Genetic and epigenetic contributions to Sjogren's syndrome

遗传和表观遗传对干燥综合征的影响

基本信息

批准号：
8991063
负责人：
Lindsey Ann Criswell
金额：
$ 23.71万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-01-01 至 2018-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8991063
关键词：
Affect Algorithms Autoantibodies Autoimmune Diseases Autoimmunity B-Lymphocytes Biological Assay Biological Markers Biopsy Blood Blood specimen Budgets CD14 gene CD19 gene CD4 Positive T Lymphocytes Carbon Cell Separation Cells Clinical Clinical Data Collection Complex Country CpG dinucleotide Cytosine DNA DNA Methylation Data Data Analyses Data Set Development Diagnosis Enrollment Epigenetic Process Etiology European Exhibits Gene Expression Genes Genetic Genome Genomic Segment Genotype Health Histocompatibility Testing Human Individual International Labial Salivary Gland Lead Machine Learning Meta-Analysis Methodology Methods Methylation Modeling Modification Molecular Genetics National Institute of Dental and Craniofacial Research Not Hispanic or Latino Oral Participant Patients Peripheral Blood Mononuclear Cell Phenotype Play Population Prevention approach Principal Component Analysis Production Research Project Grants Resources Risk Risk Factors Role SNP genotyping Sample Size Sampling San Francisco Site Sjogren&apos s Syndrome Statistical Data Interpretation Study Subject Subgroup Syndrome T-Lymphocyte Subsets Technology Tissues Transcriptional Regulation Whole Blood Work base case control cell type clinical phenotype disorder risk genome wide association study genome-wide high throughput technology human DNA interest member monocyte repository systemic autoimmune disease whole genome

项目摘要

DESCRIPTION (provided by applicant): High throughput whole genome platforms to quantitatively and efficiently assay human DNA methylation provide an extraordinary opportunity to accelerate progress in the identification of epigenetic mechanisms for complex human autoimmune diseases such as Sjogren's Syndrome (SS). Epigenetic modifications, such as methylation of the 5' carbon of cytosine which occurs in the context of CpG dinucleotides, do not affect the genetic sequence; however, they do play a critical role in transcriptional regulation of a gene and subsequent gene expression. We have applied this technology, in conjunction with whole genome SNP genotyping to a clinically well-characterized collection of SS cases and controls developed specifically for genetic and epigenetic studies. Samples from the Sjogren's International Collaborative Clinical Alliance (SICCA) repository (total n=3,500 individuals) will b utilized, given the careful phenotype characterization and standardized collection of biospecimens that has been performed for each participant. For this proposal, we have initially obtained DNA from peripheral blood mononuclear cells (PBMCs) and sorted cell populations with high purity, including CD14+ monocytes, CD19+ B cells, CD4+ T cells, as well as labial salivary gland biopsy tissue from 120 SICCA participants (100 SS cases and 20 controls). Data collected for ~450,000 highly informative CpG sites spanning 22,000 genes across the genome will provide a comprehensive assessment of DNA methylation for each individual for our proposed study Aims. As part of Aim 1, DNA methylation profiles will be examined using three main approaches: 1) Global DNA methylation profiles will be analyzed for association with SS risk in all sample types; 2) Multidimensional scaling analysis (MDS) and principal components analysis (PCA) will be performed to determine whether SS case samples can be distinguished from control samples; and 3) Local analyses will also be performed and will focus specifically on DNA methylation changes within candidate SS genes and genes demonstrating at least 1.5 fold methylation differences between cases and controls. Our proposal will take advantage of available whole genome data for each study participant and results from the largest genome wide association study (GWAS) in SS. In Aim 2, we will utilize DNA methylation profiles and methods from Aim 1 to determine whether important SS case phenotypes can be distinguished from one another. We will identify top ranked CpG sites that are either hypo or hyper methylated in specific SS case groups or that distinguish cases from controls using supervised machine learning algorithms. We will attempt replication for all top findings in an independent dataset, followed by random effects meta-analysis to incorporate other SS risk factors. Finally, we will determine whether DNA methylation profiles of interest from Aims 1 and 2 can be detected in DNA from whole blood for potential use as a biomarker. The identification of unique epigenetic profiles in SS, and an understanding of these profiles in the context of different cell and tissue types and genetic background have the potential to significantly transform our understanding of SS etiology.

描述（由申请人提供）：用于定量和有效测定人类 DNA 甲基化的高通量全基因组平台为加速干燥综合征（SS）等复杂人类自身免疫性疾病表观遗传机制的识别进展提供了绝佳的机会。表观遗传修饰，例如在 CpG 二核苷酸背景下发生的胞嘧啶 5' 碳甲基化，不会影响遗传序列；然而，它们确实在转录调控中发挥着关键作用基因和随后的基因表达。我们已将这项技术与全基因组 SNP 基因分型相结合，应用于专门为遗传和表观遗传学研究而开发的临床特征良好的 SS 病例和对照集合。鉴于已对每位参与者进行了仔细的表型表征和生物样本的标准化收集，将使用来自 Sjogren 国际合作临床联盟 (SICCA) 存储库的样本（总共 n=3,500 人）。对于这个提案，我们初步从外周血单核细胞（PBMC）中获得了DNA，并以高纯度分选了细胞群，包括CD14+单核细胞、CD19+B细胞、CD4+T细胞，以及来自120名SICCA参与者的唇唾液腺活检组织（ 100 个 SS 病例和 20 个对照）。从整个基因组中涵盖 22,000 个基因的约 450,000 个信息丰富的 CpG 位点收集的数据将为我们提出的研究目标提供每个个体 DNA 甲基化的全面评估。作为目标 1 的一部分，将使用三种主要方法检查 DNA 甲基化谱： 1) 将分析全局 DNA 甲基化谱，以确定其与所有样本类型中 SS 风险的关联； 2）进行多维尺度分析（MDS）和主成分分析（PCA）以确定是否可以将SS病例样本与对照样本区分开来； 3) 还将进行局部分析，并将特别关注候选 SS 基因内的 DNA 甲基化变化，以及证明病例和对照之间至少有 1.5 倍甲基化差异的基因。我们的提案将利用每个研究参与者可用的全基因组数据以及 SS 最大的全基因组关联研究 (GWAS) 的结果。在目标 2 中，我们将利用目标 1 中的 DNA 甲基化谱和方法来确定是否可以区分重要的 SS 病例表型。我们将确定在特定 SS 病例组中低甲基化或高甲基化的排名最高的 CpG 位点，或者使用监督机器学习算法将病例与对照区分开来。我们将尝试在独立数据集中复制所有重要发现，然后进行随机效应荟萃分析以纳入其他 SS 风险因素。最后，我们将确定是否可以在全血 DNA 中检测到目标 1 和 2 中感兴趣的 DNA 甲基化谱，以用作生物标志物。 SS 独特表观遗传谱的鉴定，以及在不同细胞和组织类型以及遗传背景背景下对这些谱的理解，有可能显着改变我们对 SS 病因学的理解。