: 2022  |  Volume : 5  |  Issue : 1  |  Page : 1--4

New changes in pathological diagnosis of brain tumors in the modern molecular era

Zhi Li 
 Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China

Correspondence Address:
Dr. Zhi Li
Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106#, Zhongshan Road II, Guangzhou 510080, Guangdong Province

How to cite this article:
Li Z. New changes in pathological diagnosis of brain tumors in the modern molecular era.Glioma 2022;5:1-4

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Li Z. New changes in pathological diagnosis of brain tumors in the modern molecular era. Glioma [serial online] 2022 [cited 2022 Jun 29 ];5:1-4
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Since 2016, the pathological diagnosis of tumors of the central nervous system (CNS) has undergone great changes, owing to the introduction of molecular pathological techniques and molecular genetic characteristics of tumors into the routine pathological diagnosis of brain tumors.[1] In 2021, the fifth edition of the World Health Organization (WHO) classification of CNS tumors (WHO CNS5) further advanced the role of molecular diagnostics.[2] The molecular characteristics of tumors not only indicate distinct tumor types or subtypes but also determine the WHO grading of certain tumors. These new changes have brought great challenges to the pathological diagnosis of CNS tumors. How to correctly interpret the molecular genetic characteristics of tumors has become an important and difficult aspect of clinical practice.

 Accurate Pathological Diagnosis Requires Adequate Intraoperative Tumor Sampling

Comprehensive histological observation of neoplastic lesions under a microscope has always been an important factor in the correct pathological diagnosis of CNS tumors. Owing to the obvious histological heterogeneity of brain tumors, especially in astrocytoma and glioblastoma, the different areas of a tumor frequently have different morphological appearances, resulting in different diagnoses with respect to histological types and the WHO grades. However, given the high conservation of molecular genetic characteristics of CNS tumors, the molecular characteristics of areas of different histological morphologies within a tumor are more consistent. This can enable the correct diagnosis of some tumors with morphological heterogeneity.[3],[4],[5] Therefore, some apparently low-grade CNS tumors can be correctly diagnosed as high-grade by detection of the molecular characteristics of high-grade tumors; such tumor types include low-grade astrocytoma-like glioblastoma, IDH-wildtype or pilocytic astrocytoma-like diffuse midline glioma, H3K27-altered.

However, this does not mean that adequate tumor sampling during surgery is no longer important. In the era of modern molecular diagnosis, comprehensive observation of the histological characteristics of CNS tumors remains the basis of accurate pathological diagnosis. The summary of the WHO CNS5 also indicates that molecular diagnostics in CNS tumor classification remain rooted in other established approaches to tumor characterization, including histology and immunohistochemistry.[2] The tumor classification system for CNS tumors includes numerous tumor types and subtypes and is very complex. Only a few distinct tumor types can be determinate by their unique molecular features (e.g., diffuse hemispheric glioma, H3G34-mutant or supratentorial ependymoma, and ZFTA fusion-positive). Complicated and extensively overlapping molecular alterations have been detected in adult- and pediatric-type diffuse gliomas, circumscribed astrocytic gliomas, and glioneuronal and neuronal tumors.[6] The tumor types or subtypes and their molecular features do not completely match each other in most CNS tumors. In other words, CNS tumors cannot be clearly classified only by their molecular alterations; thus, an integrated approach involving histological, molecular, and other key types of information is required for accurate diagnosis for CNS tumors. For example, TERT promoter mutations have been observed in adult-type IDH-wildtype glioblastoma, H3-wildtype and IDH-wildtype diffuse pediatric-type high-grade glioma, and pleomorphic xanthoastrocytoma. FGFR1 gene mutations have been reported in pediatric-type diffuse low-grade glioma, MAPK pathway-altered, or rosette-forming glioneuronal tumors. CDKN2A/B homozygous deletions can be detected in IDH-mutant adult-type astrocytoma and some high-grade meningiomas. Given this situation, it is difficult to make accurate tumor classifications when lacking comprehensive and adequate morphological observations.

In recent years, genome-wide DNA methylation analysis has become an effective auxiliary method for CNS tumor classification.[7] The role of DNA methylation profiling is becoming increasingly important for the classification and identification of unusual or newly recognized tumor types. The 2021 WHO CNS5 summary even assumes that nearly all (but not all) tumor types are aligned to a distinct methylation signature.[2] However, this does not mean there is no limit to the accuracy of tumor classification and the amount of genetic information that can be obtained by DNA methylation profiling based on small biopsies obtained from surgery or liquid biopsies through noninvasive approaches (blood, cerebrospinal fluid, etc.). DNA methylation analysis has also demonstrated tumor heterogeneity, especially in glioblastoma,[8] where tumor purity is highly variable between samples and explains a substantial part of the apparent epigenetic spatial heterogeneity.[9] Thus, the relationship between tumor purity and prediction accuracy must be taken into account for the detectable conservation in variable samples by DNA methylation analysis. This indicates a “mass requirement” in samples for DNA methylation analysis in clinical practice. Although DNA methylation profiling has certain advantages for tumor classification using small or liquid biopsies, it is an auxiliary method for CNS tumor histological classification at present, and sufficient acquisition of brain tumor samples during surgery is still a prerequisite for accurate characterization of DNA methylation.

 Clinical Significance of Correctly Interpreting Molecular Features of Central Nervous System Tumors

As well as its role in determining the classification and WHO grade of CNS tumors, accurate pathological diagnosis can be used to guide clinical treatment and evaluate patient prognosis. As integrated diagnosis is the recommended diagnostic format for CNS tumors at present, tumor molecular characteristics often have a decisive role in tumor classification. For example, when a CNS tumor is associated with IDH1/2 gene mutation and 1p/19q co-deletion, the final integrated diagnosis will be determined to be IDH-mutant astrocytoma if there is detectable IDH1/2 mutation but an absence of 1p/19q co-deletion, even though the morphological appearance is consistent with oligodendroglioma. Factually, the layered report structure of CNS tumor allows the ready separation of histological diagnosis from final integrated diagnosis (combined tissue-based histological and molecular diagnosis).[2] Under the conditions mentioned above, a histological diagnosis of “oligodendroglioma” or “diffuse glioma, not otherwise specified (NOS)” made in a pathological department or institution without molecular detection would meet the standard WHO diagnostic requirements. Clinical treatment groups should be aware that the integrated diagnosis is the final diagnosis and does not conflict with the simple histological diagnosis. Subsequent clinical management should be based on the integrated diagnosis. A pathological diagnosis with an “NOS” suffix indicates that the diagnostic information necessary to assign a specific WHO diagnosis is not available and provides an alert to the oncologist that a molecular workup should be undertaken by other institutes with qualified molecular detection platforms.

The “not elsewhere classified” (NEC) suffix is another diagnostic form; it indicates that the necessary diagnostic testing has been successfully performed but that the results do not readily allow for a WHO diagnosis.[10] Pathologists have termed such cases “descriptive diagnoses,” and they provide an alert to the oncologist that the tumor does not conform to a standard WHO diagnosis because of a mismatch in histological, immunohistochemical, and/or genetic features. For example, if a H3K27M mutation is detected in adult nonmidline IDH wildtype glioma, it is not clear whether the biological behavior of this tumor is more likely to indicate H3K27-altered diffuse midline glioma or IDH-wildtype glioblastoma.[11] The final pathological diagnosis may be “diffuse glioma, NEC,” or “hemispheric glioma with H3K27M mutation, NEC.” The WHO grade of such a tumor would be determined based on its histological features. Oncologists should be aware that this rare molecular feature has not yet been identified clearly and that its clinical significance should be verified based on more data.

Most CNS tumors are graded traditionally on the basis of tumor histological features (cellularity, mitosis, microvascular proliferation, and necrosis), and WHO grading of CNS tumor has for the decades been linked to overall expected clinical-biological behaviors, although high-grade features do not always consistently relate to overall outcome in some CNS tumors (e.g., supratentorial ependymoma and meningioma). However, in some tumor types, specific molecular features are used directly in the WHO grading or indicate that the tumor has more aggressive behavior. Therefore, the CNS WHO grading no longer simply indicates a histological grade. Oncologists should take account of the clinical significance of specific molecular characteristics and their effects on independent biological behavior in prognostic evaluation. For instance, CDKN2A/B homozygous deletions can improve adult-type diffuse IDH-mutant astrocytoma to the WHO Grade 4 regardless of the tumor's low-grade morphological features.[12] The presence of a TERT promoter mutation, EGFR amplification, or +7/−10 copy number changes in IDH-wildtype diffuse astrocytoma allows glioblastoma to have IDH-wildtype CNS WHO Grade 4 designation, even in cases that otherwise appear histologically lower grade.[4] TERT promoter mutation and/or CDKN2A/B homozygous deletion can confirm meningioma as the WHO Grade 3. Although they cannot be used to improve the WHO grade, genetic alterations including ZFTA fusion in supratentorial ependymoma, MYCN amplification in spinal ependymoma, and H3K27me3 loss in the posterior fossa ependymoma indicate aggressive tumor behaviors and tumors that are more likely to reoccur and easily disseminate throughout the CNS. In other words, a molecular parameter can sometimes add value to histological findings when assigning a grade. It is necessary to adopt more active treatment strategies when CNS tumors with high-risk genetic alterations are encountered in clinical practice.

Pediatric-type diffuse low-grade gliomas have an aggressive growth pattern with astrocytoma-or oligodendroglioma-like morphological features; owing to the histological overlap, they may be indistinguishable from adult-type astrocytomas or oligodendrogliomas. For these tumors, precise classification requires molecular characterization and integrated diagnosis.[13] Despite the similarity in morphological appearance, pediatric-type diffuse low-grade gliomas rarely progress and have a better prognosis than adult low-grade gliomas. Oncologists should be aware that most pediatric low-grade gliomas are frequently are driven by low-or intermediate-risk groups of genetic alterations, affecting genes such as MYB or MYBL1, FGFR1/2, NF1, BRAF, and IDH. These tumors progress less frequently and often eventually stop growing, with very few progressions and almost no deaths at 10–20-year follow-up.[14] Given their nonfatal disease progression, these tumors require conservative management, as therapy may have more disadvantages than the tumor itself. Therefore, careful consideration must be given to whether additional postoperative treatments, especially radiotherapy, should be adopted for patients with pediatric-type diffuse low-grade gliomas. When pediatric CNS tumors present high-risk molecular features, including H3K27M mutation, or BRAF V600E mutation with CDKN2A/B deletion, they show aggressive behavior and almost invariably progress regardless of the initial morphology and presentation.[14] Owing to their rapid progression and CNS dissemination, tumors with these molecular markers usually require immediate, aggressive treatment and the introduction of novel targeted agents. In addition, the type of molecular alteration driving the tumor should also be considered in the context of treatment strategy and prognostic assessment. Single nucleotide variant-driven pediatric low-grade gliomas are frequently associated with poorer outcomes compared with rearrangement-driven tumors.[14] The latter tumors are often diagnosed at a younger age, enriched for the WHO Grade 1 histology, infrequently progress, and rarely result in death. Multiple treatment courses and longer-term follow-up are therefore necessary for patients with single nucleotide variant-driven tumors due to the risk of late death.

In addition to tumor classification and the WHO grading, certain molecular alterations may have clinical therapeutic significance, especially in guiding the choice of targeted agents. For example, MGMT promoter methylation suggests greater sensitivity to the therapeutic effect of temozolomide. Mutation of BRAF V600E suggests that BRAF-targeted inhibitors may be more effective. PTEN gene mutation may indicate greater sensitivity to tumor treating fields therapy, a novel and effective therapy for glioblastoma.[15] It is expected that molecular targets for the clinical treatment of recurrent CNS tumors will be found using high-throughput sequencing technologies such as next-generation sequencing.

 Monitoring of Central Nervous System Tumor-Associated Genetic Tumor Syndromes

Neoplasms of the CNS and peripheral nervous system have been implicated in a wide range of genetic tumor-predisposition syndromes. Traditionally, most of these hereditary diseases have been diagnosed by clinical features and family history; however, it is increasingly possible for heritable pathogenic gene variants to be detected by high-throughput sequencing technology (next-generation sequencing assays). This requires oncologists and pathologists to consciously look for clues related to hereditary diseases in patients with CNS tumors, including symptoms, signs, and specific molecular features, followed by identification of germline alterations through further gene sequencing to confirm the initial suspicion. Some common correlations between syndromes and CNS tumors have been widely recognized, such as the close association between multiple/or plexiform neurofibroma and neurofibromatosis Type 1 (NF1), between bilateral vestibular schwannomas and neurofibromatosis Type 2 (NF2), and between hemangioblastoma and von Hippel–Lindau syndrome, as well as subependymal giant cell astrocytoma and tuberous sclerosis. However, for some rare and newly defined hereditary-syndrome-related CNS tumors, there is less awareness of the relevant molecular characteristics. For example, optic pathway glioma occurring in children may be linked to NF1.[15] Pediatric low-grade gliomas with biallelic NF1 gene loss and meningioma with NF2 gene alterations are frequently associated with NF1 and NF2, respectively.[16],[17] A large proportion of IDH-mutant astrocytomas occurring in children and young adults are constitutional mismatch repair deficiency syndrome, resulting from biallelic germline mutation in one of the mismatch repair genes and characterized by the loss of mismatch repair protein expression.[18]

When molecular detection reveals genetic germline variants in CNS tumors, diagnosis of hereditary syndromes can be confirmed. Li–Fraumeni syndrome should be considered when heterozygous germline alterations (mutation, rearrangement, or partial/complete deletion) of the TP53 gene are detected in SHH-activated medulloblastoma or choroid plexus carcinoma. Cowden syndrome should be diagnosed if germline pathogenic variants of the PTEN gene are found in dysplastic cerebellar gangliocytoma (Lhermitte–Duclos disease).[19] Nevoid basal cell carcinoma syndrome (Gorlin syndrome) is caused by germline mutations in genes involved in the Hedgehog signaling pathway (most commonly the PTCH1 gene); it seems to be exclusively associated with extensively nodular or desmoplastic/nodular types of medulloblastoma in children.[20] The purpose of discovering genetic tumor-predisposition syndromes is not only to help patients to monitor and prevent multiple lesions of the CNS or other organs but also to enable genetic disease monitoring and fertility guidance to be provided for the whole family. Therefore, it is critically important for oncologists and pathologists to be familiar with the molecular characteristics and diagnostic criteria of these hereditary-disease-associated CNS tumors.

In conclusion, in the modern molecular era, clinicopathological diagnosis has developed from a single histological diagnosis into a multifunctional diagnostic platform integrating morphological observations, guidance for treatment, prognostic assessment, and provision of genetic disease information so that patients can benefit from accurate diagnosis.

Conflicts of interest

There are no conflicts of interest.


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