Loss of LINE-1 Methylation in Cell Free DNA as a Biomarker of Aging
In recent years, transposable element activation has come to be seen as potentially important in aging. Transposable elements such as retrotransposons are DNA sequences that can copy themselves into other locations in the genome, potentially causing all sorts of disruption. These transposable elements are repressed in youth by epigenetic mechanisms such as DNA methylation, but become more active in aging. It is unclear as to the degree that this represents a rising burden of damaged and senescent cells, in which transposon activity is a part of their dysfunction, versus a more general issue across all cells that causes greater damage and senescence. Here, researchers focus on the LINE-1 retrotransposons, looking at cell-free DNA in circulation, the debris from destroyed cells, to see whether there is a clear association between the state of epigenetic marks on LINE-1 retrotransposons and the progression of aging.
LINE-1 hypomethylation, a loss of DNA methylation in the CpG-rich promoter sequences of Long Interspersed Nuclear Elements retrotransposons, occurs as "genome-wide" or "global" DNA hypomethylation in many cancer types. LINE-1 hypomethylation is therefore one of the characteristic methylation profile changes common to many cancers. LINE-1 hypomethylation often leads to LINE-1 activation, i.e., expression of LINE-1 RNA and proteins, including its potent endonuclease. This activation may elicit DNA damage and repair, stress responses, tumor progression and apoptosis, especially if additional cellular retrotransposition control mechanisms have been overcome.
Interestingly, a gradual loss of LINE-1 methylation has also been observed during aging that may likewise derepress silenced LINE-1 retroelements followed by increased genomic instability. Aging is known as a main risk factor for cancer. In this regard, we had provided additional evidence that genome-wide hypomethylation of LINE-1 retroelements in cell-free DNA (cfDNA) in blood is an epigenetic biomarker of human aging. Recently, it has been shown that LINE-1 sequences are a major component of circulating cfDNA. This finding suggests the idea that cfDNA may originate in aging or tumor cells afflicted by LINE-1 hypomethylation. Such cells would have a significantly elevated rate of LINE-1 activation and retrotransposition, affecting genomic integrity. Ultimately, this could result in apoptosis and release of their LINE-1-enriched cfDNA.
Here we present a new methodological strategy to properly and unambiguously extract DNA methylation patterns of repetitive, as well as single genetic loci from pure cell-free DNA from peripheral blood. Since this nucleic acid fraction originates mainly in apoptotic, senescent, and cancerous cells, this approach allows efficient analysis of aged and cancerous cell-specific DNA methylation patterns for diagnostic and prognostic purposes. Using this methodology, we observe a significant age-associated erosion of LINE-1 methylation in cfDNA suggesting that the threshold of hypomethylation sufficient for relevant LINE-1 activation and consequential harmful retrotransposition might be reached at higher age. We speculate that this process might contribute to making aging the main risk factor for many cancers.