Hierarchy and control of ageing-related methylation networks

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.
Author summary Aging affects all living organisms. In humans, the chronological age correlates with the methylation level of some locations of the DNA. Here we extract an interaction network between these ageing related sites, which shows signs of hierarchical organisation. In addition, modifications in the methylation of single sites of the DNA can impose cascades of changes at other sites over this network. Based on “gedanken-experiments” in a small subset of CpG sites we show that by tuning appropriately selected methylation levels the estimated biological age can be changed. When modifying the most influential locations, the resulting cascades of changes can set back the estimated biological age by more than 5 years. Our study also shows that compared to single site methylation perturbations, the propagation of the change over the interaction network leads to methylation change profiles which are more aligned with the natural direction of ageing in a high dimensional representation of the methylation levels.