REVIEWS

Adult stem cells

Cellular and epigenetic drivers

of stem cell ageing
Maria Ermolaeva1*, Francesco Neri   1*, Alessandro Ori1* and K. Lenhard Rudolph1,2*
Abstract | Adult tissue stem cells have a pivotal role in tissue maintenance and regeneration
throughout the lifespan of multicellular organisms. Loss of tissue homeostasis during post-​
reproductive lifespan is caused, at least in part, by a decline in stem cell function and is associated
with an increased incidence of diseases. Hallmarks of ageing include the accumulation of
molecular damage, failure of quality control systems, metabolic changes and alterations in
epigenome stability. In this Review , we discuss recent evidence in support of a novel concept
whereby cell-​intrinsic damage that accumulates during ageing and cell-​extrinsic changes in
ageing stem cell niches and the blood result in modifications of the stem cell epigenome. These
cumulative epigenetic alterations in stem cells might be the cause of the deregulation of
developmental pathways seen during ageing. In turn, they could confer a selective advantage to
mutant and epigenetically drifted stem cells with altered self-​renewal and functions, which
contribute to the development of ageing-​associated organ dysfunction and disease.

Quiescence
A reversible state that can
describe non-​dividing stem
cells. Cells are in the G0 phase
of the cell cycle, characterized
by very low metabolic,
transcriptional and proliferative
activities.
1
Leibniz Institute on Aging –
Fritz Lipmann Institute (FLI),
Jena, Germany.
2
Medical Faculty Jena,
University Hospital Jena
(UKJ), Jena, Germany.
*e-​mail: Maria.Ermolaeva@
leibniz-​fli.de;
Francesco.Neri@leibniz-​fli.de;
Alessandro.Ori@leibniz-​fli.de;
Lenhard.Rudolph@
leibniz-​fli.de
https://doi.org/10.1038/
s41580-018-0020-3
The ‘shadowed’ regulation of developmental path-
ways has been proposed as a new theory of ageing1–3.
According to this theory, developmental pathways
cooperate to ensure that embryonic and postnatal
development leads to optimal fitness of the organism at
reproductive age. During post-​reproductive age, there
is little evolutionary selection for the maintenance of
organisms, as the main function of the individual in
terms of evolution is fulfilled. According to this theory,
the same pathways that control organism development
to the point of optimal fitness become deregulated at
post-​reproductive age and promote the ageing process.
Given that adult stem cells (also known as tissue stem
cells) are the remnants of embryonic development
in which many of the key developmental pathways
remain actively in use to ensure postnatal organ homeo­
stasis and regeneration, these cell populations may be
particularly prone to losing accuracy in regulating
developmental pathways.
Adult stem cells are rare cells that are located in
specialized niches that contribute to the proper control
of stem cell self-​renewal and differentiation. Adult stem
cells retain the capacity to differentiate into the cell types
of the organ in which they reside, and they contribute,
throughout life, to the regeneration and homeostasis
of almost all tissues. During ageing, the functionality
of adult stem cells declines, and various types of cell-​
intrinsic damage and alterations in the niche and the
circulating blood have been demonstrated to contribute
to this age-​related decline. Adult stem cells are the long-
est living proliferative cells in multicellular organisms.
Therefore, they have an intrinsically increased risk of
acquiring DNA mutations and epigenetic alterations,
impairing the fidelity of gene expression.
Stem cells have special mechanisms to minimize
the risk of damage accumulation. These include the
suppression of metabolic activity, to reduce the intra­
cellular production of toxic metabolites, and the
maintenance of a state of quiescence to reduce
replication-​associated DNA damage4. Minimizing the
risk of DNA damage is important, as DNA repair sys-
tems generally are not more active in stem cells than in
other cells, but by contrast, DNA repair can be even more
error prone in the G0 and G1 phases of the cell cycle in
which many stem cells reside5,6. Stem cell quiescence and
the associated reduction in transcription and translation
contribute to the maintenance of a healthy proteome
(proteostasis), as the folding and refolding and the
removal of misfolded and damaged proteins are highly
energy-​consuming processes that limit the energy avail-
able to other quality control systems7,8. Stem cells employ
various damage removal systems, including autophagy
(which can remove damaged proteins and organelles),
but it is unclear whether these systems are any more
efficient in stem cells than in somatic cells or whether
stem cells rely on reducing damage load by maintaining
a quiescent state, as in the case of DNA damage9. Despite
the protective measures in place, stem cells accumulate
molecular damage and lose functionality during ageing,
which involves cell-​intrinsic processes as well as ageing-​
associated alterations in the stem cell microenvironment
(niche) and in the blood circulation10,11.

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Progenitor cells
Cells that are constantly
generated from stem cells with
reduced self-​renewal and high
proliferative activity; needed
for production of cell types for
tissue regeneration and
homeostasis.
In this Review, we first describe the types of intra-
cellular damage that accumulate in stem cells during
ageing, as well as extrinsic factors, such as systemic
factors, metabolism and changes in the stem cell niche,
that contribute to the functional decline of stem cells
during ageing. We then discuss mechanisms linking
damage accumulation to epigenome stability in ageing
stem cells and the deregulation of developmental path-
ways. We propose that this axis represents a major driver
of epigenetic drift and the selection of clonal mutations
in stem and progenitor cells, resulting in ageing-​associated
decline in the maintenance of tissue and organ function
and the onset of diseases, including cancer.
Molecular damage and quality control
Many types of damage that accumulate in stem cells
during ageing are driven by altered metabolism and a
decline in quality control pathways, which can result in
a multitude of cellular malfunctions, including genetic
and epigenetic insults (Fig. 1).
Metabolic changes in ageing stem cells
Depending on the tissue and the niche they reside in and
their activation status (for example, quiescence versus
proliferation and differentiation), the metabolic state
of stem cells can be biased towards glycolysis, such as
in quiescent haematopoietic stem cells (HSCs)12,13, or
towards oxidative phosphorylation (OXPHOS), as in
differentiating HSCs14 and intestinal stem cells (ISCs)15
(Box 1). These specific metabolic states are important
for preventing the accumulation of molecular damage
and for the maintenance of stem-​cell-specific epigenetic
landscapes.
The regulation of stem cell metabolism is disrupted
during ageing, causing cellular malfunctions. Even in
cells that rely mainly on glycolysis, mitochondria produce

Ageing
↓ Autophagy ↓ Ubiquitin-proteasome system
↓ UPRmt ↓ Asymmetric division
1 Accumulation of protein aggregates
and dysfunctional organelles,
including mitochondria

Toxic protein Mitochondrial

aggregates damage

Increase in mitochondrial damage

and dysfunction disrupts the balance
between glycolysis and OXPHOS, Increased levels
causing changes in the production of ROS and stress
of epigenetic cofactors and regulators signalling disrupt
stem cell function
Glycolysis OXPHOS ROS
2 3
p38 Nuclear DNA
Acetyl-CoA α-KG and SAM FOXO damage

NAD+

Histone DNA and histone Stress Cell Cell

acetylation methylation signalling death senescence

Epigenetic Aberrant proliferation Depletion of

alterations and differentiation stem cell pool

Fig. 1 | Molecular damage in ageing stem cells. Cell-​intrinsic changes that occur in ageing stem cells are highly
interconnected. A decline in protein quality control pathways, which include mechanisms that would normally ensure the
clearance of damaged proteins (autophagy and proteasome-​mediated degradation) and damaged organelles (mitophagy
and mitochondrial unfolded protein response (UPRmt)), as well as their asymmetric distribution during self-​renewing
divisions, leads to the accumulation of toxic protein aggregates and dysfunctional mitochondria (step 1). Damaged
mitochondria produce an excess of reactive oxygen species (ROS), which induce further mitochondrial damage (including
mitochondrial DNA damage) and lead to a metabolic imbalance between glycolysis and oxidative phosphorylation
(OXPHOS) (step 2). The glycolysis–OXPHOS balance is crucial for the homeostasis of stem cells, and its disruption leads to
inadequate levels of epigenetic cofactors and regulators (step 2). ROS accumulation induces nuclear DNA damage,
which is exacerbated by DNA replication errors and faulty DNA repair in aged stem cells, promoting cell senescence and
apoptotic cell death. Although moderate production of ROS and other stresses is required for the control of proliferation
and differentiation of stem cells in normal physiology (at young age), high levels of ROS activate stress mediators (p38 and
forkhead box protein (FOXO)), leading to aberrant stem cell function (step 3). Altogether, these changes result in defective
self-​renewal and the depletion of stem cell reserves. α-​KG, α-​ketoglutarate; SAM, S-​adenosylmethionine.

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Box 1 | Stem cell metabolism — links to niche and epigenetic state

Depending on the tissue of origin, the niches populated by adult stem
cells vary in their characteristics as does the average number of cell
divisions: intestinal stem cells (isCs) are highly proliferative and exposed
to the gut lumen, including commensal microorganisms and food
metabolites86, whereas quiescent haematopoietic stem cells (HsCs)
divide less frequently and reside in a protected and hypoxic bone
marrow niche13. Muscle stem cells (MusCs, also known as satellite cells)
are scattered on the surface of myofibres and start dividing in
response to muscle injury230. Diverse niches and specific proliferation
requirements probably determine the distinct metabolic signatures of
adult stem cells. Pluripotent stem cells, mesenchymal stem cells and
quiescent HsCs are biased towards glycolysis13,231,232, which is achieved
by inhibiting entry of pyruvate into the tricarboxylic acid (tCa) cycle,
a step that is essential for oxidative phosphorylation (OXPHOs)232,233.
in quiescent HsCs, the OXPHOs-​to-glycolysis switch is mediated by the
hypoxia-​inducible factor 1– pyruvate dehydrogenase kinase pathway
(HIF1–PKD2/PKD4 pathway), which promotes pyruvate retention in
response to low oxygen levels of the niche13,14. HsCs also inhibit
OXPHOs by removal of active mitochondria through autophagy9. High
glycolysis and low OXPHOs are critical for quiescence and self-​renewal
of HsCs: mutations that impair HiF1 signalling lead to exhaustion of the
stem cell pool by inducing untimely differentiation of HsCs14,233;
mitochondrial changes that promote OXPHOs elicit a comparable
outcome234. the ability to switch from glycolysis to OXPHOs is
equally critical for the functionality of HsCs; its loss impedes their
differentiation and repopulation capacity14. similar to activated HsCs,
which utilize OXPHOs metabolism for self-​renewal and differentiation,
isCs rely on OXPHOs supported by carbon substrates provided by niche
Paneth cells, which perform glycolysis15. Controversial data exist for
dormant versus activated and differentiating MusCs: on the one hand,
the prevalence of OXPHOs was observed in activated (versus dormant)
MusCs freshly isolated from the injured muscle235; on the other hand,
fibre culture experiments associated MusC differentiation with the
metabolic signature of enhanced glycolysis25. Potential biases related to
cell culture conditions need to be taken into account in this case. Overall,
reactive oxygen species produced via OXPHOs appear to facilitate cell
proliferation, while glycolysis renders cells sensitive to systemic nutrient
cues. the use of glycolysis over OXPHOs also affects the epigenome
of stem cells: having pyruvate excluded from mitochondria, the tCa
cycle consumes glutamate as a carbon source, reducing levels of
α-ketoglutarate (α-​KG), the cofactor of Jumonji C histone demethylases
and of methylcytosine dioxygenase tet enzymes (DNa demethylases).
Glycolytic bias increases cellular availability of acetyl-​Coa, a cofactor
of histone acetyltransferases236, and promotes biosynthesis of
S-​adenosylmethionine required for histone and DNa methylation. reduced
OXPHOs (as in quiescent HsCs) has a negative impact on the activity of
the NaD-​dependent histone deacetylase sirtuin family by affecting the
NaD+:NaDH ratio237, making chromatin less compact and increasing
exposure of DNa to modifications and damage. the metabolism of stem
cells is thus tightly linked to their epigenetic state.

HIF1–PKD2/PKD4 pathway
A signalling pathway that
adjusts cellular metabolism to
reduced levels of oxygen
(hypoxia), by suppressing the
entry of glycolytic metabolites
into mitochondria.
p38
A MAPK that regulates
expression of innate immune
molecules and stress effectors
in response to cell-​extrinsic
and cell-​intrinsic stimuli.
FOXO
A subgroup of the forkhead
family of transcription factors
regulated by the insulin–PI3K–
AKT pathway and involved in
induction of stress response
and survival genes.
Myeloid bias
Myeloid bias designates
preferential differentiation of
haematopoietic stem cells into
myeloid cells, such as
monocytes, macrophages,
neutrophils, platelets and
dendritic cells.
substantial levels of reactive oxygen species (ROS), which
damage the mitochondrial genome and cause imbal-
ance between glycolysis and OXPHOS16. The elevated
production of ROS by damaged mitochondria initiates
intracellular processes that lead to nuclear DNA damage17
(Fig. 1). High ROS levels also induce aberrant stem cell
differentiation by activating stress signalling pathways
such as p38 and forkhead box protein (FOXO)16,18–20. In
the ageing intestine of Drosophila melanogaster, high
stress levels and deregulation of stress responses induce
hyperproliferation of ISCs, leading to loss of homeostasis
and life-​limiting intestinal dysplasia21–23. Accumulation
of mitochondrial DNA mutations leads to the altered
production of mitochondrial epigenetic cofactors, which
cause epigenome changes in ageing stem cells (Fig. 1).
For example, levels of mitochondrial NAD+, an essen-
tial cofactor of the NAD-​dependent protein deacetylase
sirtuin 1 (SIRT1), are reduced during ageing24. Active
SIRT1 promotes self-​renewal and inhibits differentiation
of neuronal progenitors and muscle stem cells (MuSCs;
also known as satellite cells)25. Restoring NAD+ levels was
found to improve the functionality of aged MuSCs in a
SIRT1-dependent manner24.
A recent study linked defective self-​renewal and
myeloid bias of ageing HSCs to epigenetic changes driven
by increased mitochondrial activity9. Elevated OXPHOS
in old HSCs was attributed to the reduced removal of
active mitochondria owing to the autophagy machinery
becoming impaired9,26. Only a fraction (approximately
30%) of aged HSCs had adequate levels of autophagy
sufficient to suppress OXPHOS. Importantly, knockout
of the ATG12 autophagy gene in young adult HSCs leads
to their accelerated ageing, characterized by elevated
OXPHOS, reduced self-​renewal capacity and skewed
differentiation9. Activated HSCs, which contain active
mitochondria and resemble aged, autophagy-​impaired
cells, had increased levels of α-​ketoglutarate (α-​KG)
and reduced levels of S-​adenosylmethionine (SAM).
Fluctuations of these cofactors are probably responsible
for ageing-​associated epigenetic changes, reduced self-​
renewal and possibly myeloid bias in HSCs27. Age-​linked
epigenetic shifts in stem cells thus seem to be linked to
metabolic alterations that occur during ageing.
Ageing-​associated protein damage
At young age, proteostasis is supported by protein quality
control pathways, such as autophagy, the ubiquitin pro-
teasome system (UPS) and the unfolded protein response
in the mitochondria (UPRmt) (reviewed in ref.28) and the
endoplasmic reticulum (UPRER). The efficiency of these
protein quality control systems, which ensure the cor-
rect folding and targeting of proteins and the removal of
misfolded or mislocalized proteins, declines with ageing,
compromising cell function29 (Fig. 1). The mechanisms
of this decline are incompletely understood, but reduced
activity of regulatory transcription factors such as
FOXO30 and epigenetic silencing of effector genes such
as UPRmt components31 seem to contribute.
UPRmt and autophagy in stem cell ageing. Ageing HSCs
exhibit increased levels of mitochondrial protein folding
stress, which is counteracted by the SIRT7-dependent
branch of UPRmt (ref.32). SIRT7-deficient animals showed
early ageing of HSCs accompanied by myeloid bias
and reduced reconstitution capacity, whereas SIRT7
overexpression ameliorated ageing-​associated defects
in HSCs. Autophagy was shown to decline with ageing in
HSCs and MuSCs9,26, leading to impaired self-​renewal
and senescence. Autophagy defects in both cell types
converge at mitochondrial deregulation: in MuSCs,
impaired autophagy was linked to alterations of mito-
chondrial membrane potential and enhanced ROS

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Co-​chaperone
A protein that regulates the
activity of chaperones, such as
heat shock protein 70 (HSP70)
and HSP90, during protein
folding.
Polycomb group protein
A chromatin remodeller
implicated in the timely
silencing of developmental
genes.
Nucleotide excision repair
(NER). A DNA repair pathway
responsible for removal and
repair of DNA helix-​distorting
lesions, such as cyclobutane
pyrimidine dimers and
pyrimidine (6–4) pyrimidone
photoproducts.
Non-​homologous end
joining
(NHEJ). A DNA repair pathway
that repairs double-​strand
DNA breaks by directly ligating
the broken ends without the
use of a homologous template
(a rapid but error-​prone
process).
production by mitochondria, whereas in HSCs, it led
to elevated OXPHOS and imbalance of mitochondrial
epigenetic cofactors (SAM and α-​KG), reshaping the
epigenetic landscape of HSCs towards myeloid lineage
(Box 1; Fig. 1). A recent study linked impaired autophagy
in MuSCs to ageing-​associated reprogramming of rhyth-
mic gene expression during circadian oscillations33. It is
possible that epigenetic alterations induced by ageing-​
associated mitochondrial dysfunction contribute to the
epigenetic rewiring of circadian regulated genes.
Protein synthesis regulation in stem cells. Low rates of
protein translation support cellular proteostasis by redu­
cing pressure on protein folding and sorting machineries.
At the organism level, reduced protein synthesis (follow-
ing inactivation of protein translation genes) facilitated
reduced energy expenditure, enhanced proteostasis and
extended lifespan in yeast and animal models (reviewed in
ref.34). Nucleolar expansion, enhanced ribosomal biogen-
esis and elevated protein synthesis are hallmarks of pre-
mature ageing in humans35. In D. melanogaster germline
stem cells, elevated protein synthesis accompanies the
transition from self-​renewal to differentiation36. Unlike
other haematopoietic cells, HSCs need to maintain tightly
regulated, low rates of protein synthesis, as increases and
decreases in protein synthesis rates impair HSC self-​
renewal and function37. The crosstalk between protein
synthesis rates and the epigenetic regulation of stem cell
self-​renewal and differentiation remains to be elucidated.
UPRER, proteasome and chaperones in stem cell ageing.
UPRER ensures proper folding and sorting of newly
produced proteins in the endoplasmic reticulum, while
cytosolic chaperones and the UPS support refolding or
timely degradation of damaged proteins. UPRER regulates
the transition of D. melanogaster ISCs from a quiescent
to a proliferating state in response to intrinsic and extrin-
sic stimuli38. In old flies, overactive UPRER promotes
aberrant proliferation of ISCs and intestinal dysplasia,
leading to death, while inhibition of intestinal UPRER at
old age confers lifespan extension38. The pluripotency of
embryonic stem cells depends upon tightly controlled
proteostasis, which requires high levels of chaperones
and the protea­some39–41. A comparable protein quality
control landscape has not yet been reported for adult
stem cells. It was nonetheless shown that increased
expression of the co-​chaperone endoplasmic reticu-
lum DNA J domain-​containing protein 4 (ERDJ4; also
known as DNAJB9) enhances stemness and repopulation
capacity of HSCs by supporting protein folding in the
endoplasmic reticulum42. The activity of the proteasome
and the expression of chaperones both decline with age,
providing additional evidence for the accumulation of
protein damage in stem cell ageing29.
Segregation of damaged cellular components in ageing
stem cells. Owing to their high sensitivity to protein
damage, stem cells developed specific, efficient ways of
handling damaged proteins. During differentiation, stem
cells divide asymmetrically, giving rise to a stem cell and
a differentiating cell. In yeast, in D. melanogaster ISCs
and neuroblasts43 and in mammalian mammary gland
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stem cells44 and neural stem cells45, it was shown that dur-
ing such asymmetrical divisions, damaged proteins and
mitochondria are segregated into differentiating cells while
the stem cell daughter remains damage free43–45. The asym-
metrical distribution of damaged cellular components is
an active process involving sirtuins46, chaperones46 and
the lateral diffusion barrier in the endoplasmic reticu-
lum45, ensuring segregation before cell division. During
ageing, the mechanisms and cellular structures that sup-
port this asymmetrical partitioning decline45,46, resulting
in the accumulation of protein damage43,45 and damaged
mitochondria44 in stem cells. In some cells, the asymmet-
rical distribution of damaged cellular components works
differently: germline stem cells (in D. melanogaster)
and yeast mother cells retain damaged proteins, ensur-
ing the fitness of progenitors destined to each become a
new organism43,46. Loss of asymmetrical division during
ageing owing to altered p38 MAPK signalling has been
described in MuSCs; it remains to be investigated whether
this failure affects the segregation of damaged proteins in
ageing MuSCs47.
Protein damage and epigenetic modulators. Aside
from epigenetic changes driven by the accumulation
of protein and organelle damage during ageing, the
functionality of epigenetic regulators could also directly
depend on cellular proteostasis. For example, the stabil-
ity and turnover of chromatin modifiers such as histone
deacetylase 1 (HDAC1) and DNA (cytosine-5)-methyl-
transferase 1 (DNMT1) are regulated by the UPS, which
deteriorates during ageing48. Protein aggregation events
are more frequent in aged cells owing to proteostasis
failure, and the aggregation of Polycomb group protein
polyhomeotic was linked to a loss of coordinated repres-
sion of genes regulating cell fate during D. melanogaster
development49. The assembly of histones around DNA
and the incorporation of specific histones into chroma-
tin during replication are assisted by specific histone
chaperones (such as ASF1A/B and chromatin assembly
factor 1 (CAF1)), which become less abundant during
senescence and ageing, leading to altered chromatin
structure, loss of core histones from chromatin and gene
expression changes50,51; consistently, deletion of the ASF1
gene caused accelerated ageing in yeast52.
Accumulation of DNA damage
Here, we focus on links between DNA damage and epi­
genetic changes and refer to other reviews for an extended
discussion of ageing-​associated DNA damage in stem cells
(see refs4,53,54). Given their capacity for self-​renewal, stem
cells are at high risk of accumulating replication-​associated
DNA damage; the accumulation of genotoxic lesions in
stem cells during ageing has indeed been confirmed5,6,55.
DNA replication is believed to be the key source of
genotoxic damage during ageing56,57. In the intestine
and skin, stem cells are exposed to additional external
genotoxic insults, such as ROS, microbial products
and ultraviolet light. Analysis of HSCs from mice
deficient in telomere maintenance and DNA repair
mechanisms ( nucleotide excision repair (NER) and
non-homologous end joining (NHEJ)) revealed increased
accumulation of genotoxic damage in HSCs at old age
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Heterochronic parabiosis
An experimental procedure in
which two animals of different
age, for example, one young
and one old, are surgically
connected so that their blood
circulations are shared.
accompanied by impaired self-​renewal and loss of
regenerative potential39,58. Unlike differentiated cells with
persistent DNA lesions, genome-​damaged quiescent stem
cells avoid apoptosis and cellular senescence by activating
rapid but error-​prone NHEJ DNA repair and expression
of pro-​survival factors such as BCL-2 (refs5,6,58,59) and by
attenuating DNA damage responses55 (for review, see
ref.4). These strategies ensure the survival of quiescent
cells but prob­ably lead to accumulation of mutations in
these cells during ageing, which can cause stem cell dys-
function and promote the death of progenitor cells that
exit quiescence58,59. Chromosomal rearrangements gener-
ated by NHEJ errors may result in cancer onset and gene
mutation-​driven dysfunction of epigenetic regulators
(reviewed in ref.60).
Rapid activation of DNA repair in stem cells may have
a direct impact on their metabolism and epigenetic land-
scape: DNA repair processes involve poly(ADP-​ribose)
polymerase (PARP), which uses NAD+ as a substrate
to generate ADP-​ribose monomers. When the levels of
DNA damage become high, PARP activity might lead to
substantial depletion of intracellular NAD+ stores, disrupt-
ing mitochondrial metabolism and the activity of other
NAD+-dependent enzymes, such as sirtuins61. Elevated
glucose depletion rates and impaired mitochondrial
biogenesis have been described in telomerase-​deficient
mice with persistent DNA damage at telomeres62 (Box 1).
Gene expression marks of elevated DNA damage coincide
with global reprogramming of rhythmic gene expression
in aged epidermal stem cells, possibly owing to changes
in metabolic factors and epigenetic cues33. Moreover, per-
sistent DNA damage was linked to reduced expression of
core histones and reduced levels of histone chaperones
(ASF1A/B and CAF1) in somatic cells63, a phenotype
comparable to that of aged MuSCs64.
Stem cell-​extrinsic factors
Ageing leads to changes in cell-​extrinsic factors that
affect adult stem cell function. These include changes in
systemic, blood-​borne factors in the tissue or organ
in which they reside, as well as in their microenviron-
ment (stem cell niche). These external cues can affect
epigenetic reprogramming and gene regulation in ageing
stem cells (Fig. 2).
Systemic factors modify stem cell function
Heterochronic parabiosis experiments provided evidence
that circulating systemic factors, which change during
ageing, modify stem cell function in different com-
partments, including muscle and brain65,66. Exposure to

A Ba Haematopoietic stem cells

MPP
Hormones Systemic Diet Host • WNT3A and Vascular
inflammation microbiome WNT5A endothelial cell
• CCL5 Adipocyte
• Osteopontin
• Oestrogens
Cytokine
Systemic Stem cell ageing
factors • Metabolic changes
• Epigenetic alterations HSC MSC
Micro- • Loss of quiescence
environment • Altered developmental
pathways
Osteoblast
Neuron
ECM Macrophage

Crosstalk with Niche structure Local immune Bc Intestinal stem cells • WNT3A
niche cells (ECM) system Proliferating TA cell • cADPR
Stem cell • IL-22
• Butyrate
Bb MuSCs Paneth cell
• FGF1 and FGF2 • Sex hormones
• Fibronectin • Oxytocin CBC stem cell
• GDF11 • ECM stiffness
Repair
PAX7+
Pericryptal cell

Muscle fibre

Fig. 2 | Systemic factors and changes in the local microenvironment affect stem cell function during ageing.
a | A combination of physiological changes in hormone levels, increased inflammation and the interplay between diet
and the host microbiome leads to changes in systemic signals that regulate stem cell function in multiple compartments.
Locally , age-​related changes in cellular and molecular composition of the stem cell niche lead to aberrant stimulation of
stem cells affecting their quiescence, metabolism and differentiation potential. Extrinsic signals are often integrated into
epigenetic changes that can lead to the aberrant reactivation of developmental pathways in stem cells. Ba–Bc | Examples
of extrinsic molecules that regulate stem cell function in different stem cell compartments, the levels or properties of
which are affected by ageing or ageing-​modulating factors, such as diet and the microbiome. cADPR , cyclic ADP-​ribose;
CBC, crypt base columnar ; CCL5, CC-​chemokine ligand 5; ECM, extracellular matrix; FGF, fibroblast growth factor ; GDF11,
growth/differentiation factor 11; HSC, haematopoietic stem cell; IL-22, interleukin-22; MPP, haematopoietic multipotent
progenitor ; MSC, mesenchymal stem cell; PAX7 , paired box protein 7; TA , transit amplifying.

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Gut microbiome
The ensemble of commensal
bacterial strains that inhabit
the digestive tract of an
organism.
blood from young animals had a rejuvenating effect on
MuSCs and neuronal stem cells, as shown by enhanced
cell proliferation, regenerative capacity and increased
adult neurogenesis. These rejuvenating effects of
parabiosis are the result of enhancing developmental
pathways that become less active in aged stem cells, for
example, Notch signalling65,67 (see below). However,
it remains to be investigated whether the modulation
of developmental pathways by exposure to a youthful
systemic environment is epigenetically regulated and
whether parabiosis reprogrammes epigenetic alterations
that accumulate during ageing.
The results of parabiosis experiments sparked inter-
est in identifying systemically acting molecules that
could potentially improve the function of ageing stem
cells and tissues. Although some proteins and hormones
were identified (for example, growth/differentiation fac-
tor 11 (GDF11), eotaxin, metallopro­teinase inhibitor 2
(TIMP2) and oxytocin), the direct contribution of each
factor alone or in combination to the ageing process
remains to be elucidated68–71. Other hormonal changes
are known to influence stem cell function72. In par-
ticular, increased oestrogen levels during pregnancy
promote HSC self-​renewal73, and sex hormones drive
the conversion from dividing into quiescent MuSCs
during puberty and regeneration following injury74.
As hormones are known to influence the expression of
epigenetic-​modifying genes75, it would be interesting to
investigate whether changes in hormone levels contrib-
ute to the decline of stem cell function during ageing via
epigenetic mechanisms and whether these are reverted
by heterochronic parabiosis.
One of the long recognized but still poorly under-
stood systemic effects of ageing is the increase in
inflammatory signalling, which affects virtually all
organs. Accumulation of tissue damage and senescent
cells (Box 2) and repeated exposure to stress-​inducing
events, such as infections, lead to an increase in pro-​
inflammatory factors in the circulation as well as in the
tissue microenvironment. Infection-​induced cytokines
can impair haematopoiesis by limiting self-​renewal and
by skewing HSC differentiation towards the myeloid
lineage76,77. Inflammatory stimuli can directly influence
stem cells by altering epigenetic regulators. In MuSCs,
tumour necrosis factor (TNF)-activated p38α kinase
induces epigenetic repression of paired box protein PAX7,
the key transcription factor responsible for maintain-
ing MuSC identity, reducing stem cell self-​renewal and
increasing differentiation78. Recent data from epigenetic
reprogramming of early stage cancers by inflammatory
stimuli suggest that similar mechanisms act in the intes-
tinal epithelium79. The persistent inflammatory state that
accumulates during ageing could thus cause epigenetic
perturbation, leading to changes in stem cell identity.
Additional work is required to demonstrate whether such
mechanisms affect stem cells in other compartments.
Recent evidence indicates crosstalk between systemic
inflammation and changes in the gut microbiome, driving
stem cell ageing. In flies, ageing-​associated imbalances
in the composition of the gut microbiome can induce

Box 2 | cellular senescence during ageing

Cellular senescence, which is a permanent state of growth arrest, is a response of cells to various types of stress, including
telomere shortening, DNa replication stress, mitogen stimulation and reactive oxygen species (rOs)4. in recent years,
it has become clear that senescence has a role in ageing and tumour suppression, and during embryonic development.
senescence likely influences stem cell and tissue ageing at multiple levels.
Direct impairment of stem cell function by induction of senescence
there is evidence that cellular senescence contributes to ageing-​associated impairments in the function of muscle stem
cells (also known as satellite cells)214, haematopoietic stem cells216 and intestinal stem cells in old wild-​type mice89 and
telomerase-​deficient mice with dysfunctional telomeres238.
indirect effects of senescence on stem cell function and organ maintenance
senescent cells accumulate in ageing tissues and are a prominent source of pro-​inflammatory signals — also referred to
as the senescence-​associated secretory phenotype (sasP)91,92. studies on mice provided proof of concept that the
removal of senescent cells can improve stem cell function, tissue maintenance, metabolic performance and lifespan239–241.
senolytic treatments were shown to improve stem and progenitor cell function in blood and skeletal muscle240,241.
the studies suggested that the beneficial effects of senolytic therapies involve reductions in rOs and inflammatory
signalling — factors that were previously shown to reduce stem cell function and tissue maintenance in mouse models of
DNa damage accumulation during ageing induced by telomere dysfunction242,243 or DNa repair deficiency58.
effects of SaSP factors on epigenome and cell plasticity
sasP factors can influence stem cell plasticity, which is known to be regulated by the epigenome. interleukin-6 (iL-6)
— one of the prominent pro-​inflammatory cytokines secreted from senescent cells — is upregulated in human ageing
and in mice with shortened telomeres10,242. it was recently shown that iL-6 can promote reprogramming of cells into
pluripotent cells in vivo244, and cytokines derived from tissue-​resident immune cells have important roles in regulating
regenerative processes in various tissues85,90,245. Of note, transient pulses of partial reprogramming were shown to
improve tissue maintenance in progeroid mouse models229. Moreover, there is evidence that transient inflammation
contributes to wound healing245. in contrast to the beneficial effects of a transient induction of inflammatory signals,
chronic inflammation is associated with tissue destruction and the promotion of cancer by inducing cell fate plasticity
and self-renewal capacity in genetically altered progenitor cells246. it is conceivable that the sasP contributes to
misdifferentiation of stem cells in ageing tissues, resulting in defects such as fibrosis in muscle or adipogenesis in
bone marrow. it has been suggested that chronic inflammation (for example, as a consequence of accumulation
of senescent cells in ageing tissues) leads to stem cell exhaustion, tissue-​damagingprocesses and diseases such
as cancer91,238–240.

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Exosomes
Vesicles released by cells
containing RNAs and proteins,
which have several functions,
including cell-​cell
communication.
Fibrosis
The excessive deposition of
extracellular matrix proteins
caused by aberrant tissue
repair and chronic
inflammation.
Reserve stem cells
Pools of cells already
committed to differentiation,
generally quiescent, that upon
injury can de-​differentiate and
revert to a stem-​like state.
Nature Reviews | Molecular Cell Biology
ISC hyperproliferation, leading to accelerated tissue and
organism ageing21. In mice, changes in the gut micro-
biome affect intestinal epithelium permeability and
decrease macrophage function, leading to increased sys-
temic inflammation and tissue damage11. Importantly,
modulating the host microbiome can influence the
lifespan in various species11,80,81.
Ageing of the stem cell niche
Stem cells reside in specialized microenvironments
(known as niches), the property and nature of which vary
depending on tissue. The niche provides specific cues in
the form of differentiation and self-​renewal-regulating
signals, adhesion molecules, spatial organization and
metabolic support to stem cells82–86. As such, the niche
is essential in regulating basic functions of stem cells and
in protecting them from the accumulation of molecular
damage and toxins, for example, microorganism-​derived
factors in the intestine15,87. The intimate relationship
between stem cells and their niche can be influenced by
multiple factors, including ageing, diet and systemically
acting factors, which include metabolites from the host
microbiome (Fig. 2).
Changes in the niche may include cell-​intrinsic
changes in niche cells as well as indirect alterations
in their function, induced by secreted factors, such
as inflammatory cytokines, growth factors, adhesion
molecules and/or changes in structural components
of the extracellular matrix (ECM). An age-​dependent
increase in fibroblast growth factor 2 (FGF2) produced
by the muscle fibre has been shown to induce loss of
quiescence in MuSCs, reducing their regenerative capa­
city88. The levels of WNTs, growth factors regulating the
homeostatic proliferation and differentiation fate of
ISCs, decrease during ageing in intestinal crypts and
the surrounding mesenchyme, thereby reducing the
regenerative potential of ISCs89. In the intestinal epi-
thelium, the local immune cells can also contribute to
the regulation of stem cell function by secreting inter-
leukins, for example, interleukin-22 (IL-22), that can
directly target ISCs90. DNA damage signals in senescent
cells with dysfunctional telomeres promote the secretion
of inflammatory cytokines. This senescence-​associated
secretory phenotype 91,92 (SASP; Box  2 ) was shown
to contribute to change in bone marrow niches and
increases in inflammatory cytokines in blood, inhibit-
ing lymphopoiesis in ageing mice with dysfunctional
telomeres93. How inflammatory signals might induce
cell-​intrinsic defects in niche cells remains to be eluci-
dated. The old bone marrow niche is characterized by
low levels of osteopontin, a secreted factor that influ-
ences the polarity and epigenetic state of HSCs and
thereby their proliferation and differentiation fate94.
Ageing-​associated alterations in ECM components
were shown to impair stem cell function in skeletal
muscle and in the germ line95–97. Stem cells can con-
tribute to the remodelling of their own niche dur-
ing ageing. Activated MuSCs secrete exosomes (for
review, see ref.98) that can modulate the ECM depo-
sition by niche fibroblasts99. Although experimental
evidence is still scarce, the aberrant signals deriving
from the ageing niche are likely to be integrated into
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long-​lasting epigenetic modifications in the resident
stem cell population.
The availability of growth factors and molecules
mediating the interaction of stem cells with their niches
and the biophysical properties of the ECM can influ-
ence stem cell function100,101. In skeletal muscle, an
age-​dependent increase in fibrosis alters the cellular
and molecular composition of the stem cell niche. As
a consequence, the mechanical properties of the niche
microenvironment, such as stiffness, are changed, result-
ing in reduced MuSC self-​renewal and regenerative
capacity85. In old muscles, an alteration of the architec-
ture of collagen fibres influences the deposition of ECM
by fibroblasts, and consequently, it disrupts lineage
specification in MuSCs102. As extracellular cues, includ-
ing mechanical forces and stiffness, have been shown
to induce epigenetic alterations in stem cells103, ageing-​
associated alterations in the biophysical properties of the
ECM might contribute to epigenetic changes in adult
stem cells.
Ageing-​associated changes in the cellular composition
of the niche also occur in other stem cell compartments.
In the small intestine, it was shown that ageing is
accompanied by an increase in the number of secretory
Paneth cells in the intestinal crypts89. Additionally, injury
signals can activate reserve stem cells104, for example, via
de-​differentiation of mature enteroendocrine cells in
the intestinal epithelium105. These processes involve
a dynamic reorganization of chromatin architecture
of genomic regions controlling the expression of stem
and differentiation factors106. As the combinatorial
effect of growth factors secreted by different niche cells
determines the quiescence of ISCs by modulating their
proliferation and differentiation potential in vitro107
and in vivo108, it would be interesting to investigate
whether changes in crypt composition in old animals are
directly related to ageing-​associated epigenetic changes
in ISCs.
Influence of diet on stem cell ageing
Dietary interventions, such as intermittent fasting
and dietary restriction, have been shown to improve
health parameters and promote lifespan in multiple
organisms109. Dietary restriction has been extensively
studied, and its positive effect on regenerative capacity
has been described in multiple stem cell compartments,
including MuSCs, HSCs and ISCs110–113. A periodic diet
designed to mimic the effects of fasting was shown to
restore the expression of MuSC markers, rejuvenate the
haematopoietic system and promote adult neurogenesis
in aged mice114 and promote the reprogramming of
pancreatic cells towards insulin-​producing β-​cells in
both mice and humans115.
Dietary restriction has been shown to have a positive
effect in preserving the pool of functional stem cells
during ageing in different stem cell compartments in
flies and mice110,111,113,116. However, there seems to be a
trade-​off between the positive effects of dietary restric-
tion on extending stem cell maintenance by reducing
stem cell activity and the ability of the organism to
respond to insults and maintain tissue integrity. Indeed,
it was shown that a decrease in intestinal epithelium
Reviews
proliferation (that is, stem cell activity) correlates with
extended lifespan in D. melanogaster. Conversely, an
excessive reduction in stem cell proliferation results
in impairment of epithelial barrier function and is
ultimately detrimental to lifespan22. Similarly, in mice,
long-​term dietary restriction was shown to improve the
maintenance of the haematopoietic capacity of HSCs in
middle-​aged mice by favouring a quiescent state, but at
the same time, dietary restriction impaired the differen-
tiation potential of HSCs, resulting in immune defects
in the context of prolonged bacterial infection110,117. The
outcome of dietary regimes on stem cell function seems
to depend on the timing and duration of the regimes:
subjecting mice to lifelong dietary restriction did not
prevent the ageing-​associated functional decline of
HSCs118, in contrast to when dietary restriction was
limited to short periods of time in middle-​aged mice98.
Diet can influence stem cell function either directly
or indirectly by affecting niche cells, mainly via
nutrient-​sensing pathways. Long-​term dietary restric-
tion increases the regenerative capacity of ISCs via
reduction of mTOR complex I (mTORC1) signalling in
Paneth cells111. ISCs seem to respond to dietary restric-
tion indirectly, but dietary-​restriction-mediated changes
in paracrine signals from Paneth cells activate mTORC1 in
ISCs, thereby leading to increased protein synthesis
and proliferation119. In skeletal muscle, short-​term diet­
ary restriction increases the number and functionality
of MuSCs in both young and old mice113. Interestingly,
MuSC transplantation experiments showed that the bene­
fi­cial effects of dietary restriction are not limited to the
stem cell donor but can also be observed when the recipi­
ent animal is subjected to dietary restriction. These data
indicate that dietary restriction induces changes in the
stem cell niche that promote the engraftment of MuSCs
after transplantation113.
Diet has profound effects on the whole organism.
The way it affects stem cell function might be, at least
in part, induced by systemic factors such as decreased
level of inflammation109 or changes in the composition
of the host microbiome120. Dietary restriction can influ-
ence the epigenome by delaying age-​related changes in
DNA methylation81,121, and nutrient availability alters
the expression of chromatin modifiers in neuronal
stem cells100. Whether the duration of dietary restric-
tion (short-​term versus long-​term) and the resulting
epigenetic changes have an effect on HSC maintenance
and function (see above) remains to be investigated.
Epigenetic mechanisms are expected to also contribute to
the transgenerational effects of dietary interventions via
alteration of chromatin structure in the germ line109,122.
How and whether diet regulates the stem cell epigenome
in different compartments remain to be explored, as well
as whether specific epigenome alterations underlie the
positive and negative effects of dietary restriction on
stem cell ageing and stress resistance.
Dietary vitamins can also influence stem cell
plasticity. Vitamin A has been shown to promote the
maintenance of the quiescent state in HSCs, and a
vitamin A-​deficient diet alters the response of HSCs to
inflammatory stress stimuli by impeding the re-​entry
into quiescence, leading to stem cell pool exhaustion123.
© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
Other vitamins, such as vitamin C, can influence stem
cells by altering the activity of epigenetic modifiers124,125
and niche signalling126. However, a direct link between
age-​related vitamin deficiency and impairment of adult
stem cell function remains to be demonstrated.
In summary, changes in the epigenome seem to
integrate multiple environmental signals that influence
stem cell biology127. The mechanisms by which external
cues lead to changes in the epigenome, the activity
of developmental pathways and the functionality of
stem cells remain to be understood. As niche cells are
among the descendants of stem cells, it is possible that
niche-​induced changes in stem cells in turn aggravate
ageing-​associated remodelling of the stem cell niche. It
could be envisioned that the combination of long-​term
exposure to aberrant niche signals, incorrect activa-
tion of developmental pathways and loss of stem cell
identity might underlie the loss of regenerative capacity
in ageing.
Epigenetic drift and clonal expansion
Throughout the organismal lifespan, adult stem cells
face the challenge of being able to promptly differen-
tiate into committed progenitor cells in response to the
environmental stimuli while maintaining a functional
undifferentiated stem cell pool. Chromatin architecture
and the epigenome are instrumental in preserving stem
cell identity and function. As discussed above, the accu-
mulation of molecular damage, changes in metabolism
and alterations in the local and systemic environment of
adult stem cells that occur during ageing can lead to epi-
genetic changes that could contribute to the appearance
of altered clones, which become dominant, gradually
replacing normal cells. There is increasing evidence that
epigenome alteration and DNA mutations contribute
to the loss of stem cell function and disease develop-
ment during ageing (Fig. 3). Recent studies have revealed
mutual crosstalk between genetic and epigenetic
alterations in ageing adult stem cells (Box 3).
Epigenetic landscape of ageing stem cells
The DNA methylome of different organs and tissues
can be used to precisely predict the biological age of
mouse and human organisms121,128–131. In the haemato-
poietic system, the majority of ageing-​associated DNA
methylation changes were independent of changes in
the cellular composition of the tissues132, suggesting
that ageing-​associated DNA methylation changes in this
compartment originate at the stem or early progenitor
cell level.
Whole-​genome DNA methylation analysis in HSCs
from young and old mice showed a slight increase in
global DNA methylation levels during ageing133,134. By
contrast, somatic tissues and other adult stem cells show
a decrease in global DNA methylation levels but hyper-
methylation of CpG islands in specific loci81,121,130,135–137.
An increase in histone repressive marks, such as histone
H3 lysine 9 trimethylation (H3K9me3) and H3K27me3,
has been observed in old MuSCs and in HSCs64,138,139,
suggesting that a progressive intensification of hetero­
chromatin takes place during ageing, which could
reduce stem cell plasticity. The open (active) chromatin
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 Reviews

Tissue dysfunction

Persistent Deregulation of
epigenome-sensible
mechanisms

Young stem cell Old stem cell

population population
Cancer
Epigenetic modifiers
mutated in HSCs
• DNMT3A Mutation of epigenetic Expansion of a
• TET2 regulator or epimutation clonal stem cell
• ASXL1

Fig. 3 | epigenetic drift and clonal expansion altering adult stem cells during ageing. After reproductive age, the
epigenome of the adult stem cells undergoes an epigenetic drift, possibly driven by molecular damage, changes in
the stem cell niche or aberrant activation of developmental programmes. DNA methylation and histone modification
alterations that accumulate during ageing can be different and have different effects depending on the stem cell
compartment. Recent evidence suggests that epigenetic drift increases self-​renewal and impairs differentiation of adult stem
cells. In some stem cell compartments, persistent epigenetic drift leads to deregulation of epigenome-​sensible gene pathways
that promote stem cell dysfunctions135. In other compartments, mutations in the epigenetic modifiers (for example, DNA
(cytosine-5)-methyltransferase 3A (DNMT3A), methylcytosine dioxygenase TET2 and putative Polycomb group protein ASXL1)
have been frequently found in aged haematopoietic stem cells (HSCs) and can lead to the selection of mutant stem cells (blue)
that gain clonal dominance, leading to impairments in adult stem cell differentiation, tissue dysfunction and cancer153,158.

mark H3K4me3 is enriched in old HSCs, suggesting an
epigenetic reinforcement in the transcriptional activa-
tion of stem-​related genes139. By contrast, MuSCs display
reduced histone acetylation (a mark for open chromatin)
in old mice138. However, in contrast to young cells, old
MuSCs show a shift towards a euchromatin state follow-
ing activation, with increased histone acetylation and
decreased H3K27me3 (ref.138). Age-​dependent changes
in DNA methylation and histone modifications have
previously been reviewed140. The mechanisms of these
alterations and the functional consequences on ageing
stem cells remain largely unknown.
Specific DNA methylation and histone modifica-
tion patterns are associated with the proliferative and
differentiation status of ISCs141–143. DNA methylation is
necessary for the maintenance of asymmetrical division
of ISCs, probably by activating specific enhancers144,145.
Impaired absorptive function in the intestine of elderly
individuals has been associated with a decrease in the
number of differentiated cells relative to the number of
proliferating, undifferentiated cells146,147. These obser-
vations suggest that ageing-​induced alteration in DNA
methylation alters ISC and progenitor cell differentiation
and thus tissue composition, causing tissue dysfunction.
A study with a small cohort of patients revealed ageing-​
associated gain of DNA methylation in small intesti-
nal crypts148. Recent work has demonstrated that diet,
inflammation and the gut microbiome contribute to the
changes in the epi­genetic profile of the intestine, including
DNA methylation, that could alter the biological function
of ISCs149–152.
In summary, epigenome changes occurring during
ageing seem to be cell dependent and tissue depend-
ent and not as drastic and well coordinated as during
embryonic development, at least in mouse. However,
an epigenetic drift — which involves a specific
age-​dependent change in the CpG methylome, a rein-
forcement of open chromatin regions and progressive
heterochromatinization — can be profiled, but more
studies are required to understand the ageing-​associated
epigenetic landscape. Transcriptomic analyses have
shown that these alterations do not strongly change
the transcriptional programme and identity of adult
stem cells but can probably affect the differentiation
programme and functionality of their terminally com-
mitted progeny, causing tissue and organ dysfunction. It
has recently been reported that subpopulations of stem
cells in the haematopoietic system undergo ageing-​
associated changes in the proliferative rate153. Many
epigenetic studies have been performed in bulk stem
cell populations, which could mask cell-​to-cell hetero-
geneity and alterations acquired at the single-​cell level
during ageing. By employing single-​cell RNA sequenc-
ing, a recent study showed that whole-​transcriptome
cell-​to-cell variability, transcriptional noise and signs of
fate drift increase in human pancreas during ageing154.
Recently, single-​cell chromatin modification profiling
by mass cytometry showed that human HSC ageing is
associated with increased heterogeneity between indi-
viduals and elevated cell-​to-cell variability in chromatin
modifications155. Single-​cell analyses could therefore be
crucial to fully understand stem cell epigenetic land-
scapes during ageing. Another important question that
remains to be addressed is how the epigenetic integra-
tion of molecular damage and alteration in the stem
cell environment during ageing enable the selection of
mutant clones and/or population drifts in stem cells dur-
ing ageing. Impairment in cell differentiation and slight
changes in the self-​renewal of adult stem cells could con-
fer a minimal selective advantage to the aberrant stem
cells and to the appearance of dominant clones in the
somatic stem cell compartment (discussed below).

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Box 3 | genetics and epigenetics crosstalk in ageing stem cells
genome instability causing epigenome instability
• Genetic alterations can occur in epigenetic regulators or in non-​coding rNas that in
turn perturb the epigenome of adult stem cells. this mechanism seems to be involved in
the development of many different types of cancer for which stem cells represent the
cell of origin247. For example, the mixed-​lineage leukaemia 1 gene (MLL1; also known as
KMT2A), which encodes a histone 3 lysine 4 methyltransferase, and DNa
methyltransferase genes are frequently translocated and mutated during leukaemia
stem cell development248,249. recent noteworthy studies157,161,165 reported that
epigenetic regulators are also frequently mutated in haematopoietic stem cells of
healthy elderly individuals.
• Mutations in genes that regulate metabolism or in mitochondrial DNa lead to changes
in cellular metabolism that alter the availability of essential cofactors of chromatin
modifiers (such as S-​adenosylmethionine and α-​ketoglutarate)250,251. the resulting
impairment in the enzymatic activity of epigenome modifiers may alter the epigenome
during stem cell divisions, leading to aberrant self-​renewal, acquisition of incorrect cell
identity during differentiation and a functionally altered stem cell pool.
epigenome instability causing genome instability
• several studies report that many genes involved in DNa repair undergo epigenetic
silencing in different types of cancer252. Promoter hypermethylation of the mismatch
repair gene MLH1 leads to microsatellite instability that is responsible for
approximately 15–20% of all colorectal cancers253,254.
• Human mutation rate is associated with DNa replication timing that in turn depends on
the chromatin status of the DNa, suggesting that specific epigenetic modifications can
promote the frequency of replication-​dependent mutations255,256.
• Most of the mutations accumulated during ageing are C>t transitions, which are
characteristic of spontaneous deamination of methylated cytosine residues into
thymine at CpG sites257. this mutation spectrum is specifically enriched in highly
proliferative stem cell compartments (such as the colon and small intestine) and
suggests an additional function of DNa methylation during ageing257.
• repetitive elements in our genome are epigenetically repressed. senescent cells
and aged tissues exhibit an activation of retrotransposons, leading to genome
instability183,184.
• Mutation of epigenetic regulators
• Mutation of metabolic regulators
Genome Epigenome
instability instability
• Epigenetic silencing of DNA repair genes
• DNA replication-dependent mutations
• Deamination of methylated cytosine
• Reactivation of retrotransposons
Clonal dominance of aged mutant stem cells
Recent observations support the hypothesis that clonal
dominance is a common feature of aged stem cell
compartments 156–161. Ageing-​d ependent alterations
in the genome and epigenome of a single stem cell
may provide this cell with proliferative and metabolic
advantages, resulting in a strong benefit in cell-​to-cell
competition and compartment colonization (Fig. 3). This
mechanism highly depends on the structure and com-
partmentalization of the stem cell niche and, in some
cases, is believed to generate a precancerous stage162–164.
Deep exome-​sequencing analysis of a large human
cohort showed recurrent somatic mutations in healthy
Epimutations
Alterations of a specific
elderly individuals with clonal haematopoiesis157,161,165.
chromatin modification in Somatic mutation frequency in blood was extremely rare
a specific genomic locus. in young individuals (<1% in persons <50 years of age)
© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
and exponentially increased during age up to 30–50% in
70-year-​old people162. The presence of these mutations is
associated with a significant increase in the risk of hae-
matological cancers, ageing-​associated cardiovascular
diseases and all-​cause mortality. These associations may
even currently be underestimated owing to technical
limitations. For example, clones bearing mutations
outside the exome cannot be identified by using exon
sequencing. A whole-​genome sequencing approach
could reveal functional DNA mutations in intergenic or
intronic regions. Moreover, dominant stem cell clones
could arise from the beneficial acquisition of epimutations
due to ageing-​related epigenetic drift or sporadic but spe-
cific epigenetic events. Most of the identified mutations
were dispersed in the genome, but the protein-​coding
regions of three genes (DNMT3A, TET2 and ASXL1)
were disruptedwith very high recurrence, suggesting
that these genes are functional drivers of such clonal
haematopoiesis157,161. These three genes all encode master
epigenetic regulators, and DNMT3A and methylcytosine
dioxygenase TET2 in particular are the main contrib-
utors to de novo establishment of DNA methylation
and removal of DNA methylation, respectively, in adult
tissues. These findings indicate that alterations in the
epigenome are crucial for the development of clonal
dominance in stem cell compartments during ageing.
The most prevalent gene mutations in clonal hae-
matopoiesis — DNMT3A and TET2 — are also often
mutated in leukaemia166–169, supporting the hypothesis
that the clonal haematopoiesis originating from recur-
rently mutated genes represents a ground stage for the
development of leukaemogenesis. However, these two
enzymes are also essential regulators of normal HSC
self-​renewal and differentiation170–172, and according to
clinical studies, clonal haematopoiesis is also associated
with non-​cancerous diseases157,161. Interestingly, recent
studies reported that Tet2-deficient haematopoiesis
accelerates atherosclerosis development and cardiovas-
cular diseases in mice by enhancing IL-1b inflammatory
signalling in macrophages173,174. The association of clonal
haematopoiesis with cardiovascular diseases in aged
humans suggests that similar mechanisms are relevant
to cardiovascular disease development in humans.
Clonal haematopoiesis may by itself contribute to an
increase in inflammatory signalling in ageing, which
in turn disturbs epigenome regulation, gene regulation
and stem cell function in a variety of tissues, including
non-​mutant stem cells and non-​stem cell compartments.
The latter may also be linked to increases in cell-​to-cell
variation in stochastic alteration in gene expression in
ageing cardiomyocytes175.
Ageing-​dependent clonal dominance occurs in adult
stem cell compartments other than the blood. A recent
study performed on sun-​exposed human eyelid epider-
mis revealed a high level of somatic mutations (similar
to cancer) and a strong positive selection for cancer gene
mutations in otherwise physiologically normal cells.
A selective clonal expansion has been found in 18–32% of
normal skin cells preserving the physiological functions
of epidermis176.
Even in germ cells, which are meant to have highly
efficient protection against mutations, mutant stem cell
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Retrotransposon
A class of transposable DNA
sequences using RNA as a
mobile intermediate.
Spurious transcription
An RNA transcription process
starting from an intragenic or
intergenic region.
Nature Reviews | Molecular Cell Biology
clones emerge in an age-​dependent manner. Mutant
spermatogonial stem cells are positively selected and
progressively expand clonally in ageing testes. Although
this clonal expansion is very common, it rarely gives rise
to testicular tumours. However, mutant spermatogonial
stem cells were found to be the cause of a set of genetic
diseases affecting children of older fathers, also referred
to as paternal age effect mutations158.
In the gut epithelium, all the cells that compose a sin-
gle intestinal crypt originate from a single dominant ISC
that outcompetes other ISCs to colonize the whole stem
cell niche over time177. Although these studies reported
that ISCs follow a stochastic pattern of behaviour that
recapitulates a neutral drift dynamic, we cannot exclude
that, especially in long-​living organisms such as humans,
accumulating ageing-​dependent damage will alter this
dynamic process. There is evidence for mutated stem
cells undergoing clonal crypt dominance increasingly
during ageing159,160. Moreover, clones can expand by a
crypt fission event159,160. However, additional experi-
ments are required to assess the contribution of stem
cell DNA mutations and epigenetic alterations in field
colonization of the ageing gut epithelium.
Possible mechanisms promoting clonal dominance
In the haematopoietic system, clonally dominant HSCs
in ageing humans can be identified by the presence of
mutant clones in the peripheral blood. On the basis of the
high recurrence of mutations in the same set of genes in
population studies and experimental studies, most of these
mutations can be regarded as drivers of clonal dominance
of HSCs in ageing. Many of the drivers are directly (for
example, DNMT3A, TET2 and ASXL1) or indirectly
(for example, IDH2, TP53, JAK2, SRSF2, U2AF1 and
cohesin genes) involved in the epigenome regulation178–181.
How the epigenome is able to promote clonal dom-
inance of mutant stem and/or progenitor cells and why
epigenetic regulator mutations are selected in aged organ-
isms remain poorly understood. One hypothesis suggests
that these epimutations do not strongly affect the molecular
and metabolic machine of the adult stem cells but provoke
small but persistent epigenome changes that lead to slight
advantages to the stem cells to outcompete non-​mutant
stem cells in colonizing stem cell niches. Alternatively,
these epimutations may allow mutant adult stem cells to
adapt to the accumulation of molecular damage during
ageing (see below). Mutant clones that arise from stem cells
may escape cellular checkpoints and immune response
that contribute day by day to the reinforcement of a dom-
inant phenotype. It is currently not fully understood how
ageing affects the selection of mutant stem cell clones at
both cell-​intrinsic and cell-​extrinsic levels.
Epigenetic modifications have been demonstrated to
regulate gene transcription and many other transcription-​
associated genomic events, such as alternative promoter
usage, retrotransposon repression, spurious transcription
splicing and RNA maturation 182. Recent studies
reported that senescent cells and aged tissues undergo
epigenetic changes that result in the reactivation of
retrotransposons 183,184. Some aged stem cells show
global loss of DNA methylation in intragenic regions
that could result in increased spurious transcription
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activation to generate cryptic transcripts and aberrant
proteins185. Cryptic promoter regulation was recently
found to be a crucial mechanism for driving termi-
nal differentiation of germ cells in D. melanogaster186.
Intragenic DNA methylation can also regulate alterna-
tive splicing187–189, which plays an important part during
cellular differentiation190.
The epigenome is the major regulator of developmental
genes and pathways191. Aberrant chromatin modifications
can lead to altered expression of specific differentiation-​
associated genes. During development, adult stem cells
are generated and maintained by the activation of spe-
cific epigenetic programmes. Genes responsible for adult
stem cell self-​renewal are activated, while genes of the final
commitment are kept reversibly switched off. During age-
ing, the epigenetic programme of stem cells may slowly
evolve away from the concise regulation of developmen-
tal pathways during development leading to a ‘shadowed’
activation of developmental programmes and epigenetic
drift. This may result in hyperactivation of self-​renewal
genes and/or skewing in gene expression pathways con-
trolling lineage differentiation, thus disrupting the balance
between stem cell self-​renewal and differentiation and
leading to the selection of mutant stem clones. Another,
non-​mutually exclusive hypothesis could be that increas-
ing epigenome instability can increase the cell plasticity to
respond to an aged environment. Under selective pressure,
a new stem cell identity with a dominant phenotype can
arise in that specific aged niche.
Deregulation of developmental pathways
The deregulation of developmental pathways is increas-
ingly being recognized as underlying stem cell ageing in
different tissues (Figs 4,5). The pathways that are affected
include Notch192, WNT193,194, FGFs195, TGFβ196, p38
(ref.197) and cellular senescence signalling198,199 (Box 2).
WNT signalling
Ageing MuSCs have increased activity of canonical WNT
signalling, which promotes the erroneous differentiation
of MuSCs into fibrogenic lineages and muscle fibrosis,
as well as a decline in muscle regeneration following
injury200. In the haematopoietic system, a switch from
canonical (WNT3A) to non-​c anonical (WNT5A)
WNT signalling promotes HSC ageing by inducing the
loss of stem cell polarity — a CDC42-dependent pro-
cess important in regulating the interaction of HSCs
with the niche, self-​renewal and differentiation201,202.
As WNT3A promotes lymphopoiesis and WNT5A
enhances myelopoiesis203, the switch from canonical to
non-​canonical WNT signalling may contribute to the
ageing-​associated skewing of haematopoiesis towards
myelopoiesis204. It was also reported that activation of
non-​canonical WNT signalling maintains HSC self-​
renewal and repopulation capacity by enhancing stem
cell quiescence (which protects long-​term function of
stem cells) through reduction of intracellular levels
of ROS and suppression of Ca 2+–nuclear factor of
activated T cells (NFAT)–interferon-​γ (IFNγ) signal-
ling205–207. It remains to be investigated whether switches
in canonical to non-​canonical WNT signalling (WNT3A
to WNT5A) and the selection of subpopulations of stem
Reviews

MuSCs: p16 derepression reduces Notch and

induces CDK1 and TGFβ, reducing MuSC
Reproduction regenerative capacity
Embryogenesis Ageing
HSCs: p16 induction supresses Notch, which
impairs self-renewal of activated HSCs
WNT
MuSCs: FGF1 signalling is reduced and p38–MAPK
signalling is enhanced, impairing asymmetric cell
division of MuSCs; derepression of FGF2 can lead
to MuSC exhaustion
HSCs: administration of FGF7 or FGF21 restores
thymopoiesis
Notch
ISCs: p38–MAPK is induced by PDGF and VEGF,
Master regulators leading to hyperproliferation and
of development misdifferentiation
such as
HOX genes MuSCs: Notch reduction and TGFβ induction
impair regeneration
FGF– HSCs: Notch is suppressed, impairing self-renewal
p38–MAPK of activated HSCs
ISCs: Notch is suppressed or mutated, impairing
proliferation and differentiation
MuSCs: enhanced canonical WNT signalling drives
Senescence fibrosis
HSCs: switch from canonical to non-canonical
WNT signalling promotes myeloid bias
ISCs: DNA damage gives selective advantage to
WNTlow ISCs; low WNT impairs regeneration

Fig. 4 | Shadowed activation of developmental pathways in stem cells during ageing. Developmental pathways are
tightly regulated during embryogenesis. Master regulators of developmental pathways exhibit ageing-​associated
alteration in gene expression, which impairs the function of stem cells during ageing. These findings support the concept
that tightly controlled activity of developmental pathways, which drives embryogenesis and postnatal development until
the point of reproduction, is lost during ageing. After the reproductive age, the evolutionary pressure to maintain the
organism and its functions is reduced, and epigenetic changes that result from age-​associated increases in intracellular
damage and changes in the stem cell microenvironment and macroenvironment contribute to deregulation of these
developmental pathways in stem cells — the remnants of embryonic development in adult organisms. Aberrant expression
of master regulators of development, such as the HOX genes, which are highly responsive to changes in the epigenome,
could play a key part in causing ageing-​associated stem cell dysfunction, loss of organ homeostasis and disease. CDK1,
cyclin-​dependent kinase 1; FGF1, fibroblast growth factor 1; HSC, haematopoietic stem cell; ISC, intestinal stem cell;
MuSC, muscle stem cell; PDGF, platelet-​derived growth factor ; TGFβ, transforming growth factor-​β; VEGF, vascular
endothelial growth factor.

Progeroid mice
Mice carrying mutations in
genes that are mutated in
human progeroid syndromes
that are characterized by
segmental premature ageing
(affecting specific organs).
Aneuploidy
The irregular deviation of
chromosome numbers from
the normal situation — not
including doubling of
chromosome numbers as
in tetraploidy.
cells with high WNT5A activity are mutually exclusive
or parallel processes in HSC ageing.
In the gut, canonical WNT signalling enhances DNA
damage responses in ISCs208. In telomerase mutant mice
with critically shortened, dysfunctional telomeres, accu-
mulation of DNA damage promotes the survival of stem
cells in niche positions exposed to low levels of WNT
ligands208. Similar selection processes may contribute
to the reduction of canonical WNT signalling in ISCs
in ageing wild-​type mice89 and in hair follicle stem cells
of progeroid mice209,210. Ageing-​associated decreases in
WNT signalling reduce the differentiation and regener-
ative capacity of ISCs, thus affecting organ homeostasis.
Deregulation of Notch and WNT signalling is also seen
in HSCs and neuronal stem cells of patients with Down
syndrome211. It is possible that aneuploidy-​induced repli-
cation stress and DNA damage contribute to the selection
of stem cells with low WNT activity in these patients212.
Notch signalling
Ageing-​associated suppression of Notch signalling and
an increase in ΤGFβ/mothers against decapentaplegic
homologue 3(MAD3 also known as SMAD3) signal-
ling impair the regenerative capacity of MuSCs213. The
imbalance between ΤGFβ–SMAD3 and Notch signalling
leads to increased expression of cyclin-​dependent kinase
(CDK) inhibitors, including p16 (also known as p16INK4,
encoded by CDKN2A) and p21 (encoded by CDKN1A),
which are two well-​established activators of cellular
senescence that also have a role in development67,198,199.
Of note, ectopic expression of Notch rescued regener-
ative defects of aged MuSCs by counteracting ΤGFβ–
MAD3-driven expression of these CDK inhibitors, p15
(encoded by CDKN2B), p16, p21 and p27 (encoded by
CDKN1B)67. It is possible that decreases in Notch and
activation of TGFβ signalling contribute to the derepres-
sion of p16 in MuSCs during advanced ageing, which
inhibits cell cycle re-​entry and regenerative capacity of
MuSCs in geriatric mice214.
In the haematopoietic system, Notch promotes self-​
renewal of HSCs, which is required for WNT-​mediated
HSC proliferation215. While Notch activity is dispensable
for the proliferative response of WNT-​activated HSCs,
the inhibition of Notch results in differentiation rather
than self-​renewal of WNT-​activated HSCs. During
ageing, the deletion of p16 rescued declines in the repopu­
lation capacity of HSCs in mice, and this rescue was
associated with enhanced Notch signalling216, implying
that the suppressive regulation of gene expression
between Notch and p16 is bidirectional.

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 Reviews

Dysbiosis
In the intestine, Notch signalling controls the balance X-​linked in Drosophila, and male flies frequently exhibit
A deviation in the composition between self-​renewal and differentiation of stem and spontaneous somatic mutations of the locus resulting in
of bacterial strains and taxa in progenitor cells into different lineages of the intestinal inactivation of Notch and neoplasia formation in the
the microbiome of an organ or epithelium217. In D. melanogaster, the JUN N-​terminal ageing gut epithelium218. In contrast to the phenotypes
organism characterized by
kinase (Jnk) stress-​signalling pathway is activated by in Drosophila, Notch is important for the maintenance
decreases in overall complexity
and overgrowth of certain dysbiosis of the commensal bacteria, which occurs dur- of self-​renewal of ISCs in mice, and its deletion leads
species. ing ageing. Jnk signalling in turn activates proliferation to loss of proliferative cells in the basal crypts219. In
and aberrant differentiation of ISCs, which leads to the old mice, Notch1 signalling is decreased in ISCs, and
Lateral inhibition formation of misdifferentiated epithelial cell areas, loss there is an increase in the expression of protein atonal
A mechanism by which cells of
one type enforce a difference
of intestinal barrier function and organism death21. homologue 1 (ATOH1) — a regulator of lateral inhibition
in cell fate and/or cell identity Notch signalling in stem cell-​derived progenitor cells through δ-​like canonical Notch ligand (Dll) genes89.
in neighbouring cells. (enteroblasts) and neighbouring cells impinges on this
trajectory in two ways: it inhibits Jnk-​mediated over- FGF–p38–MAPK signalling
proliferation of ISCs but instructs misdifferentiation FGF1 signalling controls asymmetric activation of the
into dysplastic cells23. Interestingly, the Notch gene is p38–MAPK signalling pathway during MuSC divi-
sion, which regulates asymmetric cell division — the
Stem cell-intrinsic Stem cell-extrinsic p38–MAPK high-​expressing daughter cell undergoes
alterations alterations differentiation, and the p38–MAPK low-​expressing
Integrated alteration counterpart undergoes self renewal47. Ageing MuSCs
of the epigenome exhibit reduced responsiveness to FGF1 as well as ele-
vated p38–MAPK signalling. Both processes disturb
Deregulation of developmental pathways FGF1–p38–MAPK-​mediated regulation of asymmetric
• Most sensitive to epigenetic regulation MuSC divisions47,220. Enforced FGF1 signalling and inhib­
• Ground stage activity in adult stem cells
• Naturally regulated by the epigenome ition of p38–MAPK signalling, even if only transiently,
rescue the self-​renewal and regenerative capacity of aged
MuSCs47,220. MuSC niches secrete FGF2, which activates
Stem cell ageing Defects in stem cell function
stage 1 MuSCs to exit quiescence or dormancy88. Interestingly,
• Self-renewal
• Differentiation the expression of protein sprouty homologue 1 — an
Therapeutic inhibitor of FGF signalling — protects MuSC quies-
epigenetic
interventions cence, and imbalances in this regulatory system can lead
to age-​dependent MuSC exhaustion88.
Stem cell ageing In serum-​free cultured HSCs and progenitor cells,
stage 2
supplementation of FGF1 or FGF2 increased cell pro-
Epigenetic drift Mutations with altered liferation and self-​renewal221. Furthermore, in vivo
epigenome plasticity administration of FGF7 or FGF21 reversed ageing-​
Impairments in tissue associated thymic involution and enhanced thymic output
maintenance, systemic side of naive T lymphocytes in ageing mice, which could have
effects, ageing-associated
dysfunction and diseases beneficial effects for adaptive immune functions dur-
ing ageing222. However, the role of FGFs in HSC ageing
Fig. 5 | a model of stem cell ageing by epigenetic integration of damage signals and remains to be investigated. Downstream of growth factor
deregulation of developmental pathways. During ageing, stem cells accumulate stimuli, several mitogenic signalling pathways, such as
several types of molecular damage, and the stem cell environment (the stem cell niche ROS–MAPK and Janus kinase (JAK)–signal transducer
and in the blood system) undergoes several modifications. The epigenome undergoes and activator of transcription (STAT), were shown to
integrated changes in response to cell-​intrinsic and cell-​extrinsic alterations, which aggravate HSC ageing by induction of p53–Cdkn2a/
result in the deregulation of developmental signalling pathways in aged stem cells. In the p19ARF-​dependent DNA damage responses18,153.
adult organism, stem cells retain a low level of activity of signalling pathways that are FGFs contribute to the development of the intestinal
active during development and, therefore, are sensitive to ageing-​associated alterations
epithelium in various species223–226, but their role in the
of the epigenome that can deregulate these pathways. As a consequence, important
processes that are regulated by developmental pathways in stem cells are disturbed, maintenance of adult ISCs and any effects during ageing
including the control of self-​renewal, differentiation and overall stem cell capacity to remain to be investigated. There is experimental evidence
regenerate and maintain tissues. In stem cells, the stochastic integration of cell-​intrinsic that activation of ISC proliferation impairs ISC mainte-
damage and cell-​extrinsic alterations by the epigenome occurs progressively early nance and tissue homeostasis in ageing fly (see above)22.
during ageing (first stage of stem cell ageing) and leads to impairments in stem cell The activation of p38–MAPK signalling downstream of
function. This reduced stem cell function confers a selective advantage on stem cells that PDGF-​related and VEGF-​related factor 2 (PVF2) was
acquire drifts in the epigenome or mutations that increase epigenome plasticity. Both shown to aggravate this phenotype227.
processes could revert growth inhibitory effects that are imposed by the epigenetic
deregulation of developmental pathways in ageing stem cells. We propose that this is Hox genes
the second stage of stem cell ageing and represents a maladaptive change driven by
The functional impact of developmental pathways on
selection. Both stages of stem cell ageing lead to impairments in tissue maintenance,
systemic side effects (for example, increased inflammatory immune cells deriving stem cell ageing indicates that master regulators of
from mutant haematopoietic stem cells) and the development of ageing-​associated embryogenesis, such as Hox genes, could contribute
diseases. Therapeutic interventions that target epigenetic alterations during these two to stem cell ageing. Interestingly, many Hox genes are
stages of stem cell ageing may have the potential to delay the development of expressed in adult stem cells of different tissue com-
age-associated diseases. partments and have been associated with the formation

Nature Reviews | Molecular Cell Biology

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Reviews

Thymic involution
A reduction in the thymus
mass and in the output of naive
T lymphocytes.
of malignancies, for example, in the haematopoietic sys-
tem; however, functional studies of these genes in stem
cell ageing are mostly lacking. In skeletal muscle, a recent
study revealed that the Hoxa9 gene is aberrantly acti-
vated in MuSCs in response to injury. Hoxa9 induction
led to deregulation of several developmental pathways
that were previously shown to impair MuSC function
during ageing138 (see above). The role of master regu-
lators of development in the ageing of other stem cell
compartments remains to be delineated.
Conclusions and future perspectives
During ageing, stem cells that reside in different tis-
sues accumulate several defects that can prevent them
from performing the crucial functions of repairing tis-
sue damage and maintaining tissue homeostasis. These
defects include a decline in the maintenance of a healthy
proteome, metabolic changes, alterations in intrinsic
and extrinsic signalling pathways, DNA damage and
epigenetic changes.
Developmental pathways that are epigenetically
regulated and known to be crucial during embryogen-
esis have been recently proposed to contribute to stem
cell ageing. Epigenetic alterations and dysregulation of
these pathways might impair the functionality of adult
stem cells during ageing (Figs 4,5). Multiple regulators
of the epigenome were shown to have important roles
in controlling self-​renewal, differentiation and regener-
ative potential of adult stem cells (for review, see ref.228),
and these observations are raising important questions
for future research. For example, it will be important to
understand what mechanisms drive epigenome dysreg-
ulation during ageing, how molecular damage impinges
on these processes and how this leads to the aberrant
activation of developmental pathways during ageing.
In addition to these slowly evolving integrated changes,
acute modification of the epigenome in response to
tissue injury and regenerative stress seems to be per-
turbed during ageing and lead to impairments in MuSC
function and muscle regeneration by activation of
Hox genes138.
It remains to be investigated whether there are
common mechanisms that lead to changes in the epi­
genome during ageing in quiescent and activated stem
cells. Delineating acute and chronic alterations in the
control of epigenetic modification in stem cells during
ageing is also important to understand the mechanisms
underlying ageing-​associated clonal dominance of stem
cells carrying mutations in epigenome regulators — a
phenomenon that has emerged as a hallmark of the
ageing haematopoietic system in humans (Fig. 5). Lastly,
the concept of epigenetic integration of damage sig-
nals as a cause of stem cell and organism ageing holds
new promises for translational approaches, because
­epigenome alterations are in principle reversible, and
there is evidence that epigenome reprogramming can
improve tissue maintenance, regenerative capacity and
health span103,138,229.
Published online xx xx xxxx

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Acknowledgements
F.N. is supported by the Alexander von Humboldt Foundation
and the German Federal Ministry for Education and Research.
K.L.R. is supported by a European Research Council
Advanced Grant (StemCellGerontoGenes). The Fritz Lipmann
Institute is a member of the Leibniz Association and is finan-
cially supported by the federal government of Germany and
the State of Thuringia.
Author contributions
M.E., F.N., A.O. and K.L.R. contributed equally to writing,
revising, researching and discussing the article.
Competing interests
The authors declare no competing interests.
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