Human Epigenetics - By Dr. Sam Atallah
Over the past 50 years significant progress has been forged in the science of genetics.Yes, we’ve come along way from counting wide-type fruit flies in the biology lab!Let’s take a second to list some of the important milestones that have been achieved:
1865: Gregor Mendel, a monk, studies the inheritance of the garden pea.From this, we learn that all life forms have traits that can be passed on in a predictable way.In Mendilian genetics, genes can be dominant or ressessive.For some autosomal genes, simple math can predict the chances of offspring phenotypes. An excellent example of this is the inheritance of the ABO and Rh blood types.
1915:Thomas Morgan introduces the chromosomal theory of inheritance, for the first time indicating that chromosomes are what contain genetic information.
1953: Francis Crick, James Watson, and Maurice Wilkins share the nobel prize for elucidating the double-stranded helical structure of deoxyribonucleic acid (DNA) using x-ray crystallography.Essentially, the findings suggest that DNA is simply a code of only 4 base pairs, Adenine (A), Guainine (G), Cytocine (C), and Thyamine (T).Our entire genetic makeup is based on a very long sequence of AGCT.Learn the sequence, and theory has it, you should hold the blue print of a human.
Latter half of 20th Century: Prokaryotic and Eukaryotic DNA translation become understood, as does gene replication.It’s learned that DNA expresses genes with seemingly machine-like, molecular precision.In true factory style, DNA strands are first separated by the enzyme DNA gyrase to allow its translation by messenger ribonucleic acid, mRNA.The translated mRNA is then ‘read’ by Ribosomes and proteins manufactured by step-wise transfer of one amino acid at a time with the help oftransfer-RNA.These sophisticated molecules ‘read’ DNA’s translated string of A, G, C, and Ts.Each three base pairs (codons) code for a specific amino acid, which are assembles together in a chain to become functional protein.In a nutshell, specific genes make specific proteins.
2003: The Human Genome Project is completed, in effect determining the 3 billion base pair sequence of the entire human genome. Great! Every last A, G, C, and T sequenced! The Holy Grail! The Human Blue Print! But did this provide all the answers we were looking for?Well, not exactly . . .
2003-2009:Surprisingly, once the human genome was decoded, it was discovered that most of our DNA doesn’t code for anything.It’s so-called ‘junk’ DNA.Only an estimated 1.5% of the human genome codes for genes, and99% of these genes are identical to the DNA of the mouse.This leaves puzzling questions.What’s the purpose of having all this DNA if it doesn’t code for anything? How can we account for the vast phenotypic difference among man and mouse when these ‘blue prints’ are nearly identical?Why is it that cloned animals are not phenotypically identical?Why do monozygotic twins experience different susceptibility to disease and cancer?
Part of the answer to these perplexing questions lies in the rapidly evolving field of epigentics.Defined as the heritable change in gene function that occurs without changes in DNA sequence.Perhaps the best studied example of this is DNA methylation.In the human genome, DNA methylation occurs in a specific way.That is, methylation of cytosine -- but only when it precedes guanine in the DNA sequence.Often near the regulatory, 5’ end of many genes, repeat patterns of non-coding CG exist (the dinucleotide is linked by a phosphodiester“p” bond). These are refered to as CpG ‘islands.’Upstream methylation of CpG islands can effect the degree of activity of the downstream gene.
Methylation has been implicated in genomic imprinting, whereby only one of two alleles inherited are active. In most cases, both alleles are functional.When genomic imprinting occurs – secondary to CpG methylation – then either the allele inherited from the mother or from the father is turned off.Having genetic machinery operating with only one allele is analogous to a twin engine plane flying with only one of them working.In effect, imprinted genes are susceptible to gene-based disease and malignant transformation.Genomic imprinting has been implicated in Prader-Willi syndrome, Alzheimer disease, leukemia,, Beckwith-Wiedermann syndrome, and many others.
Tumors and Epigentics
An interesting finding is that tumor cells demonstrate global hypomethylation. This happens in non-coding segments ofDNA (introns), but also in the genes themselves. Even more intriguing – as a neoplasm progresses from benign to malignant, the degree of DNA hypomethylation also increases!
While global hypomethylation in gene poor regions results in a propensity towards malignant transformation, hypermethylation of CpG islands has been found to be an important genetic alteration leading to many cancers. This is because CpG repeats are in the promoter region of tumor suppressor genes, thus hypermethylation leads to down regulation of these cancer-preventing genes.This deactivation mechanism has been implicated in retinoblastoma, Hippel-Lindau disease, and BRCA-1 associated breast cancer, Colon, Lung, Esophageal, Ovarian, Liver, Bladder, Kidney, and Stomach cancer.
Perhaps one of the most interesting concepts in epigenomics is that methylation doesn’t act only as ‘a giant master switch’ turning on and offcancer related genes, but that itactually results in changes to histone proteins, which are important in packaging DNA into chromatin.Histones can be modified by methylation and acetylation, the result of which is conformantional changes in the shape of DNA itself.This global, conformantional change in DNA can lead to silencing of tumor suppressor genes.
Implications for Cancer Therapeutics
An important concept to realize is that secondary changes to DNA (ie, methylation) do not alter the sequence and are therefore considered reversible.The question is, can we control DNA methylation – particulary in cancer cells?Demethylating agents are a new and exciting area in cancer research.It has been demonstrated in vitro that it’s possible to re-express shut-off, DNA-methylated genes when these cell lines are treated with demethylating chemotherputics.Vidaza (5-azacytidine) and Decitabine (5-aza 2’-deoxycytidine) are demethylating agents which have been approved for treating leukemia and the myelodysplactic syndrome.There is also interest in histone deacetylase inhibitors which have been shown to induce cell-cycle arrest and even tumor cell apoptosis.Vorinostate (suberoylanilide hydroxamic acid) is now FDA approved from treating cutaneous T-cell lymphoma.Interestingly, valproic acid (Depakote), which is a common anti-seizure medication, is also a histone deacetylase inhibitor.There are more then 10 other agents currently being investigated in phase I/II trials.The efficacy of epigenetic inhibitors is yet to be determined.