RESEARCH ARTICLE

Single-nucleus profiling unveils a geroprotective role of the FOXO3 in primate skeletal muscle aging

  • Ying Jing 1,4 ,
  • Yuesheng Zuo 4,6,8 ,
  • Yang Yu 10,12 ,
  • Liang Sun 11 ,
  • Zhengrong Yu 13 ,
  • Shuai Ma 2,5,7 ,
  • Qian Zhao 3,9 ,
  • Guoqiang Sun 1,4 ,
  • Huifang Hu 2,5,7 ,
  • Jingyi Li 2,5,7 ,
  • Daoyuan Huang 3,9 ,
  • Lixiao Liu 4,6,8 ,
  • Jiaming Li 4,6,8,14 ,
  • Zijuan Xin 2,5,7 ,
  • Haoyan Huang 3,9 ,
  • Juan Carlos Izpisua Belmonte 16 ,
  • Weiqi Zhang , 4,5,6,8,14,15 ,
  • Si Wang , 3,9,17 ,
  • Jing Qu , 1,4,5,7 ,
  • Guang-Hui Liu , 2,3,4,5,7
Expand
  • 1. State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
  • 2. State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
  • 3. Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
  • 4. University of Chinese Academy of Sciences, Beijing 100049, China
  • 5. Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
  • 6. CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
  • 7. Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
  • 8. China National Center for Bioinformation, Beijing 100101, China
  • 9. Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
  • 10. Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
  • 11. The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing 100730, China
  • 12. Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing 100191, China
  • 13. Department of Orthopaedics, Peking University First Hospital, Beijing 100034, China
  • 14. Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
  • 15. Sino-Danish Center for Education and Research, Beijing 101408, China
  • 16. Altos Labs, Inc., San Diego, CA 94022, USA
  • 17. The Fifth People’s Hospital of Chongqing, Chongqing 400062, China
zhangwq@big.ac.cn
wangsi@xwh.ccmu.edu.cn
qujing@ioz.ac.cn
ghliu@ioz.ac.cn

Received date: 31 Jul 2022

Accepted date: 13 Sep 2022

Published date: 15 Jul 2023

Copyright

2022 The Author(s) 2022. Published by Oxford University Press on behalf of Higher Education Press.

Abstract

Age-dependent loss of skeletal muscle mass and function is a feature of sarcopenia, and increases the risk of many aging-related metabolic diseases. Here, we report phenotypic and single-nucleus transcriptomic analyses of non-human primate skeletal muscle aging. A higher transcriptional fluctuation was observed in myonuclei relative to other interstitial cell types, indicating a higher susceptibility of skeletal muscle fiber to aging. We found a downregulation of FOXO3 in aged primate skeletal muscle, and identified FOXO3 as a hub transcription factor maintaining skeletal muscle homeostasis. Through the establishment of a complementary experimental pipeline based on a human pluripotent stem cell-derived myotube model, we revealed that silence of FOXO3 accelerates human myotube senescence, whereas genetic activation of endogenous FOXO3 alleviates human myotube aging. Altogether, based on a combination of monkey skeletal muscle and human myotube aging research models, we unraveled the pivotal role of the FOXO3 in safeguarding primate skeletal muscle from aging, providing a comprehensive resource for the development of clinical diagnosis and targeted therapeutic interventions against human skeletal muscle aging and the onset of sarcopenia along with aging-related disorders.

Cite this article

Ying Jing , Yuesheng Zuo , Yang Yu , Liang Sun , Zhengrong Yu , Shuai Ma , Qian Zhao , Guoqiang Sun , Huifang Hu , Jingyi Li , Daoyuan Huang , Lixiao Liu , Jiaming Li , Zijuan Xin , Haoyan Huang , Juan Carlos Izpisua Belmonte , Weiqi Zhang , Si Wang , Jing Qu , Guang-Hui Liu . Single-nucleus profiling unveils a geroprotective role of the FOXO3 in primate skeletal muscle aging[J]. Protein & Cell, 2023 , 14(7) : 497 -512 . DOI: 10.1093/procel/pwac061

1
Aibar S, González-Blas CB, Moerman T et al. SCENIC: single-cell regulatory network inference and clustering. Nat Methods 2017;14:1083–1086.

DOI

2
Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 2015;31:166–169.

DOI

3
Anderson RM, Colman RJ. Prospects and perspectives in primate aging research. Antioxid Redox Signal 2011;14:203–205.

DOI

4
Angelidis I, Simon LM, Fernandez IE et al. An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics. Nat Commun 2019;10:963.

DOI

5
Askanas V, Engel WK. Inclusion-body myositis, a multifactorial muscle disease associated with aging: current concepts of pathogenesis. Curr Opin Rheumatol 2007;19:550–559.

DOI

6
Askanas V, Engel WK, Nogalska A. Pathogenic considerations in sporadic inclusion-body myositis, a degenerative muscle disease associated with aging and abnormalities of myoproteostasis. J Neuropathol Exp Neurol 2012;71:680–693.

DOI

7
Baskin KK, Winders BR, Olson EN. Muscle as a “mediator” of systemic metabolism. Cell Metab 2015;21:237–248.

DOI

8
Butler A, Hoffman P, Smibert P et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 2018;36:411–420.

DOI

9
Cadot B, Gache V, Gomes ER. Moving and positioning the nucleus in skeletal muscle – one step at a time. Nucleus 2015;6:373–381.

DOI

10
Cai Y, Song W, Li J et al. The landscape of aging. Sci China Life Sci 2022; 65(12), 2354–2454.

DOI

11
Calissi G, Lam EW, Link W. Therapeutic strategies targeting FOXO transcription factors. Nat Rev Drug Discov 2021;20:21–38.

DOI

12
Dalle S, Koppo K. Cannabinoid receptor 1 expression is higher in muscle of old vs. young males, and increases upon resistance exercise in older adults. Sci Rep 2021;11:18349.

DOI

13
De Micheli AJ, Spector JA, Elemento O et al. A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations. Skelet Muscle 2020;10:19.

DOI

14
Dell’Orso S, Juan AH, Ko KD et al. Single cell analysis of adult mouse skeletal muscle stem cells in homeostatic and regenerative conditions. Development 2019;146:dev174177.

DOI

15
Demontis F, Piccirillo R, Goldberg AL et al. Mechanisms of skeletal muscle aging: insights from Drosophila and mammalian models. Dis Model Mech 2013;6:1339–1352.

DOI

16
Dirks AJ, Hofer T, Marzetti E et al. Mitochondrial DNA mutations, energy metabolism and apoptosis in aging muscle. Ageing Res Rev 2006;5:179–195.

DOI

17
Domingues-Faria C, Vasson MP, Goncalves-Mendes N et al. Skeletal muscle regeneration and impact of aging and nutrition. Ageing Res Rev 2016;26:22–36.

DOI

18
Dos Santos M, Backer S, Saintpierre B et al. Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers. Nat Commun 2020;11:5102.

DOI

19
Fleming SJ, Marioni JC, Babadi M. CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets. bioRxiv 2019.

DOI

20
Frontera WR, Ochala J. Skeletal muscle: a brief review of structure and function. Calcif Tissue Int 2015;96:183–195.

DOI

21
Fuchs E, Blau HM. Tissue stem cells: architects of their niches. Cell Stem Cell 2020;27:532–556.

DOI

22
Giordani L, He GJ, Negroni E et al. High-dimensional single-cell cartography reveals novel skeletal muscle-resident cell populations. Mol Cell 2019;74:609–621.e6.

DOI

23
Gomarasca M, Banfi G, Lombardi G. Myokines: the endocrine coupling of skeletal muscle and bone. Adv Clin Chem 2020;94:155–218.

DOI

24
González JP, Queralt-Rosinach N, Bravo A et al. DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database 2015;2015:bav028.

DOI

25
Guang-Hui Liu YB, Qu J, Zhang W et al. Aging Atlas: a multi-omics database for aging biology. Nucleic Acids Res 2021;49:D825–d830.

DOI

26
He X, Memczak S, Qu J et al. Single-cell omics in ageing: a young and growing field. Nat Metab 2020;2:293–302.

DOI

27
Hershberg EA, Camplisson CK, Close JL et al. PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments. Nat Methods 2021;18:937–944.

DOI

28
Hu H, Ji Q, Song M et al. ZKSCAN3 counteracts cellular senescence by stabilizing heterochromatin. Nucleic Acids Res 2020;48:6001–6018.

DOI

29
Iizuka K, Machida T, Hirafuji M. Skeletal muscle is an endocrine organ. J Pharmacol Sci 2014;125:125–131.

DOI

30
Irrthum A, Wehenkel L, Geurts P. Inferring regulatory networks from expression data using tree-based methods. PLoS One 2010;5:e12776.

DOI

31
Jiang C, Wen Y, Kuroda K et al. Notch signaling deficiency underlies age-dependent depletion of satellite cells in muscular dystrophy. Dis Model Mech 2014;7:997–1004.

DOI

32
Jones RA, Harrison C, Eaton SL et al. Cellular and molecular anatomy of the human neuromuscular junction. Cell Rep 2017;21:2348–2356.

DOI

33
Kalinkovich A, Livshits G. Sarcopenic obesity or obese sarcopenia: a cross talk between age-associated adipose tissue and skeletal muscle inflammation as a main mechanism of the pathogenesis. Ageing Res Rev 2017;35:200–221.

DOI

34
Kanehisa M, Furumichi M, Sato Y et al. KEGG: integrating viruses and cellular organisms. Nucleic Acids Res 2021;49:D545–D551.

DOI

35
Kang W, Jin T, Zhang T et al. Regeneration Roadmap: data-base resources for regenerative biology. Nucleic Acids Res 2022;50:D1085–D1090.

36
Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods 2015;12:357–360.

DOI

37
Kim M, Franke V, Brandt B et al. Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells. Nat Commun 2020;11:6375.

DOI

38
Kishi JY, Lapan SW, Beliveau BJ et al. SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. Nat Methods 2019;16:533–544.

DOI

39
Krishnaswami SR, Grindberg RV, Novotny M et al. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc 2016;11:499–524.

DOI

40
Larsson L, Degens H, Li M et al. Sarcopenia: aging-related loss of muscle mass and function. Physiol Rev 2019;99:427–511.

DOI

41
Leger B, Derave W, De Bock K et al. Human sarcopenia reveals an increase in SOCS-3 and myostatin and a reduced efficiency of Akt phosphorylation. Rejuvenation Res 2008;11:163–175B.

DOI

42
Lei J, Wang S, Kang W et al. FOXO3-engineered human mesenchymal progenitor cells efficiently promote cardiac repair after myocardial infarction. Protein Cell 2021;12:145–151.

DOI

43
Leng SX, Pawelec G. Single-cell immune atlas for human aging and frailty. Life Med 2022:lnac013.

DOI

44
Li J, Zheng Y, Yan P et al. A single-cell transcriptomic atlas of primate pancreatic islet aging. Natl Sci Rev 2021;8:nwaa127.

DOI

45
Liberzon A, Birger C, Thorvaldsdóttir H et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst 2015;1:417–425.

DOI

46
Limbad C, Doi R, McGirr J et al. Senolysis induced by 25-hydroxycholesterol targets CRYAB in multiple cell types. iScience 2022;25:103848.

DOI

47
Lipina C, Hundal HS. Lipid modulation of skeletal muscle mass and function. J Cachexia Sarcopenia Muscle 2017;8:190–201.

DOI

48
Liu L, Liu X, Bai Y et al. Neuregulin-1β modulates myogenesis in septic mouse serum-treated C2C12 myotubes in vitro through PPARγ/NF-κB signaling. Mol Biol Rep 2018;45:1611–1619.

DOI

49
Liu Z, Li W, Geng L et al. Cross-species metabolomic analysis identifies uridine as a potent regeneration promoting factor. Cell Discov 2022;8:6.

DOI

50
Livshits G, Kalinkovich A. Inflammaging as a common ground for the development and maintenance of sarcopenia, obesity, cardiomyopathy and dysbiosis. Ageing Res Rev 2019;56:100980.

DOI

51
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014;15:550.

DOI

52
Ma S, Sun S, Geng L et al. Caloric restriction reprograms the single-cell transcriptional landscape of Rattus Norvegicus aging. Cell 2020;180:1001.e22.

DOI

53
Ma S, Sun S, Li J et al. Single-cell transcriptomic atlas of primate cardiopulmonary aging. Cell Res 2021;31:415–432.

DOI

54
Ma S, Wang S, Ye Y et al. Heterochronic parabiosis induces stem cell revitalization and systemic rejuvenation across aged tissues. Cell Stem Cell 2022;29:1005.e10.

DOI

55
Maeda S, Miyagawa S, Kawamura T et al. Notch signaling-modified mesenchymal stem cells improve tissue perfusion by induction of arteriogenesis in a rat hindlimb ischemia model. Sci Rep 2021;11:2543.

DOI

56
Maffioletti SM, Gerli MF, Ragazzi M et al. Efficient derivation and inducible differentiation of expandable skeletal myogenic cells from human ES and patient-specific iPS cells. Nat Protoc 2015;10:941–958.

DOI

57
Mammucari C, Milan G, Romanello V et al. FoxO3 controls autophagy in skeletal muscle in vivo. Cell Metab 2007;6:458–471.

DOI

58
McGinnis CS, Murrow LM, Gartner ZJ. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst 2019;8:329–337.e4.

DOI

59
McKellar DW, Walter LD, Song LT et al. Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration. Commun Biol 2021;4:1280.

DOI

60
Mercken EM, Capri M, Carboneau BA et al. Conserved and species-specific molecular denominators in mammalian skeletal muscle aging. NPJ Aging Mech Dis 2017;3:8.

DOI

61
Morris BJ, Willcox DC, Donlon TA et al. FOXO3: A major gene for human longevity — a mini-review. Gerontology 2015;61:515–525.

DOI

62
Murgia M, Toniolo L, Nagaraj N et al. Single muscle fiber proteomics reveals fiber-type-specific features of human muscle aging. Cell Rep 2017;19:2396–2409.

DOI

63
Navarro G. A guided tour to approximate string matching. ACM Comput Surv 2001;33:31–88.

DOI

64
Ohsawa N, Koebis M, Suo S et al. Alternative splicing of PDLIM3/ALP, for α-actinin-associated LIM protein 3, is aberrant in persons with myotonic dystrophy. Biochem Biophys Res Commun 2011;409:64–69.

DOI

65
Orchard P, Manickam N, Ventresca C et al. Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits. Genome Res 2021;31:2258–2275.

DOI

66
Podnar J, Deiderick H, Hunicke-Smith S. Next-generation sequencing fragment library construction. Curr Protoc Mol Biol 2014;107:7.17.11–7.17.16.

DOI

67
Rubenstein AB, Smith GR, Raue U et al. Single-cell transcriptional profiles in human skeletal muscle. Sci Rep 2020;10:229.

DOI

68
Salih DA, Brunet A. FoxO transcription factors in the maintenance of cellular homeostasis during aging. Curr Opin Cell Biol 2008;20:126–136.

DOI

69
Sandri M, Sandri C, Gilbert A et al. Foxo transcription factors induce the atrophy-related ubiquitin ligase atrogin-1 and cause skeletal muscle atrophy. Cell 2004;117:399–412.

DOI

70
Shannon P, Markiel A, Ozier O et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498–2504.

DOI

71
Simon M, Van Meter M, Ablaeva J et al. LINE1 derepression in aged wild-type and SIRT6-deficient mice drives inflammation. Cell Metab 2019;29:871–885.e5 e875.

DOI

72
Stokes T, Hector AJ, Morton RW et al. Recent perspectives regarding the role of dietary protein for the promotion of muscle hypertrophy with resistance exercise training. Nutrients 2018;10:180.

DOI

73
Tieland M, Trouwborst I, Clark BC. Skeletal muscle performance and ageing. J Cachexia Sarcopenia Muscle 2018;9:3–19.

DOI

74
Verma M, Asakura Y, Murakonda BSR et al. Muscle satellite cell cross-talk with a vascular niche maintains quiescence via VEGF and notch signaling. Cell Stem Cell 2018;23:530–543.e9.

DOI

75
Wagers AJ, Conboy IM. Cellular and molecular signatures of muscle regeneration: current concepts and controversies in adult myogenesis. Cell 2005;122:659–667.

DOI

76
Wang S, Cheng F, Ji Q et al. Hyperthermia differentially affects specific human stem cells and their differentiated derivatives. Protein Cell 2022;13:615–622.

DOI

77
Wang S, Hu B, Ding Z et al. ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells. Cell Discov 2018;4:2.

DOI

78
Wang S, Yao X, Ma S et al. A single-cell transcriptomic landscape of the lungs of patients with COVID-19. Nat Cell Biol 2021a;23:1314–1328.

DOI

79
Wang S, Zheng Y, Li J et al. Single-cell transcriptomic atlas of primate ovarian aging. Cell 2020;180:585–600.e19.

DOI

80
Wang S, Zheng Y, Li Q et al. Deciphering primate retinal aging at single-cell resolution. Protein Cell 2021b;12:889–898.

DOI

81
Wang Y, Ng S-C. Sphingolipids mediate lipotoxicity in muscular dystrophies. Life Med 2022:lnac015.

DOI

82
Wickham, H. 2016. ggplot2: Elegant Graphics for Data Analysis. Springer

DOI

83
Wilkinson DJ, Piasecki M, Atherton PJ. The age-related loss of skeletal muscle mass and function: measurement and physiology of muscle fibre atrophy and muscle fibre loss in humans. Ageing Res Rev 2018;47:123–132.

DOI

84
Yan P, Li Q, Wang L et al. FOXO3-engineered human ESC-derived vascular cells promote vascular protection and regeneration. Cell Stem Cell 2019;24:447–461.e8.

DOI

85
Yates AD, Achuthan P, Akanni W et al. Ensembl 2020. Nucleic Acids Res 2020;48:D682–D688.

86
Yu W, Clyne M, Khoury MJ et al. Phenopedia and genopedia: disease- centered and gene-centered views of the evolving knowledge of human genetic associations. Bioinformatics 2010;26:145–146.

DOI

87
Zhang W, Li J, Suzuki K, et al. Aging stem cells. A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging. Sci 2015;348:1160–1163.

DOI

88
Zhang H, Li J, Ren J et al. Single-nucleus transcriptomic landscape of primate hippocampal aging. Protein Cell 2021;12:695–716.

DOI

89
Zhang W, Wan H, Feng G et al. SIRT6 deficiency results in developmental retardation in cynomolgus monkeys. Nature 2018;560:661–665.

DOI

90
Zhang W, Zhang S, Yan P et al. A single-cell transcriptomic landscape of primate arterial aging. Nat Commun 2020a;11:2202.

DOI

91
Zhang W, Qu J, Liu G-H, Belmonte JCI. The ageing epigenome and its rejuvenation. Nat Rev Mol Cell Biol 2020b;21:137–150.

DOI

92
Zhang Y, Zheng Y, Wang S et al. Single-nucleus transcriptomics reveals a gatekeeper role for FOXP1 in primate cardiac aging. Protein & Cell 2022:pwac038.

DOI

93
Zhao D, Chen S. Failures at every level: breakdown of the epigenetic machinery of aging. Life Med 2022:lnac016.

DOI

94
Zhao J, Brault JJ, Schild A et al. FoxO3 coordinately activates protein degradation by the autophagic/lysosomal and proteasomal pathways in atrophying muscle cells. Cell Metab 2007;6:472–483.

DOI

95
Zhou Y, Zhou B, Pache L et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10:1523.

DOI

96
Zou, X., Dai, X., Mentis, A.F.A., Esteban, M.A., Liu, L., and Han, L. From monkey single-cell atlases into a broader biomedical perspective. Life Med. 2022:lnac028.

DOI

97
Zou Z, Long X, Zhao Q et al. A single-cell transcriptomic atlas of human skin aging. Dev Cell 2021;56:383–397.e8.

DOI

Outlines

/