Role of gene enhancer elements in colon cancer

描述(由申请人提供)：这项提案的总体目标是确定在结肠癌中基因增强子元件发生的遗传和表观遗传变化，并深入了解这些事件如何调节疾病进展。癌症是由于DNA突变的进行性积累，以及由潜在DNA序列突变以外的机制引起的基因表达的可遗传变化，即所谓的表观遗传改变。基因增强子元件是DNA的短区域，转录因子与其结合以增加基因的表达。几乎可以肯定，在癌症中，增强剂在遗传和表观遗传水平上都会发生改变，尽管这种改变的程度尚不清楚。利用最先进的芯片序列技术，我们确定了人类结肠癌和正常结肠细胞中基因增强子元件在整个基因组中的位置。虽然许多增强子的位置保持不变，但在正常结肠癌和结肠癌细胞中，数千个增强子基因座存在差异。我们称这些区域为增强子基因座的变异，或VEL。我们假设，VEL要么含有体细胞突变，要么纯粹源于表观遗传，对结肠肿瘤的形成和发展起到了促进作用。提出了三个具体目标。在目标1中，我们将系统地评估VEL与结肠癌进展的关系，通过对一组特征良好的原代细胞株进行表征，这些细胞株全面涵盖了结肠癌的所有临床阶段。在目标2中，我们将对肿瘤中的VEL和来自10名结肠癌患者的匹配的正常DNA进行DNA测序，以确定在癌变过程中可能发生在基因增强子元件上的体细胞突变。在目标3中，我们将通过创新的实验来评估VEL的可塑性和可逆性，在这些实验中，结肠癌细胞被恢复到胚胎状态，然后重新分化为结肠上皮。这些目标的成功完成将加速我们对表观遗传学和一类非编码功能元件在结肠癌中的作用的理解，这最终可能对旨在修复结肠癌异常表达基因的治疗研究具有重要意义。

DESCRIPTION (provided by applicant): The overall goal of this proposal is to identify genetic and epigenetic alterations occurring at gene enhancer elements in colon cancer, and to gain insights into how these events mediate disease progression. Cancer is due to the progressive accumulation of mutations in DNA, as well as heritable changes in gene expression caused by mechanisms other than mutations in the underlying DNA sequence, so called epigenetic alterations. Gene enhancer elements are short regions of DNA to which transcription factors bind in order to increase the expression of a gene. Enhancers are almost certainly altered at both the genetic and epigenetic level in cancer, although the extent by which this occurs is unknown. Using state of the art ChIP-seq technology, we identified the locations of gene enhancer elements across the entire genome in cells derived from human colon cancer and normal colon. While the locations of many enhancers remain unchanged, thousands of enhancer loci differ between normal colon and colon cancer cells. We call these regions variations at enhancer loci, or VELs. We hypothesize that VELs, which either contain somatic mutations or are purely epigenetically derived, contribute to the formation and progression of colon tumors. Three specific aims are proposed. In Aim 1 we will systematically assess the relationship between VELs and colon cancer progression through characterization of VELs in a cohort of well-characterized primary cell lines that comprehensively capture all of the clinical stages of colon cancer. In Aim 2, we will conduct DNA sequencing of VELs in tumor and matched normal DNA from ten colon cancer patients to identify somatic mutations that may have accrued at gene enhancer elements during carcinogenesis. In Aim 3, we will assess the plasticity and reversibility of the VELs through innovative experiments in which colon cancer cells are reverted to the embryonic state and then re- differentiated into colon epithelium. The successful completion of these Aims will accelerate our understanding of epigenetics and the role of a class of non-coding functional elements in colon cancer, which could ultimately have important implications for therapeutic studies aimed at targeting restoration of aberrantly expressed genes in colon cancer.