Multi-omic rejuvenation of human cells by maturation phase transient reprogramming

  1. Diljeet Gill
  2. Aled Parry
  3. Fátima Santos
  4. Hanneke Okkenhaug
  5. Christopher D Todd
  6. Irene Hernando-Herraez
  7. Thomas M Stubbs
  8. Inês Milagre  Is a corresponding author
  9. Wolf Reik  Is a corresponding author
  1. Babraham Institute, United Kingdom
  2. Chronomics Limited, United Kingdom
  3. Instituto Gulbenkian de Ciência, Portugal
  4. Altos Labs, United Kingdom

Abstract

Ageing is the gradual decline in organismal fitness that occurs over time leading to tissue dysfunction and disease. At the cellular level, ageing is associated with reduced function, altered gene expression and a perturbed epigenome. Somatic cell reprogramming, the process of converting somatic cells to induced pluripotent stem cells (iPSCs), can reverse these age-associated changes. However, during iPSC reprogramming, somatic cell identity is lost, and can be difficult to reacquire as re-differentiated iPSCs often resemble foetal rather than mature adult cells. Recent work has demonstrated that the epigenome is already rejuvenated by the maturation phase of reprogramming, which suggests full iPSC reprogramming is not required to reverse ageing of somatic cells. Here we have developed the first 'maturation phase transient reprogramming' (MPTR) method, where reprogramming factors are expressed until this rejuvenation point followed by withdrawal of their induction. Using dermal fibroblasts from middle age donors, we found that cells temporarily lose and then reacquire their fibroblast identity during MPTR, possibly as a result of epigenetic memory at enhancers and/or persistent expression of some fibroblast genes. Excitingly, our method substantially rejuvenated multiple cellular attributes including the transcriptome, which was rejuvenated by around 30 years as measured by a novel transcriptome clock. The epigenome, including H3K9me3 histone methylation levels and the DNA methylation ageing clock, was rejuvenated to a similar extent. The magnitude of rejuvenation instigated by MTPR appears substantially greater than that achieved in previous transient reprogramming protocols. In addition, MPTR fibroblasts produced youthful levels of collagen proteins, and showed partial functional rejuvenation of their migration speed. Finally, our work suggests that more extensive reprogramming does not necessarily result in greater rejuvenation but instead that optimal time windows exist for rejuvenating the transcriptome and the epigenome. Overall, we demonstrate that it is possible to separate rejuvenation from complete pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.

Data availability

DNA methylation array and RNA-seq data are available on Gene Expression Omnibus under the accession number: GSE165180.

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

Article and author information

Author details

  1. Diljeet Gill

    Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5725-2466
  2. Aled Parry

    Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5192-3727
  3. Fátima Santos

    Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3854-4084
  4. Hanneke Okkenhaug

    Imaging Facility, Babraham Institute, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0669-4069
  5. Christopher D Todd

    Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  6. Irene Hernando-Herraez

    Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
    Competing interests
    No competing interests declared.
  7. Thomas M Stubbs

    Chronomics Limited, Norwich, United Kingdom
    Competing interests
    Thomas M Stubbs, is CEO and shareholder of Chronomics.
  8. Inês Milagre

    Laboratory for Epigenetic Mechanisms, Instituto Gulbenkian de Ciência, Oeiras, Portugal
    For correspondence
    imilagre@igc.gulbenkian.pt
    Competing interests
    No competing interests declared.
  9. Wolf Reik

    Altos Labs, Cambridge, United Kingdom
    For correspondence
    wolf.reik@babraham.ac.uk
    Competing interests
    Wolf Reik, is a consultant and shareholder of Cambridge Epigenetix. Is employed by Altos Labs..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0216-9881

Funding

Biotechnology and Biological Sciences Research Council

  • Diljeet Gill
  • Fátima Santos
  • Hanneke Okkenhaug
  • Christopher D Todd
  • Irene Hernando-Herraez
  • Thomas M Stubbs
  • Inês Milagre
  • Wolf Reik

Wellcome Trust

  • Aled Parry

Milky Way Research Foundation

  • Diljeet Gill
  • Wolf Reik

Wellcome Investigator award (210754/Z/18/Z)

  • Wolf Reik

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

Copyright

© 2022, Gill 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

  • 77,295
    views
  • 9,094
    downloads
  • 106
    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. Diljeet Gill
  2. Aled Parry
  3. Fátima Santos
  4. Hanneke Okkenhaug
  5. Christopher D Todd
  6. Irene Hernando-Herraez
  7. Thomas M Stubbs
  8. Inês Milagre
  9. Wolf Reik
(2022)
Multi-omic rejuvenation of human cells by maturation phase transient reprogramming
eLife 11:e71624.
https://doi.org/10.7554/eLife.71624

Share this article

https://doi.org/10.7554/eLife.71624

Further reading

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics
    Omid Gholamalamdari, Tom van Schaik ... Andrew S Belmont
    Research Article

    Models of nuclear genome organization often propose a binary division into active versus inactive compartments yet typically overlook nuclear bodies. Here, we integrated analysis of sequencing and image-based data to compare genome organization in four human cell types relative to three different nuclear locales: the nuclear lamina, nuclear speckles, and nucleoli. Although gene expression correlates mostly with nuclear speckle proximity, DNA replication timing correlates with proximity to multiple nuclear locales. Speckle attachment regions emerge as DNA replication initiation zones whose replication timing and gene composition vary with their attachment frequency. Most facultative LADs retain a partially repressed state as iLADs, despite their positioning in the nuclear interior. Knock out of two lamina proteins, Lamin A and LBR, causes a shift of H3K9me3-enriched LADs from lamina to nucleolus, and a reciprocal relocation of H3K27me3-enriched partially repressed iLADs from nucleolus to lamina. Thus, these partially repressed iLADs appear to compete with LADs for nuclear lamina attachment with consequences for replication timing. The nuclear organization in adherent cells is polarized with nuclear bodies and genomic regions segregating both radially and relative to the equatorial plane. Together, our results underscore the importance of considering genome organization relative to nuclear locales for a more complete understanding of the spatial and functional organization of the human genome.

    1. Cell Biology
    2. Genetics and Genomics
    Keva Li, Nicholas Tolman ... UK Biobank Eye and Vision Consortium
    Research Article

    A glaucoma polygenic risk score (PRS) can effectively identify disease risk, but some individuals with high PRS do not develop glaucoma. Factors contributing to this resilience remain unclear. Using 4,658 glaucoma cases and 113,040 controls in a cross-sectional study of the UK Biobank, we investigated whether plasma metabolites enhanced glaucoma prediction and if a metabolomic signature of resilience in high-genetic-risk individuals existed. Logistic regression models incorporating 168 NMR-based metabolites into PRS-based glaucoma assessments were developed, with multiple comparison corrections applied. While metabolites weakly predicted glaucoma (Area Under the Curve = 0.579), they offered marginal prediction improvement in PRS-only-based models (p=0.004). We identified a metabolomic signature associated with resilience in the top glaucoma PRS decile, with elevated glycolysis-related metabolites—lactate (p=8.8E-12), pyruvate (p=1.9E-10), and citrate (p=0.02)—linked to reduced glaucoma prevalence. These metabolites combined significantly modified the PRS-glaucoma relationship (Pinteraction = 0.011). Higher total resilience metabolite levels within the highest PRS quartile corresponded to lower glaucoma prevalence (Odds Ratiohighest vs. lowest total resilience metabolite quartile=0.71, 95% Confidence Interval = 0.64–0.80). As pyruvate is a foundational metabolite linking glycolysis to tricarboxylic acid cycle metabolism and ATP generation, we pursued experimental validation for this putative resilience biomarker in a human-relevant Mus musculus glaucoma model. Dietary pyruvate mitigated elevated intraocular pressure (p=0.002) and optic nerve damage (p<0.0003) in Lmx1bV265D mice. These findings highlight the protective role of pyruvate-related metabolism against glaucoma and suggest potential avenues for therapeutic intervention.