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Genome-wide DNA methylation profiling in nonagenarians suggests an effect of PM20D1 in late onset Alzheimer’s disease

Published online by Cambridge University Press:  16 December 2021

Carolina Coto-Vílchez
Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
José J. Martínez-Magaña
Instituto Nacional de Medicina Genómica, Mexico City, México
Lara Mora-Villalobos
Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
Daniel Valerio
Hospital Nacional de Geriatría y Gerontología de Costa Rica, San José, Costa Rica
Alma D. Genis-Mendoza
Instituto Nacional de Medicina Genómica, Mexico City, México
Jeremy M. Silverman
Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
Humberto Nicolini
Instituto Nacional de Medicina Genómica, Mexico City, México
Henriette Raventós
Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
Gabriela Chavarria-Soley*
Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
* Author for correspondence: Gabriela Chavarria-Soley, Email:



The aim of this study is to identify differentially methylated regions (DMRs) in the genomes of a sample of cognitively healthy individuals and a sample of individuals with LOAD, all of them nonagenarians from Costa Rica.


In this study, we compared whole blood DNA methylation profiles of 32 individuals: 21 cognitively healthy and 11 with LOAD, using the Infinium MethylationEPIC BeadChip. First, we calculated the epigenetic age of the participants based on Horvath’s epigenetic clock. DMRcate and Bumphunter were used to identify DMRs. After in silico and knowledge-based filtering of the DMRs, we performed a methylation quantitative loci (mQTL) analysis (rs708727 and rs960603).


On average, the epigenetic age was 73 years in both groups, which represents a difference of over 20 years between epigenetic and chronological age in both affected and unaffected individuals. Methylation analysis revealed 11 DMRs between groups, which contain six genes and two pseudogenes. These genes are involved in cell cycle regulation, embryogenesis, synthesis of ceramides, and migration of interneurons to the cerebral cortex. One of the six genes is PM20D1, for which altered expression has been reported in LOAD. After genotyping previously reported mQTL SNPs for the gene, we found that average methylation in the PM20D1 DMR differs between genotypes for rs708727, but not for rs960603.


This work supports the possible role of PM20D1 in protection against AD, by showing differential methylation in blood of affected and unaffected nonagenarians. Our results also support the influence of genetic factors on PM20D1 methylation levels.

Original Research
© The Author(s), 2021. Published by Cambridge University Press

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