Deep sequencing reveals increased DNA methylation in chronic rat epilepsy

Abstract

Epilepsy is a frequent neurological disorder, although onset and progression of seizures remain difficult to predict in affected patients, irrespective of their epileptogenic condition. Previous studies in animal models as well as human epileptic brain tissue revealed a remarkably diverse pattern of gene expression implicating epigenetic changes to contribute to disease progression. Here we mapped for the first time global DNA methylation patterns in chronic epileptic rats and controls. Using methyl-CpG capture associated with massive parallel sequencing (Methyl-Seq) we report the genomic methylation signature of the chronic epileptic state. We observed a predominant increase, rather than loss of DNA methylation in chronic rat epilepsy. Aberrant methylation patterns were inversely correlated with gene expression changes using mRNA sequencing from same animals and tissue specimens. Administration of a ketogenic, high-fat, low-carbohydrate diet attenuated seizure progression and ameliorated DNA methylation mediated changes in gene expression. This is the first report of unsupervised clustering of an epigenetic mark being used in epilepsy research to separate epileptic from non-epileptic animals as well as from animals receiving anti-convulsive dietary treatment. We further discuss the potential impact of epigenetic changes as a pathogenic mechanism of epileptogenesis.Electronic supplementary materialThe online version of this article (doi:10.1007/s00401-013-1168-8) contains supplementary material, which is available to authorized users.

Epileptogenesis

“…Although there are studies showing altered DNA methylation of individual genes during the latent period as well as during the chronic phase, large-scale profiling data are not available on epigenome modifications in epileptogenesis (Pitkänen and Lukasiuk 2011;Kobow et al 2013;Kobow and Blümcke 2014). The only data on global changes in DNA methylation in epilepsy come from the work of Kobow et al (2013), who found alterations in DNA methylation patterns in chronically epileptic rats in the pilocarpine model of TLE. There are, however, few "omics" datasets describing alterations in miRNA expression during epileptogenesis (Table 3), indicating that, similar to mRNA, changes in miRNA expression are dynamic and time dependent.…”

The ketogenic diet for the treatment of malignant glioma

“…A recent study suggests that ␤ -hydroxybutyrate, the major ketone that is increased in the blood in animals and patients on the UKD, can alter the epigenetic landscape in mammalian cells by inhibiting histone deacetylase ( 65 ). Another study showed that the UKD reversed the major epigenetic modifi cations found in the brains of epileptic rats ( 66 ). While the effect of the KD on tumor epigenetics has yet to be studied directly, evidence warrants further exploration.…”

The New Ketone Alphabet Soup: BHB, HCA, and HDAC

“…Neither study provides direct evidence in this regard, but based on emerging lines of research (1, 2, 7), both strongly indicate that BHB (and by extension, the KD) could influence the epileptic state. In support of this, the KD has recently been shown to affect epigenetic changes in epileptic brain (17) and is also proving useful in patients with neuroinflammation-related epilepsy (18). With respect to neuroprotection, there are indeed many other KD-related mechanisms that likely play a role (3), such as ketone-mediated inhibition of vesicular glutamate release (19).…”