Abstract

Background: Meningiomas are the most common primary intracranial tumours that arise from arachnoid cap cells of the meninges and dura border cells. These tumours share a unique epigenetic and genomic landscape. The most common epigenetic event in meningiomas is the loss of chromosome 22q. About 50% of meningiomas harbour mutations in the NF2 gene that resides on chromosome 22 and codes for a protein named “Merlin”. Moreover, frequent mutations can be observed in genes including AKT1, KLF4, TRAF7, SMO, and PIK3CA. Based on mutations, meningiomas can be divided into different genomic subgroups that express unique proteomic profiles. Project aim: This project aimed to investigate the different molecular backgrounds of meningiomas and to determine the impact of gene mutations on underlying downstream processes. In addition, this study sought to integrate epigenetic, genomic, and proteomic profiles of NF2-/- meningioma subgroups to identify distinct molecular features. Furthermore, the study aimed to validate selected upregulated targets in NF2-/- and KLF4K409Q/TRAF7 mutant tumours and assess their functional role on cellular proliferation. Methods and materials: A total of 118 meningioma samples were sequenced using the Illumina TruSight Oncology 500 panel. Raw sequence data was analysed using TruSight Oncology 500 Local App and was annotated using online servers named CGI and ANNOVAR. The obtained genomic information was utilised for clinical enrichment analysis using maftools and oncoEnrichR. To identify molecular heterogeneity in NF2-/- clusters, genomic profiles were correlated with protein expression data, and results were analysed. Furthermore, this study validated upregulated targets in KLF4K409Q/TRAF7 mutant meningiomas using the Parallel Reaction Monitoring (PRM) technique, which is an antibody-independent mass spectrometry-based protein quantification method. Moreover, the study focused on the specific upregulated target ANXA3 in NF2-/- meningiomas. To explore its functional role on tumour proliferation, ANXA3 was knocked down in both low-grade as well as high-grade meningiomas using a lentivirus shRNA knockdown system. ANXA3 was knocked down in meningioma cell lines and primary cells to investigate its functional impact on cellular proliferation. The effect was further assessed by NCH93 GFP-LUC2 NF2-/- cells transplantation in an NOD scid gamma (NSG) immunodeficient mouse model. The link between ANXA3 and tumour proliferation was assessed by validating the expression of the MCM2 marker and EdU proliferation assay. Results: The study identified an average of 1161 total mutations and 7 driver mutations per sample. The top 5 driver genes observed in the study cohort were NF2 (56%), followed by TRAF7 (15%), AKT1 (12%), APC (10%) and FAT1 (9%). AKT1 and KLF4 mutations significantly co-occurred with TRAF7 mutations and were mutually exclusive of NF2 mutations, as described in previous studies. Also, our study identified co-occurring mutations such as ATM-BIVM-ERCC5, PIK3C2B-SDHD, and ERCC4-MET. Intriguingly, the integration of genomics and proteomics data of NF2-/- clusters revealed completely different mutational landscapes as well as molecular functions associated with each NF2-/- cluster, suggesting tumour heterogeneity in NF2-/- meningiomas. Moreover, samples from both clusters showed distinct histological subtypes, where most of the cluster 1 samples were of the fibrous subtype and all cluster 2 tumours were psammomatous. Additionally, NF2-/- associated ANXA3 showed significant association with cell proliferation in both ex vivo and in vivo studies using immortalised meningiomas cells. Conclusion: The study identified common and unique driver mutations in meningioma samples that were not previously reported. The identified results could help in selecting effective personalised treatments for specific genomic groups of patients. Moreover, the study revealed upregulation of Annexin-3, impacting cell proliferation. These findings offer ANXA3 as a potential target for personalised treatments in patients with NF2-/- meningioma.

Awarding Institution(s)

University of Plymouth

Supervisor

Oliver Hanemann, Matt Banton, Vikram Sharma, Claire Adams

Keywords

NF2, ANXA3, AKT1, KLF4, TRAF7, Meningioma

Document Type

Thesis

Publication Date

2026

Embargo Period

2026-03-31

Deposit Date

March 2026

Creative Commons License

Creative Commons Attribution-NonCommercial 4.0 International License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License

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