A molecular cell atlas of endocrine signaling in human neural organoids

Hormonal signaling regulates human neurodevelopment, yet its cell-type-specific effects and interactions remain poorly understood. Here, we generated a multi-omic atlas of endocrine signaling by chronically exposing developing human neural organoids to agonists and inhibitors of seven endocrine pathways: androgen, estrogen, glucocorticoid, thyroid, retinoic acid, liver X, and aryl hydrocarbon. Integrating bulk and single-cell transcriptomics, high-throughput imaging, and targeted steroidomics, we mapped endocrine responses across molecular, cellular, and morphological scales. Retinoic acid signaling had the strongest impact, promoting caudalization, neuronal maturation, and altered organoid architecture. Across pathways, androgen activation and inhibition of glucocorticoid, thyroid, and liver X signaling converged on shared gene modules involved in lipid metabolism, proteostasis, and epigenetic regulation. Single-cell analyses identified cell-type-specific endocrine responses and hormone-associated developmental states, while steroidomics revealed pathway-dependent remodeling of steroid metabolism. Together, these data establish a reference atlas for investigating endocrine disorders, developmental neurotoxicity, and environmental endocrine disruption.