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 the brain, but their contribution to AD-associated DNAm changes has been poorly investigated. In this study we considered publicly available DNAm datasets of 4 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. We showed that DNAm differences between males and females tend to be shared between the 4 brain regions, while aging differently affects cortical regions compared to cerebellum. We found that the proportion of sex-dependent probes whose methylation changes also during aging is higher than expected, but that differences between males and females tend to be maintained, with only few probes showing sex-by-age 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 changes 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 conclusion, we demonstrated that age-associated, but not sex-associated DNAm concurs to the epigenetic deregulation observed in AD, providing new insight on how advanced age enables neurodegeneration.

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

“…Importantly, four of these were not previously reported in the context of EWAS using AD Braak stage or case-control status as phenotypes and can be considered bona fide novel findings of our study. Two CpGs (cg03169557 [near the genes RPL13 and SPG7] and cg05066959 [near the genes NKX6-3, ANK1, and MIR486]) were significantly associated with both AD case-control status and AD Braak stage and 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 (λ case-control = 1.16; λ Braak = 1.24; Supplementary Figure 4), a relatively common observation in 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). Next, we used the DMP test statistics to assess the presence of DMRs, i.e., consecutive runs of differentially methylated probes which are aggregated into "regions".…”

“…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 (7)(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).…”

Epigenetic age acceleration is associated with oligodendrocyte proportions in MSA and control brain tissue

“…Our results on the varied performances of the two clocks in different tissue types and regions within the brain further support the need for the development of specific clocks for different cell types and tissues as well as clocks specifically tailored in the context of brain ageing and disease as previously suggested [2,9]. Epigenetic age acceleration in specific brain regions has been reported in other neurodegenerative diseases such as AD and HD [4,34]; however, no studies exist on epigenetic age acceleration in the brain tissues for any of the α-synucleinopathies. Our rigorous multi-step analysis of the epigenetic clocks in the context of MSA demonstrates that although increased DNAm age acceleration differences were observed in multiple brain regions in the MSA group compared to controls with both epigenetic clocks, no statistical significance was observed upon adjustment for chronological age, neuronal/oligodendrocyte proportions, and duplicated individuals with multiple datapoints.…”

“…Epigenetic age acceleration in specific brain regions has been reported in other neurodegenerative diseases such as AD and HD [4, 34]; however, no studies exist on epigenetic age acceleration in the brain tissues for any of the α-synucleinopathies. Our rigorous multi-step analysis of the epigenetic clocks in the context of MSA demonstrates that although increased DNAm age acceleration differences were observed in multiple brain regions in the MSA group compared to controls with both epigenetic clocks, no statistical significance was observed upon adjustment for chronological age, neuronal/oligodendrocyte proportions, and duplicated individuals with multiple datapoints.…”