Three-dimensional characterization of epigenomic intratumoral heterogeneity in IDH-mutant glioma

项目摘要/摘要 癌症治疗未能取得持久的疗效，通常归因于肿瘤内的异质性。 (Ith)，它促进了肿瘤的进化和耐药克隆的产生。从历史上看，IT一直是 通过体细胞突变和拷贝数改变等基因组变化进行评估。最新研究 提示表观基因组ITH也可能与肿瘤的进化和治疗耐药有关。然而， 表观基因组ITH的患病率和程度尚不清楚。低级别胶质瘤(LGG)，包括 II级星形细胞瘤和II级少突胶质细胞瘤是经手术切除治疗的生长缓慢的肿瘤， 在某些情况下，使用放射治疗和替莫唑胺化疗。这些肿瘤不可避免地复发为III级。 星形细胞瘤和III级少突胶质细胞瘤，或IV级继发性胶质母细胞瘤。LGG的特征是 通过异柠檬酸脱氢酶(IDH)基因的克隆性突变，驱动肿瘤性代谢物D- 2-羟基戊二酸(2HG)并导致表观基因组改变，包括胶质瘤CpG的发展 岛甲基化表型(G-CIMP)。我们实验室公布的数据和这里提供的初步数据 提示IDH突变型胶质瘤的表观基因组在空间上不同的肿瘤区域表现为ITH，并且 展示随着时间的推移而演变。在这个提议中，我们将检验表观基因组ITH是一个特征的中心假设 具有生物学和临床意义的IDH突变型胶质瘤。对于一群IDH突变的胶质瘤患者来说， 我们将使用一种新的地形方法在三维空间中表征ITH 与神经外科医生、神经病理学家和生物医学成像专家合作。我们将对DNA进行分析 甲基化和染色质可及性，两种互补的方法来表征 细胞的表观基因组状态。在目标1中，我们将研究表观基因组ITH相对于 基因组ITH。在目标2中，我们将通过研究表观基因组ITH的生物学意义来确定其生物学意义。 与基因调控的关系。在目标3中，我们将通过以下方法确定表观基因组ITH的临床意义 探讨其与肿瘤组织学特征及免疫细胞含量的关系，并通过对ITH的检测。 基于DNA甲基化的生物标志物，包括MGMT甲基化和表观遗传年龄。总而言之，这些 研究将提供迄今为止最全面的表观基因组ITH特征。获得的知识 这些研究将加深我们对表观基因组ITH在肿瘤进化中的贡献的理解 治疗耐药性，最终指导设计新的和改进的抗击方法 治疗失败了。这项研究的结果也可能直接影响IDH的临床治疗实践。 通过支持表观基因组签名在胶质瘤分级和诊断中的使用以及通过 指导使用免疫疗法和生物标记物进行患者分层。

Project Summary/Abstract The failure of cancer therapies to achieve durable responses is often attributed to intratumoral heterogeneity (ITH), which fosters tumor evolution and the generation of therapy-resistant clones. ITH has historically been assessed by genomic alterations such as somatic mutation and copy-number alteration. Recent studies suggest that epigenomic ITH may also contribute to tumor evolution and therapy resistance. However, the prevalence and degree of epigenomic ITH are not well understood. Low-grade gliomas (LGGs), which include grade II astrocytoma and grade II oligodendroglioma, are slow-growing tumors treated with surgical resection, and in some cases, with radiation and temozolomide chemotherapy. These tumors inevitably recur as grade III astrocytoma and grade III oligodendroglioma, or as grade IV secondary glioblastoma. LGGs are characterized by clonal mutations in isocitrate dehydrogenase (IDH) genes, which drive production of the oncometabolite D- 2-hydroxyglutarate (2HG) and result in epigenomic alterations including the development of the glioma CpG island methylator phenotype (G-CIMP). Data published by our laboratory and preliminary data presented here indicate that the epigenomes of IDH-mutant gliomas display ITH across spatially distinct tumor regions and show evolution over time. In this proposal, we will test the central hypothesis that epigenomic ITH is a feature of IDH-mutant gliomas that is biologically and clinically significant. For a cohort of IDH-mutant glioma patients, we will characterize ITH in three-dimensional space using a novel topographic approach developed in collaboration with neurosurgeons, neuropathologists, and biomedical imaging experts. We will profile DNA methylation and chromatin accessibility, two complementary approaches towards characterizing the epigenomic state of the cell. In Aim 1, we will investigate the spatial patterning of epigenomic ITH relative to genomic ITH. In Aim 2, we will determine the biological significance of epigenomic ITH by investigating its relationship with gene regulation. In Aim 3, we will determine the clinical significance of epigenomic ITH by investigating its relationship with tumor histologic features and immune cell content, and by investigating ITH of DNA-methylation based biomarkers including MGMT methylation and epigenetic age. Collectively, these studies will provide the most comprehensive characterization of epigenomic ITH to date. Knowledge gained from these studies will deepen our understanding of the contribution of epigenomic ITH to tumor evolution and therapy resistance, ultimately guiding the design of novel and improved approaches towards countering therapy failure. The results of this study may also directly impact clinical practice in the treatment of IDH- mutant glioma by supporting the use of epigenomic signatures in glioma grading and diagnostics and by guiding the use of immunotherapeutics and biomarkers for patient stratification.