Single-nucleus RNA sequencing reveals molecular determinants of functional and physiological differences between extraocular and quadriceps muscles in Macaca fascicularis.

Extraocular muscles (EOM) display distinct physiological and pathological characteristics compared with limb skeletal muscles. To define the molecular basis of these differences, we performed single-nucleus RNA sequencing on EOM and quadriceps femoris muscle (QFM) from Macaca fascicularis. Transcriptomic profiling revealed distinct cell type compositions, with EOM enriched in fast-twitch fibers (2 A/2×), fibro-adipogenic progenitors, and neural-associated cells. EOM myonuclei expressed genes involved in synaptic transmission and axon development, whereas QFM myofibers were enriched for oxidative phosphorylation and glycolysis pathways. EOM uniquely expressed diverse myosin isoforms, including MYH13 and MYH4, supporting specialized contractile function. Disease-associated genes showed differential expression between the two muscle types, suggesting distinct susceptibilities. Intercellular communication analysis further revealed neuromuscular and regenerative signaling dominance in EOM, contrasting with immune and metabolic signaling in QFM. Together, these findings provide a comprehensive molecular framework for understanding EOM specialization and disease vulnerability.