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Brain Tumor Classification: The WHO 2021 Framework

Overview

The WHO 2021 Classification of CNS Tumors (5th edition) represents a paradigm shift toward integrated diagnosis that combines morphologic features with molecular biomarkers. Many tumor types now require specific molecular alterations for definitive classification. This "layered" diagnostic approach produces an integrated diagnosis incorporating histologic type, WHO grade, and molecular features.

Integrated Diagnostic Approach

The Layered Report Structure

The WHO 2021 system uses a layered report. Layer 1 is the integrated diagnosis, combining morphologic and molecular findings into a final diagnosis (for example, "Astrocytoma, IDH-mutant, CNS WHO Grade 3"). Layer 2 is the histologic classification based on H&E morphology. Layer 3 is the CNS WHO grade (1 through 4) based on histologic and/or molecular criteria. Layer 4 provides key molecular information (IDH status, 1p/19q codeletion, MGMT methylation, and others).

"Not Otherwise Specified" (NOS) vs. "Not Elsewhere Classified" (NEC)

The NOS designation indicates that required molecular testing was not performed or was inconclusive, leaving the diagnosis based on morphology alone. NEC indicates that molecular testing was performed but results do not fit any currently defined entity, representing an acknowledged diagnostic gap.

Adult-Type Diffuse Gliomas

Astrocytoma, IDH-Mutant

This entity is defined by the presence of an IDH1 or IDH2 mutation and the absence of 1p/19q codeletion. ATRX loss by IHC and TP53 mutation are characteristic but not required for diagnosis. Grading proceeds as follows: Grade 2 has low mitotic activity without microvascular proliferation or necrosis. Grade 3 shows significant mitotic activity. Grade 4 has microvascular proliferation and/or necrosis, or CDKN2A/B homozygous deletion (a molecular grading criterion that upgrades to grade 4 even without histologic grade 4 features). IDH1 R132H immunohistochemistry is positive in approximately 90 percent of IDH-mutant gliomas; when negative, sequencing is needed. Median survival varies by grade: approximately 10 to 15 years for grade 2, 5 to 8 years for grade 3, and 3 to 5 years for grade 4.

Oligodendroglioma, IDH-Mutant, 1p/19q-Codeleted

This entity requires both an IDH1 or IDH2 mutation and whole-arm 1p/19q codeletion for diagnosis. Classic morphology includes "fried egg" cells (perinuclear halos, an artifact of FFPE processing), a delicate branching "chicken-wire" capillary network, and microcalcifications. TERT promoter mutation is present in over 95 percent of cases. Grade 2 shows low mitotic activity, while Grade 3 shows brisk mitotic activity, microvascular proliferation, and/or necrosis. No grade 4 oligodendroglioma exists. Oligodendroglioma has better prognosis than astrocytoma at equivalent grade and is chemosensitive to the PCV regimen.

Glioblastoma, IDH-Wildtype

Glioblastoma is defined by IDH-wildtype status plus at least one of the following molecular features: TERT promoter mutation, EGFR amplification, or combined whole chromosome 7 gain and chromosome 10 loss (+7/-10). If none of these molecular features are present, the tumor cannot be diagnosed as glioblastoma even with histologic grade 4 features and should be classified as NEC. Glioblastoma is always grade 4. Histologically, it is a high-grade astrocytic tumor with microvascular proliferation and/or palisading necrosis (pseudopalisading). MGMT promoter methylation predicts response to temozolomide and is assessed by pyrosequencing or methylation-specific PCR. Median survival is approximately 15 months with standard treatment (Stupp protocol). Gliosarcoma is a variant with biphasic glial and mesenchymal (sarcomatous) components.

Pediatric-Type Diffuse Low-Grade Gliomas

Diffuse Astrocytoma, MYB or MYBL1-Altered

This tumor occurs in pediatric patients and young adults, involving the cerebral hemispheres. It harbors MYB or MYBL1 rearrangement or amplification, is IDH-wildtype with retained ATRX and wild-type H3, and carries a favorable prognosis.

Polymorphous Low-Grade Neuroepithelial Tumor of the Young (PLNTY)

PLNTY shows oligodendroglioma-like areas with calcifications, harbors MAPK pathway alterations (BRAF, FGFR), and has an excellent prognosis.

Pediatric-Type Diffuse High-Grade Gliomas

Diffuse Midline Glioma, H3 K27-Altered

This tumor occurs in midline locations (thalamus, brainstem/pons, spinal cord) and is defined by H3 K27M mutation (in H3-3A or HIST1H3B/C) or EZHIP overexpression. It is always grade 4 regardless of histologic features. Prognosis is poor, with median survival under 1 year for pontine tumors (DIPG). H3 K27M IHC shows positive nuclear staining, and there is loss of H3K27me3 trimethylation.

Diffuse Hemispheric Glioma, H3 G34-Mutant

This tumor occurs in the cerebral hemispheres of adolescents and young adults, harboring H3-3A G34R or G34V mutation. It is grade 4 with GBM-like histology, ATRX loss, TP53 mutation, and IDH-wildtype status.

Circumscribed Gliomas

Pilocytic Astrocytoma

Pilocytic astrocytoma is the most common pediatric brain tumor. It shows a biphasic pattern with compact piloid areas containing Rosenthal fibers alternating with loose microcystic areas containing eosinophilic granular bodies (EGBs). MAPK pathway alterations are characteristic: BRAF::KIAA1549 fusion occurs in approximately 70 percent of posterior fossa cases, with BRAF V600E and NF1 loss being other possibilities. It is WHO grade 1 with an excellent prognosis and surgical cure in most cases.

Pleomorphic Xanthoastrocytoma (PXA)

PXA occurs superficially (temporal lobe) in children and young adults. It contains bizarre pleomorphic cells, xanthomatous (lipidized) astrocytes, EGBs, and a reticulin network around individual cells. BRAF V600E mutation is present in 60 to 70 percent of cases. It is grade 2, with anaplastic PXA (grade 3) defined by 5 or more mitoses per 10 HPFs.

Subependymal Giant Cell Astrocytoma (SEGA)

SEGA is associated with tuberous sclerosis complex (TSC1/TSC2 mutations) and occurs near the foramen of Monro, where it may cause hydrocephalus. It contains large gemistocytic/ganglioid cells that are GFAP-positive and S100-positive. It is grade 1 and treated with surgery or mTOR inhibitors (everolimus).

Ependymal Tumors

Molecular classification now defines ependymoma subgroups. Supratentorial ependymoma, ZFTA fusion-positive is the most common supratentorial form, harboring the ZFTA::RELA fusion. Posterior fossa ependymoma Group A (PFA) shows loss of H3K27me3, is pediatric, and carries a worse prognosis. Posterior fossa ependymoma Group B (PFB) retains H3K27me3, occurs in adults, and has a better prognosis. Spinal ependymoma, MYCN-amplified is aggressive.

Myxopapillary Ependymoma

Myxopapillary ependymoma occurs at the conus medullaris and filum terminale, shows papillary architecture with myxoid stroma, and is GFAP-positive. It is now classified as WHO grade 2 (upgraded from grade 1 in WHO 2021).

Embryonal Tumors

Medulloblastoma

Medulloblastoma is the most common malignant pediatric brain tumor, arising in the posterior fossa/cerebellum. Four molecular subgroups with distinct biology are recognized. WNT-activated tumors show nuclear beta-catenin positivity and chromosome 6 loss (monosomy 6) with excellent prognosis (over 95 percent survival). SHH-activated tumors harbor PTCH1, SMO, or SUFU mutations and are subdivided by TP53 status (mutant carries worse prognosis). Group 3 tumors have MYC amplification, the worst prognosis, and are frequently metastatic at diagnosis. Group 4 is the most common subgroup, has isochromosome 17q, and carries intermediate prognosis. Histologic subtypes include classic, desmoplastic/nodular, extensive nodularity, and large cell/anaplastic. Homer Wright rosettes (fibrillary core surrounded by tumor cells) are characteristic.

Meningiomas

Meningiomas are the most common primary CNS tumor overall, arising as extra-axial dura-based masses. WHO grading is based on histologic features. Grade 1 accounts for 80 percent of cases and includes meningothelial, fibrous, transitional, psammomatous, and other subtypes. Grade 2 (atypical) is defined by 4 to 19 mitoses per 10 HPFs, or brain invasion alone, or 3 or more of the following: sheeting, spontaneous necrosis, prominent nucleoli, small cells, and hypercellularity. Grade 3 (anaplastic/malignant) requires 20 or more mitoses per 10 HPFs or carcinoma/sarcoma/melanoma-like histology. Molecular features include NF2 mutation (most common) and TRAF7, KLF4, AKT1, and SMO mutations in non-NF2 meningiomas. TERT promoter mutation and/or CDKN2A/B homozygous deletion are associated with aggressive behavior and may warrant grade 3 classification even in histologically lower-grade tumors.

<image>A medical illustration of the WHO 2021 adult-type diffuse glioma classification. Three panels: Panel A (Astrocytoma, IDH-mutant): Diffuse infiltrating astrocytic tumor with IDH1 R132H IHC showing diffuse cytoplasmic positivity, ATRX IHC showing loss of nuclear staining in tumor cells with retained staining in endothelial cells, and p53 IHC showing diffuse strong positivity. Panel B (Oligodendroglioma, IDH-mutant, 1p/19q-codeleted): Classic fried-egg cells with perinuclear halos and chicken-wire capillary pattern, with 1p/19q FISH showing codeletion (single red and green signals). Panel C (Glioblastoma, IDH-wildtype): High-grade astrocytic tumor with pseudopalisading necrosis and microvascular proliferation, IDH1 R132H IHC negative, EGFR FISH showing amplification (clusters of red signals).</image>

<image>A medical illustration of pediatric-type CNS tumors. Panel A (Pilocytic astrocytoma): Biphasic pattern with compact piloid areas containing Rosenthal fibers (elongated eosinophilic fibers, arrow) and loose microcystic areas with eosinophilic granular bodies (EGBs, arrowhead). Panel B (Diffuse midline glioma, H3 K27-altered): Diffusely infiltrating glial tumor in the pons, H3 K27M IHC showing positive nuclear staining in tumor cells, H3K27me3 IHC showing loss of trimethylation. Panel C (Medulloblastoma): Densely cellular small round blue cell tumor with Homer Wright rosettes, nuclear beta-catenin IHC showing positive staining in a WNT-activated subgroup case.</image>

<image>A medical illustration of meningioma grading. Panel A (Grade 1 meningothelial): Lobular architecture of meningothelial cells with whorl formation and psammoma bodies (concentric laminated calcifications). Panel B (Grade 2 atypical): Increased cellularity with sheeting architecture, prominent nucleoli, and increased mitotic activity (4-19 mitoses per 10 HPFs highlighted by arrows). Panel C (Grade 3 anaplastic): Markedly pleomorphic cells with high mitotic rate (>=20/10 HPFs), geographic necrosis, and loss of typical meningioma architecture. Panel D: Brain invasion in a meningioma showing irregular tongues of tumor extending into brain parenchyma without an intervening leptomeningeal layer, which alone qualifies as grade 2.</image>

Clinical Pearls

IDH mutation status is the most important molecular determination in adult diffuse gliomas. IDH-mutant astrocytomas have fundamentally different biology and better prognosis than IDH-wildtype glioblastoma, even when both show grade 4 histologic features. CDKN2A/B homozygous deletion upgrades an IDH-mutant astrocytoma to grade 4 even without microvascular proliferation or necrosis; this molecular grading criterion is new in WHO 2021 and has significant prognostic implications.

In the WHO 2021 system, a histologically grade 4 diffuse glioma that is IDH-wildtype but lacks TERT promoter mutation, EGFR amplification, and +7/-10 cannot be called glioblastoma. It must be classified as "diffuse astrocytic glioma, IDH-wildtype, NEC." For medulloblastoma, molecular subgrouping is essential for risk stratification: WNT-activated has over 95 percent survival and may qualify for de-escalated therapy, while Group 3 with MYC amplification has the worst prognosis.

H3 K27M mutation defines diffuse midline glioma as grade 4 regardless of histologic features; even a histologically low-grade-appearing midline glioma with H3 K27M is biologically aggressive. TERT promoter mutation and CDKN2A/B deletion in meningiomas are emerging markers of aggressive behavior that may influence management even in histologically low-grade tumors.

References

• WHO Classification of Tumours Editorial Board. Central Nervous System Tumours. 5th ed. IARC; 2021.
• Louis DN, et al. The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro Oncol. 2021;23(8):1231-1251.
• Brat DJ, et al. cIMPACT-NOW update 3: recommended diagnostic criteria for "Diffuse astrocytic glioma, IDH-wildtype, with molecular features of glioblastoma." Acta Neuropathol. 2018;136(5):805-810.
• Ellison DW, et al. cIMPACT-NOW update 7: advancing the molecular classification of ependymal tumors. Brain Pathol. 2020;30(5):863-866.
• Taylor MD, et al. Molecular subgroups of medulloblastoma: the current consensus. Acta Neuropathol. 2012;123(4):465-472.

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