« Genomic and epigenomic regulation of adipose tissu inflammation in obesity » (Revue)
Genomic
and
epigenomic
regulation
of
adipose
tissue
inflammation
in
obesity
Amine Toubal1,3,4, Eckardt Treuter5, Karine Cle´ment1,2,3,4, and Nicolas Venteclef1,3,4
1InstituteofCardiometabolismandNutrition,Paris75013,France
2AssistancePublique-HoˆpitauxdeParis,Pitie´-Salpeˆtrie`reHospital,HeartandMetabolismDivision,Paris75013,France 3
InstitutNationaldelaSante´etdelaRechercheMe´dicale(INSERM)Unite´872,Team7Nutriomique,Paris75006,France
4Universite´PierreetMarieCurie-Paris6,CordeliersResearchCenter,Unite´MixtedeRecherche(UMR)S872,Paris75006,France 5KarolinskaInstitutet,DepartmentofBiosciencesandNutrition,14183Huddinge,Sweden
Chronic inflammationof adiposetissue is viewedas a hallmarkofobesityandcontributestothedevelopment oftype2diabetesandcardiovasculardisease.According tocurrentmodels,nutrientexcesscausesmetabolicand structural changes in adipocytes, which initiate tran- scriptionalprogramsleadingtotheexpressionofinflam- matory molecules and the subsequent recruitment of immune cells.Recent advancesin decipheringthe un- derlying mechanisms revealed that key regulatory eventsoccuratthegenomicandepigenomiclevels.Here we reviewthese advancesbecause they offer a better understandingofthemechanisms behindthecomplex obesogenicprograminadiposetissue,andbecausethey may help in defining new therapeutic strategies that prevent,restrict, and resolveinflammation inthe con- textofobesity.
Adiposetissueinflammation:ahallmarkofobesity Worldwidechangesinlifestylehavecausedaglobalobesity epidemic, with an estimate of over 700 million affected peoplein2015. Accordingly,health authoritiesincluding theWorldHealthOrganization(WHO)andtheAmerican Medical Association (AMA) promote the designation of obesityasanew‘disease’.However,theabsenceofasingle, clear,authoritative,andwidelyaccepteddefinitionofobe- sity, a concern to both clinicians and obese patients, emphasizesthe multifactorialandsometimes poorly un- derstoodnatureofthedisorder[1].
Traditionally,obesityhasbeenviewedastheresultofan imbalancebetweenenergyintakeandexpenditure,driven byincreasedconsumptionoffoodwithhighcaloriccontent andasedentarylifestyle.Interindividualdifferenceshave beenoftenascribedtogeneticvariationsingenesrelatedto energymetabolism.Indeed,manygeneticandepidemiologi- cal studiesin the1980s on cohortsoftwinsand adopted childrenrevealedastatisticallysignificantcontributionof geneticstothedevelopmentofobesity[2,3].Althoughthese
Review
Glossary
Coregulators(transcriptional): thetermcoregulatorsreferstoproteinsand multiproteincomplexesthatinteractwithDNA-boundtranscriptionfactorsto either activate (coactivators) or repress (corepressors) genetranscription. Coregulatorsaltergeneexpressionprimarilybymediatinginteractionswith thebasaltranscriptionmachineryandbymodifyingchromatinstructureand function, thereby making DNA more or less accessible to transcription. Coregulatorsratherthantranscriptionfactorsarethemainepigenomicplayers because they can reversibly write, erase, and read (translate) chromatin modificationslinkedtogeneexpression.
Enhancer-associatedRNAs(eRNAs): eRNAsarearecentlyidentifiedclassof non-codingRNAs that are transcribed from regulatory enhancerregions, distantfromthetranscriptionstart-sitesofmRNA-codinggenes.eRNAsare suspectedtoplaykeyrolesintranscriptionregulation,bothincisandintrans, buttheunderlyingmechanismsremaintobeidentified.
Epigenetics: this term was originally coined to describe ‘the study of mitoticallyand/ormeioticallyheritablechangesingenefunctionthatcannot beexplainedby changesinDNAsequence’.Initially, itwas believedthat epigeneticmodificationswereunidirectional,butrecentstudieshavedemon- stratedthattheepigenome,inotherwordsthesumofallchromatin(DNA/ histone)modificationsinagivencelltype,isinfactdynamicandreversible, changinginresponsetonutrients,physicalactivity,andwithaging.Thus, recentoperationaldefinitionsincludealltheseaspectsofepigeneticcontrolof geneexpression.
Epigenomics: thistermrefers tothegenome-wideanalysis ofepigenetic chromatinmodifications,andcurrentlyincludesthestudyofDNAmethylation aswellasofdiversehistonemodifications,thelatterbeingfarmorecomplex andexperimentallyfarmorechallengingtoapproach.
Histoneacetyltransferases(HATs): enzymeswithinmultiprotein(coactivator) complexesthat acetylatespecific lysineresidues inhistone tails,thereby promotingeuchromatinstructureandtranscriptionactivation.
Histonedeacetylases(HDACs): enzymes withinmultiprotein(corepressor) complexesthatremoveacetylgroupsfromspecificmodifiedlysineresiduesin histonetails,therebyincreasingtheiraffinityforthenegativelychargedDNA andgeneratingatightchromatinstructurerefractorytotranscription. Lipotoxicity: lipotoxicity results from intracellular accumulation of lipid species,suchasdiacylglycerols,saturatedfattyacids,andceramides,leading tocell-intrinsicand-extrinsicdysfunction.
Metaflammation: thetermwasoriginallycoinedbyGo¨khanS.Hotamisligil
[90]todescribethestateofmetabolicallydriveninflammation(alsoreferredto as‘low-grade’,‘chronic’,or‘cold’inflammation),akeyfeatureofcommon metabolicdiseasesincludingobesity.Metaflammationshareskeycomponents and signaling pathwayswith classical (‘acute’, ‘hot’) inflammationand is observedinmost‘metabolic’tissues(e.g.,fat,liver,gut,pancreas)under conditionsofdisease.
MicroRNAs(miRNAs): alargefamilyofsmallnon-codingRNAsthathave emerged as key post-transcriptional regulators of gene expression. The generationofmiRNAsistheresultoftheactivityofmultiproteincomplexes thatworksynergisticallytoinducesequentialcleavage,export,andmiRNA interactionswithsilencingcomplexes.TheyaretranscribedasRNAprecursors byRNApolymeraseII.
Transrepression: generallydescribestheabilityofatranscriptionfactorto suppresstranscriptionactivationbyotherDNA-boundtranscriptionfactorsin trans, in other words by means of protein–protein interactions, without needing to binddirectly to DNA. Transrepression accounts for the anti- 1043-2760/$–seefrontmatter
ß2013ElsevierLtd.Allrightsreserved.http://dx.doi.org/10.1016/j.tem.2013.09.006
Correspondingauthor:Venteclef,N. (nicolas.venteclef@upmc.fr).
approachesledtotheidentificationofsomecausalgenesin monogenic disease(thatareusually severewithearlyon- set), the approach was less fruitful in identifying causal genes in common formsof obesity [4–7]. In recent years obesityanditsrelatedcomplicationshavealsobeenassoci- atedwithotherfactorssuchassleep,gutflora,ornutrients, which might increase susceptibility to weight-gain and obesity-related complications through epigenetic changes
(seeGlossary)(Figure1)[8–10].
Experimentalandepidemiologicalevidencehaslinked obesity and related metabolic complication to chronic inflammation.Infact,itissuggestedthatchronicinflam- mation in the context of metabolic disorders (termed ‘metaflammation’) might be the result, at leastin part, of epigenetic alterations. Adipose tissue inflammation, a hallmark of obesity (Box 1), is present to different degreesindifferentindividuals,andmightbetheconse- quence of epigenetic alterations in response to lifestyle andotherenvironmentalfactorsthatinfluencechromatin
Lifestyle and environmental factors
Lean
Obese
Metabolic alteraons
Transcripon factors and coregulators (Chroman modifiers)
Chroman (DNA and histone)
modificaons Non-coding RNAs
Healthy adipose ssue Inflamed adipose ssue
Epigenomic response
TRENDS in Endocrinology & Metabolism
structure, transcription factor activity, and non-coding RNAregulation.
Recent progress in dissecting transcriptional altera- tions in gene networks, that are specifically linked to adiposetissueinflammationinobesity,highlighttheim- portanceofatight coordinationofsuchnetworks forap- propriate gene expression for a healthy state. These alterations include activation and promoter binding of specifictranscription factors,referredtoas genomicreg- ulators,therecruitmentofchromatinmodifyingcoregula- tors,andtheinductionofnon-codingRNAsreferredtoas epigenomicregulators(Figure1).
Herewereviewcurrent insightsintothegenomicand epigenomic regulation of adipose tissue inflammation, whichofferabetterunderstandingofthecomplexobeso- genicprogramandmayhelpindefiningnewtherapeutic strategiestoprevent,restrict,and/orresolveinflammation inthecontext ofobesity.
Genomicregulation
Transcriptionfactorsinvolvedinadiposetissue inflammationinobesity
Activationofinnateimmunitypathways. Acrucialfind- inglinking inflammationand adipose tissuedysfunction wastheobservationthattheToll-likereceptors(TLRs),a familyofpattern-recognitionreceptorsthatplayacrucial role in innate immunity, respondto dietary fatty acids. Specifically,saturatedfreefattyacids(FFAs)induceadi- posetissueinflammationthroughactivationoftheTLR4 pathway [11]. Mice lacking TLR4 are protected against high-fat diet-induced obesity, inflammation, and insulin resistancebecausetheyareresistanttothesuppressionof
[12].TLRsaswellasthetumornecrosisfactora(TNFa) receptor (TNF-R) typically activate a broad spectrum of proinflammatory markers including cytokines and tran- scription factors such as nuclear factor klight-chain-en- hancerofactivatedBcells(NF-kB),itsinhibitorIKKb,and JunN-terminalkinases(JNKs)[13](Figure2).Inhibition of IKKb or JNK by synthetic inhibitorsor theirgenetic deletion prevents adipose tissue inflammation and resolves obesity-induced insulin resistance, highlighting their key functions in adipose tissue inflammation [13]
(Figure 2). Interestingly,JNK depletion inmacrophages
reducestissueinfiltrationbymacrophages(knownasadi- posetissue-associated macrophages–ATMs),andblocks theinductionofinflammatorygeneexpressioninadipose tissue[14](Figure2).
In additiontoATMs, severalotherimmune celltypes are found in the obese adipose tissue. Inflamed adipose tissue is enriched in T lymphocytes, whichunder condi- tionsofobesitypromoteanincreaseinthelevelsofinter- ferong(IFNg).IFNgplaysacrucialroleintheregulationof adiposetissueinflammationandenhancestheproduction of various inflammatory cytokines, including TNFa
[15,16].TheincreasedIFNglevelsresultalsointheacti-
vationofinterferonregulatoryfactors(IRFs),anotherclass oftranscriptionfactorsinvolvedinadiposetissueinflam- mation(Figure2).Indeed,IRF-1,-3,-4,-7,and-9haveall beenreportedtoregulateadipogenesisandATMpolariza-
tion[17–19].Interestingly,IRFs havedual functionsbe-
causetheynotonlyactivatebutalsorepresstranscription. In particular,IRF4andIRF7appeartorepress anti- inflammatorygenesinadipocytes[20,21],thuspropagat- ingtheinflammatorystate.Althoughtheunderlyingmech- anism ofrepressionremains unclear,theinvolvement of specificcorepressorsandadistinct epigenomiclandscape specifyingtherepressivechromatinenvironmentislikelyto beonecontributingfactor(discussedbelow).
Nuclear receptors and adipose tissue inflammation. Althoughtheactivationofproinflammatorytranscription factors isaprerequisitefor adiposetissueinflammation, the concomitant suppression of anti-inflammatory tran- scriptionfactorsandtheircoregulatorsisalsopartofthe equation.Anexampleisfoundwithinthenuclearreceptor family, where various nutrient-sensing members are known for their potent anti-inflammatory activities
[22,23]. Peroxisome proliferator-activated receptor
g(PPARg),akeyregulatorofadipogenesisandthegeno- mic targetfor the anti-diabetic drugs thiadolizinediones (TZDs)[24–27],hasanti-inflammatoryaction,althoughits expression is reduced in inflamed adipose tissue [28]. Several possible mechanisms may account for the anti- inflammatory action of PPARg in the context of obese adipose tissue. For example, because PPARg activation by TZDs improves insulin sensitivity, partially through promotingfattyacidstorageastriglyceridesinadipocytes, it reduces lipotoxicity and counteracts inflammation in adiposetissue[29].Indeed,diabeticpatientstreatedwith TZDs show improvement in their inflammatory param- etersdespitegainingweight[30].
Box1.Inflammatoryeventsinobesity
Dietarymanipulationofrodentmodelshasshownthatbothhigh-fat diet(HFD)orhigh-caloricdiet(HCD)feedinginduceshort-termacute inflammationinadiposetissue.Thisphaseistermedtheearlyphase oftheinflammatoryresponseanddoesnotinvolveimmunecells [13]. The way in which this inflammation is initiated remains unclear.Storageofexcessnutrientsintheadiposetissueresultin hypertrophic adipocytes, lipid dysregulation (accumulation of diacylglycerolandceramide),mitochondrialdysfunction(oxidative stress), and endoplasmic reticulum stress [91,92]. Activation of inflammatorycascadesandanincreasedsecretionofinflammatory mediatorsisalsoobserved(Figure2)thatattractimmunecellssuch as M1 polarized (proinflammatory) macrophages [23]. This phe- nomenon is termed chemotaxis. Indeed, M1 macrophages are enrichedwithintheadiposetissueinobesity,therebyorchestrating anadaptive immuneresponse[93].Lymphocyteshave alsobeen recentlydiscoveredtoinfiltratehumanadiposetissue.Polarization oflymphocytesisdependentontheinflammatoryenvironmentand thecapacityofadiposetissue cellstopresentantigens[94]. The initial ideathatmacrophagesareresponsibleforTcellactivation was challenged byrecent evidence showingthatadipocytes can also activate T cells [95]. All these inflammatory processes contributetothedevelopmentandmaintenanceofadiposetissue inflammation in obesity. The phenotype of immune cells and adipocytesinobesitymightbetriggeredthroughspecifictranscrip- tionalcircuitsinresponsetobothgenomic(alterationsoftranscrip- tion factor binding and function)and epigenomic (alterations of chromatinmodifications)regulatoryevents.
viatransrepression,reminiscentoftheanti-inflammatory action ofPPARgandliverXreceptors(LXRs) inmacro- phages [31,32]. However, although the transrepression pathway has been validated in different macrophage populations, in the context of vascular inflammation andatherosclerosisandwithadditionalnuclearreceptors,
[33], it has not yet been established in adipocytes
(Figure3)andwarrantsmoreinvestigation.Morerecent
findingssuggestthatPPARgmaymodulateinflammation byregulating the expressionofanti-inflammatory tran- scriptionfactorsandtheircoregulatorsinadipocytes[29]. Forexample,theE-boxtranscriptionfactorTwist-related protein1(TWIST1)controlsinparttheexpressionoftwo subunitsofananti-inflammatorycomplexthatrepresses transcription,referredtoasGproteinpathwaysuppressor 2(GPS2)andsilencingmediatorforretinoidandthyroid hormonereceptor(SMRT)(describedbelowinBox2and
Figure3)[34].Interestingly,TWIST1expression,whichis
alsoregulatedbyPPARg,isreducedinobeseadipocytes andcorrelateswiththeinflammatorystatusofthetissue
[35,36].Thus,theGPS2/SMRTcorepressorcomplexcould
beamediatorofthe anti-inflammatoryaction ofPPARg
Inadditiontoitseffectsonmacrophagesandadipocytes, PPARgmayalsocontroladiposetissueinflammationand insulin sensitivity by stimulating the accumulation and function of regulatory T cells (Treg) in visceral adipose tissue[27].Finally,anotherclass oftranscription factors known as Kru¨ppel-Like factors (KLFs) appear to be in- volvedintheregulationofadiposetissueinflammationas well.AsobservedwithPPARg,reducedexpressionofKLF4 seemstobeassociatedwith elevatedexpressionofproin- flammatorymarkers[37].
Transcriptionalcoregulators
Epigenomiccheckpointsofinflammatorygene expression
The term‘coregulator’ describes astructurally andfunc- tionally diverse class of proteins and multiprotein com- plexes that do not bind directly to DNA but instead associate with DNA-bound transcription factors toregu- lategenetranscription(Figure3).Coregulatorscaneither activate(coactivators)or inhibit(corepressors)transcrip- tionthroughmodificationofthechromatinstructure.Im- portantly,manycoregulatorsmodulatetranscriptionina FFA Cytokines LPS IFNγ TNFα MAP kinase cascade Insulin signaling Insulin resistance TRAF6 JAK2 JAK1 JNK IRS JNK JNK NF-κB AP-1
Inflammatory genes Inflammatory genes
NIK
IKK
IκB IκB
Degradaon
Nucleus IL6; IL8; CCL2; CCL5; TNFα
p65 p50 p65 p50 c-JUN c-FOS MYD88 P P P P P P P P P P P P P P P P TBK1 STATs STATs STATs STATs STATs IRFs IRFs STATs TLRs IFNγ-R TNF-R Ins-R 1 2 3 P In P P TATs
TRENDS in Endocrinology & Metabolism Figure2.Inflammatorysignalinginadiposetissue.Adiposetissuesignals(lipids,cytokines,orLPS)activateimmunecellsandadipocytesthroughTNFRandTLR pathways,whichpromotepost-translationalmodificationsofNF-kBandJNK.ActivationoftheNF-kBpathwayisinducedbyactivationofIKKcomplexesanddegradationof IkBtoallowNF-kBtranslocationintothenucleusandbindingtoinflammatorygenepromoters.Activationofthesereceptorsalsopromotesphosphorylation(P)ofJNKby theMAPkinasecascade.PhosphorylatedJNKactivatesinflammatorytranscriptionfactorssuchc-Junandc-Fos(AP-1)(1).ActivationofTLRsbyadipose-derivedsignals alsoinducesthephosphorylationofIRFsviatheTRAF6/TBK1cascade.PhosphorylatedIRFscandimerizewithSTATproteins(activatedbyJAK/STATcascade)toforma regulatorycomplexwhichisrecruitedtoIFN-stimulatedgenespromotersandactivatestheirexpression(2).Theseinflammatorysignalscaninduceinsulinresistanceinthe adipocytesinparticularbytriggeringIRSphosphorylationatserineresiduesviatheJNKpathway(3).Abbreviations:IFN,interferon;IkB,inhibitorofNF-kB;IKK,IkBkinase; IRF,interferonregulatoryfactor;IRS,insulinreceptorsubstrate;JAK,Januskinase;JNK,JunN-terminalkinase;LPS,lipopolysaccharide;MAP,mitogen-activatedprotein; MYD88,myeloiddifferentiationprimaryresponsegene88;NF-kB;nuclearfactorklight-chain-enhancerofactivatedBcells;STAT,signaltransducerandactivatorof transcription;TBK1,TANK-bindingkinase;TLR,Toll-likereceptor;TNF,tumornecrosisfactor;TNFR,TNFreceptor;TRAF6;TNFreceptor-associatedfactor6.
invitroandcell-basedstudieshaveprovidedgreatinsights intothestructureandfunctionofmanycoregulatorsand theircomplexes, their in vivo function andtranscription factorspecificityremainpoorlyunderstoodpartlybecause mostofthefull-bodycoregulatorknockoutmousemodels areembryoniclethal[38].Clearly,tissue-specificknockout modelsarerequiredtostudycoregulatorfunctioninvivo and recent studies that have taken on this task have revealed novelfunctions ofsome coregulators inadipose tissue.
Coactivatorsthatdriveinflammation. Inflammatorytran- scriptionfactors suchas NF-kB, AP-1,andIRFs are de- pendenton coactivators.The coactivators CREB-binding protein/p300(CBP/P300)andswitching-defectivesucrose non-fermenting(SWI-SNF)activatetranscriptionofthese inflammatory genes by increasing histone acetylation of
target genes such as TNFa and interleukin 6 (IL-6)
[41,42],thuspropagatingtheinflammatoryprofile.Recep-
tor interacting protein 140 (RIP-140, NRIP1), originally describedasanuclearreceptorcorepressor,canalsoactas acoactivatortopromotetheexpressionofproinflammatory genes[43].RIP140isrecruitedtothepromotersofNF-kB target genes and stimulates transcription by stabilizing the formation of the trimeric ReIA and CBP/P300 com- plexes.GPS2(Gproteinpathwaysuppressor2),asubunit of the NCOR (nuclear receptor corepressor)/SMRT core- pressorcomplex,canindependentlyactasacoactivatorby directlyinteractingwithseveralnuclearreceptorsinclud- ingtheoxysterolreceptorLXR[44].Mostoftenthisregu- lationappearstobepromoter-specific,raisingthequestion ofwhatdeterminescontextselectivity.Differentchroma- tinstructuresandbindingsitecompositions,distinctpro- moter-bound transcription factor sets, and/or the
HDAC3 SMRT GPS2 TLR4 TNF-R H3K4 methylaon Inflammatory genes HDAC3 SMRT S GPS2 TLR4 TNF-R Inflammatory genes SWI-SNF CBP/P300 G TZDs PPARγ + + Transcriponal transrepression An-inflammatory genes Transcriponal acvaon Weight loss TZD treatment Transcriponal repression HDAC3 SMRT S GPS2 TLR4 TNF-R IFNγ-R IFNγ-R IFNγ-R IFNγ-R H3K4
demethylaon Inflammatory genes
An-inflammatory genes Infl In (A) (D) (B) 2 1 3 P 1 2 4 3 Inflammatory signals
Cytokines, FFA, LPS, TNFα, IFNγ
HDAC3 SMRT S GPS2 TLR4 TNF-R H3K4 methylaon Inflammatory genes IRFs I JNK IKK S 3K4 ylaon GPS Weight gain Transcriponal derepression 2 1 1 2 4 3 In SWI-SNF CBP/P300 JNK IKK
TRENDS in Endocrinology & Metabolism (C)
Figure3.Epigenomicregulationofinflammationinadiposetissue.(A)Inhealthy(lean)adiposetissueinflammatorygeneexpressionisrepressedbytheSMRT/GPS2 corepressor complex whichsuppressestheactivation ofproinflammatory transcriptionfactors (NF-kB, AP-1,C/EBP) (1).H3K4 demethylation induceschromatin condensation,therebypreventingtherecruitmentofthetranscriptionalmachinery(RNApolymeraseII)(2).ThetranscriptionfactorKLF4isrecruitedontoanti-inflammatory genepromoters,allowingtheirexpression(3).(B)Weightgaininducesmetabolicalterationsthatrepresentproinflammatorystimuli.TheactivationofTLR4,TNF-R,and IFN-Rbytheirrespectiveligands(1)inducesproinflammatorycascades(describedinFigure1)(2),thatleadtotheclearanceoftheSMRT/GPS2corepressorcomplexfrom inflammatorygene promoter(3).H3K4 methylation induceschromatindecondensation, therebyfacilitating therecruitment of thetranscription machinery(RNA polymeraseII)(4).(C)ClearanceoftheSMRT/GPS2corepressorcomplexandH3K4methylationenablestherecruitmentofCBP/P300–SWI-SNFcoactivatorcomplexes whichfurtherremodelandmodifychromatin(e.g.,byacetylation),andthuscooperatewiththetranscriptionalmachinery,toinducegenetranscription.(D)Weightlossor