Base excision repair and its implications to cancer therapy

Abstract

Base excision repair (BER) has evolved to preserve the integrity of DNA following cellular oxidative stress and in response to exogenous insults. The pathway is a coordinated, sequential process involving 30 proteins or more in which single strand breaks are generated as intermediates during the repair process. While deficiencies in BER activity can lead to high mutation rates and tumorigenesis, cancer cells often rely on increased BER activity to tolerate oxidative stress. Targeting BER has been an attractive strategy to overwhelm cancer cells with DNA damage, improve the efficacy of radiotherapy and/or chemotherapy, or form part of a lethal combination with a cancer specific mutation/loss of function. We provide an update on the progress of inhibitors to enzymes involved in BER, and some of the challenges faced with targeting the BER pathway.

Keywords: Base excision repair; Cancer therapy; DNA damage; DNA repair.

Figure 1. Overview of SP-BER and LP-BER

(A) Base damage (red flag) is recognised by one of 11 damage-specific DNA glycosylases that are monofunctional (removes base creating an AP site); bifunctional (removes base and cleaves phosphodiester backbone 3′ to the lesion) or Nei-like (cleaves phosphodiester bond either side of lesion). APE1 incises the AP site, or removes the 3′-α,β-unsaturated aldehyde remaining from bifunctional DNA glycosylase action. PNKP is required to remove 3′-phosphate termini following Nei-like DNA base excision. At this stage, PARP1 recognises SSB/gap intermediates protecting these from degradation, and facilitates repair through protein recruitment. Polβ through its lyase activity excises the 5′-dRP moiety, and simultaneously fills the one nucleotide gap (green nucleotide). XRCC1-LigIIIα complex interacts with Polβ and repairs the remaining nick in the DNA, thus completing SP-BER. (B) When the 5′-DNA end is not amenable to Polβ, LP-BER is employed. A polymerase switch to Polδ/ε stimulates strand displacement and creates a 2–8 nucleotide 5′-flap. FEN1 cleaves the flap and LigI ligates the subsequent nick, both of which are stimulated by the PCNA clamp slider. Each enzymatic step of the pathway can be targeted by small molecule inhibitors, as indicated by the red cross.

Figure 2. Functions of PARP1 and PARG during BER

PARP1 (pink) recognises SSB/gap intermediates and uses NAD+ (red hexagon) to synthesise linear and branched chains of ADP-ribose units (red circles) to itself and/or other proteins. The BRCT1 domain of XRCC1 can bind poly(ADP-ribose), and make DNA contacts, allowing access for Polβ and LigIIIα to repair the break. Accumulation of PARP1 poly(ADP-ribosyl)ation causes PARP1 to be released through electrostatic repulsion. PARG subsequently cleaves the poly(ADP-ribose) chains allowing PARP1 to bind to additional SSB/gaps. The terminal ADP-ribose unit is refractory to PARG action, so ADP-ribose hydrolases (ARH) are needed for complete removal. PARPi (red cross) can lead to a trapped PARP–DNA complex that interferes with DNA replication.