**1. Introduction**

Cells are exposed to a vast amount of exogenous genotoxic agents, such as ionizing radiation or UV light, or endogenous agents, including reactive oxygen species (ROS), derived from oxidative respiration or replication processes that can cause errors in the nucleotide chains. This damage interferes with different biological or metabolic processes, e.g., replication and transcription [1]. If these alterations are not properly repaired, then mutations, chromosomal aberrations, genomic instabilities, and other harmful effects can occur, triggering alterations such as carcinogenesis. Cells developed complex systems to deal with these problems, as they have repair systems that are activated in response to checkpoints in the cell cycle to prevent cycle progression to eliminate damage or send cells into apoptosis, when repair is no longer possible. In cancer, the response to damage is mainly activated by genotoxic agents, double-strand breaking (DSBs) repaired by homologous recombination (HR) or non-homologous end joining repair (NHEJ). Cells have signaling networks to supervise the integrity and fidelity of the major

events of the cell cycle (checkpoints) until they recognize and respond to DNA structure damage and repair. This damage response cascade is known as DNA damage response and is responsible for control of genome stability after DSBs' formation [2, 3].

Epigenetic modifications are alterations at the DNA level that do not cause permanent change in the sequence but might also cause conformational modifications. Here, chromatin plays an essential role, such that various damage response factors can gain access to the DNA sequence. Chromatin can be modified by histone changes, ATP-dependent nucleosome remodelers, and non-histone proteins, including chaperones or a high mobility group (HMG). It demonstrates that reorganization of the dynamic chromatin structure is an intrinsic component of efficient DNA repair and DDR [4–6]. Epigenetic modification has gained relevance in recent years, which involves a change in RNA. In addition, 6-methyladenosine (m6A) methylation is one of the most common RNA modifications, and is visible in eukaryotic species, such as yeast to mammals and prokaryotes and bacteria and mycoplasma. There has recently been substantial progress in m6A epitranscriptomics in its role in the initiation and progress of cancer. Studies on links between m6A and cancer yield different results in diverse tumors, suggesting that the effect of m6A modification can be variable: it affects proliferation, growth, invasion, and metastasis, but the involved pathways are just beginning to be unveiled [7, 8].

In this chapter, we will address chromatin modifications on DDR and how they function as therapeutic targets in cancer. Pathways that repair also create extraordinary work in maintaining DNA integrity, but in cancer, they are a challenge, as they represent a potential barrier to anticancer agents.

### **2. Chromatin dynamic in the DNA damage response**

The damage response triggers the rapid recruitment of repair proteins and checkpoint activation at the site of injury in DNA structure, a crucial step for DDR signaling pathway initiation. Cancer cells are characterized by deregulation in the signaling pathways that control checkpoint homeostasis, when genes associated with DDR suffer mutations, as the injury cannot be repaired correctly and is accumulated in the genome, triggering cellular transformation [9, 10]. Signaling pathways most affected will be those of apoptosis, cell cycle, and repair, contributing to harmful effects on genome integrity, thus increasing the risk of cancer [11]. Loss of function by germlines or somatic mutations of DDR-associated genes can trigger the inability of the repair single-strand break (SSBs) or DSBs, causing cell death [12]: this is the most deleterious type of DNA damage (since a single unrepaired DSB can be lethal).

The cell develops different repair mechanisms, such as base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), NHEJ and homologous recombination (HR) as well as homologous recombination repair (HRR) [2]. The specific type of DNA repair will be activated according to the lesion, the cell cycle phase, the genomic location, and the chromatin environment [3]. However, for this to occur, the processes associated with DNA repair pathways must overcome the physical chromatin condensation barrier and packaging to gain access, detect, and repair the damage. Cooperation with different histone modifications and nucleosome remodelers are involved in DNA repair [13]. The chromatin structure functions as part of the machinery regulating genome stability and provides necessary tools to carry out basic cellular processes for genetic information integrity.

Chromatin remodelers can alter or modify the chromatin structure, catalyzing the disruption of DNA-histone contacts and displacing or evicting nucleosomes

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*Epigenetics and DNA Repair in Cancer DOI: http://dx.doi.org/10.5772/intechopen.94030*

NHEJ *in vitro* [4, 5, 15, 16].

with ATP hydrolysis to gain access to DNA. They can then regulate the stiffness, flexibility, and mobility of chromatin within the nucleus [14] or facilitate the accessibility of TFs to functional DNA elements, such as promoters or enhancers. Several ATP-dependent chromatin remodeling complexes have been directly implicated in DSB response. In yeast, INO80, SWR1, switch/sucrose non-fermenting (SWI/SNF), and remodeling the structure of chromatin (RSC) complexes are recruited to the DSB and reconfigure the nucleosomes around it so as to facilitate DNA repair and/or to modulate checkpoint activation. HMG B family is specifically involved in DSBs' repair while promoting end joining in

The SWI/SNF complex regulates the correct recruitment of repair factors for NHEJ and HRR and, signaling of DDR generated by DSBs [6]. In different cancers, up to 20% of the genes, mutated or altered, belong to the SWI/SNF complex [17]. Two subunits differ according to their composition, called Brahma-related gene 1 (BRG1)-associated factor (BAF) and BRG1 polybromo-associated factor (PBAF). Further, two ATPases BRM (SMARCA2) or BRG1 (SMARCA4) are mutually exclusive but structurally related [18, 19]. On the other hand, ARID1A/1B/2, PHF10, DPF1/2/3, PBRM1 (BAF180), beta-actin, SMARCE1 (BAF57), BCL7A/B/C, BCL11A/B, SS18, and BRD9, are subunits found in mammals, so it is probable that these proteins' function are related to evolutive strategies in chromatin regulation associated with greater complexity and/or specificity to the SWI/SNF complex focalization [17]. In particular, the subunits SMARCA4, SMARCB1, ARID1A/B (BAF250A/B), PBRM1, and ARID2 have tumor suppressor function [20, 21]. this lack or silencing of a single protein, belonging to each subunit, can affect the interaction with other components of the SWI/SNF complex. The response to DNA damage was observed as nucleosome remodelers that interact through bromodo-

main with histone modifications and epigenetic marks (**Figure 1**).

Some functions for SWI/SNF subunits make it possible to understand the importance of this complex in cancer. Erket et al. [22] identified SMARCB1 as often lost or altered in malignant rhabdoid-type tumors. In addition, Agaimy et al. [23] and Nombiraan et al. [24] identified how alterations in SMACA4 compromise patients with non-small cell lung cancer, which clarified the prognosis, diagnosis, and personalized therapeutic potential in patients with mutated or altered SMARCA4. In the study by Yoshida et al. [25], SMARCA4 loss of function is related to thoracic sarcomas. However, Herpel et al. [26] suggest that SMARCA4 and SMARCA2 subunits, catalytic centers of SWI/SNF, should be added to diagnostic evaluation panels for lung adenocarcinomas, this is supported by results obtained in their work on protein expression by IHC, in more than 300 patients with non-small cell lung cancer. As earlier described, the proteins of the SWI/ SNF complex are involved in multiple mechanisms of DDR and DSB, while NER stands out, involved with other epigenetic modifications. This is demonstrated by Lee et al. [27], who observed that Brg1 subunit interacts with acetylated H3 in addition with H2AX in early stages of DNA damage, facilitating signaling, or DDR. Particularly in DNA repair, Ribeiro et al. [28] showed that both BRM and BRG1 promote normal TFIIH (ERCC2) function in transcription and NER by regulating the expression of the GTF2H1 gene and found that cells with permanent BRM or BRG1 loss can restore GTF2H1 expression levels. Therefore, DNA damage sensitivity of BRM or BRG1 deficient cells correlates with GTF2H1 protein levels and can be used to select SWI/SNF-deficient cancers that are more sensitive to platinum drug chemotherapy. In studies carried out by Decristofaro et al. [29] and Watanabe et al. [30] in breast and lung cancer cell lines, respectively, they identified that expression of ARID1A or ARID1B was decreased or absent. They also found similar behavior in other SWI/SNF subunits (BRG1, BRM, BAF60a, BAF60c, BAF53a, and

#### *Epigenetics and DNA Repair in Cancer DOI: http://dx.doi.org/10.5772/intechopen.94030*

*DNA - Damages and Repair Mechanisms*

formation [2, 3].

events of the cell cycle (checkpoints) until they recognize and respond to DNA structure damage and repair. This damage response cascade is known as DNA damage response and is responsible for control of genome stability after DSBs'

Epigenetic modifications are alterations at the DNA level that do not cause permanent change in the sequence but might also cause conformational modifications. Here, chromatin plays an essential role, such that various damage response factors can gain access to the DNA sequence. Chromatin can be modified by histone changes, ATP-dependent nucleosome remodelers, and non-histone proteins, including chaperones or a high mobility group (HMG). It demonstrates that reorganization of the dynamic chromatin structure is an intrinsic component of efficient DNA repair and DDR [4–6]. Epigenetic modification has gained relevance in recent years, which involves a change in RNA. In addition, 6-methyladenosine (m6A) methylation is one of the most common RNA modifications, and is visible in eukaryotic species, such as yeast to mammals and prokaryotes and bacteria and mycoplasma. There has recently been substantial progress in m6A epitranscriptomics in its role in the initiation and progress of cancer. Studies on links between m6A and cancer yield different results in diverse tumors, suggesting that the effect of m6A modification can be variable: it affects proliferation, growth, invasion, and metastasis, but the involved pathways are just beginning to be unveiled [7, 8].

In this chapter, we will address chromatin modifications on DDR and how they function as therapeutic targets in cancer. Pathways that repair also create extraordinary work in maintaining DNA integrity, but in cancer, they are a challenge, as

The damage response triggers the rapid recruitment of repair proteins and checkpoint activation at the site of injury in DNA structure, a crucial step for DDR signaling pathway initiation. Cancer cells are characterized by deregulation in the signaling pathways that control checkpoint homeostasis, when genes associated with DDR suffer mutations, as the injury cannot be repaired correctly and is accumulated in the genome, triggering cellular transformation [9, 10]. Signaling pathways most affected will be those of apoptosis, cell cycle, and repair, contributing to harmful effects on genome integrity, thus increasing the risk of cancer [11]. Loss of function by germlines or somatic mutations of DDR-associated genes can trigger the inability of the repair single-strand break (SSBs) or DSBs, causing cell death [12]: this is the most deleterious type of DNA damage (since a single unrepaired DSB can be lethal). The cell develops different repair mechanisms, such as base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), NHEJ and homologous recombination (HR) as well as homologous recombination repair (HRR) [2]. The specific type of DNA repair will be activated according to the lesion, the cell cycle phase, the genomic location, and the chromatin environment [3]. However, for this to occur, the processes associated with DNA repair pathways must overcome the physical chromatin condensation barrier and packaging to gain access, detect, and repair the damage. Cooperation with different histone modifications and nucleosome remodelers are involved in DNA repair [13]. The chromatin structure functions as part of the machinery regulating genome stability and provides necessary tools to carry out basic cellular processes for genetic information

Chromatin remodelers can alter or modify the chromatin structure, catalyzing the disruption of DNA-histone contacts and displacing or evicting nucleosomes

they represent a potential barrier to anticancer agents.

**2. Chromatin dynamic in the DNA damage response**

**168**

integrity.

with ATP hydrolysis to gain access to DNA. They can then regulate the stiffness, flexibility, and mobility of chromatin within the nucleus [14] or facilitate the accessibility of TFs to functional DNA elements, such as promoters or enhancers. Several ATP-dependent chromatin remodeling complexes have been directly implicated in DSB response. In yeast, INO80, SWR1, switch/sucrose non-fermenting (SWI/SNF), and remodeling the structure of chromatin (RSC) complexes are recruited to the DSB and reconfigure the nucleosomes around it so as to facilitate DNA repair and/or to modulate checkpoint activation. HMG B family is specifically involved in DSBs' repair while promoting end joining in NHEJ *in vitro* [4, 5, 15, 16].

The SWI/SNF complex regulates the correct recruitment of repair factors for NHEJ and HRR and, signaling of DDR generated by DSBs [6]. In different cancers, up to 20% of the genes, mutated or altered, belong to the SWI/SNF complex [17]. Two subunits differ according to their composition, called Brahma-related gene 1 (BRG1)-associated factor (BAF) and BRG1 polybromo-associated factor (PBAF). Further, two ATPases BRM (SMARCA2) or BRG1 (SMARCA4) are mutually exclusive but structurally related [18, 19]. On the other hand, ARID1A/1B/2, PHF10, DPF1/2/3, PBRM1 (BAF180), beta-actin, SMARCE1 (BAF57), BCL7A/B/C, BCL11A/B, SS18, and BRD9, are subunits found in mammals, so it is probable that these proteins' function are related to evolutive strategies in chromatin regulation associated with greater complexity and/or specificity to the SWI/SNF complex focalization [17]. In particular, the subunits SMARCA4, SMARCB1, ARID1A/B (BAF250A/B), PBRM1, and ARID2 have tumor suppressor function [20, 21]. this lack or silencing of a single protein, belonging to each subunit, can affect the interaction with other components of the SWI/SNF complex. The response to DNA damage was observed as nucleosome remodelers that interact through bromodomain with histone modifications and epigenetic marks (**Figure 1**).

Some functions for SWI/SNF subunits make it possible to understand the importance of this complex in cancer. Erket et al. [22] identified SMARCB1 as often lost or altered in malignant rhabdoid-type tumors. In addition, Agaimy et al. [23] and Nombiraan et al. [24] identified how alterations in SMACA4 compromise patients with non-small cell lung cancer, which clarified the prognosis, diagnosis, and personalized therapeutic potential in patients with mutated or altered SMARCA4. In the study by Yoshida et al. [25], SMARCA4 loss of function is related to thoracic sarcomas. However, Herpel et al. [26] suggest that SMARCA4 and SMARCA2 subunits, catalytic centers of SWI/SNF, should be added to diagnostic evaluation panels for lung adenocarcinomas, this is supported by results obtained in their work on protein expression by IHC, in more than 300 patients with non-small cell lung cancer. As earlier described, the proteins of the SWI/ SNF complex are involved in multiple mechanisms of DDR and DSB, while NER stands out, involved with other epigenetic modifications. This is demonstrated by Lee et al. [27], who observed that Brg1 subunit interacts with acetylated H3 in addition with H2AX in early stages of DNA damage, facilitating signaling, or DDR. Particularly in DNA repair, Ribeiro et al. [28] showed that both BRM and BRG1 promote normal TFIIH (ERCC2) function in transcription and NER by regulating the expression of the GTF2H1 gene and found that cells with permanent BRM or BRG1 loss can restore GTF2H1 expression levels. Therefore, DNA damage sensitivity of BRM or BRG1 deficient cells correlates with GTF2H1 protein levels and can be used to select SWI/SNF-deficient cancers that are more sensitive to platinum drug chemotherapy. In studies carried out by Decristofaro et al. [29] and Watanabe et al. [30] in breast and lung cancer cell lines, respectively, they identified that expression of ARID1A or ARID1B was decreased or absent. They also found similar behavior in other SWI/SNF subunits (BRG1, BRM, BAF60a, BAF60c, BAF53a, and

#### **Figure 1.**

*The SWI/SNF complex in DNA damage response (DDR). (a) The biochemical characteristics of the BAF and PBAF subunits make the SWI/SNF complex a very heterogeneous family with exclusive properties in mammals. Alterations in this group of nucleosome remodelers give rise to cancer. (b) During DDR, SWI/SNF subunits interact through their bromodomains with histone modifications and epigenetic labels. For DNA repair to occur, it is necessary to activate the kinase cascades by ATM, responsible for recruiting and phosphorylating different repair genes such as E2F1, BRCA1 or 53BP1 and thus activating NER (nucleotide excision repair), HRR (homologous recombination repair)or NHEJ (non-homologous end joining), Ub: ubiquitination, Me: methylation, Ac: acetylation, P: phosphorylation, bromo: bromodomain.*

SMARCB1). Duan et al. [31] identified that expression of ARID2 was significantly downregulated in hepatocellular carcinoma compared to adjacent nontumor tissue. Their research revealed that ARID2 inhibits cell cycle progression and tumor growth by interacting with the Rb-E2F signaling pathway. The relationship of E2F with epigenetic modifiers has become clear. Manickavinayaham et al. [32] demonstrated that the bromodomains of related acetyltransferases, p300 and CBP, specifically bind to the acetylated motif of E2F1; they found that interaction with acetylated E2F1 is critical for p300/CBP recruitment of DSBs and induction of histone acetylation at the sites of damage. They also demonstrated that in nucleosomes flanking DSBs, p300 and CBP mediate acetylation of multiple lysine residues on H3, including H3K18 and H3K56. Biswat et al. [33] and Guo et al. [34] demonstrated that E2F2 induction of histone acetylation and chromatin decondensation in response to UV radiation promote efficient NER. Lin et al. [35] shows that ATR creates induction of E2F1 in DNA damage. ATM/ATR is known to activate P53 in response to damage and plays a central role in DDR activation. ATM plays an important role in DDR and DSBs, as it regulates several pathways of cancer and epigenetic modifications.

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*Epigenetics and DNA Repair in Cancer DOI: http://dx.doi.org/10.5772/intechopen.94030*

**3. Chromatin modifications in DSB repair**

response to maintain the genome integrity [37, 39].

BAF155 subunits, potentiating the response to damage [45, 46].

Moreover, γ-H2AX recruits MDC in the chromatin, is phosphorylated by ATM, functioning as the protein coupling site of checkpoints and repair, such as 53BP1 and the UBC13-RNF8-BRCA1 complex. The protein 53BP1 is phosphorylated by ATM and helps in the BRCA1 recruitment: together with the post-translational modifications in the damage site, they help promote other repair proteins. ATM and RNF8 facilitate the repair of DNA DSBs in the phases G1 and G2 of the cell cycle, regardless of the repair pathway used [47, 48]. Similarly, ubiquitination in the DSB regulates the repair protein BRCA1 and P53, as well as BARD1 recruitment by 53BP1 [49]. BRCA1 and 53BP1 are necessary to regulate downstream histones phosphorylation and ubiquitination to direct the repair on NHEJ and HR. Thus, BRCA1 repairs DNA damage via HR, and 53BP1 plays a crucial role in the NHEJ repair pathway, ensuring DNA DSBs are repaired correctly [50, 51]. BRIT1 is required for DNA damage-induced intra-S and G2/M checkpoints, as regulation of the BRCA1 and Chk1 expression [52]. The loss of function of either of these two genes can alter

DSB repair can activate two repair pathways in mammalian cells: the HRR and NHEJ. First it is active throughout the cell cycle, and second it is active in S and G2 phases [36]. Usually, NHEJ is initiated by DSB recruitment of Ku70/80 or XRCC6 XRCC5 heterodimer. Ku70/80 is DBS sensor and facilitates the downstream factors recruitment, including DNA-PKcs, PAXX, XLF, XRCC4, and ligase IV. Recruitment of downstream factors helps complete DNA repair. However, HRR involves MRE11- RAD50-NBS1 (MRN) complex to activate ATM protein kinase [37]. Also, HRR can be influenced by PKcs and act in concert with the MRN complex and the recruitment of this complex to DNA DSB by hSSB1 (single-stranded binding protein), as well as the activities of 53BP1/RIF1 and BRCA1/CtIP [38]. Cells start a cascade of phosphorylation events in response to DNA damage, mediated by three phosphatidylinositol-3-related kinases: ATM, ATR, and DNA-dependent protein kinase catalytic subunit (DNA-PKcs). The kinases activate a rapid reaction of abundant sensors for DSBs to check injuries, recruit effectors, and generate a coordinated

Different epigenetic modifications are related to these kinases, while H2AX is an important chromatin-based substrate for phosphatidylinositol-3-related kinases, when it is phosphorylated on S139, and is named γ-H2AX. This phosphorylated form serves as a checkpoint for HR and NHEJ. The foci formation of γH2A.X is the most often observed epigenetic modification triggered by DNA damage; together with the response to DSB and the SWI/SNF complex, it promotes phosphorylation of S139 in its C-terminal region through ATM in human cells. Domains of γ-H2AX are established by contact with the DSB site. In fact, the break site defines the densities and spread of γ-H2AX [40–42]. In addition, PBAF functions in the ATM pathway silence transcription in *cis* on DSB by promoting mono-ubiquitination of H2A on K119 [43] and efficient early repair on exposure to ionizing radiation (IR), mediated by DSB and NHEJ [44]. H2AX induction by UV depends on ATR, but the formation of DSB in late stages contributes to ATM activation and the increase of H2AX. DNA-PKcs, after induction of DSB, is responsible for H2AX and chromatin remodeling factor (KAP1) phosphorylation. Furthermore, DNA-PKcs is required for chromatin remodeling in early postirradiation stages and promotes the rapid recruitment of DDR initiation proteins at DSBs sites [37]. An early modulator is BRIT, a chromatin-binding protein that forms irradiation-induced nuclear foci (IRIF) and works as a proximal factor at checkpoints in DNA, controls multiple damage sensors, and early mediators to DDR. BRIT1 colocalizes with γ-H2AX, using ATM/ATR to form the BRIT1-SWI/SNF interaction through its BAF170 and

*DNA - Damages and Repair Mechanisms*

SMARCB1). Duan et al. [31] identified that expression of ARID2 was significantly downregulated in hepatocellular carcinoma compared to adjacent nontumor tissue. Their research revealed that ARID2 inhibits cell cycle progression and tumor growth by interacting with the Rb-E2F signaling pathway. The relationship of E2F with epigenetic modifiers has become clear. Manickavinayaham et al. [32] demonstrated that the bromodomains of related acetyltransferases, p300 and CBP, specifically bind to the acetylated motif of E2F1; they found that interaction with acetylated E2F1 is critical for p300/CBP recruitment of DSBs and induction of histone acetylation at the sites of damage. They also demonstrated that in nucleosomes flanking DSBs, p300 and CBP mediate acetylation of multiple lysine residues on H3, including H3K18 and H3K56. Biswat et al. [33] and Guo et al. [34] demonstrated that E2F2 induction of histone acetylation and chromatin decondensation in response to UV radiation promote efficient NER. Lin et al. [35] shows that ATR creates induction of E2F1 in DNA damage. ATM/ATR is known to activate P53 in response to damage and plays a central role in DDR activation. ATM plays an important role in DDR and DSBs, as it regulates several pathways of cancer and

*methylation, Ac: acetylation, P: phosphorylation, bromo: bromodomain.*

*The SWI/SNF complex in DNA damage response (DDR). (a) The biochemical characteristics of the BAF and PBAF subunits make the SWI/SNF complex a very heterogeneous family with exclusive properties in mammals. Alterations in this group of nucleosome remodelers give rise to cancer. (b) During DDR, SWI/SNF subunits interact through their bromodomains with histone modifications and epigenetic labels. For DNA repair to occur, it is necessary to activate the kinase cascades by ATM, responsible for recruiting and phosphorylating different repair genes such as E2F1, BRCA1 or 53BP1 and thus activating NER (nucleotide excision repair), HRR (homologous recombination repair)or NHEJ (non-homologous end joining), Ub: ubiquitination, Me:* 

**170**

**Figure 1.**

epigenetic modifications.
