Role of DNA Methylation and Hydroxymethylation in Epidermal Homeostasis

DNA 甲基化和羟甲基化在表皮稳态中的作用

• 批准号: 9755351
• 负责人: Jeffrey B Cheng
• 金额: $ 17.6万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-01 至 2021-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9755351
• 关键词: Affect; Award; Binding; Binding Sites; Biological; Biological Assay; Biology; California; ChIP-seq; Chimeric Proteins; Chromatin; Clinical; Computational Biology; Cytosine; DNA; DNA Methylation; Data; Dermatologist; Development; Disease; EP300 gene; Enhancers; Enzymes; Epidermis; Epigenetic Process; Epithelial; Equilibrium; Foundations; Gene Expression; Gene Expression Regulation; Genes; Genomic DNA; Genomics; Goals; Grant; Homeostasis; Human; Individual; K-Series Research Career Programs; Knowledge; Lead; Location; Luciferases; Malignant Neoplasms; Malignant neoplasm of brain; Massive Parallel Sequencing; Mentors; Modification; Molecular; Molecular Conformation; Morbidity - disease rate; Pathogenesis; Pattern; Play; Process; Processed Genes; Proliferating; Proteins; Psoriasis; Regulation; Regulator Genes; Regulatory Element; Reporter; Research; Research Personnel; Role; Sampling; San Francisco; Scientist; Squamous cell carcinoma; Structure; System; Technical Expertise; Therapeutic Intervention; Training; Transcript; Transcription Coactivator; United States National Institutes of Health; Universities; Writing; base; cell type; chromosome conformation capture; deep sequencing; demethylation; epigenetic profiling; epigenome; epigenomics; experimental study; genome-wide; improved; in vivo; keratinocyte; keratinocyte differentiation; knock-down; knowledge base; mRNA sequencing; methylation pattern; neurosurgery; next generation sequencing; professor; programs; promoter; public health relevance; skills; skin disorder; transcription factor

DESCRIPTION (provided by applicant): This is an application for a K08 Clinical Scientist Mentored Career Development Award for Dr. Jeffrey Cheng, a Dermatologist at the University of California, San Francisco. The candidate's long-term goal is to become a leading independent investigator of epigenetic mechanisms in epidermal biology and disease. This grant will be invaluable in supporting Dr. Cheng's transition towards intellectual independence and direction of his own research program. Specifically, this K08 award will support an intensive 5-year training plan to develop a strong scientific knowledge base and new technical skills in computational biology, epithelial biology, and epigenetics/epigenomics and to improve grant and scientific writing skills. Dr. Joseph Costello will mentor Dr. Cheng's scientific training and carer development. Dr. Costello, a Professor of Neurosurgery at UCSF and Director of a NIH Roadmap Epigenome Mapping Center, is a leading epigenomics researcher who studies epigenetic mechanisms in brain cancer and development. Dr. Ting Wang, a computational biologist with expertise in analyzing, integrating, and displaying deep sequencing-based epigenomics data, and Dr. Theodora Mauro, who studies epidermal differentiation and barrier function, will co-mentor Dr. Cheng. The proposed research seeks to understand the role of DNA methylation and hydroxymethylation in epidermal homeostasis. While DNA methylation clearly affects epidermal homeostasis, its gene regulatory role outside of promoters remains unclear. The role of DNA hydroxymethylation in the epidermis has not been studied. Emerging evidence suggests a significant role for DNA methylation and hydroxymethylation at enhancers. Consistent with this, preliminary DNA methylation data reveals that the majority of hypomethylated regions in proliferating keratinocytes overlap with enhancers. To explore the epidermal role of DNA methylation at enhancers and DNA hydroxymethylation, Dr. Cheng will perform next generation sequencing-based epigenetic profiling assays to identify differentially methylated and hydroxymethylated regions between proliferating and differentiating keratinocytes. This will be followed by experiments to validate keratinocyte- relevant candidate enhancers identified by their DNA methylation or hydroxymethylation patterns and assess the functional consequences of epidermal DNA hydroxymethylating enzyme and 5-hyroxymethylation depletion. These data will serve as a foundation to help achieve Dr. Cheng's long-term goal of understanding how epigenetic mechanisms are dysregulated in epidermal disease.

描述（由申请人提供）：这是一份K 08临床科学家指导职业发展奖的申请，申请人是弗朗西斯科加州大学的皮肤科医生Jeffrey Cheng博士。候选人的长期目标是成为表皮生物学和疾病表观遗传机制的领先独立研究者。这笔拨款将是非常宝贵的支持郑博士的过渡到知识的独立和方向，他自己的研究计划。具体而言，该K 08奖将支持一项为期5年的强化培训计划，以发展计算生物学，上皮生物学和表观遗传学/表观基因组学方面的强大科学知识基础和新技术技能，并提高赠款和科学写作技能。约瑟夫·科斯特洛博士将指导郑博士的科学培训和照顾者发展。Costello博士是加州大学旧金山分校神经外科教授和NIH路线图表观基因组图谱中心主任，是一位领先的表观基因组学研究人员，研究脑癌和发育的表观遗传机制。Ting Wang博士是一位计算生物学家，擅长分析，整合和显示基于深度测序的表观基因组学数据，Theodora Mauro博士研究表皮分化和屏障功能，将共同指导Cheng博士。 这项研究旨在了解DNA甲基化和羟甲基化在表皮稳态中的作用。虽然DNA甲基化明显影响表皮稳态，但其在启动子外的基因调控作用仍不清楚。DNA羟甲基化在表皮中的作用尚未研究。新出现的证据表明，DNA甲基化和羟甲基化在增强子中起着重要作用。与此一致，初步的DNA甲基化数据显示，在增殖角质形成细胞中的大多数低甲基化区域与增强子重叠。为了探索DNA甲基化在增强子和DNA羟甲基化的表皮作用，郑博士将进行下一代基于测序的表观遗传分析，以确定增殖和分化角质形成细胞之间的差异甲基化和羟甲基化区域。随后进行实验以验证通过其DNA甲基化或羟甲基化模式鉴定的角质形成细胞相关候选增强子，并评估表皮DNA羟甲基化酶和5-羟甲基化耗竭的功能后果。这些数据将作为基础，以帮助实现郑博士的长期目标，了解表观遗传机制是如何在表皮疾病失调。

项目成果

Riemannian geometry and statistical modeling correct for batch effects and control false discoveries in single-cell surface protein count data.

黎曼几何和统计模型可纠正批次效应并控制单细胞表面蛋白计数数据中的错误发现。

• DOI: 10.1103/physreve.102.012409
• 发表时间: 2020
• 期刊: Physical review. E
• 作者: Zhang,Shuyi;Leistico,JacobR;Cook,Christopher;Liu,Yale;Cho,RaymondJ;Cheng,JeffreyB;Song,JunS
• 通讯作者: Song,JunS

Defining Patient-Level Molecular Heterogeneity in Psoriasis Vulgaris Based on Single-Cell Transcriptomics.

• DOI: 10.3389/fimmu.2022.842651
• 发表时间: 2022
• 期刊: Frontiers in immunology
• 影响因子: 7.3

Emergence and Evolution of Mutational Hotspots in Sun-Damaged Skin.

晒伤皮肤突变热点的出现和演变。

• DOI: 10.1016/j.jid.2017.09.007
• 发表时间: 2018
• 期刊: The Journal of investigative dermatology
• 作者: Cheng,JeffreyB;Cho,RaymondJ
• 通讯作者: Cho,RaymondJ

Single-Cell Profiling Reveals Divergent, Globally Patterned Immune Responses in Murine Skin Inflammation.

• DOI: 10.1016/j.isci.2020.101582
• 发表时间: 2020-10-23
• 期刊: iScience
• 影响因子: 5.8
• 作者: Liu Y;Cook C;Sedgewick AJ;Zhang S;Fassett MS;Ricardo-Gonzalez RR;Harirchian P;Kashem SW;Hanakawa S;Leistico JR;North JP;Taylor MA;Zhang W;Man MQ;Charruyer A;Beliakova-Bethell N;Benz SC;Ghadially R;Mauro TM;Kaplan DH;Kabashima K;Choi J;Song JS;Cho RJ;Cheng JB
• 通讯作者: Cheng JB