DNA Methylation Malleability and Dysregulation in Cancer Progression: Understanding the Role of PARP1

Abstract

Mammalian genomic DNA methylation represents a key epigenetic modification and its dynamic regulation that fine-tunes the gene expression of multiple pathways during development. It maintains the gene expression of one generation of cells; particularly, the mitotic inheritance of gene-expression patterns makes it the key governing mechanism of epigenetic change to the next generation of cells. Convincing evidence from recent discoveries suggests that the dynamic regulation of DNA methylation is accomplished by the enzymatic action of TET dioxygenase, which oxidizes the methyl group of cytosine and activates transcription. As a result of aberrant DNA modifications, genes are improperly activated or inhibited in the inappropriate cellular context, contributing to a plethora of inheritable diseases, including cancer. We outline recent advancements in understanding how DNA modifications contribute to tumor suppressor gene silencing or oncogenic-gene stimulation, as well as dysregulation of DNA methylation in cancer progression. In addition, we emphasize the function of PARP1 enzymatic activity or inhibition in the maintenance of DNA methylation dysregulation. In the context of cancer remediation, the impact of DNA methylation and PARP1 pharmacological inhibitors, and their relevance as a combination therapy are highlighted.

Keywords: DNA demethylases; DNA demethylases inhibitors; DNA methylation; PARP1; cancer cells; oncogene; poly(ADP-ribose); tumor progression; tumor suppressor gene.

Figure 1

The difference in differential DNA methylation in normal and cancer cells. In PARG or homologous DNA-repair-defective cancer cells the enzymatic activity of PARP1 is increased; therefore, auto-poly(ADP-ribosy)lated PARP1 moves away from the pre-occupied promoter of oncogenes and provides the access to transcription machinery for expression. In downstream, it facilitates DNA hypomethylation at the promoters of oncogenes and make them transcriptional active De novo DNA methyltransferases (DNMTs) promote DNA methylation by catalyzing the transfer of a methyl group from donor S-adenosyl-l-methionine (SAM) to cytosine bases to produce 5mC. The DNMT family consists of five members—DNMT1, DNMT2, DNMT3A, DNMT3B and DNMT3L (Figure 2A) [35,36]. Interestingly, DNMTs’ important actions during DNA methylation may be divided into two categories, methylation maintenance and de novo methylation. DNA methylation is predominantly maintained by DNMT1, which facilitates copying DNA methylation patterns during DNA replication in the S phase of mitosis and meiosis [37]. The epigenetic mark can then self-replicate because of DNMT maintenance, which recognizes mono-methylation and methylates the CpG site’s complementary strand, leading to a di-methylated tag. Double-stranded methylation, during which the two methyl groups accept a syn conformation in the major groove, can modulate chromatin architecture and regulate gene transcription [38]. DNMT3A and DNMT3B are de novo methyltransferases; they potentially develop a new DNA methylation signature for unmethylated CpGs of DNA and are recognized as de novo DNMT enzymes [39,40]. DNMT3A or DNMT3B catalyzes the methylation of previously unmethylated DNA (de novo methylation) in embryonic stem cells and tumor cells [41]. DNMT3A and DNMT3B can also aid in the maintenance of DNA methylation [42,43]. Accumulating evidence suggests that DNMT3L (DNMT3-like) has no catalytic activity because some crucial motifs have been lost or altered [44]. However, DNMT3L contributes as an essential cofactor for de novo methyltransferase by expediting the interaction among DNMT3A, DNMT3B and DNA, and stimulating their activity [39,40,45,46].

Figure 2

Schematic structure of human DNMT, DNMT3-like, TET family and PARP1 proteins. (A) DMAP, DMAP1-binding domain; PCNA, Proliferating Cell Nuclear Antigen domain; NLS, Nuclear Localization Signal domain; DNMT1-RFD, Cytosine-specific DNA methyltransferase replication foci domain; Zf-CXXC, CXXC zinc finger domain; BAH, Bromo adjacent homology domain; DCM, DNA-cytosine methylase; Cyt_C5_DNA_methylase, Cytosine-C5 specific DNA methylases; PWWP, domain comprising a conserved proline–tryptophan–tryptophan–proline motif; PHD, plant homeodomain; The sequences are derived from data reported under accession numbers NP_001124295 for DNMT1, NP_004403 for DNMT2, NP_783328 for DNMT3A, NP_008823 for DNMT3B and NP_037501 for DNMT3L. (B) Domain structures of ten–eleven translocation methylcytosine dioxygenases (TETs). Schematic representation of conserved domains of human TET proteins is shown, including a double-stranded-helix (DSBH) fold (all TETs), cysteine-rich (Cys-rich) domain (all TETs) and CXXC zinc fingers (Zf-CXXC; in TET1 and TET3). The sequences are derived from data reported under accession numbers NP_085128 for TET1, NP_001120680 for TET2 and NP_001274420 for TET3. (C) Domain structure of PARP1. PARP1 has four main domains, an amino (N)-terminal DNA-binding domain, an auto-modification domain, a water-binding domain and a carboxy (C)-terminal catalytic domain. ZFI, zinc finger I; ZF2, zinc finger II; ZF3, zinc finger III; NLS, nuclear localization signal; BRCT, BRCA1 C-terminal domain; PRD, PARP regulatory domain; ART, ADP-ribosyl transferase subdomain.

Figure 3

Steps for dynamic modifications of Cytosine and TET-mediated oxidation. (A) The methylation of deoxycytosine (C) residues to 5-methylcytosine (5mC) are introduced by DNA methyltransferase (DNMT) enzymes and sequentially oxidized by ten–eleven translocation (TET) enzymes via 5-hydroxymethylcytosine (5mC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). SAM, S-adenosylmethionine; SAH, S-adenosylhomocysteine; α-KG, α-ketoglutarate. (B) 5fC and 5caC are identified and excised by thymine DNA glycosylase (TDG) to produce an abasic site. The base-excision-repair (BER) pathway implicates excision of the abasic site, replacement of the nucleotide using unmodified deoxycytidine triphosphate (dCTP) by a DNA polymerase (generating pyrophosphate, PPi) and ligation to repair the nick.

Figure 4

Increased poly(ADP-ribosyl)ation precludes DNMT1 and SIRT6 enzymatic activities. In cancer cells (prostate), the poly(ADP-ribosyl)ation pathway is severely disrupted, resulting in an enhanced activity that not only poly(ADP-ribosyl)ates PARP1 but also DNMT1; therefore, it prevents the maintenance of DNA methylation on newly synthesized DNA strands. Scarcity of NAD⁺ makes SIRT6 enzymatically inactive to remove the acetyl group from histone proteins, eventually facilitating the transcription of oncogenes. The PARP1 inhibitor reverts all activities, which leads to the suppression of oncogenes.

Figure 5

Enhanced poly(ADP-ribosyl)ation maintains DNA hypomethylation by activating TET1 functions. PARP1 binds to TSGs in their promoter region in normal cells. In PARG or homologous DNA-repair-defective cells, the enzymatic activity of PARP1 is increased (although TET1 activates PARP1 independently of DNA breaks) and poly(ADP-ribosyl)ated TET1 performs its DNA de-methylation function. It leads DNA hypomethylation on the regulatory regions of genes in cancer cells. Eventually, it facilitates the expression of TSGs; although this is not quite straightforward in malignant cells, it is a model to understand the functional dependency of proteins to each other and it is helpful to develop therapies by taking advantage of them.

Figure 6

TET1 stimulates the activity of PARP1 independently of DNA damage. Poly(ADP-ribosyl)ation of TET1 by PARP1 increases TET1 enzymatic activity and regulates the hydroxylase activity of the DNA demethylation processes. Poly(ADP-ribosyl)ation of TET1 preserves the unmethylated state and activates the transcription of oncogenes. The PARP1 inhibitor inhibits the enzymatic activity of TET1, as a result, the expression of oncogenes is downregulated due to hypermethylation. Availability of NAD⁺ makes SIRT6 enzymatically active to remove the acetyl group from histone proteins, further downregulating the transcription of oncogenes.