A Meta-Analysis of Brain DNA Methylation Across Sex, Age, and Alzheimer's Disease Points for Accelerated Epigenetic Aging in Neurodegeneration

Abstract

Alzheimer's disease (AD) is characterized by specific alterations of brain DNA methylation (DNAm) patterns. Age and sex, two major risk factors for AD, are also known to largely affect the epigenetic profiles in brain, but their contribution to AD-associated DNAm changes has been poorly investigated. In this study we considered publicly available DNAm datasets of four brain regions (temporal, frontal, entorhinal cortex, and cerebellum) from healthy adult subjects and AD patients, and performed a meta-analysis to identify sex-, age-, and AD-associated epigenetic profiles. In one of these datasets it was also possible to distinguish 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) profiles. We showed that DNAm differences between males and females tend to be shared between the four brain regions, while aging differently affects cortical regions compared to cerebellum. We found that the proportion of sex-dependent probes whose methylation is modified also during aging is higher than expected, but that differences between males and females tend to be maintained, with only a few probes showing age-by-sex interaction. We did not find significant overlaps between AD- and sex-associated probes, nor disease-by-sex interaction effects. On the contrary, we found that AD-related epigenetic modifications are significantly enriched in probes whose DNAm varies with age and that there is a high concordance between the direction of changes (hyper or hypo-methylation) in aging and AD, supporting accelerated epigenetic aging in the disease. In summary, our results suggest that age-associated DNAm patterns concur to the epigenetic deregulation observed in AD, providing new insights on how advanced age enables neurodegeneration.

Entorhinal cortex epigenome-wide association study highlights four novel loci showing differential methylation in Alzheimer’s disease

“…CpGs in the AD case-control meta-analysis (Figure 1, Table 3), and nine CpGs in the Braak stage meta-analysis (Figure 2, Table 4), reached experiment-wide significance, four of which were not previously reported as AD EWAS signals. Two CpGs (cg03169557 and cg05066959) were significantly associated with both AD case-control status and AD Braak stage and both were already described in previous DNAm AD studies 8,[15][16][17] . While none of the analyses in the individual datasets analyses showed notable inflation in the test statistics (Supplementary Table 4), both meta-analyses displayed slightly increased inflation (λcase-control = 1.16; λBraak = 1.24; Supplementary Figure 4), a common observation of EWAS as already noted in Smith et al 17 .…”

“…Among these, cg25191519 showed a particularly strong association signal (P = 8.90E-06). This CpG is annotated to the genes SPG7 and RPL13, which were already reported in previous AD DNAm studies 8,[15][16][17] . Among the other suggestive association signals were also the following genes which are highlighted here owing to their moderate to high expression levels in brain tissues according to GTEx V8: MGAT3, MIEF1, VRK1, PAPOLA, PLD5, and CEP170…”

“…One of the most widely studied epigenetic marks is DNA methylation (DNAm) owing to the relative technical ease to generate these data on a(n) (epi)genome-wide scale. Since 2014, this has led to a number of epigenome-wide association studies (EWAS) assessing DNAm profiles in various AD-related phenotypes 6,[8][9][10][11][12][13][14][15][16] , culminating in a very recent meta-analysis on differential DNAm across various brain datasets 17 . Taken together, these studies identified several genomic loci (e.g., ANK1, RPL13, SPG7, and MCF2L) showing consistent changes in DNAm patterns associated with AD related phenotypes across several brain regions (e.g., EC as well as temporal and prefrontal cortex).…”

DNA Methylation in Genetic and Sporadic Forms of Neurodegeneration: Lessons From Alzheimers, Related Tauopathies and Genetic Tauopathies

“…Similar to the aging brain, global DNA hypomethylation was reported for AD, supported by decreased immunoreactivity for 5-methylcytosine (5-mC) in cortical neurons of postmortem AD brains compared to controls [84]. Reduced levels of 5mC were observed in the hippocampus, entorhinal and prefrontal cortex, as well as in the cerebellum of patients with AD [84][85][86]). In line with this, Mastroeni et al (2010) found weak staining with antibodies directed against DNA methylation maintenance factors in hippocampal tissue of AD patients compared to normal brains.…”

Sex-Specific Age-Related Changes in Methylation of Certain Genes

“…Probes lying on sex chromosomes, cross-reactive probes, and probes with SNPs according to list [13] were excluded from dataset. Since many early studies [14,15] report about gender-specific in methylation, we examined the subsets of males and females separately. Gene ontology analysis was performed for 3 groups (females, males, and duplicates) genes using PANTHER database [16].…”