Proteomic insights into myogenic progression in cultured muscle cells of Lates calcarifer (Bloch, 1790)

Muscle cell lines serve as valuable models for investigating mechanisms underlying muscle proliferation and differentiation. This study aimed to characterize proteomic changes during passage progression in a muscle cell line derived from Lates calcarifer. Comparative proteomic analysis was performed between Passage 3 (P3) and Passage 20 (P20) using label-free LC–MS/MS. Data were processed using MaxQuant, and proteins were identified against the Lates calcarifer UniProt database using the Andromeda search engine. Proteins identified with more than two unique peptides (454 proteins) were used for expression analysis. To further support these findings, immunocytochemistry was conducted to assess the expression of myogenic proteins MyoD and PAX7 at both passages. A total of 454 proteins were identified across two different passages. Hierarchical clustering of the top 25 differentially expressed proteins (fold change ≥1.5) revealed distinct expression patterns. The volcano plot highlighted key proteins, including Peroxiredoxin-1, Filamin A, Fructose-bisphosphate aldolase, and a non-selective voltage-gated ion channel. Gene ontology analysis showed enrichment of lyase activity in P3, whereas P20 proteins were associated with carbon metabolism. Protein-protein interaction analysis revealed networks related to ribosomal structure, translation, protein processing in the endoplasmic reticulum, oxidative phosphorylation, and metabolic pathways. Immunocytochemistry showed more Pax7 immunolabeled cells in P3 and more MyoD immunolabeled cells in P20. This study provides the first proteomic profile of Lates calcarifer SBM cells, highlighting molecular changes associated with the transition from proliferation to differentiation and offering a foundation for future in vitro studies.