Single-cell RNA-Seq and ATAC-Seq profiling identifies NTN5+LSAMP+ myoblasts impairing embryonic myogenesis

Prenatal myogenesis plays a crucial role in determining postnatal muscle function and mass, representing a pivotal period for understanding developmental myopathies and improving agricultural productivity. Here, we integrate single-cell transcriptomic and chromatin accessibility profiling to reveal the regulatory differences between developmental retardation and normal porcine embryonic somites. We identify a pathogenic NTN5+LSAMP+ myoblast subpopulation enriched in growth-retarded embryos, which exhibits a cell-autonomous blockade of differentiation through co-express LSAMP (Limbic System Associated Membrane Protein) and NTN5 (Netrin 5). This arrest is further reinforced by epigenetic and metabolic dysregulation: sustained chromatin accessibility at the cytoskeletal regulator TPM3 (Tropomyosin 3), suppression of the muscle-specific actin depolymerization factor CFL2 (Cofilin 2), and impaired glycolytic flux. Inhibition of the Hippo/TGF-β signaling pathway and dysregulated ligand-receptor interactions exacerbate the differentiation arrest. Our study constructs a multi-omics regulatory network that describes abnormal early embryonic myogenesis, highlighting NTN5 and LSAMP as key regulators of porcine skeletal muscle development during embryogenesis, offering novel targets to rescue myogenesis in fetal growth disorders and livestock breeding.