TET-mediated DNA oxidations in mucosal innate defense

TET 介导的粘膜先天防御 DNA 氧化

基本信息

批准号：
10525407
负责人：
Jean-Pierre Etchegaray
金额：
$ 23.55万
依托单位：
RUTGERS THE STATE UNIV OF NJ NEWARK
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-06-07 至 2024-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10525407
关键词：
Address Affect Aftercare Bacterial Infections Base Excision Repairs Biology Cell Count Cell Differentiation process Cell physiology Cells Cellular Stress Chemicals Chromatin Cytosine DNA DNA Methylation Data Dioxygenases Disease Disease susceptibility Environmental Monitoring Enzymes Epigenetic Process Epithelial Cells Equilibrium Event Exhibits Exposure to Family Gene Expression Genes Genetic Transcription Genome Health Homeostasis Human Immune Immunology Immunoprecipitation Infection Inflammation Inflammatory Inflammatory Bowel Diseases Inflammatory Response Innate Immune Response Intestines Literature Mediating Mediator of activation protein Mucous Membrane Mus Nuclear Outcome Oxidative Stress Oxides Paneth Cells Patients Pattern Phenotype Play Predisposition Reagent Research Risk Factors Role Running Stress Testing Time Tissues Ulcerative Colitis antimicrobial base biological adaptation to stress cell type commensal microbes dextran sulfate sodium induced colitis enteric pathogen environmental stressor epigenetic regulation epigenome gastrointestinal gene network gene regulatory network genome-wide genomic locus gut inflammation gut microbiota in vivo intestinal epithelium intestinal homeostasis methylation pattern microbiota mouse genetics novel nuclease oxidation pathogen postnatal programs response single-cell RNA sequencing stem cells stressor transcription factor transcriptome sequencing translational medicine translational potential

项目摘要

PROJECT SUMMARY DNA methylation pattern in the genome of intestinal epithelial cells (IECs) can be altered by gut microbiota. How the functions of various IEC types are affected by such epigenetic changes under homeostatic and stress conditions remain unclear. DNA methylation is a repressive epigenetic mark that can be actively reversed by the Ten-Eleven Translocation family of enzymes TET1, TET2 and TET3. TETs are DNA dioxygenases that successively oxidize methylated DNA - 5-methylcytosine (5mC) - into 5-hydroxy-methylcytosine (5hmC), 5- formylcytosine (5fC), and 5-carboxylcytosine (5caC). Both 5fC and 5caC can be excised by DNA based excision repair factors leading to unmodified cytosines. TET enzymes were recently implicated as new risk factors in inflammatory bowel disease (IBD) patients, but the role of TET-mediated DNA oxidation in homeostasis and in response to environmental stressors are unknown. Preliminary data show that human IECs display an elevation of 5hmC DNA oxidation upon infection by invasive pathogen, and mouse IECs lacking Tet3 had reduction of 5hmC abundance in ileal IECs. scRNA-Seq suggests that mouse Tet3 is the most abundant TET enzyme in IECs, especially in Paneth cells. Tet3DIEC mice had reduced mature Paneth cells, increased susceptibilities to inflammation caused by enteric pathogen or barrier-disrupting chemical. The project tests a central hypothesis that TET3-mediated DNA oxidations play dual roles in guiding IEC differentiation and promoting anti-microbial response via 5hmC-induced permissive chromatin while restraining differentiation via 5fC- and 5caC-induced transcriptional pausing. Aim 1 will use genome wide approaches to identify intestinal stem cell (ISC) and Paneth cell specific TET3 and DNA oxidation gene regulatory networks under homeostasis and in responding to distinct cellular stressors such as pathogen and chemical. Aim 2 will characterize how ISC and Paneth cell specific TET3-mediated DNA oxidation regulate mucosal inflammatory response. This MPI project, utilizing complementary expertise in epigenetics and intestinal biology to address how DNA oxidations regulate the epigenome in response to stressors to help resolve inflammation. The idea that TET-mediated DNA oxidations may be an integral mucosal innate immune component to cope with oxidative stresses during infection and inflammation is novel. Elucidating TET functions in specific IEC types may exert major impact on human gastrointestinal mucosal immunology and diseases. If TET enzymes are indeed uncovered by this research as key mediator and regulator of inflammatory responses, as predicted by literature and our preliminary data, the outcome can be of high relevance to translational medicine.

项目概要肠道微生物群可以改变肠上皮细胞 (IEC) 基因组中的 DNA 甲基化模式。如何各种 IEC 类型的功能受到稳态和压力下的表观遗传变化的影响情况仍不清楚。 DNA 甲基化是一种抑制性表观遗传标记，可以通过 DNA 主动逆转 TET1、TET2 和 TET3 的 10-11 易位家族。 TET 是 DNA 双加氧酶，依次将甲基化 DNA - 5-甲基胞嘧啶 (5mC) - 氧化为 5-羟甲基胞嘧啶 (5hmC)，5- 甲酰基胞嘧啶 (5fC) 和 5-羧基胞嘧啶 (5caC)。 5fC 和 5caC 都可以通过基于 DNA 的切除来切除修复因子导致未修饰的胞嘧啶。 TET 酶最近被认为是新的危险因素炎症性肠病 (IBD) 患者，但 TET 介导的 DNA 氧化在体内平衡和对环境压力的反应尚不清楚。初步数据显示，人类 IEC 显示海拔高度侵入性病原体感染后 5hmC DNA 氧化的减少，缺乏 Tet3 的小鼠 IEC 的氧化减少回肠 IEC 中 5hmC 丰度。 scRNA-Seq 表明小鼠 Tet3 是体内最丰富的 TET 酶 IEC，尤其是潘氏电池。 Tet3DIEC 小鼠成熟潘氏细胞减少，对由肠道病原体或破坏屏障的化学物质引起的炎症。该项目测试了一个中心假设 TET3 介导的 DNA 氧化在指导 IEC 分化和促进抗菌方面发挥双重作用通过 5hmC 诱导的允许染色质做出反应，同时通过 5fC 和 5caC 诱导抑制分化转录暂停。目标 1 将使用全基因组方法来识别肠干细胞 (ISC) 和潘氏细胞细胞特异性 TET3 和 DNA 氧化基因调控网络处于稳态并响应不同的细胞应激源，例如病原体和化学物质。目标 2 将描述 ISC 和潘氏细胞的特异性 TET3 介导的 DNA 氧化调节粘膜炎症反应。该 MPI 项目利用表观遗传学和肠道生物学方面的互补专业知识可解决 DNA 氧化如何调节表观基因组响应压力源，帮助解决炎症。 TET介导的DNA氧化的想法可能是粘膜固有免疫的一个组成部分，用于应对感染期间的氧化应激，炎症是新奇的。阐明特定 IEC 类型中的 TET 功能可能会对人类产生重大影响胃肠粘膜免疫学和疾病。如果这项研究确实发现了 TET 酶正如文献和我们的初步数据所预测的，炎症反应的关键介质和调节器结果可能与转化医学高度相关。