25th HUPO Human Brain Proteome Project Workshop
Program
May 3-4, 2016
Stockholm, Sweden
This workshop will provide a forum for
researchers to meet and discuss the latest
developments in neuroproteomic initiatives
to better understand brain disorders
The HUPO Human Brain Proteome Project (HBPP):
Scientific board
Lea Grinberg, UCSF, USA & Brazilian Brain Bank, São Paulo, Brazil
Katrin Marcus, Medizinisches Proteom-Center, Bochum, Germany
Oliver Schubert, University of Adelaide, Australia
Charlotte Teunissen, VU University Medical Center Amsterdam, Netherlands
Daniel Martins-de-Souza, University of Campinas, Brazil
Peter Nilsson, SciLifeLab, KTH, Stockholm, Sweden
Local organisers
Peter Nilsson and Anna Häggmark
SciLifeLab, KTH, Stockholm, Sweden
HBPP mission:
”Create and harbour a broad
and global network of
neuroproteomic researchers
with a focus of attracting
young researchers”
www.hupo.org/hbpp
Incollabora*onwith
HBPP
25th HUPO Human Brain Proteome Project Workshop
TuesdayMay3
WednesdayMay4
8.30
9.00
Session4:
Alzheimer'sdisease
9.30
10.00
10.30
11.00
11.30
Coffeeandregistration
Welcome
HBPPhistory
Session1:
Tissue-basedproteomic
profiling
Coffee
Session5:
PDandotherdementias
12.00
12.30
Lunch
Lunch
13.00
13.30
14.00
14.30
Session2:
Technicaladvancementsin
neuroproteomics
15.00
15.30
Coffeebreak
Session3:
Psychiatricdisorders
17.00
17.30
18.00
18.30
Coffeebreak
Session7:
Otherneurological
disorders
Generaldiscussionand
concludingremarks
16.00
16.30
Session6:
Autoimmunityinbrain
disorders
Pubandmingle
19.00
Dinner
25th HUPO Human Brain Proteome Project Workshop
TuesdayMay3
09.30-10.00
10.00-10.15
Coffeeandregistration
Welcome
PeterNilsson,KTH-RoyalInstituteofTechnology,Stockholm,Sweden
AnnaHäggmark,KTH-RoyalInstituteofTechnology,Stockholm,Sweden
10.15-10.30
HBPPhistory
HelmutEMeyer,ISAS-Leibniz-InstitutfürAnalytischeWissenschaften,Dortmund,Germany
YoungMokPark,CenterforCognitionandSociality,InstituteforBasicScience,Daejeon,Korea
10.30-12.00
Session1:Tissue-basedproteomicprofiling
Chair:LeaT.Grinberg
10.30-10.45
Beyondthehorizonsinneuropathology
LeaT.Grinberg,UCSF,USA&BrazilianBrainBank,SãoPaulo,Brazil
Neuropathologyisarelativelyolddisciplineknownforstillusingmethodsdevelopedoveracentury
ago.Difficultiesinprocurementandexaminationofclinicalspecimens,theadventofhighthroughput–omics,andadvancesinanimalmodelswiththeirabilitytoprovideinsightintothe
mechanismsofadiseaseprocess,ledtoawaningofinterestinneuropathologythathasbeen
renderedobsolete.Mytalkwillfocusonthetransformationofneuropathologyintoa21st-century
scienceontheforefrontofadvancesinneurosciences.Byincorporatingelementsofmolecular
biology,improvedmicroscopy,advancinggraphics,andtechnologytodealwithbigdatainthe
studyofhumanbrainspecimens,neuropathologyistransformingbiomarkerdiscoveryand
treatmentdevelopmentinseveralareasofneurologyandrapidlyreinstatingitselfasavaluable
playerinthecontemporaryneurologicalresearch.
10.45-11.00
Addressingthechallengesofquantitativemyelinproteomics
OlafJahn,ProteomicsGroup,Max-Planck-InstituteofExperimentalMedicine,
Göttingen,Germany
Rapidsignalpropagationalongvertebrateaxonsisfacilitatedbytheirinsulationwithmyelin,a
plasmamembranespecializationofglialcells.Recentinsightsfrom‘omics’approachesindicatean
activeroleofmyelinatingglialcellsasessentialsupportersofaxonalfunctions.Oncemyelinated,
thelong-termintegrityofaxonsdependsonglialsupplyofmetabolitesandneurotrophicfactors,
anditsfailureisinvolvedinmanyneurologicaldisorders.Technicaladvancesinmyelinproteomics
formthebasisforabetterunderstandingoftheseaxon-glialinteractionsandpavethewayfor
quantitativecomparisonofmyelinproteomesfrommutantmiceorpatientmaterial.
Keywords:myelinproteomics,synapticproteincomplexes,biomarkerforneurologicaldiseases
11.00-11.15
Brainstem:apromisingtargetfornewdiscoveriesinneurodegenerativediseases
RenataLeite,PhysiopathologyinAgingLabandDisciplineofGeriatrics,Universityof
SaoPauloMedicalSchool,Brazil
StudieshaveshownthatpathologicalprocessesrelatedtoParkinson’sandAlzheimer’sdisease
appearinthebrainstembeforetheyreachcorticalbrainareas.However,manyquestionsremain
abouttheinitialstages,mechanismsandprogressionofneurologicaldiseases(NDs).Inthecaseof
Parkinson’sdisease,itisknownthatneuromelanin-harboringneuronsinthesubstantianigraofthe
brainstemarevulnerabletoabnormalproteindepositionandsubstantialneuronalloss,butthe
correlationbetweenthesetwotypesoflesionshasyettobeestablished.Also,ithasbeenshown
thatproteindepositionoccursinotherbrainstemnucleievenbeforethesubstantianigrais
affected.Therefore,theanalysisofpostmortemhumanbrainstems,includingproteomicsresearch,
holdspotentialtounveilimportantinformationrelatedtotheoriginandprogressionofNDs.
Keywords:humanbrain,aging,neurodegenerativediseases
25th HUPO Human Brain Proteome Project Workshop
11.15-11.30
Antibodybasedprofilingofproteindistributioninthebrain,focusonnormal
physiologyanddisease
JanMulder,ScienceforLifeLaboratory,DepartmentofNeuroscience,Karolinska
Institutet,Stockholm,Sweden
Completionofthegenomeprojectsandrecentdevelopmentsintranscriptomicshaverevealedthe
blueprintofthehumanbody.Wenowhaveanearcompleteoverviewofallgenesandproteinsand
areabletolinkgenestoorgansandtissues.Thechallengeforthefutureistoincreasethe
resolutionofthisbody-mapbylinkingproteinstocells,cellularcompartmentsandcellular
functions.HumanProteinAtlasprojectaimstoprovidethisessentiallayerofinformationusingan
antibodybasedapproach.Mappingproteindistributioninthebrainwithitscomplexcellular
organisation,broadspectrumofphysiologicalfunctions,expressingmorethan70%ofallgenes,is
amongthespecificaimswithintheHPAproject.
11.30-11.45
Howtoexplorebrainproteinsinthenormaltissueatlas
EvelinaSjöstedt,ScienceforLifeLaboratory,Departmentofproteomics,KTH,
Stockholm,SwedenandDepartmentofImmunology,GeneticsandPathology,Uppsala
University,Uppsala,Sweden
IntheHumanProteinAtlassofar,afewselectedbrainregionsisselectedasrepresentationofthe
humannormalbrain.Thisisgraduallychangingbyaddingmoreregionsandspecializedtissue
sections,therebyprovidingabetteroverviewoftheproteinlocationinthenormalhumanbrain.
Keywords:Normalbrain,proteinlocalization,FFPEtissue
11.45-12.00
AtlasAntibodies:Advancedresearchreagentsforstudyinghumanproteins
EugeniaKuteeva,AtlasAntibodiesAB
AtlasAntibodies,acompanyfoundedbyresearchesfromtheHumanProteinAtlasproject,is
manufacturingandcommercialisingtheaffinityreagentsforstudyingthehumanproteome.Our
productportfolioincludesalargenumberofhighlyspecificandselectivepolyclonalantibodies,
coveringmorethan15000geneproducts.Inaddition,agrowingnumberofmonoclonalantibodies
forselectedtargetsisbeingdevelopedin-house.OurlatestQPrESTproductlinerepresentsanew
categoryofisotope-labelledinternalstandardsformassspectrometry(MS)-basedprotein
quantificationofferingdistinctadvantagestoexistingproducts.Thispresentationwillfocusonour
productsofrelevancefornervoussystemstudies.
Keywords:Antibodydevelopment,Immunohistochemistry,Histology
12.00-13.00
Lunch
RestaurangKönigs,Nobelsväg18
25th HUPO Human Brain Proteome Project Workshop
13.00-15.00
Session2:Technicaladvancementsinneuroproteomics
Chair:OliverSchubert
13.00-13.15
Revealingproteomicsofcerebralorganoidsfromhumanpluripotentstemcells:
aimingtounderstandthemechanismsofbraindiseases
JulianaMinardiNascimento,LaboratoryofNeuroproteomics,Departmentof
BiochemistryandTissueBiology,InstituteofBiology,UniversityofCampinas
(UNICAMP),Campinas,SaoPaulo,Brazil
Pluripotentstemcellscandifferentiateintoanycelltypeofanorganism.Moreover,theyhavea
remarkablecapacitytoself-organizeanddevelopintothree-dimensionalstructuresresembling
miniatureorgans.Cerebralorganoidsrecreateearlystepsofthehumancerebralcortex
development,showinggreatpotentialforhumanmodelingstudies,particularlythosewitha
developmentalcomponent.Analyzingglobalproteinexpressionofcerebralorganoidswefound
proteinsbroadlydistributedonfunctionalactivitiessuchascellgrowth,energymetabolismandcell
communicationandsignaling,whicharecorrelatedtocorticalbraintissue.Proteomicsadd
knowledgeaboutinformationandconnectionsbeingformed,atoparchitectureandselforganizationalreadydescribed
Keywords:neuroproteomics,pluripotentstemcells,cerebralorganoids
13.15-13.30
MRMasproteomictoolfortheanalysisofcerebrospinalfluidinneurodegenerative
diseases
PatrickOeckl,DepartmentofNeurology,UlmUniversityHospital,Ulm,Germany
Thediscoveryofnewbiomarkersincerebrospinalfluid(CSF)ishighlyappreciatedtofacilitateand
improvediagnosisofneurodegenerativediseases.Todate,immunoassaysarethefirstchoicefor
biomarkermeasurementsinCSFduetotheirconvenienceandspeed,buttheirapplicabilityis
hamperedfornewbiomarkercandidatesbyunknownspecificityandlimitedavailabilityof
antibodies.Thehighlyselectivemultiplereactionmonitoring(MRM)isanattractivealternative
whichinprincipalallowstheanalysisofanybiomarkerandalsomultiplexingbutstudiesusingMRM
fortheanalysisofCSFbiomarkersaresparse.Inthiscontext,Iwillpresentsuccessfulapplications
ofMRMforCSFbiomarkerssuchasubiquitinandalsodiscussconsiderationsandexperiences
regardingtheuniquepropertiesofCSF.
Keywords:NeurochemicalBiomarker,Proteomics,MultipleReactionMonitoring
13.30-13.45
Brainupyouranalysismethodology-ProteomeBioinformaticsandBiostatisticsin
ClinicalResearch
MartinEisenacher,MedizinischesProteom-Center,Ruhr-UniversityBochum,Bochum,
Germany
ThispresentationpresentsfacetsoftheworkintheresearchareaMedicalBioinformaticsofthe
MedizinischesProteom-Center,whicharelinkedtotheProteomicsperformedwithmass
spectrometryandthepracticalanalysisofclinicalresearchdata.Onetopicistheproteininference/
proteinambiguity,whichtakesplacein“bottom-upProteomics”,whenreportingtheproteins
explainedbytheactuallyidentifiedpeptides.Furthermorethestandardsforthedescriptionand
storageofProteomicsdataandconversionofdataandresultsintotheseformatswillbesketched.
Alsoamethodforidentifyingsamplesubgroupswillbesummarized,whichcanbeusedtodetect
yetunknown“molecularsubgroups”ofheterogeneousdiseases.Theactivitiesareavailableforthe
ProteomicscommunityinaBMBF-funded“GermanNetworkforBioinformaticsInfrastructure
(de.NBI,www.denbi.de)”.
Keywords:BioinformaticsofProteomics,ProteomicsStandardFormats,BiostatisticsinClinical
Research
25th HUPO Human Brain Proteome Project Workshop
13.45-14.00
Diagnosticandtherapeuticpotentialofextracellularvesicles
FouziElMagraoui,BiomedicalResearch,HumanBrainProteomics,Leibniz-Institutfür
AnalytischeWissenschaften–ISASe.V.,Dortmund,Germany
Extracellularvesicleshaveemergedasimportantmediatorsofvariouscellularfunctions.Theyare
secretedbyeverycelltypeandaredetectableineverybodyfluide.g.blood(serumandplasma),
urine,breastmilk,sweat,saliva,ascitesfluid,andcerebralspinalfluid.Recentresearch
demonstratetheir(patho)physiologicalrolesinvariousdiseases,includingcancer,infectious
diseasesandneurodegenerativedisorders.Incooperationwithourpartnersweperformed
differentmulti-omicsapproachestoinvestigatethepotentialoftheEVs.Thuswehavebeenable
todetectvariousADrelatedbiomarkersinplateletderivedEVs.Inotherprojectswehavebeen
abletoidentifysurrogatemarkersofStrokeandGraft-versus-Host-DiseaserelatedtherapeuticEVs.
Keywords:ExtracellularVesicles,Multi-Omics,Neurodegeneration
14.00-14.15
Clinicalproteomicsandpeptidomicsforidentificationofcerebrospinalfluid
biomarkersofneurodegenerativedisorders
JohanGobom,InstituteofNeuroscienceandPhysiology,SectionofPsychiatryand
Neurochemistry,UniversityofGothenburg
Clinicalproteomicsisanemergingfieldthathasthepotentialtocontributegreatlytoresearchinto
ourmostcommonneurodegenerativediseasesbyuncoveringbiomarkersfordiagnosisand
monitoringtreatmenteffects,andstimulatingtheformulationofnewhypothesesondisease
mechanisms.Wepresentmethodsdevelopedforproteomicandpeptidomicanalysisin
cerebrospinalfluidandtheirapplicationtobiomarkerdiscoveryinAlzheimer’sdiseaseand
Parkinsoniansyndromes.
Keywords:CSFproteomics;neurodegeneration;biomarkers
14.15-14.30
Antibody-basedCSFprofilingwithinmultiplesclerosisrevealsdisease-asociated
profilesofGAP43andSERPINA3
AnnaHäggmark,AffinityProteomics,Scilifelab,KTH-RoyalInstituteofTechnology,
Stockholm,Sweden
Antibody suspension bead arrays enable multiplexed and high-throughput protein profiling in
unfractionated body fluids through a direct labeling approach. A CSF profiling protocol was
established and applied to profile 43 selected proteins by 101 antibodies in almost 600 CSF samples
from a multiple sclerosis cohort. Two proteins, GAP43 and SERPINA3 were found with altered levels
between sample groups. The developed assay procedure offers new possibilities for broad-scale
protein profiling of CSF within neurological disorders. This technology, with its ability to screen up
to 384 samples and 384 analytes in parallel, combined with the unique antibody resources from the
Human Protein Atlas creates great potential for future research in the quest of finding disease
relatedpatterns.
Keywords:AffinityProteomics,CSF,multiplesclerosis
14.30-14.45
Effectsofhypertensiononthebrain:aninitialtop-downproteomicanalysis.
JensR.Coorssen,SchoolofMedicine,NanoscaleOrganisation&DynamicsGroup,
SchoolofScience&Health,WesternSydneyUniversity,Australia
Keywords:2DE,mousemodel,diseaseinitiationandprogression
25th HUPO Human Brain Proteome Project Workshop
14.45-15.00
QuantifyingDementia
JudithSteen,HarvardMedicalSchool,BostonChildren’sHospital,F.M.KirbyCenter
forNeurobiology,Boston,USA
Ourlaboratoryusescomputationalmethodstointerfaceandmineproteomicsandgenomicdatain
anefforttolearnaboutregenerationanddegenerationofneurons.Thisapproachallowsusto
understandhowneuronsarebornandwhatmakesthemdie.Ourmostrecenteffortshavefocused
ondementiaincludingAlzheimer’sdisease,whereneuronsdegenerateandeventuallydiecausing
thelossofmemoryandfunctioninpatients.AnewtechnologythatwedevelopedcalledFLEXITau
allowedustostratifydifferenttypesofpatientssufferingfromdementiaconnectedwithaprotein
calledTau.Thistechnologyallowedustoidentifyspecificmolecularchangesintaufrompatients
whohavedementiabutnotintaufromhealthypeople.
Keywords:Quantitative-Proteomics,Bioinformatics,Neurodegeneration
15.00-15.30
15.30-17.30
Coffeebreak
Session3:Psychiatricdisorders
Chair:DanielMartins-de-Souza
15.30-15.45
Biologicalpathwaysmodulatedbyantipsychoticsinthebloodplasmaof
schizophreniapatientsandtheirassociationtoaclinicalresponse
DanielMartins-de-Souza,LaboratoryofNeuroproteomics,DeptofBiochemistry,
UniversityofCampinas(UNICAMP),Campinas,SãoPaulo,Brazil
Ourmaingoalsareunravelingbiochemicalpathwaysmodulatedbyantipsychoticmedicationas
wellasrevealingproteinsthatcanactaspotentialbiomarkersindicatingthelikelihoodofa
successfultreatment.Ourlatestresultsshowedthatallpatientsanalysedpresentessentiallythe
samebiochemicalpathwaystriggeredindependentoftheantipsychoticresponseoutcome.
However,weobservedthatthesepathwayswereregulatedindifferentdirectionsinbloodsamples
fromthosewhorespondedwelltoantipsychotics,comparedwiththosewhohadapoorer
outcome.
Keywords:psychiatry,schizophrenia,translationalpsychiatry
15.45-16.00
PeripheralbloodgeneexpressionandproteomicanalysisimplicatesB-cell
developmentandribosomalproteinsincognitivedysfunctioninpeoplewith
remittedMajorDepression
K.OliverSchubert,NorthernAdelaideLocalHealthNetwork-MentalHealthServices,
DisciplineofPsychiatry,SchoolofMedicine,UniversityofAdelaide,Adelaide,Australia
CognitiveimpairmentsareobservedinasubstantialproportionofpatientssufferingfromMajor
DepressiveDisorder(MDD),significantlyimpactingonpatients’psychosocialfunctioningand
qualityoflife.Weutilizedwhole-bloodtranscriptomicdatafromremittedMDDpatientsfor
weightedgenecoexpressionnetworkanalysis(WGCNA),andidentified16transcriptomicmodules.
Onemodulewassignificantlycorrelatedwithpoorversusbettercognitiveperformance,containing
ribosomalgenesandmodulatorsofBcellbiology.Ontheplasmaproteinlevel,SWATH-MS
detected43%ofmodulegeneproducts,andgroupdifferenceswereconfirmed.Theexperimental
workflowmayrepresentaneffectiveapproachtobloodbiomarkerdiscoveryforpsychiatric
phenotypes.
Keywords:PsychiatricProteomics,PsychoticDisorders,YouthMentalHealth
25th HUPO Human Brain Proteome Project Workshop
16.00-16.15
Proteomicapproachestounderstandingthepostsynapticdensityinschizophrenia
andbipolardisorder
DavidCotter,RoyalCollegeofSurgeonsinIreland,Dublin,Ireland
Thepostsynapticdensity(PSD)containsacomplexsetofproteinsofknownrelevanceto
neuropsychiatricdisorderssuchasschizophreniaandbipolardisorderthroughitsrolesinsynaptic
plasticityandcognitivefunction.GenomicandclinicalsupportfortheinvolvementofthePSDin
neuropsychiatricdisordersisincreasinglyrobust.WeutilizedPSDenrichmentmethodsandlabelfreeproteomicmethodstocharacterizethedisease-associatedPSDproteomeinschizophreniaand
bipolardisorderforthefirsttime.Weenrichedforthisanatomicalstructureintheanterior
cingulatecortexof16bipolardisorder,20schizophreniacasesand20controlsfromtheStanley
MedicalResearchInstituteandusedunbiasedshotgunproteomicsincorporatinglabel-free
quantitationtoidentifydifferentiallyexpressedproteins.QuantitativeinvestigationofthePSD
revealedmorethan288differentiallyexpressedproteinsinbipolardisorderandpathwayanalysis
ofthedifferentiallyexpressedproteinsimplicatedmitochondrialassociatedproteins,oxidative
phosphorylationandthetricarboxylicacidcycleandalsocalciumsignaling,andendocytosisinboth
disorders.Proteintranslationwasimplicatedinbipolardisorderaloneandlong-termpotentiation
wasimplicatedinschizophreniaalone.OurdataproviderobustevidenceimplicatingPSDassociated
proteins,andspecificallymitochondrialfunctionwiththePSDinbipolardisorderandschizophrenia.
Calciumsignaling,longtermpotentiation,endocytosisandproteintranslationwerealsoimplicated
andtogetherthefindingsconvergetohighlightarolefortheregulationofsynapticplasticityinthe
majorpsychosis.
Keywords:neuroproteomics,plasmabiomarkers,schizophrenia
16.15-16.30
Investigatingproteinpathologyinschizophreniabyidentifyingtheinsoluble
proteome
CarstenKorth,InstitutfürNeuropathologie,HeinrichHeineUniversitätDüsseldorf,
Düsseldorf,Germany
Chronicbraindiseasesarecharacterizedbyafailureinproteostasisasseenintheclassical
neurodegenerativediseases.Sincechronicmentalillnesseslikeschizophreniaortherecurrent
affectivedisordersarealsocharacterizedbyachroniccourse,wehypothesizedthattobiologically
characterizetheseconditions,theidentificationofaproteostasisphenotypewouldberevealing.
Wepurifiedtheinsolubleproteome,i.e.thoseproteinsthatpelletafterultracentifugationanda
biochemicalmulti-stepfraction.Thisfractionwasanalyzedfor1.Candidateproteins,2.epitope
discovery,and3.ByLC-MS/MS.WefindDISC1,dysbindin,CRMP1,TRIOBP1,NKCC1asnovel
candidateproteinsforschizophreniaandconfirmtheirproteinpathologyinnovelanimalmodels.
Keywords:molecularpsychiatry,insolubleproteome,schizophrenia
16.30-16.45
Proteome-widestudyofcerebrospinalfluidbiomarkersforbipolardisorder-
multiplexedsemi-quantificationbymassspectrometry
JessicaHolménLarsson,InstituteofNeuroscienceandPhysiology,Neurochemical
pathophysiologyanddiagnosticsresearchunit,SahlgrenskaAcademyatGoteborg
University,Mölndal,Sweden
OuraimistoexplorepathophysiologicalmechanismsforBipolardisorder(BD)andtoidentifynovel
biologicalCSFmarkersfordiagnosticpurposes.ThedigestedCSFproteinsof15BDpatientsand15
matchedcontrols,werelabeledwithisobaricTandemMassTags(TMT)formultiplexedsemiquantificationandanalyzedbynano-liquidchromatography-massspectrometry.676proteinswere
semi-quantifiedand36showedsignificantly(p<0.05)alteredlevelsintheBDpatientsascompared
tocontrols.Amajorityofthealteredproteinsarebrain-specificandinvolvedine.g.cell
growth/communication/adhesion,immuneresponseandproteinmetabolism.Theresultswillnow
bevalidatedintwolargerindependentBDcohorts.
Keywords:Neuropsychiatry,Cerebrospinalfluid,Biomarker
25th HUPO Human Brain Proteome Project Workshop
16.45-17.00
AdvancingBiomarkerDiscoveryinAge12ChildrenwithPsychoticDisorder:Results
fromtheALSPACCohort
JaneAEnglish,DepartmentofPsychiatry,RoyalCollegeofSurgeonsinIreland,Dublin,
Ireland
Biomarkersofearlypsychosisareurgentlyneededtoallowtheearlyidentificationandtreatmentof
thoseatthehighestriskofdevelopingpsychosis.Wedevelopedasimultaneousdiscoveryand
targetedproteomicworkflowtoprofileandverifybiomarkercandidatesofpsychoticdisorderin
age12plasmasamplesfromtheAvonLongitudinalStudyofParentsandChildren(ALSPAC).Using
DataDependentAnalysis(DDA)ontheThermoQ-Exactive,weprofiled37plasmasamplesfromage
12childrenwithanoutcomeofpsychoticdisorder,and38agematchedcontrols.Weidentified61
proteins(p<0.05)aspotentialbiomarkercandidates,35ofwhichremainedsignificantfollowing
FDR(q=0.05).ROCanalysiswasusedtoevaluatethetop8discriminatoryVariablesofImportance
(VIP),resultinginanAUCof0.89.TargetedproteomicanalysisoftheseproteinsusingData
IndependentAnalysis(DIA)ontheThermoQ-Exactiveisunderway.
Keywords:BiomarkerDiscovery,Psychosis,ALSPACCohort
17.00-17.15
UppsalaPsychiatricPatientSamples-UPP
JanetCunningham,DepartmentofNeuroscience,Psychiatry,UppsalaUniversity,
Uppsala,Sweden
UppsalaPsychiatricPatientsamples(UPP)isabiobankwithmaterialanddatafromwellover600
individuals.Patientshavegiveninformedconsenttoresearchendocrine,immunologicaland
geneticcontributionstopsychiatricsymptoms.Thecollectionhasthreepatientsubgroups:i)a
smallscalelevelwhereindividualswithextremeandatypicalphenotypesareincludedusing
exploratorymethodsandexaminedonacase-rapportbasisii)alargescalepopulationbasedlevel
whichisimportantforestablishinggeneralizabilityoftheoriesdevelopedinthesmallscalework
andproposedbyothersandfinallyiii)collectionsinconjunctionwithotherspecifictreatment
studies.
Keywords:Psychiatry,inflammation,autoimmunity
17.15-17.30
Geneexpressionalterationsofcomplementfactorsinschizophrenia
EvaLindholmCarlström,UppsalaUniversity,Uppsala,Sweden
Ingeneral,themainfocusofmyresearchincludesgeneticanalysesandgeneexpressionstudiesto
identifygeneticcausesofschizophrenia.Wehaveperformedtranscriptomeanalysesof112brain
tissuesamplesderivedfrom65individualswithschizophreniaand47ageandsexmatchedcontrol
samples.Analysisrevealed74significantdifferentiallyexpressedgenes(adjustedp-value<0.05).
Therewasanenrichmentofimmunesystemgenes,withastrikingup-regulationofthe
complementsystem(p=49x10-7).Ourfindingssupporttheprevioushypothesisthathyperactivationofthecomplementcascadeisinvolvedinschizophreniapathology.
Keywords:Schizophrenia,genetics,geneexpression
17.30-19.00
18.00-18.30
19.00-22.00
Pubandmingle
SciLifelab,Tomtebodavägen23
AnupdateontheHumanProteinAtlas
MathiasUhlen,SciLifeLab,KTH-RoyalInstituteofTechnology,Stockholm,Sweden
Dinner
SciLifelab,Tomtebodavägen23
25th HUPO Human Brain Proteome Project Workshop
WednesdayMay4
08.30-10.00
Session4:Alzheimer'sdisease
Chair:HelmutEMeyer
08.30-08.45
BiomarkerforearlyADdiagnostics
HelmutEMeyer,Leibniz-InstitutfürAnalytischeWissenschaften–ISASe.V.,Dortmund,
Germany
Alzheimerdementia(AD)isthemostprevalentneurodegenerativedisorderoftheelderlyand
about6%ofthegeneralpopulationover65willbeaffected.Besidesalleffortstargetingthese
proteinaggregatesoverthelast20yearstodevelopeffectiveAD-therapiesnosuccesscouldbe
reportedsofar.Westartedajointeffortinfindingearlyonsetbiomarkersbyanalyzingextracellular
vesicles(EVs)inthebloodwhichareproducedbysenescentplateletsandothercellsinthe
circulation.SubfractionsoftheseEVsareenrichedinAD-relatedproteinsandlipidsandmaybethe
causativeagentoftheonsetandprogressionofAD.
Keywords:Biomarker,Alzheimer,Diagnostic
08.45-09.00
BrainenrichedproteinsinCSF–GAP43andfriends
JuliaRemnestål,AffinityProteomics,Scilifelab,KTH-RoyalInstituteofTechnology,
Stockholm,Sweden
Advancementsintranscriptomictechnologieshaveenabledcomparativestudiesallowing
identificationofgeneswithtissue-enrichedexpression.Usingantibodiesanddirectlabelingof
proteinswehaveprofiled280brain-enrichedproteinsincerebrospinalfluidfrompatientswith
Alzheimer’sdisease(AD),Parkinson’sdisease(PD)anddementiawithLewybodies(DLB)inorderto
investigatepotentialassociationstoneurodegenerativediseases.Severalproteinsdisplayed
differencesinexpressionlevelsbetweendiseasedpatientsandcontrolswiththetwosynaptic
proteinsGAP43andNRGNspecificallydemonstratingasignificantincreaseinCSFfrompatients
withADintwoindependentcohorts.
Keywords:proteinprofiling,affinityproteomics,neurodegenerativedisorders
09.00-09.15
ICharacterizationoftheAbetaandNeurograninpeptidepatterns–frombloodto
thebrain
ErikPortelius,InstituteofNeuroscienceandPhysiology,SahlgrenskaAcademyat
GoteborgUniversity,Mölndal,Sweden
Alzheimer’sdisease(AD)isthemostcommonneuropsychiatricdisorderintheagingpopulationand
ischaracterizedbyplaquesandtanglesinthebrainaswellassynapticloss.Thelastdecadeshave
witnessedanexplosioninstudiesoftheroleofamyloid-βintheprogressiontoAD.Althoughwe
nowhaveadeepknowledgeaboutthedisease,westilldonotunderstandhowthesedifferent
processesleadstothesymptomsofADorwhatitisthattriggersthedisease.Thus,adeeper
characterizationofkeyproteinsinblood,cerebrospinalfluidandbraintissueisneeded.
Keywords:Targetedproteomics;Alzheimer´sdisease;Massspectrometry
09.15-09.30
MolecularendophenotypesinAlzheimer’sdisease
PieterJelleVisser,AlzheimerCentre,VUUniversityMedicalCentre,Amsterdam,The
Netherlands
Objective:Alzheimer’sdisease(AD)isageneticallyandclinicallyheterogeneousdisorder.We
studiedwhethermolecularsubtypescanbedefinedwithadualclusteringapproachofproteinsin
cerebrospinalfluid(CSF).Methods:Datawasanalyzedof220CSFproteinsof273subjects(79
controls;130mildcognitiveimpairment(MCI);64AD)fromtheADNIstudy.Datawerenormalized
andclusteredwithnon-negativematrixfactorization.Results:Threeclusterswereidentified,which
showedasimilardistributionofdiagnosisandAPOEe4genotype.Clustersdifferedintheproportion
ofpeoplewithabnormalamyloid(Cluster1:83%;Cluster2:56%;Cluster3:74%),andabnormaltau
(Cluster1:12%;Cluster2:30%;Cluster3:57%).Conclusion:EndophenotypesbasedonCSFwere
associatedwithheterogeneityinAD.
Keywords:Alzheimer’sdisease,Cerebrospinalfluid,endophenotypes
25th HUPO Human Brain Proteome Project Workshop
09.30-09.45
ProteomicsinAlzheimer’sdisease
KimKultima,DepartmentofMedicalSciences,CARAMBA,CancerPharmacologyand
ComputationalMedicine,UppsalaUniversity,Uppsala,Sweden
Alzheimer’sdisease(AD)isachronicneurodegenerativedisorderaccountingformorethan50%of
alldementiacases.TheADneuropathologyischaracterizedbyformationofextracellularplaques
andintracellularneurofibrillarytanglesconsistingofaggregatedamyloid-βandtau,respectively.
Thediseasemechanismhasonlybeenpartiallyelucidatedandisbelievedtoinvolvemanyother
proteins.WehaveusedmassspectrometrybasedproteomicmethodstoanalyzetheAlzheimer’s
diseasebrainandCSFincombinationwithantibodybasedverificationtoincreasingourknowledge
intheADneuropathology.
Keywords:Proteomics,Alzheimer’s,Dementia
09.45-10.00
ThinkingoutsideofthebraininAlzheimer'sdiseaseusingproteomicstechnology
RenãA.S.Robinson,DepartmentofChemistry,UniversityofPittsburgh,Pittsburgh,
Pennsylvania,USA
TheperipheryisimplicatedinthepathogenesisofAlzheimer’sdiseasehoweverafull
understandingoftheroleoftheperipheryinAlzheimer’sdoesnotexist.Recentlyitwas
demonstratedthatactivationoftheperipheralimmuneresponsehelpstolowerbraininflammation
andremoveamyloid-beta.Alsoamyloid-betaproductionandclearanceinthebrainislikely
influencedbyperipheralorganssuchastheliver.Investigatingchangesinhumanperipheraltissues
canbechallengingmakinganimalmodelsofAlzheimer’sdiseaseextremelyuseful.TheRobinson
groupdevelopshighthroughputproteomicsmethodstoestablishmultiplehypothesesaboutthe
roleofperipheraltissuesinAlzheimer’sdisease.
Keywords:proteomics,Alzheimer'sdisease,massspectrometry
10.00-10.30
10.30-12.00
Coffeebreak
Session5:PDandotherdementias
Chair:KatrinMarcus
10.30-10.45
Analysisofcerebrospinalfluidusinghighresolutionmassspectrometry
KatrinMarcus,MedizinischesProteom-Center,Ruhr-UniversityBochum,Bochum,
Germany
Nowadays,themostcommonneurodegenerativedisordersareAlzheimer’sandParkinson’sdisease
(AD,PD).Althoughthesedisordersareextensivelyinvestigated,anexactdiagnosiscanonlybe
confirmedpost-mortem.Tofacilitatetherapeuticintervention,anearlydiagnosisaswellasthe
possibilitytomonitordiseaseprogressionisimportant.Sincecerebrospinalfluid(CSF)isthebody
fluidthatsurroundsthebrainitisapromisingsourceforbiomarkerdiscoveryofneurodegenerative
disorders.ForthisreasonmultipleproteomicstudiesofCSFwereperformedtoinvestigate
differencesbetweenhealthyindividualsandpatientssufferingfromneurodegenerativediseases.
Hereweshowalabel-freemassspectrometry(MS)approachtoanalyzeCSFinacross-sectionaland
longitudinaldenovoPD-cohort,whichprovidesthegreatadvantageoffastandcheapsample
preparationaswellasinterestingproteinbiomarkercandidates.
Keywords:proteomics,massspectrometry,neurodegeneration,biomarkerresearch,
25th HUPO Human Brain Proteome Project Workshop
10.45-11.00
RobustmetabolicbiomarkersforParkinson'sdisease
KarstenHiller,LuxembourgCentreforSystemsBiomedicine,Universityof
Luxembourg,Luxembourg
Thediagnosisofearly-stageParkinson’sdisease(PD)isbasedonclinicalassessmentofmotorand
non-motorsymptoms,withoutconsideringmetabolicbiomarkers.Additionaltestsarerequiredto
significantlyimprovediagnosisandpatientcare.Byusinganon-targetedgaschromatography
coupledtomassspectrometry(GC-MS)approach,weinvestigatedmetabolicchangesin
cerebrospinalfluid(CSF)fromearly-stagePDpatients,displayingthefirstmotorsymptomsofthe
disease.Wecomparedthesemetabolitelevelswithage-,gender-andeducation-matchedhealthy
controls.Wefoundthatdehydroascorbicacidlevelsweresignificantlylower(FDR<0.001)and
fructose,mannoseandthreonicacidlevelsweresignificantlyhigher(FDR=0.007,FDR<0.001,FDR
=0.004,respectively)inearly-stagePDcomparedtohealthycontrols.Thesechangesreflect
pathologicaloxidativestressresponses,aswellasproteinglycation/glycosylationreactionsinPD.
Usingamachinelearningapproachbasedonlogisticregression,wesuccessfullypredictedthe
origin(PDvs.healthycontrols)ofindependentCSFsamples,basedonabiosignaturecomposedof
mannose,threonicacidandfructose.OurresultsenhancetheunderstandingaboutthePDrelated
CSFmetabolomeandcouldbeusefulforfurtherevaluationoftheobservedchangesinother
“omics”approachesandearly-stagediagnosisofPD.
Keywords:metabolism,metabolomics,massspectrometry
11.00-11.15
RTP801/REDD1interactomeinacellularmodelofPD
CristinaMalageladaGrau,UnitofBiochemistry,DepartmentofBiomedicine,
UniversityofBarcelona,Barcelona,Spain
mTORpathwayderegulationhasbecomeahallmarkinneurodegenerativedisorders,sinceafinetunedregulationofmTORactivitiesiscrucialforneuronfunctionandsurvival.RTP801/REDD1has
becomeoneofthemostpuzzlingregulatorsofmTOR.Althoughthemechanismisnotcompletely
understood,RTP801inactivatesmTORandAktviathetuberoussclerosiscomplex(TSC1/TSC2)in
manycellularcontexts.UnderstandingthemechanismsbywhichRTP801inducescelldeathis
crucialtodesignanyeffectivetherapeuticapproaches.Here,weperformedaproteomicanalysisto
identifypotentialnewRTP801proteininteractors,tobettercomprehenditsregulatorymechanisms
overmTOR.
Keywords:neurodegenerationParkinson’sdiseasemTORsignaling
11.15-11.30
ProteomicsProfilingoftheSubstantiaNigraRevealsAssociationofRNAMetabolism
PathwaysandArp2/3-MediatedActinNucleationwithLewyBodyPresence
VladislavPetyuk,PacificNorthwestNationalLaboratory,Richland,USA
Proteinaceousaggregatescontaininga-synucleinproteinknownasLewybodiesisahallmarkof
majoritycasesofParkinson’sandanumberofotherdiverseneurodegenerativediseases.Togain
insightsonproteinsandassociatedpathwaysassociatedwiththepresenceofLewybodieswe
performedaquantitativeproteomicprofiling.Weanalyzedsubstantianigratissuefrom51subjects
arrangedintothreegroups:caseswithLewybodies,controlswithmatchingneuronallossand
controlswithnormalneuronaldensity.ThekeyfindingsaredownregulationofmRNAprocessing
pathwaysandupregulationofArp2/3complex-mediatedactinnucleationinthecasesofLewybodydependentneuronalloss.
Keywords:Parkinsons'sdisease,Lewybodies,neurodegeneration
25th HUPO Human Brain Proteome Project Workshop
11.30-11.45
IdentificationofCSFbiomarkersforspecificdementia’sbyMassspectrometry
proteomics
CharlotteTeunissen,VUUniversityMedicalCenterAmsterdam–departmentof
ClinicalChemistry,Amsterdam,Netherlands
Neurodegenerativediseasesleadingtodementiaareaclinicallyandpathologicallyheterogeneous
groupofdisorders,forwhichthereiscurrentlynocure.Diagnosisofdifferentsubtypesofdementia
relieslargelyonclinicalexamination,andthereisastrongneedforcerebrospinalfluid(CSF)
biomarkerstoaiddiagnosis.OuroverallaimistodevelopCSFbiomarkersfordementiasubtypes
withaprovenrelationtopathology.Forthis,wehavemappedchangesintheproteomeofantemortemcerebrospinalfluid(CSF)andpost-mortembraintissueofpatientsatdifferentstagesof
Alzheimer’sandfrontotemporaldementia(FTD).WewillintegratetissueandCSFproteomics
resultstoselectthemostpromisingbiomarkerproteinsforeachspecificdementiatype.
Keywords:biomarkersforneurologicaldiseases,dementiadisorders,immunoassays
11.45-12.00
IntegratedBiomarkerDiscoveryinParkinsonianDisorders
MilesTrupp,DepartmentofPharmacologyandClinicalNeuroscience,Umeå
University,Umeå,Sweden
DevelopmentofeffectivetherapeuticsforParkinson'sdisease(PD)hasbeenhinderedbythelate
stageandimprecisionofinitialdiagnosis.PDsharessimilarclinicalpresentationswithmolecularly
distinctneurodegenerativediseases,suchasmultiplesystematrophy(MSA)andprogressive
supranuclearpalsy(PSP).WeareanalyzingCSFandplasmafromtheextensivebiobanksatUmeå
UniversityHospitaltowardsidentifyingbiomarkersforParkinson'sdiseasepredictionand
progression.Weareutilizingmass-spectrometrybasedmetabolomicsandproteomicsfordiscovery
andMRMvalidationstudies.Resultsindicatethatprecise,parallelquantificationofbiomarkers
frommultiplepathwayshasthepotentialtodefinesubgroupsofParkinson'sdiseasewithdifferent
molecularetiologies.
Keywords:Mass-spectrometry,Biomarkers,Neurodegeneration
12.00-13.00
Lunch
RestaurangJönsJacob,Retziusväg22
25th HUPO Human Brain Proteome Project Workshop
13.00-14.15
Session6:Autoimmunityinbraindisorders
Chair:PeterNilsson
13.00-13.15
Anoctamin2asanovelautoimmunetargetinmultiplesclerosis
PeterNilsson,AffinityProteomics,Scilifelab,KTH-RoyalInstituteofTechnology,
Stockholm,Sweden
Weprofiledtheautoantibodyrepertoirein2,169plasmasampleswithinmultiplesclerosisusing
suspensionbeadarrays,builtwith384humanproteinfragmentsselectedfromaninitialscreening
with11,520antigens.Increasedautoantibodyreactivityagainstthechloridechannelprotein
anoctamin2(ANO2)inMScaseswasidentified.Thisfindingwasvalidatedinindependentassays
withalternativeproteinconstructsandbyepitopemappingwithpeptides.Wealsofoundastrong
interactionbetweenthepresenceofANO2autoantibodiesandtheHLAcomplexMS-associated
DRB1*15allele.ThefindingspresentedheredemonstratethatanANO2autoimmunesubphenotypemayexistinMS.
Keywords:affinityproteomics,autoantibodyprofiling,proteinmicroarrays
13.15-13.30
Newinsightsintobraindisorders
CarolineMay,MedizinischesProteom-Center,Ruhr-UniversitätBochum,Bochum,
Germany
Thebraincanbesubdividedintodifferentregions,fields,andcellularlayers.Moreover,different
neuronalandglialcellscanbedistinguished.Theseparationofbrain-derivedcellsischallenging,
becauseisolatingintactneuronsisnotfeasiblewithtraditionalmethods.Therefore,inthepast
mostofthestudieswereperformedwithwholebrainlysate.Withinthesestudiesdominantcell
types,likee.g.glialcells,canmaskneuron-specificinformation.Wepresentanewstrategyto
enrichneuronsusinglasermicrodissectionandsubsequentmassspectrometricanalysis.This
analysiswilldeepenourunderstandingofbrainfunctionandhowcertainneuronsarealteredin
braindiseases.
13.30-13.45
High-densityAntibodyandPhageMicroarrayscreeningofprefrontalcortexbrain
tissueandseraofAlzheimerDiseasePatientsfortheidentificationofspecificAD
markers
RodrigoBarderas,FunctionalProteomicsofChronicDiseases,Biochemistryand
MolecularBiologyIDepartment,ChemistryFaculty,ComplutenseUniversityof
Madrid,Madrid,Spain
Alzheimer'sDisease(AD)isasevereneurodegenerativedisorderwithahighsocioeconomicimpact.
ltisestimatedtoaffect80millionpeopleworldwidein2050.AnaccurateandearlydiagnosisofAD
isdifficultanddefinitivediagnosisrequirespost-mortemverification.Wearecurrentlyusinghighdensityantibodyandphagemicroarraysforthestudyofchangesinproteinexpressioninthe
prefrontalcortexandthehumoralresponseofADpatients,respectively.Theidentificationof
deregulatedproteinsandtargetproteinsofautoantibodiesshouldprovidenewinformationforthe
elucidationofalteredpathwaysandcellularprocessesandforthediscoveryofnewAD-specific
biomarkers.
Keywords:Quantitativeneuroproteomics,massspectrometry,protein,phageandantibody
microarrays
13.45-14.00
TBA
DoloresCahill,UniversityCollegeDublin,Dublin,Ireland
25th HUPO Human Brain Proteome Project Workshop
14.00-14.15
Profilingautoantibodyrepertoireswithinpsychiatricdisorders
DavidJust,AffinityProteomics,Scilifelab,KTH-RoyalInstituteofTechnology,
Stockholm,Sweden
Inthisprojectweaimedtoinvestigatetheautoantibodyrepertoireinpatientswithpsychiatric
disorders.Thereforewescreenedmorethan500serumsamplesinafirstdiscoveryphaseusing
differentclinicalcohorts.WeutilizedproteinfragmentsgeneratedwithintheHumanProteinAtlas
foratargetedscreeningusingthesuspensionbeadarraytechnology.Hereweselectedapprox.300
proteinfragmentswithalengthofroughly100aminoacidsthathaveaknowndiseasebackground.
Additionallyweusedtheinhousegeneratedplanararraysforanuntargetedscreeningof1152
proteinfragmentsonasubsetofourcohortcollection.Ourfindingsclearlyindicatealteredimmune
responseinpatientswithpsychiatricdisordersandbyfurthervalidatingtheseputative
autoimmunetargetswecouldgaininsightsintotheautoantigensassociatedtopsychiatric
disorders.
Keywords:Psychiatry,Autoimmunity,Microarray
14.15-14.30
14.30-15.30
Coffeebreak
Session7:Otherneurologicaldisorders
Chair:CharlotteTeunissen
14.30-14.45
Somalogic-basedproteomicstoidentifyandvalidatebiomarkersinbloodof
MultipleSclerosis
ArjanMalekzadeh,VUUniversityMedicalCenterAmsterdam,Netherlands
14.45-15.00
VascularbiomarkersinALSneurodegeneration
SebastianLewandowski,VascularBiologyGroup,DepartmentofMedicalBiochemistry
andBiophysics,KarolinskaInstitutet,Stockholm,Sweden
Humanbrainisirreversiblydependentonconstantbloodflowtomeetitshighdemandforenergy.
Asaconsequence,interruptionsinbloodflowefficiencyoftencauseorcontributeto
neurodegenerativediseases.Ouraimistostudythecerebralvesselinjuryinmousemodelsand
patientswithamyotrophiclateralsclerosis(ALS)neurodegenerationwheredecreasedcerebral
bloodflowindicatesrapiddiseaseprogression.Withthehelpofimmunebeadproteomicsplatform
wehaveidentifiedseveralvascularproteinfactorsinplasmaof360ALSpatientswiththepotential
toserveasbiomarkersforcerebralinjury.
Keywords:Neurodegeneration,cerebralbloodflow,ALS
25th HUPO Human Brain Proteome Project Workshop
15.00-15.15
MultiplexedMRMQuantitationofCandidateProteinBiomarkersinHumanCSF
ChristophBorchers,UniversityofVictoria-GenomeBritishColumbiaProteomics
Centre,Victoria,BC,Canada
Multiplexedquantitationcanexpeditetheverificationandvalidationstagesoftheprotein
biomarkerpipelineleadingtoenhancedpersonalizedmedicine.Themostpromisingstrategyfor
proteinbiomarkerverificationcentersontheMRMtechnologywithstableisotope-labeled
standards(SIS)employedwithinabottom-upproteomicworkflow.Sincecerebrospinalfluid(CSF)
isanimportantbiofluidforstudyingcentralnervoussystem(CNS)-relateddiseases,wehave
developedarapidandrobust,MRM-basedmethodtoquantifythelargestpanelofcandidateCSF
proteinbiomarkersinasingleanalyticalexperiment.Themethodisantibody-/fractionation-free
andutilizesacomplexmixtureofin-housesynthesizedinternalstandards,aswellasstandard-flow
UHPLCanddynamicMRM,forenhancedrobustnessandpeptidemultiplexing.Ourfinalmethod
enabledthereproduciblequantitationof130proteins(inferredfrom311interference-free
peptides)ina43minLC-MRM/MSrun.Severalofthesehaveputativeassociationto
neurodegenerativedisease,suchasthepotentiallydiagnosticAlzheimer’sdiseasemarkers
osteopontinandheartfattyacidbindingprotein.Overall,the130proteinsspana5orderof
magnitudeconcentrationrange(from118µg/mLto550pg/mL;asrevealedbystandardcurves),
andcanbereadilyinterrogatedasacompleteorsubsetpanelinsubsequentverificationstudiesof
patientCSFsamples.
15.15-15.30
15.30-16.30
Proteomicsinmultiplesclerosis
ClaireBridel,VUUniversityMedicalCenterAmsterdam,Netherlands
Generaldiscussionandconcludingremarks