Effects of Repeated Freeze and Thaw Cycles on the Genome-Wide DNA Methylation Profile of Isolated Genomic DNA

Kopfnagel, Verena; Klopp, Norman; Bernemann, Inga; Nizhegorodtseva, Nataliia; Wilson, Rory; Gronauer, Raphael; Seifert, Martin; Illig, Thomas

doi:10.1089/bio.2022.0045

Cited by 2 publications

(2 citation statements)

References 25 publications

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“…DNA methylation is a mechanism contributing to tumour initiation, growth, advancement, progression, recurrence, and metastasis [96,97]. DNA methylation involves the attachment of a methyl group to the C5 position of cytosine-guanine dinucleotides (CpG) [96,98,99]. CpG-rich regions are known as CpG islands, defined as regions with a GC content greater than 50%, a CpG ratio higher than 60%, and a minimum length of 200 base pairs [98,99].…”

Section: Dna Methylation Biomarkers For Crc Metastasismentioning

confidence: 99%

“…DNA methylation involves the attachment of a methyl group to the C5 position of cytosine-guanine dinucleotides (CpG) [96,98,99]. CpG-rich regions are known as CpG islands, defined as regions with a GC content greater than 50%, a CpG ratio higher than 60%, and a minimum length of 200 base pairs [98,99]. Hypermethylation (the gain of methylation) in the CpG-rich promoter regions causes the silencing of transcriptional genes in CRC [97].…”

Section: Dna Methylation Biomarkers For Crc Metastasismentioning

confidence: 99%

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Exploring Potential Epigenetic Biomarkers for Colorectal Cancer Metastasis

Ajithkumar,

Vasantharajan,

Pattison

et al. 2024

IJMS

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Metastatic progression is a complex, multistep process and the leading cause of cancer mortality. There is growing evidence that emphasises the significance of epigenetic modification, specifically DNA methylation and histone modifications, in influencing colorectal (CRC) metastasis. Epigenetic modifications influence the expression of genes involved in various cellular processes, including the pathways associated with metastasis. These modifications could contribute to metastatic progression by enhancing oncogenes and silencing tumour suppressor genes. Moreover, specific epigenetic alterations enable cancer cells to acquire invasive and metastatic characteristics by altering cell adhesion, migration, and invasion-related pathways. Exploring the involvement of DNA methylation and histone modification is crucial for identifying biomarkers that impact cancer prediction for metastasis in CRC. This review provides a summary of the potential epigenetic biomarkers associated with metastasis in CRC, particularly DNA methylation and histone modifications, and examines the pathways associated with these biomarkers.

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Section: Dna Methylation Biomarkers For Crc Metastasismentioning

confidence: 99%

Section: Dna Methylation Biomarkers For Crc Metastasismentioning

confidence: 99%

Exploring Potential Epigenetic Biomarkers for Colorectal Cancer Metastasis

Ajithkumar,

Vasantharajan,

Pattison

et al. 2024

IJMS

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Analysis of gliomas DNA methylation: Assessment of pre-analytical variables

Bomsztyk,

Mar,

Denisenko

et al. 2024

Preprint

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Precision oncology is driven by molecular biomarkers. For glioblastoma multiforme (GBM), the most common malignant adult primary brain tumor, O6-methylguanine-DNA methyltransferase (MGMT) gene DNA promoter methylation is an important prognostic and treatment clinical biomarker. Time consuming pre-analytical steps such as biospecimen storage before fixing, sampling, and processing are major sources of errors and batch effects, that are further confounded by intra-tumor heterogeneity of MGMT promoter methylation. To assess the effect of pre-analytical variables on GBM DNA methylation, tissue storage/sampling (CryoGrid), sample preparation multi-sonicator (PIXUL) and 5-methylcytosine (5mC) DNA immunoprecipitation (Matrix MeDIP-qPCR/seq) platforms were used. MGMT promoter CpG methylation was examined in 173 surgical samples from 90 individuals, 50 of these were used for intra-tumor heterogeneity studies. MGMT promoter methylation levels in paired frozen and formalin fixed paraffin embedded (FFPE) samples were very close, confirming suitability of FFPE for MGMT promoter methylation analysis in clinical settings. Matrix MeDIP-qPCR yielded similar results to methylation specific PCR (MS-PCR). Warm ex-vivo ischemia (37oC up to 4hrs) and 3 cycles of repeated sample thawing and freezing did not alter 5mC levels at MGMT promoter, exon and upstream enhancer regions, demonstrating the resistance of DNA methylation to the most common variations in sample processing conditions that might be encountered in research and clinical settings. 20-30% of specimens exhibited intratumor heterogeneity in the MGMT DNA promoter methylation. Collectively these data demonstrate that variations in sample fixation, ischemia duration and temperature, and DNA methylation assay technique do not have significant impact on assessment of MGMT promoter methylation status. However, intratumor methylation heterogeneity underscores the need for histologic verification and value of multiple biopsies at different GBM geographic tumor sites in assessment of MGMT promoter methylation. Matrix-MeDIP-seq analysis revealed that MGMT promoter methylation status clustered with other differentially methylated genomic loci (e.g. HOXA and lncRNAs), that are likewise resilient to variation in above post-resection pre-analytical conditions. These MGMT-associated global DNA methylation patterns offer new opportunities to validate more granular data-based epigenetic GBM clinical biomarkers where the CryoGrid-PIXUL-Matrix toolbox could prove to be useful.

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Effects of Repeated Freeze and Thaw Cycles on the Genome-Wide DNA Methylation Profile of Isolated Genomic DNA

Cited by 2 publications

References 25 publications

Exploring Potential Epigenetic Biomarkers for Colorectal Cancer Metastasis

Exploring Potential Epigenetic Biomarkers for Colorectal Cancer Metastasis

Analysis of gliomas DNA methylation: Assessment of pre-analytical variables

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