Transcriptional Regulators in Aging Macrophages

衰老巨噬细胞中的转录调节因子

• 批准号: 10279947
• 负责人: Deborah Rachelle Winter
• 金额: $ 60.28万
• 依托单位: NORTHWESTERN UNIVERSITY AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10279947
• 关键词: ATAC-seq; Adopted; Age; Aging; Arthritis; Bone Marrow; Cells; ChIP-seq; Chimera organism; Data; Degenerative polyarthritis; Development; Disease; Downstream Enhancer; Enhancers; Environment; Exhibits; Functional disorder; Future; Gene Expression; Gene Expression Profile; Genetic Transcription; Genomic approach; Genomics; Goals; Health; Heterogeneity; Homeostasis; Human; Immune; Immune system; Immunity; Intervention; Joints; Lead; Link; Modeling; Molecular; Mus; Myelogenous; Patients; Pattern; Phenotype; Population; Prevention strategy; Process; Publishing; Regulation; Regulatory Element; Role; Signal Transduction; Specific qualifier value; Supervision; Synovial Membrane; TNF gene; Testing; Time; Tissue-Specific Gene Expression; Tissues; To specify; Translating; Transplantation; Tumor Necrosis Factor Receptor; Wild Type Mouse; Work; age related; aged; ankle joint; cell type; chromatin remodeling; computer framework; epigenomics; functional genomics; improved; macrophage; monocyte; mouse model; receptor; residence; single-cell RNA sequencing; systemic inflammatory response; therapeutic target; transcription factor; transcriptome sequencing

As key governors of tissue integrity, macrophages are implicated in many age-related diseases. Macrophages are a plastic myeloid immune cell type found in nearly every tissue of the body where they perform critical functions for homeostasis. Tissue-resident macrophages adapt to perform specific functions through the action of tissue-specific transcription factors (TFs) that respond to signals in the local environment. In combination with cell-type-specific TFs, they specify a distinct epigenomic landscape leading to tissue-specific gene expression. Changes to the macrophage environment due to systemic inflammation and other signals in aging lead to a decline in macrophage function. In order to develop preventative strategies, we need a better understanding of how macrophages are altered in aging. However, parsing out the exact signals responsible and their indirect effects in an intractable problem. Instead, we have the opportunity to take advantage of functional genomic approaches to identify the downstream regulators, such as TFs and enhancers, that lead to age-related dysregulation. In this proposal, we will use macrophages in the synovium of murine ankle joints and computational approaches to model an aging tissue. The synovial compartment largely consists of long-lived tissue-resident macrophages but the contribution of monocyte-derived cells that originate in the bone marrow increases with age. Our preliminary analysis of the age-associated epigenomic landscape of bone marrow monocytes revealed increased activity of chromatin remodelers and decreased activity of cell-type-specific TFs. Similarly, we observe a decrease in tissue-resident synovial macrophages in the aging joint and a shift in the transcriptional profile towards monocyte-derived macrophages. Thus, we hypothesize that the aging synovial macrophage phenotype is driven by replacement with monocyte-derived cells that fail to acquire tissue- resident regulators due to epigenomic reprogramming by the aging bone marrow micro-environment. In Aim 1, we will assess age-associated changes to the synovial macrophage compartment over time. We will perform ATAC-seq, ChIP-seq, and scRNA-seq on monocyte-derived and tissue-resident macrophages subpopulations to profile their epigenomic landscape across time. By a combination of clustering and supervised approaches, we will identify temporal patterns of epigenomic reprogramming and implicate specific TFs that drive aging in each subpopulation. In Aim 2, we will quantify the impact of cell intrinsic vs. bone marrow micro- environment on aging monocyte-derived macrophages. Through analysis of their epigenomic profile, we will identify key enhancers and TFs in their genomic context. Moreover, we will compare the results with additional chimeras where TNF, one of the key signals in the aging environment, and its receptors are blocked. Together, these aims will identify key downstream regulators that drive macrophage dysfunction in aging mice with the ultimate goal of translating of our findings to human patients. Our results will provide a better understanding of the aging immune system and potential targets for interventions that improve health in aging.

作为组织完整性的关键调控者，巨噬细胞与许多与年龄相关的疾病有关。巨噬 是一种可塑性骨髓免疫细胞类型，几乎存在于身体的每一个组织中，它们在这些组织中发挥关键作用。 保持体内平衡的功能组织驻留巨噬细胞适应执行特定的功能，通过行动 组织特异性转录因子（TF）对局部环境中的信号做出反应。结合 细胞类型特异性TF，它们指定了导致组织特异性基因表达的独特表观基因组景观。 由于全身炎症和衰老中的其他信号导致巨噬细胞环境的变化， 巨噬细胞功能下降。为了制定预防战略，我们需要更好地了解 巨噬细胞在衰老过程中是如何变化的然而，解析出负责的确切信号及其间接信号， 在一个棘手的问题的影响。相反，我们有机会利用功能性基因组 方法来确定下游调节，如TF和增强子，导致年龄相关的 失调在这个提议中，我们将使用小鼠踝关节滑膜中的巨噬细胞， 计算方法来模拟老化组织。滑膜室主要由长寿命的 组织驻留巨噬细胞，但来源于骨髓的单核细胞衍生细胞的贡献 随着年龄增长。我们对年龄相关的骨髓表观基因组景观的初步分析 单核细胞显示染色质重塑活性增加和细胞类型特异性TF活性降低。 同样，我们观察到在老化关节中组织驻留的滑膜巨噬细胞减少， 对单核细胞衍生的巨噬细胞的转录谱。因此，我们假设老化的滑膜 巨噬细胞表型是由不能获得组织的单核细胞衍生细胞替代驱动的， 由于老化的骨髓微环境的表观基因组重编程而导致的常驻调节因子。在 目的1，我们将评估滑膜巨噬细胞隔室随时间的年龄相关变化。我们将 对单核细胞衍生和组织驻留巨噬细胞进行ATAC-seq、ChIP-seq和scRNA-seq 亚群来描绘它们随时间的表观基因组景观。通过聚类和监督相结合， 方法，我们将确定表观基因组重编程的时间模式，并涉及特定的TF， 推动每个亚群的老龄化。在目标2中，我们将量化细胞内在与骨髓微- 环境对老化单核细胞衍生的巨噬细胞的影响。通过分析其表观基因组图谱，我们将 在其基因组环境中鉴定关键增强子和TF。此外，我们将比较结果与其他 嵌合体，其中TNF，衰老环境中的关键信号之一，及其受体被阻断。在一起， 这些目标将确定在衰老小鼠中驱动巨噬细胞功能障碍的关键下游调节因子， 最终目标是将我们的发现转化为人类患者。我们的结果将使我们更好地了解 衰老的免疫系统和改善衰老健康的干预措施的潜在目标。