Regulation of Stem Cell Aging by Metabolism and Epigenetics.pdf

Cell MetabolismReviewRegulation of Stem Cell Aging by Metabolismand EpigeneticsRuotong Ren,1,2,3Alejandro Ocampo,4Guang-Hui Liu,1,2,3,5,*and Juan Carlos Izpisua Belmonte4,*1National Clinical Research Center for Geriatric Disorders,Xuanwu Hospital of Capital Medical University,Beijing 100053,China2National Laboratory of Biomacromolecules,CAS Center for Excellence in Biomacromolecules,Institute of Biophysics,Chinese Academy of Sciences,Beijing 100101,China3University of Chinese Academy of Sciences,Beijing 100049,China4Gene Expression Laboratory,Salk Institute for Biological Studies,10010 North Torrey Pines Road,La Jolla,CA 92037,USA5Beijing Institute for Brain Disorders,Beijing 100069,China*Correspondence:(G.-H.L.),belmontesalk.edu(J.C.I.B.)http:/dx.doi.org/10.1016/j.cmet.2017.07.019Stem cell aging and exhaustion are considered important drivers of organismal aging.Age-associateddeclines in stem cell function are characterized by metabolic and epigenetic changes.Understanding themechanisms underlying these changes will likely reveal novel therapeutic targets for ameliorating age-asso-ciated phenotypes and for prolonging human healthspan.Recent studies have shown that metabolism playsan importantrole inregulating epigeneticmodifications andthat this regulationdramatically affectstheagingprocess.This review focuses on current knowledge regarding the mechanisms of stem cell aging,and thelinks between cellular metabolism and epigenetic regulation.In addition,we discuss how these interactionssense and respond to environmental stress in order to maintain stem cell homeostasis,and how environ-mental stimuli regulate stem cell function.Additionally,we highlight recent advances in the developmentof therapeutic strategies to rejuvenate dysfunctional aged stem cells.IntroductionAging can be defined as a complex,time-dependent processthat affects multiple tissues and organs leading to a progressivereduction in physiological integrity and the degeneration of tis-sue,organ,and organismal function.Understanding the causeof aging has been an area of interest throughout human history.During the past 30 years,aging research has dramaticallyadvanced,beginning with the initial discoveries that certainCaenorhabditis elegans mutants live significantly longer thantheir wild-type counterparts(Klass,1983).The molecular andcellular mechanisms that extend C.elegans lifespan,as wellas populations of human centenarians,have been the focusof intensive investigation using interdisciplinary approaches.Several hallmarks of aging(e.g.,genomic instability,telomereattrition,epigenetic alteration,cellular senescence,stem cellexhaustion,mitochondrial dysfunction,dysregulated nutrientsensing,loss of proteostasis,and altered intercellular communi-cation)have been described as major contributors to cellularaging.In addition,aging has been identified as the primary riskfactor for the development and progression of certain diseases,such as cancer,diabetes,cardiovascular disorders,and neuro-degenerative diseases(Lopez-Otin et al.,2013).Adultstem cellsare essential forthe maintenance of tissueho-meostasis and regeneration.Consequently,the quantitativeand qualitative decline in stem cell function during life,knownas stemcell exhaustion,has beenproposed asone of the driversof aging(Lopez-Otin et al.,2013).Supporting this notion,age-associated phenotypes can be restored by the induction ofstem cell rejuvenation in vivo(Rando and Chang,2012;Lavasaniet al.,2012).Therefore,characterizing the mechanisms of stemcell aging will be critical for ultimately understanding the agingprocess and for developing novel strategies to ameliorate age-associated phenotypes and treat age-related diseases.Never-theless,the complexity of stem cell biology(compared withterminally differentiated somatic cells)may complicate ourunderstanding of the molecular mechanisms governing stemcell aging.Theroleofmetabolisminstemcellaginghasrecentlybeenthefocus of intense research.At this moment,thereis increasing ev-idence that metabolic signal pathways are strongly associatedwith aging.Evidence supporting this connection suggests that:(1)decreased nutrient signaling can extend lifespan;(2)anabolicsignaling accelerates aging;and(3)pharmacological manip-ulation of metabolic pathways extends organismal lifespan(Fontana et al.,2010;Harrison et al.,2009).In addition,recentevidence suggests that cellular metabolic pathways can alterepigenetic states and that these changes can affect organismalaging and longevity(Tatar and Sedivy,2016;Berger and Sas-sone-Corsi,2016).Here,we highlight the mechanisms by which metabolic path-ways contribute to the regulation of chromatin,and how thesespecific processes are thought to affect stem cell exhaustionand aging phenotypes.We also discuss fundamental questionsregarding stem cell aging that remain to be answered,includingwhat are the genetic or epigenetic drivers of stem cell aging,andwhether it might be possible to restore redox homeostasisand nutrient-sensing pathways to reset the epigenetic clock ofstem cell aging.Drivers of Stem Cell Exhaustion during AgingAdult stem cells play a vital role in maintaining tissue homeosta-sis through repair and regeneration during life(Goodell andRando,2015).Stem cell exhaustion,defined as the decline instem cell number and function,is observed in virtually all tissues460Cell Metabolism 26,September 5,2017 2017 Elsevier Inc.andorgansmaintainedbyadultstemcells,suchastheforebrain,bone,andmuscle(ConboyandRando,2012;Gruberetal.,2006;Molofsky et al.,2006).In addition,age-associated changesin hematopoietic stem cell(HSC)differentiation lead to the pro-duction of fewer adaptive immune cells.This potentially leadsto anemia and myeloid malignancies in aged organisms(Shawet al.,2010).Moreover,stem cell exhaustion is frequentlyobserved in human age-related diseases and rare genetic disor-ders.As an example,a premature depletion of mesenchymalstem cells(MSCs)is observed in patients with Hutchinson-Gil-fordprogeriasyndrome(HGPS)(Liuetal.,2011a,2011b),Wernersyndrome(WS)(Zhangetal.,2015),andFanconianemia(FA)(Liuet al.,2014);neural stem cells(NSCs)show defects on neuronaldifferentiation and DNA repair in patients with Parkinsons dis-ease(PD)(Liu et al.,2012c)and xeroderma pigmentosum(XP)(Fu et al.,2016);and HSCs are deregulated in FA(Liu et al.,2014).For these reasons,age-associated stem cell exhaustionis considered a hallmark of aging(Lopez-Otin et al.,2013).Theobservation that stem cell exhaustion is one of the most signifi-cant hallmarks of aging has led to many questions,including:(1)what are the mechanisms underlying stem cell senescenceand exhaustion during organismal aging?and(2)is it possibleto delay the exhaustion of stem cells or to rejuvenate senescentstem cells to ameliorate age-associated phenotypes?In this re-gard,many cellular hallmarks of aging act as major drivers ofthe quantitative and qualitative changes observed in stem cellsduring aging.These hallmarks,which are in many instancesdirectly related to the role and features of stem cells,includegenomic instability,telomere attrition,epigenetic alterations,cellular senescence,mitochondrial dysfunction,loss of proteo-stasis,and altered intercellular communication.Importantly,areversal of aging phenotypes can be induced in vivo by stemcell rejuvenation,opening the door for potential anti-aging inter-ventions based on approaches aiming at the improvement ofstem cell function(Rando and Chang,2012).Stemcellsareextremelyvulnerableandtheirhomeostasiscanbe challenged by many factors directly leading to decreasedproliferation,which is one of the major features of stem cell ag-ing.In aged mice,HSCs exhibit decreased rates of cell division,indicating a general decline in cell-cycle activity(Rossi et al.,2007).Replication stress caused by age-related cell-cycle de-fects(e.g.,DNA damage or chromosome disorganization)candiminish HSC functional activity,leading to decreased bloodproduction and impaired therapeutic potential in transplantationassays(Flach et al.,2014).As part of the underlying mecha-nisms,increased levels of p16INK4a(a cell-cycle regulator thatinhibits cell-cycle progression)and the accumulation of DNAdamage have been closely associated with declines in stemcell populations during aging(Janzen et al.,2006;Rossi et al.,2007).Consequently,rejuvenation of cell-cycle activity andengraftment capacity are observed in INK4a-deficient agedHSCs(Janzen et al.,2006).In contrast,loss of quiescence andexcessive proliferation can also cause premature exhaustion ofstem(progenitor)cells due to the accelerated exhaustion ofstem cell populations.For example,loss of p21 leads to the pre-mature exhaustion of HSCs and NSCs in mice(Cheng et al.,2000;Kippin et al.,2005).Moreover,basal levels of autophagyhelp to maintain mouse satellite cells(muscle stem cells)in aquiescent state,whereas autophagy impairment causes senes-cence of satellite cells,leading to proteostasis imbalance andmitochondrialdysfunction(Garcia-Pratetal.,2016).Additionally,autophagy has been reported to actively preserve quiescenceand stemness of old mouse HSCs by suppressing cellular meta-bolism(Ho et al.,2017).Conversely,restoration of autophagy ingeriatric satellite cells can reverse their senescent phenotype.Moreover,while dietary restriction promotes the proliferation ofintestinal stem cells(ISCs)through the cooperation of mamma-lian target of rapamycin complex 1(mTORC1)and Sirtuin 1(SIRT1)(Igarashi and Guarente,2016),rapamycin(an inhibitorof mTOR)can significantly repress the expansion of ISCs.Telo-mere attrition represents an additional driver of age-related stemcellexhaustioninmultipletissues(SharplessandDePinho,2007;Flores et al.,2005).Lastly,genome instability,as a consequenceofmultipletypesofstressordamage,constitutes anotherimpor-tant cause of the dysfunction and decline of adult stem cells dur-ing aging.For instance,deficiency of the DNA helicase WRNresults in WS,a premature aging syndrome also known as adultprogeria,which is characterized by features of physiologicalaging in young individuals(Kudlow et al.,2007;Lopez-Otinet al.,2013).Deficiency of WRN protein in human MSCs notonly triggers activation of the DNA damage response,but alsoinduces the instability of heterochromatin,which has recentlybeen suggested to drive MSC exhaustion and,subsequently,organismal aging(Zhang et al.,2015).Epigenetic Mechanisms of Stem Cell AgingThere is mounting evidence that epigenetics plays an importantrole in driving organismal aging(Lopez-Otin et al.,2013;Senet al.,2016;Benayoun et al.,2015;Booth and Brunet,2016;Pal andTyler,2016).Nucleosomes represent thebasicstructuralunits of chromatin and are composed of DNA wrapped arounda set of histone proteins.Gene expression is dynamically regu-lated by the interplay between transcription factors and epige-neticmodifiers,whichareenzymescapable of directlymodifyingDNA or the core histone variants,including H2A,H2B,H3,H4,H3.3,macroH2A,and H2A.Z.On the other hand,althoughheterochromatin domains established during early embryonicdevelopment are considered constant throughout an animalslifespan,aging triggers the loss of constitutive heterochromatinby telomere attrition,transcription changes at boundaries,anddisorganization of the nuclear periphery(Figure 1).The disorga-nizationofheterochromatincausesglobalandlocalalterationsinDNA methylation patterns,which are regularly observed in agingcells as consequences of reduced histone 3 lysine 9 trimethyla-tion(H3K9me3)levelsandheterochromatin-associatedproteins,such as heterochromatin protein 1(HP1)(Scaffidi and Misteli,2005;2006;Zhangetal.,2015).Furthermore,ithasbeendemon-strated that the aging of human adult stem cells is associatedwith diverse epigenetic alterations including global loss ofH3K9me3,decondensation of centromeric heterochromatin,physical attrition of telomeres,and changes in the nucleolusorganizer region related to ribosomal DNA(NOR-rDNA)(Renet al.,2017;Zhang et al.,2015;Liu et al.,2011a;Kubben et al.,2016;Deng et al.,2015;Ding et al.,2015;Fu et al.,2016;Yanget al.,2017;Wang et al.,2017).Unlike worms and flies,which are simple models for studyingthe regulation of aging and longevity at the organismal level,the aging process in mammalian systems is controlled by moreCell Metabolism 26,September 5,2017461Cell MetabolismReviewcomplex mechanisms in which stem cell aging may play crucialroles.Moreover,multiple lines of evidence suggest that epige-netic changes drive adult stem cell aging in mammals.Theseinclude HSCs,muscle stem cells(MuSCs)or satellite cells(Liuetal.,2013),andMSCs(Panetal.,2016;Zhangetal.,2015;Kub-ben et al.,2016).HSCsDuring aging,an increase in DNA damage and a decrease in theDNA repair capacity of HSCs has been shown to result in a pro-gressive loss of HSCs(Nijnik et al.,2007;Rossi et al.,2007).In addition,high levels of replication stress upon re-entry inthe cell cycle contribute to the functional decline in HSCs inold organisms(Flach et al.,2014).Despite the clear role ofDNA damage and replication stress during HSC aging,epige-netic dysregulation has been shown to be an important contrib-utor to HSC exhaustion.In this regard,epigenetic profiling ofyoung and old HSCs has revealed changes in H3K4me3 levelsacrossself-renewalgenesanddetectedincreaseinDNAmethyl-ation at genes related to differentiation,leading to defects in dif-ferentiation during HSC aging(Sun et al.,2014).In addition,theproliferation of mouse HSCs has been shown to be promotedby Sirtuin 6(Sirt6)deletion,as SIRT6 represses Wnt target genesby interacting with the transcription factor LEF1 and by deacety-lating H3K56Ac(Wang et al.,2016).Lastly,levels of bothH3K27me3 and H3K4me3 increase with age in mouse HSCs(Chambers et al.,2007),and changes in DNA methylation orH3K9 methylation during age induce mouse HSC differentiation(Challen et al.,2014;Mayle et al.,2015;Ugarte et al.,2015).MSCsSeveral studies have highlighted changes in the epigeneticregulation of the genome leading to a loss of self-renewal andosteoblast differentiation during aging in MSCs.As an example,a decreased expression of histone deacetylases(HDACs),together with a downregulation of polycomb group genes andupregulation of JMJD3 was observed in senescent MSCs(Jung et al.,2010).Similarly,changes in H3 acetylation but notDNA methylation were found to lead to reduced self-renewalandincreaseosteogenicdifferentiationaccompaniedbyincreased expression of osteogenic genes such as RUNX2 andALP(Li et al.,2011).On the other hand,inhibition of DNA meth-yltransferases with 5-azacytidine or small interfering RNA wasshown to induce senescence in MSCs by dysregulating notonly DNA methylation but also promoting changes in histonemarksonpromoterregions(Soetal.,2011).Importantly,patientswith WS,a disease caused by deficiency in WRN protein,whoexhibit phenotypes associated with premature cellular agingFigure 1.Interplay between Epigenetic and Genetic Instabilities in(Stem)Cell AgingDuring aging,major epigenetic ch