Combinatory Effects of Genetic Variants in Eosinophilic Esophagitis

项目总结/摘要 嗜酸性食管炎（EoE）是一种慢性过敏性炎症性食管疾病，其临床特征为： 食管功能障碍（呕吐、疼痛、吞咽困难和食物嵌塞）;组织学上通过食管 与屏障功能受损相关的嗜酸性粒细胞增多、上皮增生和细胞间隙扩张; 以及高度的遗传性。大多数遗传学研究都集中在分析常见的遗传变异 通过全基因组关联研究（GWAS），有证据表明钙蛋白酶14（CAPN 14）和胸腺 间质淋巴细胞生成素（TSLP），这是值得注意的是，都表达了相同的相关细胞类型，食管癌 上皮细胞最近，我们对EoE多重家族进行了全外显子组测序（WES）， 发现了一组与EoE有关的罕见遗传变异。尽管最近的研究进展提供了证据 对于与遗传变异相关的EoE遗传病因学，单独检测单个遗传变异不会 考虑基因复杂的相互作用景观。我们的中心假设是，一个子集的EoE结果 来自于相同生物学途径中多种变异的组合。这项研究将统计和 实验评估组合效应以及遗传变异如何对EoE做出贡献， 利用最近开发的创新技术，根据生物学途径制定风险评分，以预测EoE (e.g., WES、GWAS、RNA-seq、ChIP-seq和离体疾病建模[食管类器官和器官型 培养]）。在所附的建议中，我们概述了一套综合的多学科研究， 必要的统计和实验支持，以评估EoE之间的组合效应的影响 基因变异在目标1中，我们将检验以下假设： 罕见-罕见变异、罕见-常见变异/SNP和生物学途径。确定对风险的影响 对于EoE，我们将在变异、基因和途径水平上共同分析组合效应。在目标2中，我们将测试 DSP和PPL罕见变异体对食管屏障功能具有联合作用的假设， 基因/蛋白表达。为了探索运作机制，我们将研究这些变体是否具有 使用离体，三维培养模型（例如，食管类器官，器官型 文化）。最后，在目标3中，我们将检验遗传和基因组数据的综合将 导致能够预测谁处于发展EoE的风险、其疾病特征和/或对治疗的反应。 目标3将作为未来R01应用的基础，以进行机制研究， 会聚基因/通路的影响和病例对照研究，以进一步验证和探索临床效用 风险评分。拟议的研究将解决最近NIH研讨会概述的未满足的医疗需求， 提供了对疾病遗传机制的深入了解，从而可能有助于个性化医疗， 特别是加强筛查或预防性治疗的应用。

PROJECT SUMMARY/ABSTRACT Eosinophilic esophagitis (EoE) is a chronic allergic inflammatory esophageal disorder characterized clinically by esophageal dysfunction (vomiting, pain, dysphagia, and food impaction); histologically by esophageal eosinophilia, epithelial hyperplasia, and dilated intercellular spaces associated with impaired barrier function; and by a high degree of heritability. Most genetic studies have focused on analyzing common genetic variants by genome-wide association studies (GWAS), with evidence implicating the calpain 14 (CAPN14) and thymic stromal lymphopoietin (TSLP), which are notably both expressed by the same relevant cell type, esophageal epithelial cells. Recently, we have performed whole-exome sequencing (WES) on EoE multiplex families and identified a set of rare genetic variants involved in EoE. Though recent research progress provides the evidence for EoE genetic etiology being linked to genetic variants, testing single genetic variants separately does not consider the complex interaction landscape of genes. Our central hypothesis is that a subset of EoE results from the combination of multiple variants in the same biological pathways. This study will statistically and experimentally evaluate combinatory effects and how the genetic variants are contributing to EoE and will develop risk scores based on the biological pathways to predict EoE by using recently developed innovations (e.g., WES, GWAS, RNA-seq, ChIP-seq, and ex vivo disease modeling [esophageal organoids and organotypic culture]). In the attached proposal, we have outlined an integrated set of multidisciplinary studies with the necessary statistical and experimental support to evaluate the impact of the combinatory effects among EoE genetic variants. In Aim 1, we will test the hypothesis that the risk for EoE will be increased by the combinatory rare-rare variants, rare-common variants/SNPs, and biological pathways. To determine the impact on the risk for EoE, we will jointly analyze combinatory effects at variant, gene, and pathway levels. In Aim 2, we will test the hypothesis that DSP and PPL rare variants have combinatory effects on esophageal barrier functions and gene/protein expression. To explore the operational mechanisms, we will examine whether these variants have combinatory effects using ex vivo, 3-dimensional culture models (e.g., esophageal organoids, organotypic culture) of EoE. Finally, in Aim 3, we will test the hypothesis that the synthesis of genetic and genomic data will lead to the ability to predict who is at risk of developing EoE, its disease features, and/or response to therapy. Aim 3 will serve as the foundation for a future R01 application to conduct a mechanistic study to characterize the impact of convergent genes/pathways and a case-control study to further validate and explore the clinical utility of risk scores. The proposed study will address an unmet medical need as outlined by a recent NIH workshop, providing insight into disease genetic mechanisms and thereby potentially contributing to personalized medicine, especially the application of enhanced screening or preventive therapies.