Epigenetic alterations are reversible and, therefore, are potential targets for appropriate drugs, unlike genetic mutations that cause permanent damage to the DNA.
The hallmarks of almost every malignancy are epigenetic changes involving either a gain or loss of DNA methylation. These changes can influence the expression of cancer-related genes including apoptosis regulators and tumor suppressors. Since most of these types of epigenetic changes are reversible, they are currently being investigated as potential therapeutic targets.
Promising research from Prof Christoph Plass at the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ, Germany) and his colleagues from the Ohio State University in Columbus, OH, USA, is emerging that investigates the processes leading to the addition of different methyl labels in cancer cells. One of their pertinent research questions is when exactly the first labels occur in the development of cancer. In their latest published research, a chronic lymphocytic leukemia (CLL) murine model was used for studying the disease.
“Since first deviations in methylation occur so early in mice, we should find out whether this is also true for humans. If so, an early methylation test in high-risk individuals could provide clues about a developing cancer”, commented Prof. Plass. Therefore, in specific types of cases, drugs that inhibit methyl group attachment might delay the onset of cancer and could potentially be used as a preventive medical intervention. “This is probably most effective in a very early phase of methylation”, explained Plass.
In their study, the investigators set out to determine the mechanisms, patterns and timing of aberrant DNA methylation in the Emu-TCL1 transgenic mouse model of CLL. Their results demonstrate that CLL cells from Emu-TCL1 mice at various stages repeat the same epigenetic alterations seen in human CLL. As early as 3-month old mice showed aberrant promoter sequence methylation (including binding sites for the transcription factor FOXD3) long before the onset of disease.
The investigators of the study concluded that “specific transcriptional repression is an early event leading to epigenetic silencing of target genes in murine and human CLL … These results provide strong rationale for the development of strategies to target NF-κB components in CLL and potentially other B-cell malignancies”. The first clinical studies have already started to investigate the possibility of using this study‘s findings as a preventative medical intervention before malignancy even develops.
Source: Chen SS, Raval A, Johnson AJ et al.: Epigenetic changes during disease progression in a murine model of human chronic lymphocytic leukemia. PNAS DOI: 10.1073/pnas.0906455106 (Epub ahead of print) (2009).
A study conducted by researchers from Uppsala University, Sweden, has identified that nucleosomes are responsible for the protein coding part of genes. This research was led by Prof. Claes Wadelius at the Department of Genetics and Pathology (Uppsala University) and Prof. Jan Komorowski at the Linnaeus Centre for Bioinformatics (Uppsala University) as well as the University of Warsaw (Poland). The results of this study was recently published by the journal Genome Research and was based on massive amounts of publicly available data that had been previously published by other scientists, but not analyzed in such detail before.
“Our findings show the value of sophisticated bioinformatic analyses and the need to delve deeper into the gigantic amounts of data from modern biological research”, commented Prof. Komorowski.
The correlation between nucleosomes and exons has previously not been known or understood to exist. In the past, genome-wide nucleosome and histone modification studies have focused on transcription start sites (TSSs) where nucleosomes in RNA polymerase II (RNAPII) occupied genes are well positioned and have histone modifications that are characteristic of expression status. However, the novel results from this study demonstrate that nucleosomes are located over exons and therefore the protein code area is packed in discrete units.
“A gene can be read in several ways and create different proteins. We have now demonstrated that there is an epigenetic control that determines which parts of the gene that are read”, explained Prof. Wadelius.
In their study, they demonstrate that there is a higher nucleosome-positioning signal in internal human exons and that this positioning is independent of expression. They also observed a similarly strong nucleosome-positioning signal in internal exons of Caenorhabditis elegans. This mechanism seems to be evolutionary conserved since it is present in both primates and nematodes and can be traced back a billion years in time to a common ancestor.
Source: Andersson R, Enroth, S, Rada-Iglesias A, Wadelius C, Komorowski J: Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res. doi:10.1101/gr.092353.109 (Epub ahead of print) (2009).
The function of a gene product called amplified in liver cancer 1 (Alc1) has been unknown until the results of a study carried out by investigators from University of Kansas (KS, USA) was published in the Proceedings of the National Academy of Science (PNAS) that elucidated its function.
“We‘ve been able to demonstrate that the protein encoded by the Alc1 gene is, in fact, a chromatin remodeling enzyme”, explained Aaron Gottschalk, graduate student and lead author of the PNAS paper from the University of Kansas Medical Center conducting his research in the Stowers Institute‘s Conaway Lab. The researchers found that the enzyme is inactive by itself, but in the presence of NAD and poly (ADP-ribose) polymerase 1 (Parp1), it becomes strongly activated to move nucleosomes on DNA. From their research, they were also able to establish that the binding of a specific Alc1 region to poly(ADP-ribose) coupled to Parp1 helps recruit Alc1 to bind to and remodel nucleosomes.
The research team from the Conway laboratory has also demonstrated that Parp inhibitors block Alc1 activities in vitro and in vivo. This suggests that the therapeutic activities of these inhibitors could be partly owing to the indirect affects on Alc1.
“This finding is particularly interesting because Parp1 and poly(ADP-ribose) are known to play important roles in transcriptional regulation, DNA repair and DNA replication, but how they do so is really not at all clear” enthused Dr Ron Conaway, principal investigator.
Parp is now being investigated by medical researchers and pharmaceutical companies for its possible potential as a treatment of cancer and other diseases. If the results of this study are found to be validated, drugs that target Alc1 function may serve as a new method in the treatment of cancer and disease.
Source: Gottschalk AJ, Timinszky G, Kong SE et al.: Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. Proc. Natl Acad. Sci. USA DOI: 10.1073/pnas.0906920106 (2009) (Epub ahead of print).
Potential targets for the early detection and treatment of prostate cancer is currently an exciting area of research. A paper published by the journal Human Molecular Genetics explores how a team of scientists from the University College Dublin ([UCD], Ireland) set out to investigate and characterize the changes seen in the epigenetic signatures of prostate cells when exposed to chronic hypoxia. The aging prostate‘s characteristic feature is that of low levels of oxygen or chronic hypoxia found in its tissue, owing to the declining blood flow to the organ. This has previously been thought to contribute as a risk factor for developing cancer. The exact processes involved are not properly understood or defined and therefore research into elucidating the precise mechanism is needed.
Therefore, this study led by Dr Amanda McCann, a fellow at UCD‘s Conway Institute of Biomolecular and Biomedical Research, sort out to investigate the link between low oxygen levels and the risk of developing prostrate cancer by examining the consequences of chronic hypoxia on prostate cells. Dr Jenny Watson, a lead author of the paper, commented that “… understanding how chronic hypoxia influences global and gene-specific epigenetic programming will provide important insights into the mechanisms of hypoxia-induced cellular changes. The identification of these factors contributing to the initial development of prostate cancer represents important targets for early detection and manipulation in early stage disease”.
The scientists used PwR-1E benign prostate epithelial cells and an equal aged hypoxia-adapted PwR-1E subline to identify the phenotypic and epigenetic consequences of chronic hypoxia in prostate cells. From this, they identified a significantly altered cellular phenotype in response to chronic hypoxia which was characterized by the following features: an increased receptor-mediated apoptotic resistance, the induction of cellular senescence, increased invasion and the increased secretion of IL1b, IL6, IL8 and TNF cytokines. In addition to these phenotypic changes, they also found a significant increase in the global levels of DNA methylation and H3K9 histone acetylation in the prostate cells. These changes were also found to be associated with gene-specific changes in DNA methylation at key imprinting loci as well as increased expression of DNA methyltransferase –DMNT3b. It is hypothesized that these epigenetic processes may possibly promote tumor development by initializing and maintaining the expression of regulatory genes and activation of adaptive pathways.
The authors of the study concluded that “these epigenetic signatures may represent an additional mechanism to promote and maintain a hypoxic-adapted cellular phenotype with a potential role in tumor development”.
Source: Watson JA, Watson CJ, McCrohan AM et al.: Generation of an epigenetic signature by chronic hypoxia in prostate cells. Hum. Mol. Genet. DOI: 10.1093/hmg/ddp307 (Epub ahead of print) (2009).