Multi-omics integration analysis reveals metabolic changes during sika deer antler growth

Antler is an important economic trait of sika deer (Cervus nippon), capable of rapid growth without signs of tumorigenesis. However, the molecular mechanisms underlying its unique growth pattern remain poorly understood. This study conducted a combined transcriptomic, proteomic, metabolomic and single-cell transcriptomic analysis of tip mesenchyme of antler at three key growth stages, early, middle, and late growth (EG, MG, LG), to explore the molecular characteristics during antler growth. Active post-transcriptional and post-translational regulation likely occurred during antler growth, as characterized by significant alternative splicing (AS) events and significant enrichment of post-transcriptional and post-translational regulatory functions at the protein level. The multi-level regulatory network constructed based on differentially expressed genes, proteins, and metabolites (DEGs, DEPs, DEMs) indicated continuous and extensive metabolic reprogramming in the glycerophospholipid metabolism pathway. PLA2G3, MBOAT2, LPCAT3, DGKI, and EPT1 were positioned at core nodes within this pathway. The qRT-PCR confirmed that these genes were predominantly expressed in MG, suggesting their role as crucial candidate genes involved in regulating the metabolic reprogramming. Analysis of single-cell transcriptomic data revealed that the MBOAT2, LPCAT3, DGKI, and EPT1 genes were expressed in key cell types such as chondroblasts, chondrocytes, osteoblasts, and mesenchymal cells. Integrated multi-omics analyses indicated that the rapid growth of antlers is closely associated with continuous metabolic reprogramming, involving multi-layered regulation of glycerophospholipid metabolism. This study established a foundational multi-omics resource, providing new perspectives for elucidating the molecular mechanisms of antler growth and for subsequent functional studies, while also offering novel insights for research on organ and tissue growth in animals.