Metabolic defects provide a spark for the epigenetic switch in cancer

Abstract

Cancer is a pathology that is associated with aberrant gene expression and an altered metabolism. Whereas changes in gene expression have historically been attributed to mutations, it has become apparent that epigenetic processes also play a critical role in controlling gene expression during carcinogenesis. Global changes in epigenetic processes, including DNA methylation and histone modifications, have been observed in cancer. These epigenetic alterations can aberrantly silence or activate gene expression during the formation of cancer; however, the process leading to this epigenetic switch in cancer remains unknown. Carcinogenesis is also associated with metabolic defects that increase mitochondrially derived reactive oxygen species, create an atypical redox state, and change the fundamental means by which cells produce energy. Here, we summarize the influence of these metabolic defects on epigenetic processes. Metabolic defects affect epigenetic enzymes by limiting the availability of cofactors like S-adenosylmethionine. Increased production of reactive oxygen species alters DNA methylation and histone modifications in tumor cells by oxidizing DNMTs and HMTs or through direct oxidation of nucleotide bases. Last, the Warburg effect and increased glutamine consumption in cancer influence histone acetylation and methylation by affecting the activity of sirtuins and histone demethylases.

Fig. 1. Pyrimidine ring structures for cytosine and 5-methyl-cytosine (5-Me-C)

The addition of methyl group to position 5 of the cytosine nucleobase (dashed box) creates 5-Me-C in genomic DNA.

Fig. 2. The sites of lysine acetylation and methylation in histone tails

Histone tails protrude from the central globular domain of histone proteins and can be modified by acetylation and methylation in various ways. (* denotes lysine can be mono, di, or tri methylated)

Fig. 3. The structures of the epigenetic metabolites S-adenosylmethionine and S-adenosylhomocysteine

During transmethylation reactions the methyl group of S-adenosylmethionine (dashed box) serves as a nucleophile to attack C-5 of cytosine, and the ε-N of lysine. Once the reaction is complete, S-adenosylhomocysteine is released and utilized in other biochemical reactions.

Fig. 4. Enzymatic mechanism of DNA methyltransferases (DNMTs)

Methylation of cytosine begins with the nucleophillic attack of position 6 by a thiolate nucleophile. The resulting electron rich region at position 5 is then at attacked by the methyl group of Sadenosylmethionine (SAM). The reaction then proceeds with the removal of the hydrogen at position 5 by a basic amino acid in the active site of DNMT. In the final step, the double bond is reformed in the pyrimidine ring, resulting in elimination of bond between position 6 and the DNMT.

Fig. 5. Oxidation of nucleotide bases within methylated CpGs alters epigenetic processes

(A) Oxidation of guanine within a methylated CpG doublet abrogates MBP function, resulting in an epigenetic change. If these oxidized bases are not removed by 8-oxoguanine glycosylase 1 (OGG1) the epigenetic defect can be passed on during DNA replication and result in an unmethylated CpG. (B) Incorporation of oxidized GTP during DNA replication results in a methylated strand, and a hemimethylated CpG that is resistant to DNMTs. Removal of 8-oxoG by OGG1 and repair by base excision repair machinery (BER), creates an unmethylated CpG. (C) Oxidation of 5-methylcytosine creates 5-hydroxymethylcytosine (HMe). If this base is not removed by HMC glycosylases (HMCG) MBP function is lost at the site of oxidation and can create a hemimethylated strand following DNA replication. This epigenetic change can then persist as an unmethylated CpG in subsequent cell divisions.

Fig. 6. The oxidative demethylation of 5-Me-cytosine to cytosine

Progressive oxidation of the carbon within the methyl group of 5-methyl cytosine (5-Me-C) results in its demethylation, and formation of cytosine. Each of the intermediates produced during the oxidation process are stable within DNA and affect epigenetic processes in a unique manner.

Fig. 7. The current model for the relationship between cancer metabolic defects and epigenetic processes

(A) Tumor cells increase their production of GSH to counter mitochondrially derived oxidants such as O₂^•− and H₂O₂. To sustain GSH production, cancer cells divert metabolites away from the methionine cycle into the transsulfuration pathway, resulting in decreased SAM production. (B) Aberrant production of oxidants creates an atypical redox state by decreasing the GSH/GSSG ratio which affects the activities of SAM synthetases, DNMTs and HMTs. (C) The increased Glc (glucose) consumption of the Warburg effect decreases the NAD⁺/NADH ratio and produces Pyr (pyruvate). Decreasing this ratio creates an environment that inhibits the activity of sirtuins, and liberates genes from their negative regulation. (D) Oxidation of glutamine (Gln), and dysfunctional electron transport, alters the flow of α-KG (α-ketoglutarate) and Suc (succinate) metabolites within the Krebs cycle. These metabolites can then influence transcription in the nucleus by affecting the activity of KDMs (lysine demethylases).