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鉴定结肠癌中基因增强子元件处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。基因增强子元件是转录因子结合以增加基因表达的DNA的短区域。增强子几乎可以肯定在癌症的遗传和表观遗传水平上都发生了改变，尽管这种改变的程度尚不清楚。使用最先进的ChIP-seq技术，我们确定了来自人类结肠癌和正常结肠的细胞中整个基因组中基因增强子元件的位置。虽然许多增强子的位置保持不变，但正常结肠和结肠癌细胞之间的数千个增强子位点不同。我们称这些区域为增强子位点变异，或VEL。我们推测，VEL，无论是含有体细胞突变或纯粹的表观遗传衍生，有助于结肠肿瘤的形成和发展。提出了三个具体目标。在目标1中，我们将通过在一组充分表征的原代细胞系中表征VEL来系统地评估VEL与结肠癌进展之间的关系，所述原代细胞系全面捕获结肠癌的所有临床阶段。在目标2中，我们将对来自10名结肠癌患者的肿瘤和匹配的正常DNA中的VEL进行DNA测序，以鉴定在致癌过程中可能在基因增强子元件处产生的体细胞突变。在目标3中，我们将通过创新实验评估VEL的可塑性和可逆性，其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，这最终可能对旨在靶向恢复结肠癌中异常表达基因的治疗研究产生重要影响。

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.