Schmidl-2018-Epigenetic mechanisms regulating.pdf

Mechanisms of allergic diseasesEpigenetic mechanisms regulating T-cellresponsesChristian Schmidl,PhD,aMichael Delacher,PhD,a,bJochen Huehn,PhD,cand Markus Feuerer,MDa,bRegensburg andBraunschweig,GermanyDuring the last decade,advances in sequencing technologiesallowed production of a wealth of information on epigeneticmodifications in T cells.Epigenome maps,in combination withmechanistic studies,have demonstrated that T cells undergoextensive epigenome remodeling in response to signals,whichhas a strong effect on phenotypic stability and function oflymphocytes.In this review we focus on DNA methylation,histone modifications,and chromatin structure as importantepigenetic mechanisms involved in controlling T-cell responses.In particular,we discuss epigenetic processes in light of thedevelopment,activation,and differentiation of CD41T helper(TH),regulatory T,and CD81T cells.As central aspects of theadaptive immune system,we review mechanisms that ensuremolecular memory,stability,plasticity,and exhaustion of Tcells.We further discuss the effect of the tissue environment onimprinting T-cell epigenomes with potential implications forimmunotherapy.(J Allergy Clin Immunol 2018;142:728-43.)Key words:Epigenetics,gene regulation,enhancer,promoter,chro-matin accessibility,histone modifications,DNA methylation,tran-scription factor binding,T-cell development,T-cell function,T-cellexhaustion,regulatory T cells,tissue specificityT cells are a subtype of white blood cells,which play a majorrole in the adaptive immune system.They can be classifiedaccording to their specific function:MHC class IIrestrictedCD4-expressing T cells(CD4)can differentiate into specific THsubtypes.In contrast to this,MHC class Irestricted CD8-expressing T cells(CD8)are classically known for their potentialto destroyvirus-infected ortumorcells,hencetheirdenominationas cytotoxic T lymphocytes(CTLs).Following development inthe thymus from early T-cell precursor cells over CD4 and CD8double-negative(DN)and double-positive(DP)stages,T cellsfinally differentiate into CD4 and CD8 single-positive(SP)thy-mocytes.On recognizing MHC-peptide complexes through theirT-cell receptor(TCR),naive CD41or CD81T cells can differen-tiate into specific effector populations,which is guided by inte-grating TCR activation with a variety of other signals providedby immune and nonimmune cells.Importantly,after the initialimmune response,a persistent pool of memory T cells maintainsthe capability to respond rapidly to antigen re-encounter,providing long-lasting protection.All these phenotypic changes in T cells are accompanied bydistinct gene-expression programs that equip T cells with themolecules needed to develop and exert their function,and it is ofAbbreviations usedATAC:Assay for transposase-accessible chromatinBATF:Basic leucine zipper TF,ATF-likeCNS:Conserved noncoding sequenceCTL:Cytotoxic T lymphocyteCTLA-4:Cytotoxic T lymphocyteassociated protein 4DMR:Differentially methylated regionDN:Double-negativeDNMT:DNA methyltransferaseDP:Double positiveEZH2:Enhancer of zeste 2 polycomb repressive complex 2subunitFOXP3:Forkhead box protein P3GITR:TNF family member 18HDAC:Histone deacetylaseH3K27ac:Histone H3 lysine 27 acetylationH3K4me1:Histone H3 lysine 4 monomethylationH3K4me3:Histone H3 lysine 4 trimethylationIkzf2:Ikaros family zing finger 2IRF4:Interferon regulatory factor 4LCR:Locus control regionPD-1:Programmed cell death protein 1ROR:Retinoic acidrelated orphan receptorSTAT:Signal transducer and activator of transcriptionT-bet:T-box transcription factor 21TCF1:Transcription factor 1Tconv:Conventional TTCR:T-cell receptorTF:Transcription factorTFH:Follicular helper TTIL:Tumor-infiltrating lymphocyteTreg:Regulatory TWGBS:Whole-genome bisulfite sequencingFromathe Regensburg Center for Interventional Immunology(RCI)andbthe Chair forImmunology,University Regensburg and University Medical Center Regensburg,andcExperimentalImmunology,HelmholtzCentreforInfectionResearch,Braunschweig.Supported by grants from the European Research Council(ERC-CoG,#648145 RE-GiREG to M.F.)and the German Research Foundation(DFG)SFB/Transregio 221-B8 to M.F.and SFB738-C7 to J.H.Disclosure of potential conflict ofinterest:The authors declare that theyhave no relevantconflicts of interest.Received for publication May 3,2018;revised July 23,2018;accepted for publicationJuly 24,2018.Corresponding author:Markus Feuerer,MD,Franz-Josef-Strauss-Allee 11,93053 Re-gensburg,Germany.E-mail:markus.feuererukr.de.The CrossMark symbol notifies online readers when updates have been made to thearticle such as errata or minor corrections0091-6749/$36.00?2018 American Academy of Allergy,Asthma&Immunologyhttps:/doi.org/10.1016/j.jaci.2018.07.014Terms in boldface and italics are detailed in the glossary on page 729.728utmost importance for the integrity of the immune system that Tcells establish and maintain those states in a highly controlledmanner.This is achieved by diverse noncoding gene-regulatoryelements in the genome.Proximal and distal regulatory elements(promoters and enhancers,respectively)can be bound bytranscription factors(TFs),which cooperate with other proteins,such as remodeling complexes and epigenetic modifiers,toestablish and maintain transcription-permissive or transcription-restrictive chromatin environments in a progressive manner.Accompanied modifications of the DNA and chromatin proteinsthatcontributetomaintainingthecellstatewithoutchangesintheDNA sequence itself(so-called epigenetic modifications)havebeen described to play a major role in development,activation,and polarization of lymphocytes.In this review we focus on DNA methylation,histonemodifications,and chromatin structure and discuss the recentglobal epigenome studies on CD41THcells,regulatory T(Treg)cells,and CTLs with respect to their development and functionunder physiologic or pathologic conditions.EPIGENETIC MECHANISMS AND GENEREGULATIONDNA methylationIn mammals the base cytosine is commonly modified bymethylation of its carbon at position 5,predominantly in thecontext of CpG dinucleotides(mCpG).1The methylation markcan be written by de novo DNA methyltransferase(DNMT)3Aand DNMT3B with the help of DNMT3L.2,3Once established,methylation patterns can be stably transmitted over cell divisionsthrough maintenance DNMT1,and this inheritability designatesDNA methylation as a true epigenetic mark.4,5Long consideredextremely stable,recent discoveries regarding the ten-eleventranslocation(TET)family of proteins established the conceptof catalyzed active demethylation(Fig 1,A).6The effects ofDNA methylation on transcriptional activity are complex.AtCpG islands(regions of high CpG density),especially if locatedat promoters,DNA methylation causes repression of transcrip-tion,and high methylation levels support processes such as X-chromosome inactivation and imprinting.1In contrast,genebodies of highly expressed genes are heavily methylated,with apossible effect on splicing,whereas a low degree of methylationis found at active gene-regulatory elements that are bound byTFs.7-9Hence,usingmethodsofgenome-wideDNA-methylationprofiling,such as whole-genome bisulfite sequencing(WGBS),hasbeenprovedveryusefultodelineatecelltypespecificaspectsof gene regulation,identify cis-acting TFs,and describe cellularontologies.DNA methylation can affect gene expression in direct andindirectways(Fig1,B).Forinstance,DNAmethylationactivelyblocks the binding of certain TFs,hence restricting regulatoryelements from receiving positive transcription signals.1Further-more,it has recently been demonstrated that some TFs canactively recognize methylated DNA,and on binding,such fac-torscanrecruitotherTFstoremodelarepressedchromatinenvi-ronment toward an active one.10As an indirect mechanism,methylated DNA can be recognized by proteins,includingmethyl-CpG domainbinding(MDBs)proteins,which are ableto recruit other chromatin-modifying enzymes,such as histonedeacetylases(HDACs),11driving a repressed chromatin envi-ronment.Conversely,CXXC-type zinc finger protein 1 recog-nizesCpGislandsandrecruitsactivatinghistonemethyltransferasesthatcreateapermissivechromatinenvironment.12GLOSSARYCHROMATIN IMMUNOPRECIPITATION(ChIP):An assay used to inves-tigate interaction between proteins and DNA in the cell by evaluatingtranscription regulation through histone modification or transcriptionfactorDNA-binding interactions.DIFFERENTIALLYMETHYLATEDREGION(DMR):Regions of thegenome with different methylation states that are considered functionalregions involved in gene transcriptional regulation.Identifying DMRsamong different tissues provides a comprehensive view of epigeneticdifferences among tissues.ENHANCER OF ZESTE 2 POLYCOMB REPRESSIVE COMPLEX(EZH2):Ahistone-lysine N-methyltransferase enzyme involved in histone methyl-ation and maintaining transcriptional repression over successive cellgenerations.Mutation or overexpression of EZH2 has been associatedwith a variety of cancers,and its inhibition has been shown to beresponsible for suppressing tumor development.Thus blocking EZH2activity might slow tumor growth.PROGRAMMED CELL DEATH PROTEIN 1(PD-1):A cell-surface mole-cule that,when expressed on T cells,pro-B cells,and myeloid-deriveddendritic cells,leads to negative regulation of proliferation and activity.PD-1 and its ligand,programmed death-ligand 1(PD-L1),play a majorrole in suppressing the immune system by sending an inhibitory signalto reduce T-cell activity.SUPERENHANCER:A region of the mammalian genome comprisingmultiple enhancers in close genomic proximity to drive transcription ofgenes critical for cell-type specification and function.TEN-ELEVEN TRANSLOCATION(TET):Proteins involved in regulationof DNA methylation and transcription named for a common trans-locationbetweenchromosomes10and11,creatinganMLL-TET1fusionprotein found in patients with several forms of cancer.TOPOLOGICALLY ASSOCIATED DOMAIN(TAD):Linear units of chro-matin that fold as discrete 3-dimensional structures and tend to favorinternal,rather than external,physical chromatin interactions.It hasbeen shown that disruption of TADs leads to disease because of thetransformation of 3-dimensional organization and thus disrupting generegulation.WHOLE-GENOME BISULFITE SEQUENCING(WGBS):A type of next-generation sequencing technology that has enabled genome-wideanalysis of 5-methylcytosine(5mC)nucleotides at single nucleotideresolution by treating DNA with sodium bisulfite before sequencing.Sodium bisulfite converts unmethylated cytosines into uracil,andunconverted cytosines are methylated.This allows for detection ofunmethylated cytosines to be detected as thymines after sequencing.Methylation of DNA at cytosine nucleotides forms 5mC,which affectsvarious cellular processes involving gene expression and chromatinremodeling.The Editors wish to acknowledge Kristina Bielewicz,MS,for preparing this glossary.J ALLERGY CLIN IMMUNOLVOLUME 142,NUMBER 3SCHMIDL ET AL 729Histone modificationsDNA is wrapped around nucleosomes consisting of 8 histoneproteins(2 copies of each histone:H2A,H2B,H3,and H4)toformthebasicorganizationalstructureofgeneticinformation,thechromatin.Histone proteins have nonglobular N-terminal tailsthat can harbor manifold posttranslational modifications,such asmethylation,acetylation,phosphorylation,or ubiquitinylation.13More than a dozen classes of histone modifications are knownde novoDNA methylationrepDNMT1DNMT3maintenance DNA methylationpassivedemethylationactivedemethylationTETBERrepunmethylated CpGmethylated CpGhydroxymethylated CpGTF repelled byDNA methylationTF attracted byDNA methylationMBDCXXCrepressed chromatinenvironmentactive chromatinenvironmentH3K4me3H3K27acH3K27me3H3K9me1/2writers,e.g.H3K4me3H3K27acH3K27me3H3K9me2erasers,e.g.readers,e.g.ABDpioneer and collaborative TFssignal dependent TFsH3K4me1/2H3K27acopening/priming ofchromatinactiveregulatoryregioninacessiblechromatinMLLp300EZH2G9aHDAC1/2UTXKDM5AH3K4me3H3K27acH3K27me3H3K9me1/2SGF29BRD4EED(PCR2)CDYLLSD1protein with bromodomainprotein with chromodomainmChistone lysine methylationhistone lysineacetylationhistone tailCoactivatorcorepressorFIG 1.Epigenetic mechanisms,including DNA methylation,histone modification,and chromatin structureand their role in gene regulation.A,DNA methylation in the context of CpG dinucleotides(mCpG)is placedby the de novo DNA methyltransferase machinery(DNMT3A/B/L)and maintained by DNMT1.DNA methyl-ation can be eliminated by passive replication-dependent mechanisms or actively removed by the action often-eleven translocation(TET)enzymes,followed by further enzymatic steps that include the base excisionrepair machinery(BER).B,Direct and indirect effect of DNA methylation on transcription.C,Histone mod-ifications are placed and removed by writers and erasers and subsequently interpreted by readers thatrecognize discrete modifications of histones with specific protein domains.D,Chromatin accessibility ofnoncoding gene-regulatory elements is controlled by a complex interplay of epigenetic mechanisms andTF binding.Pioneer and collaborative TFs can open/prime inaccessible chromatin,which allows furthersignal-dependent TFs to bind,leading to their full activation.J ALLERGY CLIN IMMUNOLSEPTEMBER 2018730 SCHMIDL ET ALto date,and the corresponding enzymes that set,remove,andinterpret the marks have been identified(ie,writers,erasers,andreaders;Fig1,C).5Chromatinimmunoprecipitation(ChIP),fol-lowed by sequencing,allows genome-wide profiling of histonemodifications,even from low cell numbers,and contributedsignificantly to the understanding of distribution and functionalcorrelations of histone posttranslational modifications in generegulation.14-17In general,histone acetylation is regarded as anactivating histone modification:histone H3 lysine 27 acetylation(H3K27ac)was described to mark active promoters and en-hancers and is therefore useful to identify cis-regulatoryelements.18Histone methylation is another very well-studied modificationthat has different effects on transcription dependence on whichhistone-tail residue is modified.Histone H3 lysine 4 trimethyla-tion(H3K4me3)marks transcription-permissive promoters andtranscribed enhancers,whereas histone H3 lysine 4 monomethy-lation(H3K4me1)is associated with poised enhancers.19Mecha-nistically,asanexample,H3K4me3canbeboundbychromodomain-containing proteins,such as chromatin remodel-ers and histone acetyltransferases,which drive a relaxed chro-matin structure to enable transcription.Contrary to H3K4methylation,trimethylation of H3K27(written by enhancer ofzeste 2 polycomb repressive complex 2 subunit EZH2)is en-riched at facultative heterochromatin and marks polycomb-repressed genes involved in development,whereas constitutiveheterochromatin is marked by H3K9me3.20Interestingly,biva-lency,the co-occurrence of active and repressive histone modifi-cations,was described,providing an intermediate activity statethatcanberesolvedduringdevelopmentintoactivityorinactivityofassociated genes.21Well-establishe