A meta-analysis on age-associated changes in blood DNA methylation: results from an original analysis pipeline for Infinium 450k data.

Maria Giulia Bacalini,Enrico Giampieri,Cristina Giuliani,Alessio Boattini,Daniel Remondini,Claudio Franceschi,Davide Gentilini,Stefano Salvioli,Miriam Capri,Alberto Del Rio,Chiara Pirazzini,Elisa Fontanesi,Paolo Garagnani,Donata Luiselli,Daniela Mari,Giovanni Vitale,Gastone Castellani,Anna Maria Di Blasio

doi:10.18632/aging.100718

Abstract

Aging is characterized by a profound remodeling of the epigenetic architecture in terms of DNA methylation patterns. To date the most effective tool to study genome wide DNA methylation changes is Infinium HumanMethylation450 BeadChip (Infinium 450k). Despite the wealth of tools for Infinium 450k analysis, the identification of the most biologically relevant DNA methylation changes is still challenging. Here we propose an analytical pipeline to select differentially methylated regions (DMRs), tailored on microarray architecture, which is highly effective in highlighting biologically relevant results. The pipeline groups microarray probes on the basis of their localization respect to CpG islands and genic sequences and, depending on probes density, identifies DMRs through a single-probe or a region-centric approach that considers the concomitant variation of multiple adjacent CpG probes. We successfully applied this analytical pipeline on 3 independent Infinium 450k datasets that investigated age-associated changes in blood DNA methylation. We provide a consensus list of genes that systematically vary in DNA methylation levels from 0 to 100 years and that have a potentially relevant role in the aging process.

Highlights

In the last two years the Infinium HumanMethylation450 BeadChip (Infinium 450k) [1] has been largely used to investigate age-associated changes in DNA methylation profile of the human genome [2,3,4,5,6,7,8,9]
Illumina HumanMethylation450 BeadChip were divided in 4 classes on the basis of their genomic localization. (B) Graphic representation of how probes were grouped in BOPs
For the region-centric analysis we propose the use of multivariate analysis of variance (MANOVA) to test for general changes in methylation of a genomic region

Summary

Introduction

In the last two years the Infinium HumanMethylation450 BeadChip (Infinium 450k) [1] has been largely used to investigate age-associated changes in DNA methylation profile of the human genome [2,3,4,5,6,7,8,9]. The difficult task of extracting relevant information from microarray data can be made easier if the number of microarray features is reduced on the basis of a biologically meaningful criterion In this way the top ranking groups of features are more likely to be functionally linked to the phenotype under study than the single features. An alternative solution is to adopt a region-centric approach in which the methylation value not of the single CpG probes, but of a group of adjacent CpG probes is considered This approach is interesting as changes in DNA methylation, especially in the CpG islands, usually involve groups of adjacent CpG sites whose methylation levels are correlated, potentially affecting chromatin structure. On the contrary the biological relevance of alterations at individual CpGs, potentially interesting at specific genomic regions, is less characterized [15]

Methods

Results

Conclusion