Epigenetic Mutations Accumulate with Age, with Uncertain Consequences
Epigenetic markers, such as methylation, determine the production rates of specific proteins in a cell. These epigenetic decorations to DNA change constantly, but many changes are characteristic of aging, which has led to the generation of epigenetic clocks in recent years. Epigenetic mutations are distinct from these changes, being effectively a form of stochastic damage in which methylation is inappropriately applied to a given location in the genome. Does this cause significant issues in aging? That is an open question, and can be considered in a similar way to the question of the effects of mutation to nuclear DNA. In most cases, random methylation won't have much of an effect, as it occurs in a cell that will not replicate extensively, or changes expression of a gene that isn't all that important in the tissue in question. When an epigenetic mutation occurs in stem cells or progenitor cells, it may manage to spread widely in a tissue, however.
Epigenetic processes, among which DNA methylation is one of the most well studied, are fundamental in human aging. Studies on DNA methylation have identified age-associated changes in methylation levels shared by individuals, and have also reported an increasing divergence of methylation levels between individuals with age. While the role of DNA methylation in aging has been widely studied, epigenetic mutations, here defined as aberrant methylation levels compared to the distribution in a population, are less understood.
Epigenetic mutations may be involved in cancer development and important for human aging. Unlike age-associated changes in methylation levels that are shared among individuals, the incidences of epigenetic mutations are rare, stochastic, and inconsistent between individuals. Recently, emerging studies on methylation variability have also identified differentially varied CpG sites associated with cancer field defects. Epigenetic mutations can partly explain the increasing variability of methylation levels between individuals over time, but conversely, highly varied methylation sites do not necessarily contain extreme outliers. The extreme methylation levels may concur stronger biological consequences, such as cancer.
However, the study on epigenetic mutations and aging was based on a cross-sectional study, it needs to be validated in a longitudinal setting, where the accumulation of epigenetic mutations over time can be followed within the same individuals. It is not yet known what the clinical consequences of accumulated epigenetic mutations are, and if individuals with a high burden of epigenetic mutations are prone to develop cancer as previously suggested.
In this study, we analyzed age-related accumulation of epigenetic mutations from a longitudinal perspective in old Swedish twins, using 994 blood samples collected at up to five time points from 375 individuals in old ages. Apart from being exponentially associated with age, epigenetic mutations were also associated with sex, CD19+ B cell count, genetic background, cancer incidence, and technical factors. We showed once mutations are established, they are stable over time. Furthermore, epigenetic mutations are enriched in important regulatory sites, e.g., promoter regions of genes involved in histone modification processes, which could potentially be an explanation to why people who develop cancer have more epigenetic mutations than others do.
We further classified epigenetic mutations into High/Low Methylation Outliers (HMO/LMO) according to their changes in methylation. We also found that biological factors, including B cell compositions and genetic factors, were more strongly associated with frequent HMOs than LMOs, while frequent LMOs were more influenced by technical factors. Moreover, cancer diagnosis was significantly associated with the increase of epigenetic mutations, especially among frequent HMOs, while the same was not true for LMOs. Furthermore, we concluded that the age-related accumulation of epigenetic mutations was not related to genetic factors, hence is driven by stochastic or environmental effects.