INSIGHTS | P E R S P E C T I V E S

HYPOTHESIS

Epigenetic clocks, aging, and cancer

Global methylation changes in aging cells affect cancer risk and tissue homeostasis

By Sarah E. Johnstone1,2,3, CpG-poor regions that replicate late in S tween individual cells in a tissue, proceeding
Vadim N. Gladyshev3,4, Martin J. Aryee2,3,5, phase, particularly in rapidly dividing cells. slowly in certain progenitor populations (11).
Bradley E. Bernstein2,3,6,7 A study of replicating embryonic stem and Although the precise relationship between
HeLa cells showed that although methylation mitotic and aging clocks remains obscure,

C
ancer and aging are accompanied by was copied to daughter DNA strands, it was the cell-intrinsic properties and mechanistic
stereotyped changes to the epigenetic delayed and error prone in late-replicating underpinnings of the DNA hypomethylation
landscape, including progressive loss regions (7). Thus, global hypomethylation clock provide a complementary framework
of DNA methylation over gene-poor is a shared feature of aging and malignant for the study of human biology and aging.
genomic regions (1, 2). Global hypo- cells rooted in inefficient maintenance and What is the impact of hypomethylation?
methylation arises in cells that have gradual methylation loss as somatic cells ac- Its prominence in cancer prompted extensive
undergone many divisions, likely owing to im- cumulate divisions. exploration of potential oncogenic functions,
perfect maintenance. Evidence suggests that The mitotic hypomethylation clock is dis- yet decades of study have failed to clarify
global hypomethylation represents a “mitotic tinct from clocks that predict chronological such roles. Hypomethylation in tumor cells
clock” that counts divisions in somatic cells age from methylation in tissues. These or- may alternatively represent a scar of having
and functions to restrain aging cells and limit ganismal aging clocks have attracted con- undergone many divisions rather than being
malignant progression. Therapies that modu- siderable attention for their accuracy and a driving feature of malignancy. The recogni-
late the pace of methylation loss or eliminate potential to predict morbidity and mortality tion that hypomethylation is a consequence
hypomethylated cells could alleviate aging- (8). Machine-learning algorithms identify of accumulated divisions suggests that it
associated diseases or cancers. and integrate sets of CpGs whose methyla- might instead prune aging cells, protecting
Several lines of evidence indicate that hy- tion status correlates with age. Although ag- them from malignant progression and affect-
pomethylation represents a general mitotic ing clocks have been developed for a range of ing aging tissue homeostasis.
clock (3, 4). In tumors, hypomethylation tissues and organisms, different algorithms Substantial evidence supports several such

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affects megabase-sized intervals that are for the same tissue type incorporate different restrictive functions for hypomethylation.
CpG-poor, gene-poor, and late-replicating. CpGs. This inconsistency has hindered inter- DNA methylation plays a fundamental role in
Tissues from older individuals also exhibit pretation of the methylation changes. the transcriptional silencing of transposable
widespread hypomethylation of the same re- Organismal aging clocks presumably in- elements (TEs) such as endogenous retrovi-
gions as in cancer, albeit of lesser magnitude. corporate multiple inputs, including cell ruses (ERVs) and long interspersed nuclear
Hypomethylation is more pronounced in pro- type composition, environmental influences, elements (LINEs), which are inserted at high
liferative epithelial tissues, compared with mitotic clock features, and other disruptions copy numbers throughout mammalian ge-
brain tissue and other compartments that that arise over time. The mitotic clock input nomes (12). The expression of TEs is strongly
largely comprise postmitotic cells. Moreover, likely includes global hypomethylation as up-regulated across a range of tumors, par-
primary cells become progressively hypo- well as focal hypermethylation of specific ticularly in hypomethylated regions. In sup-
methylated with increasing passages in cul- CpG islands, which can also accumulate as port of a causal role for methylation loss, the
ture, but their methylation stabilizes when cells divide. Global hypomethylation and fo- DNMT inhibitor 5-azacytidine induces LINE
they exit the cell cycle (5). In cancer cells, the cal hypermethylation both loosely correlate and ERV expression in vitro and in vivo (13).
degree of hypomethylation correlates with with chronological age (3, 9). A relationship TE reactivation triggers innate immunity
somatic mutational burden, which is estab- between mitotic and aging clocks is also sup- through viral mimicry (13). The derepressed
lished to have mitotic clock–like properties ported by the observation that telomerase elements produce double-stranded RNAs,
because the number of mutations increases reverse transcriptase (TERT) variants that which are sensed by cytosolic sensors that
as cells accumulate divisions (6). increase telomere length are associated with trigger a type I interferon (IFN) response.
DNA methylation loss associated with cell increased epigenetic age predictions, on the DNMT inhibitors activate TEs in cancer cells,
divisions is likely a consequence of ineffi- basis of measurements of DNA methylation increase immune infiltration, and sensitize
cient epigenetic maintenance (see the figure). in human peripheral blood mononuclear tumors to immunotherapy. LINE reactivation
Methylation is copied during DNA replica- cells (8). Because these variants allow cells has also been documented in senescent cells,
tion by DNA methyltransferases (DNMTs). to undergo more divisions before telomere where it triggers IFN responses and may pro-
However, maintenance is less efficient in crisis (when telomeres become too short and mote inflammaging, a chronic inflammatory
cells arrest), a potential explanation is that state linked to aging-associated diseases (12).
1
Department of Pathology, Dana-Farber Cancer Institute,
more division increases mitotic methylation Global hypomethylation also alters chro-
Boston, MA, USA. 2Department of Pathology, Harvard changes, which accelerates the aging clock. matin topology, which can affect the phe-
Medical School, Boston, MA, USA. 3Broad Institute, The relationship between mitotic and notypes of neoplastic and aging cells. Late-
Cambridge, MA, USA. 4Division of Genetics, Department aging-associated methylation changes is con- replicating genomic regions localize to the
of Medicine, Brigham and Women’s Hospital, Harvard
Medical School, Boston, MA, USA. 5Department of Data founded by cell type heterogeneity. The pace nuclear periphery and lamina in healthy cells
Science, Dana-Farber Cancer Institute, Boston, MA, USA. of mitotic hypomethylation varies across cell but relocate to the interior and gain repres-
6
Department of Cancer Biology, Dana-Farber Cancer types, with embryonic stem cells representing sive histone modifications in hypomethyl-
Institute, Boston, MA, USA. 7Department of Cell
Biology, Harvard Medical School, Boston, MA, USA. an extreme because they remain stably meth- ated tumor cells (5, 14). These architectural
Email: bradley_bernstein@dfci.harvard.edu ylated (3, 10). Epigenetic age also varies be- changes are accompanied by transcriptional

1276 23 DECEMBER 2022 • VOL 378 ISSUE 6626 science.org SCIENCE

 changes likely to affect tumor and aging phe- lution of tumors, its net impact is more likely variability across mammals scales with life
notypes. In contrast to TEs, the expression of to restrain the proliferative capacity and plas- span (6). Moreover, the extent to which hypo-
most protein-coding genes in the reorganized ticity of aging cells and to promote their im- methylation primes downstream expression
regions is down-regulated in association mune clearance. In addition to checking ma- changes and phenotypes may represent an
with DNA methylation loss and chromatin lignant progression, effects of these sequelae additional tunable component of the mitotic
changes. The deregulated genes are enriched on tissue homeostasis may confer other adap- clock. Even to the extent that hypomethyl-
for functions related to stem cell prolifera- tive or detrimental aging phenotypes. ation is an intrinsic feature of mammalian
tion, epithelial-mesenchymal transition, and To the extent that global hypomethylation genomes predicated in imperfect mainte-
invasion (14). Their repression may restrain enacts barriers to proliferation and malig- nance, its pace and downstream integration
the proliferative and invasive potential of ag- nant progression, tumor cells must adopt by chromatin and transcriptional machinery
ing cells and hinder malignant progression. strategies to overcome them. Certain tumors have likely evolved to balance cancer resis-
Additional evidence suggests links between arise from stem cells unaffected by hypo- tance and aging phenotypes.
global hypomethylation and senescence, a methylation, whereas others acquire hyper- It should be recognized that this model of
conserved program that limits the prolifera- methylating phenotypes that may slow or re- mitotic hypomethylation and its impact on
tion of damaged cells (5). Senescent cells ex- verse mitotic hypomethylation (3). Activation cell phenotypes remains nascent and largely
hibit global hypomethylation and profound of TEs and downstream sensing pathways inferential. The hypomethylation landscape
chromatin architecture changes, including may be muted by chromatin regulators or im- has been defined from profiles of tumors,
the formation of senescence-associated het- mune factors, which are frequently altered in heterogeneous tissues, and cultured cell
lines, but the patterns and pace of methyla-
tion loss will vary according to cell lineage,
The mitotic hypomethylation clock restrains aging cells developmental stage, and environment. New
DNA hypomethylation arises from inefficient maintenance of CpG methylation in late-replicating genomic tools are needed to resolve methylation pat-
regions with low CpG density. The baseline methylation of these regions (purple circles) can gradually be terns across single cells in heterogeneous
lost (empty circles) as cells divide. Eventually, global hypomethylation may arise, which restrains aging cells tissues and to track methylation loss in real
and hinders tumor progression through the induction of transposable element expression, innate immunity time. Furthermore, downstream functional
(interferon responses), and senescence-associated chromatin alterations. consequences have been largely inferred
from correlations with chromatin states and
CpG methylation TE expression. They are supported by genet-
Aging cell phenotypes ics and the effects of DNMT inhibitors, but
• Transposable element these do not fully recapitulate the hypometh-
up-regulation

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• Type I interferon genes
ylation in aging and malignant cells. Other
• Senescence features
key questions relate to the ubiquity of hypo-
methylation in tumors and how cancer cells
overcome the associated barriers.
A more detailed understanding of the hy-
Many cell pomethylation clock could reveal biomarkers
divisions that predict disease risk or stratify tumors. It
could yield new therapeutic modalities that
prune aging or premalignant cells by exploit-
ing vulnerabilities associated with hypometh-
ylation. Alternatively, therapies that slow or
erochromatin foci (SAHFs). Key features of cancer. Cancer cells may also benefit from the reverse cell-intrinsic DNA hypomethylation
SAHFs, including their spatial redistribution derepression of certain TEs, such as the ERVs might alleviate inflammation or other aging-
and their association with repressive histone that activate oncogenes in colorectal tumors associated deficits. Interventions will need to
modifications, are reminiscent of reorganized (12). These competing forces allude to a bat- strike a balance to improve aging tissue ho-
chromatin in hypomethylated aging and ma- tle between organismal evolution and tumor meostasis without potentiating cancer risk. j
lignant cells. These parallels raise the possi- evolution, with the former yielding tumor-
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GRAPHIC: A. FISHER/SCIENCE

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harbor cytoplasmic chromatin fragments en- malian genomes, it may be “tunable” across
riched for markers of DNA damage and het- species and tissues. This is reminiscent of ACKNOWL EDGMENTS
erochromatin that are capable of activating the heterochromatin-based mitotic clock in B.E.B. has financial interests in Fulcrum Therapeutics,
HiFiBiO, Arsenal Biosciences, Chroma Medicine, Cell
the inflammatory stimulator of interferon the yeast Saccharomyces cerevisiae, whose Signaling Technologies, and Design Pharmaceuticals. M.J.A.
genes (STING) pathway (12). Hence, although modulation alters life span (5). There are also has financial interests in SeQure Dx.
hypomethylation may contribute to the evo- parallels to somatic mutational rates, whose 10.1126/science.abn4009

SCIENCE science.org 23 DECEMBER 2022 • VOL 378 ISSUE 6626 1277

 Epigenetic clocks, aging, and cancer
Sarah E. JohnstoneVadim N. GladyshevMartin J. AryeeBradley E. Bernstein

Science, 378 (6626), • DOI: 10.1126/science.abn4009

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