DNA Methylation and Histone Modification in Low-Grade Gliomas: Current Understanding and Potential Clinical Targets

Abstract

Gliomas, the most common type of malignant primary brain tumor, were conventionally classified through WHO Grades I-IV (now 1-4), with low-grade gliomas being entities belonging to Grades 1 or 2. While the focus of the WHO Classification for Central Nervous System (CNS) tumors had historically been on histopathological attributes, the recently released fifth edition of the classification (WHO CNS5) characterizes brain tumors, including gliomas, using an integration of histological and molecular features, including their epigenetic changes such as histone methylation, DNA methylation, and histone acetylation, which are increasingly being used for the classification of low-grade gliomas. This review describes the current understanding of the role of DNA methylation, demethylation, and histone modification in pathogenesis, clinical behavior, and outcomes of brain tumors, in particular of low-grade gliomas. The review also highlights potential diagnostic and/or therapeutic targets in associated cellular biomolecules, structures, and processes. Targeting of MGMT promoter methylation, TET-hTDG-BER pathway, association of G-CIMP with key gene mutations, PARP inhibition, IDH and 2-HG-associated processes, TERT mutation and ARL9-associated pathways, DNA Methyltransferase (DNMT) inhibition, Histone Deacetylase (HDAC) inhibition, BET inhibition, CpG site DNA methylation signatures, along with others, present exciting avenues for translational research. This review also summarizes the current clinical trial landscape associated with the therapeutic utility of epigenetics in low-grade gliomas. Much of the evidence currently remains restricted to preclinical studies, warranting further investigation to demonstrate true clinical utility.

Keywords: ATRX; CpG island; DNMT; G-CIMP; H3K27M; MGMT; histone acetylation; methylation; methylomics; methyltransferases; tumor suppressor.

Figure 1

A summary view of the World Health Organization (WHO) 2021 classification of central nervous system (CNS) tumors. This original figure has been created using data available from the WHO CNS5 publication.

Figure 2

Altered DNA methylation and its downstream impact in the cancer cell. Reproduced with permission from [28].

Figure 3

Cytosine methylation and demethylation cycle. C, cytosine; 5mc, 5-methylCytosine; 5hmC, 5-hydroxymethylCytosine; 5fc,5-formylCytosine; 5caC, 5-carboxylCytosine, TDG, thymine-DNA glycosylase; BER, Base Excision Repair, TET, Ten-Eleven Translocases, DNMT, DNA Methyltransferases. Reproduced with permission from [48].

Figure 4

Mechanism of action of TERT enzyme, whose regulation is impacted by methylation of promoter and upstream THOR sequence. In the figure, TERT accesses the telomere complex at the terminal end of the DNA strand, through the Shelterin complex. It then catalyzes the addition of telomere repeat segments with the help of the hTERC enzyme, in a structure called Telomerase Complex. The latter’s function of telomere elongation works against the routine telomere shortening that occurs during DNA replication. Figure reproduced under Creative Commons Attribution-Noncommercial 4.0 License from [74].

Figure 5

Potential targets in the various pathways where DNA methylation plays a role in regulating gene expression in gliomas. (Green dots are unmethylated Cytosine, red dots are 5-methylCytosine; blue dots are 5-hydroxymethylcytosine). (A) Promoter hypermethylation may prevent the binding of transcriptional factors (TF), i.e., activator, leading to gene silencing. (B) In some other cases, a hypermethylated promoter may bind to the transcriptional repressor (REP) preferentially. When active demethylation occurs, REP is unable to bind and gene expression occurs. (C) In another gene, there may occur binding by two transcriptional factors (TFs), one to a methylated sequence and another to an unmethylated sequence. (D) In normal cells, TET enzymes convert 5mc to 5hmc and later into 5cac for maintenance purposes. When 2-Hydroxyglutarate (2-HG), a byproduct of mutant IDH enzymes, inhibits TET, a state of global hypermethylation occurs. (E) Relationship between DNA methylation and chromatin compaction. The latter is regulated by chromatin chaperones that are in turn affected by DNA methylation, histone methylation, and histone acetylation. ATRX binding to methylated gene sequences leads to an increased proportion of heterochromatin, thus reducing the binding of transcriptional factors (TFs) to DNA. (F) When CTCTF binding sites on the genome are methylated, then CTCF is unable to bind, leading to alteration in chromatin compaction. This causes an exchange of an insulator by an enhancer near the said sequence. Figure reproduced, with color correction, under Creative Commons Attribution-Noncommercial 4.0 license from [45].

Figure 6

Histone modification maps for a typical chromosome in normal and cancer cells. In normal cells, DNA sequences that include the promoters of tumor-suppressor genes have more histone modification marks associated with active transcription, such as acetylation of H3 and H4 lysine residues (e.g., K5, K8, K9, K12, and K16) along with trimethylation of K4 residue of H3 protein. The normal cell also has DNA repeats and other heterochromatic regions having repressive histone marks, such as trimethylation of K27 residue and dimethylation of the K9 residue of H3, and trimethylation of K20 of H4. In cancer cells, there is a loss of the “active” histone marks on promoters of tumor-suppressor genes, leading to a tighter chromatin configuration. Additionally, the neoplastic cell has a loss of repressive marks at subtelomeric DNA and other repeat regions, causing a more “relaxed” chromatin conformation in these regions. Figure reproduced with permission from [28].