The Epigenetic World Congress is a newer, up-and-coming conference, so this year we wanted to make sure that we were there to cover the action. Thanks to avid EpiGenie reader and guest reporter, Paula Desplats from UC San Diego for covering the event and allowing us to bring you all the details.
The Epigenetics World Congress Conference
The second annual Epigenetic World Congress was held on May 6-7, 2010 in beautiful, historic and unusually warm Boston, Mass. The incredible weather was perfect for walks alongside the Park, or watching the Swan-Boats in the Boston Public Garden when there was free time. Hosted alongside the RNAi & miRNA World Congress and the Genomic Automation Congress, Epigenetics seemed to attract a smaller, but equally enthusiastic crowd. The venue presented an interesting flavor of topics, ranging from personalized medicine – including stem cell therapies- and metabolic memory, to the epigenetic legacy for future generations.
Histone methylation: the Missing Link between Chromatin and DNA Repair
Brendan Price, Dana-Farber Cancer Institute
Natural mechanisms exist for repair of DNA double-strand breaks (DNA dsb). Still, some tumors are resistant to strand breaks. When a DNA dsb occurs, ATM is recruited to the break area, cell cycle is arrested and DNA is repaired. Depending on the break, it might not be able to be repaired; cells are then targeted for apoptosis and eliminated. If a repair is successful, the cell re enters cell cycle, but occasionally a mutation is introduced in the repair that escapes quality control, then the altered cell re-enters the cell cycle but this time with oncogenic potential. ATM is a protein kinase activated by DNAdsb and phosphorylates several proteins involved in activation of cell cycle checkpoints and regulation of DNA repair. Price showed that ATM acetylation follows DNA damage, and is necessary for the activation of this kinase. They found that TIP60 histone acetyltransferase binds to ATM when the later is recruited to DNA damaged regions and acetylates ATM. Tip60 binds to methylated histones and provides docking for other regulatory factors. Overexpression of de-methylating enzymes like H3Kpme2/3 blocks Tip60 activation. Price’s group also showed that H3Kpme2/3 binds to Hp1 family. These proteins are recruited at DNA dsbs and are redistributed along the chromatin where they in turn recruit Tip60/ATM activating the DNA repair mechanism. In sum, histone methylation is critical for genome stability and alterations in histone methylation levels might directly relate to cancer etiology and progression.
Epigenetic Changes of Methyl-Writing and –Erasing Enzymes in Diabetes
Assam El-Osta, Baker IDI Heart and Diabetes Institute
This was the first in a series of reports presented at the meeting studying metabolic memory or how previous metabolic disorders or even metabolic imbalance in mothers will carry on later effects in the same organisms or its progeny. This memory is associated with persistent epigenetic gene-activating events. In these particular studies, mice were subjected to transient hyperglycemia. 6 days after the hyperglycemic event, and after a period of normal blood sugar regulation, methylation in NfkB is persistent and affects a sustained elevated expression of p65. The responsible mechanism appears to be a balance between H3K9 methyl-writer and LSD1 methyl-eraser that results in changes in histone modifications generating hyperglycemic variability in endothelial cells. This metabolic memory is sustained despite posterior diabetes therapy generating long lasting effects on p65 promoter.
Dynamic DNA Methylation Programs Persistent Adverse Effects of Early-Life Stress
Chris Murgatroyd, Max Planck Institute of Psychiatry
This was an excellent presentation well aligned with the previous talk with extensive scientific data from careful and in-depth experimental approaches. Following previous reports on the long lasting effects of early life stress on the brain, Murgatroyd showed that maternal separation in mice persistently alters the offspring’s hormonal response to stress, evident by elevated expression of vasopressin (AVP) in the hippothalamus. AVP locus contains 4 CpG islands which methylation correlates with AVP mRNA expression levels. Functional CpG methylation is persistent up to 1 year after maternal separation in CpGi3, which lies in an enhancer region. Moreover, MeCP2 binds methylated residues in CpGi3 repressing AVP enhancer. Murgatroyd went even further to show that phosphorylation of Ser438 on MeCP2, which prevents its binding to DNA, was a key event in perpetuating the effects of the early life stress: while both, control and stressed samples showed the same pattern of DNA methylation, only control samples showed higher occupancy of meCs by MeCP2. Early stress increases the phosphorylation of MeCp2 preventing its binding to CpGi3 and sustaining elevated AVP expression. This effect is only present in a very specific population of hippocampal neurons, highlighting the fine-tuning of these epigenetic controls.
Epigenomic Diversity of Colorectal Cancer Indicated by LINE-1 Methylation
Shuji Ogino, Harvard Medical School
This talk kicked off the concept of “personalized medicine” as a way of understanding the uniqueness of the patients and to address individual variability to generate better therapeutic approaches. At the molecular level, colorectal cancer is a very heterogenous disease that serves as a multistep carcinogenesis model. Alcohol consumption and levels of folate in the diet are known to influence the risk and the type of cancer manifested. The aim of the study was combine molecular and epidemiological data to determine how the negative effectors work on the disease, using a large cohort of 170,000 cases from which data about risk exposure, family history, SNPs and plasma biomarkers have been recorded. Colorectal cancer is associated with a genome-wide DNA hypomethylation that results in proto-oncogene activation and chromosomal instability. In particular LINE-1, Long Insterspersed Nucleotide Element 1, a large transposon found in Human genome, shows high variability in methylation levels and has been associated with poor prognosis, gene disruption, loss of imprinting and manifestations with more aggressive tumors. Through the analysis of epigenetic changes, risk factors and diets, Dr. Ogino reported the identification of a new cancer subtye, LINE-1 extreme hypomethylator, which represents 3% of the cases, including those more aggressive and with younger age of onset. In summary, diversity of the epigenomic status in this disease was clearly outlined, pointing to the importance of taking in consideration this epigenetic heterogeneity when developing targeted therapies.
ES Cells/iPS Cells and the Control of Pluripotency
Rudolph Jaenisch, Whitehead Institute for Biomedical Research
There is one genome, but many epigenomes…Epigenetic changes drives cells back to pluripotent status and thus, the potential of ES cells might be used to generate customized tissue repair. Through extensive epigenetic reprogramming iPS cells re-establish the core of auto-regulatory loop. Although iPS cells offer an alternative to the polemic use of embryonic ES cells, we still will need them. Jaenisch presented new data showing that subtle changes in culture conditions could have a high impact on the epigenetic status in ES cells. In particular, the induction of x-chromosome inactivation, a tightly regulated event, could be triggered earlier as a response to stress, like oxygen levels. The epigenetic state of ES cells is highly affected by derivation and culture conditions, and this is still a technical issue to be resolved in the field. Along those lines, a new option for the of generation of virus-free stem cells is gene targeting by inducing double strand breaks in specific regions driven by zinc finger proteins. Natural repair mechanisms will allow the introduction of desired genes or to correct disease-causing mutations aimed to develop customized therapies.
The Effect of EBV Transformation on Genome-Wide Methylation
Karolina Aberg, Virginia Commonwealth University
The goal of this work was to investigate if EBV infection might alter methylation patterns in human lymphocytes, aiming to determine if EBV-infected samples, which represent a big portion of the human sample collection, can still be included in analysis for potential biomarkers. Genome-wide methylation was analyzed using human tiling arrays to compare 10 whole blood samples to 10 EBV-transformed samples from the same individuals. Aberg used MethylMiner to enrich for methylated sequences and applied “complex mixing Modeling Solutions” to the entire genome to discard changes in probes not likely related to methylation. Preliminary results showed high correlation between both groups in general, but when only methylated regions are studied, it’s clear that EBV infection alters methylation patterns. Therefore inclusion of those samples might be confounding.
Maternal High Gat Diet Induced Phenotypes Persist Across Generations
Greg Duhn, University of Pennsylvania
This was a very interesting lecture that brought us back to the topic of metabolic memory, this time with a widespread concern: fat content in the diet influencing body size and insulin resistance in future generations. Recent statistics have shown changes in height and obesity rates affecting entire populations in short periods of time. The speed and extent of those changes cannot be explained only by variation in genetic determinants. The effects of maternal high fat diet in mice results in increased body length across two generations of offspring. Moreover, transmission through the paternal line is associated with alterations in miRNA in the sperm. With the third generation in the making, this study is showing already promising and exciting results.
Regulation of Gene Expression by Natural Antisense Transcripts
Claes Wahlestedt, The Scripps Research Institute, Florida
This lecture was the highlight of the whole meeting. Dr. Wahlestedt presented detailed and extensive work on natural antisense transcripts and other long RNAs with regulatory functions in gene expression. These regulatory RNAs might provide better targets for therapy and drug discovery. The best example of concordant regulation was BACE-1 AS (antisense) in field of Alzheimer’s disease, a highly conserved natural transcript that regulates B-secretase expression. The analysis of 40 postmortem hippocampi from AD patients showed increased BACE-1 AS, which might represent a novel biomarker. A series of molecular mechanisms, including nuclear retention of the antisense transcript, shorter half-life of the antisense RNA, mRNA stabilization and masking/blocking of the miR485 binding site- involved in negative regulation of B-secretase- results in concordant increase of B-secretase expression and generation of AB 1-42 toxic fragments in the brain. While too much of BACE1-AS is not a desirable effect, elevation of ApoA1-AS on the contrary, might have beneficial effects. ApoA-I is a major component of HDL-C and lower levels of this protein are associated with risk to vascular disease. ApoA1 resides in a complex locus, and histone modifications appear to relate to ApoAI-AS expression. Wahlestedt’s group succeded in increasing ApoA-I AS after i.v. injections of oligonucleotides, producing a long lasting effect in boosting the protein levels in the circulation.
Coverage provided by Paula Desplats, Assistant Project Scientist in the Neurophatology Lab at the UC San Diego School of Medicine.