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Joint ancestry and association test indicate two distinct pathogenic pathways involved in classical PDF

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RESEARCHARTICLE Joint ancestry and association test indicate two distinct pathogenic pathways involved in classical dengue fever and dengue shock syndrome MarisaOliveira1,2,3,4,WorachartLert-itthiporn5,BrunoCavadas1,2,3,Vero´nicaFernandes1,2, AmpaiwanChuansumrit6,OrlandoAnunciac¸ão2,IsabelleCasademont4,7,FannyKoeth4,7, MarinaPenova4,7,8,KanchanaTangnararatchakit6,ChieaChuenKhor9,10, a1111111111 RichardPaul4,7,11,PridaMalasit12,13,FumihikoMatsuda7,8,EtienneSimon-Lorière4,7,11, a1111111111 PrapatSuriyaphol5,LuisaPereira1,2,14‡*,AnavajSakuntabhai4,7,11‡* a1111111111 1 i3S—InstitutodeInvestigac¸ãoeInovac¸ãoemSau´de,UniversidadedoPorto,Porto,Portugal,2 Institutode a1111111111 PatologiaeImunologiaMoleculardaUniversidadedoPorto(IPATIMUP),Porto,Portugal,3 Institutode a1111111111 CiênciasBiome´dicasAbelSalazar(ICBAS),UniversidadedoPorto,Porto,Portugal,4 FunctionalGenetics ofInfectiousDiseasesUnit,InstitutPasteur,Paris,France,5 BioinformaticsandDataManagementfor Research,OfficeforResearchandDevelopment,FacultyofMedicineSirirajHospital,MahidolUniversity, Bangkok,Thailand,6 DepartmentofPediatrics,FacultyofMedicine,RamathibodiHospital,Mahidol University,Bangkok,Thailand,7 PasteurKyotoInternationalJointResearchUnitforIntegrativeVaccinomics, Kyoto,Japan,8 CenterforGenomicMedicine,KyotoUniversityGraduateSchoolofMedicine,Kyoto,Japan, OPENACCESS 9 GenomeInstituteofSingapore,A-STAR,Singapore,Singapore,10 DepartmentofBiochemistry,National Citation:OliveiraM,Lert-itthipornW,CavadasB, UniversityofSingapore,Singapore,Singapore,11 CNRS,Unite´deRechercheAssocie´e3012,Paris, FernandesV,ChuansumritA,Anunciac¸ãoO,etal. France,12 DengueHemorrhagicFeverResearchUnit,OfficeforResearchandDevelopment,Siriraj Hospital,FacultyofMedicine,MahidolUniversity,Bangkok,Thailand,13 MedicalBiotechnologyUnit, (2018)Jointancestryandassociationtestindicate NationalCenterforGeneticEngineeringandBiotechnology,NationalScienceandTechnologyDevelopment twodistinctpathogenicpathwaysinvolvedin Agency,Pathumthani,Thailand,14 DepartmentofPathology,FacultyofMedicine,UniversityofPorto,Porto, classicaldenguefeveranddengueshock Portugal syndrome.PLoSNeglTropDis12(2):e0006202. https://doi.org/10.1371/journal.pntd.0006202 ‡LPandASjointlydirectedthiswork. *[email protected](LP);[email protected](AS) Editor:BenjaminAlthouse,InstituteforDisease Modeling,UNITEDSTATES Received:August9,2017 Abstract Accepted:January2,2018 Ethnicdiversityhasbeenlongconsideredasoneofthefactorsexplainingwhythesevere Published:February15,2018 formsofdenguearemoreprevalentinSoutheastAsiathananywhereelse.Herewetake Copyright:©2018Oliveiraetal.Thisisanopen advantageoftheadmixedprofileofSoutheastAsianstoperformcoupledassociation- accessarticledistributedunderthetermsofthe CreativeCommonsAttributionLicense,which admixtureanalysesinThaicohorts.Fordengueshocksyndrome(DSS),thesignificanthap- permitsunrestricteduse,distribution,and lotypesarelocatedingenescodingforphospholipaseCmembers(PLCB4addedtoprevi- reproductioninanymedium,providedtheoriginal ouslyreportedPLCE1),relatedtoinflammationofbloodvessels.Fordenguefever(DF),we authorandsourcearecredited. foundevidenceofsignificantassociationwithCHST10,AHRR,PPP2R5EandGRIP1 DataAvailabilityStatement:Datahasbeen genes,whichparticipateinthexenobioticmetabolismsignalingpathway.Weconducted depositedattheEuropeanGenome-Phenome functionalanalysesforPPP2R5E,revealingbyimmunofluorescenceimagingthatthecoded ArchiveundertheaccessionEGAS00001002756. proteinco-localizeswithbothDENV1andDENV2NS5proteins.Interestingly,onlyDENV2- Funding:Theresearchleadingtotheseresultshas NS5migratedtothenucleus,andadeletionofthepredictedtop-linkingmotifinNS5abol- receivedfundingfromtheEuropeanCommission SeventhFrameworkProgramme[FP7/2007-2013] ishedthenucleartransfer.Theseobservationssupporttheexistenceofdifferencesbetween fortheDENFREEprojectunderGrantAgreement serotypesintheircellulardynamics,whichmaycontributetodifferentialinfectionoutcome no.282378.MOhasaPhDgrantfromFCT(The risk.ThecontributionoftheidentifiedgenestothegeneticriskrenderSoutheastandNorth- PortugueseFoundationforScienceand eastAsianpopulationsmoresusceptibletobothphenotypes,whileAfricanpopulationsare Technology—SFRH/BD/95626/2013).I3Sis PLOSNeglectedTropicalDiseases|https://doi.org/10.1371/journal.pntd.0006202 February15,2018 1/20 Independentpathogenesesandcandidategenesindenguefeveranddengueshocksyndrome financedbyFEDER—FundoEuropeude bestprotectedagainstDSSandintermediatelyprotectedagainstDF,andEuropeansthe DesenvolvimentoRegionalfundsthroughthe bestprotectedagainstDFbutthemostsusceptibleagainstDSS. COMPETE2020—Competitivenessand InternationalizationOperationalProgramme (POCI),Portugal2020,andbyPortuguesefunds throughFCT/Ministe´riodaCiência,Tecnologiae Inovac¸ãointheframeworkoftheproject"Institute Authorsummary forResearchandInnovationinHealthSciences" (POCI-01-0145-FEDER-007274).Thefundershad DenguefeverisendemicintropicalandsubtropicalareasofEastAsiaandAmerica,but noroleinstudydesign,datacollectionand globalizationandclimatechangesareintroducingvectorandvirustothenaïveregionsof analysis,decisiontopublish,orpreparationofthe EuropeandNorthAmerica.Inthisworkweconductedastatisticallyrobust,coupledasso- manuscript. ciation-admixturetestintwodenguecohortsfromThailand(classicaldenguefever,DF, Competinginterests:Theauthorshavedeclared anddengueshocksyndrome,DSS)andapublishedVietnamese(DSSonly)cohort.We thatnocompetinginterestsexist. identifiednewcandidategenesassociatedwithDFriskandconfirmedknowngenefamily associationwithDSSrisk.InDF,phosphatasecontroliscrucial,includingthroughbind- ingtoviralproteins,asweshowedforPPP2R5Eproteinco-localizationwithDENV1and DENV2-NS5proteinswithinlivercellsanddifferentialcellularlocalizationsalongtime. InDSS,cytokinedynamics,inflammationandactivationofvascularendotheliumcellsare dominantfeatures.Theparticulargeneticriskconferredbythesegenesindicatesthat SoutheastandNortheastAsiansarehighlysusceptibletobothphenotypes,whileAfricans arebestprotectedagainstDSS,andEuropeansbestprotectedagainstDFbutthemostsus- ceptibleagainstDSS. Introduction Denguevirus(DENV)isthemostcommonmosquito-borneviralinfection,infectingapproxi- mately390millionpeopleperyearworldwidewithonequarterdevelopingdenguedisease (MIM:614371)[1].Symptomsrangefromundifferentiatedfever,classicaldenguefever(DF) toshocksyndrome(DSS;hemorrhage,plasmaleakageandvitalorganimpairment)[2]. Recent-omicapproachesprovideunbiasedgenomicinsightsintomechanismsassociated withdenguedisease.Therehasbeenonlyonepublicationonclassicalgenomewideassociation study(GWAS)ofdengue[3]comparedtoaconsiderablenumberoftranscriptomicstudies [4–7].Thereasonforthisdiscrepancyisthatcohortsofthousandsofindividualsarerequired forGWAStoreachgenomewidesignificance.TheGWASworkconductedonacohortof Vietnamesechildren[3]included2,008DSSsamplesversus2,018controls,replicatedin1,737 versus2,934,andfoundSNPsingenesMICBandPLCE1associatedwithDSSphenotype. Lately,analyticalimprovementsbasedonadmixturemappinghavereducedthesamplesize requirementfromthousandstohundredsofindividualsorevenfewer[8].Mosthumanpopu- lationshavesomedegreeofancestryadmixture,whichbringstogetherhaplotypesthatoccur atdifferentfrequenciesinparentalpopulations.Admixturemappinganalysestheseblocks acrossthemosaicdescendantchromosomesandallowstocomparetheirdistributionbetween caseandcontrolcohorts.ThelowernumberofblockscomparedwithindividualSNPsreduces considerablythestatisticalburden.Wehavesuccessfullyconductedsuchanadmixturestudy indenguecohortsfromCuba[9],andidentifiedtwogenesinvolvedinlipidmetabolismwhich showedtobeprotectiveagainsttheriskofdenguehemorrhagicfever,aprotectionconferred bytheAfricaninheritedancestry.WhereasforRXRAgenetherewasalreadyfunctionalevi- denceofitsinvolvementininfection[10],wealsodemonstratedfunctionallybyshRNAthat theknockdownofOSBPL10genehadasignificantnegativeimpactinDENVreplicationrate [9]. PLOSNeglectedTropicalDiseases|https://doi.org/10.1371/journal.pntd.0006202 February15,2018 2/20 Independentpathogenesesandcandidategenesindenguefeveranddengueshocksyndrome Epidemiologicreportshaveshowntheexistenceofethnicdifferencesinsusceptibilityto denguefevernotonlyinCuba[11]butalsoinMalaysia[12]wheretheincidenceratebyethnic groupwas3.7:1:1.3forChinese,MalaysandIndians,respectively,intheyears1970’sand 1980’s,althoughnocross-evaluationwasperformedwithothersocio-demographicfactors.In thepresentstudy,wetakeadvantageoftheadmixedprofileofSoutheastAsians(inthenexus betweenSouth,NortheastandSoutheastAsia)toperformcoupledassociation-admixtureanal- yses(BMIX;[13])ofcase/controlcohortsofdenguepatients:Thaidenguepatientswhodevel- opedDF(n=252)orDSS(n=159),andacontrolblooddonorgroup(n=290);andthe publishedVietnamesedataset(2018controlsand2008DSSpatients;[3]).Althoughtheadmix- tureintheregionhasbeentakingplacealongtime,sincethefirstarrivalofmodernhuman aftertheout-of-Africamigration,aconsiderablemigrationfromsouthChinabeganinthe15th centuryandincreasedinthe19thand20thcenturies,mainlytowardsThailandwhereabout 40%ofthepopulationhassomeChineseadmixtureand14%areidentifiableThaiChinese [14].ThisisasimilarscenariototheadmixturethattookplaceintheAmericas,wherethese localadmixtureinferencetoolshavebeensuccessfullyapplied[9,15,16].Wewereableto identifydistinctcandidategenesconferringsusceptibility/resistancetotheriskofDFandDSS, arguinginfavorofindependentpathogenicmechanismsfortheestablishmentofthetwophe- notypes.WefurtherconfirmedthatoneDFcandidategenecodesforahumanproteinthatco- localizeswiththeDENV1andDENV2-NS5proteins,and,inthelattercase,transientlyrelo- catedfromthecytoplasmtothenucleus.Wealsoinferredtherelativeworldwidegeneticrisks contributedbythedetectedcandidategenesbasedontheirfrequenciesforthesusceptible/ resistanthaplotypes. Results AncestryofThaiandVietnamesecohorts Allanalyzedindividualshavesomedegreeofadmixture(Fig1;S1Fig).TheNortheast AsianbackgroundisdominantinVietnam(77.3%)anddecreasesinThailand(56.4%),incon- trasttotheSoutheastAsiancomponent,whichincreasesfrom20.7%inVietnamto35.1%in Thailand.TheSouthAsianinfluenceis8.5%inThailandand2.0%inVietnam.Withinthe denguecohorts,weobservedastatisticallysignificantincreaseintheSoutheastAsianback- groundinThailandforbothDF(4.1%increase;p-value=1.25x10−7)andDSS(4.8%increase; p-value=5.90x10−8)comparedtoThaicontrol. DSScohortsanalyses WebeganbycheckingiftheBMIXresultsonthepublishedVietnamesecohort[3]arein accordancewiththeresultsfromtheclassicalassociationmapping,atestoftherobustness ofthealgorithm.BMIXindicatesalsotheassociationofDSSwithMICBandPLCE1genes (Table1,Fig2A,S1andS4Tables).TheidentifiedregionsurroundingMICBencompasses sevensignificantSNPs,placedalong165,080bp,fromthedownstreamMICAtotheupstream LTBgene,aregionhighlyrichingenes.Threelinked(S2Fig)SNPsinMICBhavethemostsig- nificantp-values,formingtheprotectivehaplotypeGTT(OR=0.77;p-value<0.0001),which isthemostfrequenthaplotypeinworldwidepopulations(Fig3C).ThesusceptibleMICBhap- lotypeACC(OR=1.39;p-value<0.0001)ismorefrequentinEuropeansandSouthAsians (0.18to0.34).ThetwoSNPsfoundforPLCE1reachedsignificantp-valuesandarealmostin completelinkage(S5Fig).TheDSSprotectivePLCE1haplotype(CG;OR=0.75;p-value< 0.0001)ismorefrequent(Fig3B)inNortheastAsia(0.12–0.28)andSoutheastAsia(0.19),fol- lowedbyEurope(0.04–0.14)andabsentinAfrica. PLOSNeglectedTropicalDiseases|https://doi.org/10.1371/journal.pntd.0006202 February15,2018 3/20 Independentpathogenesesandcandidategenesindenguefeveranddengueshocksyndrome Fig1.GlobalancestryinferredthroughRFMixwhenusingthreeparentalancestries(South,Northeastand SoutheastAsian)fortheglobaldataset.Eachverticallinerepresentsanindividual,andthethreecoloursrepresent theproportionofthethreeparentalpopulationsineachgenome(lightorangeforSouthAsian,darkorangefor SoutheastAsianandblueforNortheastAsian). https://doi.org/10.1371/journal.pntd.0006202.g001 WefurtheranalyzedtheThaiDSSvs.controlcohort(Table1,Fig2B,S2andS5Tables), andobtainedareliablesignalofsixlinked(S3Fig)significantSNPsforPLCB4(phospholipase C,beta4;S4AFig),ageneinthesamefamilyasPLCE1,andparticipatinginmanycommon pathways,suchasdendriticcellmaturation,PI3KsignalinginBlymphocytesandPPARA/ RXRAactivation.TheDSSprotectivePLCB4haplotype(GAGAGG;OR=0.58;p-value= Table1. Oddsratios(ORs),95%confidenceintervalsandYatesp-values(correctedforcontinuity)oftheχ2testforthesignificanthaplotypes/SNPsinthepheno- typeandpopulationsforwhichassociationwasdetected. Protectivehaplotype Susceptiblehaplotype Gene Frequency Frequency OR(95CI) Pvalue Frequency Frequency OR(95CI) Pvalue Control Case Control Case VietnameseDSSstudy MICB rs2534666-rs2855807-rs3132468 G-T-T A-C-C 0.78 0.73 0.77(0.70–0.85) <1.0x10−4 0.13 0.18 1.39(1.23–1.57) <1.0x10−4 PLCE1 rs3740360-rs2274223 C-G A-A 0.27 0.22 0.75(0.68–0.84) <1.0x10−4 0.69 0.75 1.30(1.18–1.43) <1.0x10−4 ThaiDSSstudy PLCB4 rs16995800-rs2299676-rs7269910-rs1997696-rs6133707-rs6056595 G-A-G-A-G-G A-G-A-C-A-A 0.17 0.10 0.58(039–0.88) 1.3x10−2 0.61 0.70 1.48(1.10–1.98) 1.1x10−2 ThaiDFstudy CHST10 rs4850931-rs1030902-rs2241811-rs2241810-rs4149518-rs2241809-rs4149510-rs4851313-rs3828193 C-T-C-T-A-C-G-G-G T-G-T-C-G-T-A-A-T 0.26 0.17 0.59(0.44–0.79) 5.2x10−4 0.62 0.74 1.78(1.37–2.31) <1.0x10−4 AHRR rs6555205-rs2721020 T-C C-T 0.25 0.16 0.54(0.40–0.74) 1.2x10−4 0.67 0.79 1.89(1.43–2.48) <1.0x10−4 PPP2R5E rs3829766-rs6573513-rs743221-rs7144210 A-C-G-G GTAA 0.43 0.32 0.62(0.48–0.79) 2.0x10−4 0.39 0.50 1.59(1.25–2.03) 2.0x10−4 GRIP1 rs1480010 T C 0.17 0.11 0.56(0.39–0.80) 1.6x10−3 0.83 0.89 1.79(1.26–2.56) 1.6x10−3 https://doi.org/10.1371/journal.pntd.0006202.t001 PLOSNeglectedTropicalDiseases|https://doi.org/10.1371/journal.pntd.0006202 February15,2018 4/20 Independentpathogenesesandcandidategenesindenguefeveranddengueshocksyndrome Fig2. ManhattanplotsofBMIXanalysisinVietnameseDSSvsControl(A),ThaiDSSvsControl(B)andThaiDFvsControl(C)forNortheastandSoutheast Asianancestries.Theredlinerepresentsthesignificancethreshold.TheproteincodinggeneswithsignificantlyassociatedSNPsareidentified. https://doi.org/10.1371/journal.pntd.0006202.g002 0.013)israreinmostworldwidepopulations(Fig3A),reachingthehighestfrequenciesin Africa(0.21–0.28).OnlyonePLCE1SNP(rs2274223)waspresentinthechipusedintheThai denguecohortanditdidnotreachsignificance. Individually,theconventionalassociationstudywithPCAcorrectionforpopulationstrati- ficationinThaiDSSvs.controlcouldnotidentifyanycandidategenewhencorrectingfor multipletest(S6AFig–thetwosingledoutsignificantSNPsarespurioussignalsaslinkedSNPs donotdisplaysignificantp-values).Wealsotested10runsofpseudodatasets,permutating caseandcontrollabels(S1Text).NoSNPissignificantintheassociationtests,andtheBMIX PLOSNeglectedTropicalDiseases|https://doi.org/10.1371/journal.pntd.0006202 February15,2018 5/20 Independentpathogenesesandcandidategenesindenguefeveranddengueshocksyndrome Fig3.Worldwide(fromthe1000Genomesdatabase)andThaidenguecohorts(control,DFandDSS)frequencies forsignificantlyassociatedhaplotypesinthevariousgenes.A-PLCB4;B-PLCE1;C-MICB;D-CHST10;E-AHRR; F-GRIP1;G-PPP2R5E.Theprotectiveandcausativehaplotypesarehighlighted. https://doi.org/10.1371/journal.pntd.0006202.g003 algorithmidentifiedspurioussignificantSNPs(mostlyisolatedindifferentchromosomes)that donotreplicatebetweenrunsandthataredifferentfromthecase-controlcomparison.Overall posteriorp-valueswerealsolowerinthepseudodatasets.Thehigherspuriousdetectionsin BMIXthanintheassociationtestagreewiththefactthatthestatisticalburdenofthelocal ancestrytestisconsiderablylowerthantheonefortheassociationtest,whichraisesthepossi- bilityofdetectingapositivesignal.Therandomnessbetweenrunsreflectsthehighvariability betweenindividualsinadmixturepercentagesandindistributionofancestryblocksalongthe genomes.Thisarguesforadouble-carefulinterpretationofBMIXresultsinthecontextofthe disease.FortheThaiDSSvs.control,thefactthatthePLCB4genebelongstothesamefamily ofthepreviouslyindependentlyidentifiedPLCE1geneisanimportantadditionalevidencefor consideringthatgeneastrongcandidateinDSSphenotype. CalculatingthegeneticriskofDSSaccordingtotheworldwidepopulationfrequencyofthe phospholipaseCandMICBprotectiveandsusceptiblehaplotypes(Fig4A),itcanbeobserved thatAfricananddescendentCaribbeanpopulationsarebestprotected,whileEuropean,Asian andLatinAmericanpopulationsaremoresusceptibletoDSS. PLOSNeglectedTropicalDiseases|https://doi.org/10.1371/journal.pntd.0006202 February15,2018 6/20 Independentpathogenesesandcandidategenesindenguefeveranddengueshocksyndrome Fig4. Geneticriskforthevariousworldwideregionsbyconsideringanadditivemodelofprotectiveandcausativehaplotypes/SNPsforDSS(A)andDF(B). Median(middleline),mean(littlesquare),95%confidenceinterval(whiskers)andextremevalues(crosses)areindicated. https://doi.org/10.1371/journal.pntd.0006202.g004 WegenotypedtwooftheBMIX-identifiedsignificantlyassociatedPLCB4SNPsinfurther Thaicontrol(n=244)andcase(n=20)samples(S7Table),andthers1997696SNPpresentsa p-valueoverthesignificancethresholdofatraditionalGWAS(p=4.7x10-8). Denguefevercohortanalysis WhencomparingThaiDFvs.control,adistinctivegeneticsignaturewasobtained.Threegenes locatedondifferentchromosomeshadatleasttwoSNPsabovetheBMIXsignificantposterior probabilitythresholdof0.5(Fig2C),forminghaplotypes(S7,S8andS9Figs).CHST10codes forcarbohydratesulfotransferase10(S4CFig),hasninesignificantSNPs(Table1,S3andS6 Tables),formingtheprotectivehaplotypeCTCTACGGG(OR=0.59;p-value=0.0005), whereasthehaplotypeTGTCGTAATincreasedriskofDF(OR=1.78;p-value<0.0001).The protectivehaplotypeisfrequentinSouthAsianpopulations(0.38–0.57),whereasthesusceptible haplotypeisfrequentinNortheastAsia(0.61–0.74)andveryrareintheAfricanpopulations (Fig3D).AHRR(S4DFig)codesforaryl-hydrocarbonreceptor(AHR)repressor,hastwosignif- icantSNPs,andsimilarlytoCHST10,theprotectiveAHRRhaplotype(TC—OR=0.54;p- value=0.0001)ismorefrequentinSouthAsianandAfricanpopulations(between0.40–0.60) andtheoppositehaplotype(CT—OR=1.89;p-value<0.0001)ismorefrequentinNortheast Asianpopulations(0.57–0.78)(Fig3E).PPP2R5E(S4FFig)codesforproteinphosphatase2 (PP2A),regulatorysubunitB’,epsilonisoform(alsoknownasPP2A-B56),hasfoursignificant SNPs,whoseprotectivehaplotype(ACGG—OR=0.62;p-value=0.0002)showedhighfre- quencyinSouthAsianpopulations(0.76–0.86),whileAfricanpopulationshavethelowestfre- quencyofthishaplotype(0.09–0.20)(Fig3G).Interestingly,theproteinscodedbythesethree genes,andbyanothergene,GRIP1(S4EFig)thatcodesforglutamatereceptorinteractingpro- tein1,withonesignificantSNP(T;OR=0.56;p-value=0.0016),areinvolvedinthexenobiotic metabolismsignalingpathway(Fig5D).TheGRIP1protectivealleleismorefrequentinSouth Asianpopulations(0.19–0.32)andabsentinAfrica(Fig3F). Again,individually,theconventionalassociationstudywithPCAcorrectionforpopulation stratificationcouldnotidentifyanycandidategenewhencorrectingformultipletest(S6B Fig). PLOSNeglectedTropicalDiseases|https://doi.org/10.1371/journal.pntd.0006202 February15,2018 7/20 Independentpathogenesesandcandidategenesindenguefeveranddengueshocksyndrome Fig5. SignificantlyalteredgeneexpressionforPPP2R5E(A),GRIP1(B)andAHR(C)inThaidenguecohortalongthecourseofdiseasefroma transcriptomedatasetforwholeblood[17].Significantp-valuesareindicated.D)Schemeofthexenobioticmetabolismsignallingpathway(basedonIngenuity databaseinformation),highlightingthethreenucleartranscriptionfactors:theconstitutiveactivereceptor(CAR);thepregnaneXreceptor(PXR);andthearyl hydrocarbonreceptor(AHR). https://doi.org/10.1371/journal.pntd.0006202.g005 ThecontributiontothegeneticrisktoDF,inferredfromanadditivemodelcombiningthe protectiveandsusceptiblehaplotypesofthefourxenobiotic-relatedgenes(Fig4B),indicates highestprotectioninEuropeanandSouthAsianpopulationsandhighestriskinNortheast andSoutheastAsians.AfricanandLatinAmerican/Caribbeanpopulationshaveanintermedi- ateriskconferredbythesegenestoDF. ThegenotypingofsixSNPsinthesefourgenesinadditionalThaicontrols(n=245)and cases(n=55)improvesp-valuesofatraditionalassociationtestinthetotalcohorttolevelsof 10−5infourSNPsand10−4intwoSNPs(S7Table).ThesevaluesaresignificantafterBonfer- ronicorrectionfortheset-testofsixSNPs. PLOSNeglectedTropicalDiseases|https://doi.org/10.1371/journal.pntd.0006202 February15,2018 8/20 Independentpathogenesesandcandidategenesindenguefeveranddengueshocksyndrome Weanalyzedtheexpressionofthesegenesinthexenobioticpathwayinatranscriptome datasetincludingpatientssampledduringacutephaseofDF,DHFandconvalescencecom- paredwithcontrols[17].CHST10andAHRRexpressionsdidnotsignificantlychangeduring dengueinfection(S10Fig),however,therewasasignificantincreaseinPPP2R5Eexpression andasignificantdecreaseinAHR(negativelyregulatedbyAHRR)andGRIP1expressionsdur- ingacutedengueinfection(Fig5A,5Band5C).Thesefindingsarefurtherevidencethat PPP2R5E,GRIP1andAHRcanbeinvolvedindengueinfectionanddevelopmentofdengue disease.WefurthercheckedintheGTExdatabaseiftheDFcandidateSNPsactaseQTLs. AllcandidateprotectiveallelesinPPP2R5EandAHRRgenessignificantlyreducetheexpres- sionoftherespectiveproteins(S11Fig).ThecandidateSNPinGRIP1geneisnotaneQTL intheGTExcohort,andthetwoeQTLs(rs11176317andrs12322014)closetothecandidate rs1480010arenotinLDwithit.AstheGTExcohortismainlyofEuropeanancestry,wecan- notascertainifthisGRIP1SNPorotherlinkedSNPscanbeeQTLsinAsianpopulations. Immunofluorescenceco-localizationimagingofPPP2R5EandNS5protein fromDENV1and2 TherecentidentificationofconservedmotifsthatprovidebindingspecificitytothePP2A-B56 phosphatase[18]ledustofurthertestthehypothesisofthepotentialbindingofthisregulatory regionofPP2AproteintoDENVproteins.Webeganbyperforminganinsilicosearch[19]for thehigh-affinityLxxIxEmotifaswellastheintermediate-andlow-affinitymotifsinthepro- teinreferencesequencesofthefourDENVserotypes(S8TableandFig6A).NS5presents betweenthreeandsixmotifsinallfourDENVserotypes,andatleasttwoofthesemotifs (LxxIxEandLxxVxE)arehighlyconserved.Otherviralproteinsalsobearmotifs,butaremore heterogeneousbetweenDENVserotypes. WethentestedthehypothesisthatPP2A-B56caninteractwithNS5byconductingconfocal immunofluorescenceco-localizationtests.WetransfectedHuh7cellswithamammalian expressionplasmidcontainingDENV2-NS5taggedwithanorangefluorescenceprotein.We fixedandstainedwithantibodyagainstPPP2R5Eat24h,48hand72haftertransfection.In non-transfectedcells,PPP2R5Eislocalizedinthecytoplasm(Fig6B).At24hofpost-transfec- tion,bothPPP2R5EandNS5arelocalizedinthecytoplasm,butby48htheybothco-localize inthenucleus,andat72hPPP2R5EreturnstothecytoplasmwhileNS5remainsinthenucleus (Fig6C).WethendeletedthexLxxIxEmotifinourDENV2-NS5vector(Fig6D)andtrans- fectedcellsinthesameway.Thedeletionofthismotifpreventedthetranslocationoftheviral NS5proteintothenucleus(Fig6D). Testifyingtotheexistenceofdifferencesbetweenserotypes,theimmunofluorescenceco- localizationtestbetweenPPP2R5EandDENV1-NS5(Fig6E)showedthatthetwoproteins co-localizeinthecytoplasm,buttheentranceinthenucleusisalmostnegligible,andlittle accumulationofNS5canbedetectedinthenucleusat72h. Discussion Oursuccessfulassociation-admixtureanalysesinThaipopulationhaveprovidedevidencethat differentgenes/pathwayscontributetothegeneticsusceptibilityorresistancetodifferentout- comeofdengueinfection.Wesuggestthatxenobioticsandlipidmetabolism,aswellasinterac- tionofviralproteinstothesemoleculesandtoitsphosphatases,arecriticalinthedevelopment ofclassicalDF,whereasmoresevereformsofdenguearecausedbyoverreactiveimmunity leadingtocytokinestormand/ordefectinendothelialcelldysfunctionandcoagulation system. PLOSNeglectedTropicalDiseases|https://doi.org/10.1371/journal.pntd.0006202 February15,2018 9/20 Independentpathogenesesandcandidategenesindenguefeveranddengueshocksyndrome Fig6.ConfocalimagingofPPP2R5EandNS5fromDENV1andDENV2.A.ThemainlinkmotifsinNS5proteinsfromDENV1andDENV2.B.Subcellular localizationofPPP2R5EinHuh7controlcells.C.SubcellularlocalizationofPPP2R5EinHuh7controlandafter24h,48hand72hoftransfectionwithDENV2-NS5 protein.D.SubcellularlocalizationofmutatedPPP2R5EinHuh7controlandafter24h,48hand72hoftransfectionwithDENV2-NS5protein.E.Subcellular localizationofPPP2R5EinHuh7controlandafter24h,48hand72hoftransfectionwithDENV1-NS5protein.GreenimmunofluorescenceindicatesPPP2R5E,red indicatesNS5,blueflagsnucleus.Yellowsignalsindicateco-localizationofNS5andPPP2R5E,andwasobtainedbyoverlappingthetwopanels.Original magnification,×630. https://doi.org/10.1371/journal.pntd.0006202.g006 WereinforcedtheassociationofphospholipaseCgenefamilywiththeDSSphenotypein Thaipatients,ashadbeenfoundinVietnameseDSSpatients[3],butthistimethegene detectedwasPLCB4insteadofPLCE1.Theseenzymeshavebeenimplicatedinahighnumber ofsignaltransductionpathways[19]andonimmuneregulation[20].Morerecently,Linetal. PLOSNeglectedTropicalDiseases|https://doi.org/10.1371/journal.pntd.0006202 February15,2018 10/20

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Introduction. Dengue virus (DENV) is the most common mosquito-borne viral infection, infecting approxi- mately 390 million people per year worldwide PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd.0006202 February 15, 2018. 2 / 20 financed by FEDER—Fundo Europeu de.
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