA from CD138+ myeloma cells from patients with paired plasma cfDNA to determine a bone marrow-based predictive index, of which the performance will be compared with that of the cfDNA markers. In Aim 3, we will investigate change of 5hmC/5mC in serial cfDNA over time in 130 patients to characterize its therapeutic significance. The proposed research is highly significant, because it is expected to vertically advance understanding of the biological basis for early relapsed MM and promote the development of a new paradigm for epigenetic monitoring (and eventually, treatment) that has broad translational importance in the personalized management of high-risk patients.