**2. An introduction to genome instability in cancer**

Genomic instability refers to chromosomal changes, ploidy change or changes in nucleic acid sequence. In multicellular organisms, genome instability is fundamental to carcinogenesis [12]. Genome instability in cancer is associated with the ploidy change, chromosomal translocations, inversions, insertion, deletions, DNA breaks or any abnormal changes in DNA tertiary structure that can cause DNA damage, or the misexpression of genes (**Figure 1**). Ploidy change is accumulation of extra copies of chromosome(s) or parts of chromosome. Chromosomal translocations are phenomenon when a part of the chromosome breaks and get attached to some other chromosome. Inversions are breakage of a piece of DNA and getting attached to the same position in an inverted orientation. It happens when the DNA undergoes breakage and rearrangement. Insertion as the name suggests is the insertion of nucleotides on a locus in the genome. In deletions, there is deletion of nucleotide from specific loci in the genome. DNA breaks are either double stranded or single stranded depending, single stranded are easily repaired because here template is readily available but there are specific repair pathways dedicated to double stranded breaks since template is lost and the repair pathways has to bring it from the other pair and in some cases, there is error prone repair [8, 13]. Microsatellite instability is another such phenomenon influencing genomic instability. Genome instability fuels the cancer cells with changes that help it to evolve and escape death. Additionally, it also plays a critical role in cancer initiation and progression by overcoming immune surveillance, attaining uncontrolled cell division, more DNA damage, etc. [14]

In normal cells, genome is protected at every stage of the cell cycle, every step from DNA replication to chromosome packaging. Every step is very precisely monitored for faults. Several processes are involved in this such as cell cycle checkpoints, DNA damage checkpoints and DNA repair. When a normal cell turns cancerous, these fault monitoring systems are manipulated; presence of genomic instability itself indicates the failure of one or many of these safety nets (**Figure 1**) [13]. Interpreting the underlying mechanisms for imbalance in genome integrity would yield new avenues for precision therapies and clinical decision-making. Lot of research has been centered to genome instability to understand it and hold control over its initiation and progress in a hope to conquer cancer, which is the world

**Figure 1.** *Genomic instability influencing cancer.*

leading cause of death. But still a clear picture of its origin or prevalence is far from our understanding [15].

All the mutations which are results of genomic instability are not hazardous, some of them just exist without much influential function. The ones with potent negative effects are termed as driver mutations and the one without are termed as passenger mutations. Even passenger mutations contribute to tumorigenesis but has less influence. Diver mutations are usually the mutations that are present in tumor suppressors, DNA repair genes, etc. A lot of studies are done to understand these driver mutations but again there is no clear evidence [15].

In hereditary cancers, genomic instability arises from mutations in DNA repair genes that drives cancer development, as predicted by the mutator hypothesis. On the other hand, sporadic cancer, the molecular basis of genomic instability remains unclear, but recent high-throughput sequencing studies suggest that mutations in DNA repair genes is one of the major mechanisms of inducing genomic instability. Still there remains a debate on either tumor suppressor genes or the DNA repair genes are the major source for genome instability in cancer, but it is established that DNA repair mechanisms is one of the prime targets [12].

### **3. Influence of cancer on DNA repair pathways**

Source of mutation in DNA of normal cell are either from faults in DNA replication procedure or from carcinogens. The fidelity of eukaryotic DNA polymerase is very high with about 10−10 mutation per 1000 nucleotides, yet sometimes it miss, and mutation occur. Carcinogens encompasses all the factors that cause DNA damage and evoke carcinogenesis, they are such as ionizing radiations, UV radiations; some non -radiating ones are such as alcohol, tobacco, cigarette smoke and such other abusive products. These products include reactive oxygen species, deaminating agents, alkylating agents, polycyclic aromatic hydrocarbons, base analogs, intercalating agents, etc. [16]. Not only these, but there are also some microbes such as *Helicobacter pylori* and Human papilloma virus which induce inflammation leading to generation of various reactive oxygen species and generation of cancer. But still till date a specific reason for cancer cause has not been elucidated [17]. Several theories describe cancer cause but a proper picture of its causal and turning deadly is not yet established. It is very clear that cancer is not a one step process while it is complex, associated with several factors coming together to generate a system for freeing itself from crunches of checkpoints for regulating cell division. In normal cells these mutations are checked on by DNA damage checkpoints or cell cycle checkpoint, these are a series of biochemical pathways that are in constant surveillance to ensure integrity of the genome upon encountering any defects, they halt cell cycle progression and activate DNA damage repair mechanisms, then ensure repair of the faults and resume cell cycle progression [18] as shown in **Figure 2**.

There are several type of repair pathways namely: nucleotide excision repair (NER), base excision repair (BER), DNA mismatch repair (MMR) and double strand break repair which includes homologous recombination (HR) and nonhomologous end joining (NHEJ). Every one of them are specialized in a specific type of repair pathway [4]. A detailed description of them with the mutation and modifications that are present in genes involved in these pathways in cancer cells can give us much understanding of exploitation of the process by cancer.

Nucleotide excision repair (NER) repairs bulky lesions and large adducts that distorts double stranded helix under conditions when only one of the two DNA strands is affected, UV radiation and chemical mutagens include such damage. These mutagens cross-link adjacent pyrimidine bases and purine bases and creates

**193**

**Figure 2.**

to the pre-existing ones [22].

*Genomic Instability and DNA Repair in Cancer DOI: http://dx.doi.org/10.5772/intechopen.95736*

intra-strand adducts, such damage blocks basic cellular systems like DNA replication and transcription [19]. NER can adapt to many structurally unrelated types of damage, to perform its diverse work, NER employs two sub pathways: global genome repair (GG-NER) and transcription coupled repair (TC-NER). The sub pathway names hint their distinctive roles, transcription coupled repair act on lesions that block progression of an active transcription site, a locus in the genome where an RNA polymerase is actively functioning and global genome repair is active in all phases of the cell cycle, repairing damages [20]. NER first recognize the damage, gather its associated complex and unwinds that specific region of DNA locus, makes incision on both points, remove the damage, synthesizes new nucleotides using other DNA strand as template strand and ligates the DNA [21]. Several different proteins are involved in the process; a nine-unit complex called transcription factor IIH (TFIIH) executes the first phase of repair, this complex includes two helicases, XPB and XPD and two other proteins, XPA and RPA that open the helix. It remains attached to the DNA while two different endonucleases, XPG and XPF, the latter acting in conjunction with ERCC1 perform precise cutting on one side of the damaged strand, several nucleotides away from the damage. After this initial step, RPA mediates the assembly of a second repair complex where Replication factor C (RFC) binds to excision region and facilitates PCNA that binds to DNA polymerases δ and ε, preventing them from falling off the strand before the reconstruction has been done and ultimately Ligase I attaches new repaired strand

*Schematic illustration of relationship between mutations, DNA repair system and cancer.*

The base excision repair (BER) pathway corrects damage occurring from oxidation, alkylation, deamination, and ionizing radiation, these lesions produce mild damage involving few bases the mutation usually cause base mispairings [23]. In this case mutagens are usually endogenous; here by the term mutagens we mean mutation causing agents, here only the damaged nucleoside is removed by cleaving *Genomic Instability and DNA Repair in Cancer DOI: http://dx.doi.org/10.5772/intechopen.95736*

*DNA - Damages and Repair Mechanisms*

our understanding [15].

leading cause of death. But still a clear picture of its origin or prevalence is far from

All the mutations which are results of genomic instability are not hazardous, some of them just exist without much influential function. The ones with potent negative effects are termed as driver mutations and the one without are termed as passenger mutations. Even passenger mutations contribute to tumorigenesis but has less influence. Diver mutations are usually the mutations that are present in tumor suppressors, DNA repair genes, etc. A lot of studies are done to understand these

In hereditary cancers, genomic instability arises from mutations in DNA repair genes that drives cancer development, as predicted by the mutator hypothesis. On the other hand, sporadic cancer, the molecular basis of genomic instability remains unclear, but recent high-throughput sequencing studies suggest that mutations in DNA repair genes is one of the major mechanisms of inducing genomic instability. Still there remains a debate on either tumor suppressor genes or the DNA repair genes are the major source for genome instability in cancer, but it is established that

Source of mutation in DNA of normal cell are either from faults in DNA replication procedure or from carcinogens. The fidelity of eukaryotic DNA polymerase is very high with about 10−10 mutation per 1000 nucleotides, yet sometimes it miss, and mutation occur. Carcinogens encompasses all the factors that cause DNA damage and evoke carcinogenesis, they are such as ionizing radiations, UV radiations; some non -radiating ones are such as alcohol, tobacco, cigarette smoke and such other abusive products. These products include reactive oxygen species, deaminating agents, alkylating agents, polycyclic aromatic hydrocarbons, base analogs, intercalating agents, etc. [16]. Not only these, but there are also some microbes such as *Helicobacter pylori* and Human papilloma virus which induce inflammation leading to generation of various reactive oxygen species and generation of cancer. But still till date a specific reason for cancer cause has not been elucidated [17]. Several theories describe cancer cause but a proper picture of its causal and turning deadly is not yet established. It is very clear that cancer is not a one step process while it is complex, associated with several factors coming together to generate a system for freeing itself from crunches of checkpoints for regulating cell division. In normal cells these mutations are checked on by DNA damage checkpoints or cell cycle checkpoint, these are a series of biochemical pathways that are in constant surveillance to ensure integrity of the genome upon encountering any defects, they halt cell cycle progression and activate DNA damage repair mechanisms, then ensure repair of the faults and resume cell cycle progression [18] as shown in **Figure 2**. There are several type of repair pathways namely: nucleotide excision repair (NER), base excision repair (BER), DNA mismatch repair (MMR) and double strand break repair which includes homologous recombination (HR) and nonhomologous end joining (NHEJ). Every one of them are specialized in a specific type of repair pathway [4]. A detailed description of them with the mutation and modifications that are present in genes involved in these pathways in cancer cells

can give us much understanding of exploitation of the process by cancer.

Nucleotide excision repair (NER) repairs bulky lesions and large adducts that distorts double stranded helix under conditions when only one of the two DNA strands is affected, UV radiation and chemical mutagens include such damage. These mutagens cross-link adjacent pyrimidine bases and purine bases and creates

driver mutations but again there is no clear evidence [15].

DNA repair mechanisms is one of the prime targets [12].

**3. Influence of cancer on DNA repair pathways**

**192**

**Figure 2.** *Schematic illustration of relationship between mutations, DNA repair system and cancer.*

intra-strand adducts, such damage blocks basic cellular systems like DNA replication and transcription [19]. NER can adapt to many structurally unrelated types of damage, to perform its diverse work, NER employs two sub pathways: global genome repair (GG-NER) and transcription coupled repair (TC-NER). The sub pathway names hint their distinctive roles, transcription coupled repair act on lesions that block progression of an active transcription site, a locus in the genome where an RNA polymerase is actively functioning and global genome repair is active in all phases of the cell cycle, repairing damages [20]. NER first recognize the damage, gather its associated complex and unwinds that specific region of DNA locus, makes incision on both points, remove the damage, synthesizes new nucleotides using other DNA strand as template strand and ligates the DNA [21]. Several different proteins are involved in the process; a nine-unit complex called transcription factor IIH (TFIIH) executes the first phase of repair, this complex includes two helicases, XPB and XPD and two other proteins, XPA and RPA that open the helix. It remains attached to the DNA while two different endonucleases, XPG and XPF, the latter acting in conjunction with ERCC1 perform precise cutting on one side of the damaged strand, several nucleotides away from the damage. After this initial step, RPA mediates the assembly of a second repair complex where Replication factor C (RFC) binds to excision region and facilitates PCNA that binds to DNA polymerases δ and ε, preventing them from falling off the strand before the reconstruction has been done and ultimately Ligase I attaches new repaired strand to the pre-existing ones [22].

The base excision repair (BER) pathway corrects damage occurring from oxidation, alkylation, deamination, and ionizing radiation, these lesions produce mild damage involving few bases the mutation usually cause base mispairings [23]. In this case mutagens are usually endogenous; here by the term mutagens we mean mutation causing agents, here only the damaged nucleoside is removed by cleaving its *N*-glycosidic bond, leaving an abasic (AP) site [24]. One of BER's exclusivity depends on its 11 damage-sensing glycosylases, these glycosylases remain bound to the site to ensure that the fragile AP site never remains unattended, APE1/Ref1, or AP endonuclease/Redox Factor 1, process the loose ends creating special termini to accept the new base [25]. XRCC1 stabilizes the damaged area and coordinates sequential binding and release. XRCC1 also acts as a helicase, the process then includes a sliding clamp PCNA (proliferating cell nuclear antigen) and an additional stabilizer that also inserts the newly synthesized nucleotides, replication factor-C, or RFC [26].

During DNA replication, proofreading polymerases sometimes may fail to detect errors made by DNA polymerase. Mismatched repair (MMR) in a post-replicative repair mechanism steps in this scenario to clear the errors. MMR's damage sensors can differentiate between the parental DNA strand and the newly synthesized DNA strand and only remove the mismatch in newly synthesized strand, using parental strand as a template, MMR remove the mismatch and synthesizes new DNA strand [27]. MMR corrects single-base mismatches and small insertion/ deletion loops by one of the two damage recognition complexes MSH2:MSH6 or MSH2:MSH3, MSH2:MSH6 recognizes single-base substitutions and the smallest insertion/deletion loop and MSH2:MSH3 insertion/deletion loop involving up to 10 nucleotides [28]. Then they recruits a complex, comprising MutL homolog 1 (MLH1) and its binding partners, post-meiotic segregation increased protein 1or 2 (PMS1 or PMS2), MSH and MLH complexes form sliding clamp that moves along the DNA sequence till it encounters a single-strand DNA gap, replication Protein A (RPA) functions as indication at the damage site. Then MutL complex encounters the cluster, it allows a DNA exonuclease (Exo1) to enter the DNA structure, guided by the MLH:MSH complex, Exo1 removes the damage portion plus some more nucleotides and a DNA polymerase, Pol *δ* synthesizes DNA in those loci of excision. Finally, Ligase I joins the new DNA to the existing daughter strand [29].

Double-strand breaks (DSBs) are the most serious, hazardous, very complex to repair, they are rare but there are instances of its occurrences; most common ones are due to breaks in replication forks when polymerases stall at the site of unrepaired base lesions and by exogenous agents like ionizing radiations, etc. Anticancer treatments comprising of chemotherapeutics and radiation therapy can also induce multiple kinds of double-stranded DNA damage [30].

DSB repair faces many challenges such as loss of physical integrity on both strands due to which there is loss of information, like when one stand is damaged one can retrieve information from the other strand but if there is a double strand break there is no template for synthesis of the new strand, to repair such damage, human cells employ two main pathways: nonhomologous end joining (NHEJ) and homologous recombination repair (HR). Cell cycle checkpoints evaluate end processing required, which partially dictates how DSBs would be repaired [31]. NHEJ operate during any cell cycle phase but is most active in G0 and G1 (before DNA replication), whereas HR is active during S and G2 phases (after replication), its prone to error whereas HR is template based therefore its fidelity is higher and this makes the process a little complicated. Damage sensor complex is common to both NHEJ and HRR is Mre11-Rad50-Nbs1 (MRN). MRN's functionality is only one of many mysteries of DSB repair, there are still a lot to be discovered regarding HR and NHEJ. The following paragraphs summarize the main HR and NHEJ pathways [22, 32].

Nonhomologous end joining (NHEJ) rejoins DSB ends without a template, it does not search for or use a large segment of DNA for determining which bases were present before the damage occurred and search which is the other end of the breakage. Therefore, repair proceed quickly with the potential for loss of nucleotides from either side of the DSB junction, alteration of base pair sequences at

**195**

*Genomic Instability and DNA Repair in Cancer DOI: http://dx.doi.org/10.5772/intechopen.95736*

ing lymphocyte diversity [34].

the breakpoint or getting attached to some other end that does not belong to the sequence in case of multiple breaks. Thus, NHEJ can contribute to a large amount of mutation but it is preferred by the cell [33]. The main challenge of NHEJ is to collect the two free ends into immediate proximity and protect them from nucleolytic attack. The Ku heterodimer, a damage sensor and a lyase imparts protection and recruit other proteins for end processing. Then DNA-dependent protein kinase catalytic subunit (DNA-PKcs) binds to Ku and becomes DNA-PK, a docking port for various kinds of DNA end processing enzyme. Another complex XRCC4 + Ligase IV + XLF create a filament to bridge the ends. Ligase IV ligate across gaps and join processed DNA ends. Many aspects of NHEJ still remain a mystery, including whether its steps are sequential, iterative or flexible according to the complexity of the damage. The most studied form of NHEJ is V(D)J recombination, which occurs only in T and B cells and is essential for their development, maturation and generat-

Homologous recombination repair (HR) is a complex template directed DSB repair mechanism, it gets activated after DNA is copied in S phase but before it divides in M phase, so that the two strands are still together held by cohesion complex and HR takes advantage of the other full copy of adjacent DNA. This enables HR to find a large area of homology on the sister chromatid and use it as a template to reconstruct the damaged DNA strand [35]. HR plays significant role in maintaining genomic stability, in the basic step, MRN forms single-stranded DNA at the DSB end, ssDNA extends beyond the original breakpoint enabling Rad51 to attach to 3′ end, RPA binds to the naked stretch of DNA so that Rad51 can sit on the ssDNA and find DNA sequences like the 3′ overhang. When Rad51 encounters the locus with homology it invades the double strand, creating a DNA heteroduplex. Rad51 facilitates exchange of homologous DNA sequences within the sister chromatid. The overhang progressively extends as new nucleotides are generated beyond the original breakpoint, Nbs1 recruits other repair proteins to the site, Rad50 serves as a tether; MRE11 possesses both exo- and endonuclease functions [35]. During synthesis, as the loop is pushed, an X-shaped structure develops, called a Holliday junction, at the end this Holliday junction is resolved and ends are ligated Many HR genes like BRCA1, BRCA2 are involved in genomic instability generation and cancer [36]. Above mentioned facts have lightened up the understanding that cell have a very elaborately designed DNA repair system for

damages now let us see how cancer wangle it through various measures.

**4.1 Germline mutation associated with DNA repair pathways**

DNA, the genetic component of a cell, often gets damaged when exposed to any endogenous or exogenous agent like radiation, smoke, macrophages, ROS, etc. Different DNA repair pathways like base repair, mismatch excision repair, homologous recombination etc. help in repairing these DNA damages. But the expression of genes involved in these repair pathways sometimes gets reduced due to germline mutation, epigenetic alterations, somatic mutation, etc. As a result, the unrepaired DNA damage accumulates in cells. This accumulation might lead to further increase in epigenetic or somatic alteration, which helps in multiplying the altered field defects as well as different driver mutations that ultimately helps in the progression of cancer [22]. Details of few alterations affecting DNA repair genes are mentioned below.

Germline mutations of DNA repair pathways usually results in predisposing ones to cancer or having it by birth itself if abnormal gene is inherited from one

**4. Mutations in DNA repair genes in cancer**

*Genomic Instability and DNA Repair in Cancer DOI: http://dx.doi.org/10.5772/intechopen.95736*

*DNA - Damages and Repair Mechanisms*

or RFC [26].

its *N*-glycosidic bond, leaving an abasic (AP) site [24]. One of BER's exclusivity depends on its 11 damage-sensing glycosylases, these glycosylases remain bound to the site to ensure that the fragile AP site never remains unattended, APE1/Ref1, or AP endonuclease/Redox Factor 1, process the loose ends creating special termini to accept the new base [25]. XRCC1 stabilizes the damaged area and coordinates sequential binding and release. XRCC1 also acts as a helicase, the process then includes a sliding clamp PCNA (proliferating cell nuclear antigen) and an additional stabilizer that also inserts the newly synthesized nucleotides, replication factor-C,

During DNA replication, proofreading polymerases sometimes may fail to detect errors made by DNA polymerase. Mismatched repair (MMR) in a post-replicative repair mechanism steps in this scenario to clear the errors. MMR's damage sensors can differentiate between the parental DNA strand and the newly synthesized DNA strand and only remove the mismatch in newly synthesized strand, using parental strand as a template, MMR remove the mismatch and synthesizes new DNA strand [27]. MMR corrects single-base mismatches and small insertion/ deletion loops by one of the two damage recognition complexes MSH2:MSH6 or MSH2:MSH3, MSH2:MSH6 recognizes single-base substitutions and the smallest insertion/deletion loop and MSH2:MSH3 insertion/deletion loop involving up to 10 nucleotides [28]. Then they recruits a complex, comprising MutL homolog 1 (MLH1) and its binding partners, post-meiotic segregation increased protein 1or 2 (PMS1 or PMS2), MSH and MLH complexes form sliding clamp that moves along the DNA sequence till it encounters a single-strand DNA gap, replication Protein A (RPA) functions as indication at the damage site. Then MutL complex encounters the cluster, it allows a DNA exonuclease (Exo1) to enter the DNA structure, guided by the MLH:MSH complex, Exo1 removes the damage portion plus some more nucleotides and a DNA polymerase, Pol *δ* synthesizes DNA in those loci of excision.

Finally, Ligase I joins the new DNA to the existing daughter strand [29].

multiple kinds of double-stranded DNA damage [30].

Double-strand breaks (DSBs) are the most serious, hazardous, very complex to repair, they are rare but there are instances of its occurrences; most common ones are due to breaks in replication forks when polymerases stall at the site of unrepaired base lesions and by exogenous agents like ionizing radiations, etc. Anticancer treatments comprising of chemotherapeutics and radiation therapy can also induce

DSB repair faces many challenges such as loss of physical integrity on both strands due to which there is loss of information, like when one stand is damaged one can retrieve information from the other strand but if there is a double strand break there is no template for synthesis of the new strand, to repair such damage, human cells employ two main pathways: nonhomologous end joining (NHEJ) and homologous recombination repair (HR). Cell cycle checkpoints evaluate end processing required, which partially dictates how DSBs would be repaired [31]. NHEJ operate during any cell cycle phase but is most active in G0 and G1 (before DNA replication), whereas HR is active during S and G2 phases (after replication), its prone to error whereas HR is template based therefore its fidelity is higher and this makes the process a little complicated. Damage sensor complex is common to both NHEJ and HRR is Mre11-Rad50-Nbs1 (MRN). MRN's functionality is only one of many mysteries of DSB repair, there are still a lot to be discovered regarding HR and NHEJ. The following paragraphs summarize the main HR and NHEJ pathways [22, 32].

Nonhomologous end joining (NHEJ) rejoins DSB ends without a template, it does not search for or use a large segment of DNA for determining which bases were present before the damage occurred and search which is the other end of the breakage. Therefore, repair proceed quickly with the potential for loss of nucleotides from either side of the DSB junction, alteration of base pair sequences at

**194**

the breakpoint or getting attached to some other end that does not belong to the sequence in case of multiple breaks. Thus, NHEJ can contribute to a large amount of mutation but it is preferred by the cell [33]. The main challenge of NHEJ is to collect the two free ends into immediate proximity and protect them from nucleolytic attack. The Ku heterodimer, a damage sensor and a lyase imparts protection and recruit other proteins for end processing. Then DNA-dependent protein kinase catalytic subunit (DNA-PKcs) binds to Ku and becomes DNA-PK, a docking port for various kinds of DNA end processing enzyme. Another complex XRCC4 + Ligase IV + XLF create a filament to bridge the ends. Ligase IV ligate across gaps and join processed DNA ends. Many aspects of NHEJ still remain a mystery, including whether its steps are sequential, iterative or flexible according to the complexity of the damage. The most studied form of NHEJ is V(D)J recombination, which occurs only in T and B cells and is essential for their development, maturation and generating lymphocyte diversity [34].

Homologous recombination repair (HR) is a complex template directed DSB repair mechanism, it gets activated after DNA is copied in S phase but before it divides in M phase, so that the two strands are still together held by cohesion complex and HR takes advantage of the other full copy of adjacent DNA. This enables HR to find a large area of homology on the sister chromatid and use it as a template to reconstruct the damaged DNA strand [35]. HR plays significant role in maintaining genomic stability, in the basic step, MRN forms single-stranded DNA at the DSB end, ssDNA extends beyond the original breakpoint enabling Rad51 to attach to 3′ end, RPA binds to the naked stretch of DNA so that Rad51 can sit on the ssDNA and find DNA sequences like the 3′ overhang. When Rad51 encounters the locus with homology it invades the double strand, creating a DNA heteroduplex. Rad51 facilitates exchange of homologous DNA sequences within the sister chromatid. The overhang progressively extends as new nucleotides are generated beyond the original breakpoint, Nbs1 recruits other repair proteins to the site, Rad50 serves as a tether; MRE11 possesses both exo- and endonuclease functions [35]. During synthesis, as the loop is pushed, an X-shaped structure develops, called a Holliday junction, at the end this Holliday junction is resolved and ends are ligated Many HR genes like BRCA1, BRCA2 are involved in genomic instability generation and cancer [36]. Above mentioned facts have lightened up the understanding that cell have a very elaborately designed DNA repair system for damages now let us see how cancer wangle it through various measures.

### **4. Mutations in DNA repair genes in cancer**

DNA, the genetic component of a cell, often gets damaged when exposed to any endogenous or exogenous agent like radiation, smoke, macrophages, ROS, etc. Different DNA repair pathways like base repair, mismatch excision repair, homologous recombination etc. help in repairing these DNA damages. But the expression of genes involved in these repair pathways sometimes gets reduced due to germline mutation, epigenetic alterations, somatic mutation, etc. As a result, the unrepaired DNA damage accumulates in cells. This accumulation might lead to further increase in epigenetic or somatic alteration, which helps in multiplying the altered field defects as well as different driver mutations that ultimately helps in the progression of cancer [22]. Details of few alterations affecting DNA repair genes are mentioned below.

#### **4.1 Germline mutation associated with DNA repair pathways**

Germline mutations of DNA repair pathways usually results in predisposing ones to cancer or having it by birth itself if abnormal gene is inherited from one of the parents and other gene copy gets inactivated in a somatic cell later in life or both copies of a gene can get deactivated. Ultimately, that results in loss of heterozygosity which leads to a deficient response of DNA repair genes. Such affect from mutations are also seen if it is present in tumor suppressor cells [37].

Genes involved in the mismatch repair like MLH1, MSH6, MHS1 are often associated with Lynch syndrome, hereditary non-polyposis colorectal cancer (HNPCC), is the most common cause of hereditary colorectal (colon) cancer when undergoes monoallelic mutation but are associated with Constitutional mismatch repair deficiency syndrome due to biallelic mutation across children and adolescent [38].

Genes involved in homologous recombination like BRCA1/2 and BRIP1 are associated with hereditary breast and ovarian cancer syndrome when undergoes biallelic mutation. Defect in these two genes often results in breast cancer [38].

### **4.2 Somatic mutational signatures are associated with DNA repair pathways in cancer**

Somatic mutations are basic to cancer and finding their occurrence on DNA repair genes is expected, researchers have well-established effect and consequences from a few of them. The substitution mutation signatures with homologous recombination genes like BRCA leads to homologous recombination failure in breast cancer, other than that promoter methylation also contributes to BRCA gene defects in different tumors [38]. Apart from substitution, rearrangement signatures are also involved in BRCA of breast cancer, these signatures include tandem duplication, inversion, deletion, translocation, etc. For example, tandem duplication is associated with the BRCA1 mutation, whereas small deletions are associated with BRCA1/2 inactivation, indel rearrangement signature is associated with BRCA deficiency [39].

Unlike homologous recombination repair, substitution mutation signatures are also associated with the Mismatch excision repair system. For example, high rates of substitution and indels are seen in C.G to T.A transition at NpCpG sequences. Also, rearrangement signatures are associated with MMR genes, which are often found in breast cancer [39].

High expression of *XRCC-1,* interacts with DNA ligase III, polymerase beta and poly (ADP-ribose) polymerase is associated with early tumor stage in oral squamous cell carcinoma. Accumulation of single strand breaks downregulates protein APE1 responsible for DNA incision during BER helping the conversion of single strand breaks to double stranded ones [40].

Overexpression of *ERCC1* in prostate cancer has association with the formation of chromosome aberrations. It is shown to inhibit apoptosis in esophageal squamous cell carcinoma. Some of its polymorphisms also indicates prognostic markers [41].

### **5. Epigenetic alterations associated with DNA repair pathways**

Likewise mentioned earlier cancer applies several methods to take control over repair mechanism, epigenetic alteration is another such technique, here the DNA sequence remains intact, but expression and activity of the gene is affected. It's the technique due to which we have different type of cells in our body despite having the same genetic makeup and most importantly it's hereditary. Epigenetics include covalent modifications like methylation, ubiquitylation, sumoylation, phosphorylation to histones or DNA, sRNA, miRNA [41]. The following information

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*Genomic Instability and DNA Repair in Cancer DOI: http://dx.doi.org/10.5772/intechopen.95736*

**5.1 Epigenetic alterations by promoter methylation**

tomas, colon cancer, lung cancer, lymphoma etc. [44].

process, by the action of miR-155 (**Table 1**) [45].

**5.2 Epigenetic alterations due to chromosome remodeling and histone** 

modification.

ovarian, etc. [41].

ovarian, gastric, etc. [41, 42].

**modification**

is on promoter methylation, miRNAs and chromosome remodeling by histone

One of the most common ways of epigenetic alteration is by promoter methylation, this is often regulated by cytosine methyl transferases, genes get inactivated by methylation in 5-carbon of cytosine of 5′-CpG-3′ dinucleotide sequence at either promoter regions. Two of the genes involved in base excision repair namely Methyl-CpG Binding Domain 4, DNA (MBD4) and Thymine-DNA glycosylase (TDG), both are glycosylases with same function of removing mismatches by hydrolyzing carbon-nitrogen linkage between the sugar and the phosphate backbone of DNA and mis paired thymine. Due to promoter methylation in these two genes, it is found that BER pathway often gets suppressed in cancers like colorectal, myeloma,

The *XPC* gene which encodes a protein that is a key component of the XPC complex involved in GG-NER, promoter methylation of this gene often leads to NER function loss in cancers like bladder cancer. Other genes of the nucleotide excision repair pathway, RAD23A and ERCC1 genes also get inactivated by promoter methylation in different cancers like RAD23A in multiple myeloma cancers and ERCC1 in glioma cancer. Genes of the mismatch repair pathway namely MLH1, MSH2, MSH3, and MSH6 also gets suppressed by promoter methylation in various cancers like

Two genes BRCA1 and BRCA2 of homologous recombination system also have compromised activity by promoter methylation in different cancers like breast, gastric, uterine, etc. One of the genes, involved in non-homologous end-joining, XRCC5 encodes the heterodimer Ku (composed of K70/K80), which facilitates binding to nascent DNA breaks often gets epigenetically inactivated by promoter methylation is seen to be associated with cancers like adenocarcinomas [43]*.*

Direct reversal of DNA damage is the most energy efficient repair system, but its capabilities encompasses only certain damage categories such as pyrimidine dimers formed by UV radiation, O6 adducts like alkyl groups on nucleotides from chemotherapy. *O*6-methylguanine-DNA methyltransferase (MGMT), catalyzes transfer of methyl groups on DNA to its own molecule, methylation on its promoter inactivates it like the other DNA repair genes, this is often associated with cancers like glioblas-

The miRNA is synthesized as primary non-coding RNA these are then processed into mature effective ones which can alter expression of its target genes. On those target genes it influences the methylation status in the promoters and we know that the methylation status of promoters are related to their expression levels or they can directly target epigenetic factors, such as DNA methyltransferases or histone deacetylases, regulating chromatin structure for altered expression. Some genes of mismatch excision repair like MLH1, MSH2, and MSH6 are inactivated by such

Low expression of miRNA-15 suppresses promoter activity of BRCA1 by recruiting an enhanceosome mediated by HMGA1 [46]. miRNA-16 influence transcriptional activation of HMGA2 protein that again suppress ERCC1, is required for the repair of DNA lesions such as those induced by UV light or formed by electrophilic compounds including cisplatin. HMGA (High Mobility Group proteins with AT

*DNA - Damages and Repair Mechanisms*

adolescent [38].

**cancer**

deficiency [39].

breast cancer [39].

markers [41].

strand breaks to double stranded ones [40].

of the parents and other gene copy gets inactivated in a somatic cell later in life or both copies of a gene can get deactivated. Ultimately, that results in loss of heterozygosity which leads to a deficient response of DNA repair genes. Such affect from

Genes involved in the mismatch repair like MLH1, MSH6, MHS1 are often associated with Lynch syndrome, hereditary non-polyposis colorectal cancer (HNPCC), is the most common cause of hereditary colorectal (colon) cancer when undergoes monoallelic mutation but are associated with Constitutional mismatch repair deficiency syndrome due to biallelic mutation across children and

Genes involved in homologous recombination like BRCA1/2 and BRIP1 are associated with hereditary breast and ovarian cancer syndrome when undergoes biallelic mutation. Defect in these two genes often results in breast cancer [38].

**4.2 Somatic mutational signatures are associated with DNA repair pathways in** 

Somatic mutations are basic to cancer and finding their occurrence on DNA repair genes is expected, researchers have well-established effect and consequences from a few of them. The substitution mutation signatures with homologous recombination genes like BRCA leads to homologous recombination failure in breast cancer, other than that promoter methylation also contributes to BRCA gene defects in different tumors [38]. Apart from substitution, rearrangement signatures are also involved in BRCA of breast cancer, these signatures include tandem duplication, inversion, deletion, translocation, etc. For example, tandem duplication is associated with the BRCA1 mutation, whereas small deletions are associated with BRCA1/2 inactivation, indel rearrangement signature is associated with BRCA

Unlike homologous recombination repair, substitution mutation signatures are also associated with the Mismatch excision repair system. For example, high rates of substitution and indels are seen in C.G to T.A transition at NpCpG sequences. Also, rearrangement signatures are associated with MMR genes, which are often found in

High expression of *XRCC-1,* interacts with DNA ligase III, polymerase beta and poly (ADP-ribose) polymerase is associated with early tumor stage in oral squamous cell carcinoma. Accumulation of single strand breaks downregulates protein APE1 responsible for DNA incision during BER helping the conversion of single

Overexpression of *ERCC1* in prostate cancer has association with the formation of chromosome aberrations. It is shown to inhibit apoptosis in esophageal squamous cell carcinoma. Some of its polymorphisms also indicates prognostic

Likewise mentioned earlier cancer applies several methods to take control over repair mechanism, epigenetic alteration is another such technique, here the DNA sequence remains intact, but expression and activity of the gene is affected. It's the technique due to which we have different type of cells in our body despite having the same genetic makeup and most importantly it's hereditary. Epigenetics include covalent modifications like methylation, ubiquitylation, sumoylation, phosphorylation to histones or DNA, sRNA, miRNA [41]. The following information

**5. Epigenetic alterations associated with DNA repair pathways**

mutations are also seen if it is present in tumor suppressor cells [37].

**196**

is on promoter methylation, miRNAs and chromosome remodeling by histone modification.
