Trophoblasts and Inflammation: An Epigenetic Approach

描述（由申请人提供）：事实证明，人类基因组是一个非常繁忙而有趣的地方。基因组不是作为基因转录的被动模板，而是细胞功能的一个组成部分，对外部环境信号高度敏感，能够通过读取和调节自身来响应这些信号。我们假设，许多以慢性、低度炎症为特征的人类疾病之所以出现，是因为基因组读取和调节自身的能力受到环境诱导的表观遗传改变的损害。虽然对表观遗传对基因转录的影响的多项研究都集中在蛋白质编码基因上，但我们现在知道表观遗传改变和RNA表达都发生在整个基因组中，而不仅仅是在良好注释的基因内或邻近。因此，当我们的研究小组在人绒毛膜癌Jeg-3细胞的体外炎症模型中发现甲基化变化与基因表达变化相关时，我们并不惊讶地发现甲基化发生在离差异表达基因相当远的基因组区域。我们很想知道这些差异甲基化区域的情况，因为它们可能会告诉我们很多关于滋养细胞如何在全基因组的基础上对炎症做出反应的信息。然而，在我们做任何其他事情之前，我们需要在病理相关细胞中重现这些数据，即来自胎膜的足月绒毛膜滋养细胞。当我们这样做的时候，我们也有机会对滋养细胞转录组有更丰富、更好的了解。我们建议使用最先进的测序技术对term绒毛膜滋养细胞进行全基因组甲基化分析和全基因组转录组分析。我们将绘制RNA转录本到基因组，并将转录本和转录本水平与炎症引起的甲基化变化联系起来。2年后，我们将有一个非常有用的数据集，从中我们可以组织以患者为导向和体外研究，重点关注妊娠期的炎症和功能基因组学。

DESCRIPTION (provided by applicant): The human genome, it turns out, is a very busy and interesting place. Rather than serving as a passive template for gene transcription, the genome is an integral part of cell function, highly sensitive to external environmental cues and capable o responding to those cues by reading and regulating itself. We have hypothesized that many human diseases characterized by chronic, low-grade inflammation, emerge because the capacity of the genome to read and regulate itself is compromised by environmentally-induced epigenetic alterations. While multiple investigations into epigenetic effects on gene transcriptio have focused on protein-coding genes, we now know that both epigenetic alterations and RNA expression occur throughout the genome, not simply within or adjacent to well-annotated genes. Thus, when our group found methylation changes associated with gene expression changes in an in vitro model of inflammation in human choriocarcinoma Jeg-3 cells, we were not surprised to find that that methylation occurred in genomic regions quite distant from the differentially-expressed genes. We are anxious to know what's in those differentially-methylated regions, as they are likely to tell us a great deal about how trophoblasts respond to inflammation on a genome-wide basis. Before we do anything else, however, we need to reproduce these data in a pathologically-relevant cell, i.e., term chorionic trophoblasts from fetal membranes. While we're doing that, we also have the opportunity to geta richer and better understanding of the trophoblast transcriptome. We propose to perform genome-wide methylation analysis and genome-wide transcriptome analysis on term chorionic trophoblasts using state-of-the art sequencing techniques. We will map RNA transcripts to the genome and correlate transcripts and transcript levels with methylation changes that occur as a result of inflammation. After 2 years, we will have an extraordinarily useful data set from which we can organize both patient-oriented and in vitro studies focusing on inflammation and functional genomics in pregnancy.