Epigenetics

Definition

The term epi is derived from the Greek prefix meaning upon, on, over, or beside. Epigenetics looks at the extra layer of instructions that lie over or on top of DNA that control the way genes are expressed. All cells in the body contain the same genetic code. Yet each of these cells have different structures and functions. A heart cell, for example, is very different from a nerve cell. Epigenetics seeks to understand how this happens. It explores how certain chemical tags attached to different parts of DNA and its associated proteins can activate or silence genes. Such chemical changes are known as epigenetic modifications. This process does not alter the underlying genetic code. Instead it controls which genes are turned on or off in individual cells which determines the specific structure and function of the cell. Epigenetic modifications also help explain differences found between identical twins that share the same genetic code.

The epigenetics mechanism plays an important role in the normal development of the cell and maintaining the body’s equilibrium or homeostasis. Any disturbance of the epigenetic process can have major adverse health and behavioural consequences. This can be affected by internal imbalances within the body itself and wider environmental and lifestyle factors.

Most epigenetic changes only occur during the lifetime of the individual organism. Such modifications, however, can have long-term effects and be passed on to offspring and subsequent generations.

Lights marking where methtyl group molecules are binding to two cytosines in a DNA molecule. DNA methylation is one of a number of epigenetic mechanisms that cells use to control gene expression. It plays an important role in the normal development of cells and cancer. Credit: Christoph Bock, Max Planck Institute for Informatics.

Importance

Epigenetics has been a growing field since the mid 1970s. The pace of epigenetic research picked up significantly from the early 2000s. Some idea of the speed with which this happened can be gauged from the database of ISI Web of Knowledge. Between 2000 and 2010 the number of articles listed in the database that contained the word ‘epigenetics’ in their title grew from 100 to 1300. A more recent survey carried out by Enal Razvi and Gary Oosta of the number of epigenetics-focused scientific publications showed that this had an annual growth rate of 12.5 per cent in the years between 2012 and 2015.

Interest in epigenetics has been fueled by accumulating evidence that epigenetic mechanisms underpin a wide variety of illnesses, behaviours and other health issues. Epigenetic changes are now associated with a wide range of diseases. This includes nearly all types of cancer, plus respiratory, cardiovascular, autoimmune, reproductive and neurodegenerative disorders. Many factors are suspected of causing epigenetic modifications. Lifestyle behaviour such as diet, sleep and exercise are now known to cause change, as is exposure to heavy metals, pesticides, diesel exhaust, tobacco smoke, radioactivity, bacteria, and viruses.

The public visibility of epigenetics was increased by the establishment of the Human Epigenome Project (HEP). This is an international project that was launched with government funds and private investment in 2010 as a sequel to the Human Genome Project. It was set up to map DNA methylation and other epigenetic markers throughout the human genome so as to further understand gene regulation in development and disease. By 2015 the group had uncovered key information about functional elements that regulate gene expression in 127 human tissues and cell types.

Epigenetics is already making its mark in the clinic. Four drugs have already been approved by the FDA to reverse aberrant epigenetic changes that cause cancer and many more in the pipeline. A number of studies suggest that DNA methylation inbibitor drugs help increase the sensitivity of tumour cells to immune checkpoint inhibitor therapy. Many diagnostic companies are also developing tests, many using antibodies, to detect epigenetic biomarkers for diseases like cancer. Just how far the field has progressed can be seen from the fact that in 2016 analysts from Grand View Research predicted that the global market for epigenetic products would each USD 16.31 billion by 2022.

Discovery

The term ‘epigenetics’ was first coined in 1942 by Conrad H. Waddington, a British developmental biologist, embryologist and geneticist at Cambridge University. When Waddington first used the term little was known about genes and their hereditary role. Until the 1950s the term was used to describe the events that helped a fertilised egg to become a mature organism. By the mid-1980s the meaning of the word had become more precise being used to describe heritable traits that do not involve any alterations to the underlying DNA sequence.

One of the first epigenetic mechanisms to be identified was DNA methylation. This is a chemical process that involves the addition of a single carbon and three hydrogens, known as a methyl group, to a DNA strand. The methyl group addition changes the activity of a DNA segment without altering the DNA sequence. It is known as an ‘epigenetic mark’. Methylated cytosine was first detected in a preparation of calf thymus in 1948 by Rollin Hotchkiss at the Rockefeller Institute of Medical Research, New York.

It would take time however for researchers to work out what purpose the modified cytosine served. In 1969 John S Griffith and Henry R Mahler based at Indiana University suggested that it might help with memory storage in the brain. This was the first time DNA methylation was linked with a biological function. By 1975 three different groups independently suggested that DNA methylation could play a role in switching genes on and off during biological development. One was led by Arthur Riggs at the City of Hope National Medical Center, California, another by Robin Holliday at the National Institute of Medical Research, London, and the last by Ruth Sager at Harvard Medical School.

By the 1990s experimental evidence began to emerge that backed up the hypotheses about the relationship between DNA methylation and gene expression. This was helped by the development of techniques in the 1970s which enabled scientists to clone and sequence DNA. Research in the area was further aided by a method devised by an Australian group of scientists led by Marianne Frommer. This technique made it possible to isolate methylated cytosine residues in individual DNA strands by treating the DNA with the chemical sodium bisulphite. Together with the amplification of DNA by PCR, and the rise of genome sequencing technology, the bisulphite method provided the means to investigate DNA methylation and its impact on gene expression on an unprecedented scale. This could be done in pathological samples. Epigenetics research was further enhanced by the development of microarray technology and improved staining techniques using antibodies.

One of the key discoveries was made in 1985. That year Adrian Bird and his team at Edinburgh University demonstrated that DNA methylation did occur at random and took place on specific segments of DNA known as CpG islands. For a long time it was not known what the significance of this was. It subsequently emerged that methylation of CpG islands was instrumental in suppressing a gene.

The epigenetics network is now known to have many layers of complexity. Two main types of epigenetic modifications have identified. The first type, which involves DNA methylation, modifies genes, these are small sections of DNA which provide the instructions for creating a protein. DNA methylation always silences the gene. The second type of modification affects histones, a specific protein that DNA winds round. Histones help compress the long DNA molecule so that it can fit into a cell’s nucleus cell. Modification of the histones can either tighten or loosen the DNA coils. The tightness of the coil affects how much a gene is exposed or hidden from the cell’s transcription machinery. Different chemical tags added to the tail of the histone have been found to affect this process. These tags include acetyl, phosphate or ubiquitin molecules. It is not yet known exactly what types of modifications help open or tighten the DNA coils, but the acetylation of histones is known to unwind DNA and increase gene expression.

Application

With the help of new genome technologies, numerous diseases have now been linked to epigenetic disruptions, especially ones influenced by the environment. One of the first diseases to be linked to epigenetic changes was cancer. In the late 1970s Holliday and Pugh demonstrated that hypermethylation of DNA resulted in changes to normal gene regulation which led to cancer. In particular they showed that hypermethylation silenced tumour suppressor genes.

Based on this a number of cancer drugs have been developed to inhibit DNA methylation. The first such drug was Azacytidine (Vidaza). This was licensed by the FDA in 2004 for the treatment of blood cancers. Its approval marked a major milestone in the development of epigenetic cancer therapy. Since then two other DNA methylations inhibitors drugs have been approved. Three drugs have also been approved that inhibit history deacetylation. Yet, despite their success the new epigenetic drugs have certain drawbacks. The DNA methylase inhibitors, for example, have poor chemical stability and can cause severe toxic side effects in patients.

In addition to new treatments, epigenetics has opened up a new strategy for diagnosis. The chances of beating cancer are greatly improved if the disease is detected at an early stage. Diagnosing cancer early, however, is not always easy. Efforts are now underway to develop tests that can identify the presence of molecular epigenetic markers in a patient’s biological fluids to identify precursor lesions or cancer at its earliest stage. These rest on detecting abnormal DNA methylation patterns in specific genes, histone signatures and altered expression in small RNA molecules. Epigenetic markers are not only being sought for the early detection of cancer. They could also prove useful in the clinical management of patients. In 2000 it was shown that methylation levels in brain tumours could help predict patients’ responsiveness and sensitivity to certain chemotherapies.

Issues

Epigenetics research has become an indispensable tool for determining gene-environment relationships that affect risk exposure, therapeutic benefit and disease progression. Yet, despite its importance, many scientists continue to debate the parameters of epigenetics and whether this should be confined to just changes that take place at the gene level. Some are also concerned about our capacity to identify a risk. At what point, for example, can we judge when a cell or tissue has altered so much that a patient has the risk of the onset of cancer, a recurrence, tumour progression or developed resistance to treatment. Similarly, a number question the extent to which epigenetic information can provide new avenues for treatment or cures for cancer. In addition, the field is still relatively young so we still do not fully understant the full set of benefits and limitations of therapy inherent in altering epigenetic pathways.

Epigenetics: timeline of key events

William G Ruppel discovered the nucleotide while trying to isolate the bacterial toxin responsible for tuberculosis. 1898-01-01T00:00:00+0000T.B. Johnson, R.D. Coghill, 'The discovery of 5-methyl-cytosine in tuberculinic acid, the nucleic acid of the Tubercle bacillus', Journal of the American Chemical Society, 47/11 (1925, 2838–44. 1925-11-01T00:00:00+0000C.H. Waddington, 'The Epigenotype', Endeavour, 1 (1942), 18-20.1942-01-01T00:00:00+0000R.D. Hotchkiss, 'The quantative separation of purines, pyrimidines, and nucleosides by paper chromatography', J Biol Chem, 175/1 (1948), 315-32. 1948-03-10T00:00:00+0000G.R. Wyatt, 'Recognition and estimation of 5-methylcytosine in nucleic acids', Biochem J, 48/5 (1951), 581-4.1951-05-01T00:00:00+0000C.H. Waddington, The Strategy of the Genes: A Discussion of Some Aspects of Theoretical Biology (London, 1957).1957-01-01T00:00:00+0000M.F. Lyon, 'Gene action in the X-chromosome of the mouse', Nature, 190 (1961), 372–73.1961-04-22T00:00:00+0000Werner Arber, Swiss microbiologist and geneticist, and his doctoral student Daisy Dussoix propose bacteria produce restriction and modification enzymes to counter invading viruses. 1962-01-01T00:00:00+0000W. Arber, S.Linn, 'DNA modification and restriction', Annual Review Biochemistry, 38 (1969), 467-500.1969-07-01T00:00:00+0000A.D. Riggs, 'X inactivation, differentiation, and DNA methylation', Cytogenet Cell Genet, 14 (1975), 9–25; R. Sager, R. Kitchin, 'Selective silencing of eukaryotic DNA', Science, 189/4201 (1975), 426-33. 1975-01-01T00:00:00+0000R. Holliday, J.E. Pugh, 'DNA modification mechanisms and gene activity during development', Science, 187 (1975), 226–32.1975-01-01T00:00:00+0000S.J. Compere, R.D. Palmiter, 'DNA methylation controls the inducibility of the mouse metallothionein-I gene lymphoid cells', Cell, 25 (1981), 233–240. 1981-07-01T00:00:00+00001982-01-01T00:00:00+00001982-01-01T00:00:00+0000A.P. Feinberg, B. Vogelstein, 'Hypomethylation distinguishes genes of some human cancers from their normal counterparts', Nature, 301/5895 (1983), 89-92.1983-01-06T00:00:00+0000A. Bird, M. Taggart, M. Frommer, O.J. Miller, D. Macleod, ‘A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA’, Cell, 40/1 (1985 Jan;40(1):91-9. 1985-01-01T00:00:00+0000T. Bestor, A. Laudano, R. Mattaliano, V. Ingram, 'Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells', Journal Molecular Biology, 203 (1988), 971–83. 1988-10-20T00:00:00+0000V. Greger, E. Passarge, W. Hopping, E. Messmer, B. Horsthemke, 'Epigenetic changes may contribute to the formation and spontaneous regression of retinoblastoma', Human Genetics, 83 (1989), 155–58. 1989-09-01T00:00:00+0000M. Frommer, L.E. McDonald, D.S. Millar, C.M. Collis, F. Watt, G.W. Grigg, P.L. Molloy, C.L. Paul, 'A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands', PNAS, 89/5 (1992), 1827-31.1992-03-01T00:00:00+0000Mouse genetated with genes knocked out that produce the enzyme DNA methyltransfgerase involved in DNA methylation. E. Li, T.H. Bestor, R. Jaenisch, 'Targeted mutation of the DNA methyltransferase gene results in embryonic lethality', Cell, 69/6 (1992), 915-26.1992-06-12T00:00:00+0000W.F. Zapisek, G.M. Cronin, B.D. Lyn-Cook, L.A. Poirier, 'The onset of oncogene hypomethylation in the livers of rats fed methyl-deficient, amino acid-defined diets', Carcinogenesis, 13/10 (1992), 1869-72.1992-10-01T00:00:00+0000P.W. Laird, L. Jackson-Grusby, A. Fazeli, S. L. Dickinson, W. E. Jung, E. Li, R.A. Weinberg, R. Jaenisch, 'Suppression of intestinal neoplasia by DNA hypomethylation', Cell, 81 (1995),197-205, April 21, 1995,1995-04-21T00:00:00+0000M. Toyota, N. Ahuja, M. Ohe-Toyota, J.G. Herman, S.B. Baylin, J-P.J. Issa, 'CpG island methylator phenotype in colorectal cancer', PNAS, 96/15 (1999), 8681–86.1999-07-20T00:00:00+0000H.D. Morgan, H.G. Sutherland, D.I. Martin, E. Whitelaw, 'Epigenetic inheritance at the agouti locus in the mouse', Nature Genetics, 23 (1991), 314–18.1999-11-01T00:00:00+00002001-01-01T00:00:00+00002004-01-01T00:00:00+0000Drug made by MGI Pharma. approved for treatment of myelodysplastic syndromes, bone marrow disorders2006-01-01T00:00:00+0000Drug made by Merck & Co2006-10-06T00:00:00+00002009-11-01T00:00:00+00002012-09-28T00:00:00+00002015-04-01T00:00:00+0000K.B. Chiappinelli, P.L. Strissel, A. Desrichard, et al, 'Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses', Cell, 162 (2015), 974-86.2015-08-27T00:00:00+0000
Date Event People Places
1898A nucelotide called tuberculinic acid found to bind to the protein tuberculin. It is now regarded as the precursor to the discovery of DNA methylationRuppelPhilipps University of Marburg
November 1925T.B. Johnson and R.D. Coghill reported detecting a minor amount of methylated cytosine derivative as byproduct of hyrdrolysis of tuberculinic acid with sulfuric acid but other scientists struggled to replicate their results. Johnson, CoghillYale University
1942'Epigenetics' coined as a term to describe how genes interact with the environment to produce the physical traits of an organism WaddngtonCambridge University
March 1948Hotchkiss discovered the first naturally modifed DNA nucleotide, cytosine, in a chromatography of calf thymus DNAHotchkissRockefeller Institute
May 19515-methcytosine isolated in nucleic acids for the first timeWyatt 
1957Conrad Waddington develops model of epigenetic landscape to show the process of cellular decision-making during biological developmentWaddngtonCambridge University
22 Apr 1961Genes linked to X-chromosome inactivation in female mice embyosLyonCambridge University
1962Concept of restriction and modification enzymes bornArber, DussoixUniversity of Geneva
July 1969Discovery of methylase, an enzyme, found to add protective methyl groups to DNAArber, LinnUniversity of Geneva
1975DNA methylation suggested as mechanism behind X-chomosome silencing in embryosRiggs, Sager, KitchenCity of Hope National Medical Center, Harvard University
1975DNA methylation proposed as important mechanism for the control of gene expression in higher organismsHoilliday, PughNational Institute for Medical Research
July 1981First evidence provided to show that DNA methylation involved in silencing X-chromosomeCompere, PalmitterHoward Hughes Medical Institute
1982 - 1985Studies reveal azacitidine, a cytoxic agent developed by Upjohn, inhibits DNA methylation 
1982Azacitidine fails to win FDA approval for treatment of acute myelogenous leukaemia due to lack of controlled studies showing clinical benefit 
6 Jan 1983Widespread loss of DNA methylation found on cytosine-guanine (CpG) islands in tumour samplesFeinberg, VogelsteinJohns Hopkins University
January 1985DNA methylation found to occur on specific DNA segments called CpG islandsBird, Taggart, Fromer, Miller, MacleodEdinburgh University, Kanematsu Laboratories, Columbia University
20 Oct 1988Cloning of first mammalian enzyme (DNA methyltransferase, DNMT) that catalyses transfer of methyl group to DNA Bestor, Laudano, Mattaliano, IngramMassachusetts Institute of Technology
September 1989DNA methylation suggested to inactivate tumour suppressor genesGreger, Passarge, Hopping, Messmer, HorsthemkeInstitute of Human Genetics
1 Mar 1992Method devised to isolate methylated cytosine residues in individual DNA strands providing avenue to undertake DNA methylation genomic sequencing 
12 Jun 1992First transgenic mouse model created for studying link between DNA methylation and diseaseLi, Bestor, JaenischWhitehead Institute for Biomedical Research
1 Oct 1992First experimental evidence showing links between diet and DNA methylation and its relationship with cancerZapisek, Cronin, Lyn-Cook, PoirierFDA, National Center for Toxicological Research
21 Apr 1995First evidence published to demonstrate reduced DNA methylation contributes to formation of tumoursLaird, Jackson-Grusby, Fazeli, Dickinson, Jung, Li, Weinberg, JaenischMassachusetts Institute of Technology, Massachusetts General Hospital
20 Jul 1999DNA methylation of CpG islands shown to be linked to colorectal cancerToyota, Ahuja, Ohe-Toyota, Herman, Baylin, IssaJohns Hopkins University
November 1999First evidence from mammals that epigenetic changes can be passed down generations Morgan, Sutherland, Martin, WhitelawUniversity of Sydney
2001Pharmion licenses azacitidine from Pharmacia and Upjohn to Pharmacia's azacityidine technology, patents and clinical data 
2004FDA approved first DNA methylation inhibitor drug, azacitidine (Vidaza®), for treatment of rare bone marrow disorder 
2006FDA approved second DNA methylation inhibitior, decatabine (Dacogen) 
6 Oct 2006FDA approved first histone deacetylase inhibitor, Vorinostat (Zolinza), for cutaneous T-cell lymphoma 
November 2009FDA approved second histone deactylase inhibitor, Romidepsin (Istodax), for cutaneous T-cell lymphoma  
2012European approval of decatabine (Dacogen) for treatment of acute myeloid leukaemia 
April 2015Chinese regulatory authorities approved Chidamide, a histone deactylase inhibitor, for peripheral T cell lymphoma 
27 Aug 2015Experiments with mice showed that azacytidine treatment enhanced the responsiveness of tumors to anti–CTLA-4 therapy 

1898

A nucelotide called tuberculinic acid found to bind to the protein tuberculin. It is now regarded as the precursor to the discovery of DNA methylation

Nov 1925

T.B. Johnson and R.D. Coghill reported detecting a minor amount of methylated cytosine derivative as byproduct of hyrdrolysis of tuberculinic acid with sulfuric acid but other scientists struggled to replicate their results.

1942

'Epigenetics' coined as a term to describe how genes interact with the environment to produce the physical traits of an organism

Mar 1948

Hotchkiss discovered the first naturally modifed DNA nucleotide, cytosine, in a chromatography of calf thymus DNA

May 1951

5-methcytosine isolated in nucleic acids for the first time

1957

Conrad Waddington develops model of epigenetic landscape to show the process of cellular decision-making during biological development

22 Apr 1961

Genes linked to X-chromosome inactivation in female mice embyos

1962

Concept of restriction and modification enzymes born

Jul 1969

Discovery of methylase, an enzyme, found to add protective methyl groups to DNA

1975

DNA methylation suggested as mechanism behind X-chomosome silencing in embryos

1975

DNA methylation proposed as important mechanism for the control of gene expression in higher organisms

Jul 1981

First evidence provided to show that DNA methylation involved in silencing X-chromosome

1982 - 1985

Studies reveal azacitidine, a cytoxic agent developed by Upjohn, inhibits DNA methylation

1982

Azacitidine fails to win FDA approval for treatment of acute myelogenous leukaemia due to lack of controlled studies showing clinical benefit

6 Jan 1983

Widespread loss of DNA methylation found on cytosine-guanine (CpG) islands in tumour samples

Jan 1985

DNA methylation found to occur on specific DNA segments called CpG islands

20 Oct 1988

Cloning of first mammalian enzyme (DNA methyltransferase, DNMT) that catalyses transfer of methyl group to DNA

Sep 1989

DNA methylation suggested to inactivate tumour suppressor genes

1 Mar 1992

Method devised to isolate methylated cytosine residues in individual DNA strands providing avenue to undertake DNA methylation genomic sequencing

12 Jun 1992

First transgenic mouse model created for studying link between DNA methylation and disease

1 Oct 1992

First experimental evidence showing links between diet and DNA methylation and its relationship with cancer

21 Apr 1995

First evidence published to demonstrate reduced DNA methylation contributes to formation of tumours

20 Jul 1999

DNA methylation of CpG islands shown to be linked to colorectal cancer

Nov 1999

First evidence from mammals that epigenetic changes can be passed down generations

2001

Pharmion licenses azacitidine from Pharmacia and Upjohn to Pharmacia's azacityidine technology, patents and clinical data

2004

FDA approved first DNA methylation inhibitor drug, azacitidine (Vidaza®), for treatment of rare bone marrow disorder

2006

FDA approved second DNA methylation inhibitior, decatabine (Dacogen)

6 Oct 2006

FDA approved first histone deacetylase inhibitor, Vorinostat (Zolinza), for cutaneous T-cell lymphoma

Nov 2009

FDA approved second histone deactylase inhibitor, Romidepsin (Istodax), for cutaneous T-cell lymphoma

2012

European approval of decatabine (Dacogen) for treatment of acute myeloid leukaemia

Apr 2015

Chinese regulatory authorities approved Chidamide, a histone deactylase inhibitor, for peripheral T cell lymphoma

27 Aug 2015

Experiments with mice showed that azacytidine treatment enhanced the responsiveness of tumors to anti–CTLA-4 therapy