Early epigenetic changes of Alzheimer’s disease in the human hippocampus

ABSTRACT

The discovery of new biomarkers would be very valuable to improve the detection of early Alzheimer’s disease (AD). DNA methylation marks may serve as epigenetic biomarkers of early AD. Here we identified epigenetic marks that are present in the human hippocampus from the earliest stages of AD. A previous methylome dataset of the human AD hippocampus was used to select a set of eight differentially methylated positions (DMPs) since early AD stages. Next, bisulphite pyrosequencing was performed in an expanded homogeneous cohort of 18 pure controls and 35 hippocampal samples with neuropathological changes of pure AD. Correlation between DNA methylation levels in DMPs and phospho-tau protein burden assessed by immunohistochemistry in the hippocampus was also determined. We found four DMPs showing higher levels of DNA methylation at early AD stages compared to controls, involving ELOVL2, GIT1/TP53I13 and the histone gene locus at chromosome 6. DNA methylation levels assessed by bisulphite pyrosequencing correlated with phospho-tau protein burden for ELOVL2 and HIST1H3E/HIST1H3 F genes. In this discovery study, a set of four epigenetic marks of early AD stages have been identified in the human hippocampus. It would be worth studying in-depth the specific pathways related to these epigenetic marks. These early alterations in DNA methylation in the AD hippocampus could be regarded as candidate biomarkers to be explored in future translational studies.

Abbreviations

AD: Alzheimer’s disease; DMPs: Differentially methylated positions; CSF: Cerebrospinal fluid; βA42: β-amyloid 42; PET: positron emission tomography; 5mC: 5-methyl cytosine; CpG: cytosine-guanine dinucleotides; ANK1: ankyrin-1; BIN1: amphiphysin II; p-tau: hyperphosphorylated tau; CERAD: Consortium to Establish A Registry for Alzheimer’s Disease; SD: standard deviation; ANOVA: one-way analysis of variance; VLCFAs: very long-chain fatty acids; DHA: docosahexaenoic acid; mTOR: mechanistic target of rapamycin.

KEYWORDS:

• Early Alzheimer’s disease
• hippocampus
• epigenetics
• biomarkers
• DNA methylation
• ELOVL2
• GIT1
• histone
• fatty acid

Acknowledgments

We want to kindly thank Teresa Tuñón M.D., Ph.D (Department of Pathology, Complejo Hospitalario de Navarra, technical support), Federico García-Bragado M.D., Ph.D (Department of Pathology, Complejo Hospitalario de Navarra, technical support), and Isabel Gil M.D., Ph.D (Navarrabiomed BrainBank, technical support) for their help. Finally, we are very grateful to the patients and relatives that generously donor the brain tissue to the Navarrabiomed Brain Bank.

Authors’ contributions

IBL contributed to data collection, analysis of data, statistical analysis, and drafting/revising the manuscript for content. BA contributed to running experiments, acquisition, and interpretation of data and revising the manuscript for content. AUC contributed to data analysis, figure drawing, and drafting/revising the manuscript for content. JSR contributed to analysis and interpretation of data (p-tau deposits), sorting of patients into different ABC stages and acquisition of image data. JV contributed to acquisition of data, figure drawing and revising the manuscript for content. MRA contributed to drawing figures, performed bisulfite pyrosequencing experiments, and was involved in interpretation of data. AL contributed to bioinformatics analysis and drafting the manuscript. MVZ participated in revising subject diagnosis, classification of patients, and contributed to drafting/revising the manuscript for content. CC contributed to data collection, diagnosis of subjects and revising the manuscript for content. IM contributed to study concept and design, literature searching, and drafting/revising the manuscript for content. MM contributed to study concept and design, data collection, interpretation and analysis, statistical analysis, drafting/revising the manuscript for content, study supervision, and obtaining funding.

Disclosure statement

The authors report no conflict of interest.

Ethics approval and consent to participate

This study was carried out in accordance with the principles of the Declaration of Helsinki and handling of human brain samples was performed according to the current Spanish national legislation (Royal Decree RD1716/2011). Written informed consent was obtained from all subjects or next of kin. The study was approved by the Ethics Committee of the Complejo Hospitalario de Navarra and the Scientific Committee of Navarrabiomed Brain Bank, Spain.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

This work was supported by the European Regional Development Fund; Instituto de Salud Carlos III [FIS PI13/02730 and PI17/02218]; ‘la Caixa’ Foundation (ES); PRECIPITA platform (Spanish foundation for science and technology-FECYT); Fundación Caja-Navarra; The Basque Foundation for Health Innovation and Research [BIO12/ALZ/007]; Trans-Pyrenean Biomedical Research Network (REFBIOI and REFBIOII); Spanish Government [PFIS fellowship FI18/00150]; Government of Navarra [Doctorados industriales 2018-2020]; ‘la Caixa’ Foundation and Fundación Caja-Navarra [Programa de intensificación].