Integrated Transcriptomic-Proteomic Profiling Identifies Candidate Regulators of Stemness Maintenance in Skeletal Muscle Satellite Cells

Abstract Cultured meat is recognized as a sustainable alternative to animal products, but the gradual stemness loss in seed cells during in vitro culture remains a challenge for industrialization. Here, we isolated chicken embryonic skeletal muscle satellite cells and observed a pronounced decline in stemness following the third passage. Whole-transcriptome and proteome analyses, combined with weighted gene coexpression network analysis (WGCNA) and short time-series expression miner (STEM) trend analysis, identified passage-dependent molecular changes associated with proliferative and differentiation capacities. Five transcriptional and eight protein modules were significantly correlated with stemness, and 31 hub genes were enriched mainly in ECM-receptor interaction and PI3K-Akt pathways. Notably, THBS1 and LAMA5 consistently showed high connectivity and were detected at both RNA and protein levels, thereby being prioritized as core candidate regulators. Our findings offer insights into stemness-associated regulators that could contribute to enhancing stemness maintenance and optimizing long-term cultured meat production.