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

D. C. Turner; P. P. Gorski; M. F. Maasar; R. A. Seaborne; P. Baumert; A. D. Brown; M. O. Kitchen; R. M. Erskine; I. Dos-Remedios; S. Voisin; N. Eynon; R. I. Sultanov; O. V. Borisov; A. K. Larin; E. A. Semenova; D. V. Popov; E. V. Generozov; C. E. Stewart; B. Drust; D. J. Owens; I. I. Ahmetov; A. P. Sharples

doi:10.1038/s41598-020-72730-z

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

D. C. Turner, P. P. Gorski, M. F. Maasar, R. A. Seaborne, P. Baumert, A. D. Brown, M. O. Kitchen, R. M. Erskine, I. Dos-Remedios, S. Voisin, N. Eynon, R. I. Sultanov, O. V. Borisov, A. K. Larin, E. A. Semenova, D. V. Popov, E. V. Generozov, C. E. Stewart, B. Drust, D. J. OwensI. I. Ahmetov^*, A. P. Sharples^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	15360
Journal	Scientific Reports
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41598-020-72730-z
Publication status	Published - 1 Dec 2020

Bibliographical note

Funding Information:
These data were supported by a North Staffordshire Medical Institute (NMSI) grant awarded to Adam P. Sharples (PI), Daniel Turner, Mark Kitchen and Ian Dos-Remedios (Co-I’s). This work was also supported by the UK’s Engineering and Physical Sciences Research Council (EPSRC) and the UK Medical Research Council’s (MRC) centre for doctoral training, via a studentship awarded to the joint first author Piotr Gorski in the group of Adam P. Sharples (PI). Funds from Keele University and Liverpool John Moores University, UK and The Norwegian School of Sport Sciences, Oslo, Norway also supported the PhD work by Daniel Turner & Piotr Gorski in the group of Adam P. Sharples. Philipp Baumert received a fully-funded Liverpool John Moores PhD scholarship. Mohd Firdaus Maasar received a PhD studentship via the Malaysian government agency: Majlis Amanah Rakyat (MARA) via Barry Drust, Adam P. Sharples and Dr. Andrew Hulten. The physical activity and DNA methylation study was supported in part by grant from the Russian Science Foundation (Grant No. 17-15-01436: "Comprehensive analysis of the contribution of genetic, epigenetic and environmental factors in the individual variability of the composition of human muscle fibers”; DNA sample collection, genotyping, epigenetic analysis and muscle fibre typing of Russian subjects).

Publisher Copyright:
© 2020, The Author(s).

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General

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41598-020-72730-z

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Turner, D. C., Gorski, P. P., Maasar, M. F., Seaborne, R. A., Baumert, P., Brown, A. D., Kitchen, M. O., Erskine, R. M., Dos-Remedios, I., Voisin, S., Eynon, N., Sultanov, R. I., Borisov, O. V., Larin, A. K., Semenova, E. A., Popov, D. V., Generozov, E. V., Stewart, C. E., Drust, B., ... Sharples, A. P. (2020). DNA methylation across the genome in aged human skeletal muscle tissue and muscle-derived cells: the role of HOX genes and physical activity. Scientific Reports, 10(1), Article 15360. https://doi.org/10.1038/s41598-020-72730-z

@article{d9784edf00124470b73ae5218159ccb6,

title = "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.",

author = "Turner, {D. C.} and Gorski, {P. P.} and Maasar, {M. F.} and Seaborne, {R. A.} and P. Baumert and Brown, {A. D.} and Kitchen, {M. O.} and Erskine, {R. M.} and I. Dos-Remedios and S. Voisin and N. Eynon and Sultanov, {R. I.} and Borisov, {O. V.} and Larin, {A. K.} and Semenova, {E. A.} and Popov, {D. V.} and Generozov, {E. V.} and Stewart, {C. E.} and B. Drust and Owens, {D. J.} and Ahmetov, {I. I.} and Sharples, {A. P.}",

note = "Funding Information: These data were supported by a North Staffordshire Medical Institute (NMSI) grant awarded to Adam P. Sharples (PI), Daniel Turner, Mark Kitchen and Ian Dos-Remedios (Co-I{\textquoteright}s). This work was also supported by the UK{\textquoteright}s Engineering and Physical Sciences Research Council (EPSRC) and the UK Medical Research Council{\textquoteright}s (MRC) centre for doctoral training, via a studentship awarded to the joint first author Piotr Gorski in the group of Adam P. Sharples (PI). Funds from Keele University and Liverpool John Moores University, UK and The Norwegian School of Sport Sciences, Oslo, Norway also supported the PhD work by Daniel Turner & Piotr Gorski in the group of Adam P. Sharples. Philipp Baumert received a fully-funded Liverpool John Moores PhD scholarship. Mohd Firdaus Maasar received a PhD studentship via the Malaysian government agency: Majlis Amanah Rakyat (MARA) via Barry Drust, Adam P. Sharples and Dr. Andrew Hulten. The physical activity and DNA methylation study was supported in part by grant from the Russian Science Foundation (Grant No. 17-15-01436: {"}Comprehensive analysis of the contribution of genetic, epigenetic and environmental factors in the individual variability of the composition of human muscle fibers”; DNA sample collection, genotyping, epigenetic analysis and muscle fibre typing of Russian subjects). Publisher Copyright: {\textcopyright} 2020, The Author(s).",

year = "2020",

month = dec,

day = "1",

doi = "10.1038/s41598-020-72730-z",

language = "English",

volume = "10",

journal = "Scientific Reports",

issn = "2045-2322",

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Turner, DC, Gorski, PP, Maasar, MF, Seaborne, RA, Baumert, P, Brown, AD, Kitchen, MO, Erskine, RM, Dos-Remedios, I, Voisin, S, Eynon, N, Sultanov, RI, Borisov, OV, Larin, AK, Semenova, EA, Popov, DV, Generozov, EV, Stewart, CE, Drust, B, Owens, DJ, Ahmetov, II & Sharples, AP 2020, 'DNA methylation across the genome in aged human skeletal muscle tissue and muscle-derived cells: the role of HOX genes and physical activity', Scientific Reports, vol. 10, no. 1, 15360. https://doi.org/10.1038/s41598-020-72730-z

TY - JOUR

T1 - DNA methylation across the genome in aged human skeletal muscle tissue and muscle-derived cells

T2 - the role of HOX genes and physical activity

AU - Turner, D. C.

AU - Gorski, P. P.

AU - Maasar, M. F.

AU - Seaborne, R. A.

AU - Baumert, P.

AU - Brown, A. D.

AU - Kitchen, M. O.

AU - Erskine, R. M.

AU - Dos-Remedios, I.

AU - Voisin, S.

AU - Eynon, N.

AU - Sultanov, R. I.

AU - Borisov, O. V.

AU - Larin, A. K.

AU - Semenova, E. A.

AU - Popov, D. V.

AU - Generozov, E. V.

AU - Stewart, C. E.

AU - Drust, B.

AU - Owens, D. J.

AU - Ahmetov, I. I.

AU - Sharples, A. P.

N1 - Funding Information: These data were supported by a North Staffordshire Medical Institute (NMSI) grant awarded to Adam P. Sharples (PI), Daniel Turner, Mark Kitchen and Ian Dos-Remedios (Co-I’s). This work was also supported by the UK’s Engineering and Physical Sciences Research Council (EPSRC) and the UK Medical Research Council’s (MRC) centre for doctoral training, via a studentship awarded to the joint first author Piotr Gorski in the group of Adam P. Sharples (PI). Funds from Keele University and Liverpool John Moores University, UK and The Norwegian School of Sport Sciences, Oslo, Norway also supported the PhD work by Daniel Turner & Piotr Gorski in the group of Adam P. Sharples. Philipp Baumert received a fully-funded Liverpool John Moores PhD scholarship. Mohd Firdaus Maasar received a PhD studentship via the Malaysian government agency: Majlis Amanah Rakyat (MARA) via Barry Drust, Adam P. Sharples and Dr. Andrew Hulten. The physical activity and DNA methylation study was supported in part by grant from the Russian Science Foundation (Grant No. 17-15-01436: "Comprehensive analysis of the contribution of genetic, epigenetic and environmental factors in the individual variability of the composition of human muscle fibers”; DNA sample collection, genotyping, epigenetic analysis and muscle fibre typing of Russian subjects). Publisher Copyright: © 2020, The Author(s).

PY - 2020/12/1

Y1 - 2020/12/1

N2 - 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.

AB - 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.

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DO - 10.1038/s41598-020-72730-z

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

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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