**5. How the epigenetics affects genetics**

The DNA methylation takes place only at cytosine bases that are located 5' to a guanosine in a CpG dinucleotide. This dinucleotide is actually underrepresented in the genome, but short regions, known as CpG islands, are rich in CpG content. Most CpG islands are found in the proximal promoter regions of almost half of the genes in the mammalian genome and are, generally, unmethylated in normal cells. In cancer, however, the hypermethylation of these promoter regions is now the most well categorized epigenetic change to occur in tumours, it is found in virtually every type of human neoplasm and is associated with the inappropriate transcriptional silencing of genes, involving tumour-suppressor genes.

These tumour suppressor genes are predicted to be important for tumorigenesis, but seem not to be frequently mutated and *de novo* hypermethylation of CpG islands in the promoters of *MLH1* (mutL homologue 1, colon cancer, non-polyposis type 2) (Herman et al., 1998) and

Kaiso and Prognosis of Cancer in the Current Epigenetic Paradigm 111

Finally, besides DNA hypermethylation, cancer cells have also been shown to undergo dramatic global hypomethylation (Ehrlich, 2002; Cho et al., 2003) and changes in the organization of the histone protein complex that would serve as epigenetic biomarkers indicative of the carcinogenic process (He and Lehming, 2003). Many references in the literature published in the last years reviewed the importance of alterations in DNA methylation and histone modifications for better cancer diagnostics and therapeutic strategies (Jones and Baylin, 2002; Ziech et al., 2010; table 1). Further review of this subject is not within the scope of this chapter, which is aimed to show the role of proteins, like Kaiso, which interact with methylated DNA and participate in the establishment of cancer, as we

**6. The epigenetics and proteomics walking together toward the diagnosis** 

A major challenge faced by cancer therapy is to be able to predict the early stage of the disease in order to provide an appropriate treatment for the patient (Ludwig and Weinstein, 2005). In this regard, the molecular biomarkers have been useful for distinguishing different subtypes of patients with different clinical profiles and at all stages of disease, expanding

Over the past decades high-throughput technologies including genomics, epigenome, transcriptome and proteomics have been applied to improve our understanding of cancer pathogenesis in order to develop strategies aimed to improve cancer treatment (Seligson, 2005; Ocak et al., 2009). The ultimate goal of these technologies is to help develop noninvasive methods for specific and sensitive diagnosis and facilitate prediction of the response of a patient to a given therapy, as well as help identify potential therapeutic targets

The most important technologies used in the study of cancer are proteomics and epigenomics that help understand that cancer cell phenotype is primarily determined by proteins, and, thus, a genomic or transcriptome approach of the disease are extremely limited. This can be said because it is known that i. levels and protein expression have a low correlation with mRNA levels, ii. proteins undergo post-translational modifications that may alter its function, iii. in the same cell can express different proteins using a mechanism of differential splicing from the same mRNA and very important as we shall see iv. the same protein may have a different function depending on the cellular compartment where it is located. Therefore, the protein detection techniques, including immunohistochemistry (IMH), in this new context, are of vital importance for understanding cellular processes and

In order to better understand the cancer cell and the development of cancer, proteomic information projects have been created based on epigenetics in which proteins and their interactions with the epigenome inside the cell become the key aspect in the understanding of how cancer cells work (Stefanska et al., 2011; Jerónimo et al., 2011). Therefore, knowledge of machinery and all the protein interactions established by them may be important for the prognosis of the tumor and the development of a proper drug to fight cancer and to

**and prognosis of cancer, in the current epigenetic context** 

shall see later in this chapter.

(Ueda et al., 2011).

disease emergence.

determine the mechanisms of the disease.

our prognostic ability (Seligson et al., 2005).


Table 1. Summary of epigenetic modifications associated with human cancers (prospective and retrospective studies).

*MGMT* (O6-methylguanine-DNA methyltransferase) (Esteller et al., 2000b), seems to be that leads to their inactivation. Hypermethylation of the promoter of *MLH1* can lead to microsatellite instability, and hypermethylation of the promoter of *MGMT* leads to increased G →A transitions. Additionally, there is a growing list, of other tumour suppressor genes in which promoter hypermethylation is the only mechanism for the loss of function of these genes in tumorigenesis: breast cancer 1, early onset (BRCA1) (Esteller et al., 2000a), von Hippel–Lindau syndrome (VHL)(Herman et al., 1994), p16 (Herman et al., 1995; Russo et al., 2005; Sinha et al., 2009; Kim et al., 2010; Taghavi et al., 2010), death associate protein (DAP) kinase 1 (DAPK1) (Russo et al., 2005), and *RASSF1A* (Tanemura et al., 2009; Muggerud et al., 2010), which encodes a protein of unknown function that can bind to the *RAS* oncogene (Table 1).

The epigenetic modifications can also be induced by environmental and occupational exposures thus contributing to carcinogenesis. A good example is the methylation changing the absorption wavelength of cytosine, into the range of incident sunlight, resulting in CC →TT mutations, which commonly occur in skin cancers (Pfeifer et al., 2000). So, tobacco smoke has been estimated to account for 30% of all cancer deaths and 85% of lung cancer deaths due to the presence of thousands of mutagenic compounds, including polycyclic aromatic hydrocarbons and nitrosamines. In this case, methylated CpGs are also preferred binding sites for benzo(a)pyrene diol epoxide and other carcinogens that are found in tobacco smoke (Yoon et al., 2001). These cause DNA adducts and G →T transversion mutations, which are often found in the aerodigestive tumours of smokers (Ziech et al., 2010). On the other hand, one of the most well established occupational carcinogenic agents is asbestos along with a growing list of tumorigenic agents that include: wood-dust particulates, solvents, paints, dye products, gasoline, petroleum-based mixtures, benzenes, mineral oils, phthalates and metal ions (Ziech et al., 2010). For these agents, the free radicalinduced damage is suggested to be involved in aberrant epigenetic changes observed during the carcinogenic process. The understanding of epigenetic alterations has become clearer the mechanism by which lifestyle choice like smoking and drinking, diet, environment and infections affecting the DNA tissue-specific cells and altering the behavior of cells in this tissue.

**Altered genes-aberrant methylation-aberrant Distribution (p)** 

Hypermethylation- p16 (p < .0001) MINT31

**studied** 

Cho et al., 2003 Stomach CAGE CAGE- Hypomethylation

Herman et al., 1995 Many Cancers p16 p16 - Hypermethylation (the first evidence) Herman et al., 1998 Colorectal hMLH1 hMLH1-Hypermethylation (p < .001) Esteller et al., 2000 Breast, Ovary BRCA1 BRCA1- Hypermethylation (p < .0002) Esteller et al., 2000 Colorectal hMGMT MGMT (k-RAS)-Hypermethylation (p= .002)

Russo et al., 2005 Lung/Blood p16/DAPK p16/DAPK - Hypermethylation (p = .001) Sinha et al., 2009 Tongue p16 p16- Hypermethylation (p =.0361)

2009 Skin RASSF1A RASSF1A- Hypermethylation (p < .005) Daí et al., 2009 Lung Kaiso kaiso- Cyoplasmic distribution (p = .005)

Muggerud t al., 2010 Breast RASSF1A RASSF1A- Hypermethylation (p < .001) Taghavi et al., 2010 Esophagus p16 p16 - Hypermethylation (p <.001)

Table 1. Summary of epigenetic modifications associated with human cancers (prospective

*MGMT* (O6-methylguanine-DNA methyltransferase) (Esteller et al., 2000b), seems to be that leads to their inactivation. Hypermethylation of the promoter of *MLH1* can lead to microsatellite instability, and hypermethylation of the promoter of *MGMT* leads to increased G →A transitions. Additionally, there is a growing list, of other tumour suppressor genes in which promoter hypermethylation is the only mechanism for the loss of function of these genes in tumorigenesis: breast cancer 1, early onset (BRCA1) (Esteller et al., 2000a), von Hippel–Lindau syndrome (VHL)(Herman et al., 1994), p16 (Herman et al., 1995; Russo et al., 2005; Sinha et al., 2009; Kim et al., 2010; Taghavi et al., 2010), death associate protein (DAP) kinase 1 (DAPK1) (Russo et al., 2005), and *RASSF1A* (Tanemura et al., 2009; Muggerud et al., 2010), which encodes a protein of unknown function that can bind to the

The epigenetic modifications can also be induced by environmental and occupational exposures thus contributing to carcinogenesis. A good example is the methylation changing the absorption wavelength of cytosine, into the range of incident sunlight, resulting in CC →TT mutations, which commonly occur in skin cancers (Pfeifer et al., 2000). So, tobacco smoke has been estimated to account for 30% of all cancer deaths and 85% of lung cancer deaths due to the presence of thousands of mutagenic compounds, including polycyclic aromatic hydrocarbons and nitrosamines. In this case, methylated CpGs are also preferred binding sites for benzo(a)pyrene diol epoxide and other carcinogens that are found in tobacco smoke (Yoon et al., 2001). These cause DNA adducts and G →T transversion mutations, which are often found in the aerodigestive tumours of smokers (Ziech et al., 2010). On the other hand, one of the most well established occupational carcinogenic agents is asbestos along with a growing list of tumorigenic agents that include: wood-dust particulates, solvents, paints, dye products, gasoline, petroleum-based mixtures, benzenes, mineral oils, phthalates and metal ions (Ziech et al., 2010). For these agents, the free radicalinduced damage is suggested to be involved in aberrant epigenetic changes observed during the carcinogenic process. The understanding of epigenetic alterations has become clearer the mechanism by which lifestyle choice like smoking and drinking, diet, environment and infections affecting the DNA tissue-specific cells and altering the behavior of cells in this

(p < .004)

**Author Organ/tissue Genes** 

Kim et al., 2010 Intestine p16/MINT31

Tanemura et al.,

and retrospective studies).

*RAS* oncogene (Table 1).

tissue.

Finally, besides DNA hypermethylation, cancer cells have also been shown to undergo dramatic global hypomethylation (Ehrlich, 2002; Cho et al., 2003) and changes in the organization of the histone protein complex that would serve as epigenetic biomarkers indicative of the carcinogenic process (He and Lehming, 2003). Many references in the literature published in the last years reviewed the importance of alterations in DNA methylation and histone modifications for better cancer diagnostics and therapeutic strategies (Jones and Baylin, 2002; Ziech et al., 2010; table 1). Further review of this subject is not within the scope of this chapter, which is aimed to show the role of proteins, like Kaiso, which interact with methylated DNA and participate in the establishment of cancer, as we shall see later in this chapter.
