Parallel profiling of DNA methylation and hydroxymethylation highlights neuropathology-associated epigenetic variation in Alzheimer's disease

Adam R. Smith, Rebecca G. Smith, Ehsan Pishva, Eilis Hannon, Janou A. Y. Roubroeks, Joe Burrage, Claire Troakes, Safa Al-Sarraj, Carolyn Sloan, Jonathan Mill, Daniel L. van den Hove, Katie Lunnon*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

47 Citations (Web of Science)

Abstract

Background: Alzheimer's disease is a progressive neurodegenerative disorder that is hypothesized to involve epigenetic dysfunction. Previous studies of DNA modifications in Alzheimer's disease have been unable to distinguish between DNA methylation and DNA hydroxymethylation. DNA hydroxymethylation has been shown to be enriched in the human brain, although its role in Alzheimer's disease has not yet been fully explored. Here, we utilize oxidative bisulfite conversion, in conjunction with the Illumina Infinium Human Methylation 450K microarray, to identify neuropathology-associated differential DNA methylation and DNA hydroxymethylation in the entorhinal cortex.

Results: We identified one experiment-wide significant differentially methylated position residing in the WNT5B gene. Next, we investigated pathology-associated regions consisting of multiple adjacent loci. We identified one significant differentially hydroxymethylated region consisting of four probes spanning 104 bases in the FBXL16 gene. We also identified two significant differentially methylated regions: one consisting of two probes in a 93 base-pair region in the ANK1 gene and the other consisting of six probes in a 99-base pair region in the ARID5B gene. We also highlighted three regions that show alterations in unmodified cytosine: two probes in a 39-base pair region of ALLC, two probes in a 69-base pair region in JAG2, and the same six probes in ARID5B that were differentially methylated. Finally, we replicated significant ANK1 disease-associated hypermethylation and hypohydroxymethylation patterns across eight CpG sites in an extended 118-base pair region in an independent cohort using oxidative-bisulfite pyrosequencing.

Conclusions: Our study represents the first epigenome-wide association study of both DNA methylation and hydroxymethylation in Alzheimer's disease entorhinal cortex. We demonstrate that previous estimates of DNA hypermethylation in ANK1 in Alzheimer's disease were underestimates as it is confounded by hypohydroxymethylation.

Original languageEnglish
Article number52
Number of pages13
JournalClinical epigenetics
Volume11
DOIs
Publication statusPublished - 21 Mar 2019

Keywords

  • Alzheimer's disease (AD)
  • Brain
  • Ankyrin 1 (ANK1)
  • DNA methylation (5mC)
  • DNA hydroxymethylation (5hmC)
  • Entorhinal cortex (EC)
  • Epigenetics
  • Epigenome-wide association study (EWAS)
  • Illumina Infinium Human Methylation 450K microarray (450K array)
  • COMMON VARIANTS
  • 5-HYDROXYMETHYLCYTOSINE
  • PATHWAY
  • ANK1
  • SOFTWARE
  • CD2AP
  • EPHA1
  • CD33

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