Ecology and Evolution of Breast Carcinogenesis

摘要：在早期乳腺癌发生过程中，肿瘤细胞向导管内腔多层生长， 这使瘤周细胞处于低氧、低pH和营养缺乏的恶劣条件下。 适应这些恶劣的条件是初期肿瘤细胞存活的先决条件。适应最初是 急性和可逆的，但最终达尔文选择导致细胞具有硬连接的表型。一位杰出的 这方面的例子是有氧糖酵解，或沃堡效应(WE)，其中细胞与发酵紧密相连 葡萄糖，即使在氧气存在的情况下也是如此。值得注意的是，我们与癌症的转移潜能高度相关。 以及糟糕的结果。因此，致癌过程中的一个主要问题是：“一种刺激性的 微环境最终选择硬连线(可遗传)表型，如WE？“。而不是简单地 对于先前存在的表型的选择，我们认为微环境积极地诱导表型多样性 通过一套系统的表观遗传和基因改变。 为了解决这个问题，我们结合了三种不同方法的初步数据，这三种方法都是重点关注的 关于癌变过程中的生态进化动力学：首先，我们接受了良性乳腺 癌细胞和上皮细胞在严酷的条件下遇到DCIS，并观察到细胞存活 这些精选展示了一种我们。筛选出3个克隆，进行单细胞RNA测序和单细胞测序 ATAQ测序以及整个外显子组测序以绘制转录组、表观基因组和突变图 所选克隆与其亲代正常细胞的模式比较。这将形成模型系统，以 在整个当前提案中进行了分析。在第二行的调查中，我们记录了深刻的 多发性骨髓瘤(MM)从癌前病变向代谢进展过程中的表观遗传学变化 活动性疾病。我们假设MM中的这些观察结果可以提供一个框架来预测和解释 乳腺癌细胞从良性非糖酵解向侵袭性转化所经历的变化 糖酵解状态。在第三条研究线中，我们勾勒出了一个从表观遗传变化开始的连续体。 并展示了这些如何导致永久性突变或染色体变化。后一项工作提供了一个 用来预测和解释微环境引起的表观遗传变化最终如何发生的框架 导致在侵袭性糖酵解性乳腺癌中观察到的硬连接的基因变化。通过将这些组合起来 方法，我们建议破译微环境应激诱导基因组的机制 进化导致了硬连接的表型适应，以WE为代表。 在这项研究结束后，我们希望对这一问题有一个更完整和全面的了解 在致癌过程中发生的环境诱导的表观遗传和遗传变化，以及这些变化之间的关系 到硬连线的表型特征，如沃堡效应。

Abstract: In early breast carcinogenesis, neoplastic cells grow in multiple layers towards the lumens of ducts, which subjects the periluminal cells to harsh conditions of low oxygen, low pH, and nutrient deprivation. Adaptation to these harsh conditions is a pre-requisite for survival of incipient tumor cells. Adaptations are initially acute and reversible, but eventually Darwinian selection results in cells with hardwired phenotypes. A prominent example of this is aerobic glycolysis, or the Warburg Effect (WE), wherein cells are hard-wired to ferment glucose, even in the presence of oxygen. Notably, a WE is highly correlated with a cancer’s metastatic potential and poor outcome. Hence, a major question in carcinogenesis is: “What are the mechanisms by which a harsh microenvironment eventually selects for hard-wired (heritable) phenotypes, such as a WE?”. Rather than simply selection of pre-existing phenotypes, we contend that the microenvironment actively induces phenotypic diversity through a systematic set of epigenetic and genetic alterations. To address this question, we combine preliminary data from three different approaches that are all focused on the eco-evolutionary dynamics occurring during carcinogenesis: In the first, we have subjected benign breast cancer and epithelial cells to harsh conditions encountered in DCIS and have observed that the cells that survive these selections exhibit a WE. We selected three clones and applied single cell RNA sequencing and single cell ATAQ sequencing as well as whole exome sequencing to map the transcriptome, epigenome, and mutation patterns of the selected clones compared to their parental normal cells. This will form the model system to be analyzed throughout the current proposal. In the second line of investigation, we have documented the profound epigenetic changes that occur during progression of multiple myeloma (MM) from pre-malignant to metabolically active disease. We hypothesize that these observations in MM can provide a framework to predict and interpret the changes that breast cancer cells undergo as they transition from a benign non-glycolytic to an aggressive glycolytic state. In the third line of investigation, we have outlined a continuum starting with epigenetic changes and show how these result in permanent mutational or chromosomal changes. This latter work provides a framework with which to predict and interpret how microenvironment-induced epigenetic changes can eventually lead to hardwired genetic changes that are observed in aggressive glycolytic breast cancer. By combining these approaches, we propose to decipher the mechanisms whereby microenvironmental stress-induced genome evolution results in hard-wired phenotypic adaptations, represented by a WE. At the end this study, we expect to have a more complete and comprehensive understanding of the environmentally-induced epigenetic and genetic changes that occur during carcinogenesis, and how these relate to hard-wired phenotypic profiles, as exemplified by the Warburg Effect.