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

项目摘要/摘要 OC是美国最致命的妇科癌症。它由几个组织类型组成，每个组织类型在生物学上都是不同的 面临着不同的临床挑战。在父母资助的头三年半里，尽管面临挑战 在COVID的推动下，我们在实现所有目标方面取得了实质性进展。我们有 发表或提交了四篇论文，还有三篇即将提交。我们能够开发出新的 技术，新的生物信息学工具，按计划产生和分析表观基因组和转录组数据。 特别是，我们发现透明细胞卵巢癌(CCOC)和子宫内膜样癌(ENOC)， 两种密切相关的OC组织类型，类似于不同月经周期阶段的正常子宫内膜细胞 (增殖期/滤泡期、分泌期/黄体期)。传统上，起源细胞和累积的基因突变是 被认为是癌症发生和发展的最重要的决定因素。然而，这一教条确实如此 不适用于CCOC和ENOC的情况，因为这两种卵巢癌亚型都来自同一细胞- 起源(异位内膜/子宫内膜样细胞)和共享共同的基因突变(ARID1A，PIK3CA， KRAS)，但在细胞表型和临床行为上表现出显著差异。通过……案例 ENOC和CCOC，我们能够展示细胞状态(相对于细胞类型)是如何被低估的概念 在讨论细胞起源以及非遗传机制(表观遗传和转录)如何调节这一点时 进程。我们还在显微解剖的肿瘤隔间中观察到了实质性的分子异质性， 尤其是高级别浆液性卵巢癌(HGSOC)，提示存在显著的肿瘤内 原发人类肿瘤的细胞异质性，这是父母拨款无法充分解决的问题。因此， 我们建议在原发人卵巢癌中检测细胞状态的非表观遗传调节因子的单细胞变异。 样品，以及在父母资助期间开发的新技术。

PROJECT SUMMARY / ABSTRACT OC is the deadliest gynecological cancer in the US. It consists of several histotypes, each biologically distinct with different clinical challenges. In the first three and half years of the parent grant, in spite of challenges imposed by COVID, we were able to make substantial progress towards completion of all Aims. We have published or submitted four papers, with three more to be submitted soon. We were able to develop novel technologies, new bioinformatics tools, generate and analyze epigenomic and transcriptomic data as planned. In particular, we discovered that clear cell ovarian cancer (CCOC) and endometrioid ovarian cancer (ENOC), two closely related OC histotypes, resemble normal endometrial cells at different menstrual cycle phases (proliferative/follicular, secretory/luteal). Traditionally, the cell-of-origin and accumulated genetic mutations are viewed as the most important determinants in initiation and development of cancer. However, this dogma does not apply to the case of CCOC and ENOC, in that both ovarian cancer subtypes arise from the same cell-of- origin (ectopic endometrium/endometrial-like cells) and share common genetic mutations (ARID1A, PIK3CA, KRAS), yet demonstrate drastic differences in cellular phenotype and clinical behavior. Through the case of ENOC and CCOC, we were able to show how cell state (as opposed to cell type) is an underappreciated notion in the discussion of cell of origin, and how non-genetic mechanisms (epigenetic and transcriptional) regulate this process. We also observed substantial molecular heterogeneity in the microdissected tumor compartment, particularly high-grade serous ovarian cancer (HGSOC), suggesting the presence of significant intratumoral cellular heterogeneity in primary human tumors, an issue the parent grant cannot sufficiently address. Therefore, we propose to examine single-cell variations of non-epigenetic regulators of cellular states in primary human OC samples, with novel technologies developed during the parent grant.