CpG and non-CpG Presenilin1 methylation pattern in course of neurodevelopment and neurodegeneration is associated with gene expression in human and murine brain

ABSTRACT

The Presenilin1 (PSEN1) gene encodes the catalytic peptide of the γ-secretase complex, a key enzyme that cleaves the amyloid-β protein precursor (AβPP), to generate the amyloid-β (Aβ) peptides, involved in Alzheimer’s Disease (AD). Other substrates of the γ-secretase, such as E-cadherin and Notch1, are involved in neurodevelopment and haematopoiesis. Gene-specific DNA methylation influences PSEN1 expression in AD animal models. Here we evaluated canonical and non-canonical cytosine methylation patterns of the PSEN1 5ʹ-flanking during brain development and AD progression, in DNA extracted from the frontal cortex of AD transgenic mice (TgCRND8) and post-mortem human brain. Mapping CpG and non-CpG methylation revealed different methylation profiles in mice and humans. PSEN1 expression only correlated with DNA methylation in adult female mice. However, in post-mortem human brain, lower methylation, both at CpG and non-CpG sites, correlated closely with higher PSEN1 expression during brain development and in disease progression. PSEN1 methylation in blood DNA was significantly lower in AD patients than in controls. The present study is the first to demonstrate a temporal correlation between dynamic changes in PSEN1 CpG and non-CpG methylation patterns and mRNA expression during neurodevelopment and AD neurodegeneration. These observations were made possible by the use of an improved bisulphite methylation assay employing primers that are not biased towards non-CpG methylation. Our findings deepen the understanding of γ-secretase regulation and support the hypothesis that epigenetic changes can promote the pathophysiology of AD. Moreover, they suggest that PSEN1 DNA methylation in peripheral blood may provide a biomarker for AD.

KEYWORDS:

• Presenilin1
• DNA methylation
• non-CpG methylation
• MIPs (non-CpG Methylation-Insensitive Primers)
• Alzheimer’s Disease
• neurodevelopment
• neurodegeneration

Author’s contribution

AF, NM, VN, and RAC performed the experiments with animals, the mRNA expression, and the DNA methylation studies. ML, AS and FC contributed to the DNA methylation analysis and to the mRNA expression analysis in blood. MTF and GGK performed the immunohistochemical analyses. IF, FC and EA contributed to the collection of tissue samples. The overall experimental design was conceived and supervised by AF, AMT, and SS. AMT and AF prepared the manuscript for submission. All authors read and approved the final manuscript.

Acknowledgments

The authors are grateful to Viviana Ciraci, Ph.D. and to Giampiero Palladino, Ph.D., for the help with the experimental procedures. The authors would also like to thank Dr Alessandro Giuliani at Istituto Suoeriore di Sanità, Rome, Italy, for the great help with the execution of the statistical analysis.

Disclosure statement

No potential conflict of interest was reported by the authors.

Ethics approval and consent to participate

Work on human subjects:

Adult post-mortem brains used in the present study were obtained from the Institute of Neuropathology and Brain Bank (HUB-ICO-IDIBELL Biobank) following the guidelines of the Declaration of Helsinki, and according to the Spanish and Catalonian Autonomous regulations on this matter, and the approval of the local Ethics Committee of the Bellvitge University Hospital.

Embryonic and young post-mortem brains used in this study were obtained from the AMC, University of Amsterdam, and used in accordance with the Declaration of Helsinki and the AMC Research Code provided by the Medical Ethics Committee. The local ethical committees of all participating centres gave permission to undertake the study.

Blood samples were obtained from the University of Pisa (details can be found in reference) [25]. The Ethics Committee of the Pisa University Hospital approved the study (Protocol number 3618/2012) that was performed in accordance with the Declaration of Helsinki.

Work on animals:

Wild-type and transgenic animals used in the present study were bred at the Sapienza University of Rome. All procedures were carried in accordance with the European Communities Council Directive (86/609/EEC 2010/63/EU) and approved by the Italian Ministry of Health and by the local ethical committee.

Supplementary material

Supplemental data for this article can be accessed here.

Availability of data and material

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

Additional information

Funding

This study was funded by: the Seventh Framework Program of the European Commission (Grant No. 278486 [DEVELAGE project] to SS, IF, EA, GGK); the Spanish Ministry of Health, Instituto Carlos III (Fondo de Investigación Sanitaria [FIS] PI1100968, FIS PI14/00757), and CIBERNED project BESAD-P to IF; the Italian Ministry of Health (GR-2009-1606229 to FC)