Temporal transcriptomics of human 3D neuromuscular cultures reveal key signatures of neuromuscular junction development

The principal organization of mammalian neuromuscular junctions (NMJs) shares essential features across species, yet human NMJs (hNMJs) exhibit distinct structural and physiological properties. While recent advances in stem cell-based systems have significantly improved in vitro modeling of hNMJs, the extent to which these models recapitulate in vivo development remains unclear. Here, we performed spatial transcriptomic analysis of human 3D neuromuscular co-cultures, composed of iPSC-derived motoneurons and 3D skeletal muscle engineered from primary myoblasts. We found the transcriptomic analysis follows a temporally coordinated gene expression program underlying NMJ maturation. The model recapitulates key transcriptional features of NMJ development, including early myoblast fusion, sequential upregulation of presynaptic and postsynaptic maturation genes, and late-stage induction of embryonic AChR subunits. Importantly, consistent transcriptional dynamics across two independent hiPSC lines and differentiation protocols confirm the reproducibility and robustness of this system. This study provides a valuable transcriptomic resource and demonstrates that human 3D neuromuscular co-cultures are a robust and physiologically relevant model for investigating human NMJ development, function, and disease. Overall design: This project aims to perform Bulk RNA sequencing from two different lines of 3D Neuromuscular Co-culture at various time points required to establish mature NMJs.