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Aging cell
05, 2024;23 (5): e14100.

Aging clock based on nucleosome reorganisation derived from cell-free DNA.

Mariya Shtumpf, Seihee Jeong, Milena Bikova, Hulkar Mamayusupova, Luminita Ruje, Vladimir B Teif
Author Information
  1. Mariya Shtumpf: School of Life Sciences, University of Essex, Colchester, UK. ORCID
  2. Seihee Jeong: School of Life Sciences, University of Essex, Colchester, UK.
  3. Milena Bikova: School of Life Sciences, University of Essex, Colchester, UK.
  4. Hulkar Mamayusupova: School of Life Sciences, University of Essex, Colchester, UK.
  5. Luminita Ruje: School of Life Sciences, University of Essex, Colchester, UK.
  6. Vladimir B Teif: School of Life Sciences, University of Essex, Colchester, UK. ORCID
PMID: 38337183 DOI: 10.1111/acel.14100

Abstract

Aging induces systematic changes in the distribution of nucleosomes, which affect gene expression programs. Here we reconstructed nucleosome maps based on cell-free DNA (cfDNA) extracted from blood plasma using four cohorts of people of different ages. We show that nucleosomes tend to be separated by larger genomic distances in older people, and age correlates with the nucleosome repeat length (NRL). Furthermore, we developed the first aging clock based on cfDNA nucleosomics. Machine learning based on cfDNA distance distributions allowed predicting person's age with the median absolute error of 3-3.5���years.

Keywords

NRL aging cell���free DNA cfDNA liquid biopsy nucleosome positioning nucleosome repeat length nucleosomics

References

  1. Geroscience. 2024 Apr;46(2):1789-1806 [PMID: 37924441]
  2. Aging Cell. 2021 Sep;20(9):e13452 [PMID: 34415665]
  3. Genome Res. 2023 Oct;33(10):1649-1661 [PMID: 37699659]
  4. Nature. 2019 Jun;570(7761):385-389 [PMID: 31142840]
  5. Nat Struct Mol Biol. 2012 Nov;19(11):1185-92 [PMID: 23085715]
  6. Nat Aging. 2021 Aug;1(8):715-733 [PMID: 34514433]
  7. Nucleic Acids Res. 2019 Dec 2;47(21):11181-11196 [PMID: 31665434]
  8. Clin Epigenetics. 2024 Apr 1;16(1):50 [PMID: 38561804]
  9. Aging Cell. 2019 Feb;18(1):e12890 [PMID: 30575273]
  10. Chromosoma. 2022 Jun;131(1-2):19-28 [PMID: 35061087]
  11. Aging Cell. 2024 May;23(5):e14100 [PMID: 38337183]
  12. Nat Med. 2019 Dec;25(12):1928-1937 [PMID: 31768066]
  13. Gerontology. 1989;35(5-6):268-74 [PMID: 2630381]
  14. Nat Commun. 2021 May 28;12(1):3230 [PMID: 34050156]
  15. Nat Rev Genet. 2018 Jun;19(6):371-384 [PMID: 29643443]
  16. BMC Genomics. 2017 Feb 14;18(1):158 [PMID: 28196481]
  17. Exp Cell Res. 1987 Apr;169(2):458-67 [PMID: 3556427]
  18. Nature. 2023 Apr;616(7958):814-821 [PMID: 37046086]
  19. PLoS Genet. 2016 Jul 18;12(7):e1006162 [PMID: 27428049]
  20. Cell. 2016 Jan 14;164(1-2):57-68 [PMID: 26771485]
  21. Nat Methods. 2012 Mar 04;9(4):357-9 [PMID: 22388286]

Grants

  1. BB/X511171/1/Biotechnology and Biological Sciences Research Council
  2. EDDPMA-Nov21\100044/Cancer Research UK
  3. SEBPCTA-2022/100001/Cancer Research UK

MeSH Term

Nucleosomes
Humans
Aging
Cell-Free Nucleic Acids
Aged
Aged, 80 and over
Middle Aged
Male
Female
Adult

Chemicals

Nucleosomes
Cell-Free Nucleic Acids
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 66

Word Cloud

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