Epigenetics in Biology and Medicine

Manel Esteller

• Publisher: CRC Press
• Year: 2008
• ISBN:
  9781000654202
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Cell Biology
• Index: Biological Sciences

Anomalous epigenetic patterns touch many areas of study including biomedical, scientific, and industrial. With perspectives from international experts, this resource offers an all-inclusive overview of epigenetics, which bridge DNA information and function by regulating gene expression without modifying the DNA sequence itself. Epigenetics, in its

1	An Introduction to Epigenetics Manel Esteller

Genetics alone cannot explain human variation and disease. Humans with the same DNA sequence, such as monozygotic twins, and cloned animals frequently present different phenotypes and degrees of sickness penetrance. The increasingly popular term epigenetics embodies a partial explanation of both phenomena. First introduced by C.H. Waddington in 1939 to name “the causal interactions between genes and their products, which bring the phenotype into being,” it was subsequently defined as those heritable changes in gene expression that are not due to any alteration in DNA sequence. The best-known epigenetic marker is DNA methylation. From the initial characterization of global hypomethylation of human tumors and the first hypermethylated tumor suppressor, to the DNA methylation silencing of microRNAs, the ongoing human epigenome projects, and the clinical approval of therapies with DNA demethylating agents and histone deacetylase inhibitors, epigenetics has seized the attention of biomedical researchers. The scenario is further enriched because DNA methylation occurs in a highly complex chromatin network mediated by histone modifications, which are also disrupted in human diseases. Aberrant epigenetic patterns go beyond oncology to touch a wide range of fields of biomedical (immunology, neurology, metabolism, imprinting, cardiovascular, etc.), scientific (machineries for transcriptional activation and repression, high-order organization of DNA, etc.), and industrial (animal and yeast models, agriculture, nutrition) knowledge that have an impact on our lives.

The current hype of epigenetic research also relates to the introduction of powerful and user-friendly techniques for the study of DNA methylation, such as sodium bisulfite modification associated with polymerase chain reaction procedures. More recently, the advent of comprehensive epigenomic technologies has given rise to the first preliminary descriptions of the epigenomes of human cells. This book discusses the new developments, the overall main features, and the translational applications for disease in the still-young field of epigenetics, particularly regarding DNA methylation, histone modifications, noncoding RNAs, and chromatin remodeling. Enjoy!

2	Epigenetics and Cancer DNA Methylation Santiago Ropero and Manel Esteller

CONTENTS

2.1 Introduction

2.2 DNA Methylation in Healthy Cells

2.3 DNA Methylation Patterns Change in Cancer Cells

2.3.1 Global DNA Hypomethylation in Human Cancer

2.3.2 Aberrant Gene Hypermethylation in Human Cancer

2.4 miRNA Silencing in Human Cancer

2.5 DNA Methylation in Clinical Practice

2.6 DNA Methylation in Tumor Detection

2.7 The Use of DNA Methylation as a Prognostic Marker

2.8 DNA Methylation as a Predictive Factor

2.9 DNA Demethylating Agents

2.10 Conclusions

References

2.1 INTRODUCTION

Cancer can be defined in many different ways, depending on the area in which the disease is studied, and it can be understood to encompass a group of about 100 different and distinctive diseases. These diseases are characterized by an abnormal growth of cells that generally lead to an uncontrolled proliferation that, in some cases, can metastasize to other organs and tissues. In recent decades researchers have concentrated their efforts on identifying a wide variety of genomic changes, such as amplifications, translocations, deletions, and point mutations, that are involved in this uncontrolled proliferation, and thus in the development of cancer.

In the past, analysis of these genomic alterations has led to the identification of oncogenes and tumor-suppressor genes involved in tumor development. However, the occurrence of cancer is due not only to the genetic changes described above, but also to epigenetic changes. While genetics is concerned with the information transmitted on the basis of gene sequence, epigenetics deals with the inheritance of information based on gene expression levels. The main epigenetic modifications in mammals are DNA methylation and histone modification. The most widely studied epigenetic modification in humans to date has been the cytosine methylation of DNA. This consists of the covalent addition of a methyl group from the methyl donor S-adenosylmethionine to the carbon-5 position of cytosine within the CpG dinucleotide. This enzymatic reaction occurs after DNA synthesis and is performed by a family of enzymes called DNA methyltransferases (DNMTs). The proportion of CpG dinucleotides in the human genome is lower (1.2%) than expected (4%) from the abundance of cytosine and guanine (42% of the DNA bases). This lack of CpGs in our genome can be explained by a phenomenon known as CpG suppression, in which methylated CpG dinucleotides are progressively depleted due to the spontaneous deamination of methylated cytosines to thymidines during evolution.¹ The distribution of CpGs in vertebrate genomes is not uniform; they are concentrated in short stretches or clusters (500–2000 bp) called CpG islands, and are located mainly in the promoter region of approximately half of all human genes. However, the bulk of CpGs are found at low density within the intergenic and intronic regions of DNA, particularly within repeat sequences and transposable elements.

To date, most studies have focused on the role of DNA methylation in gene expression regulation under normal and pathological conditions.² Several examples illustrate the involvement of DNA methylation in disease. Rett syndrome is characterized by mutations in the methyl-binding protein MeCP.² With lupus, patients suffer severe degrees of DNA hypomethylation. It features in neurological diseases, for example, where the methylation of the fragile X mental retardation-1 (FMR) gene is the catalyst of the disorder of the same name. Aberrant patterns of DNA methylation can also be found in atherosclerosis, where protective cardiovascular genes are aberrantly hypermethylated. Patients with ICF (immunodeficiency, centromere instability, and facial anomalies) have mutations in a major DNA methyltransferase (DNMT3b). Finally, DNA methylation is also an important player in cancer development.

In this chapter we will focus on the role of DNA methylation in cancer and on the use of this epigenetic modification in clinical practice. To understand the role of DNA methylation in cancer development, first let us begin with a short introduction to the DNA methylation pattern in healthy cells.

2.2 DNA METHYLATION IN HEALTHY CELLS

In healthy cells, while repetitive genomic sequences are heavily methylated, most of the CpG islands are unmethylated, which allows genes to be expressed in the presence of the necessary transcriptional activators. However, in specific instances, gene-promoter regions are methylated in normal cells as part of normal developmental processes: imprinted genes, X chromosome genes in women, and germline-and tissue-specific genes.³ Genomic or parental imprinting is a process involving acquisition of a closed chromatin state and DNA hypermethylation in one allele of a gene (for example, a growth-suppressor gene) early in the male and female germline, which leads to monoallelic expression. A similar phenomenon of gene-dosage reduction can also be invoked with regard to the methylation of CpG islands in one X chromosome in women, where only one of two copies is active. Methylation of regulatory regions is involved in repression of expression of the silent loci.⁴ Finally, although DNA methylation is not widely used for regulating “normal” gene expression, and we certainly have more complex and specialized molecular networks to achieve this aim, sometimes DNA methylation can fulfill this purpose. There is the case, for example, of those genes whose expression is restricted to the male or female germline and which are not subsequently expressed in any adult tissue, such as the MAGE and LAGE gene families.⁵ A more controversial case may be cited for the classical tissue-specific genes; some of them contain CpG islands, while others contain only a few CpG dinucleotides scattered throughout in their 5′ regulatory region. Methylation has been postulated as a mechanism for silencing these tissue-specific genes in those cell types where they should not be expressed. A well-characterized example of this type of regulation is the methionine adenosyl transferases 1A and 2A of rodents.⁶

As will be discussed in other chapters of this book, DNA methylation regulates gene transcription in conjunction with other epigenetic modifications. Methylated DNA is recognized by methyl-CpG binding proteins. These proteins and DNMTs recruit multiprotein complexes containing chromatin remodeling enzymes such as histone deacetylases and histone methyltransferases, which are key regulators of histone modifications.⁷ However, in this chapter we will focus on the role of DNA methylation in cancer progression and its use in clinical practice.

2.3 DNA METHYLATION PATTERNS CHANGE IN CANCER CELLS

The pattern of DNA methylation changes substantially when cells became cancerous, as a result of two major phenomena. First, the tumoral genome becomes globally hypomethylated, unlike in normal cells, due mainly to the generalized demethylation in the CpGs scattered throughout the body of the genes. Second, local and discrete regions situated at the promoter region of tumor-suppressor genes undergo intense hypermethylation (Figure 2.1).

2.3.1 GLOBAL DNA HYPOMETHYLATION IN HUMAN CANCER

One of the first reports linking aberrant DNA methylation to cancer came from Lapeyre and Becker, who used HPLC to determine the 5-methylcytosine content in normal rat liver and hepatocellular carcinomas induced in rats by acetyl aminofluorene or diethylnitrosamine.⁸ The carcinogen-induced cancers displayed a decrease in overall genomic methylation of about 20–40% relative to normal liver. We now know that the genome of a cancer cell loses 20–60% of its 5-methylcytosine content in comparison to the normal tissue. The loss of methyl groups is accomplished mainly by hypomethylation of the coding regions and introns of the genes and demethylation of repetitive sequences that account for 20–30% of the human genome.⁹ Moreover, genome hypomethylation is an early event in cancer development and accumulates throughout all tumorigenic steps, from benign proliferation to invasive cancer.¹⁰ In this study, the authors described a decrease in the 5-methylcytosine content associated with the degree of tumor aggressiveness using a multistage skin cancer progression model.

Although gene-specific demethylation occurs in the context of global DNA hypomethylation, many of the effects are thought to arise through the activation of the transposable elements and endogenous retroviruses present in the human genome, and through loss of imprinting. Potentially, the reactivation of the strong promoters associated with transposable elements can globally modify the expression levels of transcription factors and/or the gene expression levels of the growth regulatory genes in which these factors reside.¹¹ It has also been suggested that unmethylated transposable elements permit genomic mutations and anomalous chromosomal recombinations. Additionally, h...

Table of contents

• Cover
• Half Title
• Title Page
• Copyright Page
• Editor
• Contributors
• Table of Contents
• Chapter 1 An Introduction to Epigenetics
• Chapter 2 Epigenetics and Cancer: DNA Methylation
• Chapter 3 Epigenetics and Cancer: Histone Modifications
• Chapter 4 Epigenetic Drugs: DNA Demethylating Agents
• Chapter 5 Epigenetic Drugs: Histone Deacetylase Inhibitors
• Chapter 6 Sirtuins in Biology and Disease
• Chapter 7 microRNAs in Cell Biology and Diseases
• Chapter 8 Chromatin Modifications by Polycomb Complexes
• Chapter 9 Epigenetics and its Genetic Syndromes
• Chapter 10 Epigenetics and Immunity
• Chapter 11 Etiology of Major Psychosis: Why Do We Need Epigenetics?
• Chapter 12 Epigenetics and Cardiovascular Disease
• Chapter 13 Plant Epigenetics
• Chapter 14 Epigenetics, Environment, and Evolution
• Chapter 15 Epigenetics and Epigenomics
• Index