IMI/INT/2013-01039 - Version 6 - 23 September 2016

IMI1 Final Project Report

Public Summary

Project Acronym: U-BIOPRED

Project Title: Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes

Grant Agreement: 115010 Project Duration: 01/10/2009 - 30/09/2015

Innovative Medicines Initiative

IMIPROJECTFINALREPORTINCLUDINGTHEPERIODICREPORTFORTHELASTPERIOD1

UnbiasedBiomarkersforthePredictionofRespiratoryDiseaseOutcomes

U-BIOPRED

115010

Prof.PeterJ.Sterk

AcademischMedischCentrumbijdeUniversiteitvanAmsterdam

Meibergdreef9NL-1105AZAMSTERDAM

Tel:+31205662695E-mail:p.j.sterk@amc.uva.nl

LastPeriodOctober/2014-September/2015

ReportingPeriod6

Durationoftheproject1stOctober2009–30thSeptember2015

Descriptionofwork–v81stJuly2014

Submissiondeadline

1 SeeArticlesII.4.1andII4.2oftheIMImodelGrantAgreement.

IMI/INT/2014-02186

Declarationofthecoordinator ............................................................................ 4

1. Executivesummary ........................................................................................ 5

1.1. Projectrationaleandoverallobjectivesoftheproject .............................................................. 5

1.2. Overalldeliverablesoftheproject .............................................................................................. 5

1.3. Summaryofprogressversusplansincelastperiod .................................................................... 9

1.4. Significantachievementssincelastreport ............................................................................... 15

1.5. Scientificandtechnicalresults/foregroundsoftheproject ..................................................... 24

1.6. Potentialimpactandmaindisseminationactivitiesandexploitationofresults ...................... 27

1.7. Lessonslearnedandfurtheropportunitiesforresearch .......................................................... 29

2. Summaryofprogressagainstobjectives ................................................... 30

2.1. Summarytable .......................................................................................................................... 30

2.2. Descriptionofprogressfordelayedmilestones/deliverablesnotcompletedpartially

completedduringthelastreportingperiod .......................................................................... 38

2.3. DeviationsfromDescriptionofWorkduringthelastreportingperiod ................................... 41

2.4. SummarystatementonallWorkPackages .............................................................................. 43

3. SummaryofMajorAchievementsandkeydisseminationactivities ........ 79

3.1. Majorachievementsforthelastreportingperiod ................................................................... 79

3.2. Keydisseminationactivitiesforthelastreportingperiod ........................................................ 82

4. Summaryofprojectoutcomes ................................................................... 93

4.1. Projectgeneralinformation ......................................................................................................... 93

4.2. Staffstatistics ................................................................................................................................ 93

4.3. ResourceInputfromtheProjectPartners ................................................................................... 93

4.4. ResourceOutputsoftheproject .................................................................................................. 94

4.5. Stakeholderengagement ........................................................................................................... 100

4.6. Collaboration .............................................................................................................................. 101

4.7. Dissemination ............................................................................................................................. 101

4.8. Ethics ........................................................................................................................................... 103

5. ResearchuseanddisseminationofForeground ...................................... 105

5.1. CurrentStatus ............................................................................................................................. 105

5.2. PlanforResearchuseanddisseminationofForeground .......................................................... 105

5.3. Planforsustainability ................................................................................................................. 119

6. ManagementofProjectandConsortium ................................................. 120

7. Finance-Cost ............................................................................................. 122

7.1. Costsummaryforthelastreportingperiod ............................................................................... 122

7.2. Descriptionofdeviationfromoriginalbudget ........................................................................... 200

8. FormCandSummaryFinancialReport .................................................... 203

Appendix1–ResponseonIMIquestionsfinancialpart

Appendix2–ResponseonIMIquestionstechnicalpart

Declarationofthecoordinator

I,thecoordinatorofthisproject,declarethat,

ThefinalreportsubmittedisinlinewiththeobligationsasstatedinArticleII.2.3oftheGrant

Agreement:

Theattachedreportrepresentsanaccuratedescriptionoftheworkcarriedoutinthisprojectfor

thelastreportingperiodaswellasforthewholedurationoftheproject;

Forthelastperiod,theproject(tickasappropriate):

X hasfullyachieveditsobjectivesandtechnicalgoals;hasachievedmostofitsobjectivesand

technicalgoalsfortheperiodwithrelativelyminordeviations2;

□ hasfailedtoachievecriticalobjectivesand/orisnotatallonschedule3.

Forthewholedurationoftheproject,theproject(tickasappropriate):

□ hasfullyachieveditsobjectivesandtechnicalgoals;

Xhasachievedmostofitsobjectivesandtechnicalgoalswithrelativelyminordeviations3;

□ hasfailedtoachievecriticalobjectivesand/orisnotatallonschedule3.

Thepublicprojectwebsitewww.ubiopred.eu3isuptodate.

Tomybestknowledge,thefinancialstatementswhicharebeingsubmittedaspartofthis final

report are in linewith the actual work carried out and are consistentwith the report on the

resources used for the project (section 7) and if applicable with the certificate on financial

statement.

All participants, in particular non-profit public bodies, secondary and higher education

establishments, research organisations and SMEs, have declared to have verified their legal

status.Anychangesordeviationshavebeenreportedundersection6(ProjectManagement)in

accordancewithArticleII.3.foftheGrantAgreement.

NameoftheCoordinator:Prof.PeterSterk

Date:30/11/2015

SignatureoftheCoordinator:

2 Ifeitheroftheseboxesisticked,thereportshouldreflecttheseandanyremedialactions taken.3 Please add the address of the public projectwebsite. The home page of thewebsite should contain the generic IMI

logo which is available in electronic format at the IMI website. The area of activity of the project should also bementioned.

1. Executivesummary

1.1. Projectrationaleandoverallobjectivesoftheproject

Context Asthmaisonecommonestchronicdiseases,affectingpatientsfromchildhoodtoelderlyage.Inmost

patientssymptomscanbesufficientlysuppressedcurrentlyavailablemedicines.However,the3-5%

ofpatientswith themost severediseasecannotbe treatedadequately,providinga largepersonal

andsocietalburden.Developmentofnewtreatmentsforindividualswithsevereasthmaisurgently

neededbuthamperedbylackofvalidatedclinicalandbiologicaldiseasemarkers,underperforming

of pre-clinical models, inadequate sub-phenotyping, and insufficient understanding of disease

mechanisms.U-BIOPRED aimed to newly discovermolecular networks operative in severe asthma

andtolinkthosetotheclinicalexpressionsofthedisease.

Hypothesis Theuseofbiomarkerprofilescomprisedofvarioustypesofhigh-dimensionaldata, integratedwith

aninnovativesystemsbiologyapproachintodistinctphenotypehandprints,willenablesignificantly

betterpredictionoftherapeuticefficacyinsevereasthmathansingleorevenclusteredbiomarkers

ofonedatatype,andwillidentifynoveltargets.

Objectives 1. Generatingconsensusandglobalstandardoperatingprocedures(SOPs)ondiagnosticcriteria,

clinicalphenotypinganddiseaseoutcomeD2.4,D5.3,

2. Creatingadult/paediatriccohortsandbiobankforcross-sectionalandlongitudinalstudiesinwell

characterizedsevereasthmaticsandcontrolsD3.2,D3.5,D3.6,M8

3. Generatingphenotypehandprintsofsevereasthmabyaninnovativesystemsbiologystrategy

D4.2,

4. ValidatingtheaccuracyofphenotypehandprintsinidentificationofnewlyincludedpatientsD8.5

5. Refiningphenotypehandprintswithpre-clinicalanimalandhumanexacerbationmodelsD6.3,

D6.4

6. Validatingthehandprintsfortheirpredictiveefficacyingoldstandardandexperimental

therapeuticinterventionD7.3

7. Refiningthediagnosticcriteriaandphenotypesofsevereasthmabyincorporatingthenewly

establishedhandprintsD8.5

8. Establishingaplatformforexchange,educationanddissemination.D1.4,D10.7

1.2. Overalldeliverablesoftheproject

Theprojectobjectivesweredividedinto10Workpackages(WP)and69deliverables(D)andthe

entireprojecttook6years(5yearsplus1yearbudgetneutralextension).Thishasallowedtodeliver

63deliverables,whilst6deliverablesarebeingfinalizedduringthefirstyearinthepost-funding

period.

Governance

AtthestartoftheprojecttheManagementOfficeandtheFinanceOfficewereinstalledandmade

operational.Thisincludedaweb-basedplatformforinteractivemonitoringprogress,aweekbyweek

scheduleofteleconferencesbasedonWPsorspecifictaskswithintheprojectandface-to-face

meetingswhenneededinadditiontothebroadannualconsortiummeetings.Thisstructured

managementservedtheprojectverywell.TheFinanceOfficewasindirectcontactwithallpartners

andassistedinpreparingtheyearlyprogressreports.Basedonthedevelopmentoftheproject,new

businesscasescouldbesubmittedtotheManagementBoard,basedonastandardtemplate,in

ordertooptimallyfacilitatethedemandsoftheWorkpackages.Both,theManagementBoardand

ScientificBoardtookalldecisionsbyconsensus.

Consensusandstandardisation

Thescientificworkstartedbyreachingconsensusamongstallacademicandindustrialpartnersabout

thedefinitionofsevereasthmaandtheclinicalalgorithmhowtoconfirmthediagnosisoftruesevere

asthmaamongstpatientswithclinically‘difficult’asthma.ThisU-BIOPREDconsensuswaspublished

in2011.HavingthosecriteriaonboardallowedthedevelopmentofStandardOperatingProcedures

(SOPs)formeasuringtheclinicalparametersofthestudy.TheseSOPswerealignedwiththeones

usedbycolleaguesintheUSandsubsequentlybecameastandardforseveralprojectsinparallelor

followingU-BIOPREDelsewhere.Eventually,afterincludingallpatients(seebelow)thecohort,the

SOPs,thebiobankandthedatabasecollectivelyformedtheU-BIOPREDregistry.Renewedconsensus

wasreachedattheendofthefundingperiod,butthiswillstillberevisedbasedonthefinalresultsof

theprojectinthefirst6monthsafterthefundingperiod(Q22016).

Adultandpaediatriccohorts

Themajorclinicaleffortwastheinclusionoftheadultandpaediatricpatients.Despitetheenormous

expertiseoftheclinicalcentresinthestudy,thisinclusionofthecohorttooktwiceaslongas

anticipated.Thiswasduetosincereoptimismbythecentresontheireligiblepatientnumbers,and

theveryintensiveandtimeconsumingproceduresrelatedtobuildingtheagreedclinicalprotocol,

theeCRFs,andthede-centralethicsapprovalinthevariouscentresandcountries.Eventually,the

cohortsweredeliveredaddingupto1025patients/controlsintotal.Duetothesedelaysthefollow-

upperiodofthesevereasthmapatientswasshortenedto12-18month,soboththebaselinedataset

andthelongitudinaldatacouldbedeliveredduringthelifespanoftheprojectandaresecuredinthe

biobankandtheTranSMARTdatabase(seebelow).

Biologicalsamples

Goodbiologicalsampleswerevitaltotheproject.Thatiswhyextensivestandardoperating

procedures(SOPs)weredevelopedforensuringthequalityofsamplesanddatafromblood,sputum

andbronchialbrushesandbronchialbiopsies.Sputuminductionandprocessingwascentrally

trained,whilstsputumcellcountingwasdonecentrallybyasinglelab.Similarly,bronchialbiopsy

specimensfromeachclinicalcentrewerefirstcheckedforqualityandonlyafteraccreditationa

particularstudycentrecouldproceed.Thebiobankwascentralizedandallthebiobanking

procedureswereaccordingtointernationalrecommendations.TheseQCstepshavelargely

contributedtothequalityofthedata.

Experimentalexacerbation

Theclinicalstudywasparalleledbyahumanexperimentalstudy,meanttomimicanasthma

exacerbationinthelab.Exacerbationsareoneofthemainunresolvedproblemsinsevereasthma

andaremostlyprimedbyarhinovirusinfection.ThatiswhyU-BIOPREDdevelopedaGood

ManufacturingPractice(GMP)rhinovirusandperformedexperimentalrhinovirusinfectionbasedon

strictSOPsasamodelofexacerbations(inmoderatelysevereasthmatics).Thedose-escalationstudy

inhealthyandasthmaticvolunteersprovidedasafeandeffectivedose(forcoldsymptoms)of

rhinovirus16(RV16)andtheasthmabiomarkerstudywithRV16hasbeenaccomplishedbyDec31,

2015.TheomicsplatformsandbioinformaticsoftheRV16studyarecurrentlybeingruninthepost-

fundingperiod.

Preclinicalmodels

AvitalaspectoftheU-BIOPREDstudywastolineupthevariouspre-clinicalmodelsof(severe)

asthmathatwereusedinacademiaandpharmaceuticalindustry.Theimmediateaddedvalueofthe

projectwastheexchangeofsuchmodelsandtheirSOPsandresultsbetweenalargenumberof

laboratories.Itappearedthatthestandardchronicallergen(house-dustmite)mousemodelisnot

matchingvitalaspectsofsevereasthma(suchassteroidinsensitivity).Butthiswasaccomplishedby

addinginfluenzavirusratherthanrhinovirusorwithCFAasadjuvant.Thesemodelsprovided

immunological(Th1,Th2,Th17),inflammatoryandgeneexpressionfeaturesthatcouldbe

suppressedbynoveltreatments(CRID3).Inadditiontomousemodels,humaninvitroandexvivo

modelscomprisingbronchialepithelialcellandairwaysmoothmusclecellculturesandalsoprecision

cutlungsliceshavedeliveredthesamplesfordetailedtranscriptomicanalysisthatwillbefinalizedby

Q22016.

‘Omics’platforms

ThecoreactivityofU-BIOPREDwastoexaminehigh-dimensionalmolecularprofilesasobtainedin

blood,sputum,bronchialbrushes,bronchialbiopsies,urineandexhaledair.Thiswasdoneatthe

RNA(transcriptomics),protein(proteomics),lipid(lipidomics)andmetabolic(metabolomicsincluding

breathomics)levels.Microbiomeanalysiswasaddedbyextra(ENSO)funding.Thefirststepwasto

implementSOPsandqualitycontrolstandardsacrosstheconsortium.Subsequently,differentially

expressedcompoundsbetweensevereasthma,mildtomoderateasthmaandhealthycontrolswere

delineated.Inparallel,unbiasedfingerprintsfromalltheseplatformsweregenerated,providing

entirelynovelsubgroupsof(severe)asthmabasedonmolecularprofiling.Forinstance,eosinophilic

andneutrophilicsevereasthmaappearstobeassociatedwith3and4differentproteomic

signatures,respectively,pointingtowardsdifferentendotypesunderlyingparticularinflammatory

profiles.Thishasdirectimplicationsforselectingtargetsforphenotype-driven,noveltreatmentsand

therebyrepresentsacoredeliverableoftheproject.SimilarpaediatricfingerprintsaredueinQ2

2016.

Bioinformatics

U-BIOPREDreliedoncutting-edgebioinformatics.Thechainbetweenrawdataandeventual

fingerprintsandhandprintswasstandardisedanddevelopedwherenecessary.Thisincludeda

detailedDataAnalysisPlanforboth‘regular’statisticsandhigh-dimensionalanalysis(U-BIOPRED

ToolBox)thatcombinedrigorousstatisticswithtopologicalanalysis.TheTranSMARTknowledge

managementsystemwasusedasstartingpointandwasfurthertailoredfortheU-BIOPREDneeds.

Thefingerprintandhandprintanalysiscoverednewgroundsindatasubsetting,featurefiltering,

omics-basedclusteringandbiomarkeridentification.Wherepossibletheanalysiswasdonebya

prioriselectionofatrainingsetandavalidationset.Platformfingerprintsweregenerated,providing

entirelynovelphenotypesof(severe)asthmathatareassociatedwith,butarealsobeyond

traditionalinflammatoryphenotyping.Thefirstcross-sectional,multi-scalehandprintsintegrating

various‘omics’platformsweregeneratedfromsputum(sputumhandprint1,2,and3)andblood

(bloodhandprint1,2,3,and4).Thesemolecularhandprintsappearedtobeassociatedwithclinical

symptomsandinflammation.ThesehandprintsareusedforbiomarkerdiscoveryusingtheU-

BIOPREDAsthmaMapofmechanisticnetworks,andarenowbeingmirroredtoalimitedbiomarker

set(analyteset)forusageintheclinicalsetting.TheseveryfinalstepswillbedeliveredinQ22016.

Deliveryofthesenewlydiscoveredhandprintsisthemajoroutcometheproject.

Disseminationandcommunication

Theprojectanditsresultswerebroughtclosertothepublicbyvariousmeans.Thepublicwebsite

wasquicklyonlineandwasconstantlyadaptedwithmaterialpromotingtheprojectanditsresults

(interviews,video’s,artcontest).PatientsparticipatinginU-BIOPREDjudgedandadjustedscientific

material(layabstracts)inordertobridgethegapbetweenprofessionalandsocietalcommunication.

Thisincreasinglyincludedsocialmedia.Theprofessionalsfollowedandarefollowingastep-wise

process,inwhichabstracts,presentationsandscientificpapersarebeingannounced,endorsedand

monitoredbyapublicationmatrix.Theopenandcollectivestrategiesbetweenpatientsand

professionalsintheprojectcanberegardedasalargeachievementbyU-BIOPRED.

Ethicsandpatientparticipation

RightfromthestartU-BIOPREDimplementedanEthicsboardandSafetyMonitoringBoardfor

independentmonitoringofprotocols,patientburden,severeadverseevents(SAEs),sample

management,publicationsandpotentialcrisissituations.Theboardsrequiredwell-definedcharters

andSOPsoftheseboards,whichareapplicableoutsideU-BIOPRED.Theactivitiesoftheboardswere

summarizedinannualreports.Theexperimentalrhinovirusstudywasmostcloselymonitoredby

weeklyinvolvementofpatientrepresentatives.ThePatientInputPlatformpublisheditsU-BIOPRED

experience,whichcanberegardedasastep-changeinpatientparticipationinbiomedicalEU

projects.

Conclusion

U-B IOPREDhasdeliveredinresponsetotheIMIcall‘Understandingofsevereasthma’:itscohorts,its

‘omics’analysis,itsfingerprintsanditsmulti-scalehandprints.Asplanned,thesearenowinputinto

newinterventionstudiesbypharmaindustries,inordertoselectpatientsforeffectivetreatment.

Thispublic-privatecollaborationhasbeenastep-changeintheresearchofsevereasthmaandthe

respiratoryfieldingeneral.

Alldeliverablesaresummarizedinthetablebelow.

Deliverables(Grey=complete)

1.1 Financeoffice 4.5 Bronchoscopicbrushingbiobank 8.2SOPs,dataformats,qualitymetrics

1.2Consortiuminteractionplatform

4.6 Bronchoscopicbiopsybiobank 8.3Analysisoflegacyandpublicdata

1.3Monitoringandplanningplatform

5.1 GMPrhinovirusinoculum 8.4 Dataintegrationmethod

1.4 Progressreports 5.2 SOP’sviralchallenge 8.5 Cross-sectionalhandprints

1.5 Yearlymeetings 5.3 Datasetviralsafetystudy 8.6Handprintspre-clinicallabmodels

1.6 Report on possible business models 5.4

Datasetviralchallengestudyinpatients

8.7Handprintsclin.models&interventionalmodel

1.7Report on initiation of business model 5.5 Standardprotocolviralchallenges 8.8

Refinedhandprintslongitudinaldata

2.1 Consensusmeeting 6.1 MeetingonanimalmodelsandSOPs 8.9Analyte,microbiomic,metabolicfingerprint

2.2Publishedconsensusdocument

6.3DatasetHDMmodel,initialRVinfection

9.1 Consortiumwebsite

2.3 GloballyagreedSOPs 6.2 Datasetexvivotissuemodels 9.2 Shortvideo2.4 Severeasthmaregistry 6.4 Meetingtorefinemodels 9.3 Artcontest2.5 Handprintrefinedconsensus 6.5 Datasetinitialhumanizedmicemodel 9.4 Materialsforlocalmeetings

2.6 Refinedcriteriaforphenotypes 6.6Analysisofpre-clinicalmodelsandhumanizedmousemodel

9.5Frameworkforwritingcommittee

3.1 Studyprotocols 6.7 Mechanismvalidation 9.6Personnelexchangeplatform

3.2 eCRFs 7.1 Summaryofbestavailableomicstech 9.7Promotion&commsstrategy

3.4 Adultcohort 7.2 SOPsforomicsassessments 10.1 CharterforEthicsBoard3.5 Paediatriccohort 7.3 Biomarkersfrompre-clinicalstudies 10.2 CharterforSafetyBoard

3.6Baselinedata-baseandbiobank

7.4 Novelindividualbiomarkers 10.3SOPsforethicalconductofscience

3.7Longitudinaldata-baseandbiobank

7.5Omicsdatasetforphenotypehandprint

10.4Harmonizedinformedconsentform

3.8Exacerbationdata-base&biobank

7.6 Datasetofanalyteresults 10.5 SOPsforsafetymonitoring

4.1SOPsbronchoscopic&nasalbiopsy

7.7 Microbiomicsdataset 10.6SOPsforsafetycrisismanagement

4.3Accreditationadult&paediatricbiopsy

7.8 DatasetofMetabolomicsresults 10.7Annualsafetyandethicsreports

4.4 Frameworkforbiobanking 8.1 KnowledgeManagementstructure

Allthedeliverablesinthetableabovehaveanassociateddeliverablereport.Thosedeliverablesin

blacktextshowreportsthatpertaintoinformationthatisexpectedtochangeasfurtherwork,inthe

legacyperiod,iscompleted.Inallcasesthisisduetothecontinuedanalysisworkonthedata.

1.3. Summaryofprogressversusplansincelastperiod

ThefinalperiodofU-BIOPREDsawthecompletionofalloftheclinicalandlaboratoryanalysis

plannedwithintheprojectperiod.TheanalysisofthedatageneratedbyU-BIOPREDwasandstillisa

large-scaletaskandthiswillprovidedatafordetailanalysisforyearstocome.However,thecore

initialanalysisasdefinedinthedeliverableshasbeenachieved,whileworkonfurtherhandprints

(includinghandprintsrelatedtoD8.7andD8.8)willbeneededpriortoarenewedpositionpaper

(D2.5andD2.6)ispublished.

Thelegacyperiodhasbeenwellpreparedfor,withthekeydatageneratingactivitiescompleteand

fundingsecuredformaintenanceofthecoreoutcomes,includingtheRhinovirusstorage,biobank,

datastorageandacoremanagementinfrastructure.

WP1:Governance

Thegovernanceoftheprojectcontinuedbyits‘managementbyconsensus’process.Proposals

byU-BIOPREDpartnersfornew,relativelysmallactivitiesthatwerenotanticipatedatthegrant

writingstage(businesscases)werejudgedbytheManagementBoard.

• Thefinancialaspectsoftheprojecthaverequiredsomeadjustmentsintermsof

partnersdeliveringtheplannedwork.Thesehavebeenimplementedwiththeapproval

oftheManagementBoardandwithintherulesforre-allocationoffundingbytheIMI.

• Inadditionandinrelationtothis,thebusinesscaseprocessforre-distributingbudget

withintheIMIrulesresultedinafurther3casesbeingawardedbytheManagement

Board.Thesecasessummarisedspecificwork,includingadditionalallergyandimmuno-

histo-chemistrytests,andpartofthefundingrelatedtofinancialresiduerelatedtolate

contributionsfromEFPIApartnerswhoseoriginalpurposehadbeenresolvedusing

additionalbeneficiarycontributions.Theproposalprocesswasmanagedbythe

ManagementBoard.

WP2:Consensus

ThisWorkpackagehaditstopactivitiesattheverybeginningandattheveryendoftheproject.

• Afterreachingitsfirstrefinementoftheconsensus,WP2continuestoiterateitscore

outputsastheproposedrefinedconsensusdocumentandrefinedcriteriawillbe

updatedasnewanalysisresultsemergeduringQ22016.

WP3:Clinicalcohorts

Thequalitycontrol(QC)oftheclinicaldataofthelongitudinalvisithasrequiredprolonged

efforts,basedondoublechecksbetweensourcedataandTranSMARTdata.Thishasalsoledto

definitivelytieupofresidualdetailsinthebaselinedataset.Thedatacleaningteamwillrelease

thelongitudinalQCdatabyendofMay2016.

• WP3hasdeliveredthepaediatricandadultcohortswiththeplannednumberof

recruitedsubjectsintotal(n=1025).

• Thecross-sectionalbaselinedatahavebeenqualitycontrolled,andthecloseddatabase

isbeingusedinTranSMARTbytheconsortiumpartners.

• ThefinalstepofWP3istodeliverthequality-controlleddatabasesforthelongitudinal

andexacerbationvisits.ThiswillbeaccomplishedbyMay2016.

WP4:Biologicalsamples

Thequalitycontrolandlaboratoryproceduresofallsampleswerefinalized.Thebiobanked

samplesweresecured,alsoforthepost-fundingperiod.

• Allbronchoscopyworkwascompletedaccordingtothedescriptionofwork.

• Thesputumandbiopsymaterialhasbeenqualitycontrolledand

immunocytochemistry/immunohistochemistryhasbeenperformed.

• Dataarenowbeingpresentedindraftpublications.

WP5:Experimentalexacerbation

Thefinalyearoftheprojectallowedaccomplishingtheexperimentalrhinovirusinfectionstudy

innormalandasthmaticvolunteers.Inordertodoso,theinvasiveprocedures(outcome

measurementsobtainedbyrepeatedbronchoscopies)wereomitted.Lastpatientoutwas

December31,2015.

• Part1ofrhinovirus16(RV16)challengestudy(Safety/Doseescalationcomponent-

D5.3)hasbeencompleted.TheviraldoseofthenewlyproducedGMPRV16,which

safelycausedviralsymptomsandviralreplicationinthenasallavage,wasselectedand

definedasthechallengedoseforpart2ofthechallengestudy(mainviruschallenge

biomarkerstudy–D5.4).Generationofthereportofpart1ofthestudyisunderway.

100TCID50wasdeterminedtobethecorrectdoselevelasitwasseentobeeffectivein

over80%ofparticipants.Thepreviousdoselevelof50TCID50wasseentohavealower

infectionratethanrequired.

• Problemswiththeportable,home-lungfunctiondeviceoccurredinpart1.

Approximately30%ofthedatawerenotreliable.Therefore,itwasnecessarytoreplace

thePIKOlungfunctiondeviceinpart2oftheviruschallengestudyviaanamendment2

ofthestudyprotocol.AnewCarefusionMicrodiarydevicewasdeployedasa

replacement,whichperformedbetter.Thehomespirometrydataobtainedwiththis

devicewereeventuallyqualitycheckedbyapanelofinvestigatorsduringtwo

teleconferencesinMarch2016.

• Thenecessityoftheamendmentcausedadelayofthestudystartofpart2.Sincethe

timelineofthestudywasalreadyseverelydelayedandrecruitmentinpart2wasfeltto

beevenmoredifficultcomparedtopart1,itwasdecidedthatthebronchoscopiesin

part2wereomittedfromtheprotocoltospeeduprecruitment.Thischangewas

includedintheamendment2.Withoutthebronchoscopydata,therhinovirus-induced

perturbationoftheasthmafingerprintswillbelessextensive.However,forfuture

applicationtheavailableandlessinvasivebloodfingerprintandhandprintwillbemuch

morerelevant.

• Thenewsite,MEU(MedicinesEvaluationUnit)Manchester,hadbeencontractedby

thesponsor(MSD)andwasactivatedbeforepart2ofthestudystarted.Thismeant

thatAmsterdam(AMST),Hannover(HANN)andMEUrecruitedallparticipantsforpart

2ofthestudy.ACROinGroningen,theNetherlands(QPS)supportedAMSTwith

referringonepatientforthestudy.

• ByDecember31,2015thestudywasclosedwhen23outof25subjectswere

challengedwithrhinovirus.Biosamples(nasalbrushings,bloodforlipidomicsand

proteomics,etc.),werecollectedandwillbeshippedtotheManchesterBiobank.In

addition,adsorbedbreathsamplesforbreathomicsweresenttoAmsterdamand

PBMCs(peripheralbloodmononuclearcell)willbesenttoMSDforgenomics.

• Afterfinishingthestudy(D5.4.)attheendofDecember2015,clinicaldataand‘omics’

platformsarebeinganalysedbyMSDinclosecollaborationwiththe‘omics’labsthat

havegeneratedtheomicsdatainU-BIOPREDandthedatawillbeimportedinto

TranSMARTforfurtheranalysis.D5.4willbedeliveredbyMay2016.

• BiosamplessenttothebiobankwillbeavailableforfurtheranalysisbyU-BIOPRED

partnerspendingsupplementaryfundingfromU-BIOPREDpartnersthemselves,

includingMSD.

• Asplanned,theRV16GMPmaterialissubjectoffurtheranalysisovertime(stabilitydata,non-infectivitydata),whicharecurrentlydeterminedatBioreliance.Thesedataarerequestedbyregulators(BfArM)beforethematerialcanbeusedasGMPmaterialinclinicaltrials.ThesedatawillbeaddedtotheavailableIMPD(InvestigationalMedicinalProductDossier).Note:Therequirementforformalsafetytestingofthevirusforfuturepost-projectusagebecameevidentduringtheproject,butthefundingisonlynowbeingprocessed(theworkisongoing)andthereforeitisnotincludedwithintheprojectperiod.

• WhentheIMPDhasbeencompletedwiththestabilitydata,thestudyprotocolpfpart2

togetherwiththeIMPDwillbereadyforfinaldeliveryasD5.5(Standardprotocolviral

challenges).D5.5willbedeliveredbyMay2016.

WP6:Pre-clinicalmodels

Thefinalyearwasusedforaligningvariousmousemodelsandforcomparisonofoutcomesin

relationtohumansevereasthma.

• InstudiesusingtheCFA/HDMmodel(CompleteFreund’sAdjuvant/HouseDustMite)we

wereabletoshowthatPenhmeasurementscorrelatedwellwithlungresistance(RL)and

acetylcholine(Ach)responsiveness(–logPC200)usingwholebodyplethysmography.Penh

was subsequentlyused to reducenumbersof animals inall longitudinal animal studies,

becausePenhcanbemeasuredveryreproducibly.

• We developed and validated a humanised mouse model of severe asthma. We

demonstrated that it is possible to model interactions between a respiratory virus

infection in the lung at very low infectious dose (100pfu – plaque forming units) and

developmentofasthma.

• Arobustmousemodelofsevereasthmaexacerbationsfollowinginfectionwithlowdose

influenzavirusA/X31H3N2wasdeveloped.

• Proofofconceptfornovelmodelofsevereasthmawasachieved.Usingamousemodelof

severe asthmabasedon chronic allergen (HDM) and adjuvant (CFA) exposure,which is

relatively steroid insensitive, we were able to demonstrate that targeting a novel

pathway, the NRLP3 inflammasome (described in human severe asthma), is highly

effectiveinreducingairwayhyperresponsivenessandinflammation.

• Inpreliminarystudieswewereabletoshowthatitispossibletomapmouse‘pawprints’

tohumanfingerprintsusingTDA(TopologicalDataAnalysis)onGSVA(GeneSetVariation

Analysis) signatures derived frommousemodels of asthma. This is a critical outcome,

sinceitcross-checkedmeasuresfromanimalmodelsagainstthosefrompatientswith

severeasthma,therebyvalidating(partsof)thesemodelsforsevereasthmaresearch.

• Wehavebegun tomaptranscriptomicdata frommousemodelsof severeasthmaunto

humansevereasthmatranscriptomicdatafromsputumusingacombinationofTDAand

GSVAapproacheseitheraloneorincombination.

WP7:‘Omics’platforms

Thefinalyearwasusedtodeliverthe‘omics’platforms.Thisrequiredactivitiesinvarious

academicandindustriallabs,whichwaseventuallyverysuccessful.

Ofthe22platformsorWorkflowsmanagedwithinWP7,20havebeendeliveredwhilst2aredelayedanddeliverywilloccurafterthisreportisdue.Theworkflowgroupswereformedaroundconcretepiecesofwork.Sometimesthiswasasingleplatform,sometimesthisrelatedtoanumberofplatforms.TheworkflowsreflectedthetypeofworkandthegroupofpeopleinvolvedandwascreatedthroughWP7andWP8discussions.ClearprogresshasbeenmadewithanalysisalreadyunderwayandaclearplanforcompletioninQ12016isinplace.Thesearethefollowing:

• Biomarkers from pre-clinical human challenge models: The primary model in U-

BIOPREDconsistedofaninvivostudyinvolvingarhinoviruschallengemodelinwhich

asthmaticparticipantswereexposedtohumanrhinovirusproducedtoGMPstandards.

AsreportedbyWP5,therewassignificantdelayinstartingtheinvivostudyandatthe

timeofwritingof this reportcollectionofall thesampleshasnotbecompleted.The

patientnumbers(n=25)andtherebythesamplenumbersareverylimitedascompared

to the samples from the U-BIOPRED clinical cohort. Therefore, the leads of all the

‘omicsplatformshaveprovidedinformationaboutthecostsandtimelinestocomplete

the analyses and there is a commitment to finalize March 2016. This will require

additionalfundingfromU-BIOPREDpharmapartnersorsomeothersourceoffunding.

Therefore,MSD‘omics’labshavebeenofferedasfeasiblealternative.Deliverywillbe

inMay2016.

• The delivery of the urine metabolomics fingerprints, derived from non-targeted

metabolomics, for which funding outside the original U-BIOPRED application was

obtained throughanENSOgrant,hasbeendelayedby forcemajeure. First, thepost-

doctoralresearcherrecruitedtoperformtheanalysisleftforanindustrialpositionafter

1monthintotheposition.Itwasthereforenecessarytorecruitanotherpost-doctoral

researcher that took an additional 4 months. Second, a major technical problem

occurred with the mass spectrometer purchased to perform the metabolomics

analyses. Themass spectrometerwas installed in February2015;however, it didnot

pass the installation specs until September 2015. Accordingly, urine metabolomics

analysescouldnotbeinitiateduntilOctober2015.Dataacquisitionhasnowbegunand

preliminary data is shown in the metabolomics deliverables section. The data have

become available inMarch 2016. Full (complete) analysiswill be available by end of

April2016.

WP8:Bioinformatics

ThekeydeliveryofU-BIOPREDisprovidingthefingerprintsandhandprintsofsevereasthma.

Usingtheavailable‘omics’datatheU-BIOPREDanalysistoolboxwasrun.Thisdeliveredseveral

fingerprints(fromtranscriptomicstobreathomics)andthesputum-andbloodhandprints.

• Initialcross-sectionalhandprints(D8.5)havebeenregeneratedwithinclusionofthe

amendedbaselineclinicaldataset.

• Theotherplannedhandprints(relatedtodeliverablesD8.6,D8.7andD8.8)arereadyto

beproduced.Theunderlyingdatatogeneratetheseareclosetobeavailableandquality

controlled.Thereafter,thestatisticalscriptscanberunsothatD8.6,D8.7andD8.8will

definitelybedeliveredbyQ22016.

WP9

BoththeexploitationsideofWP9andthedisseminationworksawmajorachievementsinthe

finalperiod.

FordisseminationU-BIOPREDpresentedadedicatedsymposiumattheERSCongress2015,with

over1000peopleinattendance.33Conferenceabstractsweresubmittedandallacceptedfor

eitherposter,symposiumororalpresentations.BaselinecohortdescriptionpapersfortheAdult

andPaediatriccohortswerepublishedintheEuropeanRespiratoryJournalandafurther10

papershavebeendraftedandareintheprocessofbeingsubmittedforpublication

o Presenceatinternationalconferenceshasensuredahighprofilefortheprojectin

thefield.U-BIOPREDfeaturedintheWorldVillageatERSandabookletofU-

BIOPREDactivitiesatCongresswasproduced.

o CommunicationsapproachisoutlinedonfinalWPdeliverableD9.7

o Thewebsiteandtwitter/LinkedInplatformscontinuetobeupdated

o Anewtailor-madevideoclearlyexplainingtheconceptanddeliveryofU-BIOPRED

tolaypersonshasbeenuploadedtothewebsite

Forexploitation,maintenancelevelfundingwassecuredfromtheERS,supporting

management,communications,biobank,datastorageandrhinovirusstorageand

publicationssupport.Updatesforthewebsiteandsocialmediaplatformssecuredinto

thesustainabilityperiod.

WP10

ThethreeboardsofthisWorkpackagefinishedandpublishedtheirwork,eventhoughongoing

patientparticipationisstillrequiredandsecured.

• TheWP10committeescompletedtheirworkinthefinalperiod.Ofthefourgroups,the

PatientInputPlatform(PIP)iscontinuingactivitythroughtothesustainabilityperiod.

Andthegrouphasproducedauniquebookletonthepatientinputexperiencewith

supportfortheprintingisfromIMI.

• TheEthicsBoardcontinuedtoadviseondevelopmentsintheRV16clinicaltrialandin

thestorageofdata.TheEthicsprocessforthedurationoftheprojecthasbeen

recorded,withpatientinputandcompletedwithallissuesresolved.

• TheSafetyMonitoringBoardfinaliseditsworkandcarriedoutareviewofallsevere

AdverseEventsformsproducedintheprojectinordertodoublechecktherewereno

outstandingfollowupissues.ThiswasprimarilyfortheWP3coreclinicalstudyasno

SAE’swerereportedinthechallengestudy.Noissueswereidentified.

• Theimpactofpatientinvolvementwaspublishedinapeerreviewjournal:‘From

tokenismtomeaningfulengagement:bestpracticesinpatientinvolvementinanEU

project.http://www.researchinvolvement.com/content/1/1/5’

1.4. Significantachievementssincelastreport

WP1

• Theknowledgeportalhasseenfinaldevelopmentsintermsoffeaturestodownload

andstoredataandalargeamountofdatahasbeenuploadedtotheU-BIOPRED

instanceoftranSMARThostedatpartner4(LOIC).

• TheProjectmanagementteamhasinitiatedanddriventhelegacyplanningprocess,

includingdevelopingalegalframeworkforcontinuingthecollaborationamong

partners,togetherwithengagingtheEuropeanRespiratorySociety(ERS)toensurethe

coreoutputs/assetsoftheproject(biobank,database,viralstorage,consortium

activities).PartnersBioSciConsultingandAMSThavemanagedthecontractualaspects

associatedtobothpiecesofwork.

• ThereportingprocesshasbeensteeredandoverseenbyWP1,withintenseeffortsin

termsofdiscussion,channellingscientificobjectivesandresultsandforming

manuscriptwritingteamsinthepastyear–andcontinuingintothelegacyperiod.

• Financialmanagementoftheconsortiumhascontinued,ledbytheAMSTwithsupport

fromBioSciConsulting.ClearinstructionsforreportingandsupportoftheCFS/FromD

processhavebeencarriedout.

• WP1hassupervisedtheuploadofallbaselineclinicaldataandomicsdatasetstotheU-

BIOPREDinstanceoftranSMART.Thishasincludedextensiveeffortstovalidatethe

datapriortoupload.

• AgreementwasobtainedfromU-BIOPREDmemberstocontinueworkingtogether

developingtheresultsandkeyoutputs/assets,initiallyonthebasisofanamended

ProjectAgreement.

• EngagementoftheERSfortheU-BIOPREDlegacywasconsolidatedwithaformal

contractsignedinordertofacilitatefinancialsupportforthesustainabilityperiod.This

isacriticalpost-projectachievementtoensurethelegacyofU-BIOPRED.

• U-BIOPREDcorefacilitatorsystemswerecarriedthroughintothesustainabilityperiod,

includingtheprojectmanagementplatforms,biobank,databasemanagement,

conferencecallfacility.Explicitmanagementsystems(boards,teleconferences)were

plannedandinstalledforthesustainabilityperiod.

• AbusinessplanandapproachtosustainabilitywasagreedandoutlinedinD1.6and

D1.7.Basedonthis,theEuropeanRespiratorySocietyhasagreedtofundthe

maintenanceofthebiobankanddatabase,whilstalsocoveringthestorageoftheGMP

rhinovirusstock.

• Collaborationhasbeeninstigatedwithmembersofa1500subjectasthmacohortin

Brazil(ProAR),whichwillenablecomparisonandcross-validationoffindingsbetween

thetwocohorts

WP2

WP3

WP4

• Meetingonconsensuspositionsandrevisedphenotypeswasheld,leadingtothefirst

iterationoftherevisedconsensusstatementandtheproposedcriteriaforphenotypes.

• TherevisedU-BIOPREDconsensusfromQ32016extendstheoriginalonepublishedinThorax2011,bystatingthatsub-classificationofasthmabasedonclusteranalysisofclinicalcharacteristicsaloneisnotaccurateenough.Duringthepast5yearsthefollowingtwomajorstepshavebeentakentoimprovethis.

o 5domainsofchronicairwaysdiseases(includingsevereasthma)shouldalwaysbeconsidered:variableairflowobstruction,fixedairflowobstruction,inflammation,infectionandremodeling.

o Biomarkerprofilesratherthansingleorevenclusteredbiomarkersofanytypeareenablingbetterpredictionoftherapeuticefficacy.Theseprofilesinclude‘omics’fingerprintsandhandprints.Thepreliminarysputumhandprints(SH1- 3)andbloodhandprints(BH1-4)ofsevereasthma,presentedattheERSAmsterdamSeptember2015(figure2.4.11),areindeeddemonstratingdifferentialclinicalexpressionprofiles.Thedefinitivehandprintswillthereforeleadtothe3rdandfinaliterationoftheU-BIOPREDconsensusinQ32016.

• Deliveryandclosureofthequalitycontrolledclinicaldatabaseofthepaediatricand

adultcohortsinTranSMART.Thisrequiredmultiplequeriesfortheindividualsite,

whichwerehandledbyWP3withtheCROCROMSource.

• Theclinicalcharacteristicshavebeenpublished.

• Clusteringofsevereasthmausingclinicalparametershasbeendone(see2.4).

• Bronchoscopysamplecollectionwascompletedwithdeliveryofbronchialbiopsies,

bronchialbrushingsandnasalbrushingsfromall4U-BIOPREDadultcohorts.

• Immunohistochemicalbiopsyanalysishasbeenperformed.

• Immunocytochemistryperformedonqualitycontrolledcytospins.

• Qualitycontrolledbronchialbiopsy,bronchialbrushingandnasalbrushingsamples

havebecomeavailablefortranscriptomicanalysis,whichhasalreadybeendone

successfullyandlinkedtotheairwayhistology(see2.4)

• Bronchoscopysamples(biopsies,bronchialbrushingsandbronchoalveolarlavage)have

beendeliveredfortheWP6programme.

• Theroleofbronchoscopicsamplesasa“goldstandard”ofasthmaphenotypeshave

beenevaluated.

• Extensivequalitycontrolhasbeenconductedon159bronchoscopyrelatedsamplesas

below.

• Thefirsthistologypaperhasbeenwrittenandisclosetosubmissiontoapeerreview

journal.

• Bronchoscopyrelatedsamples:

o GroupA–53

o GroupB–20

o GroupC–40

o GroupD-46

SAMPLE Numbertaken Passqualitycontrol Action

BronchialBiopsy

(GMA)

159 139(87.4%) Immuno-

histochemical

analysis

(inflammation)

BronchialBiopsy

(Paraffin)

159 97(61.8%) Histochemicalanalysis

(remodelling)

Bronchialbrushing 159 147(92.5%) Genearray

Bronchialbiopsy

(mRNA)

116 107(92.2%) Genearray

Nasalbrushing 100 89(89%) Genearray

WP5

• ViralchallengestudyPart1(safety&doseescalation)wascompleted.Theviral

challengedoseforpart2wasselected(100TCID50)anddefined.

• Thenewsite,MEUManchester,hasbeencontractedbythesponsor,MSD,andwas

activatedbeforepart2ofthestudystarted.

• IntheviralchallengestudyPart2(mainviruschallengebiomarkerstudy),wasfinished

bychallenging23ofthetarget25studypatients(mild/moderateasthmaticsnottaking

LABAs)withGMPRV16.FinalpatientoutwasreachedonDecember31,2015.

Biosamples(nasallavage,inducedsputum,nasalbrush,plasmaforlipidomics,serum

forproteomics,bloodforRNA(PAXgene),urineforlipidomics)werecollectedandhave

beenshippedtotheManchesterBiobank.Inaddition,breathsamplesonadsorption

tubesforbreathomicsweresenttoAmsterdamandPBMCwillbesenttoMSDfor

‘omics’analysis.

• RV16GMPstorageatFraunhoferITEM–Braunschweigissecuredforanother12

months

• RV16GMPownershipagreementbetweenAmsterdamandFraunhoferhasbeen

almostfinalized(accessdocumentforRV16GMPusebyotherpartiesisinthefinal

reviewprocess)

WP6Updates–InVivo

AMC:

• HDMmodelexacerbationwithinfluenzaandsteroidresponseprofilingcomplete

• EpithelialcellbrushingpilotstudyinmicroarraydidnotyieldsufficientRNA;RNA

preparedforanothermicroarraystudy.

Almirall:

• CFA/HDMexacerbation(polyIC)complete.

• Influenzaexacerbationmodelcomplete.

• StudywithGhent(humanizedmicemodel)finalizing.

• SecondsetoflungsamplesmRNApreparedandbeinganalysedbymicroarray.

Fraunhofer/Hannover:

• Precisioncutlungslices(PCLS)modelcharacterizationinmouseandhumanwith

HRV1bcomplete.

• Initialmicroarraystudycomplete.

• Increasingreplicatesisbeingfinalized.

ICL• FCA/HDMmodelwithvariousanti-Th2cytokinetherapeuticscomplete.

• NLRP3inhibitorstudycompletedandanalysed.

Updates-InVitro

ICL

• Culturedepithelialcellsformicroarraydone.

• Samplesawaitingmicroarrayanalysis.

• Validationofgenesinbiopsiesandsputum–RT-qPCRandIHC,ELISA/WBcompleted.

• Sampleprofiling(transcriptomics/proteomics)isbehindscheduleashumanairway

brushing/bloodsampleswereprioritized:deliveryendofApril2016.

Tableofmodels(in vivo andex-vivo utilizedbyU-BIOPREDWP6.Thelackofanadequatemodelhampers

mechanisticinsightandthedevelopmentofnewtherapeutics.

Model PurposeStageof

development/validationContextforuse

Furtherwork

Invivo

CFA/HDMsteroid Rapid,robust resistantmodel screeningmodelfor

Publishedresultsshowingsteroidinsensitiveandcanbe

possibledrugsandnoveltarget

DevelopamixedTh1/2/17modelofsteroid-resistant

asthma

exacerbatedwithpoly(I:C).Fulldescriptionofmodelisbeingwritten,includingextensivetimecourseof

assessment.Described

inflammasometargetinsubsetofsevereasthmapatients,

Willformpartofsubmission

toEMA.

immuneresponsesandeffect whichwasprevented ofanti-IL-4/13intervention byCRID3,ananti-

inflammasomeagent inthismodel.

StandardchronicHDMexacerbationmodel

Validatepreviouslypublisheddata

showingexacerbationofmodelwithRV

infection.

UnabletoshowanyexacerbationofmodelwithRV

andnoeffectonsteroidresponsivenessasreportedin

man.

Screendrugsforanti-exacerbationactivityincontextofchronic

asthmaticinflammation.

Notrobustorreproducible–nofuture

workplanned.

ChronicHDM/influenzainfection

Todeveloparobustmodelofsevere

asthmaexacerbations

Themodelledtoprolongeddeteriorationoflungfunction,aggravatedmucusproduction,peri-vascular,peri-bronchialandallergicinflammationthat

Robustscreenfornewdrugs in ICS-insensitive viral-inducedexacerbations.

Submittedforpublication.

basedonchronicHDMandinfectionwithlowdose

influenzavirusA/X31H3N2.

wasunresponsivetoinhaledcorticosteroids,butresponsivetooralcorticosteroids.Thisreflectstheclinicalsituationin

severeasthma.

Anti-IL-5 preventedthe exacerbations inthis modelrecapitulating itseffectsonsevere

WillbepartofthepackageforEMAevaluation.

Theexacerbationwasprecededbyamarkedinnate,

asthma exacerba-tions.

butnotT2responseand enhancedeosinophilia.

Alsoledtonewideas astopotentialinnate immune targets for exacerbations of humansevereasthma.

Exvivo

BronchialBiopsiesWantedtodeveloparobustmodelthat

reflectscomplexityofcellswithinthe

airwaytoexaminewhetherreflectssusceptibilityof

asthmaticairwaystoexacerbation.

PossibletodetectpresenceofsubsetsofcellswithinBiopsies

usingFACsandofsomedifferencesinmediatorreleasefollowingsteroidtreatment.However,werenotabletoexacerbatebiopsieswithRVandonlyminimallywithinfluenza.RNAqualitynot

good.

Better3Dmodelofasthma/severe

asthmainvolvingcell-cellinteractions.

Notbeing

takenfurther.

Bronchialbrushings

Theseareoftenusedasamodelandtheepitheliumwas

consideredthedriverofthedown-streamimmunedefectsin

asthma.

PossibletogetgoodRNAandproteinexpressiondata.Fewdifferencesseenatbaselineafterculturebutclear

differencesininnateimmuneresponseswithincreasing

severityofasthmawhencellsarestimulated.

Modelreflectsinnateimmunedifferencesin

severeasthmafollowingstimulation.

Maybeparticularlyusefulfortestinginnateimmune-directeddrugs

Genearraystobecompletedandlinkwithbrushingsobtained

directlyfrompatientsat

bronchoscopy.

Airwaysmoothmusclecells

ResponsibleforairwaycontractionandAHR,majorfeaturesofsevereasthma.Modelusedtodeterminewhetherdifferencesincellfunctionreflecthumanresponses.

PossibletogetgoodRNAandproteinexpressiondata.Fewdifferencesseenatbaselineafterculturebutclear

differencesininnateimmuneresponseswithincreasing

severityofasthmawhencellsarestimulated.

Modelreflectssomeaspectofseverediseaseanddata

indicatedassociationwithcough.

Paperstobesubmitted.Modelwillbecontinued.

Precisioncutlung Analternative3D slices modelofasthmabut

retainingallstructural cellsincomparison withbiopsymodel. Canshowcontraction ofairwayswiththis

model.

Peripheralblood Readilyaccessiblecell cells typethathas

previouslybeen showntoreflectsome aspectsofsevere asthmasuchas steroid responsiveness.

WP7

WP8

o Allthelaboratoryanalysesinallthe‘omicsplatformsdefinedinthegrant

applicationhavebeencompleted(exceptthedelayedurinemetabolomics,see1.3

andbelow)andthemajorityofthemhaveproducedsetsof‘omicsfingerprints,i.e.

setsofphenotypes/endotypesbasedonclustersforeachofthe‘omicstechnologies.

o Thedeliveryofurinemetabolomicfingerprints,fundedbytheENSOadditional

grant,areinproduction,withcommittedfundingandaccomplisheddeliveryby

March2016.

o TheENSO-fundedAnalyteSethasbeendeliveredasdetailedinDeliverablereport

7.6andisnowbeingevaluatedtoidentifybiomarkersofasthmaphenotypes,either

aloneorincombinationwithotherU-BIOPREDdata.

o BasedontheENSO,microbialprofilinghasdeliveredanumberofoperational

taxonomicunits(OUT)thatreflectindividualmicrobialspecieswhichwere

differentiallyabundant;clusteringoftheseisongoingandwillbecompletedbyApril

2016.

o AllanalysesbetweenWP7andWP8hadbeenspecifiedinso-calledWorkFlows

(WF),withpredefinedresearchquestions.

o AlltheacquireddatawereuploadedontotranSMARTandfingerprintsconstructed.

Fingerprintshavebeendeliveredfortranscriptomicsinblood,sputumpellets,nasal

brushings,epithelialbrushingsandbronchialbiopsies,urineeicosanoids;proteomics

ininducedsputumfluidphase(airwaysecretions)andserumandsputum

eicosanoids.

o Fullvalidationhasbeenachievedforsomeofthesefingerprintsandfurther

validationofthosefingerprintsonadditionalcohortshasbeenscheduled.

BreathomicsfingerprintscreatedbyeNoseandGC-MStechnologyhavealsobeen

generatedandeNosefingerprintshavesuccessfullybeenreplicatedusingdatafrom

thelongitudinalstudyvisit(see2.4).

o WP8hassuccessfullyproducedtwomajorhandprintsonthedatafromtheadult

cohorts:a‘bloodhandprint’on227asthmaparticipantsanda‘sputumhandprint’

on72asthmaparticipants(see2.4).Thedifferenceinnumbersofpatientsamples

availablewasduetothenumbersofsamplesavailableintherespectiveomics

platforms.Thesehandprintsthatarecombiningvarious‘omics’platformshavebeen

presentedatvarioussymposiaattheERSmeetinginAmsterdam(September2015)

andarerepresentingthecore,innovativeoutputofU-BIOPRED.

o Thebloodhandprintanalysisproduced5separatebloodhandprints(BH),

identifying5typesofasthmapatients.Eachofthe5handprintscanbeseen

asaclusterandusedasaninitialphenotypicaldefinition,withthedifferent

variablesandcharacteristicsofeachgrouppresented.Thetablebelow

showstheclusteringofdataaroundanumberofmeasurementsproducing

thehandprintgrouping.Thedatacouldalsoadequatelybeencapturedby

using4bloodhandprints.

o Thesputumhandprintproduced3clustersonthelowernumbersinvolved.

SummarytableswerepresentedattheERSCongress2015.

WP9

Figure1.4.1.Bloodhandprintvalidation.Left:Thecumulativedistributionfunctions

(CDF)forvariousnumberofclustersinthehandprint.Right:Stabilityassessmentof

thesimilaritynetworkfusion(SNF)analysis.Thedataareshowingthat4to5

handprintclustersarestable.

o U-BIOPREDagainpresentedadedicatedsymposiumattheERSCongress2015,with

over1000peopleinattendance.Thiswasavaluableopportunitytopresentonthe

projectandfocusedonproteomicsdatainrelationtoinflammationandclinical

characteristicsandonpresentingthefirstU-BIOPREDhandprint:theblood

handprint.

o 33Conferenceabstractsweresubmittedandallacceptedforeitherposter,

symposiumororalpresentations.

o Disseminationseffortscontinued,withpublicationsontheAdultandPaediatric

cohortsintheEuropeanRespiratoryJournalandaneditorialfocusingonU-BIOPRED

andSARP(USconsortium)inTheLancetRespiratoryMedicinejournal

o U-BIOPREDfeaturedintheWorldVillageatERSandabookletofU-BIOPRED

activitiesatCongresswasproduced.

o Afurther10papershavebeendraftedandareintheprocessofbeingsubmittedfor

publication

o Updatesforthewebsiteandsocialmediaplatformssecuredintothesustainability

period.

o Presenceatinternationalconferenceshasensuredahighprofilefortheprojectin

thefield

o CommunicationsapproachoutlinedonfinalWPdeliverableD9.7

o Thewebsiteandtwitter/LinkedInplatformshavebeenkeptupdatedwithnews,a

processwhichwillcontinueintothelegacyperiod.

o Anewtailor-madevideoclearlyexplainingtheconceptanddeliveryofU-BIOPRED

tolaypersonshasbeenuploadedtothewebsite.

WebsiteStatistics:1October2014–30September2015

o Totalsessions:5,631.

o Totalusers:3,693.

o Totalpageviews:23,555.

o Averagespagespersession:4.18.

o Averagesessionduration:3.44minutes.

o Mostpopularcountries:UK(28%),USA(11.5%),Belgium(8.7%),Netherlands(6.8%),

Italy(4.8%).

o Sitefoundin59%ofthecasesbyorganicsearch,in17%bydirectlyenteringthe

addressandin14%ofthecasesbyreferral.

WP10

• PatientInputPlatform(PIP)continuedactivityinPeriod6willbecontinuingthroughto

thesustainabilityperiod.

• Abookletonthepatientinputexperiencehasbeenpresented,beingledbyELFwith

veryactivepatientinputandauthorship.SupportfortheprintingisexpectedfromIMI.

• Ethicsprocessforthedurationoftheprojecthasbeenrecorded,withpatientinputand

completedwithallissuesresolved.

• TheEthicsBoardhascontinuedtoadviseondevelopmentsintheRV16clinicaltrialand

inthestorageofdata.

• ThePatientInputPlatform(PIP)hasseenitsactivityincreaseinthislastperiod,with

monthlyconferencecallsandthreefacetofacemeetingsoccurringintheperiod.The

PIPgrouparecontinuingtoworkinthelegacyperiodandareinvolvedinreviewing

publicationsanddevelopinglayabstractsaswellasassistingindisseminationwork.

• TheSafetyMonitoringBoardfinaliseditsworkandcarriedoutareviewofallsevere

adverseEventsformsinthecoreclinicalstudyasanassurancemeasure.

• Theimpactofpatientinvolvementwaspublishedinapeerreviewjournal:‘From

tokenismtomeaningfulengagement:bestpracticesinpatientinvolvementinanEU

project.http://www.researchinvolvement.com/content/1/1/5’

ENSOfundedwork–summarysupplement

Sustainability

D1.6(Reportonpossiblebusinessmodels)andD1.7(Reportoninitiationofbusinessmodel)have

beendelivered.TheteamwasledbyBioSciConsulting(ThierryNicloux/ScottWagers)andincluded

AnthonyRowe(Janssen),ChrisCompton(GSK),DavidMyles(GSK),RatkoDjukanovic(Southampton),

FanChung(LOIC),IanAdcock(LOIC),JasonHannon(Roche),JorgeBelata(Almirall),JulieCorfield

(AZ),KathrinRiemann(BI),LeonCarayannopoulos(MSD),NorbertKrug(Fraunhofer)andPeterSterk

(AMST).

FundinghasbeensecuredfromERSforamaintenancelevelofbasicprojectoutputs(biobank/data

baseanddatamanagement,consortiumactivities)for6monthswithaforthcomingbudgetreview

forafurther12months.AcontracthasbeensignedandanewsetofDeliverablesandMilestones

developedtotrackprogressinthislegacyperiod.Contactswitharangeofexternalpeoplecontinue

tofeedintotheplanningprocessforfuturework,andtheEPFIAgroupcontinuestomeet,which

shouldleadtoproposalsbeingputforwardforsupportbyothersinthegroupandeventual

endorsement.U-BIOPREDpartnersagreedinaGeneralAssemblyvotetocontinuetheircollaboration

underthetermsoftheexistingProjectAgreement.AmsterdamprovidesdailyrepresentationofU-

BIOPREDasalsoagreedduringtheGeneralAssemblymeetinginJune2015.

Fingerprint ENSO Theanalytesethascompletedanextensiveprocessofanalytenominationsandsubsequentsample

analysisplanning.Therelateddeliverablereports,D7.6andD8.9havebeencompleted.Abroad

rangeofpeoplefromacrosstheprojecthavebeeninvolvedintheprocess.AnnaJames(BIandSven-

ErikDahlen(KI)leadtheirrespectiveorganisationswork.

Microbiome:SouthamptonandJanssenhavetakenforwardthisworkandallsampleshavebeen

analysed,completingD7.7.TheleadersarePeterHowarth(SOH)andFredericBaribaud(Janssen).

Metabolomics:KIhavesuccessfullyre-establishedthemassspectrometermachineandsampleshave

beenanalysed,asreportedinD7.8.CraigWheelock(KI)isleadingthiswork.Deliveryaccomplished

byMarch2016.

1.5. Scientificandtechnicalresults/foregroundsoftheproject

• TheU-BIOPREDprojecthasaccomplishedapublic-privatecollaborationandexchangeinthe

fieldofmedicalresearch,onthetopicofunderstandingsevereasthma,inordertosubsequently

allowEFPIAcompaniestodevelopnovelinterventionstargetingpreviouslyunknownnetworks

ofbiologicalmechanismsthataredrivingthisdifficult-to-treatdisease.Thishasresultedin

injectingEFPIAexpertiseintoacademiccentresinorderdeliveracohort/registryofsevere

asthmapatientsinamongstcountriesinEuropethatmeetsthehigheststandards(GCP)interms

ofqualitycontrolintermsofmeasurementprocedures(SOPs),biobankinganddatabase

management.Alternatively,thispublic-privatecollaborationhasallowedacademiclaboratory

andbiomarkerexpertisetobesharedwithEFPIAlaboratoriesbasedonsharedprotocols.This

particularlyrelatestopre-clinicalanimalandinvitromodels,whichsimilarlyhaveforthefirst

timebeexchangedandoptimisedbetweenEFPIAcompanies.Thiswouldnothavebeen

accomplishedwithoutthisIMIproject.

• Theadultandpaediatriccohortshavealreadybeenpublishedintermsoftheirclinical

characteristics(Shawetal.ERJ2015,Flemingetal.ERJ2015),whichdefinitelyshowsthatsevere

asthmainEuropedoesnotentirelymatchsevereasthmaine.g.theUS.Thediscrepancyclinical

characteristicsofsevereasthmabetweenEuropeandUSisimportantandisrelatedto

differencesinthehealthcaresystemsbetweenEUandUS.InEuropewedealingwithtrue

severeasthma,asdefinedbyU-BIOPREDbyBeletal.Thorax2011. • TheU-BIOPREDdefinitionofsevereasthmaandthealgorithmtoclinicallydiagnosetruesevere

asthmaamongstdifficult-to-treatasthmahasbeenpublishedbyU-BIOPRED(Beletal.Thorax

2011)andhasmeantastep-changeinclinicaldecisionmaking.

• Justbyusingclinicaldata,theU-BIOPREDclusteranalysisofthedataamongsttheasthma

cohortshasproduced4clustersthatcanbedistinguishedbyroutineassessmentinclinicalcare.

Notably,theseclinicalclustersweresignificantlydifferentwithregardtothesputum

transcriptomicandproteomicnetworks.Thisshowsthatclinicalandbiologicalphenotyping

providesseparategroupsof(severe)asthmapatients,whichdefinitelyrequired(partially)

distincttherapeuticapproaches.Thisisamainaccomplishmentoftheprojectandshowsthat

severeasthmahas4distinctgroupswhichrequiredifferenttreatmentapproaches.

• ThedetailsregardingtheU-BIOPREDclinic-physiologicalclustersfortheadultcohortsarethe

following.Fourreproducibleandstableclustersofasthmaticswereidentified.Thetrainingset

clusterT1consistsofwell-controlledmoderate-to-severeasthmatics,whileclusterT2isagroup

oflate-onsetsevereasthmaticswithhistoryofsmokingandchronicairflowobstruction.Cluster

T3issimilartoclusterT2intermsofchronicairflowobstructionbutiscomposedofnon-

smokers.ClusterT4ispredominantlycomposedofobesefemaleuncontrolledsevereasthmatics

withincreasedexacerbations,butwithnormallungfunction.Thevalidationsetexhibitedsimilar

clusters,demonstratingreproducibilityoftheclassification.Thereweresignificantdifferencesin

sputumproteomicsandtranscriptomicsbetweentheclusters.Thesevereasthmaclusters,T2,

T3andT4,hadhighersputumeosinophiliathanT1withnodifferencesinsputumneutrophil

counts,exhalednitricoxideandserumIgElevels.Takentogether,thisU-BIOPREDcluster

analysisintheadultscohortshowsthatclinico-physiologicalparametersyield4stableand

reproducibleclustersthatassociatewithdifferentpathobiologicalpathways.Thispavestheway

tocriticalmechanismsandtherebypotentialtargetsfortherapyinrelationtoclinical

phenotypesofthedisease.ThemanuscriptisinrevisionintheJAllergyClinImmunol(impact

12).

• U-BIOPREDhassucceededinsamplingblood,urine,sputumandbronchialbiopsiesfromthe

sameclinicallywell-characterizedpatients.

o Duetoanumberoffactorstheoverlapfromonedatatypetoanotherdatatype,

derivedfromanalysingthevarioussamples,isvariable.Thereasonsforthisarepatient

decisions,includingoptingoutofproceduressuchasbronchoscopiesandCTscanning,

thesuccessrateofsomepatient-demandingproceduressuchassputuminductionand

thesampledataremovedduringthequalitycontrolprocess.Thesefactorsare

inevitable,andthishasnothamperedintegrativeanalysisasshownbythefirstcluster

andhandprintanalyses.Thefirstdraftpaperonlinking‘omicsplatformstohistological

outcomeshasbeenwritten,showingthecomplementaryvalueoftheU-BIOPRED

samplingprocedures.

• Duringthecourseoftheprojectitbecameevidentthatthe‘omics’platforms,requiredfor

unbiasedbiologicalphenotyping,neededcomprehensiveanalysisoftheavailabletechnologies

andvalidation.Thishasbeendoneandpublished(Wheelocketal.ERJ2013).Thisincludedthe

extensiverequirementsforadequatelyapplyingandqualitycontroloftranscriptomics,

proteomics,lipidomics,metabolomicsandbreathomics.Theintegrativeassessmentofthe

strengthsandlimitationsofthesetechnologieshadneverbeendone,andisanaccomplishment

ofU-BIOPRED.Thisisalsoapplicableoutsidetherespiratoryfield.

• ‘Omics’analysisinmedicinerequiresstringentrecommendationregardingvalidation,as

recentlypublishedbyexpertsoutsideU-BIOPRED(McShaneetal.Nature2013).Whenthe

‘omics’databecameavailableinU-BIOPRED,astepwiseDataAnalysisPlan(DAP)hasfollowed

theserecommendations.Thishasledtotheusageofso-calledTraining-andValidationSetsof

dataasobtainedby:a)apriorisplithalfprocedures,andb)temporalvalidation(usingthe

longitudinalvisitforreplicationofdataasobtainedatbaseline.Thishasensuredthequality

outputbyU-BIOPRED.

• ‘Omics’U-BIOPREDfingerprintshavethusbeenobtainedandpresentedduringtheERScongress

inSeptember2015.Themainmessageofthesefingerprintanalysisisthattraditional

clinical/inflammatoryphenotypingofpatientswithsevereasthmathathasbeendonesofar,

doesnotsufficeincapturingtherelevantunderlyingbiologyofthevariousdiseasephenotypes.

Amainparadigminasthmaduringthepastyearshasbeenthateosinophilicinflammation

representsaparticularphenotypethatrequiresseparatetherapeuticstrategieswithexisting

andnoveldrugs.U-BIOPREDnowshowsbyproteomicanalysisthatthebiologybehind

eosinophilicinflammationinsevereasthmacanbeseparatedintodistinctnetworks.Unbiased

proteomicsshows4separatemolecularclustersunderlyingeosinophilia.ThisiswhatU-BIOPRED

washeadingfor:discoveryofpreviouslyunrecognizedmolecularphenotypesunderlyinggroups

thatareclinicallysimilar(Figure2.4.8.Morerecenttranscriptomicsanalysisinsputumconfirms

andvalidatesthisfindingbyshowingdifferentnetworksunderlyingeosinophiliainsevere

asthma.Thisisamajorresult,forthefirsttimeallowingaccesstodifferingfundamental

mechanismsassociatedwithinflammatoryprofiles.Thiskindofresultismeetingthe

expectationsforEFPIApartnerswhenactuallyjoiningU-BIOPREDyearsago.

• ThehandprintsrepresentthehighestleveloutputofU-BIOPRED.Handprintsarederivedfrom

multi-scaleanalysisusingvarious‘omicsplatformsandclinicaldatainordertoestablish

comprehensivephenotypesofsevereasthma.

o Thefirsttwohandprintshavebeendeliveredandpresented(ERS2015)asderivedfrom

thebaselinedatasets:thebloodhandprintandthesputumhandprint.Thishas

generatednovelsevereasthmaphenotypes,usingalltheinformationavailable,byan

entirelyunbiasedprocedure.

o Thesehandprintsareawaitingreplicationonthelongitudinaldatasetsandwillbe

publishedin2016.Thesehandprintshavebeenderivedbyfollowingcutting-edge

analyses,whichwillbeseparatelypublished,becauseU-BIOPREDisthefirsttodosoin

themedicalfield.

Severalhandprintshavealreadybeenproduced(onbloodandsputumrelatedsamples),

whichwillberefinedwhenadditionalbaselinedatasetswillbemadeavailable.

Moreover,thesehandprintshavebeenproducedinacompletelyunbiasedmanner;

morefocusedhandprintswillalsobeproducedwithafeaturereductionstep(basedon

correlationvaluesforexample).Longitudinaldata,pendingavailabilityoftheomics

platformresults,willbeusedtoassessstabilityovertimeoftheclustersofpatients

identifiedinthebaselinehandprints.Finally,handprintsbasedonfingerprintswillbe

producedonceallrequiredfingerprintsareavailable.

o Predictivemodelsbasedonfewinformativefeaturesforallhandprintshave/willbe

built,whichwillhelpdoctorsassessinwhichclustertheirpatientsbelongto,depending

onwhichtypeofdatatheyhaveavailablefortheirpatients.Thelistoffeaturesincluded

inthemodelscanthenbeusedinclinicalpracticeusingsimpler,focusedmeasurements.

• U-BIOPREDhasvalidatedvariouspre-clinicalmodels,incloseacademic-industrialcollaboration.

ThemainoutcomeisthatthestandardchronicHDMmodelinmiceisnotrepresentativeofsevereasthmadueitbeingextremelysensitivitytocorticosteroidsandisnotrobustlyexacerbatedwithRVchallenge.Influenzachallengeappearstorepresentabetterinvivomodelofexacerbation.Thesimilaritybetweenthegenesover-expressedinthismodelandthosereportedinsevereasthmasuggestthatrelatedmodelsthataremadesteroidinsensitivearebettermodelsofdisease.

o ThedevelopmentoftheCFA/HDMmodelisonesuchapproachasthisprovidesasteroidinsensitivemixedT-cellmodelofsevereasthma.Thelimitationofthismodelistheacutenatureofthemodelincomparisontothechronicnatureofhumanasthma.Thisisoff-setbytherelativelylonginflammatorywindowseeninthismodelwhichallowstherapeuticdosing.

o Itislikelythathumantissuecellmodelssuchasprecisioncutlungslices(PCLS)andprimarycellsin3DculturemayprovidethebestdiseasemodelastheyareabletobeexacerbatedbyRVandreflectmanyaspectsofsevereasthmaincludingabnormalinnateimmuneresponses.Furtheranalysisofthesemodels,includingbioinformaticscomparisonacrossmodelsandprimarysampleshasbeenscheduled,becausethisisthefinalsteptoestablishtherationaleforthefavoureduseofprimaryhumancellsfrompatientswithsevereasthma.

1.6. Potentialimpactandmaindisseminationactivitiesandexploitationofresults

• TheimpactofU-BIOPREDonsocio-economicbenefitsforEuropeancitizensliesinitsspin-off.

Severe asthma forms 3-8%of the asthmapopulation (Hekking andBelet al. J Allergy Clin

Immunol 2015), and actually represents those patients who are consuming most of the

health budget related to asthma. Because of providing new and separate categories of

severe asthma patients, the project will allow selective usage of newly developed and

targetedmedicines.Upuntilnowbiologicaltherapiescanhardlybeusedselectivelybecause

of the absence of validatedmarkers for selecting the right patient for the right drug. The

socio-economicbenefitofthefingerprintsandhandprintsofU-BIOPREDwillbethe

avoidanceofunnecessarytreatmentstopatientswhowillnotbenefitfromnoveltherapies.

• Thereby, the projectwill contribute to health in Europe. So far, severe asthma cannot be

adequately treated. These patients represent the largest part of the burden of asthma in

Europe. U-BIOPRED has now discovered new subgroups of patients that are driven by

differentdiseasemechanisms.Thiswillnotonlyallowselectingtherightdrug for theright

patientsbutwillalsofuelpharmaceuticalresearchintofindingnewtargetsfortreatmentin

patientswhodonotrespondtoavailable(biological)drugs.Thiswilldefinitelybenefithealth

ofEuropeancitizens.

o Theseoutputshaveconcreteimplicationsforcurrentscientificandindustrialdevelopments.First,scientifically,apartfrompublishingthedataforwidedissemination,theU-BIOPREDfingerprintshavealreadybeeninputintoatleasttwonovelH2020applicationsandvariousnationalgovernmentalandindustrialgrantsbyApril2016.Second,theindustrialexploitationhasalsobeentakenup.Already3EFPIApartnersfromU-BIOPREDarenowusingtheproject’sclinicaland‘omics’fingerprintsasentrycharacteristicforthepredictionoftreatmentefficacyinnewphase2and3clinicaltrialswithbiologicalinterventions.

o Eventhoughvariousfingerprintshavealreadyshowntobeveryeffectiveinthediscoveryofnovelphenotypesofsevereasthma(e.g.4typesofeosinophilicasthmabasedonproteomics:figure2.4.8),itisenvisagedthatparticularlytheintegrationoffingerprintsandclinicaldatawillgetustheclosesttorealPrecisionMedicine.Forinstance,thesputumhandprintsS1,S2andS3appeartorepresentgroupsofpatientsthataresignificantlydifferentinlungfunction(FEV1andFEV1/FVC),sputuminflammatoryprofile(percentageeosinophils,neutrophilsandmacrophages)andcirculatorybiomarkers(periostinandIL-13).Thisindicatesthathandprintsareapowerfultooltofindgroupsthatrepresentbiologicalaswellasclinicaldifferencesthataremeaningfulforinterventionstrategies.

o TheU-BIOPREDfingerprintsandhandprintscanberegardedasnovelresearchtoolsallowingindepthphenotypingforacademiaandindustry.Atpresentthisisbeingpushedtowardstheclinicbyselectinga‘simplified’setofbiomarkers.Thisincludes:a)rapid‘omics’atpoint-of-care(suchasbreathomics)andb)theselectionofthedefinitiveU-BIOPREDAnalyteSetmirroringthemajorfingerprintsandhandprints(endofQ22016).TheAnalyteSetisbasedontheoptimalcompositeofmoreeasilyaccessibleindividualbiomarkersinbloodandurineintheclinicalsetting.ThesetwodisseminationsofU-BIOPREDwillrepresentdirectexploitationoftheproject’sresults.

• TheU-BIOPREDprojecthasboosted industrial collaborationamongst12pharma industries

and their interaction with academic centres in Europe. The shared pre-competitive new

knowledgefromtheprojectwillspeeduptheprocessofdrugdevelopmentbecauseofnewly

discoveredbiologicalnetworksinthepatientsofinterestandbecauseoftheitsvalidationof

new, compositebiomarkers for thediseasephenotypes. The latter arebeingpresented to

EMA for furtherdevelopment. Therefore, this IMIprojectwithpublic-private collaboration

willcontributetoEuropeancompetitivenessingeneralandofpharmaindustryinparticular,

since the US has lagged behind in such structured pre-competitive, academic industrial

collaboration. The fact that U-BIOPRED has delivered shows that this format represents a

successfulEuropeansignature.

1.7. Lessonslearnedandfurtheropportunitiesforresearch

• Asindicatedabove,thepublicprivatepartnership(PPP)ofU-BIOPREDhasbeencriticaltoits

success.Thisisbasedonthefollowingmodesofinteraction:

o Collaborativewritingofthefullprojectapplicationanditskeyobjectives.

o Collaborativewritingoftheclinicalprotocols,integratingacademicexperiencewith

rigourfrompharma.

o JointlyestablishingStandardOperatingProcedures(SOPs)forU-BIOPREDandfuture

usage.

o Sharingandcollaborativelyoptimizingpre-clinicalmodels,notonlybetween

academicandpharma,butalsoamongstpharmacompanies.

o JointlydevelopingandoptimizingDataAnalysisPlans.

o Generatingsharedappreciationforinclusionofthepatientperspectiveinalllayers

oftheproject.

o TheagreedConsortiumAgreement,inwhichacademiaandpharmareached

consensusonusingbackgroundandsharingforeground.

o JointManagementBoardandScientificBoards,withsynergisminthemonitoringand

steeringoftheproject.

o Weeklyjointprogressconferences,withintensivemutualexchange.

• BasedontheU-BIOREDexperience,PublicPrivatePartnerships(PPP)mayevenbereinforced

by:

o Morestrongly settling thepartnershipbefore theproject starts.Under thecurrent

IMIstructure,privatepartnersafterhavingagreedtojointheconsortiumcanleave

astheywish,withoutcommitmentuptotheleveloftheoriginalagreement.Thishas

affected U-BIOPRED, causing a sudden deficit and serious delays and unnecessary

personmonthsinensuringdelivery.

o Avoiding the need for one to one agreements and contracts between individual

EFPIA companies and individual beneficiaries within the consortium. Ensuring the

scope of the project agreement and grant agreement affords a wider basis for

collaborationandavoidstheverylengthyprocesseswhereadditionalcontractshave

to be put in place. A centralized EFPIA budget for the project will be far more

efficientasopposedtomultipleindividualcompanybudgetsanddecentralizedlocal

companydecisionsonthose.

• TheopportunitiesfornewresearchafterU-BIOPREDareenormous.Inshort,thisincludes

thefollowing

o Afurtherlongitudinalassessmentwouldthrowmorelightonboththestabilityofthe

phenotypes identified and also on the movement of individual patients between

phenotypes.

o Theplanned comparisonof findings across other asthma cohorts (such a ProAR in

Brazil) offers the opportunity to both validate the phenotypes in different patient

populations,aswellastheopportunitytoidentifypossibledifferences,perhapsdue

todifferentenvironmentalandethnicfactors.

o Similarly,combinationandmutualvalidationof ‘omics’datasetsacrossallergicand

immunologicaldiseasesisverytimely.Infact,previouspartnersfromU-BIOPREDand

otherconsortiahaveappliedforaH2020grantregardingthisinApril2016(SIMBA

project).

o Testingnewbiologicalinterventionsinphenotypesofsevereasthmaasderivedfrom

U-BIOPRED. Some of these studies have already been started and will carry the

deliverablesoftheprojecttowardsconcretetargetingofdrugsforpatients.

o Even thoughU-BIOPREDhas already started doing so in one of its ENSOs (analyte

set),researchonclinicalapplicablediagnosticsthatadequatelycapturesthecomplex

U-BIOPRED phenotypes is mandatory. Simple blood and breath tests should be

furthervalidatedandoptimized inorder toallowclinical applicationofU-BIOPRED

findingsinfirstandsecondlinecare.

o ExpandingtheU-BIOPREDconcept intoabroaderspectrumofairwaysdisease. It is

nowacknowledged thatasthmaandCOPDcannotandshouldnotbedistinguished

when it comes to the potential efficacy of new drugs. The phenotypic markers

eventually determine eventually whether a new biological will be effective.

Therefore, asthma andCOPDare now collectively lookedwhen it comes to define

treatable traits. The U-BIOPRED approach is therefore highly needed in a broad

groupofpatientsalsoincludingCOPD.Thiswilldefinitelybenefitdrugdiscoveryand

tailoredtherapy.

o Similarly, the U-BIOPRED concept is equally applicable in complex morbidities in

respiratorymedicine,suchasinterstitiallungdisease,respiratoryinfectionandeven

beyondrespiratorymedicine.Thisneedstobetakenup.Alsoinorphandiseasesthat

mostly havenot been scrutinizedwith respect to the relationship between clinical

expressionandunderlyingbiologicalnetworks.

o Starting from the U-BIOPRED handprints, pre-clinical models can now be further optimized for rapid drug assessment.Not only for drug development but even for selecting drugs for individual patients e.g. by using organoids (a three-dimensional organ-bud grown in vitro) or other in vitro systems validated against U-BIOPRED handprints.

o WiththeknowledgefromU-BIOPREDearlyphenotypingofinfantsandchildrencan

be improved, in order to come to real secondary or even primary prevention

strategies.