Epigenetic mechanisms in Alzheimer's disease

Abstract

Epigenetic modifications help orchestrate sweeping developmental, aging, and disease-causing changes in phenotype by altering transcriptional activity in multiple genes spanning multiple biologic pathways. Although previous epigenetic research has focused primarily on dividing cells, particularly in cancer, recent studies have shown rapid, dynamic, and persistent epigenetic modifications in neurons that have significant neuroendocrine, neurophysiologic, and neurodegenerative consequences. Here, we provide a review of the major mechanisms for epigenetic modification and how they are reportedly altered in aging and Alzheimer's disease (AD). Because of their reach across the genome, epigenetic mechanisms may provide a unique integrative framework for the pathologic diversity and complexity of AD.

Fig. 1. Simplified schematic of histone acetylation and DNA methylation

(Upper Left) In transcriptionally active genes the chromatin, made up of histones (blue cylinders) around which DNA is wrapped, is in a relaxed state, permitting transcriptional access to unwound DNA. This relaxed, euchromatin state is, in part, mediated by acetylation of histone tails (red rods) in which acetyl groups (green blocks) are transferred from acetyl-coenzyme A (acetyl-CoA) to the histone tails by histone acetyltransferases (HATs). (Bottom Left) Within the DNA, the cytosines of adjacent C-G/G-C dinucleotides (CpGs) may be methylated. The methyl group ultimately derives from methyltetrahydrofolate in conjunction with the methionine/homocysteine cycle, and is transferred from S-adenosylmethionine (SAM) to the cytosine and incorporated into the genome by DNA methyltransferases (DNMTs). CpG-methyl-binding-domain proteins (MBDs) and methylation complex proteins (MeCPs) (which may contain MBDs) become associated with methylated CpGs, further inhibiting transcriptional access and repression of the gene. (Upper Right). DNA methylation and histone modifications are integrally linked, because MBDs and MeCPs attract histone deacetylases (HDACs) that transfer acetyl groups on the histone tail back to CoA. Histone deacetylation, in turn, promotes the condensed, heterochromatin state characteristic of silenced or repressed genes.

Fig. 2. DNA methylation markers in AD and ND cortex

A) Typical immunoreactivity for 5-methylcytosine, a global marker of DNA methylation, in AD and ND entorhinal cortex (from Mastroeni et al., 2008, with permission). Cases were well matched for age, gender, and postmortem intervals, which were all less than 3 hours 15 minutes. Shaded bars represent means for different cases. Although glia and virtually all types of neurons exhibit 5-methylcytosine immunoreactivity, layer II “island” neurons, among the most vulnerable to AD pathology, exhibit particularly intense staining in ND cases, as shown in the upper left micrograph at low power. Such staining is weak to absent in AD cases (upper right micrograph). High power micrographs show the expected nuclear localization of immunoreactivity. Far right panel shows counts of immunoreactive neurons per total neurons per field. Normalizing to total neurons is important, as it helps to demonstrate loss of methylation within cell nuclei rather than loss of the methylated cell population itself. The significant decrement in AD (P < 0.001) is typical of dozens of AD and ND cases examined, with little to no overlap in any case. B) Representative immunoreactivity and cell counts for various MeCP1 components in AD and ND neocortex. Significant AD decrements (P < 0.05) were observed with all the markers—again with little to no overlap. C) Western blots (normalized to β-actin) for these and other methylation markers exhibit immunoreactivity at appropriate molecular weights, with AD/ND differences similar to those observed by immunohistochemistry, suggesting that the latter are not due to cross-reactivity with other antigens.

Fig. 3. Immunoreactivity for DNMT1, the most prevalent methyltransferase in adult mammals

A) Typical DNMT1 immunoreactivity and cell counts (P < 0.001) in AD and ND neocortex. Shaded bars represent means for different cases. B) Western blots (normalized to β-actin standards) show immunoreactive bands at appropriate molecular weights for DNMT1 and a significant (P < 0.01) decrement in AD cases.

Fig. 4. Decreased overall DNA methylation in monozygotic twins discordant for AD

A) Global hypomethylation (5-methylcytosine immunoreactivity) in an AD monozygotic twin compared to his normal sibling at low (upper micrographs) and high (bottom micrographs) power (Mastroeni et al., 2009) (courtesy of PLoS1). B) Similar findings have recently been observed by our group in APP transgenic mice compared to their wildtype littermates.

Fig. 5. MethylMiner methylation profile of selected flanking and initial BACE promoter sites after exposure of differentiated SK-N-BE(2) neuron-like cultures to 10 μM Aμ42

MethylMiner Methylated DNA Enrichment Kits (Invitrogen, Carlsbad, CA) were employed to enrich and fractionate double-stranded DNA based on CpG methylation density. The highly methylated region showed significant hypomethylation while poorly methylated regions exhibited hypermethylation (Grover et al., unpublished). Correlations with Aβ production can help establish the functional relevance of methylation modifications at these and other CpG sites within the BACE gene.