chromatin jc.150507-alzheimers epi-roadmap+amb
TRANSCRIPT
EpigenomicsJC150507
Gjoneskaetal.2015Nature518(365)
Lunnonetal.2015NatureNeurosci.17(9)
ÁlvaroMartínezBarrio,[email protected]/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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+ 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.