Role of gene enhancer elements in colon cancer

描述（由申请人提供）：本提案的总体目标是确定结肠癌中基因增强子元件发生的遗传和表观遗传改变，并深入了解这些事件如何介导疾病进展。癌症是由于DNA突变的逐渐积累，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。基因增强元件是DNA的短区域，与转录因子结合以增加基因的表达。几乎可以肯定，增强子在癌症的遗传和表观遗传水平上都发生了改变，尽管这种改变发生的程度尚不清楚。利用最先进的ChIP-seq技术，我们在人类结肠癌和正常结肠癌细胞的整个基因组中确定了基因增强子元件的位置。虽然许多增强子的位置保持不变，但数以千计的增强子位点在正常结肠癌细胞和结肠癌细胞之间存在差异。我们把这些区域称为增强子位点的变异，或vel。我们假设vel，要么包含体细胞突变，要么纯粹是表观遗传衍生的，有助于结肠肿瘤的形成和发展。提出了三个具体目标。在Aim 1中，我们将系统地评估vel与结肠癌进展之间的关系，通过在一组具有良好特征的原代细胞系中对vel进行表征，这些原代细胞系全面捕获了结肠癌的所有临床阶段。在Aim 2中，我们将对肿瘤中的vel和来自10名结肠癌患者的匹配正常DNA进行DNA测序，以确定可能在致癌过程中在基因增强子元件上积累的体细胞突变。在Aim 3中，我们将通过创新实验评估vel的可塑性和可逆性，在该实验中，结肠癌细胞恢复到胚胎状态，然后再分化为结肠上皮。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，这最终可能对针对结肠癌中异常表达基因的修复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.