Lineage and Organ Signals Sequentially Build Organ Intrinsic Nervous Systems [scRNA-seq]

Organ intrinsic nervous systems (OINSs) are critical components of the body–brain axis, coordinating visceral organ function with systemic physiological control. Despite their importance, how these distinct neural architectures arise from a common neural crest cell (NCC) origin has remained unclear. Here, we present a systems-level, cross-organ analysis of OINS development, integrating lineage tracing, 3D imaging, single-cell transcriptomics, and genetic perturbations across heart, pancreas, intestine, and lungs. We show that differences in NCC migratory trajectories prefigure the spatial architecture of OINSs, laying the foundation for organ-specific patterning. In contrast, molecular identity emerges largely in response to local environments, indicating that extrinsic cues play a major instructive role. Using in vitro co-cultures, we demonstrate that organ-derived cues reprogram intrinsic neurons toward organ-specific transcriptional profiles and direct neuronal differentiation, with extracellular matrix (ECM) contact identified as a central mediator. In vivo, ECM–integrin signaling supports intrinsic cardiac neuron neurogenesis, while ECM crosslinking stabilizes their stereotyped ganglionic organization. Together, these findings reveal that OINS diversity arises through a dual logic: lineage programs prefigure spatial frameworks, while organ-specific cues instruct final molecular identities and architectural precision. This work establishes a conceptual paradigm for how organs actively build their own nervous systems, illuminating principles that underpin body–brain integration.