Mutational Profile of Aggressive, Localised Prostate Cancer from African Caribbean Men Versus European Ancestry Men

(1)

HAL Id: hal-01921597

https://hal.inria.fr/hal-01921597

Submitted on 13 Nov 2018

HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are pub- lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Mutational Profile of Aggressive, Localised Prostate Cancer from African Caribbean Men Versus European

Ancestry Men

Laurie Tonon, Gaëlle Fromont, Sandrine Boyault, Emilie Thomas, Anthony Ferrari, Anne-Sophie Sertier, Janice Kielbassa, Vincent Le Texier, Aurélie

Kamoun, Nabila Elarouci, et al.

To cite this version:

Laurie Tonon, Gaëlle Fromont, Sandrine Boyault, Emilie Thomas, Anthony Ferrari, et al.. Muta- tional Profile of Aggressive, Localised Prostate Cancer from African Caribbean Men Versus European Ancestry Men. European Urology, Elsevier, 2019, 75 (1), pp.11-15. �10.1016/j.eururo.2018.08.026�.

�hal-01921597�

(2)

Platinum Priority – Brief Correspondence

EditorialbyXXXonpp.x–yofthisissue

Mutational Profile of Aggressive, Localised Prostate Cancer from African Caribbean Men Versus European Ancestry Men

Laurie Tonon

^a

, Gae¨lle Fromont

^b,d,k

, Sandrine Boyault

^j

, Emilie Thomas

^a

, Anthony Ferrari

^a

, Anne-Sophie Sertier

^a

, Janice Kielbassa

^a

, Vincent Le Texier

^a

, Aure´lie Kamoun

^l

, Nabila Elarouci

^l

, Jacques Irani

^d

, Luc Multigner

^e

, Ivo Glynne Gut

^f,g

, Marta Gut

^f,g

, Pascal Blanchet

^e,h

,

Aure´lien De Reynies

^l

, Ge´raldine Cancel-Tassin

^b,c

, Alain Viari

^a,m

, Olivier Cussenot

^b,c,i,

*

aSynergieLyonCancer,PlateformedeBioinformatique‘GillesThomas’,CentreLéonBérard,Lyon,France;^bCeRePP,Paris,France;^cSorbonneUniversité,GRC n°5,ONCOTYPE-URO,Paris,France;^dCHUdePoitiers,HôpitaldelaMiletrie,Poitiers,France;^eInsermU1085–IRSET,PointeàPitre,Guadeloupe;^fCNAG-CRG, CentreforGenomicRegulation,BarcelonaInstituteofScienceandTechnology,Barcelona,Spain;^gUniversitatPompeuFabra,Barcelona,Spain;^hCHUPointe- à-Pitre/Abymes,DepartmentofUrology,PointeàPitre,Guadeloupe;ⁱAssistancePubliqueHôpitauxdeParis,DepartmentofUrology,AcademicHospitalParis Est,Paris,France;^jCentreLéonBérard,DépartementdeRechercheTranslationnelleetdel’Innovation,GénomiquedesCancers,Lyon,France;^kCHRUdeTours, DepartmentofPathology, Tours, France;^lProgramme Cartesd’Identité desTumeurs (CIT),Ligue Nationale ContreLe Cancer,Paris,France; ^mINRIA, Montbonnot-SaintMartin,France

a v ai l a b l e a t w w w . s c i e n c e d i r e c t . c o m

j o u r n al h o m e p a g e : w w w . e u r o p e an u r o l o g y . c o m

Articleinfo

Articlehistory:

AcceptedAugust15,2018 AssociateEditor:

JamesCatto

Keywords:

Africanancestry Caribbean Mutation Prostatecancer

Abstract

Causesof highmortalityofprostate cancerin menof Africanancestrylivinginthe FrenchWestIndiesarestilldebated,betweensuspicionsofenvironmentalfactorsand geneticsusceptibility.Wereportanintegratedgenomicstudyof25tumourtissuesfrom radical prostatectomy of aggressive (deﬁned by International Society of Urological Pathology3)prostatecancerpatients(10AfricanCaribbeanand15FrenchCaucasian) using single nucleotide polymorphism arrays, whole-genome sequencing, and RNA sequencing.TheresultsshowthatAfricanCaribbeantumoursarecharacterisedbya morefrequentdeletionat1q41-43encompassingtheDNArepairgenePARP1,and a higherproportionofintrachromosomalrearrangementsincludingduplicationsassoci- atedwithCDK12truncatingmutations.Transcriptomeanalysesshowanoverexpression ofgenesrelatedtoandrogenreceptoractivityinAfricanCaribbeantumours,andofPVT1, alongnon-codingRNAlocatedat8q24thatconﬁrmsthestronginvolvementofthis regioninprostatetumoursfrommenofAfricanancestry.

Patientsummary:MortalityofprostatecancerishigherinAfricanCaribbeanmen thaninFrenchCaucasianmen.Speciﬁcitiesoftheformercouldbeexplainedbygenomic eventslinkedwithkeygenessuchasDNAdamagepathwaygenesPARP1,CDK12,andthe oncogeniclongnon-codingRNAgenePVT1atthe8q24prostatecancersusceptibility locus.

*Correspondingauthor.UrologyDepartment,TenonHospital,4ruedelaChine,75970ParisCedex 20,France.Tel.+33156016848;Fax:+33156017647.

E-mailaddress:[email protected](O.Cussenot).

https://doi.org/10.1016/j.eururo.2018.08.026

(3)

Prostate Cancer (PCa) is a majorcause of morbidity and mortality in men worldwide, causing an estimated 307 000deathsperyear.However,ethnicdisparitiesarewidely recognisedwithhigherincidenceandcancerdeathratesin blackmen thanin non-Hispanicwhitemen. Similarly, in Guadeloupe (FrenchWest Indies,FWI) where90%of the population is of African ancestry, the standardised incidence and mortality were approximately twice of that observedinmetropolitanFrance(mostlyCaucasianpopu- lation)[1].

Higher PCa incidence in men of African ancestry is largelyexplainedbygeneticfactorsastheydisplayahigher prevalenceofPCariskvariants[2].However,therelation- shipwiththehighestmortalityobservedinblackpopula- tionremainsdebated,withinvolvementofnotonlygenetic, environmental,andbiologicalfactorsbutalsosociocultural factors.Indeed,anincreasedriskofPCawasassociatedwith exposure to agricultural pesticides in epidemiological studies, including some performed in FWI [3,4]. Ethnic differencesinthefrequencyofsomegenomicalterations, suchasTMPRSS2genefusions,SPINK1overexpression,PTEN lossorSPOPmutation,havebeenreported[5],suggesting somevariabilityincarcinogenicpathwaysaccordingtothe geneticbackground.

Toprovidenewinsightsonthedifferencesobservedin molecularalterationsbetweenPCafrommenofAfricanand Caucasian ancestry, we report here the whole-genome sequencing (WGS) and RNA sequencing (RNAseq) of 25 aggressive PCa (10 from African Caribbean [AC] and 15 from French Caucasian [FC] patients) defined by International SocietyofUrologicalPathology3(Supple- mentaryTable1),aswellasapooledanalysisoftheircopy numbervariation(CNV)profileswithanadditionaldataset of 132 tumour tissues from radical both aggressive and nonaggressiveprostatectomyspecimens[6](Supplementa- rymethods).

Copynumberanalysisof157tumours(56AC+101FC) showedthatthemainsomaticCNVeventswereamplifica- tionsatlocus8q24.21(18%)encompassingconcomitantly PCAT1, MYC, andNCOA2genes,anddeletionsatloci8p21 encompassing NKX3.1 (39%), 13q14 encompassing RB1 (30%),6q14encompassingZNF292(24%),8p11encompass- ing FGFR1 (23%), and 16q23 encompassing BCAR1 (22%;

Fig.1A).Notably,homozygousdeletionof10q24(PTEN)was observedwithafrequencyof7%only.Significantcorrela- tionswerefoundbetweenthedeletionat8p21(NKX3.1)and thegainat8q24.21(PCAT1)(p=2.610 ⁴,Fisherexacttest, Benjamini-Hochbergcorrected),deletionsat10q24(PTEN) and17p13 (TP53) (p=9.510 ⁷, Fisherexacttest,Benja- mini-Hochbergcorrected),anddeletionsat5q21(NIP7P3) and 6q22 (CHD1) (p=5.3110 ⁴, Fisher exact test, Benjamini-Hochberg corrected; Supplementary Fig. 1).

Wealso observed therecurrentdeletions/lossesat SPOPL andPCDH9locirecentlyreportedinPCafromChinesemen (10%/13%forACand10%/21%forFC,respectively)[7].

Interestingly, a deletion at 1q42-43, encompassing PARP1,wassignificantlymorefrequentinACpatients(12/

56ACvs4/101FC;p=3.810 ⁴,Fisherexacttest;Fig.1B).

Using RNAseq on 25 tumours, we observed that this

haploinsufficiencywasrelatedtodecreasedexpressionof geneslocatedbetweenPARP1andTOMM20(Supplementary Fig.2).Thismoleculareventcouldbelinkedtothespecific exposure to organochlorine pesticides used for banana cultivationinFWI[3].Indeed,theSNPrs7679673,located near the gene TET2, was shownto be associated with a higherPCariskinmenwhowereexposedtohigherdoseof theorganochlorinealdrin[4].Moreover,TET2andPARP1are both implicated in early-stageepigenetic modification at pluripotency loci during somatic cell reprogramming [8]

andinandrogenregulationinPCa[9].Thislowerexpression ofPARP1suggeststhatthepatientsharbouringthisdeletion wouldnotbenefitfromtreatmentwithPARPinhibitorsand should rather be explored with therapies based on homologous recombination deficiency inhibitors such as mTorinhibitors.

Based on WGS data,we identified amean number of 4972somaticsingle-basemutations(range:1788–12576) and 603 somatic insertion/deletion (range 318–1491) mutations per samplewithout any significant difference betweenFCandACtumours(SupplementaryFigs.3and4).

WeobservedthatCDK12truncatingmutationsweremore frequent inAC thanin FCtumours(4/10vs1/15; Fig.2).

Regionsoflocalisedhypermutations,namelykataegis,were identifiedin10tumours(fourACandsixFC)for37events butwithoutanyrecurrentevent(SupplementaryFig.5).

TwogermlinemutationsoftheBRCA2gene(ACpatients) and one from PALB2 (FCpatient) were observed (Fig.2).

Notably,thetumourwithagermlineframeshiftmutation and a somatic homozygous deletion of BRCA2 had the highest chromosomal instability (large-scale statetransi- tions)scoreamongallsamples(SupplementaryFig.6).The higher frequencyofgermlineDNArepair genemutations foundinthiscohortofACpatients(20%vs6.7%inFC)could becompared tothe higher frequencyofthose mutations observedinmetastaticthaninlocalisedPCa,andsuggested that some of these patients could benefit from PARP inhibitorsorplatinum-basedchemotherapy.

UsingRNAseqdata,wefoundthatexpressionlevelofthe long non-coding RNA (lncRNA) PVT1, located at 8q24.21 near FOXA1 binding sites, was significantly higher in tumours from AC patients (p=110 ³, Mann-Whitney test;Fig.2).Concordantly,Yangetal.[10]reportedrecently that higher levels of this lncRNa were associated with pooreroverallsurvivalanddisease-freesurvival.Moreover, they showed that PVT1 knockdown by small interfering RNAtransfectionsignificantlyinhibitedPCagrowthinvivo andinvitroandpromotedcellapoptosis,suggestingthat PVT1 played an oncogenic role in PCa. PVT1 expression positivelycorrelatedwiththeandrogenactivity(Spearman

r

⁼^0.6, ^p⁼⁴10 ³) and EZH2 expression (Spearman

r

⁼^0.6,^p⁼⁴10 ³;SupplementaryFig.7).

OnlythreesamplesharbouredtheTMPRSS2-ERGfusion, whereas four others had a previously described fusion involving genes ETV1, ETV4, or SKIL, all fromFC patients (Fig.2).Thesefusionswerecorrelatedwithhighexpression ofthecorrespondinggenes(Fig.2).Wealsolookedforlarge chromosomal rearrangements in tumours and found 5093 intra- and424 interchromosomal events. The ratio

EUROPEAN UROLOGYXXX(201 8)XXX–XXX 2

(4)

Fig.1–Cumulativecopynumbervariationson157tumoursamplesforthetwoancestries.Alongthe(A)genomeand(B)chromosome1,isrepresentedthepercentageofsamplesinthecohortwithacopy numbervariationateachposition(theupperpartrepresentsthegainsandthelowerpartthelosses).EventsstatisticallymorepresentintheAfricanCaribbeansamplesarecolouredinorange,whereasthe onesmorefrequentintheCaucasiansamplesarecolouredinblue. AC=AfricanCaribbean;FC=FrenchCaucasian.

(5)

ofintra-tointerchromosomalrearrangementswassignifi- cantly higher in AC than in FC population (p=410 ², Mann-Whitney test; Supplementary Figs. 8 and 9). In addition,almosthalfoftheACsamples(40%)showedahigh proportionofduplicationsversusonlyone(6.7%)oftheFC

samples,andthisduplicatorphenotypewasassociatedwith CDK12truncatingmutations(Fig.2;SupplementaryFig.10).

Similarly,Wuetal.[11]foundrecentlythatCDK12biallelic lossisenrichedinmetastaticcastration-resistantPCaand thatthislossisassociatedwithfocaltandemduplications.

Fig.2–Summaryofbiologicalfeaturesandgenomicalterationsof25prostatetumours.Smallsomaticmutations(substitutions[SSMs]andsmall indels[SIMs])andcopynumbervariationsobservedinselectedgenes.Toprows:summaryofbiologicalfeatures:ancestry,racialmixingscore,Gleason score,relapse,andDNAmismatchrepairgermlinemutations.Bottomrows:summaryofothergenomicalterations:totalnumberofSSMsandSIMs, presenceofkataegisinthesample,ratioofintra-versusinter-chromosomalstructuralvariants,ETSgenefusiontranscripts,expressionvaluesofERG, ETV1,ETV4,SKIL,PARP1,EZH2,andPVT1representedbyquartiles,ARactivitysignaturescoreandproliferationsignaturescore,representedby quartiles.

AC=AfricanCaribbean;FC=FrenchCaucasian.

EUROPEAN UROLOGYXXX(201 8)XXX–XXX 4

(6)

Moreover, they showed that the CDK12 mutations are associatedwithanincreasedlevelofgenefusion-induced neoantigensandhighimmuneinfiltration,suggestingthat patientswiththesemutationscouldbenefitfromimmune checkpointimmunotherapy.

Thestructuralrearrangementsmorefrequentlyobservedin ACtumours,suchastandemduplicationsorPARP1haploin- sufficiency,aswellasthehigherfrequencyofgermlineDNA repairmutationssuggestthatfurtherinvestigationsdedicated tothispopulationwithspecifictherapeuticprotocolsusing checkpointinhibitorimmunotherapy,DNA-damagingthera- pies,orkinase-inhibitingagentsareneeded.

Authorcontributions:OlivierCussenothadfullaccesstoallthedatain thestudyandtakesresponsibilityfortheintegrityofthedataandthe accuracyofthedataanalysis.

Studyconceptanddesign:Cussenot.

Acquisitionofdata:Tonon,Fromont,Boyault,Kamoun,Irani,Multigner,I.

G.Gut,M.Gut,Blanchet,DeReynies,Cancel-Tassin,Viari.

Analysis and interpretation of data: Tonon, Thomas, Ferrari, Sertier, Kielbassa,Kamoun,Cancel-Tassin,Viari,Cussenot.

Draftingofthemanuscript:Tonon,Thomas,Kamoun,Irani,Multigner,I.G.

Gut,M.Gut,Blanchet,Cancel-Tassin,Viari,Cussenot.

Criticalrevisionofthemanuscriptforimportantintellectualcontent:None.

Statisticalanalysis:Tonon,Thomas,Ferrari,Sertier,Kielbassa,Kamoun, Viari.

Obtainingfunding:Cussenot,Viari.

Administrative,technical,ormaterialsupport:Elarouci,LeTexier.

Supervision:Cussenot,Cancel-Tassin,Viari.

Other:None.

Financial disclosures: Olivier Cussenot certifies that all conflicts of interest, including specific financial interests and relationships and affiliationsrelevanttothesubjectmatterormaterialsdiscussedinthe manuscript(eg,employment/affiliation,grantsorfunding,consultan- cies,honoraria,stockownershiporoptions,experttestimony,royalties, orpatentsfiled,received,orpending),arethefollowing:None.

Funding/Supportandroleofthesponsor:Thisworkhasbeenfunded, throughtheFrenchProstateICGCproject,byInstitutNationaldelaSanté etdelaRechercheMédicale(INSERM)andInstitutNationalduCancer (INCa);grantINSERMCV_2011/023(C18),withadditionalsupportfrom LYric(grantINCa-4662).Theresultspresentedinthisstudyarepartly based upon data generated by the national program CIT Cartes d’IdentitésdesTumeursfundedanddevelopedbytheLigueNationale ContreleCancer.

Acknowledgments: In memoriam ofGilles Thomas who wasat the initiativeandconceptionofthisstudy.Wethankthepatientsfortheir

participationinthisstudy,andCécileGafforyandValérieOndetfortheir technicalassistance.

AppendixA. Supplementarydata

Supplementarydataassociatedwiththisarticle canbe found, in the online version, at https://doi.org/10.1016/j.

eururo.2018.08.026.

References

[1]DeloumeauxJ,BhakkanB,EyraudR,etal.Prostatecancerclinical presentation,incidence,mortalityandsurvivalinGuadeloupeover the period2008–2013from apopulation-basedcancerregistry.

CancerCausesControl2017;28:1265–73.

[2]HaimanCA,ChenGK,BlotWJ,etal.Characterizinggeneticriskat knownprostate cancer susceptibilitylociin AfricanAmericans.

PLoSGenet2011;7:e1001387.

[3]EmevilleE,GiustiA,CoumoulX,ThoméJ-P,BlanchetP,MultignerL.

Associationsofplasmaconcentrationsofdichlorodiphenyldichlor- oethyleneandpolychlorinatedbiphenylswithprostatecancer:a case-controlstudyinGuadeloupe(FrenchWestIndies).Environ HealthPerspect2015;123:317–23.

[4]KoutrosS,BerndtSI,BarryKH,etal. Geneticsusceptibilityloci, pesticide exposure and prostate cancerrisk. PLoS One 2013;8:

e58195.

[5]KhaniF,MosqueraJM,ParkK,etal.Evidenceformoleculardiffer- encesinprostatecancerbetweenAfricanAmericanandCaucasian men.ClinCancerRes2014;20:4925–34.

[6]Kamoun A, Cancel-Tassin G, Fromont G, et al. Comprehensive molecular classiﬁcation of localized prostate adenocarcinoma revealsatumoursubtypepredictiveofanon-aggressivedisease.

AnnOncol2018;29:1814–21.

[7]Ren S,Wei GH,Liu D, etal. Whole-genomeandtranscriptome sequencing of prostate cancer identify newgenetic alterations driving disease progression [ﬁgure presented]. Eur Urol 2018;73:322–39.

[8]DoegeCA,InoueK,YamashitaT,etal.Early-stageepigeneticmodi- ﬁcationduring somatic cell reprogrammingby Parp1andTet2.

Nature2012;488:652–5.

[9]NickersonML,DasS,ImKM,etal.TET2bindstheandrogenreceptor and loss is associated with prostate cancer. Oncogene 2017;36:2172–83.

[10] YangJ,LiC,MuddA,etal.LncRNAPVT1predictsprognosisand regulatestumorgrowthinprostatecancer.BiosciBiotechnolBio- chem2017;81:2301–6.

[11] WuYM,CieslikM,LonigroRJ,etal.InactivationofCDK12delineates adistinct immunogenic classof advanced prostate cancer.Cell 2018;173,1770–82.e14.