Is NF2 a Key Player of the Differentially Expressed Gene Between Spinal Cord Ependymoma and Intracranial Ependymoma?

Although intracranial and spinal ependymomas are histopathologically similar, the molecular landscape is heterogeneous. An urgent need exists to identify differences in the genomic profiles to tailor treatment strategies. In the present study, we delineated differential gene expression patterns between intracranial and spinal ependymomas. We searched the Gene Expression Omnibus database using the term “ependymoma” and analyzed the raw gene expression profiles of 292 ependymomas (31 spinal and 261 intracranial). The gene expression data were analyzed to find differentially expressed genes (DEGs) between 2 regions. The fold change (FC) and false discovery rate (FDR) were used to assess DEGs after gene integration (|log2FC|>2; FDR P < 0.01). Enrichment and pathway analysis was also performed. A total of 201 genes (105 upregulated and 96 downregulated) were significant DEGs in the data sets. The underexpression of NF2 in spinal ependymomas was statistically significant (FDR P = 7.91 × 10−9). However, the FC of NF2 did not exceed the cutoff value (log2FC, −1.2). The top 5 ranked upregulated genes were ARX, HOXC6, HOXA9, HOXA5, and HOXA3, which indicated that spinal ependymomas frequently demonstrate overexpression of HOX family genes, which play fundamental roles in specifying anterior/posterior body patterning. Moreover, the gene ontology enrichment analysis specified “anterior/posterior pattern specification” and “neuron migration” in spinal and intracranial ependymomas, respectively. The most substantial magnitude of DEGs in ependymoma might be HOX genes. However, whether the differential expression of these genes is the cause or consequence of the disease remains to be elucidated in a larger prospective study. •Differential expression of whole exome was evaluated between intracranial and spinal ependymoma using public datasets.•Although NF2 was known to a representative DEG, the magnitude of difference was relatively low (FC, −1.2; FDR P = 7.91×10−9).•Four of top 5 DEGs were HOX family genes among 201 DEGs with statistical significance (|log2FC| >2; FDR P < 0.01).•HOX family genes might have a key role in the clinical differences between intracranial and spinal ependymomas.