Base excision repair: contribution to tumorigenesis and target in anticancer treatment paradigms

Abstract

Cancer treatments often lose their effectiveness due to the development of multiple drug resistance. Thus, identification of key proteins involved in the tumorigenic process and the survival mechanism(s), coupled with the design of novel therapeutic compounds (such as small molecule inhibitors), are essential steps towards the establishment of improved anticancer treatment strategies. DNA repair pathways and their proteins have been exposed as potential targets for combinatorial anticancer therapies that involve DNA-interactive cytotoxins, such as alkylating agents, because of their central role in providing resistance against DNA damage. In addition, an understanding of the tumor-specific genetics and associated DNA repair capacity has allowed research scientists and clinicians to begin to devise more targeted treatment strategies based on the concept of synthetic lethality. In this review, the repair mechanisms, as well as the links to cancer progression and treatment, of three key proteins that function in the base excision repair pathway, i.e. APE1, POLβ, and FEN1, are discussed.

Figure 1

The mammalian base excision repair and single-strand break repair pathways. Base excision repair (BER) begins by the removal of the damaged base by a monofunctional or bifunctional DNA glycosylase to leave an AP site (AP). After excision by a monofunctional glycosylase, APE1 cleaves the DNA backbone 5′ of the AP site. Base excision by a bifunctional DNA glycosylase is followed by incision 3′ to the AP site by either β- or β,δ-elimination via intrinsic 3′-AP lyase activity of NTH1, OGG1, or NEIL1. The 3′ or 5′ ends then undergo end processing by POLβ, APE1, or PNKP, depending on the obstructive termini. PARP1 recognizes such single-strand breaks, and end processing may utilize other factors such as TDP1 or APTX. After end processing, the BER pathway diverges into two sub-pathways: short-patch or long-patch. In short-patch BER, the single-nucleotide gap is repaired by POLβ in coordination with the scaffold protein/ligase complex of XRCC1/LIG3α. In long-patch BER, following strand-displacement synthesis of 2–13 nucleotides by POLβ and/or Polδ/ε (aided by PCNA and RFC), the 5′-DNA flap is removed by FEN1 and the backbone is subsequently ligated by LIG1. See text for additional details.

Figure 2

Protein structure of base excision repair proteins: APE1, POLβ, and FEN1 I. The human (Hu) APE1 protein has a C-terminal sequence of about 265 amino acids that is conserved across species with E. coli exonuclease III and D. melanogaster (Dros) Rpr1. This region contains the DNA repair active site of the protein. The N-terminus of APE1 differs between species. The size of the protein is denoted to the right: Hu APE1 is 318 amino acids (aa), exonuclease III is 268 aa, and Rpr1 is 679 aa. The Hu APE1 3D protein structure (PDB ID # 1DE8) is shown below. II. Hu DNA POLβ is 335 aa (designated to right) and shares multiple helix-hairpin-helix motifs that are conserved between species, including in polymerase X (PolX) from T. aquaticus (Taq) and PolX from Dros. The 3D structure of Hu POLβ is shown below (PDB ID# 3RH4), and is commonly referred to as a hand, palm, and fingers structure. III. Hu FEN1 protein is 380 aa in length (designated to right), and the N-terminus, Intermediate, and C-terminal regions of the protein are conserved in S. cervisiae and in mice. Although eukaryotic FEN1 proteins harbor these 3 regions, prokaryotic versions only contain the N-terminus and Intermediate regions [152]. The 3D structure of the Hu FEN1 protein is shown below (PDB ID# 3Q8K). In each protein structure, helices are in red, β sheets in purple, and DNA in green.