Glycative Stress Research
Online edition : ISSN 2188-3610
Print edition : ISSN 2188-3602
Received : May 17, 2018
Accepted : July 18, 2018
Published online : September 30, 2018
doi:10.24659/gsr.5.3_129

Review article

Epigenetics and aging
Yoshimasa Saito, Hidetsugu Saito
Division of Pharmacotherapeutics, Keio University Faculty of Pharmacy, Tokyo, Japan

Abstract

Epigenetics is a mechanism precisely controlling gene expression by the change in chromatin structure, notaccompanied by the change in the DNA sequence, in the processes of generation and differentiation. Representative casesof epigenetic changes are DNA methylation, histone acetylation and histone methylation. The metabolic pathway, including
folic acid metabolism and methionine metabolism, is referred to as one-carbon metabolism. The nutrients constituting thismetabolic pathway are methionine, folic acid and vitamin B12 . They have an effect on the epigenetic control mechanism andalso affect gene expression. It is reported that the failure of these epigenetic mechanisms causes various disorders including
some forms of cancer, life-style diseases and psychiatric diseases.
Recently, stem cell aging theory has been promoted, which states that the functions of stem cells are reduced withaging, and as a result the structuring and maintenance of the body tissues become difficult. It is pointed out that the epigenetic
change of tissue stem cells over time plays an important role in the decline in the function of an individual caused by aging. It
is quite likely that glycative stress affects epigenetic modification. In this research we are attempting to clarify the molecularmechanism of aging, focusing on the epigenetic change, using intestinal epithelial organoids structured by an organoid culture
system, a new 3-dimentional stem cell culture method, and also the development of a new anti-aging intervention based on
epigenome editing techniques.

KEY WORDS: epigenetics, DNA methylation, histone modification, one-carbon metabolism,		

stem cell aging, anti-aging medicine

Control of Genetic Expression by
Epigenetic Change

The epigenetic mechanism precisely controls gene
expression by the change in chromatin structure, notaccompanied by the change in the DNA sequence, and it isdeeply involved in life phenomena such as differentiation,
generation, imprinting and X-chromosome inactivation.
Epigenetics is a change normally passed down even aftercell division. If this mechanism is broken, it is reported tocause various disorders such as some forms of cancer, lifestyle diseases and psychiatric diseases 1-3). Typical examples
of epigenetic changes include DNA methylation histone
acetylation and histone methylation.
DNA methylation is only one physiological modificationof the genome of the vertebrate. It is a reaction where amethyl group is attached to the 5-position carbon atom of
the cytosine of 2-nucleotide sequence (CpG) arranged in theorder of cytosine (C) and guanine (G) from the 5’ side of theCorresponding to: Yoshimasa Saito, MD, PhD
Division of Pharmacotherapeutics, Keio University Faculty of Pharmacy,
1- 5 -30 Shibakoen, Minato- ku, Tokyo 105- 8512, Japan
TEL: + 81-3 -3434 -6241 eMail: saito-ys@pha.keio.ac.jp
Co-author: Saito H, hsaito@a2.keio.jp

DNA and it is catalyzed by DNA methyltransferase (DNMT)( Fig. 1 ) 2, 3). In many cases, the clusters of CpG sequencecalled “ CpG island” are formed in the gene promoter
region. It is known that, if the gene promoter region becomes
methylated, the gene expression downstream is suppressed.
Meanwhile, DNA demethylation can be broadly classified
into passive demethylation generated depending upon DNA
replication and active demethylation not depending upon
DNA replication. It is considered that the TET (ten-eleventranslocation) hydroxylation reaction plays an important rolein the active demethylation 4). TET hydroxylates 5-position
methyl group of cytosine (5mC: 5-mehylcytosine) and converts
it to 5hmC (5-hydroxymethyl cytosine) (Fig. 1). The converted
5hmC is converted to unmethylated cytosine through cell
division and DNA base excision repair mechanism and as aresult, it becomes demethylated. It is presumed that 5hmC
plays a role as an intermediate in DNA demethylation
pathways: however, it also possibly plays a new epigenetic
regulatory role itself. As mentioned above, 5' mC is considered_ 12 9 _Glycative Stress Research 2018; 5 (3): 129 -134
(c) Society for Glycative Stress Researchmitigates age-associated physiological decline in mice. Cell Metab. 2016; 24: 795-806.
Epigenetics and Aging

FiguresFig. 1. DNA methylation and demethylation.

A methyl group is added to the 5-position of cytosine by DNA methyltransferase (DNMT) and it becomes 5-methyl-hydroxylates andthe methylgroup of the 5-position of cytosine (5mC:5-methyl cytosine) and converts it to 5hmC
Figurecytosine.
1. DNATET
methylation
demethylation.

(5-hydroxymethyl cytosine). The converted 5hmC is converted to unmethylated cytosine through cell division and DNA baseexcision
repairmechanism
and5-position
as a result, becomes
demethylated.
A methylgroup
is added
to theof cytosine
by DNA methyltransferase (DNMT) and it becomes 5-

methyl-cytosine. TET hydroxylates the methyl group of the 5-position of cytosine (5mC:5-methyl cytosine)and converts it to 5hmC (5-hydroxymethyl cytosine). The converted 5hmC is converted to unmethylated

including folic acid metabolism and methionine metabolism.
to be “the fifth base” and 5hmC is “ the sixth base,” and it iscytosinethroughdivisionand DNA
base
excision repair
mechanism
and as thisa result,
becomes
The nutrients
constituting
metabolicpathway (methionine,presumed
that theyplay cell
extremely
importantroles
in many
folic acid and vitamin B12 ) work on the epigenetic control
fields of
the generation and progression of cancer, life-styledemethylated.
mechanism, affecting gene expression and others, so thatdiseases and neurological disorders. However, many unclear
they are considered to play a very important role in diseases
points regarding their biological roles remain.
In addition to DNA methylation, histone modification
including cancer (Fig. 3 ). S-adenosylmethionine (SAM) is ametabolite regarded as best contributing to DNA methylation.
also plays an important role in gene expression. As shown in
SAM is synthesized by methionine adenosyltransferase
Fig. 2, no DNA methylation is observed in the gene promoter(MAT) with methionine and ATP as substrates and it works
region where generally active gene expression is observed,
as a methyl group donor for DNA methylation and histone
and histone is acetylated. Meanwhile, when histone H3
methylation. The SAM that has donated its methyl group islysine 9 (H3K9) is methylated, it recruits DNMT and histone
deacetylase (HDAC), and as result, DNA is methylated
converted to S-adenosylhomocysteine (SAH) ( Fig. 3 ).
and histone is deacetylated. Chromatin structures are then
Folic acid deficiency disease decreases SAM in cells andagglutinated and gene expression is inactivated due to these
inhibits the methylation of cytosine widely, and as a result, it
modifications. Furthermore, as the controlling mechanism ofcauses the instability of the chromosome and the activation
gene expression is by an epigenetic mechanism, not throughof the cancer gene, so that it is considered to increase cancer
DNA methylation, the methylation of histone H3 lysine 27
risk 7). The epidemiologic studies so far suggest that there is(H3K27) by polycomb repressive complex (PRC) is reported
an inverse correlation between the intake volume of folate
and the risk of cancers such as colon cancer 8). According( Fig. 2 ) 2.3).
As an important point, these epigenome changes
to the cohort study, the NIH-AARP Diet and Health Study
are fundamentally reversible by utilizing drugs such as atargeting more than 525,000 Americans aged from 50 to 71,
DNA methylation inhibitor, histone deacetylase inhibitor
those whose total intake amounts of folate were more thanand histone methyltransferase inhibitor. These drugs are
900 μg/a day run a 30 % lower risk of colon cancer comparedattracting a lot of attention as molecular target drugs forwith those of less than 200 μg/a day 9). However, the details
5)diseases such as cancer for the next generation . Actually,of the effects of folate against the onset of cancer have notbeen verified by research yet. It was also pointed out that
Azacytidine (Vidaza® ), a DNA methylation inhibitor, and9a large intake volume of folic acid may possibly promote
Vorinostat (Zolinza® ), a histone deacetylase inhibitor, havethe onset of cancer and its progression 10, 11). So far, it has
been approved to be used for myelodysplastic syndromes(MDS) and cutaneous T-cell lymphoma, respectively, andbeen suggested that an appropriate intake of folate possibly
their effects have been notable 6).
lowers the risk of certain types of cancer. Meanwhile, a large
volume of folate intake may adversely increase the risk ofcancer. In order to fully clarify the roles of folate derived
from food and included in supplements, in the developmentof colon cancer and other cancers, further research is
Metabolism and Epigenetics
required.
All cells performing living activities are using a
Recently, one-carbon metabolism and the nutrients
glycolytic system as their energy source. Energy is produced
constituting it have drawn attention.
within cells using glucose taken from the outside of cells.
One-carbon metabolism refers to the metabolic pathway_ 13 0 _Glycative Stress Research

10Fig. 2. Control of gene expression by epigenetic change.

When histone
methylated, itby
recruits
DNMT and
HDAC, DNA is methylated and histone is deacetylated. ThroughFigure 2. Controlof H3K9
gene isexpression
epigenetic
change.

these modifications, the chromatin structure is agglutinated and gene expression is deactivated. Meanwhile, when histone

H3K27
is methylatedby PRC2, it itdeactivates
expression
throughDNA
DNA methylation.
When histone
H3K9
is methylated,recruitsgene
DNMT
and not
HDAC,
is methylated and histone is: Methylated DNA,: Demethylated DNA, Ac: Acetylated histone, Me: Methylated histone.

deacetylated. Through these modifications, the chromatin structure is agglutinated and gene expression isdeactivated. Meanwhile, when histone H3K27 is methylated by PRC2, it deactivates gene expression not
through DNA methylation.
●: Methylated DNA, ○: Demethylated DNA, Ac: Acetylated histone, Me: Methylated histone.

Figure 3. One-carbon metabolism and epigenetics.
Fig. 3. One-carbon metabolism and epigenetics.

One-Carbon
Metabolism
is beingmechanismcombining
nutrients
andTheepigenetics.
The
One-carbon
metabolism
is beingexaminedexamined asas
thethemechanismcombining
nutrients andepigenetics.
nutrients constituting

one-carbon metabolism bring about DNA methylation change. SAM of methionine metabolic pathway, in particular, is an

nutrients important
constituting
one-carbon
metabolism
bringgroup
about
DNA
methylationof methionine
metabolicproduct playing
a role of methyl
donor
for DNA
methylation change.
and histoneSAM
methylation.

THF: tetrahydrofolate; 5, 10-MTHF: 5, 10-methylene THF; 5, CH3-THF: 5, methyl-THF; SAM: S-adenosylmethionine; SAH:

metabolicS-adenosylhomocysteine.
pathway, in particular, is an important metabolic product playing a role of methyl group donor for10
DNA methylation and histone methylation.
THF: tetrahydrofolate; 5, 10-MTHF: 5, 10-methylene_ THF;_ 5, CH3-THF: 5, methyl-THF; SAM: S131

adenosylmethionine; SAH: S-adenosylhomocysteine．

11

11
Epigenetics and Aging

And, almost all biopolymers existing in a living body receive
senescence. For example, even though the genome sequences
glycation (glycative reaction) caused by living activities. Theof identical twins are the same, it has often been observed
effects of glycation on cells are called glycative stress. In thethat it’s possible only one of them will develop diabetes
early days, the term glycation referred to the pathway whereor cancer, and their lifespans are also different because of
the carbonyl group of reducing sugars typified by glucose
the difference in living environments and lifestyles. Theseand the amino group of protein react non-enzymatically,changes are considered to be caused by the epigenetic
which finally leads to the formation of advanced glycation
changes resulting from aging. As a result of research on theend-products (AGEs). However, in the present day, thecomparison of DNA methylation and histone acetylation ofterm is used in a broader range. As long as all proteins of aidentical twins aged 3 years and 50 years, it was reported
living body continue living activity, they possibly inevitablythat although there was almost no difference between thereceive non-enzymatical glycative reactions. In the state of
epigenomic conditions of 3 years old identical twins, clear
chronic hyperglycemia like diabetes, the glycative reactions
differences were observed between those of 50 years old
accelerate everywhere in the living body, and it results
identical twins 12). It is considered that epigenetic changes
in the accumulation of its final products, AGEs. In theaccumulated differently while they were aging underpresent aging society, the more a body has aged, the moredifferent living conditions and lifestyle habits, which affected
glycative reactions become involved in the onsets of agetheir onset of disease and life span.
related diseases including cancers. It is possible that the
Recently, a stem cell aging hypothesis has been advocatedglycative reactions also affect epigenetics. Histone lysinethat stem cell functions deteriorate with aging, so that the
carboxymethylation (HL-CM) formed under diabetic
structuring and maintenance of tissues become difficult.
conditions, in particular, possibly affects gene expression
The tissue stem cells such as blood-forming stem cells andthrough histone modification and DNA methylation
intestinal epithelial stem cell have long-term, self-replicatingchanges. Under the condition of high glucose concentrationand multipotential functions, and they are the most importantandFigureprogressiveoxidization
associatedwithdiabetes,itis
3. One-carbon metabolism and epigenetics. cells in structuring tissues. Because stem cells like these
considered that HL-CM is generated and it affects histone
replicate themselves throughout life, they are considered toacetylation.
Althoughthe relationshipbetween glycative
be goodcombining
models for nutrientsobserving theepigenetic
One-Carbon
Metabolism
is being examinedas the mechanism
andaccumulation
epigenetics.ofThereaction and epigenetics is a very important research area,changes in the process of aging. According to the research
nutrients
constituting
one-carbon
metabolism
bringmethylation
change.inSAM
methionine
almostnothing
has been clarified.
Researchin the futureis aboutsoDNA
far, theepigenetic changes
tissueofstemcells over time
expected.
play
important
roles
in
the
individualfunctional
deterioration
metabolic pathway, in particular, is an important metabolic product playing
a role of methyl group donorforcaused by aging 13). As shown in Fig. 4, the epigenetic
conditions of DNA methylation and histone modification
DNA methylation and histone methylation.
in young stem cell are almost evenly maintained. However,
THF: tetrahydrofolate; 5, 10-MTHF: 5, 10-methylene THF;
5, self-replication
CH3-THF: 5, ismethyl-THF;
SAM:
while
being repeatedwith Saging and the
Epigenetics
Changes Associated with Aging
exposuretoenvironmental
factors,
chronic
inflammation
adenosylmethionine; SAH: S-adenosylhomocysteine．
and infection with bacteria are added to them, epigenetic
It has been clarified that epigenetics plays an importantchanges are accumulated. Epigenetic changes are consideredrole not only in diseases including cancer but also aging and

Fig. 4. Epigenetic changes associated with aging of stem cells.

The epigenetic conditions of DNA methylation and histone modifications
are almost evenly maintained in young stem cells. While11
stem cells repeat self-replication with aging and the exposure to environmental factors, chronic inflammation and infection withbacteria and virus are added to it, and epigenetic changes accumulate. Epigenetic changes accelerate with aging, finally leading totissue dysfunction associated with the depletion of stem cells and the abnormal proliferation of cancer and other diseases.

_ 132 _Glycative Stress Research

to further accelerate with aging, finally leading to the tissue
dysfunction associated with the depletion of stem cells, e.g.
reduced function of tissues and abnormal proliferation ofcancer and other diseases.
Issa et al. discussed the relationship between aging andmethylation state of the estrogen-receptor (ER) gene in large
intestine mucosal tissues in a study of approximately 4 00
cases, and they reported that the level of methylation rose due
to aging 14). Generally, it is said that the amount of methylated
cytosine contained in the total genome tends to decrease withaging. Meanwhile, it is reported that the methylation statusof specific genes accelerates with aging. These changes are
considered to induce chromosome instability and inactivationof tumor suppressor genes and play an important role in
the onset of cancer. Toyota et al. precisely analyzed the
methylation status of many genes and clarified that there ismethylation caused by aging (type A) and cancer specificmethylation (type C) in abnormal methylations 15). As for type
A genes, MYOD and N33 have been reported in addition to
ER genes. There still remain unexplained points about themechanism through which the methylation status of specificgenes accelerates and further study is required.

Clarification of the Molecular Mechanism ofAging and Development of New Anti-Aging
Intervention Focusing on Epigenetic Changes
Japan is a super-aging society with the elderly, 65 years
or older, accounting for over 21% of the total population andthe aging tendency of our country is progressing in a speed
unparalleled in the world. The increased medical expenditureand care burden for the elderly are becoming a very serious
problem and it is a very important task to extent healthy life
expectancy through Anti-Aging intervention.
One of the factors inhibiting the progress of researchin aging so far was that no good model showing the true
condition of aging in vitro existed. In particular, we arefocusing on the fact that epigenetic changes and altering gene
expression accumulate in stem cells, and making efforts inclarifying the molecular mechanism of aging, using intestinal
epithelial organoids established by organoid culture. Organoidculture technique is a 3- dimentional culture method oftissue stem cells and it can reproduce in vivo characteristics
in vitro, so that it attracts worldwide attention. We have had
success in permanently culturing and maintaining the cancer
stem cells of mouse intestinal epithelial tissue and intestinal
cancer tissue of Apc Min / + mice by the means of organoidculture 16, 17). They also established organoids from biliary tract
cancer tissue, a typical refractory cancer, and had success inculturing and maintaining the cancer stem cells derived frombiliary tract cancer for more than a year 18). Owing to theorganoid culture method, it has become possible to conduct
in vitro research with high similarity to the research within vivo cells. In particular, intestinal epithelium is a dynamic
tissue because intestinal epithelial stem cells existing in cryptbase actively repeat self-duplication and differentiation, andall cells are replaced by new cells within 3-4 days. There aremany bowel diseases such as intestinal cancer which haveincreased incident rates related to aging, so the organoids
derived from intestinal epithelium are considered to be goodmodels for the observation of stem cell aging.
Life phenomenon accompanied by aging is presumed

to progress with multiple genetic changes related to eachother in a complicated manner. If these genes are to becontrolled by epigenetic changes, it is possible to control theexpression of important genes relating to aging by artificiallycontrolling epigenetic change using new low-molecularweight compounds. However, in order to apply these newly
discovered epigenome drugs to clinical use for Anti-Aging,the identification of genes associated with aging and thedevelopment of gene-specific epigenetic control are required.
Because the conventional DNA methylation inhibitor andhistone deacetylase inhibitor fundamentally demethylate
or acetylate all regions of the genome, great difficulties
remain with respect to the side effects in particular. Recently,
CRISPR-Cas9 technology was improved, and as a result, agroundbreaking epigenome editing technique was developed
to control gene-specific epigenetic changes by recruiting themethyltransferase and demethylase regions specifically 19).
It is expected that a platform for an original Anti-Aging
approach will be developed by controlling aging-specificepigenetic change, owing to epigenome editing technology.
It is possible to develop the most appropriate Anti-Aging
approach suitable for each case not only by epigenome
editing but also by verifying the effects of the epigenetic
drugs such as Nicotinamide mononucleotide (NMN) 20) of
aging control factor, which is being used in clinical trials,
DNA methylation inhibitor and histone methylation inhibitor.
If the development of these new Anti-Aging
interventions succeeds, it is expected that it will realize theextension of healthy life expectancy and QOL and lead tothe prevention of age-associated diseases such as cancer andthe improvement of organ transplantation success rates inthe elderly. Ultimately, it leads to the reduction of medical
expenditure and care burden for the elderly and it is possible
to greatly contribute to the improvement of health economics
which has become an urgent problem in Japan. It is expectedthat the developments of epigenetics and Anti-Aging
medicine lead to the realization of “rejuvenation” that peopleof all ages and countries have been pursuing.

Acknowledgement

The outline of this study was presented at the 11th
Meeting of the Society for Glycative Stress Research,
November 10, 2016, Tokyo.

Conflict of interest_ 133 _

The authors claim no conflict of interest in this study.

Epigenetics and Aging

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