Application of single-cell RNA sequencing in bone regeneration

doi:10.3969/j.issn.1674-8115.2025.08.013

Abstract

Abstract:

Bone regeneration is pivotal for restoring bone homeostasis, involving the coordinated collaboration of diverse cell types in a complex and heterogeneous process. Elucidating the molecular mechanisms at each stage to develop novel bone regeneration strategies represents a key direction in this field. Traditional high-throughput sequencing examines bulk transcriptomes, losing cellular-level resolution. Single-cell RNA sequencing (scRNA-seq) technology enables the analysis of subpopulation heterogeneity by revealing RNA expression profiles at the single-cell level. Based on single-cell atlases, researchers can further employ specific algorithms to simulate cellular differentiation trajectories, facilitating more profound mechanistic investigations. Utilizing this technology, critical cell subpopulations involved in long bone and craniofacial bone regeneration have been identified, characteristic cellular markers and potential diagnostic indicators have been defined, regenerative differences under inflammatory or aging conditions have been compared, the osteogenic mechanisms involved in guided bone regeneration procedures have been explored, and the differential bone-promoting effects of various biomaterials have been revealed. This review summarizes the applications of scRNA-seq in long bone and craniofacial bone regeneration, as well as in bone tissue engineering. It highlights its contributions in deciphering cellular heterogeneity, gene regulation, and microenvironmental interactions, consolidates key cell subpopulations and their functions identified through sequencing, and discusses current research limitations. Furthermore, it outlines future prospects for this technology in bone regeneration research, offering new perspectives for subsequent studies.

Key words: single-cell RNA sequencing, bone regeneration, craniofacial bones, bone tissue engineering

CLC Number:

HUANG Zihan, HUANG Xinzhi. Application of single-cell RNA sequencing in bone regeneration[J]. Journal of Shanghai Jiao Tong University (Medical Science), 2025, 45(8): 1053-1058.

Figures/Tables 1

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References 36

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Cell type	Key subpopulation	Location	Species	Feature	Reference
Immune cell	B cell	Hip callus	Human	Promote early-stage osteogenesis while inhibiting excessive bone formation in later stages	^[6]
	CD14⁺ dentritic cell	Hip callus	Human	Potential biomarkers of bone nonunion	^[8]
	M2 macrophage	Cranial periosteum	Swine	Secrete neuregulin-1 to recruit periosteal stromal cells	^[18]
Skeletal stem/progenitor cell	Inhba⁺progenitor cell	Femoral callus	Mouse	Promote SMAD2 phosphorylation, enhance progenitor cell proliferation and differentiation	^[10]
	CD168⁺skeletal stem cell	Femoral callus	Mouse	Osteogenic and chondrogenic differentiation	^[11]
	Ctsk⁺periosteal progenitor cell	Femoral callus	Mouse	Mechanosentive; chondrogenic differentiation	^[12]
	Sox9⁺progenitor cell	Cranial periosteum	Mouse	Osteogenic differentiation	^[19]
	Mkx⁺cell	Cranial suture	Mouse	Mechanosentive; osteogenic differentiation	^[20]
	Prrx1⁺cell	Mandibular callus	Canine	Mechanosentive; osteogenic differentiation	^[22]
	Krt14⁺Ctsk⁺cell	Maxillary sinus mucosa	Mouse	Co-expression of epithelial and mesenchymal characteristics	^[24]
	Ctsk⁺Ly6a⁺cell	Mandibular of bone marrow	Mouse	Osteogenic differentiation	^[28]
	Fat4⁺cell	Alveolar bone	Mouse	Osteogenic differentiation	^[29]
Skeletal muscle stem cell	Prrx1⁺Skeletal muscle stem cell	Femoral callus	Mouse	Promote fibrous tissue aggregation, leading to nonunion	^[13]

Cell type	Key subpopulation	Location	Species	Feature	Reference
Immune cell	B cell	Hip callus	Human	Promote early-stage osteogenesis while inhibiting excessive bone formation in later stages	^[6]
	CD14⁺ dentritic cell	Hip callus	Human	Potential biomarkers of bone nonunion	^[8]
	M2 macrophage	Cranial periosteum	Swine	Secrete neuregulin-1 to recruit periosteal stromal cells	^[18]
Skeletal stem/progenitor cell	Inhba⁺progenitor cell	Femoral callus	Mouse	Promote SMAD2 phosphorylation, enhance progenitor cell proliferation and differentiation	^[10]
	CD168⁺skeletal stem cell	Femoral callus	Mouse	Osteogenic and chondrogenic differentiation	^[11]
	Ctsk⁺periosteal progenitor cell	Femoral callus	Mouse	Mechanosentive; chondrogenic differentiation	^[12]
	Sox9⁺progenitor cell	Cranial periosteum	Mouse	Osteogenic differentiation	^[19]
	Mkx⁺cell	Cranial suture	Mouse	Mechanosentive; osteogenic differentiation	^[20]
	Prrx1⁺cell	Mandibular callus	Canine	Mechanosentive; osteogenic differentiation	^[22]
	Krt14⁺Ctsk⁺cell	Maxillary sinus mucosa	Mouse	Co-expression of epithelial and mesenchymal characteristics	^[24]
	Ctsk⁺Ly6a⁺cell	Mandibular of bone marrow	Mouse	Osteogenic differentiation	^[28]
	Fat4⁺cell	Alveolar bone	Mouse	Osteogenic differentiation	^[29]
Skeletal muscle stem cell	Prrx1⁺Skeletal muscle stem cell	Femoral callus	Mouse	Promote fibrous tissue aggregation, leading to nonunion	^[13]