The Role of The Role of Preclinical Models to Preclinical Models to

Identify Novel Identify Novel Therapeutics in Rare Therapeutics in Rare

CancersCancersPeter J. Houghton, Ph.D.Peter J. Houghton, Ph.D.

St. Jude Children’s St. Jude Children’s Research HospitalResearch Hospital

How To Select New Agents for How To Select New Agents for Clinical Trials? Clinical Trials?

Rationale for the Pediatric Preclinical Testing Rationale for the Pediatric Preclinical Testing Program (PPTP)Program (PPTP)

Drug Development Drug Development NCI/Industry/NCI/Industry/

AcademiaAcademia

Phase IPhase I

Phase IIPhase II

• Prioritization of agents for phase I

• Rational decisions to advance/stop development

• Potential to focus phase II trials• Potential to identify sensitive tumors

• Establish relevant models that encompass clinical heterogeneity

400 new drugs in development

Drug X Testing @ MTD

Panel A Panel B Panel C Panel D Panel E

Active in Model(s)?Full Dose

Response/PK

Orthotopic Models

Transgenic Models

Final Report

No

Yes

Yes

YesNo

Stage 1 Report

Other Tumor Models Available?

Houghton et al. Clin Cancer Res. (2002)Houghton et al. Clin Cancer Res. (2002)

Overview of the PPTP ScreenOverview of the PPTP Screen

6 neuroblastomas

Why Do Preclinical Why Do Preclinical Cancer Models Fail?Cancer Models Fail?

• Species Tolerance: Host tolerance leads to high Species Tolerance: Host tolerance leads to high systemic exposure to drug -overprediction. Low systemic exposure to drug -overprediction. Low tolerance leads to low systemic exposure, and tolerance leads to low systemic exposure, and underprediction of drug activity.underprediction of drug activity.

• Tumor models do not recapitulate human cancer at Tumor models do not recapitulate human cancer at the molecular levelthe molecular level

• Criteria for defining ‘activity’ is more stringent in clinical trialsCriteria for defining ‘activity’ is more stringent in clinical trials

• Preclinical tumor models do not encompass clinical heterogeneityPreclinical tumor models do not encompass clinical heterogeneity

• Clinical trials design ignores preclinical dataClinical trials design ignores preclinical data

Molecular Molecular Characterization of Characterization of

Xenograft Tumor ModelsXenograft Tumor Models• Pediatric Preclinical Testing Pediatric Preclinical Testing Program (PPTP)Program (PPTP) -Affymetrix -Affymetrix (U133A)(U133A) -SNP analysis -SNP analysis (100K)(100K) -CGH-CGH

• Pediatric Oncology Preclinical Pediatric Oncology Preclinical Protein-Tissue Array Project (POPP-Protein-Tissue Array Project (POPP-TAP)TAP) -cDNA arrays-cDNA arrays

-Tissue/Protein -Tissue/Protein arraysarrays

How well do xenograft tumors represent the respective How well do xenograft tumors represent the respective clinical disease?clinical disease?

•Tumor models do not recapitulate human cancer at Tumor models do not recapitulate human cancer at the molecular level the molecular level

KCNRKCNRASAS

Tumors Cluster Along Diagnostic Tumors Cluster Along Diagnostic TypeType

by Unsupervised Clustering by Unsupervised Clustering cDNA Array:cDNA Array: all 38,789 Good Quality Genesall 38,789 Good Quality Genes

RH1 ? EWSRH1 ? EWSRH6RH6

JHANJHAN

Javed Khan -POPP-TAP Javed Khan -POPP-TAP (subnitted)(subnitted)

SC/OrthotopicSC/Orthotopic

Identify Xenografts That Recapitulate the Identify Xenografts That Recapitulate the Tumors of Origin.Tumors of Origin.

MDS 38,789 genes of primary/xeno/cell line: EWS/NB/RMSMDS 38,789 genes of primary/xeno/cell line: EWS/NB/RMS

ANN trained on tumors predict ANN trained on tumors predict xenograftsxenografts

PPTP Lines-Rh41-Rh10-Rh28-Rh30-Rh36-Rh18

PPTP Lines-Rh41-Rh10-Rh28-Rh30-Rh36-Rh18

PPTP Lines-SK-N-AS-NB-1643-NB-1691-NB-1771-NB-EB-NB-SD-NB-1382

PPTP Lines-SK-N-AS-NB-1643-NB-1691-NB-1771-NB-EB-NB-SD-NB-1382

Panels of Xenograft TumorsPanels of Xenograft TumorsAccurately Reflect Clinical Accurately Reflect Clinical

ResponsivenessResponsiveness

Vincristine 44%Vincristine 44%Cyclophosphamide 50%Cyclophosphamide 50%Actinomycin D 25%Actinomycin D 25%

Topotecan 50% clinical responsesTopotecan 50% clinical responses

• Preclinical tumor models do not encompass clinical heterogeneityPreclinical tumor models do not encompass clinical heterogeneity

Comparison of Expression Comparison of Expression Profiles in Kidney Tumors and Profiles in Kidney Tumors and

Their Derived Xenografts ModelsTheir Derived Xenografts ModelsClustering using 543 best classifiers >1Present Clustering using 543 best classifiers >1Present

(Affymetrix U133A)(Affymetrix U133A)

CCSKCCSKFetal kidneyFetal kidneyHPLNRHPLNRWilmsWilmsXenograftXenograft

CCSKCCSKFetal kidneyFetal kidneyHPLNRHPLNRWilmsWilmsXenograftXenograft

Wilm’s Tumor Xenografts Cluster with Wilm’s Tumor Xenografts Cluster with Their Clinical SamplesTheir Clinical Samples

Chemosensitivity of Chemosensitivity of Kidney Tumor Kidney Tumor XenograftsXenografts

BMS247550

Link Expression Profiles to Link Expression Profiles to Chemosensitivity to Identify Chemosensitivity to Identify

Biomarkers of ResponseBiomarkers of Response

• Criteria for defining ‘activity’ is more stringent in clinical trialsCriteria for defining ‘activity’ is more stringent in clinical trials

Non-GBM Brain TumorsNon-GBM Brain Tumors Kidney TumorsKidney Tumors

Drug ResponseSJ-BT39 SJ-GBM2

BCNUVP-16CDDPTOPOTECANCPT-11TEMOZOLOMIDEVINCRISTINEMGI-114PS341DOXORUBICINCARBOPLATINDEPSIPEPTIDEBMS247550RII5777SU6668

umor Line OS-1 OS-2 OS-17 OS-21 OS-29 OS-31 OS-32 OS-33ncristine 4-11-05 4-11-05 4-11-05

toxan 4-11-05 4-11-05 4-11-05

ctinomycin 4-11-05 4-11-05 4-11-05

potecan 4-11-05 4-11-05

mozolomide 4-11-05

PT-11 4-11-05

G1-114 4-11-05

CNU 4-11-05 4-11-05 4-11-05

P-16 4-11-05 4-11-05 4-11-05

DDPARBOPOPLAT

XALIPLATxorubicin 4-11-05 4-11-05

-341 4-11-05

MS247550 4-11-05

R(111 ) 4-11-05 4-11-05

115777 4-11-05 4-11-05

psipeptide 4-11-05

AAG 4-11-05

-713489 4-11-05 4-11-05

HA 4-11-05

xol 4-11-05 4-11-05 4-11-05

BT-751 4-11-05 4-11-05 4-11-05

AD 001CI-779RF1042

GlioblastomaGlioblastomaOsteosarcomaOsteosarcoma

mor Line Rh10 Rh12 Rh18 Rh28 Rh30 Rh35 Rh36 Rh39 IRS56 IRS68 Rh65 Rh66stology ARMS ERMS ERMS ARMS ARMS ERMS ERMS ERMS ARMS ARMSncristinetoxanctinomycinpotecanmozolomide

PT-11PAMG1-114

CNUP-16DDP

xorubicin-341

MS247550R(111)115777psipeptideAAG-713489HAxol

BT-751AD001D1839

6668

RhabdomyosarcomaRhabdomyosarcomaNeuroblastomaNeuroblastoma

Linking ChemosensitivtyLinking ChemosensitivtyTo Expression ProfilingTo Expression Profiling

Identifying BiomarkersIdentifying BiomarkersFor Predicting Drug-For Predicting Drug-Responsive PopulationsResponsive Populations

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Hierarchical Clustering Trusted samples based on Hierarchical Clustering Trusted samples based on LogSignal CV 0.5 Max-Min>=100 at least 3 Present LogSignal CV 0.5 Max-Min>=100 at least 3 Present

(1113 probesets)(1113 probesets)

ALL

-19

BT

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56

OS

-2

BT

-28

OS

-164

OS

-166

OS

-187

SK

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EW

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WT

-12

WT

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WT

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WT

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WT

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Rh3

6

Rh1

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Rh6

5

Rh4

1

Rh2

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W-1

Rh3

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WT

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Rh1

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BT

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CH

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NB

-169

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SN

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771

NB

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NB

-164

3

NB

-132

BT

-45

BT

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BT

-56

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12

BT

-41

BT

-36

OS

-17

OS

-21

OS

-1

Group 1 versus Group 2 Osteosarcomas( Probesets >4-fold Ttest FDR<0.01)

OS#1 OS#2

keratin 18keratin 19cadherin 1, type 1, E-cadherin (epithelial)

fibronectin 1 /// fibronectin 1carboxypeptidase EIntegrin-binding sialoprotein (bone sialoprotein, bone sialoprotein II)

BT-29WT-11WT-13WT-16SKNEPWT-14WT-10WT-12EW1EW5EW8(Rh1)Rh10Rh18Rh28Rh30Rh41Rh36Rh65BT-28BT-31BT-32BT-45BT-36BT-41BT-46BT-50SJ-GBM2SJ-BT39D645D456SJ-BT56D212NB-SDNB-1771NB-1691NB-EBc1CHLA-79NB-1643NB-1382SK-N-ASOS-1OS-2OS-17OS164OS166OS187OS-21OS160ALL-2ALL-3ALL-4ALL-7ALL-8ALL-16ALL-17ALL-19ALL-10ALL-11

0501

0502

0503

0504

0505

0506

0507

0508

0

1

2

3

4

Not Determined

Neuroblastoma Osteosarcoma ALL

Progressive Disease

Kidney/Rhabdoid Sarcoma Non-GBM Brain Tumor Glioblastoma

Stable Disease

Partial Response

Complete Response

Maintained Complete Response

Chemosensitivity of Tumors in the PPTP PanelChemosensitivity of Tumors in the PPTP Panel

VincristineVincristine

The PPTPThe PPTP

• Richard Gorlick (osteosarcoma)Richard Gorlick (osteosarcoma)• John Maris (neuroblastoma)John Maris (neuroblastoma)• Henry Friedman (glioblastoma)Henry Friedman (glioblastoma)• Richard Lock (ALL)Richard Lock (ALL)• Pat Reynolds (in vitro testing)Pat Reynolds (in vitro testing)• Malcolm Smith (CTEP)Malcolm Smith (CTEP)• Javed Khan (NCI)Javed Khan (NCI)• Geoff Neale (St. Jude)Geoff Neale (St. Jude)• Chris Morton (St. Jude; coordinator)Chris Morton (St. Jude; coordinator)

ThanksThanks

Drug X Testing @ MTD

Panel A Panel B Panel C Panel D Panel E

Active in Model(s)?Full Dose

Response/PK

Orthotopic Models

Transgenic Models

Final Report

No

Yes

Yes

YesNo

Stage 1 Report

Other Tumor Models Available?

Houghton et al. Clin Cancer Res. (2002)Houghton et al. Clin Cancer Res. (2002)

Overview of the PPTP ScreenOverview of the PPTP Screen

Model Systems for Drug Model Systems for Drug SelectionSelection

Drug Development Drug Development NCI/Industry/NCI/Industry/

AcademiaAcademia

Phase IPhase I

Phase IIPhase II

•Rational decisions to Rational decisions to advance/stop development advance/stop development based on PK parametersbased on PK parameters•Potential to focus phase Potential to focus phase II trialsII trials•Potential to identify Potential to identify biomarkers for patient biomarkers for patient selectionselection

•Relevant models (panels).Relevant models (panels).-molecular -molecular

identityidentity --encompass clinical encompass clinical heterogeneityheterogeneity

Brain Tumor Panel (glioblastoma) Duke University School of Medicine SJ -GBM2 Glioblastoma SJ -BT39 Glioblastoma D645 Glioblastoma D456 Glioblastoma SJ -BT56 (extended panel) Glioblastoma D212 (extended panel) Glioblastoma Brain Tumor Panel (non-glioblastoma)

St. J ude Children’s Research Hospital

BT-28 Medulloblastoma (diagnosis) BT-31 Anaplastic medulloblastoma (diagnosis) BT-32 Medulloblastoma (diagnosis) BT-45 Medulloblastoma (diagnosis) BT-36 Anaplastic Ependymoma (diagnosis) BT-41 Ependymoma (relapse) BT-46 (extended panel) Medulloblastoma (diagnosis) BT-50 (extended panel) Medulloblastoma (diagnosis) Sarcoma Panel St. J ude Children’s Research Hospital EW1 Ewing sarcoma (relapse) EW5 Ewing sarcoma (diagnosis) EW8 Ewing sarcoma RH10 Rhabdomyosarcoma, alveolar (relapse) RH18* Rhabdomyosarcoma, embryonal (diagnosis) RH28 Rhabdomyosarcoma, alveolar (diagnosis) RH30* Rhabdomyosarcoma, alveolar (diagnosis) RH41* Rhabdomyosarcoma, alveolar (relapse) RH36 (extended panel) Rhabdomyosarcoma, embryonal (relapse) RH65 (extended panel) Rhabdomyosarcoma, alveolar (relapse) Osteosarcoma panel Albert Einstein College of Medicine OS-1 Osteosarcoma (primary/untreated) OS-2 Osteosarcoma (primary/untreated) OS-17 Osteosarcoma (primary/untreated) OS-164 Osteosarcoma (primary/previously treated) OS-166 Osteosarcoma (osteoblastic primary/relapse) OS-187 Osteosarcoma (primary/untreated) OS-21 (extended panel) Osteosarcoma (primary/untreated) OS-160 (extended panel) Osteosarcoma (lung metastasis/r elapse)

Tumor Panel: 9-10-05

Acute Lymphoblastic Leukemia panel

Children’s Cancer I nstitute of Australia

ALL-2 c-ALL /Relapse 3 (CR1 = 30 mos) ALL-3 Pre-B ALL /Diagnois (CR1 = 38 mos) ALL-4 Ph+ ALL /Diagnosis (CR1 = 10 mos) ALL-7 Biphenotypic /Diagnosis (CR1 = 7 mos) ALL-8 T-ALL /Relapse 1 (CR1 = 17 mos) ALL-16 T-ALL /Diagnosis (CR1 = 103+ mos) ALL-17 c-ALL /Diagnosis (CR1 = 25 mos) ALL-19 c-ALL /Relapse 1 (CR1 = 4 mos) ALL-10 (extended panel) c-ALL /Diagnosis (CR1 = 57+ mos) ALL-11 (extended panel) c-ALL /Diagnosis (CR1 = 120+ mos) Neuroblastoma panel Children’s Hospital of Philadelphia NB-SD MYCN amplified (previously treated) NB-1771 MYCN amplified (diagnosis) NB-1691 MYCN amplified (relapse) NB-EBc1* Not MYCN amplified (relapse) CHLA-79 Not MYCN amplified (relapse) NB-1643* MYCN amplified (diagnosis) NB-1382 (extended panel) MYCN amplified (relapse) SK-N-AS (extended panel) Not MYCN amplified (diagnosis) Kidney/ rhabdoid tumor panel St. J ude Children’s Research Hospital BT-29 Atypical teratoid rhabdoid (CNS) (diagnosis) WT-14 Rhabdoid, kidney (relapse) WT-11 Wilms favorable histology (diagnosis) WT-13 Wilms diffuse anaplastic (diagnosis) WT-16 Rhabdoid, kidney (relapse) SKNEP Wilms diffuse anaplastic (relapse) WT-10 (extended panel) Wilms favorable histology (diagnosis) WT-12 (extended panel) Rhabdoid, kidney (diagnosis)

Tumor Panel: 9-10-05 (cont.)

Volcano: Group OS1 vs Group OS2