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 肠上皮细胞（IEC）基因组中的DNA甲基化模式可以通过肠道菌群改变。如何 各种IEC类型的功能受到稳态和压力下这种表观遗传变化的影响 条件仍然不清楚。 DNA甲基化是一种抑制性表观遗传标记，可以通过 酶TET1，TET2和TET3的十个易位家族。 TET是DNA二氧酶 将甲基化的DNA-5-甲基胞嘧啶（5MC） - 依次氧化成5-羟基甲基霉素（5HMC），5-- 甲环胞嘧啶（5FC）和5-羧基霉素（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。最近将TET酶视为新的风险因素 炎症性肠病（IBD）患者，但TET介导的DNA氧化在稳态和中的作用 对环境压力源的响应尚不清楚。初步数据显示，人IEC显​​示了高程 通过侵入性病原体感染后的5HMC DNA氧化，缺乏TET3的小鼠IEC降低了 5hmc的IEC中的丰度。 scrna-seq表明小鼠TET3是最丰富的TET酶 IEC，尤其是在Paneth细胞中。 TET3DIEC小鼠减少了成熟的Paneth细胞，增加了对 由肠道病原体或屏障干扰化学物质引起的炎症。该项目检验了一个中心假设 TET3介导的DNA氧化在引导IEC分化和促进抗微生物中起双重作用 通过5HMC诱导的允许染色质反应，同时通过5FC和5CAC诱导的分化 转录暂停。 AIM 1将使用基因组范围的方法来识别肠道干细胞（ISC）和Paneth 细胞特异性TET3和DNA氧化基因调节网络在体内稳态下，并响应不同 细胞应激源，例如病原体和化学物质。 AIM 2将表征ISC和Paneth Cell特定的方式 TET3介导的DNA氧化调节粘膜炎症反应。这个MPI项目，利用 表观遗传学和肠生物学方面的互补专业知识，以解决DNA氧化如何调节 表观基因组应对压力源以帮助解决炎症。 TET介导的DNA氧化的想法 可能是应对感染过程中氧化应激的整体粘膜先天免疫成分 炎症是新颖的。在特定的IEC类型中阐明TET功能可能对人类产生重大影响 胃肠道粘膜免疫学和疾病。如果这项研究确实发现了TET酶 如文献和我们的初步数据所预测的那样，炎症反应的关键介体和调节剂 结果可能与转化医学具有很高的相关性。

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