EPCO-60. Expression of Early Progenitor Markers Within Nf2-Associated Spinal Ependymoma

Abstract

Spinal ependymomas (SP-EPNs) are intramedullary spinal tumors commonly found in patients with NF2-related schwannomatosis. Recent work using bulkRNA sequencing has suggested that SP-EPNs express a molecular signature most similar to ependymal cells. However, this type of sequencing may miss rare stem cell populations within tumors. The aim of this study was to assess the spatial heterogeneity within NF2-associated SP-EPNs and explore whether a stem cell population exists within SP-EPNs. Spatial transcriptomics (ST) was performed on a SP-EPN sample previously resected from a patient with NF2-related schwannomatosis using the 10X Genomics Visium Cytassist Platform. Libraries were sequenced on the Illumina NovaSeq 6000. 28-bp reads including spatial barcode and UMI sequences and 50-bp probe reads were generated with Illumina NovaSeq 6000 at the Center for Medical Genomics at Indiana University School of Medicine. Space Ranger 2.1 was used to process the raw files after sequencing. Data analysis was performed with R package Seurat 4.9.9.9041 following preprocessing with spaceranger. Sctransform normalized the spatial transcriptome dataset. Clusters were identified using “FindClusters” and “FindNeighbors” functions. There was diffuse expression of astrocyte and ependymal cell markers throughout the SP-EPN sample with smaller areas expressing radial glia and stem cell markers, as well as overlap between these regions. Expression of vascular and connective tissue markers varied throughout the tumor. There was minimal to no expression of neural genes in the sample. ST on our SP-EPN sample revealed a tumor with marked cellular and molecular heterogeneity. Although the primarily expressed ependymal cell and astrocyte markers, there does appear to be small, stem cell-like populations. This suggests that NF2-associated SP-EPNs may have a developmental hierarchy with radial glia-like cells and more mature progenitors within the ependymal cell lineage. This proof-of-concept study offers important findings that provide justification for further investigation using single-cell sequencing.