Proteomic Insights Into Anaplastic Meningioma Heterogeneity

Abstract

Meningiomas are the most common primary tumors of the central nervous system and show clinical heterogeneity across WHO grades. While grade 1 meningiomas are typically benign, grade 3 (anaplastic) meningiomas are rare, highly aggressive, and associated with poor prognosis. Current histopathological grading does not fully capture tumor biology, therefore molecular approaches are needed to better reflect disease behavior. Proteomic profiling provides insight into functional biological differences between tumor grades, but sample processing and analysis of formalin-fixed paraffin-embedded (FFPE) tissues remains challenging.

This study aimed to develop and implement a robust, high-throughput proteomics workflow for FFPE tissues and to apply the workflow to meningioma samples in order to characterize proteomic differences between grade 1 and grade 3 tumors, explore heterogeneity within high-grade meningiomas, and investigate associations with EZH2 expression. Multiple deparaffinization, protein extraction, and digestion methods were systematically evaluated using pilot tissues to optimize protein yield, reproducibility, and proteome coverage. The final workflow consisted of n-heptane/methanol deparaffinization, BeatBox-based protein extraction, and automated magnetic bead-based digestion on the KingFisher Apex platform.

The optimized protocol was applied to a cohort of 43 FFPE meningioma samples analyzed by data-independent acquisition mass spectrometry. Proteomic analysis revealed clear differences between grade 1 and grade 3 meningiomas, with high-grade tumors showing increased abundance of proteins involved in proliferation, DNA replication, RNA processing, and metabolic reprogramming. Pathway enrichment analyses confirmed a predominance of proliferative and biosynthetic pathways in grade 3 tumors, whereas grade 1 meningiomas were associated with homeostatic and cytoskeletal processes.

Unsupervised clustering further identified three distinct proteomic subgroups within grade 3 meningiomas, each associated with different biological pathways, EZH2 expression levels, and clinical outcomes. These findings demonstrate pronounced biological heterogeneity within high-grade meningiomas and highlight the potential of FFPE-based proteomics to refine tumor stratification beyond histological grading.

Popular Abstract

What tumor proteins reveal about the more aggressive meningiomas

Meningiomas might look similar under the microscope yet behave very differently in patients. By investigating the proteins inside these tumours, this degree project reveals hidden differences that could help doctors better predict how dangerous a tumour really is and how it might be treated in the future.

Meningiomas are the most common primary tumors of the central nervous system and show clinical heterogeneity across WHO grades. Many grow slowly and can be cured with surgery, but grade 3 meningiomas are highly aggressive and have a poor prognosis. These tumours often return after treatment and can be life-threatening. Today, doctors mainly rely on histopathological grading, done under the microscope to decide the tumor grade. However, this visual grading does not always reflect the tumour behaviour in real life.

This degree project tackled that problem by looking beyond appearances and focusing on proteins, the molecules that actually do the work inside cells. Proteins control processes such as growth, energy use and DNA repair, making them powerful indicators of how a tumour functions. The study analysed stored clinical tissue samples that had been preserved in paraffin, a format used worldwide in pathology but traditionally difficult to study at protein level.

A major part of the work was therefore technical, developing a fast, reliable way to extract thousands of proteins from these preserved samples. The final method avoided toxic chemicals and used automated steps, making it suitable for analysing large patient cohorts. Once established, the workflow was applied to 43 meningioma samples, ranging from grade 1 tumours to aggressive grade 3 ones.

The results were impressive. Grade 3 meningiomas showed much higher levels of proteins linked to rapid cell division, DNA replication and altered metabolism, compared to grade 1 meningiomas. These are classic hallmarks of aggressive cancers. In contrast, grade 1 meningiomas had higher expression of proteins involved in structural stability and normal tissue maintenance.

Even more impressive was what happened when only grade 3 tumours were compared with each other. Instead of forming one homogenous group, they split into three distinct protein patterns. One subgroup showed strong expressions for wound healing and blood clotting proteins and was associated with very poor survival outcomes. Another subgroup had a more metabolism focused profile and an intermediate outcome. The third subgroup looked biologically calmer and presented longer survival outcomes, despite all samples being grade 3 and classified as equally malignant by traditional methods.

These findings are important because they show that aggressive meningiomas are not all biologically the same. Protein profiling could one day help doctors identify which patients need the most intensive treatment and which might avoid unnecessary aggressive therapy. In addition to that, the workflow developed in this study can be applied to many other tissues preserved in paraffin besides meningiomas, turning old samples into new sources of medical insight.

• author: Cela, Ines
• supervisor: Melinda Rezeli
• organization: Division for Biomedical Engineering
• course: BMEM01 20261
• year: 2026
• type: H2 - Master's Degree (Two Years)
• subject: Technology and Engineering
• language: English
• additional info: 2026-02
• id: 9220732
• date added to LUP: 2026-02-03 12:41:58
• date last changed: 2026-02-03 12:41:58