Inflammation, Epigenetics, and Metabolism Converge To Cell Senescence and Ageing - The Regulation and Intervention

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REVIEW ARTICLE OPEN
Inflammation, epigenetics, and metabolism converge to cell

senescence and ageing: the regulation and intervention
Xudong Zhu1, Zhiyang Chen2, Weiyan Shen2, Gang Huang3, John M. Sedivy4, Hu Wang1,2 and Zhenyu Ju2
Remarkable progress in ageing research has been achieved over the past decades. General perceptions and experimental evidence
pinpoint that the decline of physical function often initiates by cell senescence and organ ageing. Epigenetic dynamics and
immunometabolic reprogramming link to the alterations of cellular response to intrinsic and extrinsic stimuli, representing current
hotspots as they not only (re-)shape the individual cell identity, but also involve in cell fate decision. This review focuses on the
present findings and emerging concepts in epigenetic, inflammatory, and metabolic regulations and the consequences of the
ageing process. Potential therapeutic interventions targeting cell senescence and regulatory mechanisms, using state-of-the-art
techniques are also discussed.
Signal Transduction and Targeted Therapy (2021)6:245 ; https://doi.org/10.1038/s41392-021-00646-9

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INTRODUCTION As the biological techniques advance, many new targets and

Individual cells face three major cell fate choices: to survive, to signaling pathways participating in cell senescence regulation
senesce, or to commit suicide. The balance between these have been identified, although some are still controversial.
processes ensures that cell turnover in an organism remains Nonetheless, the common signals and mechanisms converge
essentially in functional equilibrium (homeostasis). While cell upon dysregulated inflammation, alteration of epigenetic mod-
survival and death have been intensively investigated for long, ifications, and metabolic imbalance.8–10 Here in this review, we
cell senescence is relatively less understood due to the complexity highlight those known and yet unexploited key molecular and
of the ageing process and heterogeneity of ageing phenotypes.1 signaling pathways, particularly the inflammatory, epigenetic, and
Past investigations of cell senescence have focused on its role in metabolic aspects that link cell senescence and organismal ageing
tumor suppression, cell cycle arrest, tissue repair, and DNA (Fig. 1). Therapeutic targets and novel techniques established in
replicative stress/damage response. Many mediators are linking recent cell senescence studies are also discussed.
to intrinsic (e.g., organelle homeostasis, chronic inflammation, and
epigenetic alterations) and extrinsic factors (e.g., UV exposure, drug
toxicity, and lifestyle) that deteriorate cell physiology.2 We now DEFINITION OF CELL SENESCENCE
know many pathways involve in the regulation of cell senescence, Although research on cell senescence lasts for decades, until recently,
such as AMP-activated protein kinase (AMPK) energy-sensing,3 the field reached a consensus on the definition of cell senescence,
histone/protein (de-)acetylation,4,5 cyclic GMP–AMP synthase that is, a type of cell state that can be stimulated by multiple stress
(cGAS)–the cyclic GMP–AMP receptor stimulator of interferon signals throughout the life cycle and is characterized by cell cycle
genes (STING) signaling pathways,6 which impact the rate and arrest, senescence-associated secretory phenotype (SASP), and
extent of cell senescence. Of note, existing studies define that dysregulated metabolism and macromolecular damage1 (Fig. 2).
senescence as a relatively inert, non-proliferating, irreversible cell Consequently, many types of cell senescence have been proposed,
state.1 Although the removal of senescent cells serves as an including replicative senescence, programmed developmental senes-
attractive option to mitigate age-related functional decline and cence, and stress-induced senescence.11 Such diverse senescent
extend health span,7 researchers are trying to reprogram senescent pathways represent active and passive modes to establish a delicate
cells back to functionally healthy cells, especially for cardiomyo- balance between different cell populations—as abstract as it sounds.
cytes and neurons that are hardly proliferative. Can cell senescence It is worth noting that ageing and cell senescence are different but
be reversed? Are there different forms or stages of senescent cells closely related. Organismal ageing emphasizes the degeneration of
that exert distinct physiological effects? Does senescence have any tissues or organs caused by accumulated damages upon a period.12
yet new functions to the cells or tissues? To our knowledge, there In contrast, cell senescence can occur whenever under a specific
are still many open questions that await answers. stress condition, and it may also play a positive role in wound healing
1
Key Laboratory of Ageing and Cancer Biology of Zhejiang Province, Institute of Ageing Research, Hangzhou Normal University School of Medicine, Hangzhou, China; 2Key
Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Institute of Ageing and Regenerative
Medicine, Jinan University, Guangzhou, China; 3Division of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati,
OH, USA and 4Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
Correspondence: Hu Wang ([email protected]) or Zhenyu Ju ([email protected])
These authors contributed equally: Xudong Zhu, Zhiyang Chen
These authors jointly supervised this work: Hu Wang, Zhenyu Ju
Received: 20 November 2020 Revised: 9 May 2021 Accepted: 13 May 2021
© The Author(s) 2021

Inflammation, epigenetics, and metabolism converge to cell senescence and. . .
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Fig. 1 Dysregulated inflammation, alteration of epigenetic modifications, and metabolic imbalance converge to cell senescence and ageing.
Cross talks among epigenetic modifiers (writers, readers, and erasers), inflammatory gene expression and immune cell response, and
metabolic alterations contribute to senescent phenotypes and organ degeneration. MiDAS mitochondrial dysfunction-associated senescence,
SASP senescence-associated secretory phenotype, OXPHOS oxidative phosphorylation, ROS reactive oxygen species, TCA tricarboxylic acid
hallmarks. At present, the most commonly used senescent marker

is senescence-associated beta-galactosidase (SA-β-gal), closely
related to the lysosomal stress response, but not necessarily
dependent on senescence.15 Activation of p53, p21CIP1,
p16INK4a, ataxia telangiectasia mutated (ATM)/ATM and RAD3-
related (ATR), and retinoblastoma (RB) can be used as auxiliary
markers apart from the occurrence of morphological changes,
permanent cell cycle arrest, cell secretion, and metabolic and
chromatin remodeling.16 As none of those mentioned above
markers can solely determine the specific type of cell senescence,
various methods and hallmarks are required to clarify the exact
category of a senescent cell.17 A summary of known hallmarks of
cell senescence is shown in Table 1.
Permanent cell cycle arrest

Typically, senescent cells exhibit permanent cell cycle arrest that
differs from quiescent or differentiated cells. The current definition
of cell senescence emphasizes a state of cell cycle withdrawal
upon external stimuli.1 In contrast, quiescent cells can reenter the
cell cycle, and differentiated cells can be dedifferentiated under
certain circumstances. Besides, senescence typically accompanies
augmented p21CIP1 or p16INK4a expression, while quiescence is
Fig. 2 The hallmarks of cell senescence p27KIP1 dependent, and differentiation can involve multiple
signaling pathways (e.g., Wnt/Notch/Hedgehog/p16INK4a).
and tumor inhibition.13 The determinant that matters favorable or
lousy cell senescence largely relies on the duration: long-term type of Senescence-associated secretory phenotype
cell senescence is prone to inflammation and disease, while short- First discovered by Jean-Philippe Coppe and colleagues in 2008,
term type sometimes seems beneficial because the immune system SASP refers to a state when senescent cells release certain
can quickly scavenge the senescent cells.14 substances that mediate a series of (patho-)physiological effects,
including pro-inflammatory cytokines, chemokines, growth hor-
mones, angiogenic factors, and matrix metalloproteinases.18 The
THE HALLMARKS OF CELL SENESCENCE different biological activities induced by the components of SASP
As described above, senescent cells are categorized by differences suggest that it may interact with local and surrounding cells, and
in stress stimuli, thereby exhibiting various phenotypes and constitutes a mechanism to regulate microenvironment, which
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conditions has emerged and succeeded in rodent models. Baker
Table 1. Selected modulators of cell senescence
and colleagues have found a large number of p16INK4a-positive
Senescent modulators Circumstances References senescent cells in various tissues that cause a range of ageing
symptoms, including sarcopenia, cataracts, and lipodystrophy.7
15
SA-β-gal-positive staining Development, ageing, Accordingly, targeted clearance of p16INK4a senescent cells
all stages alleviates the adverse symptoms and successfully extend the
p21CIP1 Cell cycle arrest, ageing, 568 health span in many diseased models.7
all stages The field began to look for traces of senescent cells in common
p16INK4a Cell cycle arrest, ageing, 569 ageing diseases in humans, and successfully established a causal
all stages relationship between pathogenesis of ageing-related diseases and
p53 Cell cycle arrest, ageing, 570 cell senescence. Take atherosclerosis as an example, we have
DNA damage known that plaques composed of fat and protein gradually
Rb Cell cycle arrest, ageing, 571 accumulate on the inner arterial wall, which is prone to cause
DNA damage coronary atherosclerotic disease, stroke, or other ischemic severe
572 diseases. Next, senescence-associated macrophages were
Lamin B1 Decrease in ageing, genome
instability recruited to the arterial wall, where the plaque initially formed.
573,574 As time elapsed, other senescent cell types appeared near these
TAFs/TIFs DNA damage, telomere sites. Compared with other control cells, these senescent cells
attrition
575
expressed abundant secretory factors and metabolites that
Phospho-γH2AX DNA damage promoted the pathogenesis of atherosclerosis, concurrent with
18
SASP components Ageing, DAMPs, all stages significant alterations in epigenetic imprints.20 Using a variety of
Mitochondrial dysfunction Decrease respiration and ATP 576 approaches to remove these senescent cells attenuated the
production lesions, and thus alleviating the progress of atherosclerosis.20
Protein aggregates UPR, ageing, loss of 577 Consequently, focusing on the epigenetic and immunometabolic
proteostasis regulation of cell senescence may shed light on managing ageing-
Oxidative stress Increase ROS/RNS 576 related diseases and therapeutic interventions.21
578 In this review, we highlight the recent advances in the
Autophagy malfunction Ageing, protein toxicity
19
understanding of the inflammatory, epigenetic, and metabolic
Macromolecular Various stress, ageing basis of cell senescence, a comprehensive overview of relevant
condensates molecules and signaling pathways associated with cell senescence
579
HP1 Various stress, SAHF and organismal ageing are discussed. Finally, novel techniques
580
DNA methylation Various stress, SAHF and strategies intervening in the ageing process are briefly
Histone methylation Various stress, SAHF 581 summarized.
582
Morphology Ageing
583
Multi-omics alteration Various stress, ageing
AGEING AND INFLAMMATION
Infection-related diseases are responsible for many deaths
could be either beneficial or deleterious, depending on the globally, and aged people are more vulnerable to severe and
secretion factors, site (cell types), duration (acute or chronic), and life-threatening infections.22,23 Chronic inflammation represents
secretion-induced stimuli. an essential phenomenon in both murine and human ageing.24
Recent studies from different aspects investigations conclude that
Dysregulated metabolism inflammation is a commonly shared mark of ageing tissues. Gene
Metabolic disturbance during cell senescence manifests the loss of comparisons of young and old tissues from mice, rats, and
molecular and protein homeostasis. Several processes, such as humans revealed that age-related gene expression changes most
DNA damage response (DDR) induced by telomere attrition, remarkably involve a strong induction of inflammation and
decreased tricarboxylic acid cycle activity, and ATP production by immune response genes.25 The combination of high levels of
mitochondrial dysfunction, declined degradation of the protea- inflammatory signals, increased comorbid conditions, and reduced
some and autophagolysosome, the changes in SASP and function of the immune system increases the vulnerability of aged
epigenetic alteration, all lead to the remodeling of metabolic individuals to infection.26
signals and metabolites in the cells. Despite its crucial role in defending infections during life,
inflammation may turn into a hazardous factor to health for the
Macromolecular damage aged individuals, when it gets into chronic and persistent, such
Biomacromolecular damage is another typical phenotype of cell chronic increases in low-grade inflammation during ageing, also
senescence. Stimuli-like ionizing radiation, chemotherapeutics, known as “inflammageing”, is a hallmark of ageing.16,27 Unlike
and other drug damage, oxidative stress, and senescence-induced acute inflammation, inflammageing is characterized by maintain-
telomere dysfunction can mediate such damage, subsequently ing a low-grade, sustained background of inflammation even in
leading to the aggregation of aberrant macromolecular sub- the absence of acute infection and clinically diagnostic dis-
stances.19 Of note, the emerging concept of liquid–liquid phase ease.27,28 Increasing evidence has been shown that inflammage-
separation in cell senescence has recently made the research of ing is a risk factor that leads to reduced tissue repair and
biomacromolecule condensate in the ascendant. generative capacity, which is associated with many ageing-related
diseases.29–31
Consequently, extending the understanding of the underlying
EFFECTS OF CELL SENESCENCE ON ORGAN FUNCTION AND mechanism of inflammageing and ageing-associated diseases
DISEASES helps realize healthy ageing among the growing senile popula-
Accumulating studies have proven the relationship between tion. In this section, we summarize the current findings illustrating
senescent cells and organismal ageing. Meanwhile, the concept the cause and effect of inflammageing, and how inflammation
of eliminating senescent cells to counteract ageing-related gives rise to the evolution of ageing-related diseases. Novel

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Fig. 3 Inflammatory sources lead to senescence-associated secretory phenotype (SASP). Several pro-inflammatory sources have been
identified to trigger the chronic inflammation during cellular senescence and organismal ageing, featured by the activation of a group of
SASP-related genes, and subsequently the release of SASP components
approaches to attenuate pathophysiological conditions are also aged hematopoietic stem cells (HSCs), further stressing the
discussed, aiming at combating adverse inflammageing. immune system.48 Intriguingly, a study found that the level of
circulating mitochondrial DNA (mtDNA) is significantly increased
Source of chronic inflammation in ageing in elderly individuals and contributes to the increased systemic
High levels of pro-inflammatory cytokines shape the ageing- inflammation, although the exact source for circulating mtDNA
associated pro-inflammatory status, although the source of remains undefined.49
ageing-related chronic low-grade inflammation remains incom-
pletely understood.24,32–34 Nevertheless, a variety of source that Immunosenescence
contributes to the pro-inflammatory microenvironment has been The innate immune system gradually overtakes the adaptive
identified.35 immune system during ageing.50 In general, the function of the
immune system declines with age, collectively termed immuno-
Senescent cells senescence, featured by the reduced output of natural killer cells
Cells are driven into a senescent, nondividing state by many and thymic T cells, decreased phagocytic capacity of macro-
factors, such as telomere shortening, DNA damage, oxidative phages, as well as the impaired activation of neutrophils and
stress, genotoxic stress, and altered chromatin structure.36–39 The maldevelopment of B cells in the aged.50,51 Immunosenescence
immune system efficiently clears away the senescent cells to has been considered a dominating problem in the aged
maintain systemic homeostasis. However, the removal capacity population and is associated with inappropriate immune
declines with age (partially due to the immunosenescence), responses, resulting in the declined removal capability of
resulting in the increased SASP. Therefore, it becomes more senescent cells and DAMPs.52 Reciprocally, inflammageing leads
explicit that SASP builds a relationship connecting cellular to chronic, continuous generation of inflammatory factors that
senescent with various biological processes, where SASP repre- exhausts the adaptive immune responses, culminating with
sents a potential pharmaceutical target to manipulate the immunosenescence.10 Of note, due to the suppression of the
development of ageing and ageing-related diseases (Fig. 3). In adaptive immune response, the innate immune response could be
agreement, mounting evidence suggests that therapeutic removal reinforced as a compensatory means to protect the organism from
of senescent cells could delay or even prevent various age-related infections. Thus, the immunosenescence and inflammageing
diseases, such as atherosclerosis and osteoarthritis.7,20,40,41 could operate in parallel and form a vicious feedback loop.
Cell debris Gut dysbiosis
Cell debris, including damage-associated molecular patterns The gut mucosa barrier plays a vital role in defending against
(DAMPs), damaged organelles, and macromolecules, are recog- bacterial invasion. However, the integrity of the gut is impaired
nized and removed by the immune system. With age, cell debris with age. The permeability of the epithelial cells is damaged,
accumulates due to impaired clearance and overproduction, allowing the bacteria and other toxins to enter the blood, called
inducing augmented inflammation and impairs tissue regenera- “leaky gut”.53–55 The gut microbiota of older people also exhibits a
tion.42,43 The ageing-associated mitochondrial compromise can biased diversity.53–55 For instance, reduced anti-inflammatory
lead to a release of DAMPs, namely the secretory phenotype by bacteria like Bifidobacterium spp., while increased pro-
mitochondrial dysfunction-associated senescence (MiDAS), which inflammatory bacteria like Streptococcus spp. was found in the
causes particular attention in recent years.44–47 Congruently, aged gut.56 These changes lead to an increase in the susceptibility
ageing-associated mitochondrial stress can also lead to aberrant to infections in aged people.57 Another study also shows that gut
activation of inflammasomes and result in a functional decline in microbiota links to longevity, in which healthier seniors showed

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microbiome signatures that are similar to young people.58 In line altered.78,79 Among the transcription factors that regulate chronic
with this, the long-living (>90 years old) individuals favor inflammation across multiple diseases and tissues, NF-kB (nuclear
increased gut microbiota diversity than that in young controls, factor kappa-light-chain enhancer of activated B cells) and STAT
with several beneficial bacteria identified in the gut.59 (signal transducer and activator of transcription) are the two well
studied.80 NF-kB positively regulates many genes that encode pro-
Obesity inflammatory cytokines, therefore acting as a master regulator of
Obesity is featured by excessive fat accumulation that secret many SASP.81–83 Moreover, NF-kB drives several ageing phenotypes,
inflammatory adipokines.60,61 During ageing, immune cells particularly in the skin, spine, brain, and blood system.84–87
infiltrate into the fat tissues that can be activated upon various Notably, mTOR controls the translation of IL-1a and thus regulates
stimuli. Bernier and colleagues recently demonstrated that anti- SASP, indicative of its role in the regulation of SASP.88,89 mTOR
inflammatory Disulfiram, an FDA-approved drug treating chronic also has been manifested to control the translation of MK-2 kinase,
alcohol addiction, reversed established diet-induced obesity and which phosphorylates the specific RNA-binding protein ZFP36L1,
metabolic dysfunctions in middle-aged mice.62 Thus, bodyweight preventing the degradation of the transcripts of many SASP
control or calorie restriction (CR) that eliminates pro-inflammatory factors.89 These findings lead to the assumption that mTOR
fat deposition would reduce inflammation during ageing. accumulation helps accelerate the synthesis of SASP factors.
Sex hormones Moreover, the surroundings of senescent cells and their commu-
Existing evidence shows that sex steroids regulate the immune nications also contribute to the SASP, for instance, the NOTCH/
system by expressing their specific receptors in different immune JAG1 signaling controls the interaction between senescent cells
cells.63 With age, the levels of sex hormones, such as estrogen and with their microenvironment.90,91
progesterone in females and testosterone in males are down- Oxidative stress-induced inflammageing
regulated.64–66 Interestingly, after menopause, the number of Based on the close relationships between oxidative stress,
lymphoid cells decreases, accompanied by a strong induction of inflammation, and ageing, De La Fuente and Miquel proposed
pro-inflammatory cytokines.67–69 In contrast, postmenopausal an oxidation-inflammatory theory of ageing (oxi-inflammage-
females receiving hormone replacement therapies (HRT) showed ing).92 That is, oxidative stress leads to inflammageing and
increased B cells and reduced concentration of pro-inflammatory influences the homeostasis of the body. The redox state and the
cytokines compared with that without HRT.69,70 Despite that function of immune cells affect the velocity of ageing and life
testosterone replacement therapy has not been reported with span.92 Therefore, antioxidants treatment may improve immune
aged male individuals, one study using old nonhuman primates function. In line with this, resveratrol and metformin supplemen-
clearly showed that supplementation of androgens in aged male tation could extend life span via reducing oxidative stress.93,94
rhesus macaques partially reverted the reduced number of naive
T cells via enhancing thymic output, implicating a possible DNA damage response
connection between age-related hormone dysregulation and DNA damage induces several signaling transductions that result in
immune dysfunction.71 damage repair, cell cycle arrest, apoptosis, and cell death.95,96
Apart from the responses mentioned above, DNA damage also
Other sources triggers cellular senescent and ultimately induces SASP.97 p38 is
Apart from the sources discussed above, several lifestyle-related the primary regulator of DDR, and its activation could induce NF-
factors affect the secretory phenotypes of inflammageing.72 First, kB signaling, causing the SASP-related gene expression.98,99
long-term smoking has been associated with the increased Studies showed that p38 inhibition prevents the secretion of
susceptibility of respiratory diseases, and especially lung cancer various inflammatory factors involved in SASP.100,101 DNA damage
in the elderly, with a significantly elevated production of pro- also leads to the imbalance of systemic metabolism via inducing
inflammatory cytokines, such as interleukin (IL)-1, IL-6, TNF-alpha, tissue inflammation.102 It should be noted that DNA damage
and acute phase proteins.73,74 Second, a sedentary lifestyle among accumulated during ageing, potentially contributing to the
the aged individuals also accelerates fat accumulation and increase in chronic inflammation with age.
myeloid-biased hematopoiesis, siding with the pro-inflammatory
microenvironment. In agreement with that, a recent study found Cytosolic double-strand DNA-induced inflammageing
that regular exercise activity results in the reduced inflammatory Viral DNA in cytoplasm triggers the cGAS–STING pathway, leading
cell production, limiting the secretion of the inflammatory to the interferon (IFN) production and subsequently activates
cytokines via modulating hematopoietic and progenitor cell inflammatory response.103–105 Cytoplasmic DNA released from
proliferation in both murine and humans.75 Similarly, sleep stressed mitochondria or damaged nuclei can also lead to innate
problem perplexes aged individuals that aids mental stresses immune signaling response via inflammasome or cGAS signal-
with elevated circulating inflammatory cytokines. ing.106,107 The cGAS–STING signaling also connects genomic
instability and DNA damage to inflammation.108 Accumulated
Mechanisms involve in inflammageing evidence suggests that endogenous retroelements, such as short
Although the mechanism of inflammageing has not been interspersed nuclear elements (SINEs; including Alu) and long
thoroughly studied, many factors include oxidative stress, pro- interspersed nuclear elements (LINEs; including LINE1), play an
inflammatory cytokines, DNA damage, dysfunction of cellular essential role in initiating inflammation.109–111 De Cecco and
organelles, defects in autophagy, and stem cell ageing are colleagues demonstrated that LINE1 was transcriptionally acti-
involved in regulating inflammageing at both transcriptional and vated in senescent cells, thereby leading to type-I interferon (IFN-I)
posttranscriptional levels.76 induction and promoting SASP.112
Cytokines induction Micro-RNAs
Pathogen-associated molecular pattern receptors, such as the toll- The intracellular signaling cascades that regulate inflammageing
like receptors (TLRs) expressed on immune cells, are the principal are subject to numerous layers of regulation, including the
receptors that sense pathological stimuli and lead to cytokine regulation by micro-RNAs.113,114 For example, miRNAs participate
induction. TLRs are the first to be affected by invading pathogens in modulating TLR, retinoic acid-inducible gene I (RIG-I), and NF-kB
and mediate a series of physiological reactions, such as signaling pathways.115–118 miRNA can directly bind on TLR
inflammation, cell survival, proliferation, and apoptosis.77 During signaling or activate the RNA-sensing TLRs. In turn, the expression
ageing, the activation of TLRs downstream signaling pathways is of miRNA can also be regulated by TLRs, RIG-I, and NF-kB

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activation, revealing a feedback loop controlling the immune basal level of inflammation signal in aged animals. Therefore, the
response.117,119–121 resolution phase is much more extended than young mice.27,129
It is worth noting that inflammation has been well established
Stem cell ageing as a significant component of neurodegenerative disorders, yet it
Stem cells underlie tissue homeostasis, while ageing causes a is unclear if this is a direct cause of the disease or a consequence
functional decline in the stem cells, compromising tissue of progressive neurodegeneration.130,131 Over the past decade,
regeneration and contributing to age-related degenerative there has been a revolution in understanding how cytokines
diseases.122 Chronic inflammation is one of the main factors that contribute to the etiology of the leading neurodegenerative
induce stem cell ageing.123 During ageing, aberrant activation of disorders, including Alzheimer’s (AD) and Parkinson’s disease (PD).
the NLRP3 inflammasome restraints the function of HSCs.48 Inflammation also involves in many cardiovascular diseases,
Likewise, inflammageing is the main culprit of skeletal stem and although whether inflammation causes a heart attack or other
progenitor cell dysfunction.124 The chronic inflammatory process cardiovascular disorders require further investigation, inflamma-
accompanied by ageing leads to dysfunctional differentiation of tion serves as a universal sign for the atherogenic response.
stem cells, loss of self-renewal capacity, and results in stem cell Atherosclerosis is a chronic inflammatory condition where
ageing.123 Conversely, stem cell ageing is also responsible for atherosclerotic plaques show cellular senescence.132,133 Cytokines
systematic inflammageing. An increase in NF-kB activity has been are involved in all stages of the pathogenesis of atherosclerosis,
reported in aged HSCs, leading to enhanced sensitivity in aged having both pro- or anti-atherogenic effects.134,135 Chronic tissue
HSC to inflammatory stimuli, which result in the higher production inflammation has a vital role in the etiology and immunopatho-
of IL-6 and a myeloid-biased differentiation.87,125 Mesenchymal genesis of rheumatoid arthritis, with genetic and environmental
stromal cells (MSCs) ageing leads to adipocytes accumulation in factors contributing to a predilection to develop the disease.136,137
old bones and dysregulates hematopoiesis.126,127 A detailed Osteoporosis is a disease in which bone loses calcium and become
summary of epigenetics and ageing, particularly in stem cell fragile. Young people maintain a balance between bone loss and
ageing, is reviewed in an independent section. bone formation. However, with ageing, the balance is disturbed
Together, the possible mechanisms discussed above help toward bone loss due to the increases in chronic inflammation.138
understand how chronic inflammation accumulate and persist Sustained low-grade inflammation can be found in type 2
during ageing. These factors also provide potential drug targets diabetes due to a high concentration of circulatory inflammatory
for therapeutic interventions to delay the ageing process and cytokines.139 The inflammageing also alters the function of the
prevent inflammageing-associated diseases. blood system, leading to decreases in lymphopoiesis, over-
production of myeloid cells, cytopenias, and anemia.140–142
Inflammageing-associated chronic diseases Besides, the persistence of inflammageing intensively involves in
Inflammatory signaling has beneficial functions in many physio- hematological diseases, such as myelodysplastic syndrome and
logical processes, such as embryo development and wound acute myelogenous leukemia.143–145 Other studies also link that
healing. However, excessive and persistent inflammatory inflammageing to hypertension, frailty, dementia, and chronic
responses are detrimental, as reflected by increased morbidity kidney disease.146–148
and mortality, leading to a decline in life quality. Indeed, several On the other hand, cell senescence inhibits aberrant cell
studies have shown experimental evidence linking inflammation proliferation and tumorigenesis, yet ageing is considered the most
to chronic age-related diseases29(Fig. 4). For instance, old mice significant risk factor for cancer development. Nearly 60% of
were about 6.5-fold and fourfold more sensitive to the lethal people suffering from various kinds of cancers are 65 years old or
toxicity of lipopolysaccharide and exogenous TNF than young older. Paradoxically, although cellular senescence function as an
controls, respectively.128 The enhanced sensitivity of old mice to anticancer program, the secreted SASP factors are associated with
inflammatory stimuli is possibly due to the already existing higher malignant tumor progression.149 The mechanism that links SASP
and cancer have been extensively studied.1 For instance, IL-6 has
been shown to activate WNT signaling and promotes cell
proliferation.150,151 MPP3 (stromelysin) and vascular endothelial
growth factor drive cancer cell invasion or tumor angiogen-
esis.152,153 Besides, SASP factors have been demonstrated to
facilitate epithelial–mesenchymal transitions in the nearby pre-
malignant epithelial cells, and resulted in cancer cell invasion and
metastasis.154,155 Furthermore, many SASP factors can deteriorate
the surroundings and remodel the tissue microenvironment,
promoting cancer progression.156–159 Although the “seed and soil”
theory has established for >100 years, the internal relationship
between tumor microenvironment and cancer development
becomes a research hotspot in recent years.160 The most
abundant cells that compose the cancer microenvironment are
cancer-associated fibroblasts (CAFs).161,162 Apart from the positive
effect of CAFs on enhancing cancer proliferation and invasion,
CAFs also contribute to tumor-associated inflammation.163,164 A
study has shown that NF-kB signaling inhibition can abolish the
effect of CAFs on promoting immune cell recruitment, neovascu-
larization, and tumor growth in a mouse model of squamous skin
carcinogenesis.163 Targeting on CAFs favors a positive role in
extending life span and delaying cancer proliferation.165
Fig. 4 Inflammageing and its associated diseases. Multiple inflam-
matory signaling pathways, such as the NF-kB, NOTCH/JAG1, toll-like Therapeutic strategies to attenuate inflammageing
receptor, DNA damage response, cytosolic DNA sensing, autophagy, The pathways discussed above, which drive age-related inflam-
mRNA stabilization, and mTOR signaling pathways have been linked mation, are potential therapeutic targets to modulate inflamma-
to age-related chronic diseases in various organs geing and consequently, beneficial for the aged. One study

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indicates that switching off the immune machinery via mediating hypermethylation could be induced by senescence-associated
NLRP3 inflammasome activity could halt or even reverse these heterochromatin foci (SAHF), which recruit DNMT1 to focal
age-related diseases.166 Congruently, inhibition of NF-kB signaling sites,190,191 while oncogene-induced senescence fails to exhibit
could reduce the sensitivity of aged HSCs to inflammatory stimuli, such alterations in DNA methylation,192 reinforcing the diverse
leading to better maintenance of the hematopoietic system.87 characteristics of DNA epigenetic alterations during senescence.
Pharmaceutical or genetic removal of p16INK4a-positive senes- Interestingly, mtDNA methylation has also been changed in
cent cells delays the ageing onset and tumorigenesis in the mouse replicative senescent cells. One study reveals that 76% of mtDNA
model, although very recently p16+ liver sinusoid endothelial cells noncoding regions are hypomethylated in senescent cells,193
are found to be indispensable for the health span in mice.7,167,168 where p53-induced downregulation of mitochondrial DNMT
Furthermore, given the evidence that obesity causes increased represents a possible mechanism for the hypomethylation of
inflammation, bodyweight control, and healthy diet consumption mtDNA.194 However, no significant global DNA methylation
will be beneficial for reducing inflammageing.61 Similarly, exercise changes are observed in multiple forms of stress-induced
helps decrease inflammatory factors, which play an anti- premature senescence, including doxorubicin-induced senes-
inflammation effect across multiple systems, including cardiac, cence, irradiation-induced senescence, oncogene-induced senes-
blood, and muscle.75,169 Likewise, CR lower inflammation and cence, and nonpermissive temperature-induced senescence.195,196
protect against age-related diseases. A recent study explored the The different types of cell senescence-associated DNA methylation
effect of CR on multiple tissues at the single-cell level and found also lead to distinct gene expression patterns and cell phenotypes.
that genes related to immunity, inflammation, and lipid metabo- Further investigations are required to explore the differences
lism are most affected by the CR.170 Intake of reverse transcriptase among the epigenetic mechanisms underlying replicative senes-
inhibitor Lamivudine (3TC),112 or natural compounds represent a cence and stress-induced premature senescence.
safe and effective option that helps ameliorate many age- Of note, DNA methylation changes usually lead to a decline in
associated disabilities and diseases.93,112 Resveratrol supplement the number and function of stem cells, like self-renew ability
could reduce ovarian inflammation, attenuated spinal cord injury, defect and differentiation bias, which are often similar to those
and suppressed tumorigenesis by targeting NF-kB and mTOR observed in the ageing process.1 The effect of ageing on the DNA
signaling in a SIRT1-dependent manner.171–174 Similarly, metfor- methylome of purified adult stem cells from young and old mice
min supplementation can also reduce SASP by blocking NF-kB was detected by global methylated DNA immunoprecipitation
activity,175 although the sex-dependent effects on life span remain sequencing.197,198 These studies show that HSCs display global
controversial upon metformin treatment.176–180 Other interven- DNA hypermethylation during ageing197,198 concomitant with
tions, such as sleeping modulation, thymic replacement to decreased 5-hmC levels.198 Furthermore, ageing muscle stem cells
increase adaptive immune function, maintain gut integrity, and (MuSCs) showed a slight increase in their DNA methylation age at
to improve environmental quality, could be potentially helpful in the single-cell level.199
altering the dynamic of inflammation and preventing the Ageing-associated gains of DNA methylation were also over-
inflammageing related disease.5 occupied at loci associated with polycomb gene (PcG) binding
Although these attempts have significant impacts on treating and some transcription factors binding in old HSCs.197,198,200
ageing and inflammation-associated diseases, the spatiotemporal Similarly, PcG targets were also hypermethylated in MSCs during
regulation of pro-inflammatory cytokine release and its landscape ageing, though a predominance of ageing-associated hypomethy-
have not been completely understood. Besides, due to the limited lation as reported.201,202 The correlation between age-related
sensitivity of the current technique, many unknown age-associated changes in DNA methylation and age-related changes in
pro-inflammatory cytokines in blood await to be detected. Never- transcription was also examined in these studies, suggesting that
theless, single-cell omics and lineage tracing would surely empower the ageing process could disrupt these PcG proteins or transcrip-
a deeper understanding of inflammageing, and provide better tion factors to bind DNA and regulate transcription.201,202
solutions to counteract age-related inflammatory diseases.
Sub-telomere region DNA methylation and ageing
Senescence-associated DNA methylation alterations are engaged
AGEING AND EPIGENETICS in the regulation of telomere dysfunction. Telomere damage is not
Epigenetic regulation is used to classify heritable changes in gene only determined by the telomere length, but also controlled by
expression that are not attributable to changes in DNA the epigenetic conditions in telomeric/sub-telomeric regions.203 In
sequences.181 Mounting evidence suggests that epigenetic young wild-type cells, sub-telomeric regions are hypermethylation
dysregulation is also an essential driver for cellular senescence in CpG islands, and enriched by HP1a protein and repressive
and stem cell ageing.182–186 This part highlights the functional histone modification marks (H3K9me3 and H4K20me3), and lack
importance of epigenetic regulation in terminally differentiated of permissive histone modification marks (H3K9ac and
cells and stem cells, in the context of altered DNA methylation, H4K20ac).203 However, MEF cells from telomerase-deficient mice
changes in histone modifications, and synergistic relationships exhibit more “open” state of telomeric/sub-telomeric chromatin,
between epigenetics and metabolism in ageing. as indicated by loss of CpG island DNA methylation, loss of
repressive histone modifications (H3K9me3 and H4K20me3),
DNA methylation decreased CBX3 binding accompanied by increased H3 and H4
In mammalian cells, DNA methylation occurs predominantly at acetylation, and increase the level of H3K9ac and H4K20ac.203,204
CpG dinucleotides. Methylated cytosine (mC) is found throughout Our work discovered that the deletion of DDR factor Gadd45a
the genome at high frequency, predominantly located at rescued the heterochromatin remodeling via base excision repair-
promoter regions of genes,187 which plays a critical role in mediated active DNA demethylation in sub-telomeric regions in
transcriptional silencing.188 DNA methyltransferases (DNMTs) telomere-deficient cells, which generates an uncondensed chro-
DNMT3A and DNMT3B establish genome-wide de novo methy- matin structure to promote DDR signaling.204 Although Gadd45a
lated nucleotides, DNMT1 maintain methylated nucleotides, and has been linked to the global DNA methylation and transcriptional
TET protein family-regulated DNA demethylation.187,189 regulation, Gadd45a loss does not change the global DNA
methylation pattern in our experimental setting,204 indicating
DNA methylation during cellular senescence that manipulation of the Gadd45a gene could delay organ ageing,
During cellular senescence, the landscapes of DNA methylation and prolong the health span and life span of premature
are changed in a context-dependent manner. For instance, local ageing mice.

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DNA methylation and human ageing clocks senescence cells.237 However, the histone marker alteration
Age predictors based on a small set of CpG sites DNA methylation patterns differ in different stress-induced premature senescence
levels have been developed for humans and several other cells based on various stress factors.237 Thus, the diversity of
species.205 Early studies have found that age-related DNA histone modifications in senescence cells may cause diverse gene
hypomethylation patterns occur in many body tissues of the expression patterns and senescence phenotype.
elderly.187,205–209 However, detailed analyses of several studies The role of senescence-associated histone modification changes
uncovered CpG islands site-specific DNA hypermethylation in the senescence regulatory mechanisms has been broadly
associated with ageing tissues,200,206,210–213 and these hyper- explored. The histone methyltransferases (HMTs) complex, poly-
methylation changes are generally related to age rather than the comb repressive complex (PRC), was investigated in repressing the
tissue type,211,214,215 suggesting some level of synergetic control p16 gene expression.238 PRCs binds directly to the p16 locus and
of DNA methylome during ageing. induces H3K27me3 occurrence, which leads to transcriptional
The DNA methylome of different organs or tissues can be used suppression of p16.239 Besides, cell senescence can be delayed via
to predict the biological age.216 For example, DNA methylation in inhibition of histone acetyltransferases (HATs) and induced by
human peripheral blood has been manifested to correlate with inhibiting histone deacetylases (HDACs).240–242 A recent study
ageing.217,218 A recent analysis of human blood samples does revealed that HAT p300 is a primary driver of the replicative
confirm that, with age, most hypermethylation is not related to senescence phenotype via a high-throughput screen.242 The
changes in cell composition, but directly related to ageing.213 The depletion of p300 suppresses senescence-related gene expression,
increase in DNA methylation age of blood over 5 years was ensuing delayed senescence.242 Therefore, p300 is a candidate
associated with a 16% higher mortality rate than age.219,220 Several target for anti-ageing therapeutics.
research groups have observed an acceleration in DNA methyla- However, certain histone modifications in senescence and ageing
tion age in some age-associated diseases, including AD, cardio- may be contrasting and even paradoxical. Tissue or cells from ageing
vascular disease, and cancer.221,222 DNA methylation has been organisms show increased H4K16ac, H4K20me3, or H3K4me3, along
reported to regulate neuronal differentiation in early CNS with decreased H3K9me3 and H3K27me3, which are quite different
development. A global methylome reconfiguration was associated from cellular senescence.243 The difference in histone modification
with synaptogenesis ranging from mammalian fetal to adult brain between cellular senescence and organismal ageing may attribute to
development.187 In human, 353 CpG sites were identified to form multiple sources for ageing-associated damage, such as mutation,
an epigenetic age clock.223 The DNA methylation levels change reactive oxygen species (ROS), and environmental stress, that change
with normal ageing in many tissues, including the brain, peripheral the epigenetic pattern of ageing and differ from cell senes-
blood.223 Gene-specific DNA methylation changes are involved in cence.244,245 In turn, epigenetic therapies based on histone
rewarding in a context-dependent manner and are essential for modification that target cell senescence may inhibit the accumula-
memory formation, neurogenesis, and neuronal plasticity.224,225 tion of senescent cells. Naturally occurring activators of SIRT1,
Lower levels of DNA methylation on the promoter of target genes including resveratrol, nicotinamide riboside, and nicotinamide
in peripheral blood samples have been reported to contribute to mononucleotide, limit the accumulation of senescent cells.246–249
AD.226,227 The expression of DNMT1 and global 5mC and 5hmC
were also shown to be decreased in AD neurons and hippocam- Histone acetylation and methylation during stem cells ageing
pus.228,229 Marioni et al.230 showed that greater DNA methylation Histone associated epigenetic changes in adult stem cell ageing
acceleration is correlated with a lower cognitive score, weaker grip have been reported for numerous stem cell populations,
strength, and poorer lung function in humans during later life. remarkably HSCs and MuSCs.125,250 An increase in the level of
Horvath et al.231 found accelerated DNA methylation age in Down the repressive histone modification H3K27me3 has been observed
syndrome patients with clinical signatures of “accelerated ageing.” in both HSCs and MuSCs.251 However, H3K4me3, an active histone
There is also evidence that frailty, a syndrome with a pronounced modification mark, shows an increase in HSCs but decreases
association with age-related phenotypes, has a significant associa- marginally in MuSCs with age.250
tion with DNA methylation age, but not with telomere length.232 Many genetic studies have revealed the critical role of HDACs
Zheng et al.233 pointed out that DNA methylation age estimated and HATs activity in stem cell function. In the hematopoietic
from blood tissue can also be used to predict cancer incidence and system, the significant phenotypes related to CREB-binding
mortality. The apparent genetic clock derived from DNA methyla- protein suggest the vital role of HATs in HSC function.252–254
tion is better at estimating actual age than transcriptome and Mononuclear leukemia zinc finger protein Moz is a kind of HATs
proteomic data or telomere length.209 In conclusion, the age- translocation protein in human acute myeloid leukemia. During
related DNA methylation changes may reflect the biological age to embryo development, the gene is eliminated, resulting in the
some extent, therefore constituting the biological age clock. severe loss of HSC and other progenitors with limited lineage.255
These results strongly suggest that histone acetylation is
Histone modifications necessary for HSC self-renewal. HAT activity also plays an essential
Histone modification is an additional epigenetic regulatory layer role in the homeostasis and function of HSCs and precursor cells.
that is more complicated than DNA methylation. The unstructured Eighteen mammalian HDACs have been identified and divided
N-terminal of histones can be used for posttranslational modifica- into four families. Class I HDAC plays a role in differentiation and
tion, including acetylation, methylation, phosphorylation, sumoy- seems to have a high degree of functional redundancy.256,257 In
lation, ubiquitination, and other modifications that change the hematopoietic system, loss of HDAC class I leads to a decrease
chromatin structure and accessibility. These modifications can in bone marrow cells,258 and in some cases, causes loss of stem
regulate transcriptional activity. Here, we focus on histone cells and progenitor cells.259 In addition, the simultaneous
acetylation and methylation, which are the two most well- knockout of HDAC3, HDAC5, and HDAC7 (class I and class II
studied markers in cellular senescence and ageing. HDACs) resulted in the CDKN1A (p21) upregulation and inhibition
of cell proliferation,260 similar to p21 induction and cell cycle arrest
Histone (de-)acetylation and (de-)methylation during cellular in human mesenchymal stem cells after drug-induced inhibition
senescence of HDAC activity.261
Global decreases in H4K16Ac, H3K4me3, H3K9me3, and Class III HDAC includes the NAD+-dependent sirtuin family,
H3K27me3, while increases in the level of H3K9Ac and while other HDAC families need Zn2+ as a cofactor. In
H4K20me3 occur in replicative senescent cells.234–236 Such histone mesenchymal stem cells, SIRT1 is related to differentiation into
modifications have also been found in stress-induced premature bone and cartilage by deacetylation of β-catenin.262 In adult

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neural stem cells, the loss of SIRT1 leads to increased self-renewal chromatin in a specific DNA sequence termed the lamin A-
and proliferation with the increase of oligodendrocytes.263 associated domains (LADs).278,279 In the process of cell senescence
Similarly, SIRT2 also hinders the differentiation of oligodendro- induced by an oncogene, the remodeling of LADs results in the
cytes.264 In adult HSCs, loss of SIRT6 leads to enhanced Wnt unexpected recruitment of the decompressive sequence to the
signaling, decreased self-renewal, and over-proliferation.265 Simi- nuclear plate.280,281 Lamin A/C also promotes epigenetic changes
larly, SIRT1 guides the differentiation of epidermal stem cells by by interacting with epigenetic enzymes.282 Under physiological
promoting the production of keratinocytes.266 In HSCs and MuSCs, conditions and in young cells, lamin A/C interacts with SIRT1 and
SIRT1 loss leads to premature cell differentiation, implicating it is a enhances its deacetylase activity. It also promotes SIRT6 function
regulator of self-renewal of these cells.267–269 Robust SIRT1 activity during DNA repair and is found to recruit HDAC2.283–285
is also related to maintaining the quiescence of MuSCs, while the Importantly, the interaction of laminin with SIRT1, HDAC2, and
decrease of SIRT1 activity measured by increasing H4K16ac is SIRT6 decreased when protein A or progerin accumulated.283,285
related to the decline in NAD+ level in activated MuSCs.267 The The level of H3k9me3 in Hutchinson-Gilford progeria syndrome
increase of the H4K16ac level in these activated stem cells is due (HGPS) and mandibulofacial dysplasia type A (MADA) cells were
to the transformation of metabolism from fatty acid oxidation to decreased.286,287 HGPS cells lose heterochromatin protein HP1 and
glycolysis. Interestingly, although HSCs utilize glycolysis rather other heterochromatin markers, including H3K27me3 and
than oxidative phosphorylation (OXPHOS) and therefore have low H4K20me3.287,288 In addition, increased H4K16ac and H3K9ac
levels of available NAD+, SIRT1 activity seems to be needed to were reported in HGPS cells and MADA cells, respectively.285
regulate histone acetylation to maintain proper HSC function in Congruently, many changes in DNA methylation levels at specific
ageing.268 CpG sites were observed in the immortalized B cells of HGPS
The level of H4K16ac of aged HSCs was increased by patients.289 Interestingly, according to the epigenetic clock,231 the
immunostaining.270 Interestingly, compared with the young HSCs same cells are older than expected. LADs were also involved in the
with high-level polarized H4K16ac expression, the H4K16ac level epigenetic landscape remodeling of HGPS cells.290 In HGPS cells,
in the old HSCs decreased, concurrent with significantly changed progerin destroys the interaction of lamin A/C with SIRT1 and
cell distribution.270 The drug inhibition of Cdc42 and partial SIRT6, affecting chromatin localization and deacetylase
recovery HSC function reversed the change of H4K16ac in aged function.283,284
HSCs.270 Although the exact role of altered H4K16ac in aged HSC
remains elusive, H4K16 deacetylation has been shown to hinder Epigenetic regulation of retrotransposable elements during
DDR and repair of double-strand breaks.271 Therefore, H4K16 ageing
deacetylation in aged HSC may contribute to the accumulation of Two subtypes of non-LTR retrotransposons, LINEs and SINEs,
DNA damage.272 together make up nearly half of the human genome.291–293
In contrast to histone acetylation, histone methylation can be Heterochromatin region in young cells and organisms silences
used as a context-dependent inhibitor or permissive marker, reversible transposable factors, but due to the lack of regulation of
which indirectly regulates gene expression. Although histone higher-order chromatin structure, they are activated in the context
methylation occurs on lysine and arginine residues, most stem cell of cell senescence and tissue ageing.294 Interventions to prolong
studies detect methylation catalyzed by HMT on lysine residues.251 life, such as CR, decreased retrotransposon expression in elderly
Changes in some other chromatin features, most of which are also mice.295 In the liver and muscle cells of old mice, CR delayed the
altered with age, have been shown to regulate stem cell loss of constitutive heterochromatin and inhibited the expression
function.273 For instance, the H3K27me3 demethylase UTX is of repetitive components, including LINE1 and satellite compo-
essential for MuSC-mediated muscle regeneration.274 The increase nents, which were in the centromeric, pericentromeric, and
of histone inhibitory markers, such as H3k9me3 and H3K27me3, telomeric region. CR also inhibited the interaction between
were observed in the aged MuSCs and HSCs, which indicated that microRNA and chromodomain helicase DNA-binding protein 1,
the heterochromatin increased gradually in the ageing process.251 thus preventing the activation of retrotransposons induced by
H3K4me3, an active chromatin marker, was enriched in the old ageing and poor diet.296 Therefore, blocking the transcription of
HSCs, suggesting that epigenetic enhancement was observed in endogenous retrotransposon factors through diet restriction can
the transcriptional activation of stemness related genes.198,251 improve the age-related phenotype, and support the view that
Contrary to what was observed in HSCs, the detection of H3k4me3 retrotransposon leads to ageing and age-related diseases.
in MuSCs showed little difference between the cells isolated from SIRT6 mono-ADP ribosylates KAP1 and promotes KAP1 interac-
young and old mice.250 tion with HP1α, packaged as inhibitory heterochromatin in the
Furthermore, H3K27me3 was added by polyclonal inhibition LINE1 element. SIRT1 also binds to and inhibits major satellite
complex 2 (PRC2). When compared with the young HSCs, the level repeats in yeast and mammalian cells.297 Another known
of H3K27me3 signals in aged HSC is essentially the same, but the heterochromatin regulator, retinoblastoma protein (Rb), antag-
coverage and intensity of H3K27me3 signals in aged HSC are onizes the activation of LINE1 in senescent cells and decreases the
expanded.275 However, unlike the young MuSCs, the aged MuSCs percentage of Rb on the LINE1 promoter in senescent human cells
showed a transition to the euchromatin state after activation, with and senescent mouse tissues.298 Homologous protein transcrip-
increased histone acetylation while decreased in H3K27me3.250,276 tion factors inhibit the expression of LINE1 in adult dopaminergic
How the changes of H3K27me3 in the ageing process affect the neurons299 and prevent its degeneration. In addition, partial
function of stem cells in muscle and blood remain unanswered, overexpression of histone H3 and H4 reversed the transcription
yet this inhibitory marker may limit the regeneration potential of defects observed during ageing and reduced the reverse
these stem cells, which will decrease with age. transcriptional transposition, which indicated that the increased
reverse transcriptional transposition in old yeast was the result of
Epigenetic defects in progeroid laminopathies histone loss during ageing.291 In addition, CRISPR-Cas9 screening
The reconstruction of the chromosomal domain is also a feature of also provided a genome-wide gene investigation related to the
senescent cells. Senescent cells undergo substantial changes in retrotransposition control of LINE1, revealing that the vertebrate-
three-dimensional chromatin organization globally, as evidenced specific chromatin-modifying complex human silencing hub and
by the combination of whole-genome chromosome conformation the subunit of MORC family CW zinc finger protein 2 promoted the
capture (Hi-C), fluorescence in situ hybridization, and in silico deposition of H3K9me3 to silence the transcription of LINE1
modeling.277 Among them, lamin A/C represents an epigenetic element.300,301 Recent studies have further shown that inhibition
regulator of ageing partially due to its direct interaction with of the transposition of LINE1 by nucleoside reverse transcriptase

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inhibitors can inhibit the secretion of SASP and IFN by senescent mitochondrial stress and SIRT2 inactivation lead to the activation
human fibroblasts, and prolong the life span of the D. melanocyte of inflammatory corpuscles in NLRP3 of HSC and the decline of
model without DICR2, a heterochromatin structure regulating HSC ageing function.48 Specifically, diminished SIRT2 expression
gene.112 These findings collectively suggest that epigenetic augmented mitochondrial stress, while SIRT2 overexpression or
remodeling plays a vital role in the anti-ageing process, NLRP3/caspase-1 inactivation attenuated the impaired regenera-
preventing the activation, and mobilization of retrotransposons tive capacity of aged HSCs.48
by increasing heterochromatin stability. Genome-wide quantita-
tive analysis will provide new insights into the frequency, Mitochondrial sirtuins (Sirt3, 4, and 5)
structure, and location of retrotransposons during ageing, and In addition to the three nuclear sirtuins (Sirt1, 6, and 7),
clarify their overall contribution to ageing and rejuvenation. mitochondrial sirtuins (mtSIRT) include three members, i.e., SIRT3,
SIRT4, and SIRT5, which are all involved in regulating stem cell
Sirtuin-mediated epigenetic regulation in stem cell ageing metabolism.314 Among them, mitochondrial SIRT3 was found to
Metabolism and epigenetics are closely linked, which together be highly enriched in HSCs.315 Brown et al. suggested that SIRT3
affect the ageing of the body. The availability of key nutrients, deficiency reduced the HSC pool of old mice and impaired the
such as glucose, fatty acids, and amino acids, directly affects self-renewal of HSC during continuous transplantation stress,
organisms’ life span. Glycolysis disorders have been shown to partly due to the hyperacetylation of superoxide dismutase
prolong life span302 and supplement D-glucosamine, an antago- (SOD2) and subsequent increase in oxidative stress.315 SIRT3
nist of glucose, which can damage glucose metabolism and decreased with age and its overexpression in HSC reduced
prolong the life span of nematodes and mice.303 In addition, oxidative stress and maintained reconstructive ability.315 SIRT4
amino acid and lipid composition are closely related to age. They expression is upregulated during cell senescence of different
can be used as indicators of health span, as shown by the types.316 SIRT4 overexpression can induce trophoblast stem cell
metabonomics analysis of plasma of healthy young and old senescence.317 SIRT5 has demalonylase, deglutarylase, and desuc-
individuals.304 However, mitochondrial metabolism is the most cinylase activities318,319 that regulates ammonia detoxification.320
correlative with epigenetic regulation. Small molecules, such as Although not well studied in stem cells, SIRT5 was thought to
NAD+, alpha-ketoglutarate (α-KG), and coenzyme A derived from desuccinylate and activate SOD1 to maintain a low ROS level in
mitochondria, have changes in the content of these metabolites stem cells.321
during the ageing process and affect the activity of enzymes that SIRT6
use these metabolites as substrates for epi-modification. Specific deletion of Sirt6 in HSCs of adult mice resulted in the
The sirtuin protein family is one of the first known epigenetic amplification of HSPC, which is associated with acetylation of
enzymes and a key regulator of ageing and CR.305,306 In mammals, H3K56 and the increase of transcriptional factor in the Wnt
the sirtuin family contains seven Sir2 homologs, Sirt1–Sirt7, whose signaling pathway.265 The increased proliferation further ham-
expression or enzyme activity increases after CR. It is worth noting pered HSC quiescence and led to HSC depletion. As a result, the
that CR can prolong the life span of mice by inducing SIRT1 long-term regeneration capacity of Sirt6-defective HSCs was
expression.4 Congruently, SIRT1 overexpression mimics the severely impaired.265 Furthermore, Sirt6-mediated stress resis-
beneficial effects of CR. SIRT6 deficiency resulted in a shortened tance also helps maintain the in vitro function of MSCs.322 Human
life span in mice and early death in nonhuman primates.110,307 In bone marrow mesenchymal stem cells derived from SIRT6-
contrast, SIRT6 overexpression and CR induced SIRT6 activation deficient mice were susceptible to oxidative damage due to the
delayed ageing.282 In addition, sirtuin activators, such as SRT1720 increased level of ROS.322 Mechanistically, the SIRT6-mediated
or SRT2140, can increase the health span of obese mice and the antioxidant effect by H3K56ac deacetylation activated the Nrf2-
life span of mice on a standard diet.308,309 These longevity- mediated antioxidant gene.322 Although it is not clear how the
extending effects of sirtuins are realized mainly by their enzyme deacetylase acts as a coactivator to promote anti-oxidation genes
functions, such as deacetylase and single ADP ribosyltransferase, in MSC, this study shows that SIRT6 is crucial to mediate the anti-
especially when histone is used as the substrate. Recent findings stress and anti-ageing effect of MSC.
of sirtuins in epigenetic regulation of adult stem cells are
summarized below. SIRT7
SIRT1 Sirt7 is also highly expressed in HSC, which exerts its regenerative
SIRT1 is very important to maintain the static and regeneration ability ability by regulating the unfolded protein response in mitochon-
of HSCs under environmental stress and ageing conditions.310 Under dria.323 Quiescent HSCs are maintained in a state of inactive
normal circumstances, no abnormality was seen in the hematopoietic metabolism that can be easily activated via boosting mitochon-
cells of SIRT1-KO mice.311 However, the hematopoietic commitment drial content. Mohrin et al. showed that mitochondrial protein
of SIRT1-deficient HSC is impaired in vitro, concurrent with a reduced folding stress (PFSmt) induced the interaction between Sirt7 and
survival rate of hematopoietic progenitor cells, especially in hypoxia Nrf1, and inhibited the expression of mitochondrial ribosomal
or delayed addition of growth factor.312 Moreover, conditional protein and mitochondrial translation factor. Sirt7-deficient HSCs
exited quiescence and exhibited an ageing phenotype, including
ablation of SIRT1 in adult hematopoietic stem/progenitor cells
(HSPCs) autonomously induces HSPCs expansion and loss of long- the increase of PFSmt, apoptosis, a decrease of reproductivity, and
term repopulation under stress.310 This stress-induced loss of HSC biased bone marrow differentiation. On the contrary, the
function is associated with genomic instability, p53 activation, and upregulation of Sirt7 improved the regenerative ability of HSC in
increased DNA damage in SIRT1-deficient HSPCs.310 SIRT1 deficiency the elderly.323
also resulted in a significant increase in H4K16ac and upregulated Together, posttranscriptional and posttranslational regulation
the expression of HOXA9, a key regulator of HSPC function and via sirtuins maintains stem cell function to cope with various stress
proliferation.268,310,312 In general, SIRT1 is essential to maintain stimuli and ageing. Although mtSIRT is less studied in stem cell
different ASC pools by maintaining quiescence, self-renewal, and function, three nuclear sirtuins (Sirt1, 6, and 7) participate in the
regenerative capacity, especially in response to stress and injury. static control of stem cells, which is of considerable significance to
maintain the regenerative ability of stem cells and prevent
SIRT2 premature ageing. Pharmacological interventions targeting sir-
Sirt2 is a mammalian sirtuin, which primarily exists in the cytosol tuins may hold great promises to counteract stem cell ageing and,
and has deacetylase activity.313 Luo et al. suggested that therefore, tissue homeostasis.

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Approaches in epigenetic control of rejuvenation developed, such as single-cell sodium bisulfite sequencing for
Somatic cells are induced to restore pluripotency through various DNA methylation detection,345 single-cell chromatin immunopre-
reprogramming strategies, the most common of which is the cipitation sequencing for the identification of histone modification
overexpression of four transcription factors Oct4, Sox2, Klf4, and and protein–DNA interaction, single-cell transposable accessible
Myc (referred to as OSKM).324 The mouse nucleus reprogrammed chromatin sequencing, and Hi-C sequencing for the evaluation of
by OSKM can produce viable embryos and further develop into chromatin accessibility and chromosome conformational informa-
fertile adults without showing premature ageing, indicating that tion.346–348 These techniques have been combined with single-cell
the time sequence of the donor nucleus has been reset. transcriptome to study gene regulatory profiles and analyze cell
Consequently, core reprogramming appears to be able to reset heterogeneity. Recently, a new method has been established to
ageing clocks. Partial reprogramming of the adeno-associated record transcriptome synchronized with chromatin accessibility,
virus vector expressing OSKM can significantly improve axon thus enabling the analyses of the functional relationship between
regeneration after injury.325 The expression of OSKM leads to these two characteristics in the same cell.349
extensive remodeling of chromatin, accompanied by alterations of The intensity of the regulatory link between epigenetic
epigenetic enzymes and other transcription factors. For example, modification and transcription may vary in different develop-
as a pioneer factor, Oct4 can loosen heterochromatin and reduce mental stages and cell types, adding a layer of complexity and
the global levels of inhibitory H3K9me2, H3K9me3, and 5- uncertainty in delineating the specific spatiotemporal transcrip-
methylcytosine,326 which are obstacles in reprogramming.327,328 tional regulation. The application of these single-cell and multi-
In addition, during OSKM-mediated pluripotent reprogramming, omics techniques enables us to understand the regulation of
the epigenetic memory of the primitive cells is largely eliminated epigenetic factors on gene expression under physiological and
and rewritten in the subsequent differentiation process.329 pathological conditions.350
Many drugs, compounds, and supplements with anti-ageing In sum, stem cells residing in different tissues accumulate
properties have also been identified and attracted considerable defects during ageing, preventing stem cells from repairing
attention by pharmaceuticals, which can prolong the life span and damage, and maintaining tissue homeostasis, with altered
healthy ageing of model organisms (such as mice, Drosophila epigenetics a potential hallmark (Fig. 5). Existing evidence has
melanogaster, and Caenorhabditis elegans).330 For instance, met- suggested that the developmental pathway in embryogenesis is
formin regulates the activation of AMPK, which directly governs the key to epigenetic regulation that contributes to stem cell
the activities of several epigenetic enzymes, such as HATs, HDACs, ageing. These observations raise important issues for future
and DNMTs.331,332 In addition, metformin restores AMPK-mediated research. While it is unclear whether epigenomic changes are an
phosphorylation and stabilizes Tet2, thereby preventing changes essential element of ageing and how these changes occur during
in 5-hydroxymethylcytosine levels.333 Aspirin supplementation has ageing remain elusive, many attempts are on the way to depict
also been shown to generalize the anti-ageing effect of CR.334 The the full landscape of acute and chronic changes in the epigenetic
accumulation of senescent cells is one of the signs of ageing. modification during stem cell ageing. Given that mutations in
Senolytics selectively eliminate senescent cells, representing a epigenetic modifiers have become a marker of the ageing
new anti-ageing drug335 that may delay the ageing process. hematopoietic system, understanding the ageing-related clonal
Consistently, eliminating p16INK4a-positive senescent cells was dominance mechanism of stem cells with mutations in epigenetic
able to prolong the life span of early ageing model mice and wild- modifiers is of great interest. Finally, epigenetic integration of
type mice.167,336 damage signals, as a hardly neglected cause of stem cell and
Metabolic intermediates and by-products of the tricarboxylic organismal ageing, has brought new hope for the translational
acid cycle act as cofactors and substrates of various epigenetic pathway. Since the epigenome changes are largely reversible in
enzymes, including acetyl CoA for acetylation and S- principle, manipulating epigenetic imprints holds great prospects
adenosylmethionine (SAM) for methylation.337,338 In addition, α- in improving tissue maintenance, regeneration ability, and,
KG, an intermediate product of the tricarboxylic acid cycle, ultimately, extending health span.
induces DNA and histone demethylation by activating the
jumoniji C domain-containing demethylase and lysine demethy-
lase. A recent study showed that the increase of α-KG activated AGEING AND METABOLISM
JMJD3 (histone H3K27 demethylase) and PHF8 (histone lysine The unique metabolic signature of senescent cells shapes the
demethylase H3K9me1/2 specificity), leading to the removal of distinct senescent phenotype; for instance, augmented glycolysis
inhibitory markers and the induction of mitochondrial unfolded represents one of the metabolic hallmarks during replicative
protein response gene expression. These changes are enough to senescence. Changes in intracellular and extracellular metabolites
prolong the life span of nematodes.339,340 may lead to the consequence of senescence in adjacent cells, aka
Another important metabolite is NAD+, which is the cofactor of a bystander effect of the senescence-associated metabolic
sirtuins. It connects the gene regulation of epigenetic with pattern.351 This section will discuss the metabolic regulation of
mitochondria. High levels of NAD+ can improve mitochondrial cell senescence that interacts with many aspects of cellular
function, supplement the stem cell pool, and prolong the life span physiology, including redox balance, genomic integrity, immuno-
in mice. Supplementation of NAD+ precursor to aged mice can metabolism, proteostasis, organelle homeostasis, and metabolic
delay the decline of mitochondrial function, improve muscle, signaling pathways and interventions (Fig. 6).
nerve, and melanocyte stem cell performance, alleviate age-
related physiological decline (for example, type 2 diabetes and Metabolic regulation of redox balance in ageing
cognitive impairment), and prolong life span.341 Redox reactions occur throughout the cellular metabolism with
Apart from the investigations of novel epigenetic interventions the production of a small number of reactive oxygen radicals.352
in pursuit of rejuvenation, the study of epigenetic regulation at the Studies using model organisms, such as yeast, nematode,
single-cell resolution has deepened our understanding of the drosophila, and mouse have shown that cell senescence is closely
diversity of the single-cell state and the process of cell state related to dysregulation of redox balance.353–356 With ageing,
maintenance.342–344 Specific single-cell DNA sequencing provides increased oxidative stress featured by increased oxidized glu-
epigenetic information of DNA modification, DNA accessibility, tathione (GSSG), while lowered levels of glutathione (GSH) and
and chromosome conformation, thus deepening the understand- reduced form of nicotinamide adenine dinucleotide phosphate
ing of the impact of epigenome on the transcriptome. A variety of (NADPH) have been observed, which causes lipid, protein, and
single-cell epigenome-sequencing techniques have been DNA damages (e.g., DNA single- or double-stranded breaks, fatty

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Fig. 5 Epigenetic regulators and interventions in ageing. Age-dependent epigenetic remodeling by various (de-)methylases and (de-)
acetylases affects chromatin accessibility, thereby regulating gene transcription and expression. Interventions, such as calorie restriction and
drug treatment, may reverse the age-dependent degeneration in an epigenetic-modifying manner. HDACs histone deacetylases, DNMTs DNA
methyltransferases, TET ten–eleven translocation, HMT histone methyltransferase, TSS transcriptional start site, SAM S-adenosylmethionine, α-
KG alpha-ketoglutarate, NAD nicotinamide adenine dinucleotide
Fig. 6 Intrinsic cues to metabolic reprogramming during ageing. Six aspects, namely protein homeostasis, genetic and epigenetic instability,
organelle dysfunction, redox imbalance, immune response, and altered signaling pathways, lead to the metabolic regulation of ageing
acid chain breakage, increased membrane fluidity, and protein and nonenzyme-based (e.g., vitamins, β-carotene, selenium, GSH/
hydrolysis, inactivation of proteases, etc.). All of the above injuries GSSG, cysteine, etc.) defense systems are required to maintain
can lead to aberrant cellular metabolism and signal transduction, physiological balance. It has been generally accepted that redox
culminating by altering cell fate.357 Consequently, systemic imbalance caused by boosting of ROS and reactive nitrogen
clearance of the excess free radicals through enzyme-based, such species (RNS) production, or “oxidative stress”, and elevated
as SOD2, catalase, glutathione peroxidase, coenzyme Q10, etc.), intracellular NADH:NAD+ ratio, or “reductive stress”, reduced

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OXPHOS lead to the disorders of the mitochondrial electron levels in senescent cells also require more NADPH to maintain
transport chain (ETC), therefore, decreased ATP synthesis and cell redox balance.376
respiration.358 The causal role of oxidative damage in the ageing process
ATP synthesis utilizing various substrates is fundamental to cell remains controversial, partly because of the absence of a clear
viability. NAD+/NADH and FAD/FADH2 redox couples synthesize correlation between the efficacy of antioxidant defenses and
most ATP; in particular, NAD+ involves regulating both redox and extended cellular function or longevity.377 The lack of human
metabolic homeostasis.359 Accumulation of mitochondrial proton studies on toxic oxidative metabolites in tissue ageing also makes
donors (NADH and FADH2) attenuates OXPHOS through the ETC, scientists tiptoe cautiously at the crossroad. Nevertheless, existing
thereby causing reductive stress and increased ROS production. evidence demonstrates that ageing-related pathological fibrosis
ROS exerts multiple functions in various pathophysiological can be attenuated via the Nox-4–Nrf2 antioxidant axis.378 Other
responses closely related to augmented NADH/NAD+ ratio and interventions that promote cysteine metabolism and hydrogen
accumulation of L-2-hydroxyglutarate, a reductive metabolite that sulfide production also exhibit therapeutic benefits and delay
buffers reductive stress via inhibiting glycolysis and the Kreb’s tissue ageing.357,379 Mitochondria represent the central platform
cycle.360 Increased intracellular NADH concentration caused by of cellular metabolism and contain their own genome. The
hypoxia will generate a reverse electron transfer, resulting in accumulation of mutations in mtDNA during ageing has been
higher succinate levels and increasing oxidation, and subse- validated in many cell systems,380 with ROS as a principal cause.381
quently higher ROS levels.360 A similar process has been seen in Despite several studies implicating the role of ROS in cell
the mechanically overloaded heart. Thus, a stable ratio of NAD+/ senescence, others also suggest that it may not necessarily be
NADH is essential to maintain cellular homeostasis. Any alteration the case. One study using an empirical mathematical model
in the ratio of NAD+/NADH will cause oxidative or reductive stress, (stochastic step model of replicative senescence) suggests that
which may lead to accelerated cell senescence. Accordingly, increased mitochondrial ROS production in replicative senescent
restoration of NAD+ via precursors may reestablish the NADH/ cells is a consequence of the senescence phenotype rather than
NAD+ ratio, thereby reducing the cardiovascular injuries and the reverse.382 Another report shows that overexpression of the
attenuating cell senescence.361–363 Indeed, mounting studies have mitochondrial localized antioxidant SOD2 and the mitochondrially
shown the influence of exogenous NAD+ repletion in the targeted catalase are insufficient to inhibit the senescence
regulation and homeostasis in different models (gut, heart, phenotype in hyperoxia-induced senescent cells.383 Because
muscle, etc.).364–369 A recent study shows augmented circulating mitochondrial and non-mitochondrial enzymes produce ROS
α-hydroxybutyrate levels associated with increased NADH/NAD+ during hyperoxia (70% O2), the inability of mitochondrial
ratio and impaired glucose metabolism,370 while a normalized antioxidants to reverse growth arrest in hyperoxia-induced
NADH/NAD+ ratio can achieve by constructing LOXCAT-mediated senescence suggests that cytosolic ROS may assist growth arrest.
conversion of lactic acid to pyruvate.371 Hence, the mechanisms involved in linking mitochondrial ROS and
Although targeted regulation of the NADH/NAD+ ratio or NAD+ cell senescence still need to be further studied. Nonetheless,
level has great potential as an intervention for cell senescence and studies on genetically manipulated mouse model suggested that
organ ageing,372 there are still some critical questions about the many metabolic pathways have been found to involve oxidative
relationship between NADH/NAD+ and cell senescence. For stress management, and thus regulating cell function and
instance, in vivo NADH/NAD+ ratio and NAD+ level (particularly maintenance, including the Akt/mTOR,384 FoxO,385 AMPK,386,387
in different subcellular organelles) cannot be determined by the ATM-BID,388 Nrf2/Keap1,389 and the sirtuins,315 and so on.
conventional biochemical analysis. The exact mechanisms by Together, these studies suggest that cell senescence is closely
which exogenous NAD+ and NADH work remain elusive. correlated with the metabolic and redox state, influencing the
Furthermore, under the condition of ageing-related metabolic intracellular homeostasis of ROS and its functionalities.
remodeling, the spatiotemporal distribution of NADH/NAD+ or
NAD+ in different cellular compartments is still unclear. Given the Metabolic regulation of DNA damage in ageing
crucial roles of NADH/NAD+ and NAD+ in metabolic regulations of Cells have evolved various systems to regulate nutrient availability
redox balance and ageing, new technologies are urgently needed to maintain homeostasis, and have also developed active DNA
to provide a landscape of precise dynamics of NADH/NAD+ or repair machinery to avoid detrimental genomic instability during
NAD+ at subcellular organelle, cellular, and tissue levels. Some ageing, with two distinct cellular activities highly coordi-
attempts have successfully detected NADH/NAD+ ratio or NAD+ nated.102,390 For example, premature ageing phenotypes in
concentration in vivo by constructing genetically encoded excision repair cross-complementing group 1 knockout mice
fluorescent probes and reporter mice,373,374 which hold high and progeroid Xpg mice can be attenuated after feeding a
potentials to delineate the compartmentalized distribution of restricted diet.391 During the neonatal, a high oxygen environment
NADH/NAD+ ratio or NAD+ concentration upon various ageing- induces cardiomyocyte cell cycle arrest through DDR and directs
related stress stimuli. perinatal cardiac metabolic switch.392,393 To date, many key
Another vital player in redox balancing is the pentose regulatory molecules exerting dual roles in regulating DNA repair
phosphate pathway (PPP). PPP in the cytoplasm converts glucose and cellular metabolism have been identified, including p53,394
into 5-phosphate ribose and produces NADPH.375 The reductive sirtuins,395,396 poly(ADP-ribose) polymerases (PARPs),397 and
NADPH functions as an antioxidative mechanism produced during ATM.398 All these factors converge to the telomere at the end of
the oxidation phase, starting with the conversion of glucose-6- the chromosome in eukaryotes. Of note, telomere shortening
phosphate to 6-gluconolactone and NADPH. This is an irreversible represents one of the common mechanisms for organ ageing.399
reaction, catalyzed by glucose-6-phosphate dehydrogenase Telomerase inactivation in early life accelerates ageing pheno-
(G6PDH, a rate-limiting enzyme of this pathway), while inhibited types regardless of telomere length.400 Gene mutations in the
by NADPH feedback. Next, the lactone hydrolyzes to 6- telomerase complex cause accelerated telomere erosions, which
phosphogluconic acid that is further dehydrodecarboxylated to leads to heritable syndromes in multiple systems, takes congenital
form ribulose 5-phosphate, concomitant with another molecule of keratosis, for example, the main cause of death is DNA damage-
NADPH. NADPH is used for the reductive reactions in the synthesis related bone marrow failure.401 Consistently, telomerase gene
of biomolecules, such as fatty acids, cholesterol, deoxyribose, mutations and accelerated telomere shortening have also been
tetrahydrofolic acid, etc. NADPH is also used to reduce GSSG, thus found in patients with aplastic anemia, suggesting that telomere
maintaining redox balance in cells.375 The flux of PPP is mainly shortening is closely related to the decline in adult stem cell
determined by the amount of reduction force. Besides, high ROS regeneration, and premature ageing of tissues and organs.402 In

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high-turnover tissues, such as the hematopoietic system, we also breast cancer 1, early onset, and H2A.X variant histone. Studies
found that telomere shortening triggers cell senescence or have shown that oxidative stress can also activate ATM by
apoptosis by activating DDR,403–405 suggesting a close connection phosphorylating ATM at Ser1981, resulting in phosphorylation of
between DDR and telomere maintenance. Intriguingly, other p53 and AMPKα, therefore regulating gene expression and energy
studies have shown that telomere-related proteins can be metabolism. ATM deficiency in mice causes insulin resistance,
localized on mitochondria, thus affecting mitochondrial metabo- increased adiposity, atherosclerosis, and a variety of metabolic
lism.406 For instance, in low-turnover tissues, such as the heart, syndromes,421 while ATM activation is required in insulin-induced
telomerase dysfunction perturbs cellular energy metabolism thus glucose transport in slow and fast muscle fibers utilizing glucose
promoting ageing. The seminal study from DePinho’s lab oxidation.422 Intriguingly, the repletion of NAD also attenuated the
demonstrated a direct link between telomere dysfunction- severity of AT-induced neuropathology, suggesting that accumu-
induced DDR to mitochondrial metabolic compromise, where lated DNA damage links to dysfunctional mitochondrial metabo-
critical shortening of telomere length induces p53 activation, lism.423 ATM is the sensor for ROS in human fibroblasts, which also
thereby lowering PGC1 expression.407 Recently, another study also mediates mitochondrial ROS signaling and extends the life span of
indicates that telomere attrition can lead to p53-dependent sirtuin yeast. A more recent study demonstrated that ATM promotes
repression,408 in turn triggering a metabolic remodeling. Since antioxidant defenses and the repair of double-strand DNA breaks
telomere attrition occurs in each cell division, at some time point, by activating the PPP, representing a link between DNA repair
it will trigger a DDR (e.g., through PARP and ATM), thereby processes and cellular metabolism.
reducing the stability of the genome and eventually leading to cell
senescence. Congruently, mice with hyper-long telomeres show Sirtuins
less metabolic ageing and longer life spans.409 We also demon- Sirtuins are a cluster of NAD+-dependent enzymes involving the
strated that mild elevation of mitochondrial biogenesis regulator regulation of metabolism and genome integrity. Many proteins
PGC1α in late-generation telomerase-deficient mice was sufficient related to DNA repair have been identified as direct substrates of
to attenuate metabolic compromise and extending health span.362 sirtuins, e.g., RB-binding protein 8, endonuclease (CtIP), PARPs, and
p53.424–426 Conversely, p53 can posttranscriptionally regulate non-
p53 mtSIRT via miRNAs, while transcriptionally regulating mtSIRT
p53 represents a sophisticated molecule that wires the nuclear- through PGC1α/β.408 Existing evidence manifests that nuclear
metabolic axis during ageing; that is, p53 involves glycolysis, DNA damage signal to the mitochondria during CR with age,
OXPHOS, and regulation of the PPP and other pathways via where sirtuin network bridges such nucleus–mitochondria com-
regulating a plethora of target genes.410 Under the ageing-related munication linking genome instability to altered mitochondrial
pseudo-hypoxic state, a reduced glycolytic rate can be achieved metabolism.427 Another evidence shows that sirt3 deacetylates
through the downregulation of monocarboxylate transporter 1 and activates IDH2 to boost NADPH, thus mediating reduced
expression by p53-mediated prevention of lactate efflux.411 In oxidative stress and DNA damage.428 In addition, sirt7 deacety-
addition, p53 activates the transcription of cytochrome c oxidase lates p53 to inactivate its pro-apoptotic effect, thereby attenuating
2 synthesis, a core component of OXPHOS, and plays a key role in cardiac hypertrophy and inflammatory cardiomyopathy.429 These
the regulation of cytochrome c oxidase complex assembly.412 observations lead to attempts to boost sirtuin as an anti-ageing
p53 affects several physiological and metabolic pathways, all strategy. Indeed, sirtuin overexpression exerts a salutary effect in
heavily involved in modulating ageing and the establishment of healthy ageing by enhancing the resistance to DNA damage and
senescence.413 There is growing interest in dissecting how metabolic insult.430
metabolism affects DDR and vice versa. One hallmark of aged
cells is the deregulation of genes involving in DDR. The cell cycle, PARP
as well as senescence, can be regulated by metabolism and PARP represents another NAD+-consuming enzyme that catalyzes
mitochondrial activity through p53. For instance, vascular smooth the formation of PAR polymers. As a base excision repair protein,
muscle cell senescence-induced atherosclerosis was associated PARP overactivation has been linked to mitochondrial dysfunction
with p53-dependent degradation of telomere repeat-binding in xeroderma pigmentosum group A, as well as ataxia telangiec-
factor-2.414 Besides, mitochondrial stress in the form of increased tasia and Cockayne syndrome with similar pathogenesis involving
ROS levels also induces cell cycle arrest using mediators, such as nuclear–mitochondrial communication.426 Prolonged PARP activa-
p53 and p27.415 Meanwhile, phosphorylation of Ser-15 by ATM tion also couples NAD+ and ATP depletion, thereby triggering
activates p53 in response to DNA damage.416 Our study also cellular energy crisis and metabolic reprogramming.431,432 Some
reveals a mechanism of cell senescence, in which distinct effects metabolic transcriptional factors (e.g., HIF-1a, NRF-1, and NRF-2)
of p53 and mTORC1 pathways on HSC ageing are governed by and nuclear receptors (e.g., estrogen receptor, retinoid X receptor,
Wild-type p53-induced phosphatase 1 (Wip1), which negatively and peroxisome proliferator-activated receptors) have been
regulates several tumor suppressors and DDR pathways,417 but identified to interact with PARP, affecting glucose and lipid
also B lymphocyte maturation and tissue regeneration.418,419 metabolism and related metabolic syndromes.433 Collectively,
these data suggest a link between DNA damage-induced poly
ATM (ADP-ribosyl)ation and mammalian longevity.434
First identified in 1995, the ATM kinase contains a PI3K-like kinase In sum, the accumulation of DNA damage can promote
domain at the C-terminal and represents the core regulator for metabolic dysfunction in two ways: cell-autonomous and non-
DNA double-strand break and repair. During ageing, ATM/ATR- cell-autonomous mechanisms. Tissue regeneration is impaired by
dependent DDR, rather than the p53/p16INK4a axis, was required DNA damage-induced senescence and/or apoptosis of stem cells
for the GATA-binding protein 4-mediated senescence-associate and somatic cells, leading to metabolic dysfunction. DNA damage
secretory phenotype.420 Cells isolated from AT patients were induces non-cell-autonomous tissue inflammation through the
sensitive to radiation, indicating that ATM involves DNA repair. upregulation of cytokines and chemokines, thereby hampering
ATM is a relatively upstream kinase that phosphorylates hundreds systemic insulin signaling. DNA damage can also affect systemic
of substrates in response to DNA damage. The metabolic homeostasis through influences on cellular metabolism
MRE11–RAD50–NBS1 complex, Tip60, ATR, protein phosphatase and the endocrine system. Activation of the DDR in specific tissues
2A, and Wip1 regulate ATM activation. In turn, the activated ATM could influence the function of vital metabolic organs, thereby
can activate checkpoint kinase 2, structural maintenance of provoking systemic insulin resistance. Thus, a better under-
chromosomes-1, Fanconi anemia, complementation group D2, standing of the systemic DDR may help us develop novel

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therapeutic strategies for metabolic disorders. Additional factors health span.451 Other studies reveal that EVs participate in
await identification to shed further light on the role of DNA metabolic reprogramming during macrophage polarization,452
damage in metabolic homeostasis. wound healing,453 and fibrotic replacement.454,455 EVs derived
from immune cells contain antigen peptide–MHC complex and
Metabolic regulation of immune response in ageing various antigens, which can control the exchange of antigen
Inflammation is one of the most described ageing-related information between immune cells, thus regulating activation or
phenotypes in ageing research. Senescent cells activate innate inhibition of immune cells and other immune responses.
and adaptive immune responses that can be beneficial and
detrimental.435 Meanwhile, immune organs senesce rapidly after Metabolic reprogramming
advanced age, causing diseases such as infection, cancer, and Throughout the life of an organism, the immune system
other many chronic inflammatory diseases.436,437 In response to continually senses and responds to environmental threats, which
ageing-related intrinsic and extrinsic factors, induction into pro- is a relatively energy-consuming process.456 Altered energy
inflammatory cell senescence represents a conserved antitumor substrate (e.g., glucose, lipid, and glutamate) metabolism is
and pro-survival mechanism that promotes the clearance of commonly found in the stressed cells.339 Metabolic pathways
damaged components, restriction of fibrosis and tissue repair, control the duration and strength of innate and adaptive immune
thereby maintaining the relative homeostasis.438 However, persis- responses and the generation of memory cells.457,458 Immune cells
tently activated immunosurveillance can accelerate immune can switch between different metabolic states, preferentially using
senescence, featured by a blunted immune response, bias to different substrates (glucose, amino acids, and fatty acids) to
myeloid hematopoiesis, and impaired immunometabolism, possi- maintain various functions of specific effectors.456 Cellular
bly stem from the ageing of haematopoietic stem cells.403,439 metabolism controls the function of immune cells by controlling
Many investigations reveal that different stimuli can lead to age- key metabolic nodes, bringing new paradigms to immunology
related inflammatory manifestations, such as DDRs, telomere and prospects to treat inflammatory diseases and autoimmune
attrition, oncogene activation, oxidative stress, chemotherapy diseases through metabolism. Mills et al. demonstrated that
drugs, or radiation damage, all of which contribute to the activated macrophages experience substrate alteration for ATP
SASP.440–443 In turn, SASP causes an inflammatory microenviron- production from OXPHOS to glycolysis, concurrent with elevated
ment that dampens tissue regeneration.444 Notably, the metabolic ROS and succinate levels that triggers a pro-inflammatory cell
signatures of senescent cells have been intensively investigated, state.459 Tomas et al. demonstrated that the risk stratification of
with some typical changes in immunometabolism during ageing low- and high-risk plaque in atherosclerosis links the macrophage
discussed below. infiltration to altered mitochondrial substrate oxidation, that is,
low-risk plaque exhibits fatty acid oxidation-prone and down-
Altered secretome regulated glycolysis or anaplerosis by amino acids, while opposing
The altered secretory phenotype in inflammatory cell senescence energy preference in high-risk plaques.460 In line with this, a
includes (1) altered nucleic acid secretion, such as micronucleus similar finding was found by different investigators461 and further
formation and disruption, leakage of mtDNA, release of LINE1, evidence associates the regulation of immunometabolism of
which may activate RIG-I-MAVS or cGAS–STING signaling path- macrophages with other ageing-related diseases, such as type 2
ways to initiate an inflammatory response;110,445 (2) altered diabetes462 and macular degeneration.463 Altogether, these
protein secretion, such as inflammatory chemokines, cytokines, studies suggest that the metabolic reprogramming of immune
and other factors, which may exert tissue repairing or degrading cells might be a promising therapeutic approach to treat ageing-
effect to eliminate danger signals;446 (3) altered metabolite related diseases.
secretion, such as carnitine and low density lipoprotein, which
may correlate with risk of ageing-related oncogenic diseases, Mitochondrial dysfunction
cardiovascular, and cerebrovascular diseases.447 Of note, such In addition to their roles in cellular energy metabolism and
DAMPs can activate the cellular immune response that differs apoptosis, mitochondria are thought to be the central hub of the
from the pro-inflammatory response of immune cells induced by innate immune response,464 that is, mitochondria can not only act
pathogens (PAMP), indicating the secretome signature to be as the platform of immune response adaptors (such as MAVS and
specific and stimulus-dependent.448 Moreover, energy demand NLRP3), but also participate in the immune response by producing
changes dramatically when immune cells shift from a resting state ROS. During ageing, mtDNA, Tfam, ROS, ATP, cardiolipin, and N-
to an active state, which often causes energy deficits when cells formyl peptide can be released as DAMPs and are recognized by
become senescent and, consequently, contributes to the meta- pattern recognition receptors upon mitochondrial stress or
bolic remodeling accompanied by the altered secretion of compromise, leading to the activation of MiDAS and SASP.44 A
cytokines, chemokines, and inflammatory mediators. recent study showed that T cells with dysfunctional mitochondria
promoted ageing in mice via inducing circulating cytokines.
Extracellular vesicle secretion Blocking TNF-α, a critical cytokine released during the T cell
Extracellular vesicles (EVs) are bilayer vesicles released from cells metabolic failure, partially rescued the premature ageing pheno-
into the extracellular matrix.449 For many years, EVs have been type.465 Interestingly, He et al. demonstrated age-associated
regarded as a mechanism for excreting intracellular components acetylation of NLRP3 in macrophages might cause inflammatory
as waste products, and are important mediators for exchanging microenvironment and insulin resistance, while enhancing Sirt2
proteins and lipids between secretory cells and target cells. Two expression diminished inflammation and related disease pheno-
major types of EVs, microvesicles, and exosomes contain a variety type by directly deacetylation of NLRP3,5 indicating a possible
of components (e.g., enzymes, miRNAs, transcription factors, interplay between epigenetic regulation of inflammageing and
membrane-bound and soluble receptors, lipids, and DNA, etc.) mitochondrial metabolic reprogramming. Of note, abnormalities
and involve in cell communication, migration, angiogenesis, and between ER–mitochondrial communication (i.e., ER–mitochondrial
tumor cell growth. Mounting evidence has been suggested that dysfunction) could be another crucial player mediating the
EV secretion plays a crucial role in age-related inflammatory and ageing-related inflammatory phenotype in macrophages.466
metabolic abnormalities.450 For instance, one study demonstrates Another study has demonstrated that de novo NAD biosynthesis
that the levels of extracellular nicotinamide phosphoribosyltrans- in macrophages is the key to the homeostasis of the immune
ferase (eNAMPT) decline with age in mice and humans. Increasing response during ageing,467 while α-KG repletion could maintain
eNAMPT promotes NAD+, counteracting ageing, and extending the α-KG pool in aged mice, lower the bodyweight and fat mass,

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and improve glucose tolerance in mice fed a high-fat diet.468 suppressor AMPK. One such mechanism may be 1C metabolism
Collectively, these studies implicate that targeting mitochondrial that drives the de novo synthesis of purine nucleotides (e.g., AMP),
homeostasis in the immune cells may represent a novel avenue to suggesting that de novo biosynthesis of purine nucleotides, which
counteract inflammageing and normalize immunometabolism. is based on the metabolism of 1C compounds, is a new target for
metformin’s actions in ageing.482 Therefore, quantification and
Serum phosphate intervention of 1C metabolism metabolites may open a new
Studies performed over the past few years make it clear that avenue to further our understanding of inflammageing.
changes in serum phosphate levels have profound effects in mice
and human. Changes in extracellular and intracellular phosphate Microbial burden
concentration affect glucose metabolism, insulin sensitivity, and Ageing is correlated with a reduced abundance of salutary
oxidative stress in vivo and in vitro. High concentrations of commensal microbes that maintain the intact intestinal barrier
extracellular phosphate are toxic to cells, which induce cell and limit the amplification of pathogenic commensals by
damage and inflammation when precipitated with calcium (to secretion of specific metabolites, for instance, the short-chain
form calciprotein particles that comprised calcium–phosphate fatty acids.483 Increased attention has been paid to microbial
crystals and fetuin-A), thus potentially affect ageing pro- homeostasis that connects microbiota to the functionality of
cesses.468,469 Indeed, impaired urinary phosphate excretion multiple organs during ageing. Indeed, gut microbial dysbiosis
increases serum phosphate level and induces an inflammageing links to aberrant immune responses and miscommunication
phenotype in mice, and calciprotein particles are found in patients between gut microbes and innate immune response may cause
with chronic kidney disease associated with a (mal)adaptation of various diseases.484,485 One study implicates that microbiota-
the FGF-23-Klotho endocrine system.469 Direct evidence shows induced IFN-Is instruct a poised basal state of dendritic cells.486
that knocking out fibroblast growth factor-23, a regulator of Lloyd and Marsland propose that microbes in the host are crucial
phosphate homeostasis, causes hyperphosphatemia and vascular to establishing lung homeostasis and are affected by ageing to
calcification in mice, concurrent with multiple ageing-like reshape the immune network during chronic inflammation.487
phenotypes.470 Deletion of Klotho exhibits similar abnormalities, Ang et al. found that the ketogenic diet changed the landscape of
both could be alleviated by resolving phosphate retention (e.g., on gut microbiota by reducing intestinal pro-inflammatory Th17 cells,
a low-phosphate diet), indicating an underlying link between suggesting diet interventions could be a possible means to
phosphate and inflammageing. In line with this, augmented attenuate ageing and related metabolic diseases.488 Similarly,
circulating levels of calciprotein particles are detected in concert other studies have testified interactions between gut microbiota
with an increase in serum phosphate and age, which correlate with cerebral and cardiovascular diseases.489,490 In addition, based
positively with vascular stiffness and chronic sterile inflammation, on deep learning techniques such as neural networks, Galkin et al.
suggesting that calciprotein particles may be an endogenous pro- established a mathematical model that can reflect the relationship
ageing factor.471 Furthermore, old mice showed muscular between the microbiological profiles of gut microbiota and the
degeneration correlated with high serum phosphate concentra- biological age of host, using >3000 microbiome samples from
tion and increased levels of integrin-linked kinase and p53, 1165 healthy individuals. They concluded that 39 microbiota taxa
indicative of a possible mechanism in developing sarcopenia.472 were extracted as intestinal markers to best correlate physiological
Another study confirms that hyperphosphatemia induces age.491 In sum, these studies highlight the importance of microbes
endothelin-1-mediated senescence in human endothelial cells.473 in regulating organ function and potential effects on
In contrast, Klotho deficiency-induced heart ageing is indepen- immunosenescence.
dent of phosphate metabolism since Klotho-mutated mice exhibit
a normal range of serum phosphate.474 Metabolic regulation of protein homeostasis in ageing
Protein quality control in living organisms is essential for the
One-carbon metabolism maintenance of cell viability that maintains a relatively balanced
One-carbon (1C) metabolism formed by three reactions, namely state of the proteome in regards to synthesis, folding and
the folate cycle, the methionine cycle, and the trans-sulfuration unfolding, modification, trafficking, and degradation of specific
pathway, is of great importance to nucleotide biosynthesis, amino proteins.492 Protein homeostasis in cells is mainly coordinated by
acid homeostasis, methylation modifications, and redox bal- the molecular chaperones, and two proteolytic systems, namely
ance.475 Recent advances reveal that 1C metabolism is also the ubiquitin–proteasome system and autophagy–lysosome
associated with inflammageing. Perturbations in 1C metabolism system. The imbalance of protein homeostasis is one of the
have been linked to a biased pro-inflammatory state and may also crucial factors causing ageing and the development of ageing-
increase the risk of age-related diseases.476 Indeed, a specific related diseases.493 Cell senescence can be accelerated when
deficit in the induction of enzymes of 1C metabolism leads to the various organelles meet overloaded stress or proteotoxicity, such
accumulation of impaired naive T cells in aged mice, which could as misfolding of nuclear, ribosomal, peroxisomal, and mitochon-
be rescued by the addition of products of 1C metabolism (formate drial proteins,494–497 leading to aberrant protein aggregates that
and glycine) to the cells.477 1C units in the methionine cycle dampen the cross talk of organelles. Accordingly, several cellular
support the generation of SAM thereby a high SAM:S-adenosyl- hallmarks of proteotoxic stress have been identified, including
homocysteine (SAH) ratio, leading to enhanced histone H3 lysine dysregulated mTOR signaling and autophagy, compartment-
36 trimethylation and IL-1β expression in macrophages.478 specific unfolded protein response in mitochondria (UPRmt), and
Conversely, serine deprivation lowers IL-1β production and in the endoplasmic reticulum (UPRER).
inflammasome activation, and alters the transcriptomic and
metabolic profile in M1 macrophages via inhibited mTOR mTOR
signaling.479 Congruently, elevated homocysteine, SAM, and SAH The evolutionarily conserved mTOR is a serine/threonine kinase
levels in plasma are more susceptible to cardiometabolic that participates in the central regulation of nutrient sensing,
syndromes.480 Moreover, defect of complex I decreases mitochon- stress response, and longevity.498 Two mTOR complexes, namely
drial 1C NADPH production, which is associated with increased mTORC1 and mTORC2, have been extensively studied, and both
inflammation and cell death.481 These findings highlight a exert their functions by other kinases, such as S6 kinase and
potential regulatory mechanism for 1C metabolism to modulate Akt.499 Park et al. demonstrated that mTORC1 could influence
the inflammatory response. Notably, anti-ageing mechanisms by integrated stress response via augmenting activating transcription
which metformin can activate the gerosuppressor/tumor factor 4 (ATF4) at the posttranscriptional level by 4E-BP1.500 Zhang

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et al. revealed that mTORC1 enhances the protein synthesis regions.519 Further analysis revealed that c-JNK could bind to an
capacity, while concordantly inhibiting autophagy, promoting the AP1-binding site within the promoter regions of CHOP and C/EBP,
production of proteosomes via the activation of Nrf1.501 underscoring an indispensable role of the JNK signaling pathway
Conversely, other studies suggested mTORC1 inhibition induced in UPRmt.520 Furthermore, using the nematode model, transcrip-
an increase in proteasome abundance and protein degrada- tional factors DVE-1 and ATFS-1, along with H3K27 demethylases
tion.502,503 mTORC2 has been demonstrated to inhibit chaperone- jmjd-1.2 and jmjd-3.1 and other factors, have been identified as
mediated autophagy during ageing that can be restored by UPRmt activators.521–523 Although ample studies provide a frame-
phosphatase PHLPP1, thereby representing a lysosomal pathway work for the signal transduction of UPRmt, the exact and complete
to counteract age-associated dysfunction of protein degrada- molecular mechanism that cells (especially in mammals) sense
tion.504 Moreover, rapamycin-induced insulin resistance is trig- mitochondrial stress signals and transmit the signals to the
gered by the inhibition of mTORC2, although it is irrelevant with nucleus await further elucidation.
longevity.505
UPRER
Autophagy Response to ER stress caused by unfolded or misfolded proteins
Impairment in autophagy has linked to the derailment of (UPRER) represents another intrinsic mechanism to counteract
proteostasis that is closely associated with ageing and age- multiple stress stimuli that leads to perturbed proteostasis. The
related diseases, including macroautophagy, microautophagy, and UPRER contains three upstream stress sensors in the ER membrane,
chaperone-mediated autophagy. A significant effort has been i.e., inositol-requiring enzyme-1, PKR-like ER kinase, and ATF6,
made to elaborate on the role of autophagy in the field of cerebral which is activated by the presence of unfolded proteins within the
proteinopathies, including Huntington’s disease (HD), AD, PD, and ER, ensuring signal transduction to the well-known downstream
amyotrophic lateral sclerosis (ALS).506–508 Sorrentino et al. effector molecules.524 UPRER compromise lies at the nexus of
reported that enhancing mitophagy helped resolve amyloid-β inflammageing and metabolic dysfunction, while its constitutive
proteotoxicity in mouse and C. elegans, providing a promising activation attenuates multiple age-related diseases and extends
strategy targeting mitochondrial proteostasis to delay AD.509 longevity.525 Most of the pioneering findings regarding UPRER are
Poewe et al. showed that α-synuclein aggregation and clearance derived from the studies using worms. Taylor and Dillin revealed
of undegraded proteins were therapeutic targets for PD.510 how to rescue declined UPRER in the ageing of C. elegans and
Similarly, enhancement of cytosolic proteostasis pathways found that age-onset loss of ER proteostasis could be restored by
(through autophagy or proteasome) shows promise for HD and neural expression of a constitutively active form of X-box-binding
ALS treatments.511,512 protein 1.526 Similarly, Daniele et al. facilitated UPRER specifically in
Moreover, identifying novel mitophagy receptors or booster of neurons to promote ER function by lipid depletion through
mitophagy further enhances our understanding of the complexity lipophagy. Interestingly, this beneficial metabolic alteration is
of mitochondrial quality control. Li et al. showed that mitophagy independent of chaperone induction, but is regulated by EH
receptor protein FUNDC1 located at the mitochondrial outer domain-binding protein 1-mediated lipophagy, thereby enhan-
membrane that is associated with cytoplasmic chaperone protein cing organismal stress resistance and extending the life span.527
HSC70, leading to the recruitment of damaged or misfolded Schinzel et al. utilized a whole-genome CRISPR-based knockout
cytosolic proteins to mitochondria, and then shuttle to the screen to identify transmembrane protein 2 (TMEM2), a hyalur-
mitochondrial matrix through the TOM–TIM complex, culminating onidase that degraded hyaluronan in the extracellular matrix, was
with the degradation by matrix-localized mitochondrial protease capable of modulating ER stress through CD44, ERK, and p38.
LONP1.513 Ryu et al. identified the natural compound urolithin A as Ectopic expression of human TMEM2 promoted ER homeostasis
a mitophagy inducer, which enhanced mitochondrial and muscle and extended longevity in C. elegans, indicating a conserved
function.514 We and others have found the potential therapeutic health-promoting pathway via elevating the TMEM2–UPRER
benefits by PGC1α and TFEB upregulation in counteracting axis.528 Although more efforts are required to illustrate the
declined autophagy capacity and reduced proteostasis.362,515 orthologs of human UPRER targets and pathways, these findings
Together, these findings indicate a regulatory effect of autophagy advance our understanding of how the UPRER changes with age
in protein homeostasis necessary for proper organ function, and how this impacts disease development, thus opening new
especially in the brain and other high energy-demanding organs. therapeutic avenues to treat age-associated diseases.
UPRmt Metabolic regulation of organelle homeostasis in ageing
UPRmt is one key mechanism in mitochondrial quality control Imbalance of cellular metabolism and organelle homeostasis
involving multiple components, such as chaperones, proteases, during ageing is one of the major drivers causing ageing-related
and other stress sensors and effectors.516 Apart from cell diseases.16 Several aspects that aim to delineate the changes in
respiration and ATP production, mitochondria also participate in organelle ageing, in particular, to clarify the causal relationship
immune response, cell senescence, and apoptosis. Notably, most between organelle dysfunction and ageing and/or degenerative
proteins required by the processes above are translated from diseases, and to explore new strategies targeting organelle
nuclear-encoded genes; thus, it is crucial to orchestrate homeostasis to intervene ageing and related disorders at varying
mitochondrial–nuclear communication that ensures a precise levels of metabolism, have been investigated for long and some
transcriptional response by the UPRmt. Indeed, a plethora of critical findings are of great importance.529,530
defects within aged mitochondria that activate the UPRmt
implicates intrinsic surveillance of mitochondrial function being Mitochondria
reliant on mitochondrial stress response.517 Zhao et al. discovered For decades, mitochondrial biology lies at the center of
that the accumulation of unfolded proteins in the mitochondrial mechanistic exploration in metabolic regulation of cell senescence
matrix resulted in transcriptional upregulation of nuclear-encoded and organismal ageing.531 Mitochondrial dysfunction has been
mitochondrial stress genes, including hsp60, hsp10, mtDnaJ, and linked with mtDNA mutations, aberrant mitochondrial respiration,
ClpP, without interfering gene expression that was related to dynamics, biogenesis, autophagy, and other quality control
endoplasmic reticulum (ER) stress. Teske et al. demonstrated that machinery.532 Apart from their roles above in redox balance and
CHOP-induced ATF5 to trigger cell death in response to immune response, mitochondria also involve in proteostasis and
perturbations in protein homeostasis.518 Notably, a CHOP element, other cellular functions that intensively interact with ER and
coupled with the C/EBP domain, was found in the gene promoter nucleus.

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Guo et al. developed grazing incidence structured illumination and acyl-CoA oxidases) H2O2. Consequently, peroxisomes may serve
microscopy and found most of the mitochondrial fission events, as a direct source of oxidative stress, especially during ageing, by
while ~60% of the mitochondrial fusion events actively occurred decreased peroxisome turnover and downregulated detoxifying
at the contact sites between mitochondria and ER.533 Consistently, enzymes.545 Dixit et al. revealed that the well-known mitochondrial
Gӧbel et al. demonstrated that mitofusin 2-mediated antiviral signaling protein, MAVS, was also a peroxisome-localized
mitochondria–ER contacts in astrocytes promote repairing the adaptor that functioned in innate antiviral immunity.546 The tuberous
injured brain.534 Moreover, reduced mitochondrial fusion and sclerosis complex has also been found on the peroxisome to inhibit
Huntingtin levels were observed in impaired dendritic maturation, mTORC1 in response to endogenous ROS.547 Similar findings were
thereby leading to behavioral deficits,535 indicative of a funda- reported that a portion of extranuclear ATM was localized to
mental role of mitodynamics in tissue homeostasis. Another peroxisomes and mediated ROS-induced pexophagy,548 while AMPK
critical player, mitochondrial permeability, has been manifested as and dietary restriction extended the life span of C. elegans via
an indispensable regulator of mitochondrial function. VDAC coordinating mitochondrial and peroxisomal homeostasis.3 Of note,
oligomerization warranted an increased mitochondrial outer the peroxisomes remain the least understood of all organelles, yet
membrane permeability, which was essential to trigger released accumulating studies uncover their roles in regulating metabolism
mtDNA-induced inflammatory response.536 Ying et al. demon- and ageing in concert with mitochondria, ER, and other organelles.
strated that short-term mitochondrial permeability transition pore Further investigations on peroxisomal quality control warrant a
opening (aka mitoflash) induced a nuclear reprogramming by deeper understanding of their roles in cellular homeostasis.
histone methylation, suggesting a novel mitochondrial regulation Together, comprehensive mapping of metabolic networks
of nuclear epigenetics.537 Besides, MacVicar et al. identified that should help dissect the interaction and cross talk among different
the mTORC1–LIPIN1–YME1L regulatory axis was a posttransla- organelles, furthering our understanding of the molecular and
tional regulator of mitochondrial proteostasis at the interface cellular basis of organelle ageing.
between metabolism and mitochondrial dynamics.538
Novel interventions and techniques in metabolic ageing research
Lysosome Increasing attention has been focused on depicting the metabolic
Lysosomes are crucial cellular organelles for human health that signatures of cells from single-cell resolution, as well as the whole
function in digesting and recycling of extracellular and intracel- metabolic landscape of organisms in a dynamic manner. In
lular macromolecules. Given that many neurodegenerative particular, identifications of age-related metabolic phenotypes or
diseases (e.g., PD and AD), as well as reduced life span, are linked biomarkers that are closely correlated with overall fitness are
to lysosomal dysfunction, enhancing lysosomal function becomes increasingly being recognized as therapeutic targets. The dis-
an option to promote health span in certain circumstances, such covery of senescence-related genes and metabolites by combin-
as reduced ability to clear protein aggregates during neural stem ing transcriptomics, proteomics, epimicromics, secretomics,
cells ageing. Leeman et al. demonstrated that aged neural stem metabolomics, phenomics, and large population cohort studies
cells exhibited decreased lysosomal genes, thereby a slower sheds light on the complex senescence signaling networks.
clearance of protein aggregates. Normalization of lysosomal Among the multi-omics, single-cell RNA sequencing is the hotspot
function in these cells could restore the defects and enhance to analyze the molecular mechanism of organ ageing.549 For
the quiescent neural stem cell activation.539 Castellano et al. example, Wang et al. compared young and aged nonhuman
investigated the metabolic cue that activated mTORC1 at primate ovaries using single-cell transcriptomics. In-depth ana-
lysosome and found that SLC38A9-mediated import and lyses of gene expression dynamics of oocytes revealed oxidative
Niemann–Pick C1-mediated export of lysosomal cholesterol were damage was an important determinant in ovarian ageing.550 Bian
the drivers for mTORC1 activation.540 Further analysis found that et al. characterized a comprehensive map of human macrophage
arginine was essential for mTORC1 activation and represented as development at single-cell resolution, providing a deeper under-
the lysosomal messenger sensed by SLC38A9.541 Via developing a standing of the functions of tissue-resident macrophages.551 In
method for rapid lysosomal isolation and metabolomics, Abu- addition, the advances in metabolomics, especially single-cell
Remaileh et al. manifested that mTOR inhibition decreased the metabolomics and their applications, further add strength to the
lysosomal efflux of most essential amino acids in a V-ATPase- field of clinical pharmacology.552,553
dependent manner.542 Moreover, overexpression of the lysosomal Continuous focus on the clearance of intracellular senescence-
biogenesis regulator TFEB homolog (HLH-30) in worms has been inducing factors is a relevant direction for treating age-associated
proven beneficial. It may prolong life span through repression of disorders. Many reports manifest that removal of senescent cells
mTOR signaling and engagement of autophagic processing.543 (e.g., via senolytics) or abnormally active transposons (e.g., via
Collectively, these results reinforce the concept that regulation of inhibitors to LINE1 transposons) from ageing animal models is
lysosomal function is one of the most efficient anti-ageing salutary.7,40,112,554 Conversely, the repletion of rejuvenating factors
interventions. (NAD+) also improves various organ functions, which have been
Peroxisome experimentally proven through genetic manipulation or diet/
Peroxisomes are dynamically and metabolically active that signal supplement intervention, although detecting NAD+ levels in vivo
various intracellular events, therefore exhibiting a high degree of remains challenging. Genetically encoded fluorescent probes
plasticity, linking redox balance, and nutrient digestion to immune represent promising tools to realize high-dynamic, high-resolu-
metabolism. They are capable of autonomous replication via fission. tion, high-throughput NADH/NAD+ detection in vivo, empowering
Recent studies have revealed that beyond the essential roles in fatty a real-time visualization of compartmentalized NAD+ that facilitate
acid oxidation, anaplerotic metabolism, and production and scaven- screening for NAD-associated drug design or gene candidates
ging of ROS, peroxisomes also participate in the metabolic regulation identification.363,374 Furthermore, manipulation of melatonin,555
of cell senescence.544 Evidence shows the significant role of supplementation of compounds, such as spermidine,556 acar-
weakened peroxisomal functions, including diminished peroxisomal bose,557 and urolithin A514 may also exert an anti-ageing effect
autophagy (pexophagy), loss of communication with ER and through metabolic remodeling. Intriguingly, a controversial study
mitochondria, and dysregulation of peroxisomal proteostasis in using parabiosis demonstrated that the enhanced level or
accelerated ageing and related diseases.496 Peroxisomes not only administration of GDF11 could correct DNA damage accumulated
eliminate (mainly detoxify by peroxiredoxins, glutathione peroxidases, in ageing mouse satellite cells,558 while its paralog myostatin
and catalases), but also produce (mainly oxidize by xanthine oxidases regulates energy homeostasis in the heart and prevents heart

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Fig. 7 Approaches to alter local and systemic metabolism. Six aspects, including environmental stimuli, sleep modulation, exercise, intestinal
microbes, diet, and drug interventions, may reprogram the metabolism thereby benefiting to healthy ageing
Fig. 8 Novel techniques accelerate the discovery of anti-ageing mechanisms and therapies. Illustrations of three advanced approaches, i.e.,
single-cell sequencing, 3D-genome analysis, and genetically encoded fluorescent probes in dissecting genetic, epigenetic, and metabolic
alterations in ageing and anti-ageing research
failure.559 Although heterochronic parabiosis of young and old CR, drug intervention, microbial regulation, and sleep/exercise
mice implies the potential to attenuate the ageing process and represent simple but also noninvasive approaches to extend
improve cell function, how to rejuvenate senescent cells via health span and ameliorate age-related pathologies, at least, via
autologous rather than allogeneic resources remains a central enhancing the tissue function across a broad spectrum of animals
question to avoid issues regarding immunity and ethics. (Fig. 7). The level of CR is indeterminate from individual-by-

Zhu et al.
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individual, and long-term CR sounds impracticable to the general ADDITIONAL INFORMATION
public. In contrast, resveratrol, a naturally occurring small molecule Competing interests: The authors declare no competing interests.
that induces metabolic benefits resembling CR, increases mito-
chondrial biogenesis, partly through activation of SIRT1 and
PGC1α.560 Similarly, metformin, a hypoglycemic agent widely
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Inﬂammation, epigenetics, and metabolism converge to cell

Signal Transduction and Targeted Therapy (2021)6:245 ; https://doi.org/10.1038/s41392-021-00646-9

INTRODUCTION As the biological techniques advance, many new targets and

Received: 20 November 2020 Revised: 9 May 2021 Accepted: 13 May 2021

© The Author(s) 2021

hallmarks. At present, the most commonly used senescent marker

Permanent cell cycle arrest

Signal Transduction and Targeted Therapy (2021)6:245

Signal Transduction and Targeted Therapy (2021)6:245

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Signal Transduction and Targeted Therapy (2021)6:245

Signal Transduction and Targeted Therapy (2021)6:245

Signal Transduction and Targeted Therapy (2021)6:245

Signal Transduction and Targeted Therapy (2021)6:245

Signal Transduction and Targeted Therapy (2021)6:245

Signal Transduction and Targeted Therapy (2021)6:245

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Signal Transduction and Targeted Therapy (2021)6:245

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Signal Transduction and Targeted Therapy (2021)6:245

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Signal Transduction and Targeted Therapy (2021)6:245

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