Preclinical modeling of drug resistantacute lymphoblastic leukemia
Jean-PierreBourquin,MD-PhDDivisionof Oncology
Children‘s HospitalZürich
CRPPHumanHemato-Lymphatic Diseases
Refractory
Firstdiagnosis
DrugdevelopmentExp.TherapyInnovativeconceptse.g‚basket‘trials
Acute lymphoblastic leukemia - clinical context
Relapse
PredictivemarkersMolecularclassificationFunctionalunderstandingFunctionalclassification
15%
55%
100%
Needs
MechanismsAdaptivetreatments
Research
IntegrationofMulti-OmicsFunctionalProfiling
ModelempiryModeldefinedmoleculartypes
GeneticlandscapeofALL
Hematopoieticstemcell
Bprogenitor MatureBcell
Initiatinglesions(translocations)transcriptionfactorsKinases
Developmentalarrest(deletions)
IKZF1,PAX5,TCF3,EBF1
Cooperatinglesions(SNV,indels,others)CellcycleSignalingEpigeneticmechanisms
Leukemia
AnthonyMoorman,UKALL
MAINTENANCEINTENSIFICATIONINDUCTION
0
FirstlineALLchemo
Functionalapplicationofgenomicsstilllimitedintheclinic
Entitiesforexperimentaltreatment
day33 78 154
Very highriskMRD highatday 78MRDpos d33and IKZF1-plushypodiploidyMLL/AF4,TCF3/HLF
Genomics MinimalResidualDisease(MRD)
Patient-derived models
MSCLive ALL
DeadALL
In vivo testing
Small molecule library
Automated microscopy
MSC Primary ALL
Time(h): 0 24 48 120
- Customized drug libraries- Precise dose response curves- Combinatorials
Drugs Image analysis
ALL sample direct on MSC
Drug
resp
onse
pro
filin
gH
igh
risk
ALL
- Drug testing- Functional genetics- Microenvironment
Relevant cohorts
- First line trial- Relapse trial- Phase I setting - Refractory disease
Patient derived xenograft (PDX)
biobank
NSG mice
Frismantas etalBlood2017,inpress
Number of events (patient samples)
Num
ber o
f eve
nts
(PD
X sa
mpl
es)
BCP-ALL T-ALL
% match0255075100
0.02.55.07.510.00.02.55.07.5 10.0
2.5
5.0
7.5
10.0
Leukemia PDXare genetically stabletargeted sequencing 52genes,SNVsand indels
Frismantas etalBlood2017PamDobay,bioinformatics,IntReALL panel,C.Eckert,AMoorman,J.IrvingFP7
Drugresponse profiling identifies phenotypes
T-ALLsensitiveto Dasatinib
BCP-ALL
T-ALL
Frismantas etalBlood2017
IC50
log[
nM]
0
1
2
3
4***
BCR-ABL1
NUP214-ABL1TCF3-PBX1
BCP-ALL T-ALLinvitro
Ahighly dasatinib sensitiveT-ALLsubset
SR VHR Relapse SR VHR RelapseFrismantas etalBlood2017,inpress
dasatinib inT-ALL:validationIC
50 lo
g[nM
]
0
1
2
3
Dasatinib
40%
Day 0 Day 90
RefractoryT-ALLadultpatientDasatinib +Asparaginase
IndependentcohortJeffreyTyner,OSHU
Frismantas etalBlood2017,inpress
0 1 2 30
20
40
60
80
100
120
Control
0 1 2 30
20
40
60
80
100
120
Control
BCPALL
T-ALL
Concentrationlog[nM]
%Livingcells
Pre-T-ALL
TCF3-HLF
0 1 2 30
20
40
60
80
100
120
Control 0 1 2 30
20
40
60
80
100
120
Control
Cortical-T-ALL Mature-T-ALL
0 1 2 30
20
40
60
80
100
120
Control
MLL-AF4
AsubsetofALLrespondstoBCL2inhibitionwithvenetoclax
ABBVIEPediatric PhaseIstudy,Protocol+PIPin2017single agent and combination
Celldeathsignal
BH3-only
Apoptosis
BCL-2
BCL-XL
ABT-199venetoclax
bHLHTransactivationdomainTCF3Chr19
DNAbindingdomain
breakpoint
TCF3-HLFt(17;19)HLFbZIP
notcurable
PBX1HD
TCF3-PBX1t(1;19) favorable
GeneticlandscapestableinPDX
TCF3-HLF:aparadigmofresistantdisease
U.FischerA.Rinaldi etal,NatureGenetics 2015
Cooperativelesions(SNV)RASpathway
Hematopoieticstemcell
MatureBcell
TCF3-HLFDELPAX5,BTG1,VPREB1
Leukemia
Bprogenitor
−1 0 1 2 3 4
CYTARABINEGEMCITABINE
MERCAPTOPURINEMETHOTREXATE
THIOGUANINEDEXAMETHASONE
VINCRISTINEAT9283
BARASERTIBBI−2536
BX795TEMSIROLIMUS
TORIN−1DASATINIB
LESTAURTINIBXL228
DOXORUBICINETOPOSIDEIDARUBICIN
MITOXANTRONETOPOTECAN
BORTEZOMIBABT−199
Drugs
log IC50
E2A−HLF_T(17;19)
E2A−PBX1_ T(1;19)
Others
ZH89
ZH96
Risk
HR
MR
Others
SRZH89
ZH96
ZH96TCF3-HLF
TCF3-HLF
TCF3-PBX1
primary refractory ALL
Celldeathsignal
BH3-only
Apoptosis
BCL-2
BCL-XL
ABT-199venetoclax
A.Rinaldi,Fischeretal,NatureGenetics 2015
TCF3-HLF ALLTreatment
VEN+Dexa +VincristineFollow up leukemia
ControlVenetoclax
Treatment blocks
DEX+VCR
DEX+VCR+Venetoclax
0 20 40 60 80 100 1200
20
40
60
80
100
230
0 20 40 60 80 100 1200
20
40
60
80
100
2300 20 40 60 80 100 1200
20
40
60
80
100
230
0 20 40 60 80 100 1200
20
40
60
80
100
230hCD4
5+hC
D19+
inPB[%
]
Timeposttransplantation[days]
Survival[%
]
V.Frismantas and A.Rinaldi,Fischeretal,NatureGenetics 2015,Blood2017
3Drugminiinduction+VENcontrolsTCF3-HLFALL
SR03SR06
SR04
MNR-B03
VHR1016
959SR13
VHR03
MNR-B01
MNR-B10SR19
VHR27
MNR-B14
VHR02HR05
SR22B17SR02
SR01SR10
HR1215
00
VHR07HR03
VHR25SR08
SR12 5a
MNR-B09SR11
HR11SR14
MNR-B04 2a 7a
VHR28SR0911
c13
a
VHR06
VHR12 6a
VHR04
VHR0117
505
VHR23
MNR-B17SR17
SR21
VHR150
500
1000
1500
2000
SM IC
50 (n
M)
~20%IC50<100nM
SelectiveactivityoftheSMACmimeticbirinapant
VHR10
0 20 40 60 80 1000
20
40
60
80 ControlTreated
Day
% h
CD45
/hCD
19+
Denovo resistant (highMRDload)
B-cell precursor ALL
SMACmimeticripoptosomeapoptosis
necroptosomenecroptosis
RIP1
McCombS,Aguadé-GorgorióJ,etal.Science Translational Medicine,2016
Functional genomics:lentiviral CRISPRto target RIP1
McCombS,Aguadé-GorgorióJ,etal.Science Translational Medicine,2016
Selection with SMbirinapant
McCombS,Aguadé-GorgorióJ,etal.Science Translational Medicine,2016
SM:simultaneousapoptosisandnecroptosis
Foldchangeknockout
Biri
napa
ntLC
L161
Velc
ade
Vinc
ristin
eD
oxor
ubic
inA
BT1
99O
bato
clax
Topo
isom
eras
eEt
opos
ide
JQ1
Dex
amet
haso
neC
ytar
abin
e6-
thio
guan
ine
6-m
erca
ptop
urin
e
1
10
100
1000
10000 VHR10 ConVHR10 LC-Rip1MNRB03 ConMNRB03 LC-Rip1
IC50
(nM
)
Detection Limit
RIP1dependentdeathisnotexploitedbycurrentchemotherapeuticagents
Pat1controlPat1RIP1KOPat2controlPat2RIP1KO
McCombS,Aguadé-GorgorióJ,etal.Science Translational Medicine,2016
Preclinical modeling with PDX:
• Modelingand definition of clinically relevantcohorts
• Mechanistic studies inthe realcellular context
• Exvivoscreening,drug activity profiling,functional omics
• Proofof concept for new combination invivo
• Correlation with clinical activity of new agents
Leukemia Research GroupSeniorScientist: BeatBornhauser (CH)Biofinformatics: MariaPamelaDobay (CH)Postdocs LenaHarder(DE)
YunHuang(China)JuliaAguadé(SP)
PhD-Students:Danaelle Capron(F)Viktoras Frismantas (Lituania)VirginiaRodriguezMartinez(SP)BriceMouttet (CH)MD-PhDProgramCatarinaMezzatesta (IT)
MasterBiologie/MD: Seok YunLee(CH)GamzeAlteplin(TK)
: FabianRietmann (CH)Technician: Blerim Marovca (CH)
SilviaJenni(CH)Biobank/Labmanagement IrinaBanzola (IT)Alumni: LauraBonapace,AnnaRinaldi,PaulinaMirkowska,JeannetteBoutter,Maike Schmitz,ScottMcComb,OrrinPailKinderspitalJoelleTchinda,BeatSchaefer,FelixNiggli,NicoleBodmer
InternationalBFM-SGMartinStanulla,MartinSchrappeArnt Borkhardt,UteFischerArendvonStackelberg,ConnyEckert,AngelikaEggertVaskar Saha,AnthonyMoormannAndishe Atterbachi,RenatePanzerShaiIzraeli,RenatePfanzerBeppe Basso,Truus TeKronnieAndreaBiondi,GianniCazzanigaHeleneCavé,JeanSoulier,AndreBaruchel,UZH:MarkusManzSwissInstituteof bioinformaticsMariaPamelaDobayEPFLausanneFreddyRadtke,RajLehal,BartDeplanckeETHZurichPeterHorvath,BerndWollscheidMPIBerlinMLYaspo,MMPU/EMBL Andreas Kulozik, Paulina Richter-Pechańska, Joachim Kunz, Elena OrlovaCaroline von Knoebel Doeberitz,Tobias RauschJan Korbel, Sebastian Uhrig, G P Balasubramanian