Altuna et al. Clinical Epigenetics (2019) 11:91 https://doi.org/10.1186/s13148-019-0672-7 RESEARCH Open Access DNA methylation signature of human hippocampus in Alzheimer’s disease is linked to neurogenesis Miren Altuna1,2, Amaya Urdánoz-Casado1, Javier Sánchez-Ruiz de Gordoa1,2, María V. Zelaya3, Alberto Labarga4, Julie M. J. Lepesant5, Miren Roldán1, Idoia Blanco-Luquin1, Álvaro Perdones4, Rosa Larumbe1,2, Ivonne Jericó2, Carmen Echavarri1,2, Iván Méndez-López1,6, Luisa Di Stefano5 and Maite Mendioroz1,2* Abstract Background: Drawing the epigenome landscape of Alzheimer’s disease (AD) still remains a challenge. To characterize the epigenetic molecular basis of the human hippocampus in AD, we profiled genome-wide DNA methylation levels in hippocampal samples from a cohort of pure AD patients and controls by using the Illumina 450K methylation arrays. Results: Up to 118 AD-related differentially methylated positions (DMPs) were identified in the AD hippocampus, and extended mapping of specific regions was obtained by bisulfite cloning sequencing. AD-related DMPs were significantly correlated with phosphorylated tau burden. Functional analysis highlighted that AD-related DMPs were enriched in poised promoters that were not generally maintained in committed neural progenitor cells, as shown by ChiP-qPCR experiments. Interestingly, AD-related DMPs preferentially involved neurodevelopmental and neurogenesis- related genes. Finally, InterPro ontology analysis revealed enrichment in homeobox-containing transcription factors in the set of AD-related DMPs. Conclusions: These results suggest that altered DNA methylation in the AD hippocampus occurs at specific regulatory regions crucial for neural differentiation supporting the notion that adult hippocampal neurogenesis may play a role in AD through epigenetic mechanisms. Keywords: DNA methylation, Alzheimer’s, Hippocampus, Adult neurogenesis, Poised promoters, Homeobox, Neurodevelopment, Epigenetics Background studying epigenetic alterations in AD to shed some light on Alzheimer’s disease (AD) is the leading cause of age-related the pathogenesis of the disease. DNA methylation is a dementia and one of the major global challenges of our major epigenetic modification that involves the attachment time [1]. As knowledge about AD increases, so does the ap- of a methyl group to the 5-carbon position of a cytosine preciation of the pathogenic complexity of the disorder [2]. residue and usually occurs at cytosine-guanine dinucleo- Currently, AD is considered a complex disease that arises tides (CpG). These CpG dinucleotides are clustered in the from the interaction between environmental and genetic genome constituting CpG islands, which are enriched in factors [3], modulated through epigenetic mechanisms. the promoter of more than half of human genes and other Since epigenetics acts as an interface between the environ- important regulatory regions. ment and the genome, a major focus has been upon DNA methylation is known to be altered in complex diseases including AD. Indeed, a number of gene-specific * Correspondence: [email protected]; [email protected] differences in DNA methylation have been reported so far 1Neuroepigenetics Laboratory, Navarrabiomed, Public University of Navarre [4–8]. More recently, genome-wide approaches have un- (UPNA), IdiSNA (Navarra Institute for Health Research), c/ Irunlarrea, 3, 31008 covered additional gene-specific methylation differences Pamplona, Spain 2Department of Neurology, Complejo Hospitalario de Navarra, IdiSNA across different brain regions in AD [9, 10]. By using Illu- (Navarra Institute for Health Research), Pamplona, Spain mina Infinium HumanMethylation450K arrays, several Full list of author information is available at the end of the article © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Altuna et al. Clinical Epigenetics (2019) 11:91 Page 2 of 16 genes have been found to be differentially methylated in estimated by using the CETS R package as previously AD brain autopsy samples, including some genes previ- described [14, 21]. No statistically significant differences ously identified as harboring genetic variants for AD, such were found in cell proportions between the AD group as ANK1 (ankyrin-1) or BIN1 (amphiphysin II) [11–14]. and the control group (control mean neuronal cell pro- Importantly, a number of these DNA methylation marks portion = 0.18 versus AD mean neuronal cell propor- are present in early stages of AD, suggesting that such tion = 0.20, p value = 0.64). changes might play a role in the onset of the disorder [12]. On the whole, these reports are providing significant data Characterization of differentially methylated positions in to enrich our understanding of AD pathogenesis [15, 16]. the AD hippocampus So far, genome-wide DNA methylation studies on AD Differential methylation analysis between the AD and have been performed across different brain regions in- control hippocampus was performed by using the cluding prefrontal, frontal, and superior temporal neo- limma package (R/Bioconductor). After adjusting for cortex, along with entorhinal cortex. In this study, we age and false discovery rate (FDR) correction, the ana- have taken a complementary strategy to profile lysis revealed 118 AD-related differentially methylated genome-wide DNA methylation in the human hippo- positions (DMPs) (absolute β-difference ≥ 0.1 and ad- campus, a brain region particularly vulnerable to AD justed p value ≤ 0.05) located next to 159 genes (Fig. 1, [17–19] and the core of pathological protein tau de- Table 1). Most of the DMPs, 102 (86.4%), were hyper- posits [20]. We have applied Infinium HumanMethyla- methylated in AD cases compared to controls (Fig. 2a– tion450 BeadChip array to hippocampal samples c). Inspection of methylation patterns revealed that obtained from a homogeneous cohort of pure AD AD-related DMPs showed a mild-to-moderate effect brains and controls. As a result, we report on novel size, as the average absolute β-difference was 0.12 (SD = gene-specific DNA methylation changes, recurrent 0.02) (Fig. 2b). These results are in line with previous across multiple affected subjects, which occur in the AD methylome studies, which showed recurrent gains AD hippocampus. This DNA methylation signature of in DNA methylation of a mild-to-moderate effect size the AD hippocampus correlates with tau burden and in other brain regions [9–14]. Indeed, up to 17 (10.7%) also with specific changes in histone marks. Finally, in differentially methylated genes in our study are found silico functional analysis of these changes points to mo- among the top-ranked genes in previous AD methy- lecular and biological alterations that may be especially lome studies performed on frontal, temporal, or ento- relevant to the pathogenesis of AD, including adult rhinal cortex [11, 12, 14](Additionalfile1:TableS2). brain neurogenesis. Genomic distribution of AD-related DMPs was next analyzed. We observed that DMPs were more likely to Results locate in CpG islands, showing a 1.5-fold enrichment (p Hippocampal samples from AD patients and controls value < 0.001) compared with random expectation based DNA methylation changes were evaluated in 36 post- on all probes included in the analysis. In addition, sig- mortem hippocampal samples obtained from 26 pa- nificant enrichment was found at first exon (2.4-fold, p tients with AD and 12 control subjects. To avoid value < 0.001) and body (1.2-fold, p value < 0.05) regions spurious molecular findings related to multiprotein de- (Fig. 2d). Moreover, up to 13 (8.1%) genes were associ- posits, only AD cases with pure deposits of p-tau and ated with 2 or more AD-related DMPs which would sug- β-amyloid were eligible for the study and controls were gest the presence of hotspots of aberrant methylation free of any protein aggregates. This approach maxi- gain in the human hippocampus affected by AD. mizes the chances of finding true molecular associa- tions with AD, even though reducing the number of Validation and additional mapping of DMPs older controls. Among the 118 AD-related DMPs, we selected 7 DMPs Neuropathological and demographic features of sub- to be validated based on their genomic location in or jects, including age, gender, ABC score, and postmortem near genes relevant to brain function or AD pathology, interval (PMI), are listed in Additional file 1: Table S1. including some of the candidate hotspots, i.e., HAND2, AD subjects were older than controls (81.2 ± 12.1 versus HOXA3, HIST1H3E, NXN, PAX3, RBMS1,andRHOB. 50.7 ± 21.5; p value< 0.01), and no differences were All the selected genes were successfully validated by bi- found regarding gender (p value = 0.16). The PMI ranged sulfite cloning sequencing since a significant correlation from 1.4 to 33 h and were not significantly different be- was shown between the 450K array data and methyla- tween groups (8.2 ± 4.2 h in controls versus 7.9 ± 7.1 h in tion levels obtained by bisulfite cloning sequencing