Differential Gene Expression and Pathway Analysis of Radiation-Induced Meningiomas

Background Radiation-induced meningiomas (RIMs), a long-term sequela of cranial radiation therapy, are often clinically more aggressive and develop as multiple distinct tumors. Biologically, RIMs have been shown to have a distinct genomic landscape compared with their sporadic counterparts. Notably, RIMs have a lower frequency of NF2 mutations and absence of mutations in TRAF7, KLF4, PIK3CA, and SMO, which are commonly observed in sporadic meningiomas. A subset of RIMs has large genomic rearrangements resulting in NF2 inactivation through a fusion event with a reciprocal gene. We aimed to compare and contrast the clinical and biological profiles of RIMs with and without the NF2-fusion event.

Methods A comprehensive clinical database of 50 RIMs was created. Seven RIMs with NF2 fusion and 12 RIMs with wild-type NF2 underwent RNA sequencing on the Illumina HiSeq platform. RNA-seq expression profiles were analyzed using edgeR, available through BioConductor, and Gene Set Enrichment Analysis was performed using Cytoscape. Differential gene expression presented as log2 of fold change (logFC). Immunohistochemistry (IHC) was performed on formalin-fixed paraffin-embedded tissue samples to validate differentially expressed genes identified in pathway analysis.

Results IGF-1 (logFC = 4.14, p = 2.65E-05), MME (logFC = 3.03, p = 3.56E-03), MMP16 (logFC = 2.47, p = 8.14E-03), and AQP1 (logFC = 2.33, p = 1.19E-03) were among the top genes overexpressed in RIMs with NF2 fusion. Pathway analysis from gene expression data identified increased activity of immune and inflammatory pathways. IHC staining identified decreased expression of PD-L1 in NF2-fusion RIMs compared with NF2 wild-type RIMs (10 vs. 45%). In contrast, CCL2 had increased expression in NF2-fusion RIMs (60 vs. 10%). Imaging analysis also demonstrated a 3.8× faster growth rate in NF2-fusion RIMs compared with NF2 wild type.

Conclusion RIMs with the NF2-fusion event have a distinct gene expression profile, with upregulation of inflammatory pathways. Possibly, the increased inflammatory activity in NF2-fusion RIMs may play a role in growth rate and aggressiveness of tumor. Further studies need to be performed to validate these findings using immunohistochemistry.