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Titre: Age-Associated Methylation Suppresses SPRY1, Leading to a Failure of Re-quiescence and Loss of the Reserve Stem Cell Pool in Elderly Muscle

Auteur: Anne Bigot

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Article

Age-Associated Methylation Suppresses SPRY1,
Leading to a Failure of Re-quiescence and Loss of
the Reserve Stem Cell Pool in Elderly Muscle
Graphical Abstract

Authors
Anne Bigot, William J. Duddy, Zamalou G.
Ouandaogo, ..., Gillian Butler-Browne,
Vincent Mouly, Ste´phanie Duguez

Correspondence
vincent.mouly@upmc.fr (V.M.),
stephanie.duguez@upmc.fr (S.D.)

In Brief
Loss of muscle strength in old age is
linked to diminution of the muscle stem
cell pool. Bigot et al. show that the ageassociated increase in global DNA
methylation acts through the SPRY1
pathway to suppress human muscle stem
cell entry into quiescence, thus impairing
self-renewal of the stem cell pool.

Highlights
d

The capacity of human muscle stem cells to enter quiescence
diminishes with age

d

This reduced capacity to re-quiesce is associated with
increased DNA methylation

d

DNA methylation suppresses SPRY1, a known regulator of
quiescence

d

Senescence, a feature of late cell division counts, is not
increased with age

Bigot et al., 2015, Cell Reports 13, 1172–1182
November 10, 2015 ª2015 The Authors
http://dx.doi.org/10.1016/j.celrep.2015.09.067

Accession Numbers
GSE52699
GSE53302

Cell Reports

Article
Age-Associated Methylation Suppresses SPRY1,
Leading to a Failure of Re-quiescence and Loss of
the Reserve Stem Cell Pool in Elderly Muscle
Anne Bigot,1,4 William J. Duddy,1,4 Zamalou G. Ouandaogo,1,4 Elisa Negroni,1 Virginie Mariot,1 Svetlana Ghimbovschi,2
Brennan Harmon,2 Aurore Wielgosik,1 Camille Loiseau,1,3 Joe Devaney,2 Julie Dumonceaux,1 Gillian Butler-Browne,1
Vincent Mouly,1,* and Ste´phanie Duguez1,*
1Sorbonne Universite
´ s, UPMC University of Paris 06, INSERM UMRS974, CNRS FRE3617, Centre de Recherche en Myologie (CRM), GH Pitie´

^trie`re, Paris 13, France
Salpe
Proteomics, and Bioinformatics (GPB) Core of the Intellectual and Developmental Disabilities Research Center (IDDRC),
Children’s National Medical Center, Washington, DC 20010, USA
3Sorbonne Universite
´ s, UPMC University of Paris 06, INSERM, UMR-S 1158, Neurophysiologie Respiratoire Expe´rimentale et Clinique,
Paris 13, France
4Co-first author
*Correspondence: vincent.mouly@upmc.fr (V.M.), stephanie.duguez@upmc.fr (S.D.)
http://dx.doi.org/10.1016/j.celrep.2015.09.067
This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
2Genomics,

SUMMARY

The molecular mechanisms by which aging affects
stem cell number and function are poorly understood. Murine data have implicated cellular senescence in the loss of muscle stem cells with aging.
Here, using human cells and by carrying out experiments within a strictly pre-senescent division count,
we demonstrate an impaired capacity for stem cell
self-renewal in elderly muscle. We link aging to an
increased methylation of the SPRY1 gene, a known
regulator of muscle stem cell quiescence. Replenishment of the reserve cell pool was modulated experimentally by demethylation or siRNA knockdown of
SPRY1. We propose that suppression of SPRY1 by
age-associated methylation in humans inhibits the
replenishment of the muscle stem cell pool, contributing to a decreased regenerative response in old
age. We further show that aging does not affect muscle stem cell senescence in humans.
INTRODUCTION
Aging is characterized by a progressive decline in the physiology
and turnover of adult tissues. Tissue renewal requires stem cells,
which show declining functional properties with age (Pollina and
Brunet, 2011; Signer and Morrison, 2013). Over a lifetime, adult
tissues present an accumulation of cellular damage as follows:
genomic mutations, epigenetic alterations, mitochondrial dysfunctions, imbalance of protein synthesis and degradation, telomere shortening, accumulation of senescent cells, and altered
intercellular communication (see Lo´pez-Otı´n et al., 2013 for review). In skeletal muscle, aging is characterized by a decline in
mass and strength due to a decrease in the number, size, and
quality of contractile myofibers (Klein et al., 2003; Nilwik et al.,

2013), as well as a loss of regenerative capacity (Pollina and
Brunet, 2011).
Once activated, the muscle stem cell divides asymmetrically
to maintain a pool of muscle precursor cells and produce a progeny that will fuse with damaged myofibers to form new muscle
contractile tissue (Conboy and Rando, 2002; Olguin and Olwin,
2004; Zammit et al., 2004). This process is at least partly cell
autonomous since muscle stem cells in vitro can fuse to form
myotubes while a minority remain undifferentiated as reserve
cells (Zammit et al., 2006). The decline of the muscle regenerative capacity with age (Carlson et al., 2008) has been attributed
to a decline in the number of muscle stem cells in mouse (Brack
et al., 2005; Chakkalakal et al., 2012; Collins et al., 2007; Conboy
et al., 2005) and humans (Malmgren et al., 2000; Renault et al.,
2002), and also to extrinsic environmental influences and to the
intrinsic regenerative potential of the cells themselves (Collins
et al., 2007; Conboy et al., 2005). When old murine muscle
stem cells are exposed to a young environment or to growth factors, their capacities to proliferate and differentiate are partly
restored (Brack et al., 2007; Collins et al., 2007; Conboy et al.,
2005), suggesting that functional deregulations with age may
be reversible.
Loss of the stem cell population with aging may involve cell
death, although this has never been evidenced, or a progressive
loss of the cell’s potential to self-renew. A decline of muscle stem
cell function also was associated with a process of senescence
in geriatric mice (Sousa-Victor et al., 2014). Multiple regulatory
mechanisms determine stem cell fate (Collas, 2010; Krishnakumar and Blelloch, 2013), including the epigenetic status, which
is defined by DNA and histone methylation as well as the expression of regulatory RNAs (Krishnakumar and Blelloch, 2013).
Although DNA methylation regulates gene expression (Jones,
2012) and correlates with aging (Bocklandt et al., 2011; Horvath,
2013) in many tissues, little is known about muscle stem cell
methylation status with aging and the mechanism(s) by which
it could regulate stem cell fate. Here we demonstrate that ageassociated changes in methylation of a quiescence regulator,

1172 Cell Reports 13, 1172–1182, November 10, 2015 ª2015 The Authors

Figure 1. Muscle Stem Cells from Young
and Elderly Subjects Have Similar Characteristics of Proliferation and Senescence
(A) Rate of division and (B) maximum division
number were similar in myogenic precursors
derived from young and elderly subjects, as
determined by cell counts throughout culture, until
proliferative arrest (n = 5–10 subjects per group).
(C) Similar levels of b-galactosidase, a marker of
senescence. (Top) Representative image shows
b-galactosidase staining. (Bottom) Percentage of
b-galactosidase-positive cells is shown (n = 3
subjects per group). Scale bar, 50 mm.
(D) Levels of p16 expression, quantified by qRTPCR and with results normalized to B2M transcript
level, are shown (n = 5 subjects per group).
(E) Telomere length, as measured by qRT-PCR at
five to ten divisions, is shown (n = 5 subjects per
group).
Each data point represents a single muscle progenitor culture derived from one subject. Values
are means ± SEM. See also Figure S1.

SPRY1, cause a failure of re-quiescence in activated stem cells,
leading to a decline of the stem cell pool in elderly human
muscle.
RESULTS
The Replicative Potential of Muscle Stem Cells Is
Unaffected by Age
Cultures isolated from muscle biopsies of elderly subjects
presented less myogenic cells (desmin-expressing cells;
Figure S1A) than those of young ones. We tested whether
this could be explained by earlier replicative senescence or
cell death. For this purpose, we enriched the CD56-positive
myogenic population up to 82%–99% purity (Figure S1B),
and we investigated the proliferative potential and markers of
senescence.
The capacity of elderly muscle precursor cells to proliferate
was equal to that of young subjects: muscle precursors underwent the same number of divisions per day (Figure 1A) and
divided homogenously, reaching a similar number of generations after 5 days (generation 7; Figure S1C). In contrast to
what is described in muscle stem cells of geriatric mice
(Sousa-Victor et al., 2014), there was no greater propensity toward senescence in human elderly cells, as we observed a
comparable replicative lifespan (Figure 1B), a similar percentage of b-galactosidase-positive cells (a marker of senescence;
Figure 1C), an unaltered expression of p16 (which can hamper
the proliferative capacity of human myoblasts; Zhu et al., 2007;
Figure 1D), and equal telomere length (Figure 1E). This is
consistent with our previous work (Barberi et al., 2013) showing
that both young and aged human muscle stem cells exhibit
increasing expression of p16 and shortening of telomeres
throughout their replicative lifespan, which terminates at around
20 cell divisions independently of subject age. Cell death
was unaffected by age, both during proliferation (less than

4% of cell death in both age groups) and at the exit of the
cell cycle toward differentiation (similar level of PARP-1 cleavage; Figure S1D).
We conclude that human muscle stem cells maintain their
proliferative capacity with aging, and are prone to neither proliferative senescence nor cell death. Importantly, all subsequent
analyses were done in the first half of the lifespan, at division
counts of less than 12.
Self-Renewal Is Impaired in Elderly Muscle Precursors
In Vitro
Since cell death or senescence was ruled out, we hypothesized
that the reduced size of the muscle stem cell population with
age is due to a loss of its capacity to self-renew. Reflecting
muscle regeneration in vivo, the majority of muscle stem cells
in vitro fuse to form differentiated plurinucleated myotubes,
while a minority do not fuse but self-renew to constitute the
pool of reserve cells that express PAX7, a marker of muscle
progenitor fate (Zammit et al., 2006). We observed that cultures
of elderly muscle stem cells generated a significantly lower proportion of reserve (PAX7-expressing) cells at both 3 and 6 days
of differentiation (Figure 2A). Although mononucleated cells
were observed in elderly cultures, most of these were positive
for myosin heavy chain (MyHC), a marker of engagement in differentiation, and did not express PAX7 (Figure 2A). To test
whether these MyHC-expressing elderly cells retained their capacity to expand and differentiate, fused myotubes were
removed by differential trypsinization and mononucleated cells
were re-plated. Upon re-plating, elderly mononucleated cells
presented a low proportion of desmin-expressing myogenic
cells, 2%–20%, in contrast to up to 90% in young cultures (Figure 2B), indicating that, in elderly culture, mononucleated
cells positive for MyHC were terminally differentiated and unable to reattach and proliferate, thus confirming that the pool
of reserve cells was depleted.

Cell Reports 13, 1172–1182, November 10, 2015 ª2015 The Authors 1173

Figure 2. Muscle Precursor Pool Is Diminished in Elderly Muscle Stem Cells In Vitro
and In Vivo
(A) Reserve cell marker PAX7 is lost in elderly cultures of differentiated muscle cells. Cultures were
labeled for PAX7 (green) and myosin heavy chain
(MyHC) (red). Differentiated myotubes (multinucleated cells positive for MyHC) are present in both
cultures. Reserve cells (mononucleated and PAX7
expressing) are observed in young-derived (arrows)
but rarely in elderly derived cultures, whereas
MyHC-expressing mononucleated cells (asterisks)
were abundant in elderly cultures. Counts of
reserve cells and of MyHC-expressing mononucleated cells are expressed as a percentage of
mononucleated cells (bottom; mean ± SEM).
(B) The mononucleated cell population can give
rise to new myotubes. Diagram summarizes
workflow to test the myogenic capacity of mononucleated cells. Re-plated desmin-positive cells
were able to differentiate and form myotubes, but
their numbers were much lower in elderly derived
cultures. Desmin, green; MyHC, red; nuclei, blue.
(C) Elderly derived human muscle precursors engrafted into mouse muscles participate less in the
reserve cell niche. Tibialis anterior muscles were
harvested 4 weeks after cryodamage and subsequent injection of 5 3 105 human cells. Human cells
participating in the reserve cell compartment (white
arrows) are defined by nuclear expression of PAX7
(red) and human lamin A/C (green). Laminin (white)
and nuclei (blue) are visualized. Human reserve cells
are counted as a percentage of the total number of
human lamin A/C nuclei (bottom). Significant differences with young-derived cells are indicated
(*p < 0.05 and **p < 0.01). Scale bar, 50 mm.

Self-Renewal of Elderly Muscle Stem Cells Is Impaired
In Vivo
Human muscle stem cells from both young and old subjects were injected into regenerating muscles of immunodeficient mice and able to fuse with the murine muscle host
fibers (Figures 2C and 3B). Post-engraftment, muscle fibers
were found expressing human spectrin, and sub-laminal
cells containing human nuclei (expressing human lamin A/C)
also were detected. While 8.09% ± 0.43% of the nuclei
derived from young human muscle stem cells expressed
PAX7 and, thus, participated in stem cell renewal, only
3.53% ± 1.29% (p < 0.01) of the nuclei derived from elderly
human muscle stem cells did this (Figure 2C). Thus, selfrenewal of the quiescent stem cell population was impaired
in vivo in mouse-engrafted human muscle stem cells derived
from elderly subjects.
Elderly Muscle Stem Cells Strongly Express Markers of
Differentiation
Since the late-differentiation marker MyHC was expressed by a
higher proportion of mononucleated cells in elderly derived
differentiated cultures, we explored further the differentiation
fate of these elderly cells. Muscle precursors from elderly cells
show a high capacity to fuse, with a fusion index of 88%
compared with 71% for young-derived cells (Figure S2A);

in vitro they form larger myotubes containing a significantly
greater number of nuclei (Figure 3A); and, following in vivo
engraftment, they form significantly much larger fibers than
young-derived cells (Figure 3B).
To further explore this observation at the molecular level,
transcriptomic analysis was performed on myotubes after 1
and 3 days of differentiation (Tables S1 and S2). Genes
that previously were shown to be upregulated during differentiation of human primary myoblasts presented a strongly
increased expression in elderly derived as compared with
young-derived cells at both day 1 and day 3 (Figure S2B).
By day 3 of differentiation, genes that are known to be upregulated during murine C2C12 myoblast differentiation, in
myoblast response to known triggers/enhancers of differentiation (MyoD or IGF-1), or in general muscle development
processes were all found to be more strongly expressed in
elderly derived compared with young-derived differentiated
cells (Figure 3C; muscle differentiation-related gene sets
mentioned in the text are highlighted in yellow). Correspondingly, genes induced by starvation or atrophy of myotubes
were downregulated in myotubes derived from elderly as
compared to those derived from young cells. We confirmed
by qRT-PCR that elderly differentiated myoblasts have a
higher level of MyHC 3 and myosin light chain 1 mRNA (Figure 3D), markers of late stages of myogenic differentiation.

1174 Cell Reports 13, 1172–1182, November 10, 2015 ª2015 The Authors

Figure 3. Elderly Muscle Stem Cells Strongly Express Markers of Differentiation and Form Large Myotubes
(A) Differentiated myotubes are larger when formed by elderly muscle stem cells. (Left) Representative images show young and elderly myotubes. Nuclei, blue;
desmin, green. Scale bar, 50 mm. (Right) Cumulative rank plots show the higher nuclear number per myotube in elderly cultures (p < 0.001).
(B) Engrafted elderly muscle stem cells form large myotubes in vivo. (Left) Myofibers (asterisks) formed by the differentiation of engrafted cells are positive for
human spectrin (red) and contain human myonuclei (human lamin A/C, green). (Right) Cumulative rank plots show the larger Feret diameters of myofibers formed
by elderly compared with young muscle stem cells (p < 0.001).
(C) Upregulation of differentiation-related molecular signatures in elderly derived cultures. Of 1,053 gene sets, including all biological processes of the gene
ontology, only those whose distributions in the transcriptome profile were significantly non-random (p < 0.05 and FDR < 0.025) are shown, colored red or blue in
proportion to up- or downregulation in elderly compared with young cells (differentiation day 3). Node size represents number of significantly altered genes, and
edge width represents the number of altered genes that are shared between connected gene sets. References of each gene set are given in Table S3. Differentiation-related gene sets are indicated.
(D) qRT-PCR for markers of early to late myogenic differentiation. The mRNA levels were normalized to desmin. Values are means ± SEM (n = 3–4 per group).
Significant differences with young-derived cells are indicated (*p < 0.05 and **p < 0.01). See also Figure S2 and Tables S1, S2, and S3.

In addition, western blot analyses confirmed a greater level of
MyHC in elderly stem cell cultures (Figure S2C). On the other
hand, PITX3 and PITX2 mRNA levels, described as markers
for proliferation and early stage of differentiation (Knopp
et al., 2013), were similar between young and elderly myotubes (Figure 3D).

Capacity for Self-Renewal Is Regulated by DNA
Methylation
Elderly muscle stem cells presented an overall significantly
increased level of methylated DNA (Figures 4A and 4B; Figure S3A; Table S4), and a whole DNA methylome array showed
that hypermethylated CpGs were distributed throughout the

Cell Reports 13, 1172–1182, November 10, 2015 ª2015 The Authors 1175

Figure 4. DNA Methylation Regulates the Size of the Reserve Cell Pool
(A) DNA from elderly muscle stem cells is hypermethylated. An ELISA assay was used to measure the level of methylated DNA in muscle progenitors derived from
young and elderly subjects (one data point per subject; n = 5–8 per group). Values are means ± SEM. ***p < 0.001.
(B) Genomic visualization of DNA methylation. Chromosome numbers, chromosomal positions (in units of 1 Mb), and cytogenetic bands are shown at the
outermost circle. Within this are displayed counts of hypermethylated CpG sites in muscle stem cells from old compared with young subjects (inner ring), and from
young compared with old subjects (outer ring). Darker reds represent higher counts.
(C) Experimental demethylation of DNA increased the number of muscle reserve cells in elderly cultures. Elderly cells were treated with 5-Aza-20 -deoxycytidine.
(Left) Representative immunostaining shows treated (top) and untreated (bottom) elderly cells. PAX7, green; MyHC, red; nuclei, blue. Reserve cells (expressing
PAX7, white arrows) and mononucleated cells positive for MyHC (asterisks) are indicated. (Right) Percentage of mononucleated cells that are PAX7 or MyHC
positive is shown (n = 3 per condition). Values are means ± SEM. Significantly different from untreated cells, *p < 0.05 and **p < 0.01. Scale bar, 50 mm. See also
Figure S3 and Table S4.

genome (Figure 4B). Importantly, a higher DNA methylation also
was confirmed on human biopsies (Figure S3B). When we demethylated DNA using 5-Aza-20 -deoxycytidine in in vitro cultures up
to day 6 of differentiation, the number of reserve (PAX7-expressing) cells generated was restored in elderly cultures (an increase
of about 2.7-fold; Figure 4C), whereas the number of mononucleated cells positive for MyHC was significantly decreased (Figure 4C). Fusion into myotubes was unaffected since the number
of nuclei per myotube was similar in both conditions (Figure S3C).
Thus, DNA methylation is increased in elderly muscle stem cells,
inhibiting reserve pool self-renewal, which can be restored by
demethylation.
Sprouty1 Regulates Self-Renewal in Muscle Stem Cells
The genome-wide methylation analysis revealed a general hypermethylation of gene bodies in elderly muscle stem cells,
whereas upstream transcription start sites and promoter regions
were hypomethylated (Figures S4A and S4B), suggesting that an
overall activation of transcription underlies both their engagement into the myogenic differentiation program (Figure 3) and
their reduced quiescence (Figure 2). Genes involved in myogenic
differentiation pathways, such as elements of the WNT3A
pathway, were hypomethylated (Figure 5A; Table S4). This is
concordant with results in the previous section showing that

the myogenic program is upregulated in elderly muscle stem
cells (Figures 3C and 3D; Figures S2 and S4C). Conversely,
genes involved in self-renewal pathways, such as SPRY1 and
NOTCH1 (Brack et al., 2008; Chakkalakal et al., 2012; Conboy
and Rando, 2002; Shea et al., 2010; Wen et al., 2012),
were hypermethylated (Figure 5A). Lower mRNA levels of
SPRY1, NOTCH1, and its co-regulator mastermind-like protein
1 (MAML1) were detected in elderly cultures; delta-like protein
1 (DLL1), a second regulator of NOTCH1, was unchanged
(Figure 5B).
5-Aza-20 -deoxycytidine treatment, which rescued self-renewal
in vitro, also rescued the expression level of SPRY1 (Figure 5C),
whereas the mRNA level of NOTCH1 was highly variable and
its cofactor MAML1 remained unchanged (Figure 5C). Following
small interfering RNA (siRNA) knockdown of SPRY1 to about
5% in elderly muscle stem cells treated with 5-Aza-20 -deoxycytidine, their capacity to renew the reserve cell compartment was
abolished (Figure 5D). Similarly, knocking down the expression
of SPRY1 to 55% in young muscle stem cells diminished their
capacity to self-renew the reserve cell pool to a level similar to
that observed in elderly cells (Figure 5D). It is noteworthy that
the number of mononucleated differentiated cells (expressing
MyHC) remained low (about 3%; Figure S4D) and the number
of nuclei per myotube was unchanged (Figure S4E), suggesting

1176 Cell Reports 13, 1172–1182, November 10, 2015 ª2015 The Authors

Figure 5. Shutdown of Quiescence Pathways in Elderly Muscle Stem Cells Is Rescued by Demethylation; Knockdown of SPRY1 Diminishes
the Pool of Reserve Cells
(A) Change in DNA methylation of genes involved in myogenic differentiation and quiescence. Each bar represents a significantly altered CpG site (multiple sites
for some genes); asterisks indicate sites within upstream regulatory regions.
(B) Transcript levels and protein localization of genes involved in quiescence pathways. The mRNA levels are means ± SEM (n = 5–7 per group) and were
normalized to B2M. Significance against young-derived cells is indicated (*p < 0.05, **p < 0.01).
(C) DNA demethylation with 5-Aza-20 -deoxycytidine in elderly cultures increased the mRNA levels of SPRY1. The mRNA levels are means ± SEM (n = 3 per group)
and were normalized to B2M. Significantly different from young cells, **p < 0.01.
(D) Inhibition of SPRY1 expression in elderly muscle stem cells treated with 5-Aza-20 -deoxycytidine diminished their capacity to form a pool of reserve cells. In
aged cells treated with 5-Aza-20 -deoxycytidine, the pool of reserve cell was diminished at day 3 of differentiation following knockdown of SPRY1 (si-Sprouty)
compared to controls (Cont and si-Luc). White arrows indicate reserve cells. PAX7, green; MyHC, red; nuclei, blue. Scale bar, 50 mm. Mean values (±SEM) are as a
percentage of the mononucleated cells. Significant differences with controls are indicated (*p < 0.05 compared with si-Luc).
(E) Inhibition of SPRY1 expression in young muscle stem cells diminished their capacity to form a pool of reserve cells. In young cells at day 3 of differentiation, the
reserve cell pool was diminished following knockdown of SPRY1 (si-Sprouty) compared to controls (Cont and si-Luc). White arrows indicate reserve cells. PAX7,
green; MyHC, red; nuclei, blue. Scale bar, 50 mm. Mean values (±SEM) are as a percentage of the mononucleated cells. Significant differences with controls are
indicated (**p < 0.01 compared with si-Luc; ***p < 0.001 compared with Cont). See also Figure S4 and Table S4.

that the sprouty1 pathway, despite its strong regulation of quiescent fate, does not regulate myogenic differentiation. Altogether,
our data evidence a downregulation of the sprouty1 self-renewal
pathway by DNA methylation in elderly muscle stem cells, which
inhibits quiescence and may contribute to the age-associated
decrease in the pool of muscle stem cells.
In this context, we wanted to check whether FGF2, an antagonist regulator of sprouty1 pathway that is secreted by myofibers
(Chakkalakal et al., 2012), was differently expressed between
young and elderly murine myotubes. We could not detect any
differences in FGF2 mRNA level between young and elderly myotubes (Figure S4F). However, we observed a significantly higher

level of FGF2 mRNA in elderly muscle biopsies (Figure S4G),
suggesting that FGF2 is differentially regulated in vivo and may
act synergistically with DNA methylation to repress the quiescence pathway in elderly stem cells.
DISCUSSION
Changes in stem cell content play a key role in tissue homeostasis, regulating the balance between growth and atrophy in skeletal muscle (Brack et al., 2005; Verdijk et al., 2014). However,
although a loss of stem cells has been evidenced with aging,
little is known about the mechanisms involved. In this study,

Cell Reports 13, 1172–1182, November 10, 2015 ª2015 The Authors 1177

performed on human muscle stem cells isolated from seven
young and 14 elderly subjects while carefully controlling for division number to avoid artifacts due to senescence, we showed
that DNA methylation is an age-sensitive upstream regulator of
genes controlling cell quiescence and that it acts chiefly through
suppression of the sprouty1 pathway to impair the self-renewal
capacity of the elderly muscle stem cell compartment.
Two key features of this work were that, first, we verified the
myogenic purity immediately following each thawing of frozen
stocks; this was important because contaminant populations
such as fibroblasts may senesce more rapidly than myoblasts,
thereby giving a false impression of myoblast senescence and
potentially introducing bias into measures such as the fusion index. Second, and more importantly, all experiments were carried
out at a division number of less than 12. We have shown previously that later divisions begin to show signs of senescence,
including a lower proliferation rate even in strong proliferationinducing media (20% fetal bovine serum [FBS]) (Barberi et al.,
2013). It is important to distinguish control of division number
(as calculated here and in previous work [Barberi et al., 2013])
from control of passage number: primary isolates from elderly
subjects are less numerous, thus initial culture is usually at lower
cell density so that more divisions are required to reach the first
passage. These two features of our work may be relevant to the
fact that, like several previous studies (Alsharidah et al., 2013;
Renault et al., 2002) but unlike a recent report by Sousa-Victor
et al. (2014), we did not observe senescence in elderly primary
myoblasts. We also note that our previous study of these same
primary human myoblasts showed that levels of p16 expression,
while increasing markedly with division number, remained unchanged between young and elderly cultures (Barberi et al.,
2013).
Consideration also should be given to the physiological history of muscle. Muscle growth during early post-natal development results from muscle precursor cells fusing with the
muscle fiber, as shown in rat (Moss and Leblond, 1971) and
mice (White et al., 2010), but this accretion is completed by
21 days postnatally in mice (Duddy et al., 2015; White et al.,
2010). Similarly, muscle growth is complete in young human
adults (Verdijk et al., 2014) and subsequent myonuclear turnover is then low during adulthood, with myonuclear turnover
being estimated at 15 years (Spalding et al., 2005). Our observations of similarity between cells of elderly and young subjects, in terms of capacity to proliferate, lifespan, p16 expression, and telomere length, confirm that their mitotic age is
largely unaffected by aging in accordance with a very slow
turnover during adulthood.
Our study shows that the sprouty1 pathway is an important
regulator of human myoblast quiescence and that this pathway
is suppressed by methylation during aging. This was confirmed
by both SPRY1 knockdown and demethylation in young and
old cells and by in vivo transplantations. A further confirmation
would have been to transduce young myoblasts with a small
hairpin RNA (shRNA) SPRY1 knockdown construct and then
carry out in vivo transplantation. However, the lengthy antibiotic
selection required for this assay places it at the technical limits of
what could be achieved without reaching cell senescence,
potentially leading to artifactual findings.

It is important to note that the age-associated changes in stem
cell fate identified by our study in no way challenge the existence
of asymmetric division in human myoblasts. Our results consistently show that a proportion of reserve cells is maintained in
both young and old cultures—what changes is the size of this
proportion. In both young and old cultures, a percentage of
mononucleated cells continued to express the PAX7 quiescence
marker after differentiation was induced (12% of all nuclei in
young cultures and 3.6% in elderly cultures). Thus, asymmetric
division is present but less frequent in elderly cultures.
Several mechanisms have been proposed to be responsible
for muscle stem cell loss with aging, including apoptosis and
cellular senescence. Collins et al. (2007) showed that aged murine muscle stem cells are prone to in vitro apoptosis with an
accumulation of damaged DNA. In contrast, more recent studies
did not observe any sign of apoptosis or cell death in cultured
elderly murine and human muscle stem cells (Alsharidah et al.,
2013; Cousin et al., 2013). Comparing cultures derived from
young and old adult human subjects, we confirmed in vitro that
apoptosis is a very rare event.
DNA methylome analysis of elderly compared to youngderived cells identified an increased methylation of certain quiescence pathways, but reduced methylation of a marker of differentiation. This was consistent with observations of downstream
processes, such as the following: (1) an overall transcriptomic
molecular signature of increased myogenic differentiation (Figure 3; Figure S2B); (2) changes in the expression of myogenic
differentiation markers (Figure 3; Figures S2C and S4C); and
(3) the downregulation of quiescence pathways, such as that
of sprouty1 (Figure 5). This latter finding in human cells is in
agreement with the recent report that elderly murine muscle
stem cells lose markers of quiescent fate, such as sprouty1
and Pax7 (Chakkalakal et al., 2012). The downregulation of
quiescence pathways results in a decreased number of reserve
cells in elderly cultures and a failure to self-renew the stem cell
pool in vivo. Our results distinguish two major characteristics
of the aged muscle progenitors as follows: (1) myogenic potential
is preserved in elderly human muscle stem cells, as shown previously in the mouse (Brack et al., 2007; Collins et al., 2007; Conboy et al., 2005) and in humans (Alsharidah et al., 2013); and (2)
elderly muscle stem cells have an impaired ability to return to
quiescence once they are activated, due to the suppression of
quiescence pathways, chiefly SPRY1, by DNA methylation.
The impact of this on the stem cell population is modeled in Figure 6 and explains its disappearance with age.
Several pathways are implicated in muscle stem cell quiescence, including notch 1 (Brack et al., 2007; Bro¨hl et al., 2012;
Conboy et al., 2003; Wen et al., 2012) and sprouty1 (Abou-Khalil
and Brack, 2010; Shea et al., 2010). In this study, the loss of the
reserve pool in elderly muscle stem cells correlates with an upregulation of WNT3A (Figure S4C), WNT being an antagonist of
notch pathways (Brack et al., 2007; Bro¨hl et al., 2012; Conboy
et al., 2003; Wen et al., 2012), and with a downregulation of
NOTCH1 and its co-regulator MAML1 (Figure 5). Notch has
been shown to upregulate Pax7 (Wen et al., 2012). Demethylating the DNA did not markedly rescue expression levels of the
notch 1 pathway, despite rescuing reserve cell commitment.
FGF2 is secreted by murine myofibers (Chakkalakal et al.,

1178 Cell Reports 13, 1172–1182, November 10, 2015 ª2015 The Authors

Figure 6. A Model for the Inhibition of Quiescence by DNA Methylation and Its Consequences on the Maintenance of the Stem Cell Pool
During Tissue Repair
DNA methylation increases with aging in muscle stem cells. During regeneration/reparation, muscle stem cells are activated in both young and elderly subjects.
Once activated, the cells proliferate. In youth, the sprouty1 pathway is activated upon exit from the cell cycle, driving some cells toward quiescence, thus replenishing the pool of reserve cells. In contrast, hypermethylation of DNA in elderly stem cells suppresses sprouty1, inhibiting re-quiescence to prevent full
replenishment of the reserve cell population, which results in its gradual loss with aging.

2012) and by murine cardiac fibroblasts (Thum et al., 2008), and it
stimulates an antagonist pathway of sprouty1. Our failure to
observe any age-associated change in muscle stem cell FGF2
expression supports methylation as a cell-intrinsic regulator of
the sprouty1 pathway, but it does not rule out the possibility
that FGF2 (which we did observe to be increased with age in
muscle biopsies) exerts an influence in vivo.
The downstream effects of SPRY1 demethylation or siRNA
knockdown in young human cells (present work), or genetic
knockout in the mouse (Shea et al., 2010), show the importance
of this pathway in driving the quiescence fate of muscle stem
cells and, thus, in the maintenance of the stem cell pool. As
noted above, the expression level of SPRY1 does not interfere
with the differentiation pathway, since knockdown did not
change the number of nuclei per myotube (Figure S4E). Similarly,
a sprouty1 knockout murine model showed the same capacity
as control mice to regenerate, with unchanged myofiber number
and cross-section area after induction of the degeneration/
regeneration process (Shea et al., 2010). Shea et al. (2010) and
Abou-Khalil and Brack (2010) suggested that sprouty1 is
required for the self-renewal of muscle stem cells. Based on
the results presented in this report, we propose that the role of
sprouty1 is to trigger the commitment of cells toward a quiescent
fate, without interfering with myogenic differentiation, the latter
instead being driven by an aging-associated reinforcement of
myogenic specialization, as discussed above.

Our findings follow those of others showing that stem cell
behavior is affected by age-related changes in epigenetic status
(Liu et al., 2013; Oberdoerffer et al., 2008; Rando and Chang,
2012), but we have linked this to a specific pathway. Modulation
of stem cell renewal by methylation may not be restricted to muscle stem cells: we note, for instance, that the number of hematopoietic stem cells increases with aging (Pollina and Brunet, 2011)
while their DNA becomes globally hypomethylated (Bocker et al.,
2011). A fundamental question is whether the epigenetic status of
the stem cell is regulated by its local environmental niche. Accumulated evidence suggests that muscle fibers secrete growth
factors, microRNAs, and components of the extracellular matrix
into their environment (Le Bihan et al., 2012; Duguez et al.,
2013; Henningsen et al., 2010; Roca-Rivada et al., 2012). Another
environmental factor is oxidative stress, which can have local effects on the activity of histone-deacetylases and DNA methylases (Cencioni et al., 2013). Oxidative stress in aging muscle is
well characterized and is related to mitochondrial dysfunction in
muscle fibers (Marzetti et al., 2013) and increased inflammation
(Franceschi et al., 2007; see Thorley et al., 2015 for review). We
have shown that epigenetic manipulation of the pathways
involved in quiescence can modulate the formation of the reserve
cell pool. Determining if the muscle secretome changes with aging, and in turn alters the epigenetic status of these stem cells,
may suggest strategies to improve human health in age-related
diseases associated with stem cell dysfunction.

Cell Reports 13, 1172–1182, November 10, 2015 ª2015 The Authors 1179

EXPERIMENTAL PROCEDURES
See the Supplemental Experimental Procedures for descriptions of the cell
culture conditions, qRT-PCR, methylated DNA quantification, muscle cell injection in mice, telomere length measurement, proliferation and senescence
assays, immunolabeling, 5-Aza-20 -deoxycytidine treatment, and knockdown
of SPRY1 using siRNA.
Participants and Ethical Approval
Seven muscle biopsies were obtained from the Bank of Tissues for Research
(BTR, a partner in the EU network EuroBioBank) in accordance with European
recommendations and French legislation. Fifteen muscle biopsies were obtained from Leiden University Medical Center (LUMC) after approbation of
the local medical ethical committee in the context of a European study
(HEALTH-2007-2.4.5-10: Understanding and combating age related muscle
weakness ‘‘MYOAGE’’). Written informed consent was obtained from all
patients. All biopsies were isolated from quadricep muscle. Seven young
(15–24 years old) and 14 old (72–80 years old) healthy subjects were included.
Samples and Cell Culture
Briefly, the muscle biopsies were dissociated mechanically and cultured as
previously described (see the Supplemental Experimental Procedures for
more detailed information).
Gene Expression Profiling
An aliquot of 150 ng high-quality total RNA from each sample was used for the
mRNA expression profiling. Samples were analyzed using Illumina Gene
Expression BeadChip Array technology). See the Supplemental Experimental
Procedures for more details.
GSEA and Enrichment Mapping
Gene set enrichment analysis (GSEA) was applied to genes that were significantly altered in elderly versus young muscle stem cells at day 1 and day 3
of differentiation. Probe sets were first filtered for p value < 0.05; then, in cases
where multiple probe sets for a given gene were significantly altered, the probe
set with the greatest absolute fold change was retained. Fold-change values
were log2 transformed and subjected to pre-ranked GSEA using the GSEA
tool. A total of 1,053 gene sets were tested for their positive or negative enrichment. The majority of these were downloaded from the Molecular Signatures
Database (MSigDB, http://www.broadinstitute.org/gsea/msigdb/), including
866 gene ontology biological processes and 46 sets identified by a search
of the MSigDB for muscle-related sets. Several custom-made sets derived
from publications chosen by us also were added, including those listed in
the Results. For statistical testing, data were permuted 1,000 times and the
‘‘meandiv’’ normalization algorithm was applied. A gene set was tested if
10–500 genes from the significantly altered list were present in the gene set.
Gene sets that were found by enrichment analysis to be highly significantly
enriched (p < 0.05 and false discovery rate [FDR] < 0.025) were graphically presented using the enrichment mapping plugin for Cytoscape. The overlap coefficient was set to 0.2 with a combined constant of 0.5.
Global DNA Methylation Studies
Genomic DNA extracted from young and elderly muscle cells differentiated for
24 hr was used in the DNA methylation studies (n = 3 per group). The Infinium
HumanMethylation 450 BeadChip (Illumina), which includes 485,577 cytosine
positions in the human genome, was utilized for genome-wide DNA methylation screening. See the Supplemental Experimental Procedures for more
details.
DNA Methylation Data Analysis
The p values were calculated to identify failed probes as per Illumina’s recommendations and no arrays exceeded our quality threshold of >5% failed
probes. In addition, we removed CpG sites on the X and Y chromosomes
(and removed from the analysis CpG sites that contained a SNP or a SNP
within 10 bp of the methylation probe). Raw data were normalized using Illumina’s control probe scaling procedure and background subtracted.

The b values were imported into Partek Genomics Suite (version 6.6) and underwent a logit transformation (M value). The M value is calculated as the log2
ratio of the intensities of the methylation probes versus unmethylated probe.
The problem of heteroscedasticity in the high and low ranges of methylation
(<0.2 and R0.8) is resolved with the transformation of b value to M value.
The data were analyzed using ANOVA models, with M value for each site as
the dependent variable and response (old versus young) as the independent
variable. For Circos visualization, counts of significantly altered CpG sites
within bins of equal size (10 Mb) were calculated across all chromosomes using R. Bins were then displayed using Circos and colored according to counts,
with color incrementally darkening from white to red in increments of 25, up to
a maximum darkness of red at counts >150.
The lists of genes hypermethylated (200%–15%) and hypomethylated
(30%–200%) were imported into DAVID functional annotation software developed by Huang et al. (2009a, 2009b) mapped to their official gene symbol. We
used the clustering algorithm of DAVID (version 6.7) with high clustering stringency (initial and final group membership, 5; similarity term overlap, 3; multiple
linkage threshold, 0.5; and similarity threshold, 0.85). This identified several
functional annotation clusters with a Fisher exact p value < 3.7 3 102 and
an enrichment score above 2 (geometric mean in log scale of member’s p
values, significance being considered at 1.5). See the Supplemental Experimental Procedures for more details.
Statistical Analysis
All values are presented as means ± SEM. Student’s t test was used to
compare differences between young and elderly samples. A KolmogorovSmirnov test was used to compare the distribution of myotube nuclear
numbers in young and elderly cell culture and the distribution of the fiber
size containing human nuclei from young or elderly donor. One-way ANOVA
was used to evaluate the time course changes in reserve cells and in mononucleated cells positive for MyHC, followed by a Newman-Keuls multiple
comparison test. Differences were considered to be statistically different at
p < 0.05.
ACCESSION NUMBERS
The accession numbers for the data reported in this paper are GEO:
GSE52699 and GSE53302.
SUPPLEMENTAL INFORMATION
Supplemental Information includes Supplemental Experimental Procedures,
four figures, and four tables and can be found with this article online at
http://dx.doi.org/10.1016/j.celrep.2015.09.067.
AUTHOR CONTRIBUTIONS
S.D., V. Mouly, and G.B.-B. conceptualized the study. V. Mouly and G.B.-B.
obtained funding for the project. S.D. performed and analyzed the experiments. W.J.D. performed the bioinformatics analysis. E.N. performed the
transplantation experiments. S.G. performed the microarray analysis. B.H.
and J. Devaney performed the DNA methylome assay and associated statistical analysis. S.D., Z.G.O., C.L., and A.B. measured the cell division speed.
A.W. measured the telomere length. A.B. extracted the cells from human biopsies and measured their lifespans. A.B., V. Mariot, and S.D. performed the
5AZA and siRNA knockdown experiments. S.D. and Z.G.O. performed qRTPCR and immunostaining. A.B., W.J.D., Z.G.O., G.B.-B., V. Mouly, J. Dumonceaux, and S.D. wrote, discussed, and edited the manuscript. S.D. supervised
the project.
ACKNOWLEDGMENTS
We would like to thank Drs. Capucine Trollet and Denis Furling for fruitful discussion. We thank Nicolas Martin and Kamel Mamchaoui for their technical
support. We thank the Human Cell Culture Platform of the Institute of Myology.
This work was financed by the EU FP7 Programme project MYOAGE (contract

1180 Cell Reports 13, 1172–1182, November 10, 2015 ª2015 The Authors

HEALTH-F2-2009-223576), the ANR Genopath-INAFIB, the Agence Franc¸aise
pour la Lutte contre le Dopage (AFLD), the CNRS, INSERM, the University
Pierre and Marie Curie Paris 6, and the Association Franc¸aise contre les
Myopathies (AFM). It also partially was supported by NIH National Center for
Medical Rehabilitation Research (NCMRR)/National Institute of Neurological
Disorders and Stroke (NINDS) 2R24HD050846-06 and Eunice Kennedy
Shriver National Institute of Child Health and Human Development (NICHD)/
NINDS 5R24HD050846-08 (NCMRR-DC Core Molecular and Functional
Outcome Measures in Rehabilitation Medicine), NIH National Center for
Research Resources (NCRR) UL1RR031988 (GWU-CNMC CTSI), and NIH
NINDS (DDRC 1P30HD40677-06). Contents are solely the responsibility of
the authors and do not necessarily represent the official views of the NIH.
The monoclonal antibodies Pax7 and MF20 developed by A. Kawakami and
D.A. Fischman, respectively, were obtained from the Developmental Studies
Hybridoma Bank developed under the auspices of the NICHD and maintained
by The University of Iowa, Department of Biology.

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