eISSN: 1509-572x
ISSN: 1641-4640
Folia Neuropathologica
Current issue Archive Manuscripts accepted About the journal Special Issues Editorial board Reviewers Abstracting and indexing Subscription Contact Instructions for authors Ethical standards and procedures
Editorial System
Submit your Manuscript
SCImago Journal & Country Rank
Search
Editorial Policies
Sarajevo Declaration on Integrity and Visibility of Scholarly Publications
4/2024
vol. 62
 
Share:
Send email
Share:
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
Article file
- Classification.pdf  [0.34 MB]
Get citation
 
PlumX metrics:
 
1. Afflerbach AK, Albers A, Appelt A, Schweizer L, Paulus W, Bockmayr M, Schüller U, Thomas C. Nanopore sequencing from formalin-fixed paraffin-embedded specimens for copy-number profiling and methylation-based CNS tumor classification. Acta Neuropathol 2024; 147: 74.
2. Bertero L, Mangherini L, Ricci AA, Cassoni P, Sahm F. Molecular neuropathology: an essential and evolving toolbox for the diagnosis and clinical management of central nervous system tumors. Virchows Arch 2024; 484: 181-194.
3. Braczynski AK, Capper D, Jones DTW, Schittenhelm J, Stichel D, von Deimling A, Harter PN, Mittelbronn M. High density DNA methylation array is a reliable alternative for PCR-based analysis of the MGMT promoter methylation status in glioblastoma. Pathol Res Pract 2020; 216: 152728.
4. Buckland ME, Sarkar C, Santosh V, Al-Hussaini M, Park SH, Tihan T, Ng HK, Komori T. Announcing the Asian Oceanian Society of Neuropathology guidelines for Adapting Diagnostic Approaches for Practical Taxonomy in Resource-Restrained Regions (AOSNP-ADAPTR). Brain Pathol 2024; 34: e13201.
5. Capper D, Jones DTW, Sill M, Hovestadt V, Schrimpf D, Sturm D, Koelsche C, Sahm F, Chavez L, Reuss DE, Kratz A, Wefers AK, Huang K, Pajtler KW, Schweizer L, Stichel D, Olar A, Engel NW, Lindenberg K, Harter PN, Braczynski AK, Plate KH, Dohmen H, Garvalov BK, Coras R, Hölsken A, Hewer E, Bewerunge-Hudler M, Schick M, Fischer R, Beschorner R, Schittenhelm J, Staszewski O, Wani K, Varlet P, Pages M, Temming P, Lohmann D, Selt F, Witt H, Milde T, Witt O, Aronica E, Giangaspero F, Rushing E, Scheurlen W, Geisenberger C, Rodriguez FJ, Becker A, Preusser M, Haberler C, Bjerkvig R, Cryan J, Farrell M, Deckert M, Hench J, Frank S, Serrano J, Kannan K, Tsirigos A, Brück W, Hofer S, Brehmer S, Seiz-Rosenhagen M, Hänggi D, Hans V, Rozsnoki S, Hansford JR, Kohlhof P, Kristensen BW, Lechner M, Lopes B, Mawrin C, Ketter R, Kulozik A, Khatib Z, Heppner F, Koch A, Jouvet A, Keohane C, Mühleisen H, Mueller W, Pohl U, Prinz M, Benner A, Zapatka M, Gottardo NG, Driever PH, Kramm CM, Müller HL, Rutkowski S, von Hoff K, Frühwald MC, Gnekow A, Fleischhack G, Tippelt S, Calaminus G, Monoranu CM, Perry A, Jones C, Jacques TS, Radlwimmer B, Gessi M,
6. Pietsch T, Schramm J, Schackert G, Westphal M, Reifenberger G, Wesseling P, Weller M, Collins VP, Blümcke I, Bendszus M, Debus J, Huang A, Jabado N, Northcott PA, Paulus W, Gajjar A, Robinson GW, Taylor MD, Jaunmuktane Z, Ryzhova M, Platten M, Unterberg A, Wick W, Karajannis MA, Mittelbronn M, Acker T, Hartmann C, Aldape K, Schüller U, Buslei R, Lichter P, Kool M, Herold-Mende C, Ellison DW, Hasselblatt M, Snuderl M, Brandner S, Korshunov A, von Deimling A, Pfister SM. DNA methylation-based classification of central nervous system tumours. Nature 2018; 555: 469-474.
7. Capper D, Stichel D, Sahm F, Jones DTW, Schrimpf D, Sill M, Schmid S, Hovestadt V, Reuss DE, Koelsche C, Reinhardt A, Wefers AK, Huang K, Sievers P, Ebrahimi A, Schöler A, Teichmann D, Koch A, Hänggi D, Unterberg A, Platten M, Wick W, Witt O, Milde T, Korshunov A, Pfister SM, von Deimling A. Practical implementation of DNA methylation and copy-number-based CNS tumor diagnostics: the Heidelberg experience. Acta Neuropathol 2018; 136: 181-210.
8. Capper D, Weissert S, Balss J, Habel A, Meyer J, Jäger D, Ackermann U, Tessmer C, Korshunov A, Zentgraf H, Hartmann C, von Deimling A. Characterization of R132H mutation-specific IDH1 antibody binding in brain tumors. Brain Pathol 2010; 20: 245-254.
9. Drexler R, Brembach F, Sauvigny J, Ricklefs FL, Eckhardt A, Bode H, Gempt J, Lamszus K, Westphal M, Schüller U, Mohme M. Unclassifiable CNS tumors in DNA methylation-based classification: clinical challenges and prognostic impact. Acta Neuropathol Commun 2024; 12: 9.
10. Galbraith K, Vasudevaraja V, Serrano J, Shen G, Tran I, Abdallat N, Wen M, Patel S, Movahed-Ezazi M, Faustin A, Spino-Keeton M, Roberts LG, Maloku E, Drexler SA, Liechty BL, Pisapia D, Krasnozhen-Ratush O, Rosenblum M, Shroff S, Boué DR, Davidson C, Mao Q, Suchi M, North P, Hopp A, Segura A, Jarzembowski JA, Parsons L, Johnson MD, Mobley B, Samore W, McGuone D, Gopal PP, Canoll PD, Horbinski C, Fullmer JM, Farooqui MS, Gokden M, Wadhwani NR, Richardson TE, Umphlett M, Tsankova NM, DeWitt JC, Sen C, Placantonakis DG, Pacione D, Wisoff JH, Teresa Hidalgo E, Harter D, William CM, Cordova C, Kurz SC, Barbaro M, Orringer DA, Karajannis MA, Sulman EP, Gardner SL, Zagzag D, Tsirigos A, Allen JC, Golfinos JG, Snuderl M. Clinical utility of whole-genome DNA methylation profiling as a primary molecular diagnostic assay for central nervous system tumors-A prospective study and guidelines for clinical testing. Neurooncol Adv 2023; 5: vdad076.
11. Gliński B, Urbański J, Hetnał M, Małecki K, Jarosz M, MuchaMałecka A, Chrostowska A, Jakubowicz E, Frączek-Błachut B, Dymek P. Prognostic value of the interval from surgery to initiation of radiation therapy in correlation with some histo-clinical parameters in patients with malignant supratentorial gliomas. Contemp Oncol (Pozn) 2012; 16: 34-37.
12. Han S, Liu Y, Cai SJ, Qian M, Ding J, Larion M, Gilbert MR, Yang C. IDH mutation in glioma: molecular mechanisms and potential therapeutic targets. Br J Cancer 2020; 122: 1580-1589.
13. Hegi ME, Genbrugge E, Gorlia T, Stupp R, Gilbert MR, Chinot OL, Nabors LB, Jones G, Van Criekinge W, Straub J, Weller M. MGMT promoter methylation cutoff with safety margin for selecting glioblastoma patients into trials omitting temozolomide: A pooled analysis of four clinical trials. Clin Cancer Res 2019; 25: 1809-1816.
14. Jaunmuktane Z, Capper D, Jones DTW, Schrimpf D, Sill M, Dutt M, Suraweera N, Pfister SM, von Deimling A, Brandner S. Methylation array profiling of adult brain tumours: diagnostic outcomes in a large, single centre. Acta Neuropathol Commun 2019; 7: 24.
15. Karimi S, Zuccato JA, Mamatjan Y, Mansouri S, Suppiah S, Nassiri F,
16. Diamandis P, Munoz DG, Aldape KD, Zadeh G. The central nervous system tumor methylation classifier changes neuro-oncology practice for challenging brain tumor diagnoses and directly impacts patient care. Clin Epigenetics 2019; 11: 185.
17. Kling T, Wenger A, Beck S, Carén H. Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours. Clin Epigenetics 2017; 9: 33.
18. Kotredes KP, Razmpour R, Lutton E, Alfonso-Prieto M, Ramirez SH, Gamero AM. Characterization of cancer-associated IDH2 mutations that differ in tumorigenicity, chemosensitivity and 2-hydroxyglutarate production. Oncotarget 2019; 10: 2675-2692.
19. Lee M, Kang SY, Suh YL. Genetic alterations of epidermal growth factor receptor in glioblastoma: The usefulness of immunohistochemistry. Appl Immunohistochem Mol Morphol 2019; 27: 589-598.
20. Liu C, Tang H, Hu N, Li T. Methylomics and cancer: the current state of methylation profiling and marker development for clinical care. Cancer Cell Int 2023; 23: 242.
21. Louis DN, Perry A, Reifenberger G, von Deimling A, Figarella-Branger D, Cavenee WK, Ohgaki H, Wiestler OD, Kleihues P, Ellison DW. The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary. Acta Neuropathol 2016; 131: 803-820.
22. Louis DN, Perry A, Wesseling P, Brat DJ, Cree IA, Figarella-Branger D, Hawkins C, Ng HK, Pfister SM, Reifenberger G, Soffietti R, von Deimling A, Ellison DW. The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro Oncol 2021; 23: 1231-1251.
23. Lutsik P, Slawski M, Gasparoni G, Vedeneev N, Hein M, Walter J. MeDeCom: discovery and quantification of latent components of heterogeneous methylomes. Genome Biol 2017; 18: 55.
24. Lv SQ, Fu Z, Yang L, Li QR, Zhu J, Gai QJ, Mao M, He J, Qin Y, Yao XX, Lan X, Wang YX, Lu HM, Xiang Y, Zhang ZX, Huang GH, Yang W, Kang P, Sun Z, Shi Y, Yao XH, Bian XW, Wang Y. Comprehensive omics analyses profile genesets related with tumor heterogeneity of multifocal glioblastomas and reveal LIF/CCL2 as biomarkers for mesenchymal subtype. Theranostics 2022; 12: 459-473.
25. Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 1988; 16: 1215.
26. Miratashi Yazdi SA, Bakhshi N, Nazar E, Moradi Tabriz H, Gorji R. Epidermal growth factor receptor (EGFR) expression in high grade glioma and relationship with histopathologic findings, a cross sectional study. Int J Surg Open 2022; 46: 100527.
27. Moore LD, Le T, Fan G. DNA methylation and its basic function. Neuropsychopharmacology 2013; 38: 23-38.
28. Moran S, Vizoso M, Martinez-Cardús A, Gomez A, Matías-Guiu X, Chiavenna SM, Fernandez AG, Esteller M. Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray. Epigenetics 2014; 9: 829-833.
29. Morris TJ, Butcher LM, Feber A, Teschendorff AE, Chakravarthy AR, Wojdacz TK, Beck S. ChAMP: 450k chip analysis methylation pipeline. Bioinformatics 2014; 30: 428-430.
30. Nassiri F, Ajisebutu A, Patil V, Mamatjan Y, Liu J, Wang JZ, Voisin MR, Nejad R, Mansouri S, Karimi S, Chakravarthy A, Chen E, De Carvalho DD, Aldape K, Zadeh G. Metabologenomic characterization uncovers a clinically aggressive IDH mutant glioma subtype. Acta Neuropathol 2024; 147: 68.
31. Park JW, Lee K, Kim EE, Kim SI, Park SH. Brain tumor classification by methylation profile. J Korean Med Sci 2023; 38: e356.
32. Pratt D, Sahm F, Aldape K. DNA methylation profiling as a model for discovery and precision diagnostics in neuro-oncology. Neuro Oncol 2021; 23 (23 Suppl 5): S16-S29.
33. Priesterbach-Ackley LP, Boldt HB, Petersen JK, Bervoets N, Scheie D, Ulhøi BP, Gardberg M, Brännström T, Torp SH, Aronica E, Küsters B, den Dunnen WFA, de Vos FYFL, Wesseling P, de Leng WWJ, Kristensen BW. Brain tumour diagnostics using a DNA methylation-based classifier as a diagnostic support tool. Neuropathol Appl Neurobiol 2020; 46: 478-492.
34. Sahm F, Brandner S, Bertero L, Capper D, French PJ, FigarellaBranger D, Giangaspero F, Haberler C, Hegi ME, Kristensen BW, Kurian KM, Preusser M, Tops BBJ, van den Bent M, Wick W, Reifenberger G, Wesseling P. Molecular diagnostic tools for the World Health Organization (WHO) 2021 classification of gliomas, glioneuronal and neuronal tumors; an EANO guideline. Neuro Oncol 2023; 25: 1731-1749.Sejda A, Grajkowska W, Trubicka J, Szutowicz E, Wojdacz T, Kloc W,
35. Iżycka-Świeszewska E. WHO CNS5 2021 classification of gliomas: a practical review and road signs for diagnosing pathologists and proper patho-clinical and neuro-oncological cooperation. Folia Neuropathol 2022; 60: 137-152.
36. Spiegl-Kreinecker S, Pirker C, Filipits M, Lötsch D, Buchroithner J, Pichler J, Silye R, Weis S, Micksche M, Fischer J, Berger W. O6-Methylguanine DNA methyltransferase protein expression in tumor cells predicts outcome of temozolomide therapy in glioblastoma patients. Neuro Oncol 2010; 12: 28-36.
37. Suwala AK, Stichel D, Schrimpf D, Maas SLN, Sill M, Dohmen H, Banan R, Reinhardt A, Sievers P, Hinz F, Blattner-Johnson M, Hartmann C, Schweizer L, Boldt HB, Kristensen BW, Schittenhelm J, Wood MD, Chotard G, Bjergvig R, Das A, Tabori U, Hasselblatt M, Korshunov A, Abdullaev Z, Quezado M, Aldape K, Harter PN, Snuderl M, Hench J, Frank S, Acker T, Brandner S, Winkler F, Wesseling P, Pfister SM, Reuss DE, Wick W, von Deimling A, Jones DTW, Sahm F. Glioblastomas with primitive neuronal component harbor a distinct methylation and copy-number profile with inactivation of TP53, PTEN, and RB1. Acta Neuropathol 2021; 142: 179-189.
38. Tang K, Kurland D, Vasudevaraja V, Serrano J, Delorenzo M, Radmanesh A, Thomas C, Spino M, Gardner S, Allen JC, Nicolaides T, Osorio DS, Finlay JL, Boué DR, Snuderl M. Exploring DNA methylation for prognosis and analyzing the tumor microenvironment in pleomorphic xanthoastrocytoma. J Neuropathol Exp Neurol 2020; 79: 880-890.
39. Thakkar JP, Dolecek TA, Horbinski C, Ostrom QT, Lightner DD, Barnholtz-Sloan JS, Villano JL. Epidemiologic and molecular prognostic review of glioblastoma. Cancer Epidemiol Biomarkers Prev 2014; 23: 1985-1996.
40. Torre M, Vasudevaraja V, Serrano J, DeLorenzo M, Malinowski S, Blandin AF, Pages M, Ligon AH, Dong F, Meredith DM, Nasrallah MLP, Horbinski C, Dahiya S, Ligon KL, Santi M, Ramkissoon SH, Filbin MG, Snuderl M, Alexandrescu S. Molecular and clinicopathologic features of gliomas harboring NTRK fusions. Acta Neuropathol Commun 2020; 8: 107.
41. Tran PMH, Tran LKH, Nechtman J, Dos Santos B, Purohit S, Satter KB, Dun B, Kolhe R, Sharma S, Bollag R, She JX. Comparative analysis of transcriptomic profile, histology, and IDH mutation for classification of gliomas. Sci Rep 2020; 10: 20651.
42. Trubicka J, Łastowska M, Karkucińska-Więckowska A, Niemira M, Ejmont M, Sowińska A, Pronicki M, Matyja E, Grajkowska W. BCOR expression in paediatric pineoblastoma. Folia Neuropathol 2023; 61: 121-128.
43. Vij M, Cho BB, Yokoda RT, Rashidipour O, Umphlett M, Richardson TE, Tsankova NM. P16 immunohistochemistry is a sensitive and specific surrogate marker for CDKN2A homozygous deletion in gliomas. Acta Neuropathol Commun 2023; 11: 73.
44. Watkins SH, Ho K, Testa C, Falk L, Soule P, Nguyen LV, FitzGibbon S, Slack C, Chen JT, Smith GD, De Vivo I, Simpkin AJ, Tilling K, Waterman PD, Krieger N, Suderman M, Relton C. The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip. Epigenetics 2022; 17: 2366-2376.
45. Weller M, Felsberg J, Hentschel B, Gramatzki D, Kubon N, Wolter M, Reusche M, Roth P, Krex D, Herrlinger U, Westphal M, Tonn JC, Regli L, Maurage CA, von Deimling A, Pietsch T, Le Rhun E, Reifenberger G. Improved prognostic stratification of patients with isocitrate dehydrogenase-mutant astrocytoma. Acta Neuropathol 2024; 147: 11.
46. Whitfield BT, Huse JT. Classification of adult-type diffuse gliomas: Impact of the World Health Organization 2021 update. Brain Pathol 2022; 32: e13062.
47. Wojdacz TK, Dobrovic A. Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res 2007; 35: e41.
48. Wojdacz TK, Dobrovic A, Hansen LL. Methylation-sensitive high-resolution melting. Nat Protoc 2008; 3: 1903-1908.
49. Wu Z, Abdullaev Z, Pratt D, Chung HJ, Skarshaug S, Zgonc V, Perry C, Pack S, Saidkhodjaeva L, Nagaraj S, Tyagi M, Gangalapudi V, Valdez K, Turakulov R, Xi L, Raffeld M, Papanicolau-Sengos A, O’Donnell K, Newford M, Gilbert MR, Sahm F, Suwala AK, von Deimling A, Mamatjan Y, Karimi S, Nassiri F, Zadeh G, Ruppin E, Quezado M, Aldape K. Impact of the methylation classifier and ancillary methods on CNS tumor diagnostics. Neuro Oncol 2022; 24: 571-581.
Copyright: © 2024 Mossakowski Medical Research Centre Polish Academy of Sciences and the Polish Association of Neuropathologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License (http://creativecommons.org/licenses/by-nc-sa/4.0/), allowing third parties to copy and redistribute the material in any medium or format and to remix, transform, and build upon the material, provided the original work is properly cited and states its license.
EVENTS
Termedia
About us Contact
Copyright notice Privacy policy Advertising policy Contact us
Quick links
Journals Books eBooks Events
© 2025 Termedia Sp. z o.o.
Developed by Bentus.