DNA methylation and cancer

DNA methylation and cancer; A Review Article

Maruf Raza A.K.M.¹ *

1. Assistant Professor of Pathology, Jahurul Islam Medical College, Kishoregonj, Bangladesh.

Abstract

Epigenetics is the study of the changes in gene expression that are heritable and do not involve a change in the DNA sequence. DNA methylation is one of the key epigenetic mechanisms that is clearly understood. DNA methylation is the process that add methyl group to the 5th carbon atom of the cytosine base at CpG dinucleotides without changing the nucleotide sequence. Transcriptional silencing in X inactivation and genomic imprinting are two important epigenetic mechanisms where DNA methylation plays a major role. It is well known that DNA hypermethylation and hypomethylation are directly associated with tumor formation. Hypomethylation leads to the inappropriate and increased levels of gene expression in tumors. Trancriptional repression that is seen in cancers is also mostly due to hypermethylation. DNA methylation plays a major role in transcriptional silencing in X inactivation, genomic imprinting and tumor or cancer formation. Changes in the pattern of DNA methylation have been a consistent finding in cancer cells. DNA methylation plays an important role in the generation of mutations in human tumors. The high incidence of C-to-T transitions found in the p53 tumor-suppressor gene. DNA methylation plays a crucial role in the regulation of gene expression and chromatin organization within normal eukaryotic cells. In cancer patterns of DNA methylation are altered with global hypomethylation and hypermethylation of a subset of CpG-dense gene-associated regions (CpG islands).

Key words: Epigenetics, DNA methylation, Cancer

1. Introduction

Cancer is essentially a genetic and environmental disease arising from a series of germ-line and/ or somatic DNA changes. DNA methylation is the process that add methyl group to the 5th carbon atom of the cytosine base at CpG dinucleotides without changing the nucleotide sequence. Transcriptional silencing in X inactivation and genomic imprinting are two important epigenetic mechanisms where DNA methylation plays a major role. It is well known that DNA hypermethylation and hypomethylation are directly associated with tumor formation. Hypomethylation leads to the inappropriate and increased levels of gene expression in tumors. Trancriptional repression that is seen in cancers is also mostly due to hypermethylation (1). DNA methylation involves a modification of DNA and has been found to influence a variety of processes that affect DNA integrity and function. It has therefore long been speculated that DNA methylation might play a role in the onset of cancer. In the past decade a solid foundation for this view has been laid by a series of reports documenting various changes in the DNA methylation patterns in transformed cells in vitro and in vivo. DNA methylation plays an essential role in normal development through its effects on gene imprinting, X-chromosome inactivation, and transcriptional silencing of repetitive elements (2). In the Human Genome, most of the 5-methylcytosines occur in CpG dinucleotides. DNA methylation is carried out by DNA methyltransferases (DNMTs) - DNMT1, DNMT3A and DNMT3B (3).

2. Biological Significance of DNA Methylation

It is nearly 15 years since scientists recognized the significance of DNA methylation in tumors. Studies have shown that methylation patterns in tumor cells are significantly different from those in normal cells (4). Tumor cells may even display hypomethylation in genomic DNA even before tumor formation which leads to increased and inappropriate gene expression (5). Hypermethylation of CpG islands is the most commonly observed alteration in DNA methylation in cancers. Transcriptional repression due to hypermethylation of promoters of tumor suppressor genes is identified as one of the couses of tumor formation. In colorectal, lung and breast carcinomas, cell cycle inhibitor P16 INK4a is heavily hypermethylated (6). Hypermethylation profiling over more than 15 tumor types (colon, stomach, pancreas, liver, kidney, lung, head and neck, breast, ovary, endometrium, kidney, bladder, brain, and leukemia and lymphomas) has shown that all the metabolic pathways are affected by promoter hypermethylation- associated silencing (3).

3. DNA Methylation in Mammals

DNA methylation in mammals is found as a covalent modification at the fifth carbon position of cytosine residues within CpG dinucleotides. Most of the CpG dinucleotides in the human genome are methylated. CpG islands are about 1 kb long and are not only CpG-rich, but generally G/C-rich as well and are found at the 5' end of genes (7). All known housekeeping genes and some tissue-specific genes have associated CpG islands. However, 5-methylcytosine makes up less than 1% of all nucleotides and CpG dinucleotides and 5-methylcytosine are unevenly distributed in the genome. Most of the genome is heavily methylated with a corresponding deficit in CpG dinucleotides (8).

4. Changes in the DNA Methylation Pattern in Cancer Cells

Changes in methylation levels as well as modifications of methylation patterns of individual genes have been seen as a characteristic trait in a great variety of tumor cells. These findings, however, have not lead to simple conclusions regarding the role of methylation in carcinogenesis, since both DNA hypomethylation and hypermethylation have been associated with cancer in numerous investigations (9).

5. Hypomethylation

Reduced levels of global DNA methylation have been reported for a variety of malignancies in the past decade (9). Gama Sosa and coworkers found that in a wide variety of tumors, hypomethylation not only correlated with tumour transformation, but also with tumor progression and suggested an early role for DNA hypomethylation in colorectal cancer (3). Hypomethylation of proto-oncogenes has been observed particularly in liver tumors and leukemias. A variety of proto-oncogenes, such as the c-fos gene, the c-myc gene and the Ha-ras and Ki-ras genes have shown reduced levels of DNA methylation in liver tumors. Other examples of proto-oncogenes being hypomethylated in various human leukemias include the Erb-A1 gene and the bcl-2 gene (9).

6. Hypermethylation

There have also been many reports of regional increases in DNA methylation levels. Baylin and coworkers have found regional hypermethylation on chromosomes 3p, 11p and 17p in a variety of human tumors. These include CpG island areas that are normally never methylated in vivo, but are found to be methylated in tumor tissues (9).

There is evidence for inactivation of tumor-suppressor gene function through hypermethylation of the Rb gene in sporadic retinoblastoma. It is possible, therefore, that hypermethylation of tumor-suppressor genes leading to gene inactivation results in a selective growth advantage of the transformed cells (10).

7. Significance of DNA methylation changes in carcinogenesis

Changes in DNA methylation consisting of either DNA hypomethylation or hypermethylation are commonly seen in cancer cells. The significance of these alterations in the genesis of cancer is an ongoing research. The crucial question is whether hypomethylation of specific growth-promoting genes such as proto-oncogenes or the hypermethylation of growth-suppressing genes such as tumor-supressor genes contributes to a selective advantage of the cancer cell and therefore may represent one of the steps in the sequence of events leading to malignancy (9). Hypermethylation of tumor suppressor genes might indeed be involved in maintaining transcriptional repression and thus might provide a selective growth advantage (3).

8. Clinical Applications of DNA Methylation

Recent advances in our understanding of cancer-associated DNA methylation underlie many promising clinical applications including the development of molecular markers for early detection of cancer, prediction of prognosis and prediction of treatment outcomes. Current genome-wide methylation profiling technology which permits the rapid and simultaneous analysis of thousands of loci will likely help identify novel, superior methylation markers with higher sensitivity and specificity (2). Combinations of multiple methylation markers may provide even more prognostic potential. Since genes involved in the repair of DNA damage are frequently targeted by hypermethylation in cancers, the study of these loci may be useful in predicting response to chemotherapy (3).

9. Summary

Epigenetics is the “study of the changes in gene expression that are mitotically and/or meiotically heritable and do not involve a change in the DNA sequence”11. DNA methylation is the process that add methyl group to the 5th carbon atom of the cytosine base at CpG dinucleotides without changing the nucleotide sequence is one of the key processes in epigenetic mechanisms. Transcriptional silencing in X inactivation and genomic imprinting are two important epigenetic mechanisms where DNA methylation plays a major role. It is well known that DNA hypermethylation and hypomethylation are directly associated with tumor formation. Hypomethylation leads to the inappropriate and increased levels of gene expression in tumors. Trancriptional repression that is seen in cancers is also mostly due to hypermethylation.

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