Multiplatform Molecular Profiling of Vestibular Schwannoma Reveals Immune Enrichment after Radiosurgery and a Methylation-Based Predictor of Recurrence

Abstract

Vestibular schwannomas (VS) can cause significant morbidity from cranial nerve deficits and mass effect. Broad molecular differences have been described for intracranial versus spinal axis schwannomas, but little is known about the molecular heterogeneity of VS or predictors of VS recurrence. The objective of this study was to understand VS biology and identify molecular predictors of VS recurrence. Sixty-six sporadic VS from 59 consecutive patients with available tissue who underwent initial resection (44), resection for recurrence after prior surgery (5), resection for recurrence after prior stereotactic radiosurgery (SRS) (11), or resection after both prior surgery and prior SRS (6) at a single institution from 2003-2017 were profiled using Illumina 850K DNA methylation arrays (median follow-up: 4.2 years, median volumetric resection: 91%). Twenty-four VS were further characterized using RNA sequencing (RNA-seq), and 7 were analyzed by single nuclei RNA-seq. Molecular subtyping was performed by hierarchical clustering of differentially-methylated DNA probes and validated using transcriptomic data. In vitro functional experiments were performed using human VS cells. Clustering of genome-wide DNA methylation probes revealed that VS are comprised of 2 subgroups that are delineated by enrichment of neural crest or immune genes. Fifteen of 35 immune-enriched VS (43%) had prior SRS, while only 2 of 31 neural crest-enriched VS (6%) had prior SRS (p<0.001). Analysis of 6 patients with matched primary and recurrent VS samples revealed that all recurrent VS after prior SRS exhibited similar methylation profiles and were enriched in immune genes. In contrast, the methylation profile of VS that recurred after prior surgery did not deviate from the primary tumor. Hypomethylation of G protein-coupled estrogen receptor 1 (GPER) promoter was prognostic for local failure in multivariate regression irrespective of primary treatment modality (p<0.0001). Radiation of VS cells in vitro recapitulated gene expression of immune-enriched VS. VS are comprised of 2 molecular subgroups characterized by differential enrichment of neural crest or immune genes. VS with prior SRS are associated with immune-enrichment. GPER promoter hypomethylation is prognostic for VS recurrence. These data illuminate the biology of VS and shed light on potential molecular therapies.