TET-mediated DNA oxidations in mucosal innate defense

TET 介导的粘膜先天防御 DNA 氧化

• 批准号: 10841231
• 负责人: Jean-Pierre Etchegaray
• 金额: $ 19.63万
• 依托单位: RUTGERS THE STATE UNIV OF NJ NEWARK
• 依托单位国家: 美国
• 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/10841231
• 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; Mucous Membrane; Mus; Nuclear; Outcome; Oxidative Stress; Paneth Cells; Patients; Pattern; Phenotype; Play; Predisposition; Reagent; Research; Risk Factors; Role; Running; Stress; Testing; Time; Tissues; Ulcerative Colitis; antimicrobial; biological adaptation to stress; cell type; commensal microbes; coping; 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; permissiveness; postnatal; programs; response; restraint; single-cell RNA sequencing; stem cells; stressor; transcription factor; transcriptome sequencing; translational medicine; translational potential

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.

项目摘要 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类型的功能在稳态和应激下受到这种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甲基化逆转。 TET 1、TET 2和TET 3酶的10 - 11易位家族。胰蛋白酶是DNA双加氧酶， 将甲基化DNA - 5-甲基胞嘧啶（5 mC）-依次氧化成5-羟基-甲基胞嘧啶（5 hmC）、5- 甲酰胞嘧啶（5 fC）和5-羧基胞嘧啶（5caC）。5 fC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。泰特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氧化的作用，在体内平衡， 对环境压力的反应是未知的。初步数据显示，人类的IEC显示出 感染侵袭性病原体后，5 hmC DNA氧化的减少，缺乏Tet 3的小鼠IEC减少了5 hmC DNA氧化的减少。 回肠IEC中的5 hmC丰度。scRNA-Seq表明小鼠Tet 3是小鼠中最丰富的泰特酶。 IEC，尤其是潘氏细胞。Tet 3DIEC小鼠具有减少的成熟潘氏细胞，增加的对 由肠道病原体或屏障破坏化学物质引起的炎症。该项目测试了一个核心假设 TET 3介导的DNA氧化在引导IEC分化和促进抗微生物作用方面发挥双重作用， 通过5 hmC诱导的允许染色质的反应，同时通过5 fC和5caC诱导的抑制分化 转录暂停。目的1将使用全基因组方法鉴定肠干细胞（ISC）和Paneth 细胞特异性TET 3和DNA氧化基因调控网络在稳态和响应不同的 细胞应激源，如病原体和化学物质。目的2将描述ISC和潘氏细胞特异性 TET 3介导的DNA氧化调节粘膜炎症反应。这个MPI项目，利用 在表观遗传学和肠道生物学的补充专业知识，以解决如何DNA氧化调节 表观基因组对压力源的反应，以帮助解决炎症。TET介导的DNA氧化 可能是一个完整的粘膜先天免疫成分，以科普感染期间的氧化应激， 炎症是新的。阐明特定IEC类型中的泰特功能可能会对人体产生重大影响 胃肠道粘膜免疫学和疾病。如果这项研究确实发现了泰特酶， 正如文献和我们的初步数据所预测的那样， 结果可能与转化医学高度相关。

项目成果

Self-assembly of DNA parallel double-crossover motifs.

• DOI: 10.1039/d3nr05119f
• 发表时间: 2024-01-25
• 期刊: NANOSCALE
• 影响因子: 6.7
• 作者: Lee, Jung Yeon;Yang, Qi;Chang, Xu;Jeziorek, Maciej;Perumal, Devanathan;Olivera, Tiffany R.;Etchegaray, Jean-Pierre;Zhang, Fei
• 通讯作者: Zhang, Fei