Spatial Transcriptomics of Spinal Ependymoma in NF2-related Schwannomatosis

Abstract

Spinal ependymoma (SP-EPN) is a central nervous system (CNS) tumor that is associated with high morbidity. The only effective treatment for end-stage SP-EPN is surgery, but this is associated with high risk of injury to the sensorimotor spinal tracts and paralysis. There is a critical need to understand the cellular origins of this tumor so that disease models of tumor progression can be generated for drug development. Recent genomic studies with bulkRNA sequencing suggest the molecular signature of SP-EPN matches that of ependymal cells (EPCs). However, large-scale genomic studies can often misrepresent rare cancer stem cell populations within the tumor. In this study, we performed spatial transcriptomics (ST) on a SP-EPN resected from a patient with NF2-related neurofibromatosis to examine the spatial heterogeneity within the tumor. The SP-EPN sample exhibited cellular heterogeneity with diffuse expression of astrocytic and EPC markers, and smaller pockets with RGC or stem cell markers, as well as overlap between progenitor cell and mature cell markers. These findings suggest that there may be a developmental hierarchy within the EPC lineage in SP-EPN tumors, which may stem from aberrant radial glia cells.