Recombinational DNA repair and human disease

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Abstract

We review the genes and proteins related to the homologous recombinational repair (HRR) pathway that are implicated in cancer through either genetic disorders that predispose to cancer through chromosome instability or the occurrence of somatic mutations that contribute to carcinogenesis. Ataxia telangiectasia (AT), Nijmegen breakage syndrome (NBS), and an ataxia-like disorder (ATLD), are chromosome instability disorders that are defective in the ataxia telangiectasia mutated (ATM), NBS, and Mre11 genes, respectively. These genes are critical in maintaining cellular resistance to ionizing radiation (IR), which kills largely by the production of double-strand breaks (DSBs). Bloom syndrome involves a defect in the BLM helicase, which seems to play a role in restarting DNA replication forks that are blocked at lesions, thereby promoting chromosome stability. The Werner syndrome gene (WRN) helicase, another member of the RecQ family like BLM, has very recently been found to help mediate homologous recombination. Fanconi anemia (FA) is a genetically complex chromosomal instability disorder involving seven or more genes, one of which is BRCA2. FA may be at least partially caused by the aberrant production of reactive oxidative species. The breast cancer-associated BRCA1 and BRCA2 proteins are strongly implicated in HRR; BRCA2 associates with Rad51 and appears to regulate its activity. We discuss in detail the phenotypes of the various mutant cell lines and the signaling pathways mediated by the ATM kinase. ATM’s phosphorylation targets can be grouped into oxidative stress-mediated transcriptional changes, cell cycle checkpoints, and recombinational repair. We present the DNA damage response pathways by using the DSB as the prototype lesion, whose incorrect repair can initiate and augment karyotypic abnormalities.

Introduction

One of the hallmarks of tumor cells is their highly rearranged karyotypes with respect to both chromosome number and the structural integrity of each homologous pair. Numerous rearrangements can be visualized in vivid detail using spectral karyotyping, which specifically colors each chromosome, e.g. [1]. These changes presumably reflect the selective outgrowth of outlaw cells whose rearrangements have conferred growth advantages during the evolution of the tumor. Chromosomal rearrangements are a consequence of the loss of fidelity in repairing double-strand breaks (DSBs). These dangerous lesions are corrected by the two primary pathways of nonhomologous end-joining (NHEJ) and homologous recombinational repair (HRR) (reviewed in [2], [3], [4], [5], [6], [7]). Recent studies employing mouse models have shown that the absence of either pathway leads to genomic instability, including potentially oncogenic translocations [8]. In humans, inherited genetic defects in these pathways are often manifest as increased radiosensitivity [9] since DSBs are the major contributor to cell lethality and mutation produced by ionizing radiation (IR).

The NHEJ pathway involves a “duct-tape” approach to mending a DSB that can result in the gain or loss of nucleotide sequence [10]. DNA-dependent protein kinase (DNA-PK, composed of DNA-PKcs catalytic subunit and the Ku70–Ku86 heterodimer), along with the ligation factors LIG4 and XRCC4, are five critical components of this repair process. Besides their role in DSB repair, Ku and DNA-PKcs proteins provide another level of chromosome stability by participating in capping chromosome ends, or telomeres, thereby protecting them from end-to-end fusions [11], [12], [13], [14]. However, in the absence of one of the NHEJ proteins in mutant cells, residual end-joining reactions still operate as evidenced by chromosomal translocations [15], [16], [17]. During normal V(D)J recombination in B and T lymphocytes, DSBs created by the site-specific cleavage by the RAG proteins are subsequently processed and rejoined by components of the nonhomologous DNA end-joining pathway [18].

A prominent role for the HRR pathway in maintaining chromosome stability has become apparent from biochemical [10] and genetic studies on a variety of mutant cell lines (reviewed by [5], [19], [20]). An emergent concept is that the formation of DSBs is a normal by-product of DNA replication, especially in higher eukaryotes, which have much larger chromosomes than yeast. Replication forks encountering single-strand breaks (SSBs) or other lesions may undergo collapse with the formation of a “one-sided” DSB. Restoration of the fork can be accomplished by break-induced replication to re-establish strand continuity. In addition, replication-blocking lesions such as bulky adducts may result in gaps in one of the nascent strands. A free single-stranded end associated with the gap may pair with the intact sister DNA duplex and undergo recombination to achieve an error-free elimination of the gap with the adduct still in place.

Section snippets

Ataxia telangiectasia (AT)

AT is a rare human genetic disorder that is characterized by progressive neuronal degeneration with loss of cerebellar function, immunodeficiency, sterility, cancer predisposition, and clinical radiation sensitivity [21]. Along with the cerebellar ataxia, telangiectasis (dilation of small blood vessels and capillaries) of the sclera, face, and ears are a characteristic feature of AT. The increased risk of cancer is estimated to be 60–180-fold higher than the general population, with ∼70% of

Werner syndrome gene (WRN)

Like Bloom syndrome, Werner syndrome is a rare recessive genetic disorder associated with a greatly increased risk of cancers. Although WS shares a number of similarities with BS, including having a defect in a RecQ-related helicase, there are many differences. WS individuals are short in stature like BS individuals. However, unlike BS, WS is an adult progeria syndrome that includes a wide range of age-related traits having greatly accelerated onset although generally occurring after puberty.

BRCA1 cancer suppressor gene

Mutations in the BRCA1 tumor suppressor gene are found in ∼70% of all of the families with inherited breast and ovarian cancers and ∼20% of the families with only breast cancer [185]. Considerable evidence supports the idea that BRCA1 and BRCA2 proteins have multiple, complex roles in cellular responses to DNA damage. They participate in the processes that implement cell cycle checkpoints in response to DSB, help coordinate the repair of those breaks, facilitate transcription coupled repair of

RAD51, RAD52, RAD54, and RAD54B

As a homolog of RecA, Rad51 is the major strand-transfer protein in eukaryotic cells. It is assisted in recombination by the Rad52, Rad54, and Rad54B proteins, as well as the Rad51 paralogs discussed below. Rad51 has been extensively characterized and found to interact with many proteins, including c-Ab1, BRCA2, RPA, BLM, Rad52, Rad54, and XRCC3 [5]. The enzymatic activities of the Rad51, Rad52, and Rad54 proteins, as well as their interactions with other proteins, were recently reviewed [5]

Elevated DSBs and homologous recombination associated with replication arrest in the XP variant

The classical DNA repair disorder xeroderma pigmentosum is caused by two different types of biochemical defects associated with either excision repair or the cell’s ability to replicate across cis-syn cyclobutane pyrimidine dimers efficiently without making mutations. Only the gene affected in the XP variant (XP-V) is associated with defective lesion bypass. The XP-V polymerase was identified as Pol η, which is encoded by the PolH/RAD30A gene [335], [336]. XP-V cells have mild UV sensitivity to

Concluding remarks

It is apparent that a complex network of highly evolved proteins governs the repair of DNA lesions, particularly DSBs. In addition to the multi-faceted Tp53 [340], [341], several large regulatory proteins (ATM, ATR, BRCA1, and BRCA2) participate in numerous, complex functional interactions. Several of the key players (BRCA1, BRCA2, and Tp53) are not represented by homologs in lower eukaryotes, suggesting that their origin is tied to the development of larger genomes that must support great

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