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SfN 2011—Lessons From a Tumor: Cancer Research Foreshadows CNS Epigenetics

7 December 2011. Heritability is no longer just about DNA. A large body of research implicates epigenetic alterations—mitotically heritable changes that control gene activity without altering the DNA sequence—in a number of major illnesses, including schizophrenia. The role of epigenetics in disease was the subject of a 15 November 2011 Presidential Special Lecture at the 41st annual Society for Neuroscience Meeting by Andrew Feinberg of Johns Hopkins University School of Medicine in Baltimore, Maryland. Feinberg’s talk, entitled “The Epigenetic Basis of Common Human Disease,” detailed a role for alterations in DNA methylation in cancer, and discussed interesting issues that may be relevant to schizophrenia research.

Epigenetics is the study of non-sequence, heritable information in DNA and chromatin. A major epigenetic mechanism is DNA methylation, the transfer of a methyl group to a cytosine residue at the dinucleotide sequence CpG (adjacent cytosine and guanine nucleotides on the same DNA strand connected by a phosphodiester bond) that generally leads to gene repression. In general, CpG sites are heavily methylated, although clusters of CpG sites (termed CpG islands) at promoter regions tend to be less methylated. Substantial evidence points to a role for epigenetic alterations in psychiatric illness (see SRF Current Hypothesis paper by Dennis Grayson, as well as an interview with Art Petronis), and studies suggest that epigenetics may, at least in part, account for the high discordance for schizophrenia among identical twins. For example, a recent twin study has demonstrated altered DNA methylation patterns associated with schizophrenia (see SRF related news story).

In his talk, Feinberg pointed out that heart and brain tissue are very different, despite carrying the same DNA sequence, and that such differences may be mediated by epigenetic mechanisms. In an attempt to elucidate the role of DNA methylation in these differences, Feinberg determined regions of the genome that are differentially methylated across tissue types. Using a novel technique they dubbed CHARM, which stands for “comprehensive high-throughput arrays for relative methylation” (Irizarry et al., 2008), Feinberg’s group identified over 16,000 regions in the genome that contained DNA methylation differences among brain, liver, and spleen tissue (Irizarry et al., 2009). This novel technique is notable for its agnostic approach regarding the location of genes and CpG content, and thus the ability to explore DNA methylation in regions beyond the usually studied CpG islands (which are generally enriched on arrays owing to their high CpG content). In fact, the majority of tissue-specific methylation was not found in CpG islands, but in adjacent regions (within 2 kb), termed “CpG island shores” (Irizarry et al., 2009). These data suggest that the popular CpG island-centered approach for hunting epigenetic changes in disease may need to be reconsidered (Jones and Baylin, 2007), a point that may also be applicable to schizophrenia methylomic studies. For example, in a 2011 study by Dempster and colleagues (Dempster et al., 2011), the top psychosis-associated methylation site identified was not located within a CpG island.

Feinberg also discussed his work examining colon cancer-related changes in DNA methylation using CHARM. Specifically, he detailed his finding that many of the regions that exhibit altered methylation in cancer (cancer-specific differentially methylated regions, or cDMRs) also show methylation differences among tissue types (Irizarry et al., 2009). Additionally, these same cDMRs are differentially methylated during stem cell reprogramming of induced pluripotent stem cells (Doi et al., 2009), suggesting that the sequences that govern the differentiation of disparate tissues are also altered in cancer. Moreover, the cDMRs are not just specific to colon cancer: the same regions are also differentially methylated in a variety of cancers including those of the breast, lung, and thyroid, which is suggestive of a general disruption of the cancer methylome (Hansen et al., 2011). Especially of interest, in contrast to the low variability in methylation levels observed in normal tissue, these regions exhibit high levels of stochastic variation in methylation levels within each cancer type (Hansen et al., 2011). The most variable cDMRs are located within genes implicated in tumor heterogeneity and progression. If epigenetic variation plays a role in cancer, could it also be involved in schizophrenia? Ongoing studies by Feinberg’s and other labs examining methylation variability in schizophrenia may answer that question.—Allison A. Curley.

Comments on Related News

Related News: Epigenetic Forces May Blaze Divergent Heritable Paths From Same DNA

Comment by:  Shiva SinghRichard O'Reilly
Submitted 2 February 2009
Posted 3 February 2009

The methylation difference between twins is clearly demonstrated using newer methods in this publication. However, conceptually it’s an old story now. A quick PubMed search for "monozygotic twins and non-identical" yielded a total of 7,653 publications. There is no doubt that the more we look, the more difference we will find between monozygotic twins. Also, monozygotic twin differences in methylation and gene expression are expected to increase with age. It is also affected by a variety of genetic and environmental factors. We have come a long way in genetic research on twins and the time has come to modify our thinking about monozygotic twins as "non-identical but closest possible" rather than as "identical." They started from a single zygote, but have diverged during development and differentiation including upbringing.

The implication of the published results is that the methylation (epigenetic) differences (in monozygotic twins) will be powerful in any genetic analysis of disease(s). Once again, it is probably more problematic than usually assumed. Also, it is particularly problematic for behavioral/psychiatric disorders including schizophrenia. The reason is multi-fold and includes the effect of (known and unknown) environment including pregnancy, upbringing, drugs, life style, food, etc. All these are known to affect DNA methylation and gene expression. As a result, they add unavoidable confounding factors to the experimental design. It does not mean that epigenetics is not involved in these diseases. Rather, directly establishing a role for methylation in schizophrenia will be challenging. A special limitation is the fact that methylation is known to be cell-type specific, and perfectly matched affected and normal (twin) human brain (region) samples for necessary experiments are problematic and methylation studies on other cell types may or may not be informative.

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Related News: Twins Tell Story of Epigenetic Alterations in Schizophrenia and Bipolar Disorder

Comment by:  Schahram Akbarian
Submitted 7 October 2011
Posted 7 October 2011

The genetic risk architecture is still very difficult to "capture" for a large majority of patients diagnosed with schizophrenia or related diseases. Therefore, studies like that of Dempster et al., who profiled DNA methylation (a type of "epigenetic" modification of cytosine that residues mostly at sites of CpG dinucleotides in the genome) in blood cells of monozygotic twins discordant for schizophrenia, provide an important additional layer of information. The idea is that the disease process in the affected twin leaves behind a molecular signature (in the study by Dempster et al., this would be a change in DNA methylation) that is not found in the healthy twin, with the implication that this signal is related to disease etiology or disease process and treatment, etc.

Dempster and colleagues screened approximately 20 twin pairs. I believe the Illumina bead system they used probes primarily annotated promoters; on a genomewide level, they found, overall, quite subtle changes. One of the more prominent findings is hypomethylation of one specific CpG dinucleotide associated with ST6GALNAC1, a gene regulating protein glycosylation, with additional changes in a dozen or so genes. Hypomethylation of ST6GALNAC1 (which the authors further verified in postmortem brains of subjects with schizophrenia) at sequences proximal to promoters is generally associated with increased expression, but it is not clear if this is the case in the twin blood or the postmortem brain. Interestingly, as the authors point out, the same gene (ST6GALNAC1) may harbor an excess copy in some subjects on the psychosis spectrum. This is a good example of the possibility that some of the genes that are potentially linked to psychosis because of DNA sequence and copy number changes may also show up in epigenetic studies such as that of Dempster and colleagues. Whether a genetic variation or mutation somewhere else in the genome "drives" the epigenetic changes at ST6GALNAC1 and other genes is, of course, hard to prove.

The most important challenge to the epigenetics and psychosis fields is, at least in my opinion, that of reproducibility and independent replication. In other words, will we be able to replicate, in independent studies, epigenetic alterations in blood or postmortem brain tissue, reported to be "highly significant" for cohorts comprising a few dozen or fewer cases? With fewer than five published studies (to the best of my knowledge) that measured DNA methylation on a genomewide scale in mood and psychosis spectrum disorders, it is still hard to predict whether DNA and histone modification mapping will provide valuable clues to the underlying neurobiology of disease. I take an optimistic view, and would like to predict that DNA methylation and histone modification mapping will provide a very important additional layer of information when paired with whole-genome sequencing and transcriptome (RNA expression) profiling.

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