PanNETs-胰腺神经内分泌肿瘤的全基因组图谱nature

Whole-genomelandscapeofpancreaticneuroendocrinetumoursNATURE,师煜井佳瑜,PanNETs,Pancreaticneuroendocrinetumours(PanNETs)：thesecondmostcommonepithelialneoplasmofthepancreasandhaveamortalityrateof60%.WHOclassification：lowgrade(G1),intermediategrade(G2),highgrade(G3)G3tumoursareinvariablylethal90%ofPanNETsaregradeG1orG2,PanNETs,PanNETs:sporadic,threehereditarysyndromes:multipleendocrineneoplasiatype1(MEN-1),vonHippel-Lindausyndrome(VHL),andoccasionallytuberoussclerosiscomplex(TSC)MEN-1:35%ofPanNETsmTORsignalling:14%ofpatients,Everolimus(advancedPanNET)apoptoticregulatorDAXXorthechromatinmodifierATRX:40%ofPanNETs,promotealternativelengtheningoftelomeres(ALT,端粒替代延长机制)andchromosomalinstability,PanNETs,102clinicallysporadicPanNETs：candidatemechanismsthatactivatemTORsignallingWehaveuncoveredanimportantroleforgermlineMUTYHvariantsInaddition,wehaveidentifiedalarger-than-anticipatedgermlinecontri-butiontoclinicallysporadicPanNETs,delineatingfuturechallengesintheclinicalassessmentofsusceptibility.,GenomiclandscapeofPanNETs,PatientswererecruitedandconsentforgenomicsequencingobtainedaspartoftheInternationalCancerGenomeConsortium().AllcaseswereclassifiedaccordingtoWHOcriteria98resectedPanNETs:36tumoursclassifiedasG1,57asG2,and5asG3.FouradditionalPanNETsandonecoloncancerfromapatientwithMUTYH-associatedpolyposis(MAP)weresequencedtovalidatemutationalsignatures.,GenomiclandscapeofPanNETs,MutationalmechanismsinPanNET,lowermutationburdenthanexocrinecounterpartFivesignatures(AE):A:MUTYHB:APOBEC(minimal)C:BRCA(breast,pancreaticductal,ovarianandoesophagealcarcinomas)D:Age(deamination)E:signature5(unknown)ValidationofMUTYHsignatureinfouradditionalPanNETsandonecolontumour.ThreePanNETsandthecolontumourcontainedadominantMUTYHsignatureandharbouredagermline-damagingMUTYHmutation,MutationalmechanismsinPanNET,MutationalmechanismsinPanNET,MutationalmechanismsinPanNET,MUTYH:Anovelmutationalsignature,composedofG:CT:Atransversions,predominatedinfivePanNETs(range0.24.2mutationsperMb),whichboreaknownpathogenicornovelinactivatinggermlinemutationinthebase-excision-repairgeneMUTYH,coupledwithlossofheterozygosity.ThismutationalsignatureorpatternofbiallelicMUTYHinactivationwasnotobservedin100pancreaticductaladenocarcinomas.,MutationalmechanismsinPanNET,MUTYH:3/62Italiancohort,themostcommonMAP-linkedvariantsinpopulationsofEuropeanorigin80familieswithMAPfromItalyandGermanyThesedatasuggestthat,inadditiontopredisposingtocolonic,gastricandavarietyofnon-gastrointestinalcancers,MUTYHdeficiencyplaysaroleinPanNET.,MutationalmechanismsinPanNET,MutationalmechanismsinPanNET,MutationalmechanismsinPanNET,Clustersofbreakpoints:ninetumours(9%),structuralvariationsandcopy-numberchangesconsistentwithchromothripsis.Fouroftheseninetumourshadrecurrentcatastrophicrearrangementsonchromosome11q,allinvolving11q13,andtwooftheserearrangementsledtolossofMEN1.TP53:noTP53mutationswerepresentinPanNETs.,Germlinemutations,ThediscoveryofgermlinedeleteriousmutationsinMUTYHandBRCA2promptedustoscreenthegermlinesofallpatientsformutationsinDNAdamagerepairgenesorgenesassociatedwithhereditarysyndromes.Germlinemutations:MEN1:sixpatients(fourframeshifts,onesplicesitemutation,andonecopy-numberloss).CDKN1B:onepatient.(CDKN1Bgermlinemutationscausemultipleendocrineneoplasiatype4andsomaticmutationsoccurinintestinalneuroendocrinetumours.)VHL:onepatient.(anegativeregulatorofhypoxiasignallingthatpromotesneuroendocrineproliferationandPanNETs.)Ineverycase,germlinealterationswerecoupledwithsomaticLOH.,Germlinemutations,CHEK2:DNA-damagerepairgenetumoursuppressorinbreastcancerandothercancertypesfourindividuals(4%):anonsensemutation,a15-basepairin-framedeletion,amissensemutationinexon2implicatedinprostatecancerpredisposition,amissensevariantinexon4.,Germlinemutations,ToinvestigatethefunctionalconsequencesofCHEK2mutations,wegeneratedapanelofFlagCHEK2constructsencodingthewild-type,P85L,D177H,E282Kand7782variants.,Somaticdrivermutations,Atotalof15,751somaticcodingmutations(7,703non-silent)weredetectedin2,787genes.Sixteensignificantlyandrecurrentlymutatedgenesweredefined.MEN1:themostfrequentlymutatedofthesegenes,37%oftumours.DAXX:22samplesATRX:11samplesPTEN(n=7)andDEPDC5(n=2),mTORpathwayDEPDC5havenotbeenpreviouslydescribedinPanNETs,wesurveyedanadditional62casesandidentifiedafurther2tumoursthatharbouredDEPDC5mutationsTP53:uncommon(n=3).SETD2:fivesamples(previousobservationsinrenalcellcarcinoma),Somaticdrivermutations,Copynumberchanges,Copynumberof98PanNETs:group1:recurrentpatternofwholechromosomalloss,affectingspecificchromosomes(1,2,3,6,8,10,11,15,16and22);enrichedinG2PanNETsgroup2:sampleswithalimitednumberofevents,manywithlossaffectingchromosome11;group3:polyploidtumours,withgainofallchromosomes;group4:aneuploidtumours,containingpredominantlywholechromosomegainsaffectingmultiplechromosomes).,Copynumberchanges,broadregionsofloss:MEN1(chromosome11q13.1)andCDKN2A(chromosome9q21.3)focallosses:EYA1(chromosome8q13.3;aknowntargetofMEN1),FMBT1(chromosome3p21.1;encodingakeycomponentofhistonemodificationmachineryimplicatedincancer)RABGAP1L(chromosome1q25.1;frequentlydeletedinneurofibromas).amplifiedregions:PSPN(chromosome19p13.3),PIK3CAsignalling,thyroidmedullarycancersULK1(chromosome12q24.33),mTORsignalling,autophagy,Chromosomalrearrangements,StructuralrearrangementsarelesscommoninPanNETs(mean,29eventspertumour)thaninpancreaticductaladenocarcinoma(119pertumour).InactivationoftumoursuppressorgenesthroughrearrangementoccurredinMTAP(n=4),ARID2(n=5),SMARCA4(n=3),MLL3(n=3),CDKN2A(n=1),andSETD2(n=1).Rearrangementscanalsocreateoncogenicdriversthroughin-framegenefusions.TheEWSR1genewasinvolvedinfusioneventsinthreePanNETs.,Chromosomalrearrangements,EWSR1EWSR1BEND2fusiongenes:2tumours,definingBEND2asanovelEWSR1fusionpartner(afusionpartnerofMN1).EWSR1FLI1genefusion:1tumourEWSR1FLI1fusionsoccurinsarcomas:adistinctive,high-grade,undifferentiatedroundcellmorphologyalongwithstrongmembraneexpressionoftheglycoproteinCD99.Inactivationoftumoursuppressorgenes(STAG2,TP53,andCDKN2A)andspecificchromosomalcopy-numberalterations(gainsofchromosome1and8q)EWSR1FLI1fusion:1tumour,strongimmunostainingforCD99andmutationsinMEN1,ATRXandTSC2.,Chromosomalrearrangements,TelomereintegrityandPanNETmolecularsubtypes,ATRXorDAXXIntotal,22of26ATRXorDAXXmutanttumoursdisplayedALT,andinDAXXmutationsweremorefrequent(19/22)thanATRXmutations(3/22),incontrasttoinvitrostudiesinwhichATRXalterationsaremoreprevalent.MEN1somaticmutations:increasedtelomerelength,suggestingthatMEN1hasaroleinchromosomemaintenance.ALTtumourshavebeenreportedtoundergorecurrentregionsofgenecopygainandlossinapanelofhumancancercelllinesinvitro;incontrast,whole-chromosomelossofspecificchromosomespredominatesinPanNETs.,TelomereintegrityandPanNETmolecularsubtypes,IntegratedanalysisofPanNETcancerpathways,3subtypes:insulinoma胰岛素型intermediate中间型metastasis-like(MLP)转移样型,IntegratedanalysisofPanNETcancerpathways,3subtypes:insulinoma胰岛素型intermediate中间型metastasis-like(MLP)转移样型,IntegratedanalysisofPanNETcancerpathways,Fourpathways：DNAdamagerepair:MUTYH,CHEK2,BRCA2,11%ofpatientsChromatinremodelling:MEN1,SETD2,ARID1AandMLL3，transcriptionaldysregulationTelomeremaintenance:MEN1bindstheTERTpromoterupregulationDAXXorATRX:onethirdofPanNETs,correlatedstronglywithtelomerelength,apoorprognosisintheG2subgroupTumourswithunalteredtelomerelengthhadabetteroutcome.d.mTORsignallingactivation:,IntegratedanalysisofPanNETcancerpathways,d.mTORsignallingactivation:InactivatingmutationsinnegativeregulatorsofmTORsignalling(PTEN,TSC2,andTSC1andDEPDC5reportedhere)werepresentin12%ofpatients,andwereassociatedwithapoorprognosisintheG2subgroupofpatients.Thesemutationsmayrepresentputativebiomarkersfortheselectionofpatients.Consistentwithpreviousreports,inactivatingmutationsformTORinhibitortherapy.threepotentialnovelmTORpathwayactivationmechanisms:inactivatingmutationsofthetumoursuppressorDEPDC5,whichencodesasubunitoftheGATOR1complex,asuppressorofmTORsignalling;aputative