chromatin jc.150507-alzheimers epi-roadmap+amb

EpigenomicsJC150507

Gjoneskaetal.2015Nature518(365)

Lunnonetal.2015NatureNeurosci.17(9)

ÁlvaroMartínezBarrio,PhDmartinezbarrio.alvaro@gmail.comlinkedin.com/in/ambarrio@ambarrio

ExtendedFigure1

ExtendedFigure1

Cyclin-dependentkinase5,regulatorysubunit1(CDK5R1->p35)

cyclin-dependentkinase5(CDK5)

ExtendedFigure1

Cyclin-dependentkinase5,regulatorysubunit1(CDK5R1->p35)

cyclin-dependentkinase5(CDK5)calpain

(p25)+relocalizationfromthecellperipherytonuclearandperinuclearregions

ExtendedFigure1

Cyclin-dependentkinase5,regulatorysubunit1(CDK5R1->p35)

cyclin-dependentkinase5(CDK5)

(p25)

+ deregulatesCDK5activitybyprolongingitsactivationandchangingitscellularlocation.

+ p25formaccumulatesinthebrainneuronsofpatientswithAD.

+ accumulationcorrelateswithanincreaseinCDK5kinaseactivity

+ mayleadtoaberrantlyphosphorylatedformsofthemicrotubule-associatedproteintau,whichcontributestoAD.

ExtendedFigure1

Cyclin-dependentkinase5,regulatorysubunit1(CDK5R1->p35)

cyclin-dependentkinase5(CDK5)

(p25)

ExtendedFigure1

+ Tripletransgenic(Tg)miceover-expressinghumanp35,Cdk5,andtau,despitesignificantincreasesinCdk5activityinthesemice,donotdisplayanincreaseintauphosphorylation(VandenHauteetal.,2001).!

+ GenerationofInducibleTgMiceoverexpressinghumanp25inthePostnatalForebrainusingthetetracycline-controlledtransactivator(tTA)systemunderthecontroloftheCamKIIpromoter,whichdriveshightransgeneexpressionintheforebrain(Mayfordetal.,1996).!

+ Inthepresenceofthetetracyclinederivativedoxycycline,expressionofthep25transgeneisinhibited.!

+ Allmiceareconceivedandraisedinthepresenceofdoxycyclinebeforeinductionofp25topreventanypotentialdevelopmentalconsequencesfromtheexpressionofp25.

5. Cruz,J.C.,Tseng,H.-C.,Goldman,J.A.,Shih,H.&Tsai,L.-H.AberrantCdk5activationbyp25triggerspathologicaleventsleadingtoneurodegenerationandneurofibrillarytangles(NFTs).Neuron40,471–483(2003).

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2.Blalock,E.M.,Buechel,H.M.,Popovic,J.,Geddes,J.W.&Landfield,P.W.Microarrayanalysesoflaser-capturedhippocampusrevealdistinctgrayandwhitemattersignaturesassociatedwithincipientAlzheimer’sdisease.J.Chem.Neuroanat.42,118–126(2011).

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4.Lambert,J.C.etal.Meta-analysisof74,046individualsidentifies11newsusceptibilitylociforAlzheimer’sdisease.NatureGenet.45,1452–1458(2013).

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+ Among20genome-widesignificantADloci,11non-codingAD-associatedSNPinLD.5/11localisew/iincreased-levelenhancers(e.g.PICALM,BIN1)andthree(INPP5D,CELF1/SPI1,PTK2B)bycombiningallADcohorts.!

+ Additional22weaklyassociatedregionscontainsvariantsw/iincreased-levelenhancerorthologues,17lackprotein-alteringvariantsinLD(e.gABCA1,prologueofAD-associatedABCA7).

Figure3

29. Krimbou,L.etal.MolecularinteractionsbetweenapoEandABCA1:impactonapoElipidation.J.LipidRes.45,839–848(2004).

ApolipoproteinE(ApoE)

+ ClassofapolipoproteinfoundinthechylomicronandIntermediate-densitylipoprotein(IDLs)thatisessentialforthenormalcatabolismoftriglyceride-richlipoproteinconstituents.

+ Inperipheraltissues,ApoEisprimarilyproducedbytheliverandmacrophages,andmediatescholesterolmetabolisminanisoform-dependentmanner.

+ IntheCNS,ApoEismainlyproducedbyastrocytes,andtransportscholesteroltoneuronsviaApoEreceptors,whicharemembersofthelowdensitylipoproteinreceptorgenefamily.

+ ADaffects26mpeopleworldwide.!+ Accumulationofamyloidplaques>NFTbyhyperphosphorylatedtau>gliosis>synapticdysfunction>neuronalcelldeath!

+ Progressiveneurodegenerationacrossthecortex,withareasofearlyneuropathologyastheentorhinalcortex(EC)andothersresistanttoneuronaldamagelikethecerebellum(CER).!

+ EtiologyofADfocusedprimarilyonDNAsequencevariation.JonathanMillisanadvocateofepigenome-wideassociationstudies(EWAS).

• StudyDESIGN:onediscoverycohort(n=122)withfourbrainregions(EC,STC,PFC,CERandbloodpre-mortem),2confirmationones(n=144andn=62).

!• TOOL:Illumina450KHumanMethylationarrayandsometargetedbisulfite-pyrosequencing.

!• CATEGORIES:Braakstaging(0-VI),astandarizedmeasureofneurofibrillarytangleburdendeterminedatautopsy.

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SupplementaryFigure1

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+ EWASofADpathologyin708corticalsamples

21. DeJager,P.L.etal.Alzheimer’sdiseasepathologyisassociatedwithearlyalterationsinbrainDNAmethylationatANK1,BIN1andotherloci.Nat.Neurosci.doi:10.1038/nn.3786(17August2014).

SupplementaryFigure2

+ Althoughnotpreviouslyimplicatedindementia,geneticvariationinANK1isassociatedwithdiabeticphenotypes,establishinglinksbetweenT2DandAD.

SupplementaryFigure3

SupplementaryFigure4(N=36)

+ ClinicalbiomarkerswithdiagnosticandprognosticutilityduringAD-development.+ Pre-mortemwhole-bloodDNAfromthediscoverycohort(n=57).+ Durationbetweenbloodsamplingandmortality(avg=4.15±3.00years).+ AnalysesrestrictedtoidentificationofDMPsassociatedwithclinicaldiagnosisofADinsteadofBraakscore.+ IdentifyanumberifAD-associatedDMPs,manyinthevicinityofrelevanttoADgenes(e.g.DAPK1,GAS1,NDUFS5).

+ However,thetop-rankedDMPsinbloodaredistinctfromthoseidentifiedinthebrainastheyshownosignificantoverlapwitheithercortexorCER.

+ AD-associatedDMPsinbloodareunlikelyrelatedtotheactualneurodegenerativeprocess.+ However,usingpreviousblood-basedtranscriptomicdata(ref.38),theyobserve18oftheirtop-rankedbloodDMPslocatedinthevicinityofknowndifferentiallyexpressedtranscripts.

Figure4

Gjoneskaetal. Lunnonetal.2015

• ContrastingchangesinimmuneandneuronalgenesandregulatoryregionsduringAD-likedegeneration

• Surprisingdepletionofneuronalpromotersandenhancersforacognitivedisorderwithwell-establishedconnectionstoenvironmentalandexperientialfactors

• Modelofinteractionsbetweengeneticallydrivenimmunecelldysregulationandenvironmentallydrivenepigeneticalterationinneuralcells

• PoweroftheCK-p25mousemodelforthestudyofADhumandiseaseprogression.Molecularchangesinbothgenesandregulatoryregionsarehighlyconserved.

• SpecifictherapeutictargetsforAD(e.g.PU.1)

• Largestcross-tissuestudyofADusingmatchedDNAfrombothaffectedandunaffectedbrainregions.Firstsequentialreplicationwith3independentstudycohortsand2independenttechnologies.

• Cortex-specifichypermethylationacrossanANK1regioninseveralindependentcohortssuggestiveofthelocusbeingrelevanttoAD-pathogenesis.MostsubstantialinEC.ReplicationofthesameDMRinanotherlargeEWASofAD(DeJageretal.).

• Mostbrain-identifiedDMPs,includingANK1,notdetectedinblood.ButmanyDMPsinbloodlocatedinvicinityofgenesfoundalteredinpatientswithMCI.

• CarefulcontroloftechnicalartefactsinEWASwithIllumina450Karray.

• PowercalculationsfromEWASinstudydesign.Theystatetobepoweredtoidentifyrelativelysmall(~5%)DNAmethylationdifferencesbetweengroups.

• Conventionalmethodsformultiple-testcorrectionlikelytobeoverlystringentandinappropriategivennon-independenceoflociandlackofinter-individualvariation.