Recalibrating the cerebellum DNA methylation clock: implications for ageing rates comparison

Abstract

BackgroundDNA methylation (DNAm) based age clocks have been studied extensively as a biomarker of human ageing and risk factor for age-related diseases. Despite different tissues having vastly different rates of proliferation, it is still largely unknown whether they age at different rates. It was previously reported that the cerebellum ages slowly, however, this claim was drawn from a single clock using a small sample size and so warrants further investigation. ResultsWe collected the largest cerebellum DNAm dataset (N=752). We found the respective epigenetic ages are all severely underestimated by six representative DNAm age clocks, with the underestimation effects more pronounced in the four clocks whose training datasets do not include brain-related tissues. We identified 613 age-associated CpGs in the cerebellum, which accounts for only 14.5% of the number found in the middle temporal gyrus from the same population (N=404), of which only 201 CpGs are both age-associated in the two tissue types. We built a highly accurate age prediction model for the cerebellum named CerebellumClockspecific (Pearson correlation=0.941, MAD=3.18 years). Furthermore, based on the 201 age-associated CpGs, we built two other clocks CerebellumClockcommon and CortexClockcommon for the cerebellum and non-cerebellar brain cortex tissues separately, they both support that the cerebellum has a relative lower DNAm ageing rate. ConclusionsThe large underestimation for the cerebellum by previous clocks mainly reflects the improper usage of the age clocks. There exist strong and consistent ageing effects on the cerebellar methylome despite the cerebellum having unique age-dependent methylome changes. The DNAm clock based ageing rates comparisons are valid only upon models constructed on a small group of CpGs, therefore, more evidence is required to support the idea that different DNAm ageing rates represent different biological ageing rates.