Elucidating Neurodevelopmental Trajectories in Cancer with Topic Modeling: Revealing Persistent External Granule...

The cerebellar rhombic lip generates cerebellar progenitors and neurons that ultimately differentiate to comprise over half of all neurons in the adult human brain. Standard clustering approaches often fragment or miss rhombic lip progenitor populations entirely due to their transient nature, small size, and rapid state transitions, leaving fundamental questions unanswered about normal cerebellar development and how such processes may be hijacked in pediatric brain cancer. Medulloblastoma, the most common malignant pediatric brain tumor, affects approximately 500 children annually in the United States with overall survival rates varying dramatically by subgroup. Sonic hedgehog (SHH) medulloblastoma, comprising 25-30% of cases, arises from rhombic lip-derived granule neuron precursors (GNP) within the external granule layer (EGL) and has particularly poor outcomes in several subtypes (5-year survival ~41%). Using our topic modeling framework on over one million fetal cerebellar nuclei, we identify proliferative rhombic lip and EGL states that bifurcate into distinct glial and neuronal lineages through intermediate progenitors and capture a portion of the developmental spectrum form outer EGL (oEGL) proliferation through inner EGL (iEGL) differentiation. These developmental signatures (topics) persist in medulloblastoma, validating GNP origins of SHH tumors and revealing age-specific molecular programs that correspond to distinct stages of EGL development within SHH subtypes. Our transferable framework enables systematic comparison of developmental and disease states across technologies without data integration, solving a fundamental challenge as genomic atlases expand.