Which molecular assays should be performed in meningioma for diagnostic and prognostic evaluation?

Molecular Testing in Meningioma

For meningiomas, you should prioritize testing for CDKN2A/B homozygous deletion and TERT promoter mutations as these directly upgrade tumors to WHO grade 3, followed by assessment of 1p/22q co-deletion status which upgrades morphologically benign tumors to grade 2. 1

Essential Molecular Markers by Priority

Tier 1: Grade-Defining Alterations (Test First)

• CDKN2A/B homozygous deletion: Automatically designates WHO grade 3 regardless of histology 1, 2
• TERT promoter mutations: Defines WHO grade 3 when present 1, 3
• 1p deletion with concurrent 22q deletion/NF2 mutation: Upgrades morphologically benign meningiomas to WHO grade 2 2

Tier 2: Prognostic and Therapeutic Markers

For targeted therapy selection (particularly in recurrent/progressive disease):

• mTOR pathway activation (ESCAT II level - highest actionability) 1
• NF2 alterations (ESCAT II level) 1
• Driver mutations: AKT1, SMO, TRAF7, KLF4, PIK3CA 1
• SMARCE1 loss: Defines clear cell meningioma subtype, automatically grade 2 2
• BAP1 mutation: Associated with aggressive behavior 1, 2

Additional therapeutic targets:

• SSTR2A expression: For radioligand therapy consideration 1
• PD-L1 expression: For immunotherapy selection 1
• Progesterone receptor (PR): Favorable prognostic marker 4

Tier 3: Emerging Prognostic Markers

• DNA methylation profiling: Provides molecular classification into risk groups (benign, intermediate, high-risk) 5, 6
• Copy number variations: Losses of 1p, 6p/q, 10q, 14q, 18p/q indicate higher grade 2
• Ki-67/MIB-1: Proliferation index correlates with recurrence 4

Clinical Algorithm for Testing

When to Test:

1. Mandatory testing scenarios 2:

   • All WHO grade 2 and 3 meningiomas (histologically)
   • Brain-invasive but otherwise morphologically benign (BIOB) meningiomas
   • Cases with borderline morphological grading criteria
   • Recurrent meningiomas
   • Young patients or those with family history (consider germline testing)

2. Consider testing for grade 1 meningiomas 5:

   • Approximately 10% of histologic grade 1 tumors fall into higher molecular risk groups
   • Testing may be warranted if clinical concern exists, though not cost-effective for all grade 1 cases

Testing Methodology:

Preferred platforms 1, 7:

• Next-generation sequencing (NGS): Most comprehensive, detects point mutations and CNVs
• Chromosomal microarray analysis (CMA): Reliable for copy number alterations
• DNA methylation arrays: Provides molecular classification and CNV profile 5

Alternative when resources limited 7, 3:

• FISH: Can detect CDKN2A/B deletion and chromosomal losses, but lower concordance than CMA/NGS
• Targeted sequencing: Focus on TERT promoter mutations (most cost-effective single test) 3
• Immunohistochemistry: For SMARCE1, BAP1, PR, SSTR2A, PD-L1 (though less reliable for some markers)

Critical Pitfalls to Avoid

1. Intratumoral heterogeneity: TERT promoter mutations and CDKN2A/B deletions can be subclonal; ensure adequate sampling of aggressive-appearing areas 1

2. Don't grade brain-invasive meningiomas before molecular testing: BIOB meningiomas require molecular data before grade assignment 2

3. FISH limitations: Shows lower concordance with CMA for detecting chromosomal arm losses; interpret cautiously and consider confirmatory testing if clinically discordant 7

4. H3K27me3 and p16 immunohistochemistry: Currently lack sufficient prognostic value for routine clinical use 3

5. Hemizygous CDKN2A/B deletion: Insufficient evidence for grading implications; only homozygous deletion upgrades to grade 3 2

Reporting Requirements

Molecular reports should include 1:

• Exact test type performed
• Sample details (FFPE vs frozen, tumor cell content)
• For NGS: genes/regions interrogated, variant details per HGVS standards, read depth, variant allele frequencies
• For RNA sequencing: fusion reads and functional plausibility of gene fusions

The most pragmatic approach in resource-limited settings is to prioritize TERT promoter mutation testing for all grade 2 meningiomas, as this single test provides the highest clinical yield for identifying grade 3 cases 3, followed by CDKN2A/B assessment and comprehensive molecular profiling when feasible.