Integrative Single-Cell RNA-Seq and ATAC-Seq Identifies Transcriptional and Epigenetic Blueprint Guiding Osteoclastogenic Trajectory

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 ChIP-seq, to comprehensively define the regulatory landscape of osteoclastogenesis in wild-type (WT) and Irf8 conditional knockout (cKO) mice. We uncovered a highly structured and sequential differentiation trajectory from hematopoietic stem and progenitor cells (HSPCs) 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 toward 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.

Keywords: ChIP-seq; IRF8; chromatin accessibility; monocytes; osteoclasts; single cell RNA-seq; single-cell ATAC-seq; transcriptional regulation.