Senescence: A gradual path to mortality

Many of the features associated with senescence appear steadily over time before cells stop dividing.
  1. Na Yang
  2. Payel Sen  Is a corresponding author
  1. Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, United States

In 1961, Hayflick and Moorhead discovered that human fibroblast cells cultured in the laboratory could only divide a limited number of times, after which they stopped multiplying but remained metabolically active (Hayflick and Moorhead, 1961). It did not matter how the cells were cultured – whether they were repeatedly transferred, or ‘passaged’, into a fresh environment, or if their growth was interrupted by episodes of freezing – the number of divisions they could make was always finite. This state was termed replicative senescence and was found to occur in a range of cell types.

Further research revealed that senescence is caused by the shortening of caps, or ‘telomeres’, on the end of chromosomes (Bodnar et al., 1998). Every time a cell divides, its telomeres shrink until they reach a critical length that stops the cell from multiplying. Once senescent, cells display unique features such as expressing certain proteins, releasing inflammatory molecules, and loosening tightly packed regions of DNA known as heterochromatin (Hernandez-Segura et al., 2018). New evidence showed that senescence is induced by cell stress as well as successive divisions, and that the number of senescent cells increases as tissues age (van Deursen, 2014).

Despite almost 60 years of research, many questions still remain about senescence; for instance, what happens to cells as they transition in to the senescent state? How does their metabolism change during this shift, and do they take on a new cell identity? Now, in eLife, David Botstein, David Hendrickson and colleagues from Calico Life Sciences – including Michelle Chan as first author – report the results of experiments that exquisitely profile the roadmap cells take on their path to senescence (Chan et al., 2022).

The team used a new experimental design to survey the entire genome and repertoire of RNAs, proteins, and metabolites present in fibroblasts cultured in the laboratory. These patterns were traced over time as the cells grew until they stopped dividing. Chan et al. then used a range of control conditions to pinpoint which changes were specific to replicative senescence. This included repeating the experiment on cells growing at a similar density to senescent cultures, cells that had only been passaged a few times (and therefore unlikely to be senescent), cells that never become senescent, and cells made senescent by radiation-induced stress.

To begin with, Chan et al. measured the level of unique RNAs in single cells to investigate how the genes that fibroblasts expressed changed over time. The data revealed that RNAs known to be expressed in fully senescent cells progressively accumulate throughout the cell cycle. This suggests that senescent cells in vivo may be slowly amassing these features, but not yet expressing the classic biomarkers associated with the end-point of senescence, such as the beta-galactosidase enzyme. This may explain why previous studies found less than 20% of cells in old tissues exhibited these biomarkers, which has led researchers to question the role of senescence in aging (Biran et al., 2017; Idda et al., 2020). Chan et al. also found cells that had experienced replicative senescence (but not senescence induced by radiation) expressed genes related to a subtype of epithelial-to-mesenchymal transition (EMT). This process, which sees epithelial cells lining surfaces of the body lose their identity and become mesenchymal, is common in development and cancer.

Further experiments revealed that cells change how they use and generate energy as they progress towards replicative senescence. Similar metabolic changes have also been observed in models of EMT, further validating the connection between replicative senescence and this transition. Chan et al. discovered that the protein complex YAP1/TEAD1 and its target, the growth factor protein TGFβ2, drove this shift in energy. Applying a drug that stops YAP1 and TEAD1 from assembling (Wang et al., 2016) reduced the expression of signatures associated with mesenchymal cells and senescence.

Finally, Chan et al. identified another signature of replicative stress: the increased expression of Nicotinamide N-methyltransferase (NNMT). This enzyme catalyzes chemical reactions that ultimately prevent certain proteins from condensing DNA. It is possible that by reducing the activity of these proteins, NNMT is able to open up closed regions of the genome, which may explain the reported loss of heterochromatin in senescent cells (Yang and Sen, 2018).

The findings of Chan et al. suggest that cells gradually acquire a number of changes on the path to replicative senescence: they express different genes, rewire their metabolic reactions and take on a new identity similar to mesenchymal cells (Figure 1). Previous studies have shown that removing senescent cells can increase the health- and life-span of mice (Di Micco et al., 2021). Therefore, interventions that target these early changes could help improve the wellbeing of individuals by stopping the cascade of events that lead to replicative senescence.

The journey to replicative senescence.

Healthy cells cultured in the laboratory (left) will undergo continuous rounds of division until they reach a state of growth arrest called replicative senescence (right; shown in blue). To begin with (early and early-middle stages), cells express factors associated with cell cycle progression and growth as well as proteins that maintain chromatin stability. As they progress towards replicative senescence (middle-late stage), they undergo an epithelial-to-mesenchymal transition (EMT) and change their cell identity: this transition is driven by the growth factor protein TGFβ2 and the protein complex YAP1/TEAD1. As cells near replicative senescence (late stage), they exhibit a pro-inflammatory phenotype and secrete cytokines, in addition to expressing a beta-galactosidase enzyme which is detected by a reaction that turns cells blue.

Image credit: Figure created using BioRender.

References

    1. Wang C
    2. Zhu X
    3. Feng W
    4. Yu Y
    5. Jeong K
    6. Guo W
    7. Lu Y
    8. Mills GB
    (2016)
    Verteporfin inhibits YAP function through up-regulating 14-3-3sigma sequestering YAP in the cytoplasm
    American Journal of Cancer Research 6:27–37.

Article and author information

Author details

  1. Na Yang

    Na Yang is in the Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, United States

    Competing interests
    No competing interests declared
  2. Payel Sen

    Payel Sen is in the Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, United States

    For correspondence
    payel.sen@nih.gov
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2809-0901

Publication history

  1. Version of Record published:

Copyright

© 2022, Yang and Sen

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

Metrics

  • 2,433
    views
  • 266
    downloads
  • 1
    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. Na Yang
  2. Payel Sen
(2022)
Senescence: A gradual path to mortality
eLife 11:e77749.
https://doi.org/10.7554/eLife.77749
  1. Further reading

Further reading

    1. Chromosomes and Gene Expression
    2. Evolutionary Biology
    Gülnihal Kavaklioglu, Alexandra Podhornik ... Christian Seiser
    Research Article

    Repression of retrotransposition is crucial for the successful fitness of a mammalian organism. The domesticated transposon protein L1TD1, derived from LINE-1 (L1) ORF1p, is an RNA-binding protein that is expressed only in some cancers and early embryogenesis. In human embryonic stem cells, it is found to be essential for maintaining pluripotency. In cancer, L1TD1 expression is highly correlative with malignancy progression and as such considered a potential prognostic factor for tumors. However, its molecular role in cancer remains largely unknown. Our findings reveal that DNA hypomethylation induces the expression of L1TD1 in HAP1 human tumor cells. L1TD1 depletion significantly modulates both the proteome and transcriptome and thereby reduces cell viability. Notably, L1TD1 associates with L1 transcripts and interacts with L1 ORF1p protein, thereby facilitating L1 retrotransposition. Our data suggest that L1TD1 collaborates with its ancestral L1 ORF1p as an RNA chaperone, ensuring the efficient retrotransposition of L1 retrotransposons, rather than directly impacting the abundance of L1TD1 targets. In this way, L1TD1 might have an important role not only during early development but also in tumorigenesis.

    1. Chromosomes and Gene Expression
    Shihui Chen, Carolyn Marie Phillips
    Research Article

    RNA interference (RNAi) is a conserved pathway that utilizes Argonaute proteins and their associated small RNAs to exert gene regulatory function on complementary transcripts. While the majority of germline-expressed RNAi proteins reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here, we find that the small RNA biogenesis machinery is spatially and temporally organized during Caenorhabditis elegans embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we further demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.