Integrative single-cell RNA-seq and ATAC-seq identifies transcriptional and epigenetic blueprint guiding osteoclastogenic trajectory.

IF 5.9 1区 医学 Q1 ENDOCRINOLOGY & METABOLISM
Amitabh Das, Keita Saeki, Stefania Dell'Orso, Xiaobei Wang, Kim C Mansky, Joseph Stains, Keiko Ozato, Hong-Wen Deng, Vivek Thumbigere-Math
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引用次数: 0

Abstract

Osteoclasts (OCs) are multinucleated bone resorbing cells essential for skeletal development and remodeling. In adulthood, OCs originate from the serial fusion of monocytes, yet the transcriptional and epigenetic mechanisms shaping their osteoclastogenic potential at a single-cell resolution remain poorly understood. Here, we present an integrative multi-omics analysis, combining single-cell (sc) RNA-seq, scATAC-seq, bulk RNA-seq, and Chromatin Immunoprecipitation (ChIP)-seq, to comprehensively define the regulatory landscape of osteoclastogenesis in WT and interferon regulatory factor 8 (IRF8) conditional KO mice. We uncovered a highly structured and sequential differentiation trajectory from hematopoietic stem and progenitor cells to common monocyte progenitors (cMoPs) to mature monocytes, with each stage exhibiting distinct transcriptional and epigenetic signatures. cMoPs and monocytes are the critical stages when OC lineage priming occurs, characterized by transcriptional and epigenetic activation of cytoskeletal, immune, and cell migration pathways. This priming is tightly regulated to prevent premature OC differentiation and IRF8 acts as a negative regulator of osteoclastogenesis by maintaining monocyte identity and restricting chromatin accessibility at osteoclastogenic loci. IRF8 deficiency disrupts this balance, leading to chromatin reprogramming characterized by increased accessibility at OC-promoting loci (Nfatc1, Cebpe) and reduced accessibility at monocyte-specific genes (Mafb, Klf4), thereby priming precursors towards pre-mature osteoclastogenesis. Just as NFATc1 is recognized as a master activator of osteoclastogenesis, our findings position IRF8 as a master negative regulator of osteoclastogenesis, maintaining the delicate balance required for proper bone homeostasis. Collectively, this study provides unprecedented resolution into the molecular mechanisms shaping OC precursor identity and offers novel insights into potential therapeutic targets for osteolytic disorders.

综合单细胞RNA-Seq和ATAC-Seq鉴定指导破骨细胞生成轨迹的转录和表观遗传蓝图。
破骨细胞(OCs)是一种多核骨吸收细胞,对骨骼发育和重塑至关重要。在成年期,OCs起源于单核细胞的一系列融合,然而在单细胞分辨率下形成其破骨细胞潜能的转录和表观遗传机制仍然知之甚少。在这里,我们提出了一个综合多组学分析,结合单细胞(sc) RNA-seq, scATAC-seq,散装RNA-seq和ChIP-seq,全面定义野生型(WT)和Irf8条件敲除(cKO)小鼠破骨细胞发生的调控环境。我们发现了从造血干细胞和祖细胞(HSPCs)到普通单核细胞祖细胞(cops)再到成熟单核细胞的高度结构化和顺序分化轨迹,每个阶段都表现出不同的转录和表观遗传特征。cops和单核细胞是OC谱系启动的关键阶段,其特征是细胞骨架、免疫和细胞迁移途径的转录和表观遗传激活。这种启动受到严格调控,以防止OC过早分化,IRF8通过维持单核细胞身份和限制破骨细胞形成位点的染色质可及性,作为破骨细胞发生的负调节因子。IRF8缺乏破坏了这种平衡,导致染色质重编程,其特征是oc促进位点(Nfatc1, Cebpe)的可及性增加,而单核细胞特异性基因(Mafb, Klf4)的可及性降低,从而引发了成熟的破骨细胞发生的前体。正如NFATc1被认为是破骨细胞生成的主要激活因子一样,我们的研究结果将IRF8定位为破骨细胞生成的主要负调节因子,维持适当的骨稳态所需的微妙平衡。总的来说,这项研究为形成OC前体身份的分子机制提供了前所未有的解决方案,并为溶骨疾病的潜在治疗靶点提供了新的见解。
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来源期刊
Journal of Bone and Mineral Research
Journal of Bone and Mineral Research 医学-内分泌学与代谢
CiteScore
11.30
自引率
6.50%
发文量
257
审稿时长
2 months
期刊介绍: The Journal of Bone and Mineral Research (JBMR) publishes highly impactful original manuscripts, reviews, and special articles on basic, translational and clinical investigations relevant to the musculoskeletal system and mineral metabolism. Specifically, the journal is interested in original research on the biology and physiology of skeletal tissues, interdisciplinary research spanning the musculoskeletal and other systems, including but not limited to immunology, hematology, energy metabolism, cancer biology, and neurology, and systems biology topics using large scale “-omics” approaches. The journal welcomes clinical research on the pathophysiology, treatment and prevention of osteoporosis and fractures, as well as sarcopenia, disorders of bone and mineral metabolism, and rare or genetically determined bone diseases.
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