Review
Evidence for base excision repair processing of DNA interstrand crosslinks

https://doi.org/10.1016/j.mrfmmm.2012.11.007Get rights and content

Abstract

Many bifunctional alkylating agents and anticancer drugs exert their cytotoxicity by producing cross links between the two complementary strands of DNA, termed interstrand crosslinks (ICLs). This blocks the strand separating processes during DNA replication and transcription, which can lead to cell cycle arrest and apoptosis. Cells use multiple DNA repair systems to eliminate the ICLs. Concerted action of repair proteins involved in Nucleotide Excision Repair and Homologous Recombination pathways are suggested to play a key role in the ICL repair. However, recent studies indicate a possible role for Base Excision Repair (BER) in mediating the cytotoxicity of ICL inducing agents in mammalian cells. Elucidating the mechanism of BER mediated modulation of ICL repair would help in understanding the recognition and removal of ICLs and aid in the development of potential therapeutic agents. In this review, the influence of BER proteins on ICL DNA repair and the possible mechanisms of action are discussed.

Highlights

BER pathway is mainly involved in the excision of damaged bases from the DNA. ► BER is also involved in the processing of bulky lesions and interstrand crosslinks. ► BER proteins process ICLs, mostly based on the distinct DNA structural distortions.

Introduction

Cellular DNA is under constant threat from endogenous sources such as reactive oxygen species (ROS) and exogenous sources such as environmental oxidants, alkylating agents and anticancer drugs. The most common DNA lesions are base modifications such as alkylation, oxidation, loss of bases and single strand breaks. Complex and more toxic lesions include crosslinks and double strand breaks [1], [2]. Cells are endowed with the inherent capacity to respond to and eliminate these DNA lesions. The lesions are typically recognized and removed by various DNA repair pathways [3]. The base excision repair (BER) pathway as its name suggests is mainly involved in the excision of damaged bases from the DNA. It is considered as the predominant repair system in the protection of cells against a broad range of small base lesions resulting from oxidation, alkylation and deamination [4]. The BER pathway is a highly conserved, multistep process which requires the concerted action of several proteins [5]. It has been estimated that cells encounter ∼10,000 damaged bases per day, most of which are removed by BER [6], [7], [8].

The initiation of BER occurs by the action of DNA glycosylases which recognize alterations to the DNA bases and remove the altered bases by hydrolyzing the N-glycosidic bond. Once the damaged base is removed by a glycosylase, the resulting sugar–phosphate backbone without the base is called an apurinic/apyrimidinic (AP) site [9], [10]. AP endonuclease1 (APE1) cleaves the phosphate backbone resulting in a nick with a 3′ hydroxyl group and 5′deoxyribose phosphate (dRP) residue. The oxidation/reduction state of this 5′deoxyribose is a crucial factor in determining the subsequent downstream processing. If the dRP is not oxidized/reduced, this will lead to the activation of the short-patch BER pathway with the recruitment of DNA Polymerase β (Pol β). The dRP is cleaved by the lyase activity of Pol β and the one nucleotide gap is also filled by Pol β. The final nick is subsequently ligated by the DNA ligase III and XRCC1 complex [10]. If there is any change in the oxidative state of the dRP residue, this leads to the inhibition of the lyase activity of Pol β and activation of other polymerase activity resulting in strand displacement which leads to a 2–10 nucleotide flap intermediate, which is cleaved by FEN1 and joined by DNA Ligase-I [11]. The latter process is termed long-patch repair and requires the action of PCNA [10]. In addition to the oxidized state of the dRP residue, lesion specificity, protein–protein interaction and cell cycle status can also influence the specific choice of BER sub-pathways [12], [13]. The nucleotide incision pathway (NIR) is suggested to be the backup of the BER pathway where Ape1 incises the damaged DNA independent of glycosylase cleavage [14].

Recent studies indicate that BER proteins have broad substrate specificity and they interact with each other to catalyze the repair of DNA lesions [15], [16]. However, in the context of drug therapy, effective BER can render cells resistant to alkylating agents by repairing the DNA adducts that would otherwise be cytotoxic [17], [18]. For example, BER repairs the DNA lesions induced by alkylating agents such as methyl methane sulphonate (MMS) and temozolomide and over expression of BER proteins enhance resistance to these drugs [19], [20]. Therefore, several attempts have been made to target the BER proteins to increase cell sensitivity to alkylating agents [21], [22]. Generation of knock-out mice and identification of small molecule inhibitors of BER proteins have proven to be useful tools to dissect the mechanisms of drug resistance. Several small molecule inhibitors of APE1, Pol β and PARP were tested extensively for their ability to enhance the cytotoxicity of alkylating anticancer agents and some of them have been successful in clinical trials [23], [24], [25], [26], [27], [28]. BER proteins interact with proteins from other DNA repair pathways and this cross-talk/co-ordination has implications for combination therapy targeting two DNA repair pathways simultaneously [29], [30].

Section snippets

Interstrand crosslinks (ICLs)

DNA interstrand crosslinks are formed between both strands of DNA and these covalent links are highly toxic to cells [31], [32]. It has been shown that it takes only a single ICL to kill repair-deficient bacteria and yeast, and about 40 ICLs to kill repair-deficient mammalian cells [33], [34]. The ICLs form an absolute block to metabolic processes such as DNA replication and transcription, trigger cell cycle arrest and apoptosis, ultimately resulting in cell death [35]. In addition, ICLs are

Glycosylases

In BER, specific DNA glycosylases recognize corresponding damaged bases and cleave the N-glycosidic bond between abnormal bases and deoxyribose, leaving either an abasic site or a DNA single-strand break [78]. Several DNA glycosylases are identified in humans, which bind specifically to the modified base initiating the BER pathway. Cell survival assays display differential effects of glycosylases on the sensitivity of ICL inducing agents. 3-alkyladenine-DNA glycosylase (AAG), also called

Endonucleases

Ape1/Ref1 performs complex functions in cells through redox dependent and independent mechanisms. It acts as a transcriptional coactivator, regulates apoptosis, proliferation, differentiation, and production of ROS. In the BER pathway, it acts as an endonuclease that cleaves the abasic sites generated by the action of DNA glycosylases [92], [93]. Over expression of Ape1 has been observed in cancer cells and tumor samples which serves as a diagnostic and prognostic marker and also correlates

Polymerases

Polymerase β (Pol β) belongs to the X family DNA polymerases and is well characterized for a role in DNA repair [125]. Studies have established the role of Pol β in both short-patch and long-patch BER [126]. Pol β has dRP lyase activity which is shown to be a rate-limiting step in the BER pathway [127]. This gap filling polymerase has been identified as being error prone which is evident by increased mutagenesis when it is over expressed. Over-expression of Pol β leads to bifunctional DNA

Other BER proteins

BER proteins including XRCC1 and PARP are also involved in processing ICLs. XRCC1 is involved in the repair of single strand breaks (SSB) generated during BER and acts as a scaffold, connecting other BER proteins such as PARP, Pol β and DNA ligase III [151]. Polymorphisms in the XRCC1 gene have been associated with increased risk of developing certain cancers and also used as a prognostic marker in platinum-treated lung and gastric cancer patients [151], [152], [153]. Down regulation of XRCC1

Conclusion

ICLs covalently link the two strands of DNA and block the denaturing cellular processes that occur during DNA replication and transcription. ICLs are cytotoxic DNA lesions that are formed by a variety of anticancer drugs such as cisplatin, mitomycin C, psoralen, nitrosureas and nitrogen mustard derivatives. These crosslinking agents distort the DNA double helix, each in a unique manner. The repair of ICLs is still not completely understood in eukaryotes and the participation of different DNA

Conflict of interest

None declared

Acknowledgement

We thank members of the Patrick lab for critical reading of the manuscript. This study was supported by a grant from the National Institutes of Health (1R01-GM088249) to SMP.

References (156)

  • P.D. Lawley et al.

    DNA adducts from chemotherapeutic agents

    Mut. Res. Fundam. Mol. Mech. Mutagen.

    (1996)
  • V.S. Jonnalagadda et al.

    Interstrand crosslink-induced homologous recombination carries an increased risk of deletions and insertions

    DNA Repair

    (2005)
  • V.J. Spanswick et al.

    Repair of DNA interstrand crosslinks as a mechanism of clinical resistance to melphalan in multiple myeloma

    Blood

    (2002)
  • M. Raschle et al.

    Mechanism of replication-coupled DNA interstrand crosslink repair

    Cell

    (2008)
  • V. Mladenova et al.

    Enhanced repair of DNA interstrand crosslinks in S phase

    FEBS Lett.

    (2006)
  • P.A. Muniandy et al.

    Repair of laser-localized DNA interstrand cross-links in G(1) phase mammalian cells

    J. Biol. Chem.

    (2009)
  • P.H. Clingen et al.

    Chemosensitivity of primary human fibroblasts with defective unhooking of DNA interstrand cross-links

    Exp. Cell Res.

    (2007)
  • I. Kuraoka et al.

    Repair of an interstrand DNA cross-link initiated by ERCC1-XPF repair/recombination nuclease

    J. Biol. Chem.

    (2000)
  • X. Shen et al.

    REV3 and REV1 play major roles in recombination-independent repair of DNA interstrand cross-links mediated by monoubiquitinated proliferating cell nuclear antigen (PCNA)

    J. Biol. Chem.

    (2006)
  • M. Kartalou et al.

    Recognition of cisplatin adducts by cellular proteins

    Mutat. Res. Fundam. Mol. Mech. Mutagen.

    (2001)
  • D.M. Wilson et al.

    A novel link to base excision repair?

    Trends Biochem. Sci.

    (2010)
  • A. Kothandapani et al.

    Novel role of base excision repair (BER) in mediating cisplatin cytotoxicity

    J. Biol. Chem.

    (2011)
  • A. Maor-Shoshani et al.

    3-methyladenine DNA glycosylase ill important for cellular resistance to psoralen interstrand cross-links

    DNA Repair

    (2008)
  • G.E. Kisby et al.

    DNA repair modulates the vulnerability of the developing brain to alkylating agents

    DNA Repair

    (2009)
  • B. Liu et al.

    Real-time monitoring of uracil removal by uracil-DNA glycosylase using fluorescent resonance energy transfer probes

    Anal. Biochem.

    (2007)
  • R. Abbotts et al.

    Human AP endonuclease 1 (APE1): from mechanistic insights to druggable target in cancer

    Cancer Treat. Rev.

    (2010)
  • K.A. Robertson et al.

    Altered expression of Ape1/ref-1 in germ cell tumors and overexpression in NT2 cells confers resistance to bleomycin and radiation

    Cancer Res.

    (2001)
  • F. Altieri et al.

    DNA damage and repair: from molecular mechanisms to health implications

    Antioxid. Redox Signal.

    (2008)
  • M.C. Reddy et al.

    Repair of genome destabilizing lesions

    Radiat. Res.

    (2005)
  • C.L. Peterson et al.

    Cellular machineries for chromosomal DNA repair

    Genes Dev.

    (2004)
  • D.O. Zharkov

    Base excision DNA repair

    Cell. Mol. Life Sci.

    (2008)
  • D.M. Wilson et al.

    Life without DNA repair

    Proc. Natl. Acad. Sci. U.S.A.

    (1997)
  • J. Baute et al.

    Base excision repair and its role in maintaining genome stability

    Crit. Rev. Biochem. Mol. Biol.

    (2008)
  • S.S. David et al.

    Base-excision repair of oxidative DNA damage

    Nature

    (2007)
  • S. Maynard et al.

    Base excision repair of oxidative DNA damage and association with cancer and aging

    Carcinogenesis

    (2009)
  • M.L. Hegde et al.

    Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

    Cell Res.

    (2008)
  • A.J. Podlutsky et al.

    Human DNA polymerase beta initiates DNA synthesis during long-patch repair of reduced AP sites in DNA

    EMBO J.

    (2001)
  • N.A. Timofeyeva et al.

    Conformational dynamics of human AP endonuclease in base excision and nucleotide incision repair pathways

    J. Biomol. Struct. Dyn.

    (2009)
  • R.A.O. Bennett et al.

    Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway

    Proc. Natl. Acad. Sci. U.S.A.

    (1997)
  • B. Kaina et al.

    DNA repair in resistance to alkylating anticancer drugs

    Int. J. Clin. Pharmacol. Ther.

    (2002)
  • G. Damia et al.

    Mechanisms of resistance to alkylating agents

    Cytotechnology

    (1998)
  • R.W. Sobol et al.

    Mutations associated with base excision repair deficiency and methylation-induced genotoxic stress

    Proc. Natl. Acad. Sci. U.S.A.

    (2002)
  • R.N. Trivedi et al.

    The role of base excision repair in the sensitivity and resistance to temozolomide-mediated cell death

    Cancer Res.

    (2005)
  • D.M. Wilson et al.

    Small molecule inhibitors of DNA repair nuclease activities of APE1

    Cell. Mol. Life Sci.

    (2010)
  • A.M. Reed et al.

    Small-molecule inhibitors of proteins involved in base excision repair potentiate the anti-tumorigenic effect of existing chemotherapeutics and irradiation

    Future Oncol.

    (2009)
  • S. Madhusudan et al.

    Isolation of a small molecule inhibitor of DNA base excision repair

    Nucleic Acids Res.

    (2005)
  • P.C. Fong et al.

    Inhibition of poly(ADP-Ribose) polymerase in tumors from BRCA mutation carriers

    N. Engl. J. Med.

    (2009)
  • S. Banerjee et al.

    Making the best of PARP inhibitors in ovarian cancer

    Nat. Rev. Clin. Oncol.

    (2010)
  • A. Guainazzi et al.

    Using synthetic DNA interstrand crosslinks to elucidate repair pathways and identify new therapeutic targets for cancer chemotherapy

    Cell. Mol. Life Sci.

    (2010)
  • N. Maganaschwencke et al.

    The fate of 8-methoxypsoralen photoinduced crosslinks in nuclear and mitochondrial yeast DNA – comparison of wild-type and repair-deficient strains

    Proc. Nat. Acad. Sci. U.S.A. Biol. Sci.

    (1982)
  • Cited by (0)

    View full text