Amitabh Das, Keita Saeki, Stefania Dell'Orso, Xiaobei Wang, Kim C Mansky, Joseph Stains, Keiko Ozato, Hong-Wen Deng, Vivek Thumbigere-Math
{"title":"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。","authors":"Amitabh Das, Keita Saeki, Stefania Dell'Orso, Xiaobei Wang, Kim C Mansky, Joseph Stains, Keiko Ozato, Hong-Wen Deng, Vivek Thumbigere-Math","doi":"10.1093/jbmr/zjaf084","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":185,"journal":{"name":"Journal of Bone and Mineral Research","volume":" ","pages":"1127-1143"},"PeriodicalIF":5.9000,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Integrative single-cell RNA-seq and ATAC-seq identifies transcriptional and epigenetic blueprint guiding osteoclastogenic trajectory.\",\"authors\":\"Amitabh Das, Keita Saeki, Stefania Dell'Orso, Xiaobei Wang, Kim C Mansky, Joseph Stains, Keiko Ozato, Hong-Wen Deng, Vivek Thumbigere-Math\",\"doi\":\"10.1093/jbmr/zjaf084\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>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.</p>\",\"PeriodicalId\":185,\"journal\":{\"name\":\"Journal of Bone and Mineral Research\",\"volume\":\" \",\"pages\":\"1127-1143\"},\"PeriodicalIF\":5.9000,\"publicationDate\":\"2025-09-28\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Bone and Mineral Research\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1093/jbmr/zjaf084\",\"RegionNum\":1,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"ENDOCRINOLOGY & METABOLISM\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Bone and Mineral Research","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1093/jbmr/zjaf084","RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"ENDOCRINOLOGY & METABOLISM","Score":null,"Total":0}
Integrative single-cell RNA-seq and ATAC-seq identifies transcriptional and epigenetic blueprint guiding osteoclastogenic trajectory.
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.
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.