Proteomic dynamics in endochondral ossification: insights from antler tip analysis

Background The antler primary growth center, located at the distal tip of the growing antler, comprises five consecutive tissue zones beneath the velvet skin. Because the outermost reserve mesenchyme contains blastema progenitor cells with multipotent differentiation capacity, antler regeneration recapitulates embryonic skeletal development through endochondral ossification (ECO). The molecular mechanisms governing cell fate decisions and tissue morphogenesis across these zones remain poorly understood. Methods We profiled the proteome of the sika deer ( Cervus nippon ) antler growth center across all five tissue zones using the Orbitrap Astral platform in data-independent acquisition (DIA) mode. Protein identification and quantification were performed with DIA-NN. Proteome dynamics were analyzed by integrating three complementary clustering approaches including weighted gene co-expression network analysis (WGCNA), Fuzzy C-means clustering, and monotonic feature selection. Differentially expressed proteins were annotated by gene ontology (GO) enrichment analysis. Transcriptomic data from the same tissue zones were reanalyzed to assess mRNA–protein concordance. Results A total of 8,173 proteins were identified across the five tissue zones, representing the most comprehensive proteomic coverage of the antler growth center. Clustering analyses resolved distinct protein expression modules corresponding to sequential ECO stages from mesenchymal proliferation in the reserve mesenchyme to cartilage mineralization in the innermost zone. Deep proteome coverage enabled detection of low-abundance chondrogenic transcription factors SOX9, SOX6, and RUNX3, whose spatial expression matched their known roles in chondrogenesis. At the protein level, the reserve mesenchyme co-expressed 11 embryonic and 23 mesenchymal stem cell markers, indicating that antler stem cells represented a unique mesenchymal stem cell (MSC) population possessing partial embryonic stem cell (ESC)-like features. Conclusions This study provides a spatially resolved proteomic atlas of the complete antler growth center and identifies key regulatory proteins at each stage of endochondral ossification. The findings offer new insights into progenitor cell characteristics, transcription factor activity, and protein dynamics during bone development, with potential relevance to bone repair and regenerative medicine.