Essay: Epigenetics

Epigenetics are heritable changes in gene expression that are not occupied by changes in the DNA sequence itself. These changes are crucial for key eukaryotic processes of development and differentiation and may help to explain the mechanism by which one tissue is differentiated form another developmentally. Physiological these processes include: the control of gene expression, X chromosomal inactivation, maintenance of chromatin structure and genomic imprinting. 12
Epigenetic transcriptional silencing is a process wherein the methylation of gen promoters has been noted to be involved. Abnormal gene methylation of tumor suppressor genes has been shown to stimulate the development of malignancy. There is shown that the profiles of gene methylation have been different in various malignant tumors and that the profiles of gene methylation are linked with clinical outcomes. Specific gene methylation profiles may exist between different pathways of ovarian tumorigenesis. 3
DNA methylation
An example of an epigenetic modification is DNA methylation. DNA methylation is well-associated with transcription repression. DNA methylation takes place on the C5 position of cytosines that precede guanines (CpG dinucleotides). The CpG dinucleotides are unequally distributed across the human genome. They can exist as CpG islands, this are sequences of 1 kb in length with an elevated G+C content of more than 50 percent and observed frequency of more than 0.60. Usually most of the CpG-rich repetitive DNA sequences and heterochromatin are methylated, but CpG islands which are located within the 5′ promotor regions of genes are normally unmethylated. This is the reason why active gene transcription is here possible. Pathologically leads aberrant silencing of expression to diseases such as cancer. There is seen that differentially methylated regions that are associated with normal tissue differentiation overlap substantially with regions where methylation changes lead to cancers. This fact supports the ‘epigenetic progenitor model of cancer’, this model states that methylation changes that drive normal cell development and differentiation are the main mechanism by which epigenetic changes drive cancer. 12
Histone modifications
There are different kinds of histone modifications, examples are histone acetylation, histone methylation and histone phosphorylation. Histone acetylation is the acetylation of lysines and it is highly dynamic and regulated by two opposing action families of enzymes: histone acetyltransferases (HATs) and histone deactylases (HDACs). Histone phosphorylation is highly dynamic. It takes predominantly place on serines, threonines and tyrosines, in the N-terminal histone tails. The levels of the modification are controlled by kinases and phosphatases that add and remove the modification respectively. All of the identified histone kinases transfer a phosphate group form ATP to the hydroxyl group of the target amino-acid side chain. In this way adds the modification a significant negative charge to the histone that undoubtedly influences the chromatin structure. Histone methylation occurs most of the time on the side chains of lysines and arginines. Acetylation and phosphorylation do alter the charge of the histone protein, histone methylation on the other hand does not alter the charge of the histone protein. There are different kind of methylations that could take place: lysines may be mono-, di-or tri-methylated whereas arginines may be mono-, symmetrically or asymmetrically di-methylated. 17 Histone modifications can sometimes lead to cancer. This can occur via two mechanisms: by altering gene expression programmes, including the abnormal regulation of oncogenes and tumor suppressor genes or by histone modifications which may affect genome integrity and/or chromosome segregation. 17
Chromatin
Chromatin regulates transcriptional processes through coordinated covalent modifications of DNA and its associated nucleosomal histones. 17 The basic unit of chromatin is the nucleosome. A nucleosome consists of nuclear DNA wrapped around a histone octamer. Making the DNA compact through dynamic coiling confers an access barrier to the transcriptional machinery. 4 The modifications which are regulated by chromatin include acetylation, methylation and ubiquitination. Post-translational modifications of histones play crucial roles in the dynamics of chromosomes. Chromatin remodelling complexes are master regulators of transcription factor action and enable gene transcription by supporting in the coordination of the binding of transcription factors to promotors and enhancers. Chromatin remodelling complexes are involved in various processes such as DNA repair, DNA synthesis, mitosis and genomic stability. There is shown that alterations in the subunits of these complexes play a role in cancer. Core components of the chromatin remodelling complexes are potent tumor suppressors, which are specifically inactivated in cancers. 17 Chromatin modifying complexes can be grouped in two classes: those that covalently modify nucleosomes and those that consume ATP to mobilize nucleosomes and modulate chromatin compaction, for example the SWI/SNF complex. 4
Ovarian Clear Cell Carcinoma
Analysis of individual genes has led to a large number of targets of DNA methylation which are now reported in ovarian cancer. When the methylation profiles of ovarian cancer and noncancerous cells were compared it indicated that of the 2,003 genes that showed differential levels of methylation, 93.4% showed hypermethylation in the cancer cell lines. There is already demonstrated that addition of methylation occurs more frequently than loss of methylation in almost all types of primary tumors. Genome wide methylation analysis have shown that ovarian CCC has a distinct methylation profile relative to the other histological subtypes of epithelial ovarian cancer. The OCCC-specific methylation profile includes synchronous gain of promoter methylation for multiple genes in the ERalpha pathway and loss of promoter methylation for multiple genes in the HNF1 pathway. 10 Four genes that could lead to OCCC when they are aberrantly methylated are: 14-3-3- sigma as SFN, PYCARD, WT1 and HNF1B. 10 About HNF-1?? (hepatocyte nuclear factor 1B) is known that it not only would be an excellent OCCC-specific molecular marker but also a molecular target for the therapy of ovarian CCC.20 HNF-1B expression is epigenetically regulated and its protein product is involved in glucose homeostasis. 5 In OCCC HNF1B is upregulated at both mRNA and protein level. 19
Another pathway that seemed to play a prominent role in OCCC is the MET/P13K pathway. MET gene amplification takes place in 30% of the primary OCCC and 20% of the OCCC show AKT2gene amplification. AKT2 is a downstream component of the MET/P13K pathway. 1
Another couple of genes that are frequently mutated in OCCC tumors are ARID1A, PIK3CA, PPP2R1A and KRAS. PIK3CA encodes a subunit of phosphatidylinositol-3 kinase, and KRAS encodes an oncoprotein. 22 PPP2R1A encodes a regulatory subunit of serine/threonine phosphatase. This is involved in the negative control of cell growth and division. ARID1A encodes AT-rich interactive domain-containing protein 1a, which plays a role in chromatin remodelling. 22
The ARID1A gene product is part of an ubiquitin ligase complex, this complex targets H2B for ubiquitination and proteasomal degradation.19 ARID1a is the gene which seemed to be most frequently disrupted in OCCC. ARID1A acts as a tumor suppressor gene and its mutation leads to the loss of BAF250A. There is speculated that the somatic mutation of ARID1A is an early event in the transformation of endometriosis into cancer. Sequence mutations of ARID1A seem to occur in 43-57% of the OCCC cases. 19