Tissue Block-Resolved Spatiotemporal Transcriptomic Atlas of Human Fetal Brainstem Reveals Gene Modules and Paradigms Linked to Neurological Disorders

The brainstem serves as a critical structural and functional hub connecting cerebral and spinal regions, yet its gene regulatory dynamics during fetal development remain poorly characterized. This study employed RNA-seq to map spatiotemporal transcriptomes across 107 tissue blocks from 18 human fetal brainstems (gestational weeks 9-33). Weighted gene co-expression network analysis (WGCNA) identified 22 functionally annotated modules. We quantitatively assessed their spatiotemporal activity gradients across developmental stages and anatomical subdomains, systematically classifying genes with significant temporal trajectories by phase-specific signatures. Crucially, we validated expression patterns of neurodevelopmental disorder-associated genes (e.g., Parkinson's, ALS, schizophrenia) within fetal brainstem tissues. Our integrated approach constructs a developmental transcriptomic profile, revealing stage-specific regulatory networks and dynamic transcriptional trajectories governing ontogeny. This work advances understanding of brainstem development and provides a foundational resource for neurological disorder research. Overall design: RNA-seq profiling of 107 tissue blocks from distinct anatomical regions of 18 human fetal brainstem samples across gestational weeks 9 to 33.