The epigenetics of inflammaging-The contribution of age-related heterochromatin loss and locus-specific remodelling and the modulation by environmental stimuli.pdf

Contents lists available at ScienceDirectSeminars in Immunologyjournal homepage: epigenetics of inflammaging:The contribution of age-relatedheterochromatin loss and locus-specific remodelling and the modulation byenvironmental stimuliChristine Nardinia,b,c,Jean-Francois Moreaud,e,Nomie Gensousf,Francesco Ravaiolif,Paolo Garagnanif,g,h,i,j,Maria Giulia Bacalinik,aDepartment of Laboratory Medicine,Karolinska Institutet,Stockholm,SwedenbCNR IAC“Mauro Picone”,Roma,ItalycPersonal Genomics S.r.l.,Verona,ItalydUniversity of Bordeaux,CNRS-UMR5164,146 rue Lo Saignat,33076 Bordeaux,FranceeCHU Bordeaux,Place Amlie Raba-Lon,Bordeaux,FrancefDepartment of Experimental,Diagnostic and Specialty Medicine(DIMES),University of Bologna,Bologna,ItalygClinical Chemistry,Department of Laboratory Medicine,Karolinska Institutet at Huddinge University Hospital,Stockholm,SwedenhLaboratory of Cell Biology,Rizzoli Orthopaedic Institute,Bologna,ItalyiCNR Institute of Molecular Genetics,Unit of Bologna,Bologna,ItalyjCenter for Applied Biomedical Research(CRBA),St.Orsola-Malpighi University Hospital,Bologna,ItalykIRCCS Istituto delle Scienze Neurologiche di Bologna,Bologna,ItaliaA R T I C L E I N F OKeywords:EpigeneticsHistonesMethylationInflammagingA B S T R A C TA growing amount of evidences indicates that inflammaging the chronic,low grade inflammation statecharacteristic of the elderly is the result of genetic as well as environmental or stochastic factors.Some of these,such as the accumulation of senescent cells that are persistent during aging or accompany its progression,seemto be sufficient to initiate the aging process and to fuel it.Others,like exposure to environmental compounds orinfections,are temporary and resolve within a(relatively)short time.In both cases,however,a cellular memoryof the event can be established by means of epigenetic modulation of the genome.In this review we will specifically discuss the relationship between epigenetics and inflammaging.In parti-cular,we will show how age-associated epigenetic modifications concerned with heterochromatin loss and gene-specific remodelling,can promote inflammaging.Furthermore,we will recall how the exposure to specific nu-tritional,environmental and microbial stimuli can affect the rate of inflammaging through epigenetic me-chanisms,touching also on the recent insight given by the concept of trained immunity.1.IntroductionInflammaging is a major and ubiquitous characteristic of humanaging 1 conserved across a remarkable phenotypic variability 2,3.Increased basal levels of circulating pro-inflammatory factors,such asIL-6,TNF-,IL-1R,and C-reactive protein(CRP),hallmark of in-flammaging,have been described during aging and have been asso-ciated with the development of a wide range of age-related pathologiesand with higher risks of mortality 4,5.Inter-individual variations ininflammaging and in its functional readouts rely on the intrinsic plas-ticity of the immune system and are the result of an entangled networkof factors that operate during the life course on the genetic backgroundof each individual.Some inflammaging sources 6 are intimately linked to time ero-sion:for example,cellular divisions unavoidably occur during devel-opment and maintenance of tissue homeostasis and lead to telomeresshortening,which in turns induces cellular senescence 7.The Senes-cence-Associated Secretory Phenotype(SASP)includes a number ofpro-inflammatory cytokines that sustain a pro-inflammatory micro-environment,potentially contributing to inflammaging as shown invitro 4 and recently in vivo 8.Other sources of inflammaging are notmechanistically related to the passing of time.These include lifestyle,https:/doi.org/10.1016/j.smim.2018.10.009Received 2 August 2018;Received in revised form 12 October 2018;Accepted 15 October 2018Corresponding author at:IRCCS Istituto delle Scienze Neurologiche di Bologna,Via Altura 3,40139 Bologna,Italia.Corresponding author at:Department of Experimental,Diagnostic and Specialty Medicine(DIMES),University of Bologna,Via S.Giacomo,12,40126 Bologna,Italy.E-mail addresses:paolo.garagnani2unibo.it(P.Garagnani),mariagiuli.bacalini2unibo.it(M.G.Bacalini).Seminars in Immunology 40(2018)4960Available online 03 November 20181044-5323/2018 The Authors.Published by Elsevier Ltd.This is an open access article under the CC BY-NC-ND license(http:/creativecommons.org/licenses/BY-NC-ND/4.0/).Texposure to environmental factors and to infections 9,10.The accu-mulation of the individual response during lifespan(starting from fe-cundation and possibly earlier in parental gametes)can shape the pro-and anti-inflammatory phenotype of each individual,finally de-termining the extent of inflammaging in adulthood and old age.The intra-and extra-cellular environments experienced by each cellduringreplications and quiescence,possibly contributing to in-flammaging,can be recorded by an important molecular writer:epi-genetic modifications.Epigenetics comprises the study of mitotically(and sometimes meiotically)heritable alterations in gene expressionthat do not imply changes in DNA sequence,but that rely on chemicalmodifications of DNA and histone proteins.Epigenetic modificationsare essential mechanisms of developmental processes and are involvedin the establishment of tissue-specific cells identity.Such modificationsare stable across cell divisions,but also reversible,and hence guaranteephenotypic plasticity and ability to respond relatively quickly to sti-muli.Owing to their heritability,epigenetic changes are tied to cellsmemory,a metaphor to indicate the ability to somehow record eventsthat occurred in earlier cells generations.It is therefore not surprising that epigenetic patterns undergo duringaging profound rearrangements 1114 that have been associated withthe onset of age-related diseases 15.The technological advances forthe analysis of epigenetic molecular markers achieved in the last twodecades showed that,in humans,all tissues,including immune cells16 undergo profound epigenetic changes during aging.However,ourunderstanding of how these changes are mechanistically related toaging and age-related phenotypes including inflammaging is far tobe complete.Epigenetics and inflammaging are two active research areas in agingand the existence of a reciprocal relationship is almost given forgranted.Nevertheless,only a relatively limited number of studies hasspecifically addressed this issue,investigating how age-associated epi-genetic remodelling sustains inflammaging and,vice versa,how in-flammaging can modulate epigenetic patterns.The aim of this review isto recapitulate these evidences.We will briefly recall changes in DNAmethylation and histone modifications that occur during aging.Then,we will review and discuss the available studies on the epigenetics ofinflammaging,focusing on those that describe age-dependent changesin genes relevant for inflammaging and/or associations of the epige-netic patterns with the levels of pro-and anti-inflammatory markers17,18.Finally,the effect of environmental factors on the epigeneticsof inflammaging will be discussed.2.Epigenetic modifications and their remodelling during aging2.1.Epigenetic modificationsIn this review we will focus on DNA methylation and histonemodifications.RNA-mediated transcriptional and post-transcriptionalgene silencing is often referred to as an epigenetic mechanism 19.However,its role in inflammaging has been extensively reviewedelsewhere 20,21 and therefore will not be discussed here.DNA methylation consists in the covalent addition of a methylgroup to a cytosine,mainly within a CpG dinucleotide.In mammals,CpG dinucleotides tend to be globally under-represented but enrichedin regions,known as CpG islands,typically located close to gene pro-moters 22,23.CpG sites out of CpG islands tend to be methylated,while methylation of CpG islands is dynamically regulated during de-velopment 24.DNA methylation is catalysed by DNA methyl-transferase enzymes(DNMTs),while demethylation can occur passivelyduring cell divisions or actively through the combination of oxidative/deamination reactions and DNA repair mechanisms 2527.The most studied histone modifications include acetylation,me-thylation and phosphorylation of histone tails 28.Each type ofmodification can occur at different residues of the histone tails and isestablished and removed by specific classes of enzymes.A complex and only partially characterized crosstalk governs therelationship between DNA methylation and histone modifications 29.The ultimate consequence of this interplay is the regulation of chro-matin structure and the expression of the underlying DNA sequences.Aging is characterized by a marked remodelling of epigenetic sig-natures.Two types of changes have been widely characterized:1)general loss of heterochromatin and 2)reproducible gain or loss ofepigenetic markers at specific genomic locations.More recently,sto-chastic epigenetic modifications(that is,not shared among individuals)and increase in epigenetic variability have been described during aging3032,but their relevance for inflammaging has not yet been ad-dressed and as such will not be further discussed in this review.2.2.Age-associated heterochromatin lossHeterochromatin,a tightly packaged chromatin structure,ensurestranscriptional silencing and genomic stability at specific genomic do-mains,including telomeres,centromeres,repetitive regions and trans-posable elements 33.Assembly and maintenance of heterochromatinis governed by a complex crosstalk of epigenetic modifications,thatinclude trimethylation of lysine9 on histone H3(H3K9me3)and DNAmethylation 34.During cell senescence a profound reorganization of chromatinstructure occurs,characterized by loss of long-range chromosome in-teractions and gain of short-range interactions 3537.These re-arrangements lead to a global loss of constitutive heterochromatin,arecognized hallmark of aging 38,39 occurring at the centromeric andpericentromeric regions and in retrotransposons(Alu,SVA and LINE-1)that show an increase in transcription rates and genomic copy number40,41.These events,observed in several eukaryotic models of cellsenescence,are likely to contribute to genomic instability and to in-crease mutation rates by retro-transposition 42,43.Heterochromatinloss is sustained by a decrease in histones synthesis and histones levels,as observed in cellular models of replicative senescence and in humanfibroblasts from different age donors 44.Furthermore,both histones post-translational modifications andDNA methylation undergo profound changes during aging.H3K9me3levels are reduced with aging and replicative senescence 45,46 and inhuman models of age acceleration,including Hutchinson-Gilford pro-geria syndrome 47,48 and Werner Syndrome 49.Concomitantly,global hypomethylation of DNA has been extensively observed in tis-sues from aged individuals 50 and in cellular models of senescence51,fostered by age-associated changes in the expression and activityof enzymes involved in epigenetic modifications contributing to het-erochromatin loss.For instance,expression of the histone methyl-transferase SUV39H1/2 is downregulated during aging 45,46,as isthe expression of DNMT1 52.At present it is not clear if heterochromatin loss is a side-effect of thedysregulation of the epigenetic maintenance machinery during aging orif it is-at least in part-the result of a regulated,programmed process.Indeed,although usually referred to as“global”,age-associated loss ofheterochromatin is not a-specific and occurs preferentially at Alu re-peats compared to LINE-1 sequences 50,53,54.However,age-asso-ciated decrease in LINE-1 methylation has also been reported 55,56.2.3.Reproducible age-associated epigenetic changesIn addition to the prominent whole genome loss of heterochromatinat repetitive sequences,several non-repetitive genomic regions,oftenlocated in genes,gene promoters and surrounding sequences also un-dergo epigenetic remodelling during aging.Depending on the genomicregion,these changes can consist in a gain or in a loss of specific epi-genetic markers(for example,acquisition or loss of DNA methylation,referred as hyper-or hypo-methylation,respectively)11.Epigenome-wide association studies(EWAS)have provided a consistent repertoirefor the so called normative changes in epigenetic marks associated withC.Nardini et al.Seminars in Immunology 40(2018)496050aging,that is changes at specific genomic loci that reproducibly char-acterize the epigenome of aged people.Most of these epigenetic mar-kers of aging actually are DNA methylation markers,while ourknowledge of locus-specific histone changes during human aging isscarcer 14,57,58.This is mainly due to technical reasons,as pur-ification of genomic DNA from whole blood and other human tissues ismuch simpler compared to chromatin recovery and histones analysis.Furthermore,EWAS studies on DNA methylation have enormouslybenefited from the availability of Illumina Infinium microarrays,morecost-effective than sequencing approaches,that have been used toquantitatively measure methylation in thousands of subjects of differentages.The chip assesses CpG sites(evolving from roughly 27,000 to480,000 and up to 850,000 with the last version of the array)re-presenting only a minor fraction of the 28 million CpG sites in thehuman genome.However,the design of the microarray has proven tobe highly informative in reproducibly identifying hundreds of loci thatspecifically undergo hypermethylation or hypomethylation with aging5961.The drivers of these site-specific age-associated DNA methylationchanges,as well as their functional and phenotypical consequences,arelargely unknown.Plausible hypotheses include that at least a fraction ofthese changes is related to the accumulation of mitotic divisions62,63 or is the result of the purposeless continuation of develop-mental programs 64.On the other hand,it has also been hypothesisedthat stochastic events,including molecular damage,converge in ste-reotyped epigenetic changes at specific loci 14.2.4.The epigenetic clocksIn the past years,normative changes in DNA methylation at specificCpG sites have been combined in mathematical models able to estimatechronological age 60,61,6568.The most popular among thesemodels are Horvaths,based on 353 Infinium CpG probes 61 andHannums epigenetic clock,based on 71 Infinium CpG probes 60.While Horvaths clock can be applied to estimate epigenetic age in awide range of human tissues,Hannums clock is specific to whole blood.The epigenetic age predicted according to these clocks is highly cor-related with chronological age in physiological conditions,while de-viations from this correlation can be informative of the presence ofbiological signs of accelerated or decelerated aging.This is relevant as,for example,epigenetic age acceleration that is,an older biologicalthan chronological age has been found in individuals affected by age-related conditions such as Down Syndrome,Werner Syndrome,Par-ki