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Folia Neuropathologica
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4/2024
vol. 62
 
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abstract:
Original paper

Classification of gliomas based on genome-wide DNA methylation profiles and immunohistochemical analysis: a short study

Olga Taryma-Leśniak
1
,
Kamil Buczkowski
2
,
Tomasz Klepinowski
3
,
Maciej Jankowski
4
,
Szymon Retfiński
1
,
Bartłomiej Sagan
3
,
Leszek Sagan
3
,
Ewa Szutowicz
5
,
Kacper Winiarski
5
,
Marta Masztalewicz
6
,
Przemysław Nowacki
6
,
Marta Sobalska-Kwapis
7
,
Dominik Strapagiel
7
,
Wojciech Kloc
8, 9
,
Beata Lipska-Ziętkiewicz
4
,
Ewa Iżycka-Świeszewska
2
,
Tomasz K. Wojdacz
1

  1. Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Poland
  2. Department of Pathology and Neuropathology, Medical University of Gdansk, Poland
  3. Department of Neurosurgery, Pomeranian Medical University in Szczecin, Poland
  4. Department of Biology and Genetics, Medical University of Gdansk, Poland
  5. Department of Oncology and Radiotherapy, Medical University of Gdansk, Poland
  6. Department of Neurology, Pomeranian Medical University in Szczecin, Poland
  7. Biobank Laboratory, Department of Molecular Biophysics, University of Lodz, Poland
  8. Department of Neurosurgery, Copernicus Hospital, Gdansk, Poland
  9. Department of Psychology and Sociology of Health and Public Health, School of Public Health, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Poland
Folia Neuropathol 2024; 62 (4): 362-375
DOI: https://doi.org/10.5114/fn.2024.147538
Online publish date: 2024/12/31
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Methylation profiling is one of the diagnostic methods included in the 2021 World Health Organization Classification of Central Nervous System Tumors (WHO CNS5). In the present short study, we performed methylation analysis of 16 archival diffuse gliomas, including seven glioblastomas (GB) with long survival and three GB with early disease presentation. The formalin-fixed paraffin-embedded (FFPE) and freshly frozen (FF) samples were analyzed using Infinium Methylation-EPIC microarrays. The diagnosis was changed in two cases, and two other cases were classified as control tissue due to the low content of neoplastic cells in examined frozen samples. No differences were found between the usefulness of FF and FFPE material for methylation profiling. Copy number variation analysis and comparative immunohistochemical and molecular studies were also performed. The MGMT promoter methylation assessment was consistent between the micro-array and methylation-sensitive high-resolution melting (MS-HRM) testing. The performed analyses did not supply new data according to the unexpected clinical course of the selected cases. Immunohistochemical evaluation with p16 and PTEN antibodies was consistent with the CDKN2A and PTEN status in most cases.

In conclusion, the classification of gliomas based on genome-wide methylation profiles increases the precision of histopathological diagnosis but has limitations, and pathological and clinical consistency is always necessary. Furthermore, immunohistochemical surrogates of molecular alterations are suitable and widely available diagnostic tools.
keywords:

WHO CNS5, glioma, glioblastoma, DNA methylation, classifier
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