Epigenomic influences of diet on intestinal neoplasia

描述（由申请人提供）：在这个项目中，我们提出通过小鼠模型系统来探索饮食是否影响癌症的发展。我们的假设是，饮食对基因调控产生慢性和累积效应，即所谓的表观遗传效应，导致从正常的调控模式向早期癌症形成模式转变。一个关键的基因调控机制是基因组中胞嘧啶的甲基化，通常与基因沉默有关。胞嘧啶甲基化已被观察到在许多癌症中发生了深刻的改变，这与导致细胞不受调节生长的基因表达变化有关。添加到胞嘧啶上的甲基的底物是单碳供体分子，如叶酸。研究表明，饮食中叶酸水平的改变对基因组中胞嘧啶甲基化的总体水平有实质性影响，但受影响的确切位点尚未确定。我们开发了一种全基因组分析方法来检测小鼠基因组中约60万个胞嘧啶甲基化位点，使我们能够确定在这种情况下受影响的位点。我们提出了一项研究，我们测试来自小肠空肠区域的正常细胞和来自同一区域的腺瘤，使用喂食正常或单一碳供体缺乏饮食的小鼠。我们将确定发生的表观遗传变化：(a)作为对叶酸、胆碱和蛋氨酸缺乏的饮食的反应，以及(b)来自同一小鼠的良性肿瘤（使用Apc1638模型）。我们将定义每种情况下的变化程度，一种我们称之为表观基因组距离的测量方法，并通过寻找每种情况下涉及的基因座的一致性，确定正常细胞中饮食诱导的变化是否代表了肿瘤转化过程中的中间状态。该项目的成功结果将揭示癌症形成的早期阶段的见解，将特定类型的饮食缺乏与异常甲基化和癌症易感性联系起来，并为诊断和预防试验的人类研究奠定基础——可以想象，由于长期饮食影响而获得的表观遗传变化可以通过药理学或仅通过改变饮食来逆转。这个试点项目将作为处理这些可能性的扩大项目的基础。虽然饮食在引起胃肠道癌症方面明显有影响，但饮食与导致正常细胞变成癌细胞所需的基因变化之间的联系仍然难以捉摸。在这项研究中，我们建议使用小鼠模型系统来测试当暴露于影响基因表达调节剂之一胞嘧啶甲基化的饮食中时，肠道肿瘤中的基因调控是否受到干扰。这项研究将是第一次对胞嘧啶甲基化进行全基因组研究，以确定饮食引起的变化是否代表癌症发展的中间阶段。

DESCRIPTION (provided by applicant): In this project, we propose to explore whether diet influences the development of cancer using a mouse model system. Our hypothesis is that diet exerts chronic and cumulative effects on gene regulation, so-called epigenetic effects, to cause a change from a normal pattern of regulation towards the pattern in early cancer formation. One key gene regulatory mechanism is the methylation of cytosines in the genome, usually associated with gene silencing. Cytosine methylation has been observed to be profoundly altered in a number of cancers, associated with gene expression changes that contribute to the cell's unregulated growth. The substrate for the methyl group added to cytosine are single carbon donor molecules like folic acid. It has been shown that altered folate levels in diet have substantial effects on overall levels of cytosine methylation in the genome, but the precise loci affected have not been identified. We developed a genome-wide assay to test ~600,000 sites in the mouse genome for cytosine methylation, allowing us to identify the loci affected in such situations. We propose a study in which we test normal cells from the jejunal area of the small intestine and adenomas from the same area, using mice that have been fed normal or single carbon donor-deficient diets. We will identify the epigenetic changes that occur (a) as a response to the diet deficient in folate, choline and methionine, and (b) in benign tumors from the same mice (using the Apc1638 model). We will define the degree of change in each case, a measure we call epigenomic distance, and determine whether diet-induced changes in normal cells represent an intermediate state on the way to neoplastic transformation by looking for consistency of the loci involved in each case. The successful outcome of this project will reveal insights into the early stages of cancer formation, link a specific type of dietary deficiency with aberrant methylation and cancer susceptibility, and create the basis for human studies for diagnostic and for prophylactic trials - it is conceivable that acquired epigenetic changes due to prolonged dietary influences could be reversed pharmacologically or through changed diet alone. This pilot project will serve as the foundation for an expanded project to address these possibilities. While diet is clearly influential in causing cancer of the gastrointestinal tract, the link between diet and the genetic changes required to cause a normal cell to become a cancer cell have remained elusive. In this study, we propose to use a mouse model system to test whether gene regulation is disturbed in intestinal tumours when exposed to a diet that influences one of the regulators of gene expression, cytosine methylation. The study will be the first genome-wide study of cytosine methylation to see whether diet-induced changes represent an intermediate stage in the development of cancer.