3D Genome Reorganization and Epigenome Dynamics of Clonal Hematopoiesis

克隆造血的 3D 基因组重组和表观基因组动力学

• 批准号: 10674252
• 负责人: Sheng Li
• 金额: $ 34.31万
• 依托单位: JACKSON LABORATORY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-15 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10674252
• 关键词: 3-Dimensional; Age; Aging; Anti-Inflammatory Agents; Bone Marrow; Candidate Disease Gene; Cardiovascular Diseases; Cell physiology; Cells; Chromatin; Clinical; Clonal Expansion; Clonal Hematopoietic Stem Cell; DNA Methylation; DNA Modification Methylases; DNMT3a; Data; Development; Disease; Early Intervention; Elderly; Enhancers; Entropy; Epigenetic Process; Gene Expression; Gene Expression Regulation; Gene Targeting; Genes; Genetic Transcription; Genome; Genome Mappings; Genomics; Genotype; Goals; Hematology; Hematopoiesis; Hematopoietic; Hematopoietic Neoplasms; Hematopoietic Stem Cell heterogeneity; Hematopoietic Stem Cell subsets; Hematopoietic stem cells; Heterogeneity; Human; Impairment; Individual; Induced Mutation; Inflammation; Inflammation Process; Inflammatory; Intervention; Link; Measures; Molecular; Molecular Conformation; Mus; Mutant Strains Mice; Mutate; Mutation; Older Population; Persons; Pharmaceutical Preparations; Population; Regulator Genes; Research; Role; STAT3 gene; Somatic Mutation; Testing; Therapeutic; Therapeutic Intervention; Transplantation; age related; aged; cell age; efficacy evaluation; epigenetic therapy; epigenome; epigenomics; evidence base; healthspan; hematopoietic differentiation; hematopoietic stem cell aging; hematopoietic stem cell expansion; hematopoietic stem cell self-renewal; high risk; improved; in vivo; leukemia; middle age; mortality; mouse model; multiple omics; mutant; novel therapeutics; preempt; prevent; progenitor; programs; promoter; response; self-renewal; stem cell biology; stem cell function; stem cell genes; targeted treatment; therapeutic target; transcription factor; transcriptome; transcriptome sequencing; transcriptomics

PROJECT SUMMARY Clonal hematopoiesis (CH) commonly occurs with aging and is associated with increased mortality, a higher risk of leukemia, and cardiovascular disease. As the population of older adults expands in the US, there is an urgent unmet need to mitigate CH. Age-related CH is the abnormal expansion of hematopoietic cells that have somatic mutations, mostly in genes encoding the DNA methyltransferase DNMT3A and the demethylase TET2. These 'CH-mutations' change the hematopoietic stem cell (HSC) epigenome (i.e., DNA methylation and chromatin accessibility) at promoters and enhancers. To better understand how these changes impact gene regulation to confer a competitive advantage to a subset of HSCs and contribute to CH development, we propose a multi- omics approach that considers the effects of epigenomic changes on the physical interactions between enhancers and promoters, which are critical to activating transcription. By mapping the genome's 3D chromatin interactions, we will identify the specific enhancer-promoter pairs that control key HSC cellular functions such as self-renewal and response to inflammation. Although it is known that the epigenome organization of HSCs changes with age, it remains unclear how aging and CH-mutations jointly remodel the '3D epigenome' (3D chromatin organization and epigenome) of HSCs and contribute to CH. Our central hypothesis is that the 3D epigenome is remodeled with age and impacts transcriptional programs critical for HSC function. Thus, to identify therapeutic targets for elongating healthspan and delaying or preventing the occurrence of CH-associated disease in the aging US population, this proposal seeks to systematically uncover the 3D epigenomic configurations of cellular competition in CH and to prioritize candidate gene targets that emerge in early aging. Using mouse models of CH and human primary cells, we will test this hypothesis via bulk and single-cell multi- omics mapping (including RNA-seq, chromatin accessibility, and chromatin interactions) of normal and mutant HSCs to systematically determine their 3D epigenome remodeling during early aging. In Aim 1, we will determine whether 3D epigenome organization is linked to an aging transcriptional program in mouse and human HSCs by identifying and integrating HSC-specific 3D genomic, epigenomic, and transcriptomic signatures from young, middle-age, and old individuals of both species and validate the roles of top candidate genes in HSC aging in vivo. In Aim 2, we will define age-dependent 3D epigenome remodeling in HSCs of CH mouse models and validate the roles of top candidate genes in clonal expansion of mutant HSCs in vivo. Aging signatures that emerge at middle age will likely be the initial cause of functional changes in aged HSCs. Thus, the study will reveal primary and modifiable targets for therapeutic intervention. In Aim 3, we will determine the response of CH-associated chromatin reorganization in aged HSCs to epigenetic therapy and anti-inflammatory drugs in vivo. We anticipate that the findings from this study will accelerate the development of early interventions to preempt CH-associated disease in aging individuals.

项目摘要 克隆造血（CH）通常发生在衰老中，与死亡率增加有关，风险更高 白血病和心血管疾病。随着老年人的人口在美国的扩张，紧急 未满足减轻CH的需求。与年龄相关的CH是具有体细胞的造血细胞的异常膨胀 突变，主要是编码DNA甲基转移酶DNMT3A和脱甲基酶TET2的基因。这些 “ CH-Mutations”改变造血干细胞（HSC）表观基因组（即DNA甲基化和染色质） 发起人和增强子的可访问性）。更好地了解这些变化如何影响基因调节 赋予HSC子集的竞争优势并为CH开发做出贡献，我们提出了一个多竞争优势 OMICS方法认为表观基因组变化对物理相互作用的影响 增强子和启动子，对于激活转录至关重要。通过映射基因组的3D染色质 相互作用，我们将确定控制关键HSC蜂窝函数（例如 自我更新和对炎症的反应。尽管众所周知，HSC的表观基因组组织 随着年龄的变化，尚不清楚衰老和CH-Mutations如何共同重塑“ 3D表观基因组”（3D HSC的染色质组织和表观基因组，并为CH做出了贡献。我们的中心假设是3D 表观基因组随着年龄的增长而重塑，并影响对HSC功能至关重要的转录程序。因此，确定 延长健康范围并延迟或阻止CH相关的治疗靶标 美国老年人口的疾病，该提案试图系统地揭示3D表观基因组学 CH中细胞竞争的构型，并优先考虑早期衰老中出现的候选基因靶标。 使用CH和人类原代细胞的小鼠模型，我们将通过批量和单细胞多多核 正常和突变体的OMICS映射（包括RNA-Seq，染色质可及性和染色质相互作用） HSC在早期衰老期间系统地确定其3D表观组的重塑。在AIM 1中，我们将确定 3D表观基因组组织是否与鼠标和人类HSC中的老化转录程序相关联 识别和整合HSC特异性3D基因组，表观基因组和转录组学特征 中年和种类的老个人，并验证顶级候选基因在HSC衰老中的作用 体内。在AIM 2中，我们将在CH鼠标模型的HSC中定义依赖年龄的3D表观组重塑 验证顶级候选基因在体内突变HSC的克隆膨胀中的作用。老化的签名 在中年，出现可能是老化HSC功能变化的最初原因。因此，研究将 揭示用于治疗干预的主要和可修改靶标。在AIM 3中，我们将确定 老年HSC中的CH耦合染色质重组，以表观遗传疗法和抗炎药 体内。我们预计这项研究的发现将加速早期干预措施的发展 衰老个体中的先发制人相关疾病。