Hierarchy and control of ageing-related methylation networks

PLoS Comput Biol. 2021 Sep 17;17(9):e1009327. doi: 10.1371/journal.pcbi.1009327. eCollection 2021 Sep.

Abstract

DNA methylation provides one of the most widely studied biomarkers of ageing. Since the methylation of CpG dinucleotides function as switches in cellular mechanisms, it is plausible to assume that by proper adjustment of these switches age may be tuned. Though, adjusting hundreds of CpG methylation levels coherently may never be feasible and changing just a few positions may lead to biologically unstable state. A prominent example of methylation-based age estimators is provided by Horvath's clock, based on 353 CpG dinucleotides, showing a high correlation (not necessarily causation) with chronological age across multiple tissue types. On this small subset of CpG dinucleotides we demonstrate how the adjustment of one methylation level leads to a cascade of changes at other sites. Among the studied subset, we locate the most important CpGs (and related genes) that may have a large influence on the rest of the sub-system. According to our analysis, the structure of this network is way more hierarchical compared to what one would expect based on ensembles of uncorrelated connections. Therefore, only a handful of CpGs is enough to modify the system towards a desired state. When propagation of the change over the network is taken into account, the resulting modification in the predicted age can be significantly larger compared to the effect of isolated CpG perturbations. By adjusting the most influential single CpG site and following the propagation of methylation level changes we can reach up to 5.74 years in virtual age reduction, significantly larger than without taking into account of the network control. Extending our approach to the whole methylation network may identify key nodes that have controller role in the ageing process.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aging / genetics*
  • CpG Islands
  • DNA Methylation*
  • Humans

Grants and funding

The research was partially supported by the Velux Foundation 00018310 (JB) and by the Hungarian National Research, Development and Innovation Office K128780 (PG, PP) and by the Hungarian National Research, Development and Innovation Office NVKP\_16-1-2016-0004 (JB, AM, BM, ICs) and by the Research Excellence Programme of the Ministry for Innovation and Technology in Hungary, within the framework of the Digital Biomarker thematic programme of the Semmelweis University (GP, PP) and the NRDI Office within the framework of the Artificial Intelligence National Laboratory Program (ICs). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.