Genomic Landscape of Intramedullary Spinal Cord Gliomas

Abstract

Intramedullary spinal cord tumors (IMSCTs) are rare neoplasms that have limited treatment options and are associated with high rates of morbidity and mortality. To better understand the genetic basis of these tumors we performed whole exome sequencing on 45 tumors and matched germline DNA, including twenty-nine spinal cord ependymomas and sixteen astrocytomas. Though recurrent somatic mutations in IMSCTs were rare, we identified NF2 mutations in 15.7% of tumors (ependymoma, N = 7; astrocytoma, N = 1), RP1 mutations in 5.9% of tumors (ependymoma, N = 3), and ESX1 mutations in 5.9% of tumors (ependymoma, N = 3). We further identified copy number amplifications in CTU1 in 25% of myxopapillary ependymomas. Given the paucity of somatic driver mutations, we further performed whole-genome sequencing of 12 tumors (ependymoma, N = 9; astrocytoma, N = 3). Overall, we observed that IMSCTs with intracranial histologic counterparts (e.g. glioblastoma) did not harbor the canonical mutations associated with their intracranial counterparts. Our findings suggest that the origin of IMSCTs may be distinct from tumors arising within other compartments of the central nervous system and provides the framework to begin more biologically based therapeutic strategies.

Figure 1

Whole exome mutational burden of intramedullary spinal cord tumors. (A) astrocytic tumors, (B) ependymomas. One subependymoma was discovered to harbor 315 unique somatic mutations and was held out from this analysis. Unpaired t-test was used to test for significance between high-grade gliomas (HGG) and low-grade gliomas (LGG). ANOVA was used to test for significance between ependymoma subtypes. SNVs, single-nucleotide variants. GBM, glioblastoma. AA, anaplastic astrocytoma. LG2, Grade II glioma. PA, pilocytic astrocytoma. Classic, classic ependymoma. MPE, myxopapillary ependymoma. SE, subependymoma.

Figure 2

Heatmap depicting recurrent mutations and clinicopathologic correlates of IMSCT. NA, not available.

Figure 3

Circos plots depicting structural variants in 12 IMSCT selected for WGS and one brain stem glioma with recurrence in the cervical spine. PA, pilocytic astrocytoma. LG2, Grade II glioma.