title: Effects of rapamycin on chromatin – implications for ageing and tumour suppression
Creators: name: Adam, Field
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: Cancer, epigenetics, ageing, chromatin, senescence, rapamycin.

description: The role of mTORC1 in ageing is well established, with reduction in mTORC1 associated signalling being an accepted longevity assurance mechanism. Rapamycin, a potent inhibitor of mTORC1, has been shown to extend lifespan in a range of models, inhibit tumorigenesis and ameliorate symptoms of age associated decline. Rapamycin has been shown to prevent age associated epigenetic change on histones (Gong et al., 2015) and DNA methylation (Cole et al., 2017; Wang et al., 2017). However, these previous studies do not propose a robust mechanism by which rapamycin may promote epigenome stability. Here we hypothesise that the epigenetic change observed during ageing is the result of a stochastic process driven by the rate of epigenome turnover. We propose that rapamycin slows this rate of turnover through direct effects on the epigenetic machinery and indirectly through effects on transcription. This investigation sought to characterise novel effects of rapamycin which may lead to epigenome stability and decelerate age associated epigenetic change. SILAC labelling in senescent IMR90 fibroblasts of histones in-vitro showed that rapamycin lowers histone incorporation into nuclei of senescent cells. Rapamycin also prevents incorporation of 13C labelled methyl groups onto DNA suggesting that rapamycin may reduce turnover of 5-methylcytosine on DNA. This data suggests that rapamycin may prevent age associated changes in the epigenome by reducing stochastic error inherent in histone exchange and the writing and removal of DNA methylation. Rapamycin may exert these effects in senescent cells, through effects on the linker histone H1.0. In the same model, rapamycin is shown to alter the abundance of histone PTMs H3K56ac, H3K36me3, H3K4me1 and H3K27ac potentially suggesting a role for these modifications in rapamycin’s effects. Rapamycin alters the senescent transcriptome effecting a number of chromatin modifying enzymes. SILAC labelling in mouse ex-vivo hepatocytes shows significant reductions in histone incorporation, similar to the senescent cell model. I found that metabolites associated with chromatin modifying enzymes are significantly altered in the livers of mice treated with rapamycin. In mice treated with life-long rapamycin, multiple histone post-translational modifications are significantly altered based on age and treatment. Preliminary multivariate analysis of histone PTMs suggests that rapamycin may reverse age associated changes in H3 methylation. I present a number of promising avenues, in both human and mouse models, for understanding rapamycin’s effects on the epigenome in both dynamic and static readouts. I propose a model where rapamycin alters binding of H1.0, alters chromatin gene expression and alters histone PTMs, reducing nucleosome turnover. Rapamycin’s effects on metabolic co-factors such as succinate, citrate and SAH, may indicate increased DNA methylation. Together these effects may reduce age associated epigenetic change at the histone and DNA methylation levels.