High-throughput Epigenomic Mapping of Regulatory Elements in Ovarian Cancer at Basepair Resolution

卵巢癌调控元件碱基对分辨率的高通量表观基因组图谱

• 批准号: 10436903
• 负责人: Hui Shen
• 金额: $ 30.25万
• 依托单位: VAN ANDEL RESEARCH INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10436903
• 关键词: ARID1A gene; Address; Area; BRCA1 gene; Behavior; Binding Sites; Bioinformatics; Biological Assay; Categories; Clear Cell; Clinical; Clinical Management; DNA; DNA Methylation; DNA Repair Pathway; DNA Sequence Alteration; Data; Data Set; Dependence; Diagnosis; Disease; Elements; Enhancers; Enzymes; Epigenetic Process; Epithelial ovarian cancer; Freezing; Genes; Genetic Transcription; Genome; Histologic; Human; Hybrids; Knowledge; Lasers; Light; Literature; Malignant - descriptor; Malignant Female Reproductive System Neoplasm; Malignant Neoplasms; Malignant neoplasm of ovary; Maps; Methods; Methylation; Molecular; Mutation; Neoplasm Metastasis; Nucleosomes; Oncogenic; Ovarian Clear Cell Tumor; Ovarian Endometrioid Adenocarcinoma; Ovarian Serous Tumor; PIK3CA gene; Pathway interactions; Patients; Phenotype; Platinum; Process; Prognosis; Publishing; RAD51C gene; RNA; Recurrence; Regulatory Element; Research; Research Priority; Resistance development; Resolution; Role; Sampling; Serous; Signal Transduction; Specimen; Standardization; Stratification; TP53 gene; Technology; The Cancer Genome Atlas; Therapeutic; Tissues; Transcriptional Regulation; Tumor Suppressor Genes; United States; Untranslated RNA; base; bioinformatics pipeline; bioinformatics tool; bisulfite; chemotherapy; chromatin remodeling; cost effective; endometriosis; epigenetic profiling; epigenetic regulation; epigenome; epigenomics; genome-wide; innovation; interest; methylome; neoplastic cell; promoter; response; subclonal heterogeneity; therapeutically effective; tool; transcription factor; transcription regulatory network; transcriptome; transcriptome sequencing; transcriptomics; tumor

PROJECT SUMMARY / ABSTRACT Epithelial ovarian cancer (OC) is the deadliest gynecological cancer in the US. It consists of several histotypes, each biologically distinct with different clinical challenges. Clear cell OC (CCOC) represents a much understudied histotype marked by low response rates to standard chemotherapies and a lack of effective therapeutic options. Endometrioid OC (ENOC) is a closely related histotype. CCOC and ENOC share a common tissue of origin (endometriosis) and key genetic mutations but differ markedly in their clinical behavior. Our recently published study showed that most of these mutations were detectable in untransformed endometriosis, suggesting further distinct mechanisms of malignant transformation. We seek to delineate the contributions of altered epigenetics and transcriptional control in this process. The most prevalent histotype, high grade serous OC (HGSOC) harbors epigenetic inactivation of key tumor suppressor genes BRCA1 and RAD51C in the homologous DNA repair (HR) pathway, a pathway highlighted for its therapeutic relevance. These tumors often recur within five years despite initial good response to platinum therapy. Past epigenetic studies of primary OC have usually been conducted without stratification of histotypes, or heavily biased towards the most common histotype HGSOC. Even for HGSOC, epigenetic profiling has been performed with only limited genome coverage, focused primarily on gene promoters. Enhancers have incurred much interest in recent literature as the most dynamically used compartment of the genome, but enhancer studies of primary human OC samples, especially those of distinct histotypes, are generally lacking. This is attributable in part to limitations of existing technology. To address this knowledge gap, we propose to implement an innovative cost-effective tool, compatible with primary human samples, to profile enhancers and other regulatory elements using a targeted technology that jointly profiles DNA methylation and nucleosome occupancy (Target-NOMe Seq). We will also develop the associated bioinformatic pipeline needed to apply this technology (Aim 1). We will use Target-NOMe Seq and transcriptome profiling to analyze 300 bulk OC tumor samples, as well as microdissected tumor and supportive stromal compartments on a subset of samples (Aim 2). With this rich dataset we hope to address the research and clinical questions described above (Aim 3). We will use enhancer and promoter epigenetic states, and a new category of non-coding RNA - enhancer RNA (eRNA), as well as the expression levels of transcription factors and candidate target genes to define transcriptional regulatory networks. By analyzing which networks are altered in the different histotypes, we will gain a better understanding of the distinct molecular makeup of each of these histotypes. The relatively high sequencing depth of our focused Target-NOMe Seq technology will also allow us to assess intertumor and subclonal heterogeneity to shed light on potential mechanisms of tumor recurrence.

项目概要/摘要 上皮性卵巢癌（OC）是美国最致命的妇科癌症。它由几部分组成 组织型，每种组织型在生物学上都不同，具有不同的临床挑战。透明电池 OC (CCOC) 代表了很多 未充分研究的组织型，其特点是对标准化疗的反应率低且缺乏有效的治疗 治疗选择。子宫内膜样 OC (ENOC) 是一种密切相关的组织型。 CCOC和ENOC有一个共同点 起源组织（子宫内膜异位症）和关键基因突变，但其临床行为显着不同。我们的 最近发表的研究表明，大多数突变在未转化的子宫内膜异位症中是可检测到的， 进一步揭示了恶性转化的独特机制。我们力求描绘出以下贡献： 在此过程中改变了表观遗传学和转录控制。最常见的组织型，高级别浆液性 OC (HGSOC) 具有关键肿瘤抑制基因 BRCA1 和 RAD51C 的表观遗传失活 同源 DNA 修复 (HR) 途径，该途径以其治疗相关性而突出。这些肿瘤常 尽管最初对铂类治疗反应良好，但五年内复发。原发性 OC 过去的表观遗传学研究 通常是在没有组织型分层的情况下进行的，或者严重偏向于最常见的组织型 组织型 HGSOC。即使对于 HGSOC，表观遗传分析也仅在有限的基因组覆盖范围内进行， 主要关注基因启动子。增强剂引起了人们对最近文献的极大兴趣，因为它们是最 动态使用基因组区室，但主要人类 OC 样本的增强剂研究，特别是 通常缺乏那些具有不同组织型的细胞。这部分归因于现有技术的局限性。 为了解决这一知识差距，我们建议实施一种创新的具有成本效益的工具，与 主要人类样本，使用有针对性的技术来分析增强子和其他调控元件 联合分析 DNA 甲基化和核小体占据（Target-NOMe Seq）。我们还将开发 应用该技术所需的相关生物信息管道（目标 1）。我们将使用 Target-NOMe Seq 和 转录组分析可分析 300 个大量 OC 肿瘤样本以及显微解剖肿瘤和支持性样本 样本子集上的基质区室（目标 2）。借助这个丰富的数据集，我们希望能够开展研究 以及上述临床问题（目标 3）。我们将使用增强子和启动子表观遗传状态，以及 新一类非编码RNA——增强子RNA（eRNA），以及转录表达水平 因子和候选靶基因来定义转录调控网络。通过分析哪些网络 在不同的组织型中发生改变，我们将更好地了解不同的分子组成 这些组织型中的每一个。我们专注的 Target-NOMe Seq 技术相对较高的测序深度将 还允许我们评估肿瘤间和亚克隆异质性，以揭示肿瘤的潜在机制 复发。