Stem cell aging in adult progeria

Epigenetic modifications on DNA and histones change with age and vary in different
cell types, disease states (e.g., cancers), and developmental and differentiating
stages 27]. Epigenetic marks that link to aging include gain of H3K4 and H4K20 trimethylation,
H4K16 acetylation, and decrease in H3K9 and H3K27 trimethylation (Fig. 1a) 28]. H4K20 trimethylation is a marker for constitutive heterochromatin. Increase of H4K20
trimethylation is found in aging tissues of rats and also in patients of HGPS 29], 30]. Epigenetic changes on histone in WS are largely unknown. A recent report suggests
that heterochromatin alteration, as reflected by global loss of H3K9 trimethylation
and reduction of SUV39H1 (protein that trimethylates H3K9) and HP1?, is found in WRN knockout cells 31]. The group concludes heterochromatin disorganization is a potential determinant of
premature aging in WRN-deficient cells.

Fig. 1. Aging-associated epigenetic changes on histone modifications. a In aged somatic and stem cells, chromatin is progressively changed. H3K4me3, H4K20me3,
and H4K16ac are increased whereas H3K9me3, H3K27me3, and H3K9ac are decreased. Chromatin
remodeling proteins (e.g., HP1? and NuRD) and DNA methylation are also decreased globally
(not shown). Changes of chromatin structure and organization affect transcriptional
activity and genomic stability related to aging. b SIRT1 and SIRT6 are important aging regulators. SIRT1 deacetylates H3K9 and H4K16
and increases H3K9me3 through SUV39H1. SIRT6 also deacetylates H3K9 at telomeric regions.
Hyperacetylation of telomeric H3K9 impairs association of the WRN protein with telomeres,
hence, leading to premature aging

DNA methylation is also drifted in aged cells. Globally, hypomethylation is found
at various organs/cell types with advanced age, for examples, blood and dermal fibroblasts.
Repetitive sequences such as Alu and LINE-1 show decreased 5mC content with age, suggesting a mechanistic link to the increased
genomic instability due to the loss of global methylation 32]. However, some locus-specific regions, especially for those at CpG islands, show
hypermethylation as cells age 33]. Some of the hypermethylated genes are putative tumor suppressor genes, extrapolating
that epigenetic silencing is another risk factor for increased neoplastic events in
elderly people. By profiling a number of WS and HGPS patients, aberrant DNA methylation
profile is detected. For WS, differential methylation on CpG sites is located in genes
enriched for the IKB kinase/NF-kappaB signaling and proteinaceous extracellular matrix
formation 34]. These candidate genes may be involved in the phenotypic changes observed during
premature aging. Interestingly, WRN itself is also controlled by epigenetic regulation. Epigenetic downregulation of
the WRN gene is found in many age-related diseases, e.g., cataract and cancer 35], 36].

Unlike genetic mutations, epigenetic modifications are reversible, raising the question
of whether aging and longevity can be changed if we are able to change the age-associated
epigenome. A family of genes known to promote longevity are actually enzymes for epigenetic
modifications. The sirtuin gene family plays a critical role in regulating aging.
Among the seven mammalian sirtuin genes, SIRT1, SIRT3, and SIRT6 have been shown to improve health through regulating diverse processes 37]. Here we briefly discuss the roles of SIRT1 and SIRT6 in stem cells and aging.

As a histone deacetylase, SIRT1 not only deacetylates H4K16 and H3K9 but also regulates
the histone methyl-transferase SUV39H1 during heterochromatin formation 38]. Loss of SIRT1 reduces H3K9 trimethylation and impairs localization of heterochromatin
protein 1 (HP1), an epigenetic alteration associated with aging. Although Sirt1 overexpression in mice does not increase longevity, it does improve healthy aging
such as wound healing and reduced incidence of cancer 39]. In another study, Sirt1 overexpression specifically in the brain extends lifespan through upregulation of
Ox2r by cooperation with Nkx2-1 40]. In addition to the epigenetic regulatory role, Sirt1 also participates in repairing
DSB in response to oxidative stress and helps to combat genomic instability and age-dependent
transcriptional changes 41]. The role of SIRT1 in regulation of adult stem cell aging and homeostasis is evident.
SIRT1-deleted young HSCs show skewed differentiation with reduced lymphoid compartment,
anemia, and expression pattern similar to aged HSCs 42]. In human MSC derived from various adult tissues, SIRT1 demonstrates a beneficial
effect on long-term growth and differentiation potential 43], 44]. Because SIRT1 is able to delay premature senescence, it also plays a role in progeria.
Lamin A, the mutant form causing laminopathy-based premature aging, interacts with
and activates Sirt1. Such interaction is interrupted in progeroid cells, leading to prominent decline
of adult stem cells in the progeria mouse model 45]. For WS, expression and localization of WRN is modulated by SIRT1 and PML 46]. SIRT1 is reported to deacetylate WRN 47]. Acetylation of the WRN protein enhances its stability by inhibiting ubiquitination
48]. SIRT1 affects translocation of the WRN protein from nucleolus to nucleoplasm when
DNA repair is required 49].

SIRT6, another important member of the sirtuin family, has other unique biological functions.
SIRT6 expression declines significantly in the aged brain, which is associated with
increased H3K9 acetylation 50]. Decreased SIRT6 expression is also found in HGPS and senescent cells but unknown
for WS cells 51]. Sirt6 knockout mice exhibit premature aging and developmental abnormalities including profound
lymphopenia and metabolic defects 52]. On the other hand, overexpression of Sirt6 increases lifespan in male but not female
mice. Transgenic male mice have a lower serum level of IGF1, higher level of IGF-binding
protein 1, and altered phosphorylation levels of major components of IGF1 signaling
53]. Restoring SIRT6 expression in HGPS cells impedes premature senescence and formation
of dysmorphic nuclei 51]. SIRT6 is a histone H3K9 deacetylase that maintains repressive telomeric chromatin.
Repressive heterochromatin at telomeres is an epigenetic mechanism for silencing telomere-proximal
genes, which is disrupted in the absence of SIRT6 54]. Mechanically, SIRT6 specifically associates with telomeres where it deacetylates
H3K9 which is required for stable association with WRN. SIRT6-depleted cells show
telomere dysfunction with premature cellular senescence that resembles WS cells 55]. Besides the role in telomere function, SIRT6 also helps maintain genomic stability
and regulates metabolic homeostasis, another two hallmarks of aging 56]. In summary, SIRT1 and SIRT6 are the most well-known Sir2 orthologs that contribute to aging partially through epigenetic regulation of the
“aging” epigenome (Fig. 1b).