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 克隆性造血（CH）通常与衰老有关，与死亡率增加有关， 白血病和心血管疾病。随着美国老年人口的增加， 未满足的需要，以减轻CH。与CH相关的是造血细胞的异常扩增， 突变，主要在编码DNA甲基转移酶DNMT 3A和脱甲基酶TET 2的基因中。这些 “CH-突变”改变造血干细胞（HSC）表观基因组（即，DNA甲基化和染色质 可及性）。为了更好地了解这些变化如何影响基因调控， 赋予竞争优势的一个子集的HSC，并有助于CH的发展，我们提出了一个多- 一种考虑表观基因组变化对生物体间物理相互作用的影响的组学方法， 增强子和启动子，它们对激活转录至关重要。通过绘制基因组的3D染色质 相互作用，我们将确定控制关键HSC细胞功能的特定增强子-启动子对， 自我更新和炎症反应。尽管已知HSC的表观基因组结构 随着年龄的变化，仍然不清楚衰老和CH突变如何共同重塑“3D表观基因组”（3D 我们的中心假设是，3D染色质组织和表观基因组）的HSC，并有助于CH。 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，为了识别 用于延长健康寿命和延迟或预防CH相关性疾病发生的治疗靶点 疾病的老龄化美国人口，这项建议旨在系统地揭示3D表观基因组 CH中的细胞竞争配置，并优先考虑在早期衰老中出现的候选基因靶点。 使用小鼠CH和人原代细胞模型，我们将通过大量和单细胞多克隆抗体来验证这一假设。 正常和突变体的组学作图（包括RNA-seq、染色质可及性和染色质相互作用） HSC系统地确定其在早期衰老过程中的3D表观基因组重塑。在目标1中，我们将确定 3D表观基因组组织是否与小鼠和人类HSC中的衰老转录程序相关， 鉴定和整合来自年轻人的HSC特异性3D基因组、表观基因组和转录组特征， 中年和老年人的两个物种，并验证了顶级候选基因在HSC衰老中的作用， vivo.在目标2中，我们将定义CH小鼠模型HSC中年龄依赖性的3D表观基因组重塑， 验证在体内突变型HSC克隆扩增中最佳候选基因的作用。老化的签名， 在中年时出现可能是老化HSC功能改变的最初原因。因此，研究将 揭示了治疗干预的主要和可修改的目标。在目标3中，我们将确定 老年HSC中CH相关染色质重组对表观遗传治疗和抗炎药物的影响 vivo.我们预计，这项研究的结果将加速早期干预的发展， 预防老年人的CH相关疾病。