Brain Tumor Study Investigates TRDMT1's Influence on DNA Methylation in Glioblastoma

Glioblastoma is a highly aggressive brain tumor with poor survival rates despite available treatments like surgery and chemotherapy. The tumor exhibits complex heterogeneity at various levels, including genomics, transcriptomics, and epigenomics, potentially contributing to drug resistance and cancer recurrence. However, the interplay between these alterations remains unclear, which has limited the progress in developing more effective therapies.

Prior studies have demonstrated that TRDMT1 knockout (KO) significantly affects the response of cancer cells to chemotherapy. Initially identified as a DNA methyltransferase, TRDMT1 is now known to be a 5-methylcytosine RNA methyltransferase involved in cellular responses to stress. This multifaceted protein not only influences chemotherapy responses but also affects genetic stability and cellular diversity within glioblastoma cells. It also plays a role in the regulation of microRNAs during times of cellular stress. However, there remains a lack of comprehensive information about how TRDMT1 specifically influences DNA methylation and related pathways in cancer cells.

In a study featured in the Journal of Neuro-Oncology, scientists from Poland’s National Research Institute of Animal Production and the University of Rzeszow's Institute of Biotechnology aimed to investigate the impact of knocking out the TRDMT1 gene on DNA methylation patterns. Their primary objective was to determine whether the removal of this gene would lead to significant changes in DNA methylation, which could shed light on its role in glioblastoma cells and potentially uncover new insights into the disease.

Using a CRISPR-based approach to obtain TRDMT1 KO glioblastoma cells, the researchers measured total 5-methylcytosine levels in DNA, DNMT1 enzyme availability, and DNMT activity using EpigenTek’s commercial ELISAs, including our MethylFlash™ Global DNA Methylation (5-mC) ELISA Easy Kit, DNMT1 Assay Kit, and DNA Methyltransferase Activity/Inhibition Assay Kit. Reduced representation bisulfite sequencing (RRBS) was also used to comprehensively evaluate the DNA methylome in glioblastoma cells with TRDMT1 KO.

Figure Assessing A) 5-mC in gDNA, B) DNMT1 levels, and C) DNMT activity. [Zabek T et. al. PMID: 37169948]

The results indicated that TRDMT1 KO in glioblastoma cells decreased global DNA methylation, lowered DNMT1 levels, and reduced DNMT activity. RRBS analysis revealed significant differences in DNA methylation patterns in TRDMT1 KO glioblastoma cells, particularly affecting genes associated with methylation and telomere biology.

Further bioinformatics analysis identified multiple gene ontology categories affected by TRDMT1 KO, including processes related to the nervous system, apoptosis, mTOR signaling, cellular senescence, and more. Hypomethylated genes were associated with the homeobox domain and cell junctions, while hypermethylated genes were linked to transcription and developmental proteins.

Overall, the findings indicate that TRDMT1 may have a role in modulating DNA methylation in glioblastoma cells, potentially impacting various cellular processes and pathways. While more research is needed to uncover the molecular mechanisms behind this gene’s influence on DNA methylome and its implications in cancer, the study suggests TRDMT1 levels and mutation status could serve as novel prognostic markers during glioblastoma progression.

For researchers investigating DNA methylation, EpigenTek offers a range of convenient kits, including the ones utilized in this study. See our full range of DNA methylation kitsand explore the services we offer for Representation Bisulfite Sequencing (RRBS).

Source: Zabek T et. al. (May 2023). Knockout of TRDMT1 methyltransferase affects DNA methylome in glioblastoma cells. J Neurooncol.