Abstract

Largemulti-centerGWAstudieshavefoundassociationsbetweenover20genomiclociandlate-onset Alzheimer?sdisease(LOAD).However,theprecisetargetgenes,thecausalgeneticvariantsandtheir molecularmechanismsofactionthroughwhichtheyexerttheirpathogeniceffectsremainlargelyunknown. Ourlong-termgoalistoelucidatecausalgeneticfactorsandtheirfunctionaleffectsthatcontributetotheriskof developingLOAD.Ourcentralhypothesisisthatchangesinexpressionlevelsofcriticaldiseasegenesisan importantmolecularmechanismunderlyingLOADetiologyandthatcausalvariantsmodulateexpressionof thesediseasegenes,andbythatcontributetoLOADrisk.ChangesingeneexpressioninLOADvs.healthy controlsweredescribedinbraintissuesbyourteamandothersandpreviousstudiesreportedthecis- associationsoftaggingSNPswithexpressionofnearbyLOAD-riskgenes,providingastrongscientificpremise fortheproposedstudy.Inthisstudy,wewillemployamultifacetedapproachthatcombinesinsilico,invitro andinvivomethodstoinvestigateregionsinthegenomethatweresignificantlyassociatedwithLOAD-riskin GWAstudies.
In Aim1 wewillidentifytargetgeneswithinLOAD-associatedregionsthatshowdifferential expressionalongtheneuropathologicalprogressionofLOAD.Wewilldeterminetheexpressionprofileof geneswithintheseregionsinneurons,astrocytesandmicrogliaisolatedfromaffectedandunaffectedrapidly autopsiedhumanbraintissuesusinglasercapturemicrodissection(LCM)coupledwithnCountersinglecell geneexpressiontechnology(NanoString).
Aim2 willdiscoverregulatorynoncodingsequenceswithinLOAD- associatedregions.First,wewillprioritizecandidateregulatoryelementsusingbioinformaticstoolsandhuman genomedatabases,aswellasATAC-sequencingexperimentsusingNeuN+/-nucleifromaffectedand unaffectedhumanbraintissuestodeterminechromatinaccessibilityprofilesincelltype-andpathological stage-specificmanners.Thefunctionalityofthecandidatenoncodingsequenceswillbethencharacterized usingiPSC-derivedmodelsystemsthatwillbegenomeeditedtocarrydeletionsofthepredictedregulatory sequences.
Aim3 willfocusonShortStructuralVariants(SSVs)andwillinvestigatethefunctionaleffectsand causalityofSSVsinthecandidateregulatorysequences.WewilluseSMRTsequencingcombinedwithCas9 system(PacBio)toaccuratelydeterminetheSSVsgenotypeandhaplotypesinLOADcomparedtocontrol subjects,andwillexaminetheirregulatoryeffectsusinggenomeeditedisogeniciPSC-derivedneuronsand/or astrocytesmodelsthatcarrydifferentalleles/haplotypesattheSSVsite.Ourstudywilladvancethe identificationofcausalgeneticfactorsandtheunderstandingoftheirmoleculareffectsthatcontributetothe riskofdevelopingLOAD.Thisknowledgewillprovideinsightregardingactionabletargetsfordevelopmentof noveltherapiesforLOAD.Furthermore,theidentifiedSSVswilladvancethedevelopmentofgenetic biomarkersforearlydiagnosisandforenrichmentofclinicaltrialswithsubjectsathighrisk.

Public Health Relevance

LateonsetAlzheimer?sdisease(LOAD)isacriticalunmetmedicalneed.Thediseaseprocessstartsdecades beforeplaquesortangleneuropathologiesaredetectable,andalthoughgeneticscontributestotheriskto developLOADtheprecisegeneticfactorsandtheirmechanismsofactionremainlargelyunknown.Ourstudy seekstouncoverthegeneticdeterminantsandmolecularmechanismsunderpinningLOAD.Understandingthe geneticfactorsaffectingtheetiologyofLOADwillleadtothediscoveryofpreventivetherapiestargeting moleculareventsthatoccurearly;?yearsbeforethemanifestationofneuropathologicalchangesandclinical symptoms.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute on Aging (NIA)
Type
Research Project (R01)
Project #
5R01AG057522-03
Application #
9719711
Study Section
Special Emphasis Panel (ZAG1)
Program Officer
Wise, Bradley C
Project Start
2017-09-15
Project End
2022-05-31
Budget Start
2019-06-01
Budget End
2020-05-31
Support Year
3
Fiscal Year
2019
Total Cost
Indirect Cost

  Institution

Name
Duke University
Department
Neurology
Type
Schools of Medicine
DUNS #
044387793
City
Durham
State
NC
Country
United States
Zip Code
27705