Bisulfite profiling of the MGMT promoter and comparison with routine testing in glioblastoma diagnostics

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• dc.contributor.author Tierling, Sascha
• dc.contributor.author Jürgens-Wemheuer, Wiebke M.
• dc.contributor.author Leismann, Alea
• dc.contributor.author Becker-Kettern, Julia
• dc.contributor.author Scherer, Michael
• dc.contributor.author Wrede, Arne
• dc.contributor.author Breuskin, David
• dc.contributor.author Urbschat, Steffi
• dc.contributor.author Sippi, Christoph
• dc.contributor.author Oertel, Joachim
• dc.contributor.author Schulz-Schaeffer, Walter J.
• dc.contributor.author Walter, Jörn
• dc.date.accessioned 2022-04-05T10:07:26Z
• dc.date.available 2022-04-05T10:07:26Z
• dc.date.issued 2022
• dc.description.abstract Background: Promoter methylation of the DNA repair gene O6-methylguanine-DNA methyltransferase (MGMT) is an acknowledged predictive epigenetic marker in glioblastoma multiforme and anaplastic astrocytoma. Patients with methylated CpGs in the MGMT promoter benefit from treatment with alkylating agents, such as temozolomide, and show an improved overall survival and progression-free interval. A precise determination of MGMT promoter methylation is of importance for diagnostic decisions. We experienced that different methods show partially divergent results in a daily routine. For an integrated neuropathological diagnosis of malignant gliomas, we therefore currently apply a combination of methylation-specific PCR assays and pyrosequencing. Results: To better rationalize the variation across assays, we compared these standard techniques and assays to deep bisulfite sequencing results in a cohort of 80 malignant astrocytomas. Our deep analysis covers 49 CpG sites of the expanded MGMT promoter, including exon 1, parts of intron 1 and a region upstream of the transcription start site (TSS). We observed that deep sequencing data are in general in agreement with CpG-specific pyrosequencing, while the most widely used MSP assays published by Esteller et al. (N Engl J Med 343(19):1350-1354, 2000. https://doi.org/10.1056/NEJM200011093431901 ) and Felsberg et al. (Clin Cancer Res 15(21):6683-6693, 2009. https://doi.org/10.1158/1078-0432.CCR-08-2801 ) resulted in partially discordant results in 22 tumors (27.5%). Local deep bisulfite sequencing (LDBS) revealed that CpGs located in exon 1 are suited best to discriminate methylated from unmethylated samples. Based on LDBS data, we propose an optimized MSP primer pair with 83% and 85% concordance to pyrosequencing and LDBS data. A hitherto neglected region upstream of the TSS, with an overall higher methylation compared to exon 1 and intron 1 of MGMT, is also able to discriminate the methylation status. Conclusion: Our integrated analysis allows to evaluate and redefine co-methylation domains within the MGMT promoter and to rationalize the practical impact on assays used in daily routine diagnostics.
• dc.description.sponsorship Funding: Open Access funding enabled and organized by Projekt DEAL. This work was supported by the German Epigenome Programme (DEEP) of the Federal Ministry of Education and Research in Germany (BMBF) (01KU1216F). MS is supported by the BMBF project de.NBI-epi (031L0101D) and the EU H2020 project SYSCID (733100)
• dc.format.mimetype application/pdf
• dc.identifier.citation Tierling S, Jürgens-Wemheuer WM, Leismann A, Becker-Kettern J, Scherer M, Wrede A et al. Bisulfite profiling of the MGMT promoter and comparison with routine testing in glioblastoma diagnostics. Clin Epigenetics. 2022 Feb 18;14(1):26. DOI: 10.1186/s13148-022-01244-4.
• dc.identifier.doi http://dx.doi.org/10.1186/s13148-022-01244-4
• dc.identifier.issn 1868-7075
• dc.identifier.uri http://hdl.handle.net/10230/52828
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/733100
• dc.rights © Sascha Tierling et al. 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri https://creativecommons.org/licenses/by/4.0/
• dc.subject.other Glioblastoma multiforme
• dc.subject.other ADN -- Metilació
• dc.subject.other Diagnòstic
• dc.title Bisulfite profiling of the MGMT promoter and comparison with routine testing in glioblastoma diagnostics
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion