DNA methylation across the genome in aged human skeletal muscle tissue and muscle-derived cells: the role of HOX genes and physical activity

Abstract

Skeletal muscle tissue demonstrates global hypermethylation with age. However, methylome changes across the time-course of differentiation in aged human muscle derived cells, and larger coverage arrays in aged muscle tissue have not been undertaken. Using 850K DNA methylation arrays we compared the methylomes of young (27 ± 4.4 years) and aged (83 ± 4 years) human skeletal muscle and that of young/aged heterogenous muscle-derived human primary cells (HDMCs) over several time points of differentiation (0, 72 h, 7, 10 days). Aged muscle tissue was hypermethylated compared with young tissue, enriched for; pathways-in-cancer (including; focal adhesion, MAPK signaling, PI3K-Akt-mTOR signaling, p53 signaling, Jak-STAT signaling, TGF-beta and notch signaling), rap1-signaling, axon-guidance and hippo-signalling. Aged cells also demonstrated a hypermethylated profile in pathways; axon-guidance, adherens-junction and calcium-signaling, particularly at later timepoints of myotube formation, corresponding with reduced morphological differentiation and reductions in MyoD/Myogenin gene expression compared with young cells. While young cells showed little alterations in DNA methylation during differentiation, aged cells demonstrated extensive and significantly altered DNA methylation, particularly at 7 days of differentiation and most notably in focal adhesion and PI3K-AKT signalling pathways. While the methylomes were vastly different between muscle tissue and HDMCs, we identified a small number of CpG sites showing a hypermethylated state with age, in both muscle tissue and cells on genes KIF15, DYRK2, FHL2, MRPS33, ABCA17P. Most notably, differential methylation analysis of chromosomal regions identified three locations containing enrichment of 6–8 CpGs in the HOX family of genes altered with age. With HOXD10, HOXD9, HOXD8, HOXA3, HOXC9, HOXB1, HOXB3, HOXC-AS2 and HOXC10 all hypermethylated in aged tissue. In aged cells the same HOX genes (and additionally HOXC-AS3) displayed the most variable methylation at 7 days of differentiation versus young cells, with HOXD8, HOXC9, HOXB1 and HOXC-AS3 hypermethylated and HOXC10 and HOXC-AS2 hypomethylated. We also determined that there was an inverse relationship between DNA methylation and gene expression for HOXB1, HOXA3 and HOXC-AS3. Finally, increased physical activity in young adults was associated with oppositely regulating HOXB1 and HOXA3 methylation compared with age. Overall, we demonstrate that a considerable number of HOX genes are differentially epigenetically regulated in aged human skeletal muscle and HDMCs and increased physical activity may help prevent age-related epigenetic changes in these HOX genes.

The methylome and comparative transcriptome after high intensity sprint exercise in human skeletal muscle

“…Importantly, we identified VEGFA to possess enriched hypomethylated in its promoter in the current study. Interrogation of aged skeletal muscle tissue methylome in our recent studies, also suggests one of the same VEGFA CpG sites (cg04629501) is oppositely regulated (hypermethylated) with age 25 compared with exercise (hypomethylated) in the present study. Therefore, VEGFA is hypomethylated in its promoter and is associated with its own increased gene expression (as well as highly correlated with PGC1-α, NR4A1…”

“…is hypermethylated with aging 25 as compared with the hypomethylated response seen with exercise in the present study. Something, that requires future investigation with COD exercise in elderly populations.…”

“…Others have suggested that it is well tolerated and also extremely practical, given a reduced time-burden of the exercise regime 27 . Furthermore, aging is associated with hypermethylation in skeletal muscle tissue 25,28 and muscle stem cells 25 . With increased physical activity and resistance exercise demonstrated to somewhat reverse the hypermethylated signature observed with age 25,29 .…”

“…Furthermore, aging is associated with hypermethylation in skeletal muscle tissue 25,28 and muscle stem cells 25 . With increased physical activity and resistance exercise demonstrated to somewhat reverse the hypermethylated signature observed with age 25,29 . Therefore, as COD exercise evokes greater hypomethylation than ST running, change of direction exercise may also have a beneficial epigenomic impact in reversing the hypermethylation observed in skeletal muscle tissue of aged individuals.…”

Systematic Review of Multi-Omics Approaches to Investigate Toxicological Effects in Macrophages

“…Noteworthy, the temporal behavior can differ between phosphopeptides [ 182 ]. In the case of epigenomics [ 183 ] in general and DNA methylation [ 184 ] in particular, there is no one correct time point to be investigated since the modifications are regulated dynamically. Thus, for those approaches, the explored time points have to be chosen depending on the research question as well, keeping in mind that an integrative analysis is facilitated by the use of paired samples [ 60 ].…”