**2. Genomic instability and cancer**

It should be noted that a state of genomic instability prevails in cancer. In certain cases, such as overexpression of licensing factors (hCdt1 and hCdc6), prolonged overexpression of these factors lead to a more aggressive phenotype, bypassing the antitumor barriers of accelerated senescence and apoptosis. The link between activation of DNA-damage response and tumorigenesis implies that continuous DNA damage checkpoint activation could lead to selective suppression of the DNA-damage response-induced antitumor barriers by inactivating mutations resulting in genomic instability and tumor progression (Bartkova et al. 2005, Bartkova et al. 2006, Gorgoulis et al. 2005, Di Micco et al. 2006, Halazonetis, Gorgoulis and Bartek 2008). Cells possessing re-replicated DNA above a critical threshold are typically neutralized by either senescence or apoptosis. However, cells with re-replicated elements below a critical threshold are prone to recombination processes leading to genomic instability. These events favor the selection of resilient cells and lead to therapeutic resistance (Liontos et al. 2007).

Proteins involved in DNA repair pathways have garnered attention because mutations causing dysfunction can lead to increased genetic instability and ultimately to increased cancer risk. Indeed, several studies have demonstrated alterations of these genes are associated with susceptibility to cancer (Berwick and Vineis 2000). Identification of factors associated with prognosis is an ever important process for both an escalation and deescalation of therapies for appropriately selected patients. Additionally if alterations of these genes impact development of cancer, they are possible targets for therapy.

#### **2.1 DNA damage and repair**

The human body is under continuous attack from both external and internal insults which ultimately generates thousands of DNA lesions per day. But it has evolved its own defense mechanism to combat these lesions. The cellular response to DNA damage is critical for maintaining genomic integrity and for preventing carcinogenesis. Since DNA lesions can block genomic replication and transcription and lead to mutations it is imperative that DNA is repaired without any errors. Failure to repair any damage to the nucleic acid results in cell death in the form of apoptosis or necrosis. To combat threats posed by DNA damage, cells have evolved mechanisms, collectively termed the DNAdamage response, to detect DNA lesions, signal their presence, and promote DNA repair. Cells defective in these mechanisms generally display heightened sensitivity towards DNA-damaging agents. While this may be exploited for cancer therapy [e.g. poly ADPribose polymerase (PARP) inhibitors in breast cancer susceptibility protein (BRCA) deficient ovarian and breast tumors] it should also be noted that many such defects can lead to human disease, such as cancer.

#### **2.2 DNA repair pathways**

In an effort to repair the damaged DNA and avoid passing the damaged DNA onto the progeny cells, the cell has evolved several repair pathways. These repair pathways include base excision repair (BER), nucleotide excision repair (NER), double strand break (DSB) repair via homologous recombination (HR) or non-homologous end joining (NHEJ), and mismatch repair (MMR) (Polo and Jackson 2011, Stratton 2011, Stricker, Catenacci and Seiwert 2011). Though it is not clear what determines the choice of repair pathway, it is an area of active research.

It should be noted that a state of genomic instability prevails in cancer. In certain cases, such as overexpression of licensing factors (hCdt1 and hCdc6), prolonged overexpression of these factors lead to a more aggressive phenotype, bypassing the antitumor barriers of accelerated senescence and apoptosis. The link between activation of DNA-damage response and tumorigenesis implies that continuous DNA damage checkpoint activation could lead to selective suppression of the DNA-damage response-induced antitumor barriers by inactivating mutations resulting in genomic instability and tumor progression (Bartkova et al. 2005, Bartkova et al. 2006, Gorgoulis et al. 2005, Di Micco et al. 2006, Halazonetis, Gorgoulis and Bartek 2008). Cells possessing re-replicated DNA above a critical threshold are typically neutralized by either senescence or apoptosis. However, cells with re-replicated elements below a critical threshold are prone to recombination processes leading to genomic instability. These events favor the selection of resilient cells and lead to therapeutic resistance (Liontos et al. 2007). Proteins involved in DNA repair pathways have garnered attention because mutations causing dysfunction can lead to increased genetic instability and ultimately to increased cancer risk. Indeed, several studies have demonstrated alterations of these genes are associated with susceptibility to cancer (Berwick and Vineis 2000). Identification of factors associated with prognosis is an ever important process for both an escalation and deescalation of therapies for appropriately selected patients. Additionally if alterations of these

genes impact development of cancer, they are possible targets for therapy.

The human body is under continuous attack from both external and internal insults which ultimately generates thousands of DNA lesions per day. But it has evolved its own defense mechanism to combat these lesions. The cellular response to DNA damage is critical for maintaining genomic integrity and for preventing carcinogenesis. Since DNA lesions can block genomic replication and transcription and lead to mutations it is imperative that DNA is repaired without any errors. Failure to repair any damage to the nucleic acid results in cell death in the form of apoptosis or necrosis. To combat threats posed by DNA damage, cells have evolved mechanisms, collectively termed the DNAdamage response, to detect DNA lesions, signal their presence, and promote DNA repair. Cells defective in these mechanisms generally display heightened sensitivity towards DNA-damaging agents. While this may be exploited for cancer therapy [e.g. poly ADPribose polymerase (PARP) inhibitors in breast cancer susceptibility protein (BRCA) deficient ovarian and breast tumors] it should also be noted that many such defects can

In an effort to repair the damaged DNA and avoid passing the damaged DNA onto the progeny cells, the cell has evolved several repair pathways. These repair pathways include base excision repair (BER), nucleotide excision repair (NER), double strand break (DSB) repair via homologous recombination (HR) or non-homologous end joining (NHEJ), and mismatch repair (MMR) (Polo and Jackson 2011, Stratton 2011, Stricker, Catenacci and Seiwert 2011). Though it is not clear what determines the choice of repair pathway, it is an

**2. Genomic instability and cancer** 

**2.1 DNA damage and repair** 

lead to human disease, such as cancer.

**2.2 DNA repair pathways** 

area of active research.

Whereas some lesions are subject to direct protein-mediated reversal, most are repaired by a cascade of catalytic events mediated by multiple proteins. In MMR-mediated repair, detection of mismatches and insertion/deletion loops triggers a single-strand incision that is then worked upon by nuclease, polymerase and ligase enzymes. In BER-mediated repair, a damaged base is often recognized by a DNA glycosylase enzyme that mediates base removal before nuclease, polymerase and ligase proteins complete the repair in processes overlapping with those used in single strand break repair. In contrast, NER-mediated repair recognizes helix-distorting base lesions. It includes two sub-pathways that differ in the mechanism of lesion recognition: transcription-coupled NER, which specifically targets lesions that block transcription, and global-genome NER. A key aspect of NER is that the damage is excised as a 22–30-base oligonucleotide, producing single-stranded DNA that is acted upon by DNA polymerases and associated factors before ligation proceeds.

In NHEJ, DSBs are recognized by the Ku protein that then binds and activates the protein kinase DNA-PKcs, leading to recruitment and activation of end-processing enzymes, polymerases and DNA ligase IV. NHEJ repair, predominantly utilized in the repair of radiation induced DNA damage, is a highly efficient but error-prone process that often results in mutations in the repaired DNA. The NHEJ repair process is dependent on the DNA-dependent protein kinase (DNA-PK) catalytic subunit (DNA-PKcs), the Ku70/Ku80 heterodimer, and the XRCC4–ligase IV complex and ultimately rejoins the ends of DSBs with little or no homology. In response to radiation, DNA-PKcs is autophosphorylated at threonine 2609. This is required for the functional activation of the NHEJ repair pathway. Consistent with the role of NHEJ repair in the repair of radiation-induced DSBs, cells deficient in any NHEJ repair protein have been shown to be hypersensitive to radiationmediated cytotoxicity (Iliakis et al. 2004, Yang et al. 2009, van Gent, Hoeijmakers and Kanaar 2001). A less-well-characterized Ku-independent NHEJ pathway, called micro-homologymediated end-joining (MMEJ) or alternative end-joining, results in sequence deletions. Although both NHEJ and MMEJ are error-prone, they can operate in any phase of the cell cycle.

In contrast, HR is generally restricted to S and G2 because it uses sister-chromatid sequences as the template to mediate faithful repair. Although there are several HR sub-pathways, HR is always initiated by single strand DNA generation, which is promoted by various proteins including the MRE11–RAD50–NBS1 (MRN) complex. In events catalyzed by RAD51 and the breast-cancer susceptibility proteins BRCA1 and BRCA2, the single strand DNA then invades the undamaged template and, following the actions of polymerases, nucleases, helicases and other components, DNA ligation and substrate resolution occur. HR is also used to restart stalled replication forks and to repair inter-strand DNA crosslinks, the repair of which also involves the Fanconi anaemia protein complex. This high-fidelity, error-free process is also critical in the repair of lesions resulting from replicative stress (Yang et al. 2009, Jiang et al. 2011, Wang et al. 2010).

#### **2.2.1 Cell cycle checkpoints**

Checkpoints are also put in place throughout the cell cycle that halt further progression of DNA replication and cell division upon detection of damaged DNA. This can arrest the cell either transiently or permanently (senescence), as well as activate specific DNA repair pathways in response to certain types of DNA damage. Some of the proteins in these

p53 in breast cancer. A number of changes are observed in lung cancer including P16INK4a, H-cadherin, Death-associated protein kinase 1 (DAPK1), MDM2, and p53. Modification in p14ARF is observed in lung, esophageal and colorectal cancers while changes in hHML1 are seen in colorectal cancer. RASSF1A modification are present in lung and nasopharyngeal

Besides changes in DNA methylation patterns, the chromatin has also been shown to regulate transcriptional activity. To this end, any modifications in core histone proteins (e.g. H2A, H2B, H3 and H4) can have an impact in the activation and/or repression of transcription. Such modifications can include, among others, methylation, acetylation, deacetylation, phosphorylation, and ubiquitination. Histone acetylation and/or deacetylation are observed in breast, prostate, colon, testicular, renal and pancreatic cancers. Histone demethylation is observed in breast, prostate, colon, testicular and esophageal cancers while histone H3 lysine 27 tri-methylation is observed in breast, ovarian, colon and pancreatic cancers. Histone H3 lysine 9 and/or Histone H4 lysine 20 tri-methylations are present in breast, lung and hepatocellular cancers. Histone H3 lysine 4 methylation is often observed in breast, ovarian, colorectal and hepatocellular cancers

Perhaps, the most noted molecular marker for cancer is mutations in the BRCA family of genes. The BRCA family of proteins is essential for HR-mediated repair of DNA double strand breaks (Jackson and Bartek 2009, Bartek, Lukas and Lukas 2004, Wang et al. 2010, Jiang et al. 2011). As little as one unrepaired DNA double strand break is fatal to the cell (Yang et al. 2009, Aziz, Nowsheen and Georgakilas 2010). Thus, it is not surprising that certain mutations in the BRCA gene lead to an increased risk for breast cancer as part of a hereditary breast-ovarian cancer syndrome. Women with mutated BRCA1 or BRCA2 gene have up to a 60% risk of developing breast cancer (King et al. 2003, Graeser et al. 2009). Similarly, 55% increased risk of developing ovarian cancer is observed with BRCA1 mutations and about 25% for women with BRCA2 mutations (King et al. 2003). Research suggests hypermethylation of the BRCA1 promoter may be an inactivating mechanism for BRCA1 expression not only in breast and ovarian cancer but also lung and oral cancer (Esteller et al. 2000, Marsit et al. 2003). Due to the lack of reliable biomarkers, many women with breast cancer end up being over-treated or under-treated for the disease. Epigenetic modifications have been detected in critical genes involved in breast cancer that could potentially serve as specific clinical molecular markers. These include promoter DNA hypomethylation in c-myc, CAGE, Urokinase-type plasminogen activator, EPO and γ-Synuclein genes and promoter DNA hypermethylation in BRCA1, BRCA2, Von Hippel–

In addition to breast cancer, mutations in the BRCA1 gene also increase the risk of developing ovarian, fallopian tube, and prostate cancers (Brose et al. 2002, Thompson, Easton and the Breast Cancer Linkage 2002). Mutations in BRCA also increase the risk for a subset of leukemia and lymphoma (Friedenson 2007). Women having inherited a defective BRCA1 or BRCA2 gene have risks for breast and ovarian cancer that are so high

Lindau tumor suppressor (VHL) and p53 genes (Ziech et al. 2010).

cancers (Ziech et al. 2010).

(Ziech et al. 2010).

**2.5 BRCA1 and cancer** 

**2.4.2 Modifications in chromatin structure in cancer** 

pathways are mutated or non-functional in human tumors causing cancer cells to be more reliant on an intact DNA repair pathway for survival. Key DNA damage signaling components in mammalian cells are the protein kinases ATM and ATR. ATM is recruited to and activated by DSBs. In contrast, ATR is recruited to and activated by replication protein A-coated double stranded DNA. Two of the best studied ATM/ATR targets are the protein kinases CHK1 and CHK2. Together with ATM and ATR, these proteins reduce cyclindependent kinase (CDK) activity by various mechanisms, often mediated by p53. Inhibition of CDKs slows down or arrests cell-cycle progression at the G1–S, intra-S and G2–M cellcycle checkpoints. This allows more time for DNA repair before replication or mitosis. In parallel, ATM/ATR signaling enhances repair by a variety of methods: inducing DNArepair proteins transcriptionally or post-transcriptionally, by recruiting repair factors to the damage-site, and by activating DNA-repair proteins by modulating their phosphorylation, acetylation, ubiquitylation or SUMOylation. The aforementioned proteins can be exploited for cancer therapy as well.

#### **2.3 Epigenetic modifications in cancer**

Both genotoxic and non-genotoxic mechanisms have been implicated in malignant transformation. Genotoxic mechanisms involve changes in genomic DNA sequences leading to mutations. On the other hand, non-genotoxic mechanisms modulate gene expression directly (Franco et al. 2008). Epigenetic pathway which involves changes in DNA methylation patterns and histone modifications is considered to be a non-genotoxic mechanism capable of modulating gene expression and thus promoting malignant transformation. Thus, it is vital to determine such epigenetic modifications in a way that we can expand on cancer biological marker development with clinical relevance (Franco et al. 2008). Epigenetic molecular marker development has been a hot topic in cancer research because of the ability to contribute to cancer diagnosis and/or prognosis due to their high sensitivity and specificity. A number of epigenetic modifications have been detected in critical genes involved in various cancers that can potentially serve as specific clinical biomarkers.

#### **2.4 DNA hypomethylation and cancer**

Promoter DNA hypomethylation modification has been observed for a number of genes including H-ras in prostate and thyroid cancers and cancer-testis antigen gene (CAGE) in prostate, breast, lung and laryngeal cancers. The X-inactive specific transcript (XIST) modification is observed in prostate cancer while erythropoietin (EPO) is found in prostate and breast cancers. Maspin changes are detected in ovarian, pancreatic and lung cancers. Changes in γ-Synuclein are prevalent in ovarian and breast cancers while c-myc modifications are found in breast and lung cancers. Urokinase-type plasminogen activator modification is observed in breast cancer, S100P in pancreatic cancer and Melanomaassociated antigen A (MAGE-A) in lung cancer (Ziech et al. 2010).

#### **2.4.1 DNA hypermethylation and cancer**

Promoter DNA hypermethylation modification has been associated with altered expression of critical genes associated with various cancers including BRCA1/BRCA2 in prostate, breast, pancreatic and ovarian cancers, Von Hippel–Lindau tumor suppressor (VHL) and

pathways are mutated or non-functional in human tumors causing cancer cells to be more reliant on an intact DNA repair pathway for survival. Key DNA damage signaling components in mammalian cells are the protein kinases ATM and ATR. ATM is recruited to and activated by DSBs. In contrast, ATR is recruited to and activated by replication protein A-coated double stranded DNA. Two of the best studied ATM/ATR targets are the protein kinases CHK1 and CHK2. Together with ATM and ATR, these proteins reduce cyclindependent kinase (CDK) activity by various mechanisms, often mediated by p53. Inhibition of CDKs slows down or arrests cell-cycle progression at the G1–S, intra-S and G2–M cellcycle checkpoints. This allows more time for DNA repair before replication or mitosis. In parallel, ATM/ATR signaling enhances repair by a variety of methods: inducing DNArepair proteins transcriptionally or post-transcriptionally, by recruiting repair factors to the damage-site, and by activating DNA-repair proteins by modulating their phosphorylation, acetylation, ubiquitylation or SUMOylation. The aforementioned proteins can be exploited

Both genotoxic and non-genotoxic mechanisms have been implicated in malignant transformation. Genotoxic mechanisms involve changes in genomic DNA sequences leading to mutations. On the other hand, non-genotoxic mechanisms modulate gene expression directly (Franco et al. 2008). Epigenetic pathway which involves changes in DNA methylation patterns and histone modifications is considered to be a non-genotoxic mechanism capable of modulating gene expression and thus promoting malignant transformation. Thus, it is vital to determine such epigenetic modifications in a way that we can expand on cancer biological marker development with clinical relevance (Franco et al. 2008). Epigenetic molecular marker development has been a hot topic in cancer research because of the ability to contribute to cancer diagnosis and/or prognosis due to their high sensitivity and specificity. A number of epigenetic modifications have been detected in critical genes involved in various cancers that can potentially serve as specific clinical

Promoter DNA hypomethylation modification has been observed for a number of genes including H-ras in prostate and thyroid cancers and cancer-testis antigen gene (CAGE) in prostate, breast, lung and laryngeal cancers. The X-inactive specific transcript (XIST) modification is observed in prostate cancer while erythropoietin (EPO) is found in prostate and breast cancers. Maspin changes are detected in ovarian, pancreatic and lung cancers. Changes in γ-Synuclein are prevalent in ovarian and breast cancers while c-myc modifications are found in breast and lung cancers. Urokinase-type plasminogen activator modification is observed in breast cancer, S100P in pancreatic cancer and Melanoma-

Promoter DNA hypermethylation modification has been associated with altered expression of critical genes associated with various cancers including BRCA1/BRCA2 in prostate, breast, pancreatic and ovarian cancers, Von Hippel–Lindau tumor suppressor (VHL) and

associated antigen A (MAGE-A) in lung cancer (Ziech et al. 2010).

for cancer therapy as well.

biomarkers.

**2.3 Epigenetic modifications in cancer** 

**2.4 DNA hypomethylation and cancer** 

**2.4.1 DNA hypermethylation and cancer** 

p53 in breast cancer. A number of changes are observed in lung cancer including P16INK4a, H-cadherin, Death-associated protein kinase 1 (DAPK1), MDM2, and p53. Modification in p14ARF is observed in lung, esophageal and colorectal cancers while changes in hHML1 are seen in colorectal cancer. RASSF1A modification are present in lung and nasopharyngeal cancers (Ziech et al. 2010).

#### **2.4.2 Modifications in chromatin structure in cancer**

Besides changes in DNA methylation patterns, the chromatin has also been shown to regulate transcriptional activity. To this end, any modifications in core histone proteins (e.g. H2A, H2B, H3 and H4) can have an impact in the activation and/or repression of transcription. Such modifications can include, among others, methylation, acetylation, deacetylation, phosphorylation, and ubiquitination. Histone acetylation and/or deacetylation are observed in breast, prostate, colon, testicular, renal and pancreatic cancers. Histone demethylation is observed in breast, prostate, colon, testicular and esophageal cancers while histone H3 lysine 27 tri-methylation is observed in breast, ovarian, colon and pancreatic cancers. Histone H3 lysine 9 and/or Histone H4 lysine 20 tri-methylations are present in breast, lung and hepatocellular cancers. Histone H3 lysine 4 methylation is often observed in breast, ovarian, colorectal and hepatocellular cancers (Ziech et al. 2010).

#### **2.5 BRCA1 and cancer**

Perhaps, the most noted molecular marker for cancer is mutations in the BRCA family of genes. The BRCA family of proteins is essential for HR-mediated repair of DNA double strand breaks (Jackson and Bartek 2009, Bartek, Lukas and Lukas 2004, Wang et al. 2010, Jiang et al. 2011). As little as one unrepaired DNA double strand break is fatal to the cell (Yang et al. 2009, Aziz, Nowsheen and Georgakilas 2010). Thus, it is not surprising that certain mutations in the BRCA gene lead to an increased risk for breast cancer as part of a hereditary breast-ovarian cancer syndrome. Women with mutated BRCA1 or BRCA2 gene have up to a 60% risk of developing breast cancer (King et al. 2003, Graeser et al. 2009). Similarly, 55% increased risk of developing ovarian cancer is observed with BRCA1 mutations and about 25% for women with BRCA2 mutations (King et al. 2003). Research suggests hypermethylation of the BRCA1 promoter may be an inactivating mechanism for BRCA1 expression not only in breast and ovarian cancer but also lung and oral cancer (Esteller et al. 2000, Marsit et al. 2003). Due to the lack of reliable biomarkers, many women with breast cancer end up being over-treated or under-treated for the disease. Epigenetic modifications have been detected in critical genes involved in breast cancer that could potentially serve as specific clinical molecular markers. These include promoter DNA hypomethylation in c-myc, CAGE, Urokinase-type plasminogen activator, EPO and γ-Synuclein genes and promoter DNA hypermethylation in BRCA1, BRCA2, Von Hippel– Lindau tumor suppressor (VHL) and p53 genes (Ziech et al. 2010).

In addition to breast cancer, mutations in the BRCA1 gene also increase the risk of developing ovarian, fallopian tube, and prostate cancers (Brose et al. 2002, Thompson, Easton and the Breast Cancer Linkage 2002). Mutations in BRCA also increase the risk for a subset of leukemia and lymphoma (Friedenson 2007). Women having inherited a defective BRCA1 or BRCA2 gene have risks for breast and ovarian cancer that are so high

2010). Mutations in the FANC gene, a marker of Fanconi anemia, leads to deficient DNA crosslink repair and subsequent increased risk of acute myeloid leukemia, head and neck cancer, gynecological malignancies, and gastrointestinal squamous cell carcinoma (Aziz et al. 2010). DNA Lig4 deficiency, a mutation in a key NHEJ repair protein, leads to pancreatic and lung cancers (Aziz et al. 2010). Other defects in NHEJ mediated repair pathways, e.g. Rag1 and Rag2 or Artemis, lead to an increased incidence of lymphoma. XCIND and RS-SCID syndromes are characterized by the aforementioned defects (Aziz et al. 2010). Mutations in XLF, a marker of Cernunnos deficiency and a key NHEJ-mediated repair protein, lead lymphoma while defects in ATR, a key DSB repair protein, lead to ATR-Seckel

Another protein, OGG1, an enzyme involved in DNA repair, has been shown to have predictive value for lung cancer (Hatt et al. 2008). OGG1 levels can be easily assayed in blood samples and low levels correlate with higher chance of developing lung cancer. In a recent study, 40% of people with lung cancer had low levels of the enzyme compared to 4%

Progression of any cancer is accompanied by genetic alteration(s) which leads to altered protein structure and function. In the last several years, the association between human papilloma virus (HPV) and head and neck cancer has been solidified (Wansom et al. 2010, Albers et al. 2005, Sirianni et al. 2004, Sirianni, Wang and Ferris 2005, Kumar et al. 2007, Kumar et al. 2008, Sisk et al. 2002). Interestingly, HPV associated head and neck cancers exhibit better prognosis and appear to respond better to chemo-radiation. Saliva or serum of head and neck cancer patients can be analyzed for p53, EGFR, and HPV status and microsatellite alterations. In addition, a number of epigenetic modifications have been detected in critical genes involved in this particular cancer type that could potentially serve as specific clinical biological markers. These include promoter DNA hypomethylation in Hras and CAGE genes in thyroid and laryngeal cancers respectively and promoter DNA hypermethylation in p14ARF and RASSF1A genes in esophageal and nasopharyngeal

Billions of dollars are spent each year to research new therapeutic strategies against cancer. Still, millions of people die from the disease each year. Thus, successful prevention appears to be the better option and requires attacking the root causes of the disease. The best way to control cancer is to prevent it from happening in the first place. Geographic and economic differences in cancer incidence and mortality are striking. The types of cancer vary greatly between the developed and developing countries. Lung, prostate, breast and colorectal cancer are common in the developed countries like the US while ovarian, cervical, hepatocellular, and head and neck cancer are wide-spread in the poorer nations (Ott et al. 2011). **Table 1** lists the common cancers and their associated risk factors which can be

syndrome which predisposes the individual to leukemia (Aziz et al. 2010).

of healthy individuals (Paz-Elizur et al. 2003).

**2.7 Other modifications in cancer** 

cancers respectively (Ziech et al. 2010).

avoided to prevent these malignancies.

**3. The role of lifestyle choices in cancer** 

and seem so selective that many mutation carriers choose to have prophylactic surgery. Promoter DNA hypomethylation in Maspin and γ-Synuclein genes and promoter DNA hypermethylation in BRCA1 and BRCA2 genes have been reported in ovarian cancer (Ziech et al. 2010). A number of epigenetic modifications have been detected in critical genes involved in pancreatic cancer that could potentially serve as specific clinical biomarkers including promoter DNA hypermethylation in BRCA1 and BRCA2 genes (Ziech et al. 2010). Thus, the tumor suppressor genes BRCA1 and BRCA2 are critical for the maintenance of our genome.

#### **2.6 Mutations in DNA repair genes and cancer**

Patients with underlying cellular defects in the response to DNA DSBs often exhibit genomic instability, increased cancer predisposition and radiation sensitivity. There are a number of other genetic disorders that predisposes an individual to cancer via defects in DNA repair pathways. For example, mutations in Ataxia telangiectasia mutated (ATM), a critical DNA repair protein, leads to Ataxia Telangiectasia (AT). ATM is a serine/threonine protein kinase that is recruited and activated by DNA DSB. It phosphorylates several key proteins that initiate activation of the DNA damage checkpoint, leading to cell cycle arrest, DNA repair or apoptosis. Several of these targets, including p53, CHK2 and H2AX are tumor suppressors (Shiloh 2003). Thus AT sufferers are predisposed to lymphoma, breast, brain, stomach, bladder, pancreas, lung, ovaries, T cell prolymphocytic leukemia, B cell chronic lymphocytic leukemia and sporadic colon cancers (Aziz et al. 2010). They are also extremely sensitive to radiation, a source of DNA damage (Alderton 2007).

Nijmegen breakage syndrome (NBS) is a rare autosomal recessive congenital disorder causing chromosomal instability and DNA repair deficiency. NBS1 codes for a protein that stops cell cycle progression following DNA damage and interacts with FANCD2 that can activate the BRCA1/BRCA2 pathway of DNA repair (Stavridi and Halazonetis 2005). Thus, mutations in the NBS1 gene lead to higher levels of cancer, primarily lymphoma (Aziz et al. 2010). Similarly, Lynch syndrome is marked by defects in MMR genes such as MSH1, MSH2, MSH6, and PMS2 (Vasen and de Vos tot Nederveen Cappel 2011). This leads to increased incidence of colorectal cancer, cancers of the stomach, small intestine, liver, gallbladder ducts, upper urinary tract, brain, skin, prostate, endometrium and ovary (Aziz et al. 2010). Li-Fraumeni patients demonstrate mutations in Chk2 and p53 and defects in MMR. They have a higher incidence of osteosarcoma (Aziz et al. 2010). Werner syndrome, on the other hand, is marked by mutations in WRN and Rad51 genes leading to deficiency in HR- and NHEJ mediated DSB repair. This syndrome leads to a number of cancers including osteosarcoma, colon, rectal, lung, stomach, prostate, breast, thyroid and soft tissue sarcomas (Aziz et al. 2010). Xeroderma Pigmentosum is marked by mutations in XPD gene, defects in NER-mediated repair and higher incidence of skin cancer (Aziz et al. 2010). Bloom is caused by mutations in Blm gene and leads to leukemia, lymphoma, melanoma, and bladder cancer due to defects in HR-mediated repair (Aziz et al. 2010). Mutations in RECQL4, a key BER and HR-repair protein, leads to Rothmund Thompson, Baller Gerold and Rapadilino syndromes which are marked by predisposition to osteosarcoma (Aziz et al.

and seem so selective that many mutation carriers choose to have prophylactic surgery. Promoter DNA hypomethylation in Maspin and γ-Synuclein genes and promoter DNA hypermethylation in BRCA1 and BRCA2 genes have been reported in ovarian cancer (Ziech et al. 2010). A number of epigenetic modifications have been detected in critical genes involved in pancreatic cancer that could potentially serve as specific clinical biomarkers including promoter DNA hypermethylation in BRCA1 and BRCA2 genes (Ziech et al. 2010). Thus, the tumor suppressor genes BRCA1 and BRCA2 are critical for

Patients with underlying cellular defects in the response to DNA DSBs often exhibit genomic instability, increased cancer predisposition and radiation sensitivity. There are a number of other genetic disorders that predisposes an individual to cancer via defects in DNA repair pathways. For example, mutations in Ataxia telangiectasia mutated (ATM), a critical DNA repair protein, leads to Ataxia Telangiectasia (AT). ATM is a serine/threonine protein kinase that is recruited and activated by DNA DSB. It phosphorylates several key proteins that initiate activation of the DNA damage checkpoint, leading to cell cycle arrest, DNA repair or apoptosis. Several of these targets, including p53, CHK2 and H2AX are tumor suppressors (Shiloh 2003). Thus AT sufferers are predisposed to lymphoma, breast, brain, stomach, bladder, pancreas, lung, ovaries, T cell prolymphocytic leukemia, B cell chronic lymphocytic leukemia and sporadic colon cancers (Aziz et al. 2010). They are also extremely sensitive to radiation, a source of DNA

Nijmegen breakage syndrome (NBS) is a rare autosomal recessive congenital disorder causing chromosomal instability and DNA repair deficiency. NBS1 codes for a protein that stops cell cycle progression following DNA damage and interacts with FANCD2 that can activate the BRCA1/BRCA2 pathway of DNA repair (Stavridi and Halazonetis 2005). Thus, mutations in the NBS1 gene lead to higher levels of cancer, primarily lymphoma (Aziz et al. 2010). Similarly, Lynch syndrome is marked by defects in MMR genes such as MSH1, MSH2, MSH6, and PMS2 (Vasen and de Vos tot Nederveen Cappel 2011). This leads to increased incidence of colorectal cancer, cancers of the stomach, small intestine, liver, gallbladder ducts, upper urinary tract, brain, skin, prostate, endometrium and ovary (Aziz et al. 2010). Li-Fraumeni patients demonstrate mutations in Chk2 and p53 and defects in MMR. They have a higher incidence of osteosarcoma (Aziz et al. 2010). Werner syndrome, on the other hand, is marked by mutations in WRN and Rad51 genes leading to deficiency in HR- and NHEJ mediated DSB repair. This syndrome leads to a number of cancers including osteosarcoma, colon, rectal, lung, stomach, prostate, breast, thyroid and soft tissue sarcomas (Aziz et al. 2010). Xeroderma Pigmentosum is marked by mutations in XPD gene, defects in NER-mediated repair and higher incidence of skin cancer (Aziz et al. 2010). Bloom is caused by mutations in Blm gene and leads to leukemia, lymphoma, melanoma, and bladder cancer due to defects in HR-mediated repair (Aziz et al. 2010). Mutations in RECQL4, a key BER and HR-repair protein, leads to Rothmund Thompson, Baller Gerold and Rapadilino syndromes which are marked by predisposition to osteosarcoma (Aziz et al.

the maintenance of our genome.

damage (Alderton 2007).

**2.6 Mutations in DNA repair genes and cancer** 

2010). Mutations in the FANC gene, a marker of Fanconi anemia, leads to deficient DNA crosslink repair and subsequent increased risk of acute myeloid leukemia, head and neck cancer, gynecological malignancies, and gastrointestinal squamous cell carcinoma (Aziz et al. 2010). DNA Lig4 deficiency, a mutation in a key NHEJ repair protein, leads to pancreatic and lung cancers (Aziz et al. 2010). Other defects in NHEJ mediated repair pathways, e.g. Rag1 and Rag2 or Artemis, lead to an increased incidence of lymphoma. XCIND and RS-SCID syndromes are characterized by the aforementioned defects (Aziz et al. 2010). Mutations in XLF, a marker of Cernunnos deficiency and a key NHEJ-mediated repair protein, lead lymphoma while defects in ATR, a key DSB repair protein, lead to ATR-Seckel syndrome which predisposes the individual to leukemia (Aziz et al. 2010).

Another protein, OGG1, an enzyme involved in DNA repair, has been shown to have predictive value for lung cancer (Hatt et al. 2008). OGG1 levels can be easily assayed in blood samples and low levels correlate with higher chance of developing lung cancer. In a recent study, 40% of people with lung cancer had low levels of the enzyme compared to 4% of healthy individuals (Paz-Elizur et al. 2003).
