**1. Introduction**

566 DNA Repair

Yin, J., Vogel, U., Ma, Y., Guo, L., Wang, H. & Qi, R. (2006). Polymorphism of the DNA

Yokoi, M., Masutani, C., Maekawa, T., Sugasawa, K., Ohkuma, Y. & Hanaoka, F. (2000). The

You, J.S., Wang, M. & Lee, S.H. (2003). Biochemical analysis of the damage recognition process in nucleotide excision repair. *J.Biol.Chem.,* Vol. 278, No. 9, pp. (7476-7485) Zienolddiny, S., Campa, D., Lind, H., Ryberg, D., Skaug, V., Stangeland, L., Phillips, D.H.,

non-small cell lung cancer. *Carcinogenesis,* Vol. 27, No. 3, pp. (560-567)

population. *Cancer Genet.Cytogenet.,* Vol. 169, No. 1, pp. (27-32)

Vol. 275, No. 13, pp. (9870-9875)

repair gene ERCC2 Lys751Gln and risk of lung cancer in a northeastern Chinese

xeroderma pigmentosum group C protein complex XPC-HR23B plays an important role in the recruitment of transcription factor IIH to damaged DNA. *J.Biol.Chem.,* 

Canzian, F. & Haugen, A. (2006). Polymorphisms of DNA repair genes and risk of

Oxidative DNA damage is one of the earliest detectable events in several neurodegenerative diseases, often preceding the onset of the clinical symptoms. Moreover, neurons in the adult human brain can re-enter the cell division cycle, likely allowing DNA repair. Impairments of DNA repair pathways are reported in neurons of patients suffering from one of several neurodegenative diseases and might result in the accumulation of mutations critical for neurodegeneration. Current investigation aims at understanding the causes of such impairment (Coppedè & Migliore, 2010). One of the most robust set of data that demonstrates association between DNA repair and neurodegenerative diseases comes from studies on early onset ataxia with ocular motor apraxia and hypoalbuminemia/ataxia with oculomotor apraxia type 1 (EAOH/AOA1), an autosomal recessive form of cerebellar ataxia caused by mutations in the aprataxin (*APTX*) gene. It was shown that aprataxin participates in DNA repair suggesting that genes involved in DNA repair pathways might have a role in neurodegeneration (Hirano et al., 2007; Takahashi et al., 2007). Also parkin, encoded by one of the causative genes of Parkinson's disease (PD), seems to contribute to DNA repair (Kao, 2009). Variants and polymorphisms of DNA repair genes, particularly DNA base excision repair (BER) genes, have been investigated as possible risk factors for Alzheimer's disease (AD), Parkinson's disease, amyotrophic lateral sclerosis (ALS), and other neurodegenerative diseases (Coppedè & Migliore, 2010). There is also evidence that BER could contribute to CAG repeat expansion in Huntington's disease (HD) (Kovtun et al., 2007). Most of the genetic association studies have been performed in the last few years and gave often conflicting or inconclusive results, their power was limited by the sample size of casecontrol groups, gene-gene interactions were missing, and only common polymorphisms have been included with little or no attention paid to rare gene variants (Coppedè, 2011). In this chapter I discuss the current knowledge on DNA repair gene variants and polymorphisms and major neurodegenerative disorders.

### **2. DNA repair pathways**

A brief overview of the major DNA repair pathways in mammals is shown in Table 1. It is estimated that our cells are subjected to a daily average of about one million lesions that, if not properly repaired, can drive mutagenesis, disrupt normal gene expression or create aberrant protein products. Cells have therefore developed several repair systems that can be

Variants and Polymorphisms of DNA Repair Genes and Neurodegenerative Diseases 569

takes places either in nuclei and mitochondria, and mitochondria have independent BER machinery encoded by nuclear genes. Indeed, several BER enzymes have been identified which have both nuclear and mitochondrial forms. The gaps generated by the action of AP endonucleases/lyases are filled in by Pol γ in the mitochondria, and ligation is mediate by ligase III. To date, there is no evidence of long-patch BER in mitochondria

The nucleotide excision repair pathway (NER) is required for the removal of a wide variety of forms of DNA damage, including UV induced photoproducts, DNA crosslinks, and other bulky lesions. NER involves at least 20-30 proteins or complexes of proteins, and is divided into global genome repair (GGR) and transcription coupled repair (TCR). The two pathways mainly differ in the initial steps that recognize the DNA lesion, and different initial recognition factors are involved. NER senses the presence of a lesion through the distortion it causes to the DNA structure. In GGR DNA damage recognition requires the xeroderma pigmentosum (XP) complementing protein XPC-HR23B-centrin complex. The DNA damage is verified by opening of the DNA strands surrounding the lesion by the transcription factor TFIIH. This is followed by recruitment of XPA and other components of the transcription factor TFIIH to the lesion site. In TCR the recognition step is initiated when a RNA polymerase stalls at a lesion site and requires the Cockayne's syndrome proteins CSA and CSB. After a correct assembly of the NER complex, a fragment of 24-32 nucleotides is incised and removed from the damaged strand by the simultaneous action of the DNA excision repair cross complementing (ERCC) proteins ERCC5 (XPG; 3' endonuclease) and ERCC4 (XPF; 5' endonuclease) complexed with ERCC1. Repair is completed by new DNA synthesis mediated by DNA Pol δ/ε, DNA Pol κ, and ligation (DNA ligase I, DNA ligase III) of the nascent DNA to the parental strands using the undamaged strand as a template. The GGR pathway removes damages overall in the genome irrespective of genome location and point in the cell cycle, whereas TCR is required for the specific repair of bulky lesions in the transcribed strand of active genes. Mitochondria have been shown to lack NER, which operates in the nucleus removing the

majority of DNA lesions (Fleck & Nielsen, 2004; Subba Rao, 2007).

DNA Pol δ and a DNA ligase, for DNA repair (Kunkel & Erie, 2005).

**2.4 Homologous recombination (HR) and non homologous end joining (NHEJ)** 

Non homologous end joining (NHEJ) is the major pathway for the repair of DSBs because it can function throughout the cell cycle and does not require a homologous chromosome. Rather, NHEJ involves rejoining of what remains of the two DNA ends, tolerating nucleotide loss or addition at the rejoining site. When a DSB occurs during G0, G1, and early

Mismatch repair (MMR) corrects mismatches and small insertions or deletions during DNA replication, thus eliminating potentially pre-mutagenic bases. Repair involves recognition of the mismatch by MutSα (MSH2 and MSH6 proteins), or by MutSβ (MSH2 and MSH3 proteins) in the case of small insertions/deletions (1-10 nucleotides). MutLα (a heterodimer of MLH1 and PMS2 proteins) is then recruited and serves to coordinate the process that involves, among others, the PCNA protein for strand discrimination and exonuclease 1,

(Weissman et al., 2007).

**2.3 Mismatch repair (MMR)** 

**2.2 Nucleotide excision repair (NER)** 


generally divided into single stand break (SSB) and double strand break (DSB) repair pathways (Table 1).

Table 1. Major DNA repair pathways in mammalian cells

#### **2.1 Base excision repair (BER)**

The DNA base excision repair pathway deserves a detailed description since it is believed to be the major pathway for repairing DNA base modifications caused by oxidation, deamination and alkylation. DNA glycosylases catalyze the first step in the BER process by cleaving the N-glycosylic bond between a damaged base and the sugar moiety; after the cleavage the damaged base is released resulting in the formation of an abasic site which is then cleaved by an AP lyase activity or by the major mammalian apurinic/apyrimidinic endonuclease (APEX1). Repair can then proceed through short or long-patch BER. In shortpatch BER, which is the most common sub-pathway, a single nucleotide is incorporated into the gap by DNA polymerase β (Pol β) and ligated by the DNA ligase III/ X-ray repair crosscomplementing group 1 (XRCC1) complex. In long-patch BER several nucleotides (two to seven-eight) are incorporated, followed by cleavage of the resulting 5' flap structure and ligation. It has been suggested that after Pol β adds the first nucleotide into the gap, it is substituted by Pol δ/ε which continues long-patch BER. DNA ligase I completes the longpatch pathway. Several other proteins, including the proliferating cell nuclear antigen (PCNA), the RPA protein, and the 5'-flap endonuclease (FEN-1) participate in long-patch BER. Recent evidence suggests that XRCC1 acts as a scaffold protein in short-patch BER, regulating and coordinating the whole process. XRCC1 recruits DNA Pol β and DNA ligase III required for filling and sealing the damaged strand. Moreover, it also interacts with DNA glycosylases and APEX1, mediating their exchange at the damaged site. XRCC1 also interacts with PARP-1, which is one of the cellular sensors of DNA SSBs and DSBs. BER takes places either in nuclei and mitochondria, and mitochondria have independent BER machinery encoded by nuclear genes. Indeed, several BER enzymes have been identified which have both nuclear and mitochondrial forms. The gaps generated by the action of AP endonucleases/lyases are filled in by Pol γ in the mitochondria, and ligation is mediate by ligase III. To date, there is no evidence of long-patch BER in mitochondria (Weissman et al., 2007).
