1. Computational and Systems Biology

Lack of evidence for increased transcriptional noise in aged tissues

  1. Olga Ibañez-Solé
  2. Alex M Ascensión
  3. Marcos J Araúzo-Bravo  Is a corresponding author
  4. Ander Izeta  Is a corresponding author
  1. Biodonostia Health Research Institute, Spain
https://doi.org/10.7554/eLife.80380
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  1. Olga Ibañez-Solé
  2. Alex M Ascensión
  3. Marcos J Araúzo-Bravo
  4. Ander Izeta
(2022)
Lack of evidence for increased transcriptional noise in aged tissues
eLife 11:e80380.
https://doi.org/10.7554/eLife.80380
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Abstract

Aging is often associated with a loss of cell type identity that results in an increase in transcriptional noise in aged tissues. If this phenomenon reflects a fundamental property of aging remains an open question. Transcriptional changes at the cellular level are best detected by single-cell RNA sequencing (scRNAseq). However, the diverse computational methods used for the quantification of age-related loss of cellular identity have prevented reaching meaningful conclusions by direct comparison of existing scRNAseq datasets. To address these issues we created Decibel, a Python toolkit that implements side-to-side four commonly used methods for the quantification of age-related transcriptional noise in scRNAseq data. Additionally, we developed Scallop, a novel computational method for the quantification of membership of single cells to their assigned cell type cluster. Cells with a greater Scallop membership score are transcriptionally more stable. Application of these computational tools to seven aging datasets showed large variability between tissues and datasets, suggesting that increased transcriptional noise is not a universal hallmark of aging. To understand the source of apparent loss of cell type identity associated with aging, we analyzed cell type-specific changes in transcriptional noise and the changes in cell type composition of the mammalian lung. No robust pattern of cell type-specific transcriptional noise alteration was found across aging lung datasets. In contrast, age-associated changes in cell type composition of the lung were consistently found, particularly of immune cells. These results suggest that claims of increased transcriptional noise of aged tissues should be reformulated.

Data availability

Code availabilityThe Decibel and Scallop repositories can be found at https://gitlab.com/olgaibanez/decibel and https: //gitlab.com/olgaibanez/scallop, respectively. The reproducible Jupyter notebooks with the analyses carried out in this study can be found in figshare (https://doi.org/10.6084/m9.figshare.20402817.v1).

The following previously published data sets were used

Article and author information

Author details

  1. Olga Ibañez-Solé

    Computational Biology and Systems Biomedicine Group, Biodonostia Health Research Institute, San Sebastian, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0552-9793

  2. Alex M Ascensión

    Computational Biology and Systems Biomedicine Group, Biodonostia Health Research Institute, San Sebastian, Spain
    Competing interests
    The authors declare that no competing interests exist.

  3. Marcos J Araúzo-Bravo

    Computational Biology and Systems Biomedicine Group, Biodonostia Health Research Institute, San Sebastian, Spain
    For correspondence
    mararabra@yahoo.co.uk
    Competing interests
    The authors declare that no competing interests exist.

  4. Ander Izeta

    Tissue Engineering Laboratory, Biodonostia Health Research Institute, San Sebastian, Spain
    For correspondence
    ander.izeta@biodonostia.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1879-7401

Funding

la Caixa" Foundation " (LCF/BQ/IN18/11660065)

  • Olga Ibañez-Solé

Instituto de Salud Carlos III (AC17/00012)

  • Olga Ibañez-Solé
  • Alex M Ascensión
  • Ander Izeta

Instituto de Salud Carlos III (PI19/01621)

  • Olga Ibañez-Solé
  • Alex M Ascensión
  • Ander Izeta

Ministerio de Ciencia e Innovación (PID2020-119715GB-I00)

  • Olga Ibañez-Solé
  • Alex M Ascensión
  • Ander Izeta

European Regional Development Fund (MCIN/AEI/10.13039/501100011033)

  • Olga Ibañez-Solé
  • Alex M Ascensión
  • Ander Izeta

H2020 Marie Skłodowska-Curie Actions (713673)

  • Olga Ibañez-Solé

Eusko Jaurlaritza (PRE_2020_2_0081)

  • Alex M Ascensión

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

Reviewing Editor

  1. Marcus M Seldin, University of California, Irvine, United States

Publication history

  1. Received: May 18, 2022
  2. Accepted: December 23, 2022
  3. Accepted Manuscript published: December 28, 2022 (version 1)

Copyright

© 2022, Ibañez-Solé 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. Olga Ibañez-Solé
  2. Alex M Ascensión
  3. Marcos J Araúzo-Bravo
  4. Ander Izeta
(2022)
Lack of evidence for increased transcriptional noise in aged tissues
eLife 11:e80380.
https://doi.org/10.7554/eLife.80380

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