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

项目总结 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，临床上 特征、预后和对治疗的反应。尽管有最好的治疗方法，多发性骨髓瘤通常是不治之症 而患者最终会患上复发/难治性疾病。早期复发与临床表现差有关 结果和总体存活率。目前还没有有效的标记物可以预测哪些患者 有早期复发。长期目标是更好地理解表观遗传学在治疗结果中的作用。 MM，并开发一种非侵入性的、临床上方便的方法来预测复发。总的目标是 这项应用是为了评价循环中的5-羟甲基胞嘧啶(5HmC)和5-甲基胞嘧啶(5mC MM患者外周血中游离DNA(CfDNA)作为预测早期复发高危人群的指标 诊断时间。众所周知，表观遗传的异质性越大，存活率和复发率越低。 我们认为，敏感和强大的基于cfDNA的表观遗传标记可能会提供更大的便利和 预测MM早期复发的最小侵袭性除了5mC，5hmC的变化，一个丰富的 和稳定的修饰胞嘧啶，具有与5mC截然不同的基因调控功能，已被认为与癌症有关 发育和病理生物学。然而，由于技术限制，以前对癌症的研究 表观遗传学在很大程度上将修饰的胞嘧啶解释为5mC，还没有研究评估不同的 5HmC和5mC在MM治疗意义中的作用填补当前研究和技术空白 考虑到开发一种针对多发性骨髓瘤的微创血液检测的高影响，我们将利用一种高度 由我们的团队开发的敏感和强大的技术，Nano-Seal-Seq(一种化学标记技术 与下一代测序集成)，以准确确定cfDNA和 CD138+骨髓瘤“癌”细胞来源于骨髓。中心假设是5hmC/5mC签名 在诊断时，cfDNA可根据MM患者的早期复发情况区分MM患者。在目标1中，我们将分析5hmC和 约240名MM患者(12个月内复发[早期复发，n=120]与12个月[晚期复发]的cfDNA中的5mC 复发)，以开发早期复发的综合预测指数。我们会 在约750名MM患者的两个独立复制人群中验证5hmC/5mC标志物。在目标2中，我们 将对来自配对血浆患者的CD138+骨髓瘤细胞的300基因组DNA中的5hmC/5mC进行分析 CfDNA来确定一个基于骨髓的预测指数，其中的性能将与 CfDNA标记的同源性。在目标3中，我们将研究130中序列cfDNA中5hmC/5mC随时间的变化 来描述它的治疗意义。这项拟议的研究意义重大，因为它 有望纵向推进对早期复发多发性骨髓瘤生物学基础的了解，并促进 开发一种新的表观遗传学监测(并最终进行治疗)范例，具有广泛的 翻译在高危患者个性化管理中的重要性。

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.