Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity

  1. Siming Ma
  2. Akhil Upneja
  3. Andrzej Galecki
  4. Yi-Miau Tsai
  5. Charles F Burant
  6. Sasha Raskind
  7. Quanwei Zhang
  8. Zhengdong D Zhang
  9. Andrei Seluanov
  10. Vera Gorbunova
  11. Clary B Clish
  12. Richard A Miller
  13. Vadim N Gladyshev  Is a corresponding author
  1. Brigham and Women's Hospital, Harvard Medical School, United States
  2. University of Michigan Medical School, United States
  3. Albert Einstein College of Medicine, United States
  4. University of Rochester, United States
  5. Broad Institute, United States

Abstract

Mammalian lifespan differs by >100-fold, but the mechanisms associated with such longevity differences are not understood. Here, we conducted a study on primary skin fibroblasts isolated from 16 species of mammals and maintained under identical cell culture conditions. We developed a pipeline for obtaining species-specific ortholog sequences, profiled gene expression by RNA-seq and small molecules by metabolite profiling, and identified genes and metabolites correlating with species longevity. Cells from longer-lived species up-regulated genes involved in DNA repair and glucose metabolism, down-regulated proteolysis and protein transport, and showed high levels of amino acids but low levels of lysophosphatidylcholine and lysophosphatidylethanolamine. The amino acid patterns were recapitulated by further analyses of primate and bird fibroblasts. The study suggests that fibroblast profiling captures differences in longevity across mammals at the level of global gene expression and metabolite levels and reveals pathways that define these differences.

Article and author information

Author details

  1. Siming Ma

    Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Akhil Upneja

    Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Andrzej Galecki

    Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Yi-Miau Tsai

    Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Charles F Burant

    Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Sasha Raskind

    Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Quanwei Zhang

    Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Zhengdong D Zhang

    Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Andrei Seluanov

    Department of Biology, University of Rochester, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Vera Gorbunova

    Department of Biology, University of Rochester, Rochester, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Clary B Clish

    Broad Institute, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Richard A Miller

    Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Vadim N Gladyshev

    Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
    For correspondence
    vgladyshev@rics.bwh.harvard.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0372-7016

Funding

NIH Office of the Director (AG047745)

  • Vadim N Gladyshev

National Institutes of Health (AG047200)

  • Zhengdong D Zhang
  • Andrei Seluanov
  • Vera Gorbunova
  • Vadim N Gladyshev

National Institutes of Health (AG023122)

  • Vadim N Gladyshev

National Institutes of Health (DK089503)

  • Vadim N Gladyshev

National Institutes of Health (DK097153)

  • Vadim N Gladyshev

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

Copyright

© 2016, Ma 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.

Metrics

  • 4,523
    views
  • 917
    downloads
  • 69
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Siming Ma
  2. Akhil Upneja
  3. Andrzej Galecki
  4. Yi-Miau Tsai
  5. Charles F Burant
  6. Sasha Raskind
  7. Quanwei Zhang
  8. Zhengdong D Zhang
  9. Andrei Seluanov
  10. Vera Gorbunova
  11. Clary B Clish
  12. Richard A Miller
  13. Vadim N Gladyshev
(2016)
Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity
eLife 5:e19130.
https://doi.org/10.7554/eLife.19130

Share this article

https://doi.org/10.7554/eLife.19130

Further reading

    1. Cell Biology
    Tamás Visnovitz, Dorina Lenzinger ... Edit I Buzas
    Short Report

    Recent studies showed an unexpected complexity of extracellular vesicle (EV) biogenesis pathways. We previously found evidence that human colorectal cancer cells in vivo release large multivesicular body-like structures en bloc. Here, we tested whether this large EV type is unique to colorectal cancer cells. We found that all cell types we studied (including different cell lines and cells in their original tissue environment) released multivesicular large EVs (MV-lEVs). We also demonstrated that upon spontaneous rupture of the limiting membrane of the MV-lEVs, their intraluminal vesicles (ILVs) escaped to the extracellular environment by a ‘torn bag mechanism’. We proved that the MV-lEVs were released by ectocytosis of amphisomes (hence, we termed them amphiectosomes). Both ILVs of amphiectosomes and small EVs separated from conditioned media were either exclusively CD63 or LC3B positive. According to our model, upon fusion of multivesicular bodies with autophagosomes, fragments of the autophagosomal inner membrane curl up to form LC3B positive ILVs of amphisomes, while CD63 positive small EVs are of multivesicular body origin. Our data suggest a novel common release mechanism for small EVs, distinct from the exocytosis of multivesicular bodies or amphisomes, as well as the small ectosome release pathway.

    1. Cell Biology
    Yajun Zhai, Peiyi Liu ... Gongzheng Hu
    Research Article

    Discovering new strategies to combat the multidrug-resistant bacteria constitutes a major medical challenge of our time. Previously, artesunate (AS) has been reported to exert antibacterial enhancement activity in combination with β-lactam antibiotics via inhibition of the efflux pump AcrB. However, combination of AS and colistin (COL) revealed a weak synergistic effect against a limited number of strains, and few studies have further explored its possible mechanism of synergistic action. In this article, we found that AS and EDTA could strikingly enhance the antibacterial effects of COL against mcr-1- and mcr-1+ Salmonella strains either in vitro or in vivo, when used in triple combination. The excellent bacteriostatic effect was primarily related to the increased cell membrane damage, accumulation of toxic compounds and inhibition of MCR-1. The potential binding sites of AS to MCR-1 (THR283, SER284, and TYR287) were critical for its inhibition of MCR-1 activity. Additionally, we also demonstrated that the CheA of chemosensory system and virulence-related protein SpvD were critical for the bacteriostatic synergistic effects of the triple combination. Selectively targeting CheA, SpvD, or MCR using the natural compound AS could be further investigated as an attractive strategy for the treatment of Salmonella infection. Collectively, our work opens new avenues toward the potentiation of COL and reveals an alternative drug combination strategy to overcome COL-resistant bacterial infections.