Abstract

Accumulation of somatic mutations in the mitochondrial genome (mtDNA) has long been proposed as a possible mechanism of mitochondrial and tissue dysfunction that occurs during aging. A thorough characterization of age-associated mtDNA somatic mutations has been hampered by the limited ability to detect low frequency mutations. Here, we used Duplex Sequencing on eight tissues of an aged mouse cohort to detect >89,000 independent somatic mtDNA mutations and show significant tissue-specific increases during aging across all tissues examined which did not correlate with mitochondrial content and tissue function. G→A/C→T substitutions, indicative of replication errors and/or cytidine deamination, were the predominant mutation type across all tissues and increased with age, whereas G→T/C→A substitutions, indicative of oxidative damage, were the second most common mutation type, but did not increase with age regardless of tissue. We also show that clonal expansions of mtDNA mutations with age is tissue and mutation type dependent. Unexpectedly, mutations associated with oxidative damage rarely formed clones in any tissue and were significantly reduced in the hearts and kidneys of aged mice treated at late age with Elamipretide or nicotinamide mononucleotide. Thus, the lack of accumulation of oxidative damage-linked mutations with age suggests a life-long dynamic clearance of either the oxidative lesions or mtDNA genomes harboring oxidative damage.

Data availability

The Duplex-Seq-Pipeline is written in Python and R, but has dependencies written in other languages. The DuplexSeq-Pipeline software has been tested to run on Linux, Windows WSL1, Windows WSL2 and Apple OSX. The software can be obtained at https://github.com/KennedyLab-UW/Duplex-Seq-Pipeline. Raw mouse sequencing data used in this study are available at SRA accension PRJNA727407. The data from Arbeithuber et al. are available at SRA accension PRJNA563921. The final post-processed data, including variant call files, depth information, data summaries, and mutation frequencies, as well as the scripts to perform reproducible production of statistics and figure generation (with the exception of Figure 5C-E) are available at https://github.com/Kennedy-Lab-UW/Sanchez_Contreras_etal_2022.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Monica Sanchez-Contreras

    Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3092-2781
  2. Mariya T Sweetwyne

    Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States
    For correspondence
    sandu@uw.edu
    Competing interests
    No competing interests declared.
  3. Kristine A Tsantilas

    Department of Biochemistry, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4274-6930
  4. Jeremy A Whitson

    Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
  5. Matthew D Campbell

    Department of Radiology, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
  6. Brenden F Kohrn

    Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9948-2131
  7. Hyeon Jeong Kim

    Department of Biology, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
  8. Michael J Hipp

    Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1904-0670
  9. Jeanne Fredrickson

    Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
  10. Megan M Nguyen

    Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
  11. James B Hurley

    Department of Biochemistry, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7754-0705
  12. David J Marcinek

    Department of Radiology, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
  13. Peter S Rabinovitch

    Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7169-3543
  14. Scott R Kennedy

    Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States
    For correspondence
    scottrk@uw.edu
    Competing interests
    Scott R Kennedy, is an equity holder and paid consultant for Twinstrand Biosciences, a for-profit company commercializing Duplex Sequencing. No Twinstrand products were used in the generation of the data..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4444-1145

Funding

National Institute on Aging (P01AG001751)

  • David J Marcinek
  • Peter S Rabinovitch

National Institute on Aging (K01AG062757)

  • Mariya T Sweetwyne

National Institute of Diabetes and Digestive and Kidney Diseases (R21DK128540)

  • Monica Sanchez-Contreras
  • Mariya T Sweetwyne

Congressionally Directed Medical Research Programs (W81XWH-16-1-0579)

  • Scott R Kennedy

National Human Genome Research Institute (R21HG011229)

  • Scott R Kennedy

National Cancer Institute (R21CA259780)

  • Scott R Kennedy

National Institute on Aging (T32AG000057)

  • Kristine A Tsantilas
  • Jeremy A Whitson

National Institute on Aging (T32AG066574)

  • Kristine A Tsantilas

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: This study was performed in accordance to the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to an approved institutional animal care and use committee (IACUC) protocol (2174-23) at the University of Washington.

Reviewing Editor

  1. William Copeland, National Institute of Environmental Health Sciences, United States

Publication history

  1. Preprint posted: September 1, 2022 (view preprint)
  2. Received: September 11, 2022
  3. Accepted: February 15, 2023
  4. Accepted Manuscript published: February 17, 2023 (version 1)

Copyright

© 2023, Sanchez-Contreras et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Monica Sanchez-Contreras
  2. Mariya T Sweetwyne
  3. Kristine A Tsantilas
  4. Jeremy A Whitson
  5. Matthew D Campbell
  6. Brenden F Kohrn
  7. Hyeon Jeong Kim
  8. Michael J Hipp
  9. Jeanne Fredrickson
  10. Megan M Nguyen
  11. James B Hurley
  12. David J Marcinek
  13. Peter S Rabinovitch
  14. Scott R Kennedy
(2023)
The multi-tissue landscape of somatic mtdna mutations indicates tissue specific accumulation and removal in aging
eLife 12:e83395.
https://doi.org/10.7554/eLife.83395

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